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Cited by 460Sepsis Diagnosis and TreatmentGut microbiota and healthNosocomial Infections in ICU

The microbiome and critical illness

Open access
Dickson, Robert P·2016·The Lancet Respiratory Medicine
DOI 10.1016/s2213-2600(15)00427-0PMC PMC4752077
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Abstract

The central role of the microbiome in critical illness is supported by a half century of experimental and clinical study. The physiological effects of critical illness and the clinical interventions of intensive care substantially alter the microbiome. In turn, the microbiome predicts patients’ susceptibility to disease, and manipulation of the microbiome has prevented or modulated critical illness in animal models and clinical trials. This Review surveys the microbial ecology of critically ill patients, presents the facts and unanswered questions surrounding gut-derived sepsis, and explores the radically altered ecosystem of the injured alveolus. The revolution in culture-independent microbiology has provided the tools needed to target the microbiome rationally for the prevention and treatment of critical illness, holding great promise to improve the acute and chronic outcomes of the critically ill.

AI snapshot

Written from the paper’s full text.

TL;DR

This review argues that critical illness and intensive-care interventions substantially alter the gut and lung microbiomes, and that these altered communities contribute to sepsis, ARDS, pneumonia, and exacerbations of chronic lung disease. It synthesizes historical and modern culture-independent evidence to propose the microbiome as an underrecognized diagnostic, prognostic, and therapeutic target in critical care.

Key findings

  • Critical illness collapses gut bacterial diversity: the stomach and proximal small intestine become overgrown by a few species such as *E coli*, *P aeruginosa*, and *Enterococcus* spp, while the lower gastrointestinal tract loses diversity and can be overrun by a few or even one species; butyrate-producing bacteria are uncommon or absent and butyrate production is at a minimum.
  • Gut-derived sepsis evidence is strong: minimizing gut bacterial burden with enteric antibiotics or germ-free animals lessens distal organ inflammation and injury across species and shock types; selective decontamination of the digestive tract has been tested in more than 65 randomised controlled trials studying more than 15000 patients, with patients less likely to develop multiorgan failure or die.
  • In more than 10000 hospital inpatients, a strong dose–response relation was found between estimated intestinal dysbiosis and subsequent severe sepsis.
  • Injured alveoli become ecologically more like the gut: sterile lung injury in mice increases lung bacterial content and shifts community membership, and bacteria from injured lungs provoke more inflammation and injury in healthy mice than bacteria from uninjured lungs; intraoperative larger tidal volumes increased postoperative pneumonia fivefold, from 1·5% to 8·0%.
  • Exacerbations of chronic lung disease are not acute bacterial infections: culture-independent studies consistently report no increase in bacterial burden and no decrease in community diversity during exacerbations, while azithromycin decreases exacerbation frequency in COPD, cystic fibrosis, and bronchiectasis.

Methods

  • Narrative review; no primary data collection. It surveys the microbial ecology of critically ill patients, focusing on the gut and lungs, and discusses sepsis, ARDS, pneumonia, and exacerbations of chronic lung disease.
  • Evidence base includes experimental animal models (mice, rats, rabbits, dogs), clinical trials, meta-analyses, population studies, and culture-independent microbiome studies, with tables summarizing ecological effects of critical illness and intensive-care interventions.
  • Main analytic framework is community ecology—immigration, elimination, and relative reproduction rates—applied to gut and lung microbiomes; it is a conceptual synthesis rather than a systematic review or meta-analysis.

Limitations

  • The paper states that mechanisms of gut-derived sepsis remain controversial and incompletely understood; the three hypotheses (systemic translocation, gut-lymph translocation, and in-situ virulence) probably explain complementary features but are unresolved.
  • The paper states that observational human studies alone cannot disentangle the effects of critical illness from its treatment (eg, antibiotics), so future investigation requires animal studies and prospective controlled human trials; effects on viruses, archaea, and eukaryotes are unknown, as are the clinical consequences of butyrate loss and the natural history of microbiome recovery.
  • Evident from the text: as a narrative review, it does not report a systematic search strategy, risk-of-bias assessment, or new primary outcomes, and some cited evidence comes from animal models or indirect associations.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1016/s2213-2600(15)00427-0

Cites

168 of 168 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 215 cited sources checked · 0 supported · 0 flagged

  • Findingcitation

    In critically ill patients, healthy oral microbiota are displaced by gram-negative aerobes, including prominent members of the Proteobacteria phylum.

    “in critically ill patients, healthy oral microbiota are displaced by gram-negative aerobes (figure 1), including prominent members of the Proteobacteria phylum”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [4] Johanson, 1969, Changing pharyngeal bacterial flora of hospitalized patients. Emergence of gram-negative bacilli, N Engl J Med source

      Not checked in the free run.

    • cites [7] Bahrani-Mougeot, 2007, Molecular analysis of oral and respiratory bacterial species associated with ventilator-associated pneumonia, J Clin Microbiol source

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  • Findingcitation

    Exposure to the hospital setting has minimal effect on the bacterial communities of the upper respiratory tract.

    “Exposure to the hospital setting has minimal effect on the bacterial communities of the upper respiratory tract”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [4] Johanson, 1969, Changing pharyngeal bacterial flora of hospitalized patients. Emergence of gram-negative bacilli, N Engl J Med source

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  • Findingcitation

    In critical illness, the stomach and proximal small intestine become overgrown by a small number of species, such as E coli, P aeruginosa, and Enterococcus spp.

