The DOI matches its Crossref record; 261 of the 261 references it cites were found in a registry or an index; 6 of the 219 sources its claims cite were checked for support.
Understanding the Holobiont: How Microbial Metabolites Affect Human Health and Shape the Immune System
Open accessAbstract
SUMMARY The human gastrointestinal tract is populated by a diverse, highly mutualistic microbial flora, which is known as the microbiome. Disruptions to the microbiome have been shown to be associated with severe pathologies of the host including metabolic disease, cancer and inflammatory bowel disease. Mood and behavior are also susceptible to alterations in the gut microbiota. A particularly striking example of the symbiotic effects of the microbiome is the immune system, whose cells depend critically on a diverse array of microbial metabolites for normal development and behavior. This includes metabolites that are produced by bacteria from dietary components; metabolites that are produced by the host and biochemically modified by gut bacteria; and metabolites that are synthesized de novo by gut microbes. In this review, we highlight the role of the intestinal microbiome in human metabolic and inflammatory diseases and focus in particular on the molecular mechanisms that govern the gut-immune axis.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
This review argues that gut microbes and their metabolites form a composite holobiont with the host, influencing metabolic and inflammatory disease as well as immune cell development. It surveys mechanisms by which dietary-, host-, and microbe-derived metabolites shape the intestinal immune system, while emphasizing unresolved mechanistic and ecological questions.
Key findings
- Microbiome composition and function are linked to obesity, type 2 diabetes, and atherosclerosis. Obesity associates with increased Firmicutes relative to Bacteroidetes; transferring obese microbiota to germ-free mice causes greater weight gain than lean transfer. Type 2 diabetes microbiota produces fewer short-chain fatty acids, increasing mucosal permeability and LPS-driven inflammation; TMAO from phosphatidylcholine and l-carnitine predicts cardiovascular risk and promotes atherosclerosis in mice, though fish/TMAO and l-carnitine contradictions remain.
- Short-chain fatty acids are major anti-inflammatory mediators. Acetate, propionate, and butyrate signal via FFAR2/FFAR3/HCAR2 and HDAC inhibition; they support epithelial barrier, neutrophils, macrophages, dendritic cells, B cells, and regulatory T cells. Different short-chain fatty acids have distinct effects: acetate/propionate expand existing colonic regulatory T cells, while propionate/butyrate promote de novo regulatory T cell differentiation. In vivo concentrations varied from 36 to 300 mM; butyrate at 150 mM in drinking water increased colonic regulatory T cells, 36 mM did not, and 50 mM by enema did.
- Other metabolites include indole derivatives activating AhR and PXR to support IL-22/ILC3 and barrier function; polyamines modulating NLRP6/IL-18 and macrophage cytokines; bile acids signaling through BAR/FXR and GPBAR1/TGR5 to reduce pro-inflammatory cytokines; microbially derived ATP driving TH17 and P2X7-dependent IgA regulation; and polysaccharide A from Bacteroides fragilis inducing IL-10 and Treg/TH1 responses.
- Reported quantities include: average male colonized by about 3.8×10^13 microbes versus 3.0–3.7×10^13 host cells; female about 4.4×10^13 bacteria versus 2.1×10^13 host cells; metagenomic catalog of 3.3×10^6 nonredundant microbial genes from up to 1,150 species, about 150-fold human protein-coding genes; each person hosts at least 160 species; about 10% of blood metabolites are microbiota-derived. In mouse colonic lumen, 179 metabolites were detected, 48 absent from food, 35 of those altered in germ-free mice, plus 88 food-present metabolites altered. Of 79 human intestinal strains screened, 9 (11.4%) produced TMA from choline.
Methods
- Narrative review, not primary research; synthesizes prior human, animal, in vitro, and metagenomic/metabolomic studies.
- Covers microbiome links to metabolic disease and immune modulation by three metabolite classes: bacterial products from diet, host metabolites modified by bacteria, and de novo microbial products.
- Main analysis is conceptual synthesis and mechanistic discussion; no systematic search, inclusion criteria, or meta-analysis described.
Limitations
- The paper states many mechanisms remain unresolved: most intestinal bacterial metabolome is unidentified, many known metabolites are functionally uncharacterized, bioavailability and epithelial crossing are poorly understood, TMAO mechanisms are elusive, bile-acid causality in IBD is not established, and short-chain fatty acid dosing/route effects are unclear.
