The DOI matches its Crossref record; 147 of the 147 references it cites were found in a registry or an index; 4 of the 216 sources its claims cite were checked for support.
Respiratory viral infection-induced microbiome alterations and secondary bacterial pneumonia.
Open accessAbstract
Influenza and other respiratory viral infections are the most common type of acute respiratory infection. Viral infections predispose patients to secondary bacterial infections, which often have a more severe clinical course. The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system. Studies over the past 15 years have demonstrated that unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract, which have both direct and indirect effects on host defense against viral infections. In addition, antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function ("dysbiosis") in the respiratory and gastrointestinal tract, which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. In this review, we summarize the literature on the interactions between host microbial communities and host defense, and how influenza, and other acute respiratory viral infections disrupt these interactions, thereby contributing to the pathogenesis of secondary bacterial infections.
Overview
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TL;DR
This review synthesizes evidence that acute respiratory viral infections—especially influenza—induce dysbiosis in the gut and respiratory tract microbiomes, which in turn alters host immune priming and inter-microbial competition, contributing to secondary bacterial pneumonia. It argues that these microbiome shifts are driven largely by systemic antiviral immune signals rather than direct viral presence at distant sites.
Key findings
- Respiratory viral infection alters the gut microbiome despite no detectable virus in the GI tract: murine influenza models show reduced segmented filamentous bacteria and Lactobacillus/Lactococcus with increased Enterobacteriaceae/Proteobacteria, effects mediated by type I and type II interferons and possibly by reduced caloric intake.
- Viral infection is associated with increased colonization by potential pathogens in the upper respiratory tract: in adults with influenza A, *S. aureus*, *S. pneumoniae*, and *H. influenzae* were present in 12%, 24%, and 32% of infected patients versus 5%, 11%, and 10% of uninfected patients; in children, influenza was associated with a 15-fold increase in nasopharyngeal *S. pneumoniae* titer.
- In a mouse model, intranasal live attenuated influenza vaccine increased nasopharyngeal bacterial density up to 100,000-fold and prolonged *S. pneumoniae* or *S. aureus* carriage 2- to 5-fold.
- Gut microbiome depletion (antibiotics or germ-free status) impairs antiviral and antibacterial immunity—reduced antibody and CD4+/CD8+ T cell responses, defective macrophage IFN responses, decreased phagocytosis and TNF-α—while commensal re-colonization (e.g., *Lactobacillus reuteri*, *Enterococcus faecalis*, *Lactobacillus crispatus*, *Clostridium orbiscindens*) protected against bacterial pneumonia via GM-CSF.
- Inter-microbial competition matters: nasal implantation of a *Corynebacterium* strain eradicated *S. aureus* in 71% of persistent carriers, and *C. accolens* inhibits *S. pneumoniae* growth in vitro via a lipase releasing free fatty acids.
Methods
- Narrative literature review (not a primary study) covering human and animal studies on gut and respiratory tract microbiomes during respiratory viral infection, with a stated focus on the bacterial microbiome because of a paucity of mycobiome and virome studies.
- Synthesizes cross-sectional and longitudinal human studies (16S rRNA sequencing, qPCR, metagenomics, culture-independent pyrosequencing) alongside murine, ferret, and in vitro models, organized by anatomic niche (gut, URT, LRT) and by mechanism (host immune effects, inter-microbial effects, direct viral effects on bacteria).
- No systematic search strategy, inclusion criteria, or quantitative synthesis is reported.
Limitations
- Stated by the paper: protocols for sampling, processing, and bioinformatics of the respiratory microbiome are not standardized; most studies are in animal models, and human studies are small and largely limited to the URT; fungi and viruses (including phages) are largely omitted because 16S rRNA analysis cannot capture them; species-composition studies are insufficient without functional transcriptomic/proteomic characterization; long-term effects of microbiome-modulating therapies (especially antibiotics) are unknown.
- Stated by the paper: cross-sectional human studies are poorly controlled and small relative to confounding variables (age, gender, oral hygiene, smoking, medication, healthcare employment, exposure to children), and are confounded by viral type, sampling timing, infection severity, and antimicrobial use.
- Evident from the text: the central mechanistic claim—that viral-induced microbiome changes cause secondary bacterial pneumonia in humans—is explicitly described as not yet examined ("the effects of these alterations on risk of secondary bacterial pneumonia have not been studied"), and much of the supporting evidence is from murine models under SPF conditions that may not reflect more diverse human or wild-mouse microbiota.
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Claims the paper makes
128 Not checked yet · 23 No basis given · 20 Own interpretation · 3 Partly supported · 3 Own method · accuracy not yet measured
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In the paper
“The most frequently detected pathogens were methicillin-resistant Staphylococcus aureus (MRSA), M. catarrhalis, and coronavirus.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Partly supportedcites [116] Hassoun, 2015, Seasonal variation of respiratory pathogen colonization in asymptomatic health care professionals: A single-center, cross-sectional, 2-season observational study, Am J Infect Control sourceExperimental — accuracy not yet measured
The Abstract Results identify MRSA, Moraxella catarrhalis, and coronavirus as the most frequently detected agents in winter. The claim omits that seasonal qualification: the same section identifies MRSA and Klebsiella pneumoniae as the most prevalent bacteria in summer, and the Results report no summer coronavirus detections. (LLM, conf=0.86)
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In the paper
“antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function (“dysbiosis”) in the respiratory and gastrointestinal tract”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Abstract
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In the paper
“Influenza and other respiratory viral infections predispoxsse patients to secondary bacterial super-infections”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
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In the paper
“which have both direct and indirect effects on host defense against viral infections”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Abstract
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In the paper
“over half of patients with severe infections in the 1957 H2N2 and 1968 H3N2 pandemics had bacterial complications”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
What the sources say
- Not checked yetcites [8] Bisno, 1971, Pneumonia and Hong Kong influenza: a prospective study of the 1968-1969 epidemic, Am J Med Sci source
- Not checked yetcites [9] Hers, 1958, Bacteriology and histopathology of the respiratory tract and lungs in fatal Asian influenza, Lancet source
- Not checked yetcites [10] Oswald, 1958, Pneumonia complicating Asian influenza, Br Med J source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“influenza infection has been found to result in significant changes in the gut microbiome, despite the lack of detectable virions in the GI tract”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
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In the paper
“The severity of infection was associated with reductions in dendritic cell migration rate and the number of local T cells.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
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In the paper
“flu-infected mice had increased IL-17A levels and numbers of Th17 cells in the small intestine and colon, which appeared to contribute to intestinal injury”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of acute respiratory viral infection on gut microbiome
What the sources say
- Not checked yetcites [43] Wang, 2014, Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation, J Exp Med source
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In the paper
“influenza infection alters intestinal microbiota composition through type II IFN produced by lung-derived T cells recruited to the intestine”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of acute respiratory viral infection on gut microbiome
What the sources say
- Not checked yetcites [43] Wang, 2014, Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation, J Exp Med source
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In the paper
“These mice also had higher viral titers in their lungs”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
- Not checked yetcites [51] Ichinohe, 2011, Microbiota regulates immune defense against respiratory tract influenza A virus infection, Proc Natl Acad Sci USA source
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In the paper
“During viral infections, the degree of macrophage response to respiratory viruses depends on the presence of gut microbes.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
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In the paper
“changes in the gut microbiome appear to result not from direct viral effects but from systemic inflammatory signals that travel from the lung and trigger local inflammatory responses in the gut”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of acute respiratory viral infection on gut microbiome
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In the paper
“Using animal models of pulmonary infections by influenza and respiratory syncytial virus (RSV), multiple groups have shown that the gut microbiome is clearly impacted by respiratory viral infections, despite the lack of detectable respiratory virus in the gut”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of acute respiratory viral infection on gut microbiome
What the sources say
- Not checked yetcites [43] Wang, 2014, Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation, J Exp Med source
- Not checked yetcites [44] Deriu, 2016, Influenza Virus Affects Intestinal Microbiota and Secondary Salmonella Infection in the Gut through Type I Interferons, PLoS Pathog source
- Not checked yetcites [45] Bartley, 2017, Impact of age, caloric restriction, and influenza infection on mouse gut microbiome: an exploratory study of the role of age-related microbiome changes on influenza responses, Front Immunol source