    “The stomach and proximal small intestine, which are usually sparsely populated, become overgrown by a small number of species, such as E coli, P aeruginosa, and Enterococcus spp.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [67] Marshall, 1988, The microbiology of multiple organ failure. The proximal gastrointestinal tract as an occult reservoir of pathogens, Arch Surg source

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    • cites [68] de la Cal, 2013, Selective digestive decontamination and bacterial resistance, Lancet Infect Dis source

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  • Findingcitation

    Dominant species in the lower gastrointestinal tract of critically ill patients include S aureus, Enterococcus spp, and members of the Enterobacteriaceae family.

    “Dominant species include S aureus, Enterococcus spp, and members of the Enterobacteriaceae family (including E coli and Klebsiella spp).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [20] Zaborin, 2014, Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness, MBio source

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    • cites [69] Shimizu, 2011, Altered gut flora are associated with septic complications and death in critically ill patients with systemic inflammatory response syndrome, Dig Dis Sci source

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    • cites [70] Madan, 2012, Gut microbial colonisation in premature neonates predicts neonatal sepsis, Arch Dis Child Fetal Neonatal Ed source

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  • Findingcitation

    In critically ill patients, transit time is substantially slowed by various pathophysiological and therapeutic factors.

    “In critically ill patients, transit time is substantially slowed by various pathophysiological (glucose and electrolyte disturbances8,9 and endogenous opioid production) and therapeutic (sedatives, opiates, and systemic catecholamines21) factors.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [8] Björnsson, 1994, Effects of hyperglycemia on interdigestive gastrointestinal motility in humans, Scand J Gastroenterol source

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    • cites [9] Lowman, 1971, The potassium depletion states and postoperative ileus. The role of the potassium ion, Radiology source

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    • cites [21] Dive, 2000, Effect of dopamine on gastrointestinal motility during critical illness, Intensive Care Med source

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  • Classified as probably not a substantial claim. 6
  • May combine two claims. 42

  • Probably not a substantial claim: may not pass S4 (based).

    Findingnone given

    Decades of research into the diseases of critical illness have yielded no targeted therapies.

    “decades of research into the diseases of critical illness have yielded no targeted therapies”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    Normally rare fungi such as Candida spp bloom in the gut of critically ill patients, and culture-based detection of candidaemia is a marker of disease severity and predictive of a poor outcome.

    “normally rare fungi, such as Candida spp, bloom and thrive;20 culture-based detection of candidaemia is a marker of disease severity and predictive of a poor outcome.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [20] Zaborin, 2014, Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness, MBio source

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    • cites [72] Wey, 1988, Hospital-acquired candidemia. The attributable mortality and excess length of stay, Arch Intern Med source

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  • May combine two claims.

    Findingcitation

    In critical illness, bile salt production drops, IgA production is impaired, and the dense mucosal barrier of secreted antimicrobial peptides is lost.

    “bile salt production drops,17 IgA production is impaired,31 and the dense mucosal barrier of secreted antimicrobial peptides is lost.”
    Quote in the paperSubstantial claim0 of 5 sources checked
    • cites [17] de Vree, 1999, Lack of enteral nutrition during critical illness is associated with profound decrements in biliary lipid concentrations, Am J Clin Nutr source

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    • cites [31] Coutinho, 1997, Intra-abdominal sepsis: an immunocytochemical study of the small intestine mucosa, J Clin Pathol source

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    • cites [25] Lu, 2011, The anatomic sites of disruption of the mucus layer directly correlate with areas of trauma/hemorrhagic shock-induced gut injury, J Trauma source

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    • cites [26] Rupani, 2007, Relationship between disruption of the unstirred mucus layer and intestinal restitution in loss of gut barrier function after trauma hemorrhagic shock, Surgery source

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    • cites [32] Book, 2007, Inducibility of the endogenous antibiotic peptide beta-defensin 2 is impaired in patients with severe sepsis, Crit Care source

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  • May combine two claims.

    Findingcitation

    In studies of the gut microbiome in critically ill patients, butyrate-producing bacteria are uncommon or absent, and butyrate production is at a minimum.

    “In studies of the gut microbiome in critically ill patients, butyrate-producing bacteria are uncommon or absent,20,69–71 and butyrate production is at a minimum.”
    Quote in the paperSubstantial claim0 of 4 sources checked
    • cites [20] Zaborin, 2014, Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness, MBio source

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    • cites [69] Shimizu, 2011, Altered gut flora are associated with septic complications and death in critically ill patients with systemic inflammatory response syndrome, Dig Dis Sci source

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    • cites [70] Madan, 2012, Gut microbial colonisation in premature neonates predicts neonatal sepsis, Arch Dis Child Fetal Neonatal Ed source

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    • cites [71] Shimizu, 2006, Altered gut flora and environment in patients with severe SIRS, J Trauma source

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  • May combine two claims.

    Findingcitation

    Increased nitrate concentrations and an altered mucosal oxygen gradient favour the growth of microbes in the Proteobacteria phylum and some members of the Firmicutes phylum.