- The paper notes functional studies mostly examine single species or metabolites, whereas real gut communities may interact additively, synergistically, redundantly, or subtractively; up to 1,150 species and at least 160 per person make network complexity enormous.
- Evident from the text: as a narrative review, it does not systematically assess study quality or bias, and many conclusions rest on mouse models, in vitro systems, or small human studies, such as the small FMT study in type 2 diabetes.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
132 Not checked yet · 11 No basis given · 9 Own interpretation · 4 Sources not found · 3 Partly supported · 1 Supported so far · accuracy not yet measured
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“administration of synthetic NR1I2 agonists exerts protective effects in mouse models of colitis (Dou et al., 2013; Garg et al., 2016; Shah et al., 2007; Terc et al., 2014; Venkatesh et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Partly supportedcites Dou et al., 2013 sourceExperimental — accuracy not yet measured
The Abstract and Discussion report that chrysin activated PXR (NR1I2) and reduced chemically induced colitis in mice. But the Introduction identifies chrysin as a naturally occurring flavonoid, not a synthetic agonist; this study therefore does not support the claim's synthetic-agent qualifier. (LLM, conf=0.88)
- Supportedcites Garg et al., 2016 source
The Experimental Colitis section identifies PCN as a mouse-specific PXR (NR1I2) agonist administered to mice with DSS-induced colitis. The Results report that PCN significantly reduced colonic damage, thickening, and barrier dysfunction in that model. This paper therefore supports the protective-effect claim as one example among the sentence’s multiple citations. (LLM, conf=0.90)
- Not checked yetcites Shah et al., 2007 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.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“it was demonstrated that expression of IL-22 requires the AhR (Martin et al., 2009; Veldhoen et al., 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Martin et al., 2009 source
- Partly supportedcites Veldhoen et al., 2008 sourceExperimental — accuracy not yet measured
The Abstract section (page not indicated) reports that AhR-deficient CD4 T cells differentiated into TH17 cells but lacked IL-22 expression; it also reports that AhR reconstitution restored IL-22 expression under TH17 conditions. This supports a requirement for AhR in the TH17-cell conditions studied, but not the unqualified claim that all IL-22 expression requires AhR. (LLM, conf=0.85)
boosteddirect- 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 sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“Nr1h4−/− mice also develop spontaneous hepatic inflammation and liver tumors (I. Kim et al., 2007; Yang et al., 2007).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Supportedcites I. Kim et al., 2007 source
The Discussion (p. 3) describes sustained chronic inflammation in Fxr-null mice and reports liver tumors in 38% of the mice at 12 months. The Introduction (p. 1) also says the mice spontaneously developed liver lesions, adenomas, and carcinomas. (LLM, conf=0.92)
- Not checked yetcites Yang et al., 2007 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.
- Supported
None of the sources cited for this claim have been checked yet.
In the paper
“This observation also holds true when the microbiota from obese or lean humans is transferred to germ-free mice (Ridaura et al., 2013; Tremaroli et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
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.
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
“When a germ-free mouse receives the microbiota of an obese individual, the ability to effectively utilize high-caloric nutrients is transferred along with it, resulting in obesity of the recipient.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
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 composition of the microbiome differs between obese and lean individuals in humans and in animal models: obesity is associated with a relative increase in Firmicutes at the expense of Bacteroidetes (Ley et al., 2005; 2006).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not matchedcites Ley et al., 2005; 2006
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
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.
- Not matched
In the paper
“In addition to changes in energy metabolism, obesity has also been linked to a deterioration of the intestinal mucosa and resultant chronic, systemic inflammation, analogous to type 2 diabetes (see below) (Boutagy et al., 2016).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not checked yetcites Boutagy et al., 2016 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.
In the paper
“They found that l-carnitine and its metabolite γ-butyrobetaine also promoted atherosclerosis in mice, and that elevated plasma levels of l-carnitine were associated with increased risk of cardiovascular disease in individuals with elevated TMAO plasma levels (Koeth et al., 2013; 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
What the sources say
- Not matchedcites Koeth et al., 2013; 2014
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
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.