- Not checked yetcites [46] Yildiz, 2018, Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis, Microbiome source
- Not checked yetcites [47] Groves, 2018, Respiratory disease following viral lung infection alters the murine gut microbiota, Front Immunol source
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In the paper
“Mice pretreated with an antibiotic cocktail showed increased morbidity and mortality during influenza infection”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“administration of Lactobacillus reuteri, Enterococcus faecalis, Lactobacillus crispatus, and Clostridium orbiscindens, which are strong stimulators of NOD2 (i.e., cytosolic receptor for muramyl dipeptide, which is found in cell walls of certain bacteria), are able to protect against bacterial pneumonia by enhancing GM-CSF production”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
What the sources say
- Not checked yetcites [66] Brown, 2017, The microbiota protects against respiratory infection via GM-CSF signaling, Nat Commun source
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In the paper
“activation of antiviral immune responses, including type I and type II IFNs, have been associated with increased susceptibility to secondary bacterial pneumonia”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
What the sources say
- Not checked yetcites [64] Sun, 2008, Inhibition of pulmonary antibacterial defense by interferon-gamma during recovery from influenza infection, Nat Med source
- Not checked yetcites [65] Shahangian, 2009, Type I IFNs mediate development of postinfluenza bacterial pneumonia in mice, J Clin Invest source
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In the paper
“These effects might be mediated in part by decreased Nod1 sensing of meso-DAP (diaminopimelic acid)-containing peptidoglycan found in gut microbiota, which previously was shown to be essential for priming innate immune responses to S. pneumoniae”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
- Not checked yetcites [56] Clarke, 2010, Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity, Nat Med source
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In the paper
“Other Lactobacillus strains are known to enhance TNF-α and IFN-γ production by nasal lymphocytes upon influenza infection”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
What the sources say
- Not checked yetcites [61] Hori, 2002, Augmentation of cellular immunity and reduction of influenza virus titer in aged mice fed Lactobacillus casei strain Shirota, Clin Diagn Lab Immunol source
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In the paper
“Clostridium orbiscindens, a member of the human gut microbiome, has been found to produce desaminotyrosine (DAT) from metabolism of flavonoids and amino acids.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
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In the paper
“antibiotic-induced disruptions in the normal gut microbial community alter multiple aspects of normal host defense against acute respiratory pathogens”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
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In the paper
“bacterial colonization of the URT is generally considered as the first step in the development of invasive bacterial infections (83, 84), including secondary bacterial infections following respiratory viral infection”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
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In the paper
“Higher pneumococcal colonization density has been linked to respiratory virus co-infection and invasive pneumococcal pneumonia, after adjusting for age and sex”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [85] Wolter, 2014, High nasopharyngeal pneumococcal density, increased by viral coinfection, is associated with invasive pneumococcal pneumonia, J Infect Dis source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“In experimental in vitro models, viral infections increase the colonization rates of various bacteria in the URT (90–95), including S. pneumoniae and H. influenzae (86–88).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [90] Hirano, 1999, Effects of influenza A virus on lectin-binding patterns in murine nasopharyngeal mucosa and on bacterial colonization, Otolaryngol Head Neck Surg source
- Not checked yetcites [91] McCullers, 2010, Influenza enhances susceptibility to natural acquisition of and disease due to Streptococcus pneumoniae in ferrets, J Infect Dis source
- Not checked yetcites [92] Wadowsky, 1995, Effect of experimental influenza A virus infection on isolation of Streptococcus pneumoniae and other aerobic bacteria from the oropharynges of allergic and nonallergic adult subjects, Infect Immun source
- Not checked yetcites [93] Wren, 2014, Influenza A virus alters pneumococcal nasal colonization and middle ear infection independently of phase variation, Infect Immun source
- Not checked yetcites [94] Nakamura, 2011, Synergistic stimulation of type I interferons during influenza virus coinfection promotes Streptococcus pneumoniae colonization in mice, J Clin Invest source
- Not checked yetcites [95] Diavatopoulos, 2010, Influenza A virus facilitates Streptococcus pneumoniae transmission and disease, FASEB J source
- Not checked yetcites [86] Ishizuka, 2003, Effects of rhinovirus infection on the adherence of Streptococcus pneumoniae to cultured human airway epithelial cells, J Infect Dis source
- Not checked yetcites [87] Avadhanula, 2006, Respiratory viruses augment the adhesion of bacterial pathogens to respiratory epithelium in a viral species- and cell type-dependent manner, J Virol source
- Not checked yetcites [88] Wang, 2009, Rhinovirus enhances various bacterial adhesions to nasal epithelial cells simultaneously, Laryngoscope source
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In the paper
“Impaired airway clearance due to intrinsic or extrinsic factors leads to the proliferation of bacterial species that can exploit this growth opportunity”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
- Not checked yetcites [82] Rogers, 2013, Interpreting infective microbiota: the importance of an ecological perspective, Trends Microbiol source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“One possible mechanism by which influenza and other viral infections might predispose infected hosts to secondary bacterial pneumonia is by altering the microbial composition of the upper respiratory tract, fostering enhanced growth of pathogens, and facilitating the subsequent entry of large bacterial loads into the LRT”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [85] Wolter, 2014, High nasopharyngeal pneumococcal density, increased by viral coinfection, is associated with invasive pneumococcal pneumonia, J Infect Dis source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“In healthy individuals, the microbial community richness (i.e., the total number of bacterial taxa) is lower in the LRT than that in the URT”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
- Not checked yetcites [70] Charlson, 2011, Topographical continuity of bacterial populations in the healthy human respiratory tract, Am J Respir Crit Care Med source
- Not checked yetcites [74] Dickson, 2017, Bacterial topography of the healthy human lower respiratory tract, MBio source
- Not checked yetcites [75] Abreu, 2012, Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis, Sci Transl Med source
- Not checked yetcites [76] Bassis, 2015, Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals, MBio source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Given the effects of viruses on enhancing bacterial adherence to the epithelium (86–88), it is perhaps not surprising that multiple studies of human subjects as well as in animal models have shown that viral infections are associated with increased colonization by potentially pathogenic bacteria”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [86] Ishizuka, 2003, Effects of rhinovirus infection on the adherence of Streptococcus pneumoniae to cultured human airway epithelial cells, J Infect Dis source
- Not checked yetcites [87] Avadhanula, 2006, Respiratory viruses augment the adhesion of bacterial pathogens to respiratory epithelium in a viral species- and cell type-dependent manner, J Virol source
- Not checked yetcites [88] Wang, 2009, Rhinovirus enhances various bacterial adhesions to nasal epithelial cells simultaneously, Laryngoscope source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“In children, influenza is associated with a 15-fold increase in nasopharyngeal titer of S. pneumoniae”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [96] Vu, 2011, Association between nasopharyngeal load of Streptococcus pneumoniae, viral coinfection, and radiologically confirmed pneumonia in Vietnamese children, Pediatr Infect Dis J source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Animal models have similarly confirmed that viral infection, particularly influenza, increases bacterial colonization rates in the URT, enhancing the risk of secondary bacterial infections”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [97] Takase, 1999, Facilitated expansion of pneumococcal colonization from the nose to the lower respiratory tract in mice preinfected with influenza virus, Microbiol Immunol source
- Not checked yetcites [98] Tong, 2000, Effect of adenovirus type 1 and influenza A virus on Streptococcus pneumoniae nasopharyngeal colonization and otitis media in the chinchilla, Ann Otol Rhinol Laryngol source
- Not checked yetcites [99] Peltola, 2006, Bacterial sinusitis and otitis media following influenza virus infection in ferrets, Infect Immun source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“A comparative analysis using qPCR to detect specific bacteria in adult patients with or without influenza A infection showed that Staphylococcus aureus, S. pneumoniae, and H. influenzae were present in 12, 24, and 32% of infected patients, respectively as compared to 5, 11, and 10% of uninfected patients”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [89] Safaeyan, 2015, Quantitative detection of Staphylococcus aureus, Streptococcus pneumoniae and Haemophilus influenzae in patients with new influenza A (H1N1)/2009 and influenza A/2010 virus infection, GMS Hyg Infect Control source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“An examination of the oropharyngeal microbiome of pneumonia patients with and without 2009 influenza A H1N1 pandemic viral infection showed that Firmicutes (which include Staphylococcus and Streptococcus spp.) and Proteobacteria (mainly Pseudomonas amygdali, P. fluorescens, Pseudomonas sp. UK4, Acinetobacter baumanii and A. junii)—were significantly enriched in patients with influenza (108).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [108] Leung, 2013, Modulation of potential respiratory pathogens by pH1N1 viral infection, Clin Microbiol Infect source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Based: passes — The paper gives a reason why it holds.