    “Increased nitrate concentrations13 and an altered mucosal oxygen gradient29 favour the growth of microbes in the Proteobacteria phylum”
    Quote in the paperSubstantial claim0 of 5 sources checked
    • cites [13] Winter, 2013, Host-derived nitrate boosts growth of E. coli in the inflamed gut, Science source

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    • cites [29] Albenberg, 2014, Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota, Gastroenterology source

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    • cites [14] Lupp, 2007, Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae, cell Host Microbe source

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    • cites [15] Honda, 2012, The microbiome in infectious disease and inflammation, Annu Rev Immunol source

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    • cites [16] Grootjans, 2010, Human intestinal ischemia-reperfusion-induced inflammation characterized: experiences from a new translational model, Am J Pathol source

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  • May combine two claims.

    Findingcitation

    In the stomach of critically ill patients, transit time slows and pH is neutralised by the use of agents that suppress gastric acid production.

    “In the stomach, which is normally fast to empty and extremely acidic, transit time slows36 and pH is neutralised by the use of agents to suppress the production of gastric acid.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [36] Moore, 1988, Effect of body posture on radionuclide measurements of gastric emptying, Dig Dis Sci source

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    • cites [38] Lombardo, 2010, Increased incidence of small intestinal bacterial overgrowth during proton pump inhibitor therapy, Clin Gastroenterol Hepatol source

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    • cites [39] Du Moulin, 1982, Aspiration of gastric bacteria in antacid-treated patients: a frequent cause of postoperative colonisation of the airway, Lancet source

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  • May combine two claims.

    Findingcitation

    Topical oral decontamination decreases the bacterial burden of the oropharynx and decreases immigration from the source community.

    “topical oral decontamination, decrease the bacterial burden of the oropharynx and decrease immigration from the source community”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [44] Benus, 2010, Impact of digestive and oropharyngeal decontamination on the intestinal microbiota in ICU patients, Intensive Care Med source

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  • May combine two claims.

    Findingcitation

    The upper gastrointestinal tract becomes a stagnant reservoir of potential pathogens whose presence is predictive of extra-abdominal infections and multiorgan failure.

    “The upper gastrointestinal tract becomes a stagnant reservoir of potential pathogens, the presence of which is predictive of extra-abdominal infections and multiorgan failure.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [64] Marshall, 1993, The gastrointestinal tract. The “undrained abscess” of multiple organ failure, Ann Surg source

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    • cites [67] Marshall, 1988, The microbiology of multiple organ failure. The proximal gastrointestinal tract as an occult reservoir of pathogens, Arch Surg source

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  • May combine two claims.

    Findingcitation

    The lower gastrointestinal tract in critical illness loses diversity and the community is overrun by a few bacterial species.

    “The lower gastrointestinal tract, which in healthy people contains hundreds of distinct bacterial species, loses diversity, and the community is overrun by a few (in some cases only one) bacterial species.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [20] Zaborin, 2014, Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness, MBio source

      Not checked in the free run.

    • cites [69] Shimizu, 2011, Altered gut flora are associated with septic complications and death in critically ill patients with systemic inflammatory response syndrome, Dig Dis Sci source

      Not checked in the free run.

    • cites [70] Madan, 2012, Gut microbial colonisation in premature neonates predicts neonatal sepsis, Arch Dis Child Fetal Neonatal Ed source

      Not checked in the free run.

  • May combine two claims.

    Findingcitation

    Elevation of the head of the bed decreases immigration of gastric microbiota to the lungs but also impedes microbial elimination from the lungs.

    “Elevation of the head of the bed decreases the immigration rate of gastric microbiota,58 but it also impedes microbial elimination”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [58] Torres, 1992, Pulmonary aspiration of gastric contents in patients receiving mechanical ventilation: the effect of body position, Ann Intern Med source

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    • cites [59] Li Bassi, 2008, Following tracheal intubation, mucus flow is reversed in the semirecumbent position: possible role in the pathogenesis of ventilator-associated pneumonia, Crit Care Med source

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  • May combine two claims.

    Findingcitation

    In trauma patients at high risk of multiorgan failure, serial blood cultures from indwelling portal vein catheters show minimum evidence of bacterial translocation and no association between portal vein bacteraemia and subsequent illness.

    “in a study of trauma patients at high risk of multiorgan failure,101 serial blood cultures drawn from indwelling portal vein catheters have shown minimum evidence of bacterial translocation and no association between portal vein bacteraemia and subsequent illness.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [101] Moore, 1991, Gut bacterial translocation via the portal vein: a clinical perspective with major torso trauma, J Trauma source

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  • May combine two claims.

    Findingcitation

    Depressed consciousness and sedation blunt the cough reflex, and endotracheal intubation and acute illness impair the mucociliary escalator.

    “Depressed consciousness and sedation blunt the cough reflex,46 and endotracheal intubation and acute illness impair the mucociliary escalator.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [46] Sekizawa, 1990, Lack of cough reflex in aspiration pneumonia, Lancet source

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    • cites [47] Nakagawa, 2005, Mucociliary clearance is impaired in acutely ill patients, Chest source

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  • May combine two claims.

    Findingcitation

    Since the first randomised controlled trial in 1987, selective decontamination of the digestive tract has been tested in more than 65 randomised controlled trials studying more than 15000 patients.

    “Since the first (which was also the first positive) randomised controlled trial in 1987,95 SDD has been tested in more than 65 randomised controlled trials studying more than 15000 patients.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [95] Unertl, 1987, Prevention of colonization and respiratory infections in long-term ventilated patients by local antimicrobial prophylaxis, Intensive Care Med source

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    • cites [96] Silvestri, 2012, Selective decontamination of the digestive tract: the mechanism of action is control of gut overgrowth, Intensive Care Med source

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  • May combine two claims.