- Not matched
In the paper
“Elimination of the gut microbiota by treatment with antibiotics negated the choline-induced exacerbation of atherosclerosis, confirming the importance of the gut microbiome in this process (Z. Wang et al., 2011).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
What the sources say
- Not checked yetcites Z. Wang et al., 2011
boosteddirect- 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
“Hazen and colleagues separately investigated l-carnitine, an amino acid found in red meat that is also converted to TMAO after processing by gut bacteria.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
What the sources say
- Not matchedcites Koeth et al., 2013; 2014
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
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.
- Not matched
None of the sources cited for this claim have been checked yet.
In the paper
“First, the gut microbiota associated with T2D produces lower levels of short-chain fatty acids (SCFAs, discussed in detail below), which have been shown in vitro and in vivo to support the integrity of the intestinal mucosa in a variety of ways (Fukuda et al., 2011; Gaudier et al., 2004; Macia et al., 2015; Willemsen et al., 2003; Wrzosek et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
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.
In the paper
“Consistent with this finding, supplementing food with choline or TMAO promoted atherosclerosis in mice.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
What the sources say
- Not checked yetcites Z. Wang et al., 2011
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Bacteria of the gut microbiota process dietary phosphatidylcholine to yield trimethylamine (TMA), which is absorbed by the host and oxidized in the liver to trimethylamine N-oxide (TMAO).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Host genetic variation has been shown to be associated with variation in the microbiome composition, but genome-wide approaches to identify individual genes and their role in shaping the microbiome are only beginning to emerge (Blekhman et al., 2015; Spor et al., 2011).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
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.
None of the sources cited for this claim have been checked yet.
In the paper
“which have been shown in vitro and in vivo to support the integrity of the intestinal mucosa in a variety of ways (Fukuda et al., 2011; Gaudier et al., 2004; Macia et al., 2015; Willemsen et al., 2003; Wrzosek et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
What the sources say
boosteddirect- 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
“A seminal study by Hazen and colleagues discovered that plasma levels of TMAO and its precursors choline and betaine predicted the risk of cardiovascular disease in humans, thus identifying a novel connection between the microbiome and metabolic health.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
What the sources say
- Not checked yetcites Z. Wang et al., 2011
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.
In the paper
“Correspondingly, patients suffering from T2D have been reported to exhibit increased plasma levels of LPS (Creely et al., 2007).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
What the sources say
- Not checked yetcites Creely et al., 2007 source
hedgedcorrelational- 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
“Recently, Plovier et al. reported that much of this effect could be replicated by administration of a membrane protein purified from A. muciniphila, suggesting the appealing possibility of a novel therapeutic application (Plovier et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not checked yetcites Plovier et al., 2017 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.
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 vivo studies use widely varying methods of administration and concentrations of SCFAs, including oral uptake via enriched starch or drinking water, enema, and intraperitoneal injection.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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
“Concentrations of SCFAs provided with drinking water ranged from 36 mM to 300 mM in the studies cited above.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
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 particularly striking example of the symbiotic effects of the microbiome is the immune system, whose cells depend critically on a diverse array of microbial metabolites for normal development and behavior.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > 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: unclear — It is unclear why the paper says 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
“Disruptions to the microbiome have been shown to be associated with severe pathologies of the host including metabolic disease, cancer and inflammatory bowel disease.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Abstract
boostedcorrelational- 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
“This is consistent with the notion that the intestinal microbiome is an important regulator of mucosal barrier function, which will be discussed in further detail in subsequent sections.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
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
“Ffar2−/− mice had a similar defect, although no FFAR2 expression could be detected on microglia, leaving the connection between SCFAs and microglia unresolved (Erny et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Erny et al., 2015 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
“Therefore, atherosclerosis is at least in part a disease of chronic inflammation, not unlike T2D.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Second, microbiota-derived LPS has been suggested to traverse the mucosal barrier of the intestine on chylomicrons, lipoprotein complexes that transport long-chain fatty acids from the gut lumen to the lymph and blood (Ghoshal et al., 2009; Khan et al., 2014; Sonnenburg and Bäckhed, 2016).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
What the sources say
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Beyond these general mechanisms, the gut microbiome affects atherogenesis more specifically through its degradation of phosphatidylcholine, which is abundant in eggs, cheese, seafood and red meat (Jonsson and Bäckhed, 2017; Sharon et al., 2014; Sonnenburg and Bäckhed, 2016).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
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.