In the paper
“A recent study of subjects with and without respiratory viral infections demonstrated lower overall bacterial reads from nasopharyngeal samples in virally-infected subjects compared with uninfected controls”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [100] Edouard, 2018, The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens, Eur J Clin Microbiol Infect Dis source
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The relationship between acute viral infections and bacterial colonization appears to be bidirectional.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“A French study of children admitted to the hospital with influenza revealed increased diversity of the nasopharyngeal microflora with increased influenza severity (105).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [105] Langevin, 2017, Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study, J Gen Virol source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Conversely, a French study of nasopharyngeal samples and a South Korean study of oropharyngeal samples from patients with acute respiratory viral infections both displayed decreases in diversity indices during viral infections compared to healthy controls (71, 100).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [71] Yi, 2014, Profiling bacterial community in upper respiratory tracts, BMC Infect Dis source
- Not checked yetcites [100] Edouard, 2018, The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens, Eur J Clin Microbiol Infect Dis source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“colonization of the URT with S. aureus drastically reduced influenza-induced acute lung injury and mortality in mice by recruiting a C-C chemokine receptor type 2+ cluster of differentiation (CD)11b+ monocyte subset to the lungs and inducing an M2 macrophage phenotype”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [104] Wang, 2013, Bacterial colonization dampens influenza-mediated acute lung injury via induction of M2 alveolar macrophages, Nat Commun source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“A recent metagenomics-based study in France reported enrichment of S. aureus, S. pneumoniae, H. influenzae, Moraxella catarrhalis and Klebsiella pneumoniae in nasopharyngeal samples of subjects with confirmed respiratory viral infections compared to healthy controls (100).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [100] Edouard, 2018, The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens, Eur J Clin Microbiol Infect Dis source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“The presence of a nasopharyngeal commensal protected mice against RSV-induced airway hyperresponsiveness.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [103] Ni, 2012, Pharyngeal microflora disruption by antibiotics promotes airway hyperresponsiveness after respiratory syncytial virus infection, PLoS ONE source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Results from microbiome analyses have not demonstrated consistent changes in diversity when comparing virally infected subjects with healthy controls.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“In some studies, increased bacterial diversity appeared to be associated with influenza severity.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [105] Langevin, 2017, Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study, J Gen Virol source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Viral replication in the respiratory tract can be enhanced by exposure to S. pneumoniae”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [101] Verkaik, 2011, Streptococcus pneumoniae exposure is associated with human metapneumovirus seroconversion and increased susceptibility to in vitro HMPV infection, Clin Microbiol Infect source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Patients harboring S. pneumoniae are more likely to experience subsequent acute respiratory illness episodes than those without colonization”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [102] DE, 2016, Co-colonization by Streptococcus pneumoniae and Staphylococcus aureus in the throat during acute respiratory illnesses, Epidemiol Infect source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Longitudinal studies conducted in healthy volunteers who underwent experimental self-innoculation with rhinovirus also failed to demonstrate significant changes in diversity of the URT microbiome”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [73] Allen, 2014, Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge, Microbiome source
- Not checked yetcites [107] Tarabichi, 2015, The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles, Microbiome source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“while administration of LAIV vaccine to healthy adults led to increases in diversity measures following viral challenge (73, 107).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [73] Allen, 2014, Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge, Microbiome source
- Not checked yetcites [107] Tarabichi, 2015, The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles, Microbiome source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“A 16s rRNA sequencing-based study conducted in infants with acute RSV or hRV respiratory infections reported that infants with RSV had significantly higher abundance of Staphylococcus spp. compared to hRV-infected infants (113).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [113] Rosas-Salazar, 2016, Differences in the nasopharyngeal microbiome during acute respiratory tract infection with human rhinovirus and respiratory syncytial virus in infancy, J Infect Dis source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Another study examining the presence of 20 respiratory viruses by PCR panel and prevalence of bacterial carriage in the nasopharynx of children found a strong positive association between S. aureus colonization and influenza virus (112).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [112] van, 2012, Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria, PLoS ONE source
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“H. influenzae was positively associated with hRV and RSV;”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [112] van, 2012, Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Moreover, in 87.5% of patients, operational taxonomic units (OTUs) in patients varied significantly between time points (115).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [115] Pérez-Losada, 2017, Nasopharyngeal microbiome diversity changes over time in children with asthma, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Moreover, S. pneumoniae colonization was positively associated with the presence of hRV and enteroviruses;”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [112] van, 2012, Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“These findings are supported by another group who found that Moraxella and Enterobacter spp. (which are classified as Proteobacteria) were the most highly represented bacteria in nasopharyngeal samples obtained from patients with pandemic H1N1 influenza (110).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [110] Greninger, 2010, A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Another study of patients with 2009 pandemic H1N1 influenza infection revealed that the predominant phyla of the upper respiratory tract (nasal and nasopharyngeal samples) in patients harboring pandemic H1N1 were Actinobacteria, Firmicutes, and Proteobacteria although normal controls were not included;”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [109] Chaban, 2013, Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“and M. catarrhalis colonization was positively associated with coronaviruses and adenoviruses.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [112] van, 2012, Associations between pathogens in the upper respiratory tract of young children: interplay between viruses and bacteria, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This may underlie the highly variable and sometimes discrepant observations from microbiome studies in patients with viral infections.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“However, another analysis of two nasopharyngeal washes collected 5.5–6.5 months apart from 40 children and adolescents with asthma showed no significant differences in nasopharyngeal microbiome diversity across seasons”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [115] Pérez-Losada, 2017, Nasopharyngeal microbiome diversity changes over time in children with asthma, PLoS ONE source
plainn = 40- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“By 60 days, abundance of these bacteria had returned to baseline.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [119] Hofstra, 2015, Changes in microbiota during experimental human Rhinovirus infection, BMC Infect Dis source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“However, the number of subjects were small in both studies, limiting the power to detect changes over time.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“A longitudinal study of healthy subjects found a significant association between the presence of Lactobacillus helveticus, Prevotella melaninogenica, Streptococcus infantis, Veillonella dispar, and Bacteroides ovatus and influenza-specific H1 and H3 IgA antibody response (122).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [122] Salk, 2016, Taxa of the nasal microbiome are associated with influenza-specific IgA response to live attenuated influenza vaccine, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“These changes were not observed in subjects given saline nasal spray.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [107] Tarabichi, 2015, The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles, Microbiome source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Mean density of all bacterial species was significantly higher at each visit when a virus was detected.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [117] DeMuri, 2018, Dynamics of bacterial colonization with streptococcus pneumoniae, haemophilus influenzae, and moraxella catarrhalis during symptomatic and asymptomatic viral upper respiratory tract infection, Clin Infect Dis source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Nasopharyngeal microbiota composition has been shown to be altered by influenza vaccination (Figure 3).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [120] Thors, 2016, The effects of live attenuated influenza vaccine on nasopharyngeal bacteria in healthy 2 to 4 year olds. a randomized controlled trial, Am J Respir Crit Care Med source
- Not checked yetcites [107] Tarabichi, 2015, The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles, Microbiome source
- Not checked yetcites [121] Mina, 2014, Live attenuated influenza vaccine enhances colonization of Streptococcus pneumoniae and Staphylococcus aureus in mice, MBio source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“One clinical investigation assessed the presence and density of S. pneumoniae, H. influenzae, and M. catarrhalis in the nasopharynx of children during URT infection and in the healthy state, and reported that the proportion of children colonized with these bacteria was higher during infection than during asymptomatic surveillance visits.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [117] DeMuri, 2018, Dynamics of bacterial colonization with streptococcus pneumoniae, haemophilus influenzae, and moraxella catarrhalis during symptomatic and asymptomatic viral upper respiratory tract infection, Clin Infect Dis source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“No differences in Staphylococcus were observed.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [73] Allen, 2014, Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge, Microbiome source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“These studies reported no significant changes in total read counts or of the main phyla (e.g., Actinobacteria, Firmicutes, and Proteobacteria) over time in nasopharyngeal samples (73) or throat swabs (119).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Data from a mouse model of influenza infection seem to indicate that flu infection has only a modest effect on bacterial counts, diversity and composition of the lung microbiome (46).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [46] Yildiz, 2018, Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis, Microbiome source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“However, this effect was not observed in uninfected animals.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [97] Takase, 1999, Facilitated expansion of pneumococcal colonization from the nose to the lower respiratory tract in mice preinfected with influenza virus, Microbiol Immunol source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“This suggests that pneumococcal infection may sequentially develop from the URT to the LRT in influenza virus-infected subjects (97).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [97] Takase, 1999, Facilitated expansion of pneumococcal colonization from the nose to the lower respiratory tract in mice preinfected with influenza virus, Microbiol Immunol source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“In a mouse model of S. aureus nasal colonization, the absence of type I IFN receptor was associated with decreased persistence of bacteria (107).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [107] Tarabichi, 2015, The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles, Microbiome source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, it is possible that some individuals with influenza infection might develop changes in their lung microbiome as a result of changes in their URT microbial communities.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Type III IFN, which is also induced during influenza infections, led to changes in the nasal microbiome, including increased numbers of culturable bacteria.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [123] Planet, 2016, Lambda interferon restructures the nasal microbiome and increases susceptibility to staphylococcus aureus superinfection, MBio source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, it is remarkable that a relatively mild viral stimulus such as flu vaccine can lead to detectable changes in the URT microbiome.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“S. pneumoniae intranasally inoculated into mice pre-infected with influenza virus first colonized the nose, followed by the trachea and lungs several days later with purulent inflammation.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [97] Takase, 1999, Facilitated expansion of pneumococcal colonization from the nose to the lower respiratory tract in mice preinfected with influenza virus, Microbiol Immunol source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“The researchers observed that the growth of bacteria seemed to arise from the existing community.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [124] Molyneaux, 2013, Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease, Am J Respir Crit Care Med source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Although the data are still preliminary, animal studies have suggested that antiviral immune activation contributes to changes in the URT microbiome and facilitate colonization by potential pathogens, such as S. aureus.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [107] Tarabichi, 2015, The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles, Microbiome source
- Not checked yetcites [123] Planet, 2016, Lambda interferon restructures the nasal microbiome and increases susceptibility to staphylococcus aureus superinfection, MBio source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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In the paper
“An early study in Japan reported on the effects of introducing a Corynebacterium strain into the nares of healthy adult hospital workers who were persistent carriers of S. aureus, with successful eradication in 71% of subjects (137).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [137] Uehara, 2000, Bacterial interference among nasal inhabitants: eradication of Staphylococcus aureus from nasal cavities by artificial implantation of Corynebacterium sp, J Hosp Infect source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Prior viral infections dysregulate both alveolar macrophages (64, 131–136) and neutrophils (65, 128, 129), thereby inhibiting bactericidal activity.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [64] Sun, 2008, Inhibition of pulmonary antibacterial defense by interferon-gamma during recovery from influenza infection, Nat Med source
- Not checked yetcites [131] Astry, 1984, Influenza virus-induced immune complexes suppress alveolar macrophage phagocytosis, J Virol source
- Not checked yetcites [132] Franke-Ullmann, 1995, Alteration of pulmonary macrophage function by respiratory syncytial virus infection in vitro, J Immunol source
- Not checked yetcites [133] Ghoneim, 2013, Depletion of alveolar macrophages during influenza infection facilitates bacterial superinfections, J Immunol source
- Not checked yetcites [134] Jakab, 1982, Immune impairment of alveolar macrophage phagocytosis during influenza virus pneumonia, Am Rev Respir Dis source
- Not checked yetcites [135] Kleinerman, 1976, Effect of virus infection on the inflammatory response. Depression of macrophage accumulation in influenza-infected mice, Am J Pathol
- Not checked yetcites [136] Nickerson, 1990, Pulmonary antibacterial defenses during mild and severe influenza virus infection, Infect Immun source
- Not checked yetcites [65] Shahangian, 2009, Type I IFNs mediate development of postinfluenza bacterial pneumonia in mice, J Clin Invest source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Innate immune cells including macrophages and neutrophils are recruited to the lung by cytokines and chemokines for phagocytosis and bactericidal activity.