    Findingcitation

    The intestinal wall of critically ill patients is permeable, and the degree of permeability correlates with subsequent risks of organ injury and death.

    “The intestinal wall of critically ill patients is permeable, and the degree of permeability correlates with subsequent risks of organ injury and death.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [100] Doig, 1998, Increased intestinal permeability is associated with the development of multiple organ dysfunction syndrome in critically ill ICU patients, Am J Respir Crit Care Med source

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  • May combine two claims.

    Findingcitation

    Patients who receive selective decontamination of the digestive tract are less likely to develop multiorgan failure or die than patients who do not.

    “patients who receive SDD are less likely to develop multiorgan failure91 or die96 than patients who do not”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [91] Silvestri, 2010, Impact of selective decontamination of the digestive tract on multiple organ dysfunction syndrome: systematic review of randomized controlled trials, Crit Care Med source

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    • cites [96] Silvestri, 2012, Selective decontamination of the digestive tract: the mechanism of action is control of gut overgrowth, Intensive Care Med source

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  • May combine two claims.

    Findingcitation

    In alveolar injury, the bactericidal surfactant layer is inactivated and microbial elimination is slowed by impairment of mucociliary clearance.

    “The bactericidal surfactant layer is inactivated55,57 and microbial elimination is slowed by impairment of mucociliary clearance.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [55] Günther, 1996, Surfactant alterations in severe pneumonia, acute respiratory distress syndrome, and cardiogenic lung edema, Am J Respir Crit Care Med source

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    • cites [57] Wu, 2003, Surfactant proteins A and D inhibit the growth of Gram-negative bacteria by increasing membrane permeability, J Clin Invest source

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    • cites [47] Nakagawa, 2005, Mucociliary clearance is impaired in acutely ill patients, Chest source

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  • May combine two claims.

    Findingnone given

    Pneumonia is the most common cause of sepsis, whereas exacerbations rarely or never provoke a septic response.

    “whereas pneumonia is the most common cause of sepsis, exacerbations rarely or never provoke a septic response.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    The cells of innate immunity increase in number and activation in alveolar injury, causing the alveolar concentration of molecules related to the host stress response to increase.

    “The cells of innate immunity (macrophages and neutrophils) increase in number and activation, which causes the alveolar concentration of molecules related to the host stress response to increase.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [117] Meduri, 1995, Inflammatory cytokines in the BAL of patients with ARDS. Persistent elevation over time predicts poor outcome, Chest source

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  • May combine two claims.

    Findingcitation

    Culture-independent studies comparing bacterial communities at baseline and during exacerbations in the airways of patients with COPD, cystic fibrosis, or bronchiectasis consistently report no increase in bacterial burden and no decrease in community diversity during exacerbations.

    “With remarkable consistency, all studies report no increase in bacterial burden and no decrease in community diversity during exacerbations.”
    Quote in the paperSubstantial claim0 of 8 sources checked
    • cites [132] Huang, 2014, Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease, J Clin Microbiol source

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    • cites [133] Millares, 2014, Bronchial microbiome of severe COPD patients colonised by Pseudomonas aeruginosa, Eur J Clin Microbiol Infect Dis source

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    • cites [134] Stressmann, 2011, Does bacterial density in cystic fibrosis sputum increase prior to pulmonary exacerbation?, J Cyst Fibros source

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    • cites [135] Zhao, 2012, Decade-long bacterial community dynamics in cystic fibrosis airways, Proc Natl Acad Sci USA source

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    • cites [136] Carmody, 2013, Changes in cystic fibrosis airway microbiota at pulmonary exacerbation, Ann Am Thorac Soc source

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    • cites [137] Price, 2013, Unique microbial communities persist in individual cystic fibrosis patients throughout a clinical exacerbation, Microbiome source

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    • cites [138] Carmody, 2015, The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation, Microbiome source

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    • cites [139] Tunney, 2013, Lung microbiota and bacterial abundance in patients with bronchiectasis when clinically stable and during exacerbation, Am J Respir Crit Care Med source

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  • May combine two claims.

    Findingcitation

    Raising the head of the patient's bed decreases immigration to the lungs of gastric microbiota compared with supine positioning, but this practice also compromises microbial elimination from the lungs.

    “Raising of the head of the patient’s bed decreases immigration to the lungs of gastric microbiota compared with supine positioning,149 but this practice also compromises microbial elimination from the lungs”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [149] Drakulovic, 1999, Supine body position as a risk factor for nosocomial pneumonia in mechanically ventilated patients: a randomised trial, Lancet source

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    • cites [59] Li Bassi, 2008, Following tracheal intubation, mucus flow is reversed in the semirecumbent position: possible role in the pathogenesis of ventilator-associated pneumonia, Crit Care Med source

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  • May combine two claims.

    Findingcitation

    Early intensive-care studies of probiotics suggest that they decrease the risk of pneumonia and shorten the length of stay in the intensive-care unit for ventilated patients and decrease systemic infections in high-risk postoperative patients.