None of the sources cited for this claim have been checked yet.
In the paper
“The primary cause of cardiovascular disease is atherosclerosis, a process in which the microbiome has been implicated as well (Jonsson and Bäckhed, 2017; Sharon et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
What the sources say
- Not checked yetcites Jonsson and Bäckhed, 2017
- Not checked yetcites Sharon et al., 2014 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
“Beyond intestinal macrophages, SCFAs have also been reported to be functionally important for microglia, a macrophage-like cell type of the central nervous system.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Erny et al., 2015 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.
In the paper
“although no FFAR2 expression could be detected on microglia”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Erny et al., 2015 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
“Germ-free mice exhibited microglia dysfunction that could be rescued by treatment with SCFAs.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Erny et al., 2015 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Several studies have demonstrated that butyrate and propionate inhibit the maturation of dendritic cells (DCs), which form a central bridge between the innate and adaptive immune systems (Lu Liu et al., 2012; Millard et al., 2002; Singh et al., 2010; B. Wang et al., 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
boosteddirect- 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
“It is hence not surprising that the same systemic, pro-inflammatory events that promote T2D also promote atherosclerosis (see above).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Atherosclerosis
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
“In summary, microbiome-derived SCFAs are key regulators of virtually every aspect of the intestinal immune system.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Nr1i2−/− mice exhibit impaired epithelial barrier function”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
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
“there is evidence that these differences affect experimental outcomes.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
In the paper
“Arpaia et al. detected no significant changes at a concentration of 36 mM”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Arpaia et al., 2013 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
“A role for SCFA in the regulation of B-cell function was reported nearly 20 years ago (Kudoh et al., 1998).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Kudoh et al., 1998 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
“In Ido1−/− mice, which cannot produce the endogenous AhR ligand l-kynurenine, bacteria that are able to metabolize dietary tryptophan and produce indole derivatives gain a selective advantage due to the increased availability of tryptophan.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Zelante et al., 2013 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
“Smith et al. reported an increase in cTregs after providing butyrate at a concentration of 150 mM with drinking water”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Smith et al., 2013 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
“Dietary tryptophan, for instance, is processed to several different indole derivatives, which can act as ligands for the aryl hydrocarbon receptor (AhR) in host cells (Wikoff et al., 2009).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Wikoff et al., 2009 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.
None of the sources cited for this claim have been checked yet.
In the paper
“whereas propionate and butyrate, but not acetate, increase the de novo differentiation of naive T cells into Tregs (Arpaia et al., 2013; Furusawa et al., 2013; Singh et al., 2014; Smith et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
In the paper
“Direct application of 50 mM butyrate by enema, however, did elicit an increase in cTregs”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Arpaia et al., 2013 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
“Intriguingly, they further found that SCFAs in parallel modulate the energy metabolism of B cells to promote production of antibodies (M. Kim et al., 2016).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites M. Kim et al., 2016 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.
None of the sources cited for this claim have been checked yet.
In the paper
“likely because this lower quantity of butyrate was largely absorbed by the upper gastrointestinal tract before reaching the colon (Arpaia et al., 2013; Smith et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
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.
None of the sources cited for this claim have been checked yet.
In the paper
“acetate and propionate, but not butyrate, stimulate the expansion of pre-existing colonic Tregs (cTregs)”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
In the paper
“The expansion of pre-existing cTregs is mediated by activation of FFAR2, which is not triggered effectively by butyrate (Smith et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Smith et al., 2013 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 promiscuous nuclear receptor subfamily 1 group I member 2 (NR1I2, also known as pregnane X receptor, PXR) has been identified as a functional receptor for indole-3-propionic acid (IPA)”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Venkatesh et al., 2014 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
“Separately, butyrate has also been shown to enhance Treg generation by promoting an anti-inflammatory phenotype in macrophages and DCs through activation of HCAR2 (Singh et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Singh et al., 2014 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.
None of the sources cited for this claim have been checked yet.