In the paper
“For example, S. epidermidis and Propionibacterium acnes abundance in the nares has been shown to be negatively associated with S. aureus carriage (67).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [67] Frank, 2010, The human nasal microbiota and Staphylococcus aureus carriage, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, with multiple aspects of pulmonary host defense impaired, it would not be entirely surprising if a subset of influenza infected patients developed secondary bacterial pneumonia as a result of being unable to clear aspirated pathobionts from the URT.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Rests on an assumption: Bacterial pneumonia frequently arises as a result of aspirated bacterial pathogens.
- Rests on an assumption: Innate immune cells including macrophages and neutrophils are recruited to the lung by cytokines and chemokines for phagocytosis and bactericidal activity.
In the paper
“A metagenomic analysis showed that pH1N1-associated airway microbiotas were enriched in genes associated with cell motility, transcriptional regulation, metabolism, and response to chemotaxis compared to the same bacteria in non-infected patients (108).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [108] Leung, 2013, Modulation of potential respiratory pathogens by pH1N1 viral infection, Clin Microbiol Infect source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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In the paper
“In comparison, S. epidermidis implantation did not have an effect.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [137] Uehara, 2000, Bacterial interference among nasal inhabitants: eradication of Staphylococcus aureus from nasal cavities by artificial implantation of Corynebacterium sp, J Hosp Infect source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Third, respiratory viral infections impair innate immune responses against bacteria (128–130).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [128] Abramson, 1982, Depression of monocyte and polymorphonuclear leukocyte oxidative metabolism and bactericidal capacity by influenza A virus, Infect Immun source
- Not checked yetcites [129] Didierlaurent, 2008, Sustained desensitization to bacterial Toll-like receptor ligands after resolution of respiratory influenza infection, J Exp Med source
- Not checked yetcites [130] McNamee, 2006, Both influenza-induced neutrophil dysfunction and neutrophil-independent mechanisms contribute to increased susceptibility to a secondary Streptococcus pneumoniae infection, Infect Immun source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Finally, direct effects of the infecting virus on bacteria that comprise the microbiome may facilitate the transition from pathobiont to pathogen.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In addition to enabling us to determine what is present during states of health, large-scale sequencing-based microbiome analyses have also revealed who is not present during disease.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Activation of influenza-induced antiviral interferon pathways can lead to inadequate innate immune cell responses during host defense against secondary bacterial infections, resulting in the proliferation of potentially pathogenic bacterial species.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Conclusion
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: unclear — It is unclear why the paper says it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, direct effects of viruses on bacterial transcriptional patterns might be a mechanism by which colonizing bacteria acquire invasive potential, thereby leading to bacterial superinfections.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“Influenza has been shown to affect the S. pneumoniae transcriptome in terms of downregulating expression of genes associated with the colonizer state and upregulations of bacteriocins (142).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [142] Pettigrew, 2014, Dynamic changes in the Streptococcus pneumoniae transcriptome during transition from biofilm formation to invasive disease upon influenza A virus infection, Infect Immun source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although the picture is incomplete, recent microbiome literature provides additional insights into the pathogenesis of dysregulated immune responses following acute viral infections, that may promote the development of secondary bacterial pneumonias (Figure 4).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Conclusion
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Respiratory viral infections can initiate a cascade of host immune responses that alter microbial growth conditions in the URT, LRT, and the gut (Supplemental Table 1).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Conclusion
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Probably not a substantial claim. 38
- It may state two separate claims as one. 68
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“caloric restriction also results in increased relative abundance of Proteobacteria and increased Bacteroidetes to Firmicutes ratio, raising the possibility that decreased oral intake during influenza may contribute to changes in the microbiome”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of acute respiratory viral infection on gut microbiome
What the sources say
- Partly supportedcites [45] Bartley, 2017, Impact of age, caloric restriction, and influenza infection on mouse gut microbiome: an exploratory study of the role of age-related microbiome changes on influenza responses, Front Immunol sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Partly supportedcites [47] Groves, 2018, Respiratory disease following viral lung infection alters the murine gut microbiota, Front Immunol sourceExperimental — accuracy not yet measured
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
- Not checked yetcites [49] Ley, 2006, Microbial ecology: human gut microbes associated with obesity, Nature source
- Not checked yetcites [50] Ruiz, 2017, One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents, Environ Microbiol source
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Second, viral infections can also reduce ciliary beat frequency and the number of ciliated cells, disrupt the coordinated movement of cilia, and impede the repair of respiratory epithelial cells, further leading to reduced mucociliary clearance (126, 127).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [126] Pittet, 2010, Influenza virus infection decreases tracheal mucociliary velocity and clearance of Streptococcus pneumoniae, Am J Respir Cell Mol Biol source
- Partly supportedcites [127] Smith, 2014, Ciliary dyskinesia is an early feature of respiratory syncytial virus infection, Eur Respir J sourceExperimental — accuracy not yet measured
The Discussion reports that RSV caused ciliary dyskinesia and cilia loss, which the authors say are likely to reduce mucociliary clearance. But it explicitly says ciliary beat frequency and the number of motile ciliated cells were not reduced. The paper does not establish that RSV impeded epithelial-cell repair. Page numbers were not supplied in our copy. (LLM, conf=0.90)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Bacterial co-infection was also detected in ~30% of cases in the 2009 H1N1 pandemic, with high mortality rates despite administration of appropriate antibiotics”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
What the sources say
- Not checked yetcites [11] Cillóniz, 2012, Bacterial co-infection with H1N1 infection in patients admitted with community acquired pneumonia, J Infect source
- Not checked yetcites [12] Gill, 2010, Pulmonary pathologic findings of fatal 2009 pandemic influenza A/H1N1 viral infections, Arch Pathol Lab Med source
- Not checked yetcites [13] Jain, 2009, Hospitalized patients with 2009 H1N1 influenza in the United States, April-June 2009, N Engl J Med source
- Not checked yetcites [14] Kumar, 2009, Critically ill patients with 2009 influenza A(H1N1) infection in Canada, JAMA source
- Not checked yetcites [15] Martín-Loeches, 2011, Community-acquired respiratory coinfection in critically ill patients with pandemic 2009 influenza A(H1N1) virus, Chest source
- Not checked yetcites [16] Palacios, 2009, Streptococcus pneumoniae coinfection is correlated with the severity of H1N1 pandemic influenza, PLoS ONE source
- Not checked yetcites [17] Shieh, 2010, 2009 pandemic influenza A (H1N1): pathology and pathogenesis of 100 fatal cases in the United States, Am J Pathol source
- Not checked yetcites [18] Domínguez-Cherit, 2009, Critically Ill patients with 2009 influenza A(H1N1) in Mexico, JAMA source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Abstract
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“the so-called “Spanish Flu” pandemic of H1N1 influenza A virus from 1918 to 1919 resulted in more than 50 million deaths, with many caused by bacterial super-infection leading to secondary pneumonia”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
What the sources say
- Not checked yetcites [1] Brundage, 2006, Interactions between influenza and bacterial respiratory pathogens: implications for pandemic preparedness, Lancet Infect Dis source
- Not checked yetcites [2] Chien, 2009, Bacterial pathogens and death during the 1918 influenza pandemic, N Engl J Med source
- Not checked yetcites [3] Johnson, 2002, Updating the accounts: global mortality of the 1918-1920 “Spanish” influenza pandemic, Bull Hist Med source