    “Early intensive-care studies of probiotics suggest that they decrease the risk of pneumonia and shorten the length of stay in the intensive-care unit for ventilated patients150 and decrease systemic infections in high-risk postoperative patients.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [150] Siempos, 2010, Impact of the administration of probiotics on the incidence of ventilator-associated pneumonia: a meta-analysis of randomized controlled trials, Crit Care Med source

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    • cites [151] Pitsouni, 2009, Does the use of probiotics/synbiotics prevent postoperative infections in patients undergoing abdominal surgery? A meta-analysis of randomized controlled trials, Eur J Clin Pharmacol source

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    Findingcitation

    Proton-pump inhibitors decrease elimination of gastric microbiota and increase immigration of bacteria into the lungs, which increases the risk of pneumonia.

    “proton-pump inhibitors decrease elimination of gastric microbiota38 and increase immigration of bacteria into the lungs, which increases the risk of pneumonia.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [38] Lombardo, 2010, Increased incidence of small intestinal bacterial overgrowth during proton pump inhibitor therapy, Clin Gastroenterol Hepatol source

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    • cites [148] Herzig, 2009, Acid-suppressive medication use and the risk for hospital-acquired pneumonia, JAMA source

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  • May combine two claims.

    Interpretationreasoning

    Critical illness substantially alters the physiology of the host, which in turn alters the environmental conditions and community structures of resident microbes.

    “Critical illness substantially alters the physiology of the host, which in turn alters the environmental conditions and community structures of resident microbes.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    The pathophysiological consequences of low butyrate in critical illness are predictable (epithelial cell death and dysregulated inflammation), but the clinical consequences are unknown.

    “The pathophysiological consequences of this condition are predictable (epithelial cell death and dysregulated inflammation), but the clinical consequences are unknown.”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [75] Donohoe, 2011, The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon, Cell Metab source

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    • cites [76] Furusawa, 2013, Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells, Nature source

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  • May combine two claims.

    Interpretationcitation

    The catabolic starvation state of critical illness results in decreased immigration of food-associated bacteria and decreased nutritional supply for commensal microbes.

    “The catabolic starvation state of critical illness results in decreased immigration of food-associated bacteria and decreased nutritional supply for commensal microbes.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [6] David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature source

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  • May combine two claims.

    Interpretationreasoning

    The net effect of altered elimination in critical illness is reduced elimination of bacteria, especially in the upper gastrointestinal tract, which becomes a pH-neutral reservoir overgrown by Gram-negative bacteria.

    “The net effect is reduced elimination of bacteria, especially in the upper gastrointestinal tract, which is transformed into a pH-neutral reservoir that quickly becomes overgrown by Gram-negative bacteria.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [64] Marshall, 1993, The gastrointestinal tract. The “undrained abscess” of multiple organ failure, Ann Surg source

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    • Rests on an assumption: The composition of every community, microbial or otherwise, is determined by the balance of three ecological factors: immigration into the community, elimination of members from the community, and the relative reproduction rates of the community's members.
    • Rests on an assumption: In healthy individuals, the primary means of microbial elimination from the gut microbiome is transit through and from the gastrointestinal tract.

  • May combine two claims.

    Premisecitation

    The lower gastrointestinal tract drains into the portal circulation and mesenteric lymph nodes; these nodes drain to the thoracic duct, which empties into the left subclavian vein.

    “The lower gastrointestinal tract drains not only into the portal circulation but also into mesenteric lymph nodes. These nodes drain to the thoracic duct, which in turn empties into the left subclavian vein.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [12] Deitch, 2012, Gut-origin sepsis: evolution of a concept, Surgeon source

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  • May combine two claims.

    Interpretationcitation

    In acute illness, the normally nutrient-poor alveolus is flooded with nutrient-rich oedema, oxygen and temperature gradients are established, and host stress signalling molecules selectively promote the growth of potential pathogens.

    “The normally nutrient-poor environment of the alveolus is flooded with nutrient-rich oedema,55 pockets of oxygen and heterogeneous temperature gradients are established,48,49 and the signalling molecules of the host stress response selectively promote the growth of potential pathogens.”
    Quote in the paperSubstantial claim0 of 6 sources checked
    • cites [55] Günther, 1996, Surfactant alterations in severe pneumonia, acute respiratory distress syndrome, and cardiogenic lung edema, Am J Respir Crit Care Med source

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    • cites [48] Worlitzsch, 2002, Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients, J Clin Invest source

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    • cites [49] Schmidt, 2014, Neutrophil elastase-mediated increase in airway temperature during inflammation, J Cyst Fibros source

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    • cites [23] Meduri, 1999, Cytokines IL-1beta, IL-6, and TNF-alpha enhance in vitro growth of bacteria, Am J Respir Crit Care Med source

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    • cites [50] Dickson, 2015, Intraalveolar catecholamines and the human lung microbiome, Am J Respir Crit Care Med source

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    • cites [51] Freestone, 2012, Pseudomonas aeruginosa-catecholamine inotrope interactions: a contributory factor in the development of ventilator-associated pneumonia?, Chest source

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  • May combine two claims.

    Interpretationreasoning

    The predicted effect of ecological forces in the lungs of critically ill patients is a state of increased immigration, decreased elimination, and favourable growth conditions for potential pathogens.