In the paper
“However, SCFAs have also been shown to affect DC maturation and function through HCAR2 and FFAR3, depending on the context (Singh et al., 2014; Trompette et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
plainconditional- 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
“Under homeostatic conditions, IL-22 is primarily produced by a specialized subset of intraepithelial lymphocytes, the type 3 innate lymphoid cells (ILC3s) (Melo-Gonzalez and Hepworth, 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Melo-Gonzalez and Hepworth, 2017
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
“Kim et al. shed further light on this observation and demonstrated that SCFAs support antibody responses by regulating gene expression through HDAC inhibition.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites M. Kim et al., 2016 source
boosteddirect- 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
“Conversely, the de novo differentiation of cTregs relies on HDAC inhibition in both DCs and T cells, which acetate does not promote (Arpaia et al., 2013; Furusawa et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
In the paper
“mice deficient for Card9, a gene that in humans is associated with IBD susceptibility, have an altered microbiota that produces lower amounts of indole derivatives, similar to the microbiota of IBD patients (Lamas et al., 2016).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Lamas et al., 2016 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
“SCFAs have also been reported to promote generation of both effector and regulatory T cells, depending on the immunological context (Park et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Park et al., 2015 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
“spermine administration exhibits protective anti-inflammatory effects in mouse models of both localized and systemic inflammation (Steege et al., 1999; M. Zhang et al., 1997; S. Zhu et al., 2009).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
None of the sources cited for this claim have been checked yet.
In the paper
“activation of GPBAR1 on macrophages and Kupffer cells by synthetic agonists inhibits the expression of LPS-induced pro-inflammatory cytokines by interfering with NF-κB-dependent transcription.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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.
In the paper
“Spermine and the monoamine histamine both inhibit activation of the NLRP6 inflammasome, a protein complex expressed by epithelial cells that regulates IL-18 secretion.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Levy et al., 2015 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
“Consequently, the gut microbiota plays an important role in regulating the extent to which bile acids can be recycled by the host.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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.
None of the sources cited for this claim have been checked yet.
In the paper
“blocking endogenous production of polyamines with a chemical inhibitor of ornithine decarboxylase negatively affects maintenance, repair and function of the intestinal epithelium”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
None of the sources cited for this claim have been checked yet.
In the paper
“the composition of bile acids varies dramatically between germ-free and control animals in feces, liver, heart, kidney and plasma (Duboc et al., 2013; Sayin et al., 2013; Swann et al., 2011).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
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.
In the paper
“Levy et al. recently reported that exogenous polyamines can reduce the release of IL-18, a cytokine that promotes epithelial repair and barrier function.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Levy et al., 2015 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
“The highly reactive polyamines putrescine (a diamine, N2), spermidine (N3) and spermine (N4) all are arginine derivatives produced and secreted by intestinal bacteria (Michael, 2016).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Michael, 2016 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.
None of the sources cited for this claim have been checked yet.
In the paper
“the inflammatory effects of BAR deficiency on the liver may not only be mediated by Kupffer cells, but also by hepatocytes and NKT cells (Mencarelli et al., 2009; Y.-D. Wang et al., 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Mencarelli et al., 2009 source
- Not checked yetcites Y.-D. Wang et al., 2008
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
“These effects are primarily mediated by two different host receptors, the bile acid receptor (BAR; also known as nuclear receptor subfamily 1 group H member 4, NR1H4, or farnesoid X-activated receptor, FXR) and the G-protein-coupled bile acid receptor 1 (GPBAR1; also known as membrane-type receptor for bile acids, M-BAR, or TGR5).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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 cellular protein alpha-2-HS-glycoprotein (AHSG, also known as Fetuin-A) has been reported to be a required co-factor for the anti-inflammatory activity of spermine”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites H. Wang et al., 1997 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Germ-free mice retain significantly higher amounts of arginine in their intestines than mice colonized by gut microbes.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
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.
None of the sources cited for this claim have been checked yet.