- Not checked yetcites [4] McCullers, 2006, Insights into the interaction between influenza virus and pneumococcus, Clin Microbiol Rev source
- Not checked yetcites [5] Morens, 2007, The 1918 influenza pandemic: insights for the 21st century, J Infect Dis source
- Not checked yetcites [6] Morens, 2008, Predominant role of bacterial pneumonia as a cause of death in pandemic influenza: implications for pandemic influenza preparedness, J Infect Dis source
- Not checked yetcites [7] The origin and virulence of the 1918 “Spanish” influenza virus86112 TaubenbergerJK 17526158Proc Am Philos Soc1502006
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“which often have a more severe clinical course”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Abstract
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Abstract
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“microbial metabolites are integral for promoting immune responses in the gut against pathogens, including inducing secretion of IL-18 (36) and defensins (37, 38)”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
What the sources say
- Not checked yetcites [36] Kalina, 2002, Enhanced production of IL-18 in butyrate-treated intestinal epithelium by stimulation of the proximal promoter region, Eur J Immunol source
- Not checked yetcites [37] Schauber, 2003, Expression of the cathelicidin LL-37 is modulated by short chain fatty acids in colonocytes: relevance of signalling pathways, Gut source
- Not checked yetcites [38] Schauber, 2004, Histone-deacetylase inhibitors induce the cathelicidin LL-37 in gastrointestinal cells, Mol Immunol source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“SCFAs promote the development of naive CD4+ T cells into regulatory T cells (31, 32), induce “tolerogenic” dendritic cells in the intestinal mucosa (33), and limit autoimmity (34, 35).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
What the sources say
- Not checked yetcites [31] Smith, 2013, The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis, Science source
- Not checked yetcites [32] Arpaia, 2013, Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation, Nature source
- Not checked yetcites [33] Goverse, 2017, Diet-derived short chain fatty acids stimulate intestinal epithelial cells to induce mucosal tolerogenic dendritic cells, J Immunol source
- Not checked yetcites [34] Mariño, 2017, Gut microbial metabolites limit the frequency of autoimmune T cells and protect against type 1 diabetes, Nat Immunol source
- Not checked yetcites [35] Haase, 2018, Impacts of microbiome metabolites on immune regulation and autoimmunity, Immunology source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“potential mechanisms by which these changes might modulate susceptibility to secondary bacterial infections include alterations in the nature and magnitude of the immune response in the host (microbiome on host effects) and facilitating growth of pathogens in the absence of normal commensals (inter-microbial effects)”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Germ-free (GF) mice (which lack microbiota) have markedly underdeveloped gut-associated lymphoid tissues, decreased number and smaller-sized Peyer's patches and mesenteric lymph nodes, and defects in antibody production, compared to specific pathogen free (SPF) mice.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“Wild-living mice exhibit more diverse microbiomes, with significant abundance of Proteobacteria as well as Firmicutes and Bacteroidetes”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
What the sources say
- Not checked yetcites [21] Rosshart, 2017, Wild mouse gut microbiota promotes host fitness and improves disease resistance, Cell source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“While the effects of these alterations on risk of secondary bacterial pneumonia have not been studied”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
In the paper
“germ-free animals exhibit increased susceptibility to multiple types of infections, including viruses, bacteria, and parasites”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
What the sources say
- Not checked yetcites (22,–27)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate are fermentation products of dietary fiber and carbohydrates by large intestinal bacteria”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
What the sources say
- Not checked yetcites [30] Cummings, 1983, Fermentation in the human large intestine: evidence and implications for health, Lancet source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This raises the possibility that disruptions in the normal microbial communities by an acute viral infection might contribute to the development of post-viral bacterial pneumonia.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“During health, the human gut bacterial community is diverse, with each individual harboring over 100 trillion bacteria, comprised of over 150 different species.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The gastrointestinal microbiota is dominated by Firmicutes (e.g., Lactobacillus, Bacillus, and Clostridium) and Bacteroidetes (e.g., Bacteroides), with lower abundances of Proteobacteria (e.g., Escherichia) and Actinobacteria (e.g., Bifidobacterium)”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
What the sources say
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“segmented filamentous bacteria are critical promoters of intestinal mucosal IgA production (39, 40)and Th17 cell induction (41, 42)”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
What the sources say
- Not checked yetcites [39] Klaasen, 1993, Apathogenic, intestinal, segmented, filamentous bacteria stimulate the mucosal immune system of mice, Infect Immun source
- Not checked yetcites [40] Talham, 1999, Segmented filamentous bacteria are potent stimuli of a physiologically normal state of the murine gut mucosal immune system, Infect Immun source
- Not checked yetcites [41] Ivanov, 2009, Induction of intestinal Th17 cells by segmented filamentous bacteria, Cell source
- Not checked yetcites [42] Gaboriau-Routhiau, 2009, The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses, Immunity source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The gut microbiome, in particular, has been shown to play an integral role in shaping the immune system starting early in life, with continued influence on priming the nature and robustness of immune responses throughout one's lifetime.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“compared to free-living mice or laboratory animals exposed to gut flora from wild mice, SPF animals have a more limited microbial community and are also more susceptible to inflammatory diseases, with a reduced immune repertoire including deficits in memory responses”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
What the sources say
- Not checked yetcites [21] Rosshart, 2017, Wild mouse gut microbiota promotes host fitness and improves disease resistance, Cell source
- Not checked yetcites [28] Reese, 2016, Sequential infection with common pathogens promotes human-like immune gene expression and altered vaccine response, Cell Host Microbe source
- Not checked yetcites [29] Beura, 2016, Normalizing the environment recapitulates adult human immune traits in laboratory mice, Nature source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“emerging evidence suggests that our microbial communities residing on our mucosal surfaces likely shape the rigor of our immune responses and shape the ecological relationships between host and pathogens”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“bacterial metabolites generated by gut commensals contribute to the maintenance of intact epithelial integrity, regulatory T-cell development, and a relatively anti-inflammatory immune state”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The pathogenesis of super-infection has been attributed to direct mucosal/epithelial damage by influenza virus, increased bacterial colonization of the upper and lower respiratory tracts (URT and LRT, respectively), and dysregulation of immune responses, which all lead to increased susceptibility to secondary bacterial infections.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“the effects of viral infection on the respiratory microbiome appear to be relatively modest, but detectable”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The respiratory tract also harbors distinct communities of microbes, with multiple discrete ecological niches (e.g., nasal cavity, oropharynx, upper airways) that vary in terms of temperature, pH, oxygen tension, mucus production, and other factors.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Introduction
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The gut microbiome, in addition to its metabolic functions in the host, plays an integral role in the development, instruction, and priming of the immune system.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“The increase in Proteobacteria appears to be mediated by type I interferons (IFNs) (18), which not only depleted anaerobic bacteria but also increased susceptibility to secondary Salmonella colitis.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of acute respiratory viral infection on gut microbiome
What the sources say
- Not checked yetcites [18] Domínguez-Cherit, 2009, Critically Ill patients with 2009 influenza A(H1N1) in Mexico, JAMA source
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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It may state two separate claims as one.