    “The predicted effect of these ecological forces in the lungs, therefore, is a state of increased immigration, decreased elimination, and favourable growth conditions for potential pathogens.”
    Quote in the paperSubstantial claim0 of 4 sources checked
    • cites [61] Muscedere, 2011, Subglottic secretion drainage for the prevention of ventilator-associated pneumonia: a systematic review and meta-analysis, Crit Care Med source

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    • cites [82] Bousbia, 2012, Repertoire of intensive care unit pneumonia microbiota, PLoS One source

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    • cites [83] Lu, 2014, Increased constituent ratios of Klebsiella sp., Acinetobacter sp., and Streptococcus sp. and a decrease in microflora diversity may be indicators of ventilator-associated pneumonia: a prospective study in the respiratory tracts of neonates, PLoS One source

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    • cites [84] May, 2015, A pilot study of the noninvasive assessment of the lung microbiota as a potential tool for the early diagnosis of ventilator-associated pneumonia, Chest source

      Not checked in the free run.

    • Rests on an assumption: The composition of every community, microbial or otherwise, is determined by the balance of three ecological factors: immigration into the community, elimination of members from the community, and the relative reproduction rates of the community's members.

  • May combine two claims.

    Interpretationcitation

    Clinical use of selective decontamination of the digestive tract remains uncommon, especially in North America, due to perceived risk of antimicrobial resistance, although this concern is not supported by large clinical trials and meta-analyses.

    “clinical use of SDD remains uncommon, especially in North America, due to perceived risk of antimicrobial resistance, although this concern is not supported by large clinical trials and meta-analyses.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [97] Daneman, 2013, Effect of selective decontamination on antimicrobial resistance in intensive care units: a systematic review and meta-analysis, Lancet Infect Dis source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    All three hypotheses (systemic translocation, gut-lymph translocation, and in-situ virulence) probably explain complementary features of a complex pathogenesis of multiorgan failure.

    “All three hypotheses (systemic translocation, gut-lymph translocation, and in-situ virulence) probably explain complementary features of a complex pathogenesis of multiorgan failure”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    The toxicity of mesenteric lymph does not depend on the presence of endotoxin or of detectable bacteria, suggesting that other bacterial or tissue injury factors are important mediators of injury.

    “the toxicity of this lymph does not depend on the presence of endotoxin or of detectable bacteria,104 which suggests that other bacterial or tissue injury factors are important mediators of injury.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [104] Reino, 2011, Trauma hemorrhagic shock-induced lung injury involves a gut-lymph-induced TLR4 pathway in mice, PLoS One source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    The alveolar space in healthy individuals is an ecologically unfavourable environment for most bacteria and reproduction is minimal.

    “the alveolar space is an ecologically unfavourable environment for most bacteria and reproduction is minimal.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [77] Dickson, 2015, Spatial Variation in the healthy human lung microbiome and the adapted island model of lung biogeography, Ann Am Thorac Soc source

      Not checked in the free run.

    • cites [112] Venkataraman, 2015, Application of a neutral community model to assess structuring of the human lung microbiome, MBio source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    Many daily therapies and interventions in intensive care increase intestinal permeability, bacterial translocation, and bacterial virulence.

    “Many daily therapies and interventions in intensive care increase intestinal permeability (eg, nonsteroidal anti-inflammatory drugs109 and parenteral feeding55,82), bacterial translocation (eg, antibiotics,65 corticosteroids,110 and opiates111), and bacterial virulence (eg, opiates19 and catecholamines22,51).”
    Quote in the paperSubstantial claim0 of 9 sources checked
    • cites [109] Bjarnason, 1986, Effect of non-steroidal anti-inflammatory drugs and prostaglandins on the permeability of the human small intestine, Gut source

      Not checked in the free run.

    • cites [55] Günther, 1996, Surfactant alterations in severe pneumonia, acute respiratory distress syndrome, and cardiogenic lung edema, Am J Respir Crit Care Med source

      Not checked in the free run.

    • cites [82] Bousbia, 2012, Repertoire of intensive care unit pneumonia microbiota, PLoS One source

      Not checked in the free run.

    • cites [65] Knoop, 2015, Antibiotics promote inflammation through the translocation of native commensal colonic bacteria, Gut

      Not checked in the free run.

    • cites [110] Alverdy, 1991, The effect of glucocorticoid administration on bacterial translocation. Evidence for an acquired mucosal immunodeficient state, Ann Surg source

      Not checked in the free run.

    • cites [111] Meng, 2013, Morphine induces bacterial translocation in mice by compromising intestinal barrier function in a TLR-dependent manner, PLoS One source

      Not checked in the free run.

    • cites [19] Zaborina, 2007, Dynorphin activates quorum sensing quinolone signaling in Pseudomonas aeruginosa, PLoS Pathog source

      Not checked in the free run.

    • cites [22] Alverdy, 2000, Gut-derived sepsis occurs when the right pathogen with the right virulence genes meets the right host: evidence for in vivo virulence expression in Pseudomonas aeruginosa, Ann Surg source

      Not checked in the free run.

    • cites [51] Freestone, 2012, Pseudomonas aeruginosa-catecholamine inotrope interactions: a contributory factor in the development of ventilator-associated pneumonia?, Chest source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Injured alveoli begin to resemble the gut more than healthy lungs, and most pathogens that arise in critical illness are of enteric origin.