In the paper
“bile acids reduce the expression of pro-inflammatory cytokines from monocytes, macrophages, DCs and the hepatic macrophages known as Kupffer cells (Brestoff and Artis, 2013; Martinot et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Both receptors can be activated by primary and secondary bile acids alike (Kawamata et al., 2003; Makishima et al., 1999; Maruyama et al., 2002; Parks et al., 1999; H. Wang et al., 1999).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Oral administration of polyamines enhances the development and maintenance of the intestinal mucosa and resident immune cells (Buts et al., 1993; Dufour et al., 1988; Löser et al., 1999; Pérez-Cano et al., 2010).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
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
“Specifically in the gut mucosa, P2X7 has been shown to be an important regulator of IgA secretion into the intestinal lumen.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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
“Binding of ATP to P2X7 results in the influx of Na+ and Ca2+ ions with simultaneous K+ efflux.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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
“However, no conclusive evidence for a causative role of bile-acid imbalances in the pathogenesis of IBD has been uncovered so far.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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
“presentation of SFB-derived antigens by intestinal APCs was shown to be sufficient for TH17 cell development (Goto et al., 2014; Panea et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
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.
In the paper
“intraperitoneal injection of ATP exacerbated experimental colitis in mice (Atarashi et al., 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Atarashi et al., 2008 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
“Specifically, ATP elicits the production of cytokines that favor TH17 differentiation by CD70high CD11clow antigen-presenting cells (APCs) in the lamina propria (Atarashi et al., 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Atarashi et al., 2008 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
“Perruzza et al. recently demonstrated that microbially derived ATP can in fact modulate the host immune response through this pathway.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Perruzza et al., 2017 source
boosteddirect- 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 subsequent reduction in B1-cell stimulation is believed to cause increased susceptibility of P2rx7−/− mice to polymicrobial sepsis (Proietti et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Proietti et al., 2014 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
“A study evaluating genetic variations in NR1H4 found no association between single-nucleotide polymorphisms in this gene and IBD risk (Nijmeijer et al., 2011).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Nijmeijer et al., 2011 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
“Monocolonization with a Shigella flexneri mutant unable to secrete ATP was associated with a significant increase in Tfh and germinal-center B cells, as well as elevated levels of bacteria-specific IgA in the intestine, compared to colonization with the ATP-secreting wild-type S. flexneri (Perruzza et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Perruzza et al., 2017 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Gpbar1−/− mice, like their Nr1h4−/− counterparts, develop more severe disease than wildtype controls in several animal models of inflammatory disorder, including colitis, hepatitis and gastritis (Cipriani et al., 2011; C. Guo et al., 2015; Y.-D. Wang et al., 2011).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Another important microbial immune modulator is the zwitterionic PSA, produced by the common gut bacterium Bacteroides fragilis (Pantosti et al., 1991; Sharma et al., 2017) (Fig. 3).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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.
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, microbially derived ATP appears to protect the intestinal microbiota from excessive antibody production under physiological conditions, which allows for mutually beneficial colonization of the host.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Long-term activation of P2X7, however, results in formation of a large membrane pore and cell death (Nuttle and Dubyak, 1994; Smart et al., 2003).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Nuttle and Dubyak, 1994
- Not checked yetcites Smart et al., 2003 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
“Entpd1−/− mice, which cannot remove extracellular ATP through this mechanism, where highly susceptible to experimental colitis (Friedman et al., 2009).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Friedman et al., 2009 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
“They found that previous observations made in vivo could be robustly reproduced, while being able to extract compelling new insights due to the tightly controlled nature of their system (Yissachar et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Concluding remarks
What the sources say
- Not checked yetcites Yissachar et al., 2017 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.