In the paper
“antibiotic treatment prior to influenza infection ameliorated the degree of intestinal injury, but not lung injury, suggesting that gut dysbiosis contributed to local but not systemic inflammation”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of acute respiratory viral infection on gut microbiome
What the sources say
- Not checked yetcites [43] Wang, 2014, Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation, J Exp Med source
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Dysbiosis, or an imbalance in the normal composition of the microbiome, is associated with a variety of chronic diseases, many of which are characterized by chronic inflammation or abnormal metabolism, including inflammatory bowel disease, cardiovascular disease, and diabetes.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
In the paper
“Macrophages from animals treated with antibiotics exhibited defective responses to type I and II IFNs and impaired capacity to limit viral replication, suggesting that intestinal microbiota provide immune stimulation that establishes an “activation threshold” for innate antiviral immune responses”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
- Not checked yetcites [52] Abt, 2012, Commensal bacteria calibrate the activation threshold of innate antiviral immunity, Immunity source
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Mice given a 4 week oral course of broad-spectrum antibiotics before respiratory viral infection mounted an attenuated anti-PR8 antibody response, were incapable of inducing CD4+ T cell-mediated IFN-γ response to PR8 antigen, and had fewer influenza-specific CD8+T cells”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In a murine model of influenza infection, the investigators found that although the total numbers of bacteria in the gut did not decrease, there was a reduction in the quantities of segmented filamentous bacteria (SFB) and Lactobacillus/Lactococcus, accompanied by increases in Enterobacteriaceae.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of acute respiratory viral infection on gut microbiome
What the sources say
- Not checked yetcites [43] Wang, 2014, Respiratory influenza virus infection induces intestinal immune injury via microbiota-mediated Th17 cell-dependent inflammation, J Exp Med source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Short-term perturbations in the gut microenvironment caused by illness, antibiotic usage, or dietary changes (e.g., starvation) can alter the gut microbiome and subsequently lead to transient alterations in immune responses.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
In the paper
“Germ-free mice and antibiotic-treated mice also exhibit impaired antibody responses to seasonal influenza vaccination, which was restored by oral administration of flagellated E. coli, demonstrating a dependence on TLR5-mediated sensing of the host microbiota”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
- Not checked yetcites [53] Oh, 2014, TLR5-mediated sensing of gut microbiota is necessary for antibody responses to seasonal influenza vaccination, Immunity source
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The respiratory tract is the main site of continuous contact with exogenous microbes.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Skin and oral cavity lineages are represented in the nasopharynx—e.g., Streptococcus, Staphylococcus, Corynebacterium, and Prevotella”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
- Not checked yetcites [70] Charlson, 2011, Topographical continuity of bacterial populations in the healthy human respiratory tract, Am J Respir Crit Care Med source
- Not checked yetcites [72] Ling, 2013, Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates, BMC Genomics source
- Not checked yetcites [73] Allen, 2014, Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge, Microbiome source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“Oral administration of a probiotic cocktail containing Lactobacillus restored the immune response and enhanced the activation of signaling pathways associated with recognition of single-stranded RNA virus”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
What the sources say
- Not checked yetcites [62] Wu, 2013, Microbiota regulates the TLR7 signaling pathway against respiratory tract influenza A virus infection, Curr Microbiol source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“clinical studies have shown that although probiotics do not influence the incidence of respiratory tract infection, they do reduce the severity of symptoms and duration of the illness”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
What the sources say
- Not checked yetcites [57] de, 2006, Probiotic bacteria reduced duration and severity but not the incidence of common cold episodes in a double blind, randomized, controlled trial, Vaccine source
- Not checked yetcites [58] Vouloumanou, 2009, Probiotics for the prevention of respiratory tract infections: a systematic review, Int J Antimicrob Agents source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Antibiotic-pretreated animals displayed altered cytokine profiles in the lung compared to untreated controls following S. pneumoniae infection, including significantly decreased TNF-α levels at 6 and 24 h after infection.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
- Not checked yetcites [55] Schuijt, 2016, The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia, Gut source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“animals fed a high fiber diet had increased generation of SCFAs, leading to enhanced antiviral CD8+ T cell immune responses and attenuated neutrophil-mediated lung injury during influenza infection, resulting in improved survival”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
What the sources say
- Not checked yetcites [63] Trompette, 2018, Dietary fiber confers protection against flu by shaping Ly6c- patrolling monocyte hematopoiesis and CD8+ T cell metabolism, Immunity source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The oropharynx contains members of Firmicutes, Proteobacteria, and Bacteroidetes, including Streptococcus, Neisseria, Haemophilus, and Lachnospira spp.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
- Not checked yetcites [68] Lemon, 2010, Comparative analyses of the bacterial microbiota of the human nostril and oropharynx, MBio source
- Not checked yetcites [70] Charlson, 2011, Topographical continuity of bacterial populations in the healthy human respiratory tract, Am J Respir Crit Care Med source
- Not checked yetcites [71] Yi, 2014, Profiling bacterial community in upper respiratory tracts, BMC Infect Dis source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
None of the sources cited for this claim have been checked yet.
In the paper
“In healthy adults, bacteria present in the nasal cavity are typically those associated with skin, predominantly members of the Actinobacteria (e.g., Corynebacterium spp., Propionibacterium spp.), followed by Firmicutes (e.g., Staphylococcus spp.), and Proteobacteria”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
- Not checked yetcites [67] Frank, 2010, The human nasal microbiota and Staphylococcus aureus carriage, PLoS ONE source
- Not checked yetcites [68] Lemon, 2010, Comparative analyses of the bacterial microbiota of the human nostril and oropharynx, MBio source
- Not checked yetcites [69] Bassis, 2014, The nasal cavity microbiota of healthy adults, Microbiome source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
In the paper
“oral administration of Lactobacillus plantarum enhanced the type I IFN response and lowered viral titers in the lungs in a murine model of influenza infection”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
What the sources say
- Not checked yetcites [60] Maeda, 2009, Oral administration of heat-killed Lactobacillus plantarum L-137 enhances protection against influenza virus infection by stimulation of type I interferon production in mice, Int Immunopharmacol source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Antibiotic-treated mice exhibited markedly decreased fecal and serum DAT levels, which was associated with attenuated type I IFN responses to influenza infection and increased mortality”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Gut microbiome: therapeutic avenues for acute respiratory infections
What the sources say
- Not checked yetcites [59] Steed, 2017, The microbial metabolite desaminotyrosine protects from influenza through type I interferon, Science source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“microbiome depletion led to decreased survival, increased lung bacterial burden, and increased systemic dissemination of bacteria”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
- Not checked yetcites [55] Schuijt, 2016, The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia, Gut source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Several factors are known to influence airway microbiome composition including infection history, age, genetics, and structural lung disease.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
In the paper
“SFB-deficient animals have increased lung bacterial burdens and more severe pneumonia when challenged with methicillin-resistant Staphylococcus aureus (MRSA) (54), which was associated with decreased IL-17-mediated responses in the lung.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
- Not checked yetcites [54] Gauguet, 2015, Intestinal Microbiota of Mice Influences Resistance to Staphylococcus aureus Pneumonia, Infect Immun source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“in the microbiota-depleted group, alveolar macrophages and blood neutrophils exhibited decreased phagocytic activity, and decreased inflammatory cytokine production following ex vivo stimulation by Toll-like receptor (TLR) ligands such as lipoteichoic acid (LTA)”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The gut microbiome and respiratory infections > Effects of gut microbiome on host immune responses
What the sources say
- Not checked yetcites [55] Schuijt, 2016, The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia, Gut source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The URT and LRT have similar microbial community compositions, although microbe densities are much higher in the former in healthy hosts.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Individuals with chronic airway diseases (e.g., cystic fibrosis, COPD) have increased bacterial populations in the lungs (77) and differences in the relative abundance of certain species”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The major phyla in healthy lungs are Bacteroidetes and Firmicutes, which mainly include Prevotella, Veillonella, and Streptococcus”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
- Not checked yetcites [78] Morris, 2013, Comparison of the respiratory microbiome in healthy nonsmokers and smokers, Am J Respir Crit Care Med source
- Not checked yetcites [79] Segal, 2013, Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation, Microbiome source
- Not checked yetcites [80] Dickson, 2015, Spatial variation in the healthy human lung microbiome and the adapted island model of lung biogeography, Ann Am Thorac Soc source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Contrary to dogma that normal healthy lungs are a sterile environment, a distinct, and somewhat dynamic lung microbiome can be identified using sequencing technology, with microaspiration serving as the primary route of microbial immigration from the URT to the LRT”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
What the sources say
- Not checked yetcites [76] Bassis, 2015, Analysis of the upper respiratory tract microbiotas as the source of the lung and gastric microbiotas in healthy individuals, MBio source
- Not checked yetcites [77] Venkataraman, 2015, Application of a neutral community model to assess structuring of the human lung microbiome, MBio source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“A limited number of pathogens including Streptococcus pneumoniae, Neisseria meningitides, and Haemophilus influenzae are commensal bacteria of the URT.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
None of the sources cited for this claim have been checked yet.