    “Ecologically, the injured alveoli begin to resemble the gut more than healthy lungs and, therefore, it is unsurprising that most pathogens that arise in critical illness are of enteric origin.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationcitation

    Any source of alveolar injury and inflammation, whether direct or indirect, can trigger a cascade of inflammation leading to increased concentrations of intra-alveolar catecholamines, which in turn promote the growth and virulence of select bacterial community members and a disordered bacterial community that perpetuates alveolar inflammation.

    “Thus any source of alveolar injury and inflammation, whether direct (eg, aspiration or ventilator-induced lung injury60) or indirect (eg, sepsis or shock) can trigger a cascade of inflammation leading to increased concentrations of intra-alveolar catechol amines,120 which in turn promote the growth and virulence of select bacterial community members and a disordered bacterial community that perpet”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [120] Flierl, 2007, Phagocyte-derived catecholamines enhance acute inflammatory injury, Nature source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    The role of bacteria in the pathogenesis of exacerbations of chronic lung disease has been controversial for decades.

    “the role of bacteria in the pathogenesis of exacerbations has been controversial for decades.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [126] Dickson, 2014, The role of the microbiome in exacerbations of chronic lung diseases, Lancet source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Bacterial pneumonia is characterised by increased bacterial burden and low community diversity, generally one dominant pathogen.

    “Bacterial pneumonia, a true lung infection, exemplifies these features: it is characterised by increased bacterial burden and low community diversity (generally one dominant pathogen).”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [62] Flanagan, 2007, Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa, J Clin Microbiol source

      Not checked in the free run.

    • cites [83] Lu, 2014, Increased constituent ratios of Klebsiella sp., Acinetobacter sp., and Streptococcus sp. and a decrease in microflora diversity may be indicators of ventilator-associated pneumonia: a prospective study in the respiratory tracts of neonates, PLoS One source

      Not checked in the free run.

    • cites [130] Dickson, 2014, Analysis of culture-dependent versus culture-independent techniques for identification of bacteria in clinically obtained bronchoalveolar lavage fluid, J Clin Microbiol source

      Not checked in the free run.

    • Rests on an assumption: Ecologically, infections are characterised by an increase in microbial burden and a decrease in community diversity, coupled with increased host inflammation and tissue injury.

  • May combine two claims.

    Interpretationreasoning

    The web of interactions between the lung microbiome and alveolar inflammation is complex, dynamic, and bidirectional.

    “The web of interactions between the lung microbiome and alveolar inflammation is complex, dynamic, and bidirectional.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisereasoning

    The microbiome can be manipulated therapeutically, as shown by the success of faecal microbiota transplantation in the treatment of refractory Clostridium difficile infection.

    “The microbiome can be manipulated therapeutically, as has been shown by the success of faecal microbiota transplantation in the treatment of refractory Clostridium difficile infection.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    None of host genetics, immune responses, and exposures accounts for the differences in outcomes attributable solely to differences in patients' microbiota.

    “None of these accounts for the differences in outcomes attributable solely to differences in patients’ microbiota (figure 2).”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Differences in outcomes attributable solely to differences in patients' microbiota exist.

  • May combine two claims.

    Premisecitation

    Survivors of ARDS and sepsis have chronic deficits in cognitive function and functional status.

    “Survivors of ARDS and sepsis have chronic deficits in cognitive function and functional status”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [164] Prescott, 2015, Readmission diagnoses after hospitalization for severe sepsis and other acute medical conditions, JAMA source

      Not checked in the free run.

  • May combine two claims.

    Interpretationcitation

    Selective decontamination of the digestive tract is the most thoroughly studied intervention in critical care research and has unambiguous benefits in the prevention of infections, multiorgan failure, and death.

    “SDD is the most thoroughly studied intervention in critical care research, and has unambiguous benefits in the prevention of infections, multiorgan failure, and death.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [91] Silvestri, 2010, Impact of selective decontamination of the digestive tract on multiple organ dysfunction syndrome: systematic review of randomized controlled trials, Crit Care Med source

      Not checked in the free run.

    • cites [96] Silvestri, 2012, Selective decontamination of the digestive tract: the mechanism of action is control of gut overgrowth, Intensive Care Med source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    The importance of the microbiome in critical illness has been established for a half century.

    “Although the importance of the microbiome in critical illness has been established for a half century”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationcitation

    Airway inflammation leads to altered microbial growth conditions, and the resulting disordered bacterial community further drives airway inflammation.

    “Airway inflammation leads to altered microbial growth conditions and the resulting disordered bacterial community further drives airway inflammation.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [126] Dickson, 2014, The role of the microbiome in exacerbations of chronic lung diseases, Lancet source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    The predictive relationship between early gut microbiome composition and neonatal sepsis can be plausibly explained by enteric harbouring of potential pathogens or by systemic immune derangements provoked by intestinal dysbiosis.

    “which can be plausibly explained by either enteric harbouring of potential pathogens or systemic immune derangements provoked by intestinal dysbiosis.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S4 (based).

    Interpretationnone given

    The microbiome is central to the biology of critical illness.

    “The microbiome is central to the biology of critical illness”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    The revolution in culture-independent microbiology has yielded tools capable of determining the microbiome's contribution to the pathogenesis of sepsis, ARDS, and multiorgan failure.

    “the revolution in culture-independent microbiology has at last yielded tools capable of determining its contribution to the pathogenesis of sepsis, ARDS, and multiorgan failure.”
    Quote in the paperNot a substantial claim
48 of 48

  • The paper relies on this without support.