In the paper
“The presence of PSA is a prerequisite for effective colonization of the colonic mucosa by its producer B. fragilis”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Round et al., 2011 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
“This process is supplemented by direct binding of PSA to TLR2 expressed on FoxP3+ Tregs, further enhancing IL-10 production (Round et al., 2011).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Round et al., 2011 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
“the gut microbiota appears to influence nearly every aspect of host physiology, including energy balance, cardiovascular health, chronic inflammation, development of adaptive immune cells and many more systems that fall outside of the scope of this review (Rooks and Garrett, 2016; Sharon et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Concluding remarks
What the sources say
- Not checked yetcites Rooks and Garrett, 2016
- Not checked yetcites Sharon et al., 2014 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
“the up-regulation of ENTPD1 has been implicated in the protective effect of PSA in experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis (Ochoa-Reparaz et al., 2010; Y. Wang et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Ochoa-Reparaz et al., 2010 source
- Not checked yetcites Y. Wang et al., 2014
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
“Yissachar et al. recently reported the development of a highly functional, microfluidics-based intestinal organ culture system.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Concluding remarks
What the sources say
- Not checked yetcites Yissachar et al., 2017 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
“an increase in ENTPD1 expression on peripheral-blood Tregs has been associated with remission of IBD (Gibson et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Gibson et al., 2015 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 confirms that the immunomodulatory effects of PSA are not restricted to the intestinal compartment but have systemic consequences.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
boosteddirect- 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. 65
- Probably not a substantial claim. 6
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“The capability of other TH17-inducing gut bacteria to produce ATP has not been determined yet, but a common property appears to be their ability to adhere to the intestinal epithelium (Atarashi et al., 2015; Tan et al., 2016).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Partly supportedcites Atarashi et al., 2015 sourceExperimental — accuracy not yet measured
The Discussion (page unavailable) identifies epithelial adhesion as a shared characteristic of the Th17-inducing microbes studied, including SFB and 20 human-derived strains. Our copy does not state that the ATP-producing ability of other Th17-inducing gut bacteria remains undetermined; a search for ATP found only a cited reference about ATP and Th17 differentiation. (LLM, conf=0.85)
- Partly supportedcites Tan et al., 2016 sourceExperimental — accuracy not yet measured
The Results (page unavailable) report that B. adolescentis, like SFB, closely associated with the ileal epithelium and suggest that tight epithelial association may be a conserved feature of Th17-inducing microbes. Our copy does not address whether other Th17-inducing bacteria produce ATP, so it does not establish the claim about their ATP-production status. (LLM, conf=0.85)
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.
- Partly supported
In the paper
“Crucially, the transfer of the microbiota from obese mice to germ-free animals results in a significantly larger weight increase than an equivalent transfer from lean mice, clearly demonstrating that body weight is in part controlled by the microbiome (Turnbaugh et al., 2008; 2006).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not matchedcites Turnbaugh et al., 2008; 2006
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
boosteddirect- 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.
- Not matched
In the paper
“Interestingly, a small study of FMTs from lean, healthy donors to obese recipients with type 2 diabetes found no reduction in weight but a significant increase in insulin sensitivity in the recipient population six weeks after transplantation (Vrieze et al., 2012).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not checked yetcites Vrieze et al., 2012 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
“Consistent with this model of microbial selection based on biochemical capacity, the representation of biochemical pathways in the collective genome of the gut microbiome is remarkably similar between healthy individuals, whereas the composition of the microbiome on a species level varies significantly.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
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
“Abundance of A. muciniphila is decreased in obese (and diabetic) mice, while reintroduction of the bacterium by oral gavage improves epithelial barrier function and reduces diet-induced obesity (Everard et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not checked yetcites Everard et al., 2013 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
“Interestingly, mice chronically exposed to low levels of LPS for four weeks gained weight and became insulin-resistant (Cani et al., 2007).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
What the sources say
- Not checked yetcites Cani et al., 2007 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
“Obese individuals share a functionally similar gut microbiome between them, with reduced but still considerable species diversity (Human Microbiome Project Consortium, 2012; Kurokawa et al., 2007; Qin et al., 2010; Turnbaugh et al., 2009).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not checked yetcites Turnbaugh et al., 2009 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Unexpectedly, the gut microbiome can be an active driver of obesity, either in combination with the interrelated factors of diet and genetic predisposition, or by itself (Cox and Blaser, 2013; Shapiro et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not checked yetcites Cox and Blaser, 2013
- Not checked yetcites Shapiro et al., 2017 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
“the microbiota extracts energy from dietary components that are not digested by the host and converts that energy to nutrients the host can absorb, thereby altering the overall energy balance of the host.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not checked yetcites Sonnenburg and Bäckhed, 2016 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
“An obesity-inducing, Western-style diet, which is typically low in fiber and high in caloric content from sucrose and unsaturated fat, thus selects for a less diverse microbiota that efficiently extracts energy from these nutrients (mostly members of the Firmicutes). Conversely, a plant-based diet promotes the enrichment of microbial species that efficiently ferment fiber (Bacteroidetes) (De”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Obesity
What the sources say
- Not checked yetcites De Filippo et al., 2010 source
- Not checked yetcites Wu et al., 2011
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 human gastrointestinal tract is populated by a diverse, highly mutualistic microbial flora, which is known as the microbiome.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > 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.