In the paper
“Both studies included subjects ranging from infants to adults >80 years of age, limiting conclusions about age-related effects.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [71] Yi, 2014, Profiling bacterial community in upper respiratory tracts, BMC Infect Dis source
- Not checked yetcites [100] Edouard, 2018, The nasopharyngeal microbiota in patients with viral respiratory tract infections is enriched in bacterial pathogens, Eur J Clin Microbiol Infect Dis source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, unlike other diseases where decreased diversity is considered deleterious to the host, the effects of viral infections on diversity per se are variable and not presently considered a good indicator of risk for complications, including secondary bacterial pneumonias.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Children with severe influenza showed decreased relative abundance of S. aureus and increased abundance of Prevotella, Streptobacillus, Porphyromonas, Granulicatella, Veillonella, Fusobacterium, and Haemophilus.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [105] Langevin, 2017, Early nasopharyngeal microbial signature associated with severe influenza in children: a retrospective pilot study, J Gen Virol source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“RSV-infected mice who underwent antibiotic-mediated depletion of Streptococcus viridans in the nasopharynx exhibited increases in number of inflammatory lymphocytes and airway hyperresponsiveness, and decreases in regulatory T cell number and transforming growth factor-β production”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [103] Ni, 2012, Pharyngeal microflora disruption by antibiotics promotes airway hyperresponsiveness after respiratory syncytial virus infection, PLoS ONE source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In a study of mice colonized with S. pneumoniae and then infected with influenza A virus 3 days after, S. pneumoniae transmission occurred only when all mice were infected with influenza and was blocked by an influenza-neutralizing antibody”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [95] Diavatopoulos, 2010, Influenza A virus facilitates Streptococcus pneumoniae transmission and disease, FASEB J source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In healthy children, the major phyla among nasopharyngeal microbiotas are Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria, with Moraxella, Haemophilus, Streptococcus, Flavobacteria, Dolosigranulum, Corynebacterium, and Neisseria as predominant genera.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [114] Bogaert, 2011, Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis, PLoS ONE source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Another complicating factor particularly in cross-sectional studies examining the microbiome during viral infections is that the groups are not well-controlled and the sample numbers are relatively small considering the number of variables that could affect the respiratory tract microbiome–such as age, gender, oral hygiene and nose-picking habits, healthcare-based employment status, smoking status”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“although mean relative abundances of Haemophilus, Moraxella, Staphylococcus, and Corynebacterium varied significantly between summer and fall samples and between age groups.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [115] Pérez-Losada, 2017, Nasopharyngeal microbiome diversity changes over time in children with asthma, PLoS ONE source
plaincorrelationaln = 40- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The underlying type of viral infection, sampling timepoint after onset of infection, severity of infection, and concomittant antimicrobial usage are other confounding factors.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“However, these studies demonstrated that there was considerable inter-subject variability, highlighting the need for longitudinal studies to decipher changes following viral infection.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [108] Leung, 2013, Modulation of potential respiratory pathogens by pH1N1 viral infection, Clin Microbiol Infect source
- Not checked yetcites [109] Chaban, 2013, Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza, PLoS ONE source
- Not checked yetcites [110] Greninger, 2010, A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America, PLoS ONE source
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“An investigation of the frequency and seasonal variation in bacterial and viral load in asymptomatic healthcare professionals during the winter and summer months showed that of the 100 subjects tested during the winter, 34 were colonized with at least one bacterial species and 11 tested positive for at least one virus.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [116] Hassoun, 2015, Seasonal variation of respiratory pathogen colonization in asymptomatic health care professionals: A single-center, cross-sectional, 2-season observational study, Am J Infect Control source
plainn = 100- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In the nasopharyngeal compartment of Aboriginal and non-Aboriginal children in Australia, positive associations were detected between hRV and S. pneumoniae, H. influenza, and Moraxella catarrhalis carriage as well as between adenovirus and M. catarrhalis (111).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [111] Jacoby, 2007, Kalgoorlie Otitis Media Research Project Team. Modelling the co-occurrence of Streptococcus pneumoniae with other bacterial and viral pathogens in the upper respiratory tract, Vaccine source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“These profiles, however, were not associated with virus type but were linked to the age of subjects (71).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [71] Yi, 2014, Profiling bacterial community in upper respiratory tracts, BMC Infect Dis source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Changes in nasopharyngeal microbiome diversity were observed across seasons, with a predominance of Proteobacteria and Fusobacteria in fall-winter and Bacteroidetes and Firmicutes in spring; these differences were independent of recent antibiotics and viral co-infection (114).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [114] Bogaert, 2011, Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis, PLoS ONE source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In a mouse model, bacterial density in the nasopharynx after LAIV administration was increased as much as 100,000 times compared to influenza-naive hosts, and the duration of carriage of S. pneumoniae or S. aureus was also increased 2 to 5-fold (121).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [121] Mina, 2014, Live attenuated influenza vaccine enhances colonization of Streptococcus pneumoniae and Staphylococcus aureus in mice, MBio source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In healthy adult volunteers, it was demonstrated that intranasal LAIV administration induced an increase in the diversity of the nasopharyngeal microbiome, as well as relative abundances of Staphylococcus and Bacteroides (107).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [107] Tarabichi, 2015, The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles, Microbiome source
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Nasopharyngeal sampling showed completely opposite results, with decreased relative abundance of Haemophilus and Neisseria spp., but an increase in the normal nasal commensal, Propionibacterium, in subjects following hRV infection (73).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [73] Allen, 2014, Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge, Microbiome source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Administration of live attenuated influenza vaccine (LAIV), which is nasally instilled, to healthy children increased the nasal colonization density of S. pneumoniae in subjects who harbored this bacterium at the time of vaccination, and transiently increased rates of colonization by H. influenza (120).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [120] Thors, 2016, The effects of live attenuated influenza vaccine on nasopharyngeal bacteria in healthy 2 to 4 year olds. a randomized controlled trial, Am J Respir Crit Care Med source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In contrast, of the 100 subjects tested during the summer, 37 harbored at least one bacterium (mainly MRSA and K. pneumoniae) and four tested positive for one virus (116).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [116] Hassoun, 2015, Seasonal variation of respiratory pathogen colonization in asymptomatic health care professionals: A single-center, cross-sectional, 2-season observational study, Am J Infect Control source
plainn = 100- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In the oropharyngeal compartment, rhinovirus infection was associated with a strong trend toward transient increases in the relative abundances of H. parainfluenzae, Neisseria subflava and a weak trend toward an increase in S. aureus (119).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [119] Hofstra, 2015, Changes in microbiota during experimental human Rhinovirus infection, BMC Infect Dis source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Another study of 31 families with small children using longitudinal nasal swab sampling demonstrated that rhinovirus infection was associated with increased acquisition of S. pneumoniae from the community as well as increased transmission of S. pneumoniae within the family (118).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [118] Karppinen, 2017, Acquisition and transmission of streptococcus pneumoniae are facilitated during rhinovirus infection in families with children, Am J Respir Crit Care Med source
boostedcorrelationaln = 31- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Interestingly, the percentage of colonized children and bacterial density were also higher at asymptomatic visits in which virus was detected than at those in which virus was not detected (117).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [117] DeMuri, 2018, Dynamics of bacterial colonization with streptococcus pneumoniae, haemophilus influenzae, and moraxella catarrhalis during symptomatic and asymptomatic viral upper respiratory tract infection, Clin Infect Dis source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“In subjects with chronic obstructive pulmonary disease (COPD) after hRV infection but not in healthy individuals, there was an increase in bacterial burden and growth of bacteria present at baseline, particularly H. influenzae (124).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [124] Molyneaux, 2013, Outgrowth of the bacterial airway microbiome after rhinovirus exacerbation of chronic obstructive pulmonary disease, Am J Respir Crit Care Med source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“First, mucus production in the respiratory tract is increased to facilitate viral clearance during infections. However, excessive mucus production can lead to airway obstruction by impeding mucociliary clearance (125).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [125] Vareille, 2011, The airway epithelium: soldier in the fight against respiratory viruses, Clin Microbiol Rev source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Increased upper respiratory tract persistence of S. aureus as well as increased risk of S. aureus pneumonia was observed in flu-infected wildtype mice compared to mice lacking the type III IFN receptor (123).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the URT microbiome during respiratory viral infection
What the sources say
- Not checked yetcites [123] Planet, 2016, Lambda interferon restructures the nasal microbiome and increases susceptibility to staphylococcus aureus superinfection, MBio source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Respiratory viruses not only alter the bacterial community in the URT, but also promote bacterial colonization of the LRT by a variety of mechanisms that impair bacterial clearance.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Compared to studies of the URT microbiome, studies of the LRT microbiome following viral infections are relatively scarce due to the difficulty of obtaining uncontaminated samples from the lung.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Samples of convenience, such as sputum, suffer from oral contamination, but bronchoscopic samples are invasive and expensive to obtain on a regular basis.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > The respiratory tract microbiome > Studies of the LRT microbiome during respiratory viral infection
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“Subsequent studies by another group reported that C. pseudodiphtheriticum inhibited S. aureus growth, whereas C. accolens and S. aureus appeared to support each other's growth (139).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [139] Yan, 2013, Nasal microenvironments and interspecific interactions influence nasal microbiota complexity and S. aureus carriage, Cell Host Microbe source
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“These data imply that influenza infection perturbs the respiratory microbiome, leading to the production of secondary metabolites including immune-modulating molecules.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [108] Leung, 2013, Modulation of potential respiratory pathogens by pH1N1 viral infection, Clin Microbiol Infect source
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Interestingly, a recent preclinical study using a murine model of RSV and S. pneumoniae superinfection employed nasal priming by a C. pseudodiphtheriticum strain to augment host defense against the viral infection, which enhanced clearance of secondary bacterial challenge and reduced lung injury measures (140).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [140] Kanmani, 2017, Respiratory commensal bacteria corynebacterium pseudodiphtheriticum improves resistance of infant mice to respiratory syncytial virus and streptococcus pneumoniae superinfection, Front Microbiol source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Conversely, other investigators observed that Corynebacterium spp. were enriched in children who were not nasally colonized with pneumococcus, and demonstrated that C. accolens inhibit S. pneumoniae growth in vitro by expressing a lipase that releases free fatty acids from skin surface triacylglycerols, which inhibit pneumococcal growth.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“The mechanism appeared to be bacteriocin-independent.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [137] Uehara, 2000, Bacterial interference among nasal inhabitants: eradication of Staphylococcus aureus from nasal cavities by artificial implantation of Corynebacterium sp, J Hosp Infect source
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, it is possible that the immune response incited by acute viral infections, changes in the host epithelial surface caused by the virus, or the virus itself might lead to elimination of a host commensal that is responsible for keeping pathobionts in check.”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
- Rests on an assumption: Interspecies competition maintains homeostasis of the microbial community, preventing one microbe from dominating the community.