    The composition of every community, microbial or otherwise, is determined by the balance of three ecological factors: immigration into the community, elimination of members from the community, and the relative reproduction rates of the community's members.

    “The composition of every community, microbial or otherwise, is determined by the balance of three ecological factors: immigration into the community, elimination of members from the community, and the relative reproduction rates of the community’s members.”

  • The paper relies on this without support.

    The primary route of immigration of microbes into the gut microbiome is via the oropharynx.

    “The primary route of immigration of microbes into the gut microbiome is via the oropharynx”

  • The paper relies on this without support.

    In healthy individuals, the primary means of microbial elimination from the gut microbiome is transit through and from the gastrointestinal tract.

    “In healthy individuals, the primary means of microbial elimination from the gut microbiome is transit through and from the gastrointestinal tract”

  • The paper relies on this without support.

    The resident microbes of the lower gastrointestinal tract normally serve essential metabolic and immunomodulatory functions.

    “The resident microbes of the lower gastrointestinal tract normally serve essential metabolic and immunomodulatory functions.”

  • The paper relies on this without support.

    Ecologically, infections are characterised by an increase in microbial burden and a decrease in community diversity, coupled with increased host inflammation and tissue injury.

    “Ecologically, infections are characterised by an increase in microbial burden and a decrease in community diversity, coupled with increased host inflammation and tissue injury.”

  • The paper relies on this without support.

    Differences in outcomes attributable solely to differences in patients' microbiota exist.

    “None of these accounts for the differences in outcomes attributable solely to differences in patients’ microbiota (figure 2).”

  • The paper relies on this without support.

    Premature neonates are subjected to numerous microbiome-altering exposures and lack mature innate and adaptive immune responses.

    “Premature neonates are subjected to innumerable microbiome-altering exposures (eg, antibiotics and formula feeding) and lack mature innate and adaptive immune responses.”

  • The paper relies on this without support.

    The mechanisms underlying postintensive-care syndrome are poorly understood.

    “The mechanisms underlying this so-called postintensive-care syndrome are poorly understood”

  • The paper relies on this without support.

    How quickly or completely the microbiome recovers after the insults and disruptions of critical illness is unknown.

    “how quickly or completely the microbiome recovers after the insults and disruptions of critical illness are unknown.”
9 of 9

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?

  • Pneumonia is the most common cause of sepsis.

    “Pneumonia is the most common cause of sepsis (Dickson, 2017).”

    From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as Dickson, 2017

  • ICU interventions increase intestinal permeability and bacterial translocation.

    “Beyond the impact on the body’s resident microbial populations, ICU interventions also increase intestinal permeability (e.g., non-steroidal anti-inflammatory drugs and parenteral feeding) and bacterial translocation – the movement of bacteria through the gut mucosa to normally sterile tissues (Dickson, 2017).”

    From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as Dickson, 2017

  • Even after survival of ARDS and sepsis, patients have a high risk of re-admission in the months after discharge from ICU.

    “Even after survival of ARDS and sepsis, patients have an unfortunately high risk of re-admission in the months after discharge from ICU (Dickson, 2017).”

    From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as Dickson, 2017

  • Respiratory failure may be caused by exacerbation of chronic airway diseases, and viruses are unambiguous precipitants.

    “Respiratory failure may also be caused by exacerbation of chronic airway diseases (e.g., asthma, chronic obstructive pulmonary disease, and cystic fibrosis), and whereas bacteria play a controversial role in their pathogenesis, viruses are unambiguous precipitants (Dickson, 2017).”

    From Viral Infections, the Microbiome, and Probiotics (2021) · cites this paper as Dickson, 2017

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Authors
Dickson, R. P.
Affiliations
University of Michigan (US)
Corresponding author
Dickson, Robert P
ORCID
Dickson, Robert P
Venue
The Lancet Respiratory Medicine
Publisher
Elsevier BV
Published
2016-01
Volume
4
Issue
1
Pages
59-72
ISSN
2213-2600 (ISSN-L)
DOI
10.1016/s2213-2600(15)00427-0
PMC
PMC4752077
OpenAlex
W2199095759
Semantic Scholar
4bef5426a27f9ace8e1af8d39d90aefa1d07b8ea
Cited by
460
References
168
Citations by year
2026: 47 · 2025: 40 · 2024: 43 · 2023: 55 · 2022: 59 · 2021: 62 · 2020: 54 · 2019: 35 · 2018: 32 · 2017: 22 · 2016: 11
FWCI
2.79
Type
journal article
Language
en
Open access
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations
  • The Lancet Respiratory Medicine (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
National Institutes for Health (UL1TR000433)
Topics
  • Health Sciences › Medicine › Epidemiology › Sepsis Diagnosis and Treatment
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
  • Health Sciences › Medicine › Critical Care and Intensive Care Medicine › Nosocomial Infections in ICU
Keywords
microbiome, critical illness, gut microbiota, gut-derived sepsis, intensive care, lung injury, microbiota-targeted interventions, disease susceptibility
MeSH terms
Gastrointestinal Microbiome, Animals, Asthma, Bronchiectasis, Cystic Fibrosis, Humans, Lung, Pneumonia, Respiratory Distress Syndrome, Critical Illness, Disease Progression, Sepsis, Pulmonary Disease, Chronic Obstructive, Microbiota

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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-09.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-09.

Statistics and arithmetic are recomputed, not judged.

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