None of the sources cited for this claim have been checked yet.
In the paper
“Viruses have also been found to impair bacterial biofilm formation and disrupt existing biofilm (141–144).”
§ Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia > Intermicrobial interactions and postviral secondary infections
What the sources say
- Not checked yetcites [141] Reddinger, 2016, Host physiologic changes induced by influenza a virus lead to staphylococcus aureus biofilm dispersion and transition from asymptomatic colonization to invasive disease, MBio source
- Not checked yetcites [142] Pettigrew, 2014, Dynamic changes in the Streptococcus pneumoniae transcriptome during transition from biofilm formation to invasive disease upon influenza A virus infection, Infect Immun source
- Not checked yetcites [143] Marks, 2013, Interkingdom signaling induces Streptococcus pneumoniae biofilm dispersion and transition from asymptomatic colonization to disease, MBio source
- Not checked yetcites [144] Reddinger, 2018, Streptococcus pneumoniae modulates staphylococcus aureus biofilm dispersion and the transition from colonization to invasive disease, MBio source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper relies on this without support.
Bacterial pneumonia frequently arises as a result of aspirated bacterial pathogens.
“Given that bacterial pneumonia frequently arises as a result of aspirated bacterial pathogens, a potential mechanism by which viral infections might increase the risk of secondary bacterial infections is through increased colonization of the upper respiratory tract by bacterial pathogens.”
The paper relies on this without support.
Interspecies competition maintains homeostasis of the microbial community, preventing one microbe from dominating the community.
“However, interspecies competition also maintains homeostasis of the microbial community, either through their abilities to capture scare resources (e.g., iron), or targeted killing of other bacteria (e.g., bacteriocins), preventing one microbe from dominating the community.”
The paper relies on this without support.
Mechanisms have evolved in bacteria that confer competitive advantages, permitting them to survive in an otherwise inhospitable host environment.
“It has long been appreciated that mechanisms have evolved in bacteria that confer competitive advantages, permitting them to survive in an otherwise inhospitable host environment.”
The paper relies on this without support.
Innate immune cells including macrophages and neutrophils are recruited to the lung by cytokines and chemokines for phagocytosis and bactericidal activity.
“Innate immune cells including macrophages and neutrophils are recruited to the lung by cytokines and chemokines for phagocytosis and bactericidal activity.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Influenza is the most common type of acute respiratory infection (Hanada et al., 2018)”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Hanada et al., 2018
Citations
Cites
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785
The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T reg Cell Homeostasis
Smith, P. M., Howitt, M. R., Panikov, N., Michaud, M., Gallini, C. A., Bohlooly-Y, M., Glickman, J. N., & Garrett, W. S. (2013) · Science · doi:10.1126/science.1241165 · Cited by 5,413
Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation
Arpaia, N., Campbell, C., Fan, X., Dikiy, S., van der Veeken, J., deRoos, P., Liu, H., Cross, J. R., Pfeffer, K., Coffer, P. J., et al. (2013) · Nature · doi:10.1038/nature12726 · Cited by 4,838
Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria
Ivanov, I. I., Atarashi, K., Manel, N., Brodie, E. L., Shima, T., Karaoz, U., Wei, D., Goldfarb, K. C., Santee, C. A., Lynch, S. V., et al. (2009) · Cell · doi:10.1016/j.cell.2009.09.033 · Cited by 4,554
The role of nasal carriage in Staphylococcus aureus infections
Wertheim, H. F., Melles, D. C., Vos, M. C., van Leeuwen, W., van Belkum, A., Verbrugh, H. A., & Nouwen, J. L. (2005) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(05)70295-4 · Cited by 2,685
Updating the accounts: global mortality of the 1918–1920 "Spanish" influenza pandemic.
Johnson, N. P. A. S., & Mueller, J. (2002) · Bulletin of the History of Medicine · doi:10.1353/bhm.2002.0022 · Cited by 1,980
Streptococcus pneumoniae colonisation: the key to pneumococcal disease
Bogaert, D., de Groot, R., & Hermans, P. (2004) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(04)00938-7 · Cited by 1,929 · cited 1×
“Nonetheless, bacterial colonization of the URT is generally considered as the first step in the development of invasive bacterial infections (83, 84), including secondary bacterial infections following respiratory viral infection.”
BackgroundHospitalized patients with 2009 H1N1 influenza in the United States, April-June 2009
Jain, S., Kamimoto, L., Bramley, A. M., Schmitz, A. M., Benoit, S. R., Louie, J., Sugerman, D. E., Druckenmiller, J. K., Ritger, K. A., Chugh, R., et al. (2009) · New England Journal of Medicine · doi:10.1056/nejmoa0906695 · Cited by 1,700
Morens, D. M., Taubenberger, J. K., & Fauci, A. S. (2008) · The Journal of Infectious Diseases · doi:10.1086/591708 · Cited by 1,625 · cited 1×
“It is estimated that the so-called "Spanish Flu" pandemic of H1N1 influenza A virus from 1918 to 1919 resulted in more than 50 million deaths, with many caused by bacterial superinfection leading to secondary pneumonia (1) (2) (3) (4) (5) (6) (7) .”
Background
Cited by
Sorted by citations
Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization
Zuo, T., Zhang, F., Lui, G. C. Y., Yeoh, Y. K., Li, A. Y. L., Zhan, H., Wan, Y., Chung, A. C. K., Cheung, C. P., Chen, N., et al. (2020) · Gastroenterology · doi:10.1053/j.gastro.2020.05.048 · Cited by 1,537
Coronavirus disease 2019 (COVID-19) pandemic and pregnancy
Dashraath, P., Wong, J. L. J., Lim, M. X. K., Lim, L. M., Li, S. W. L., Biswas, A., Choolani, M. A., Mattar, C. N. Z., & Su, L. (2020) · American Journal of Obstetrics and Gynecology · doi:10.1016/j.ajog.2020.03.021 · Cited by 1,521
Iddir, M., Alex Brito, O., Dingeo, G., Sosa, S., Samouda, H., Frano, M. R. L., & Bohn, T. (2020) · Nutrients · doi:10.3390/nu12061562 · Cited by 825
Shen, Z., Xiao, Y., Kang, L., Ma, W., Shi, L., Zhang, L., Zhou, Z., Yang, J., Zhong, J., Yang, D., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa203 · Cited by 513
Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies
Aggarwal, N., Kitano, S., Puah, G. R. Y., Kittelmann, S., Hwang, I. Y., & Chang, M. W. (2022) · Chemical Reviews · doi:10.1021/acs.chemrev.2c00431 · Cited by 571
Metadata
- Authors
- Hanada, S., Pirzadeh, M., Carver, K. Y., & Deng, J. C.
- Affiliations
- University of Michigan (US)
- Corresponding author
- Deng, Jane C.
- Venue
- Frontiers in Immunology
- Publisher
- Frontiers Media SA
- Published
- 2018-11-16
- Volume
- 9
- Pages
- 2640-2640
- ISSN
- 1664-3224 (ISSN-L)
- PMC
- PMC6250824
- OpenAlex
- W2900850632
- Semantic Scholar
- 8c97d3d01a4d77e5f4f458ed46ba5399f3647a74
- Cited by
- 495
- References
- 147
- Citations by year
- 2026: 29 · 2025: 53 · 2024: 58 · 2023: 77 · 2022: 89 · 2021: 110 · 2020: 72 · 2019: 7
- FWCI
- 4.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Frontiers in Immunology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Veterans Affairs
- National Institutes of Health
- National Heart, Lung, and Blood Institute (R01HL108949)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Epidemiology › Influenza Virus Research Studies
- Health Sciences › Medicine › Epidemiology › Respiratory viral infections research
- Keywords
- respiratory viral infections, influenza, secondary bacterial pneumonia, airway microbiome, dysbiosis, gut microbiota, mucosal microbiota, host defense, viral-bacterial interactions, antiviral immunity
- MeSH terms
- Gastrointestinal Microbiome, Host Microbial Interactions, Humans, Immunity, Innate, Respiratory Tract Infections, Virus Diseases, Pneumonia, Bacterial, Coinfection, Microbiota, Dysbiosis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-09, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-09 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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