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
“These can broadly be grouped into three categories: (i) metabolites that are produced by bacteria directly from dietary components; (ii) metabolites that are produced by the host and biochemically modified by gut bacteria; and (iii) metabolites that are synthesized de novo by gut microbes (Table 1).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System
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
“In the absence of adequate SCFA production, the permeability of the intestinal mucosa increases, allowing gut bacteria to cross and enter the bloodstream.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
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 microbiome of patients suffering from T2D, which is also markedly different from healthy individuals, is believed to promote these inflammatory events by two distinct mechanisms (Karlsson et al., 2013; Qin et al., 2012).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
What the sources say
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.
In the paper
“T2D is associated with inflammation of the insulin-producing β cells of the pancreatic islets and the white adipose tissue itself, which results in decreased insulin production and increased insulin resistance, respectively (comprehensively reviewed by (Donath et al., 2013)).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
What the sources say
- Not checked yetcites Donath et al., 2013 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
“In addition to obesity, the gut microbiome has also been implicated directly in the development of the two primary complications of Metabolic Syndrome, type 2 diabetes (T2D) and cardiovascular disease (Fändriks, 2016; Jonsson and Bäckhed, 2017; Khan et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > The Role of the Microbiome in Metabolic Diseases > Type 2 Diabetes
What the sources say
- Not checked yetcites Fändriks, 2016
- Not checked yetcites Jonsson and Bäckhed, 2017
- Not checked yetcites Khan et al., 2014 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 AhR is in fact required for postnatal maintenance of IL-22-producing ILC3s, as well as the formation of isolated lymphoid follicles (Kiss et al., 2011; Lee et al., 2011; Y. Li et al., 2011; J. Qiu et al., 2012).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
boosteddirect- 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
“Perhaps the most potent anti-inflammatory property of SCFAs is their promotion of regulatory T cells (Tregs), which suppress the activity of effector T cells.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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
“Each of these functions operates independently, as numbers of cTregs in germ-free mice, which are starkly reduced in the absence of treatment, can be rescued by separate provision of acetate, propionate or butyrate (Arpaia et al., 2013; Smith et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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
“The AhR is a ligand-activated transcription factor with a central role in the intestinal mucosa (Stockinger et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Stockinger et al., 2014 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.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“which is produced in mice monocolonized with Clostridium sporogenes but absent in the gut of germ-free mice (Venkatesh et al., 2014; Wikoff et al., 2009).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
None of the sources cited for this claim have been checked yet.
In the paper
“Atarashi et al. showed that exposure of a colorectal cancer cell line to a mixture of SCFAs could elicit the production of transforming growth factor beta (TGF-β), which promotes the differentiation of naive T cells into Tregs (Atarashi et al., 2013; Fu et al., 2004).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Atarashi et al., 2013 source
- Not checked yetcites Fu et al., 2004
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
“emphasizing the importance of administration route and SCFA concentration for in vivo experiments (Arpaia et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Arpaia et al., 2013 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Ahr−/− mice suffer from multiple immunological deficits, including reduced resistance to infection with the bacteria Listeria monocytogenes or Citrobacter rodentium, as well as the fungus Candida albicans; exacerbated DSS-induced colitis; and even altered susceptibility to experimental autoimmune encephalomyelitis (EAE)”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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
“Indole derivatives produced by these bacteria can then compensate for the lack of endogenously produced AhR ligands, reflecting an interesting mutualistic balance between the needs of microbiome and host (Zelante et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Zelante et al., 2013 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
“This appears to be primarily mediated by HDAC inhibition, as the effect is dependent on the SCFA transporter SLC5A8 (Singh et al., 2010).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Singh et al., 2010 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
“free taurine generated by deconjugation can enhance the activation of the NLRP6 inflammasome and thereby increase production of IL-18 by the intestinal epithelium, which supports epithelial barrier function and maintenance (Levy et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Levy et al., 2015 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
“This indicates that the microbiome metabolizes substantial quantities of dietary arginine and may thus regulate the availability of arginine to the immune system to a certain extent (Mardinoglu et al., 2015; Matsumoto et al., 2012).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
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.
It may state two separate claims as one.
In the paper
“Primary bile acids are converted to secondary bile acids by the local microbiota, partly in the small intestine and predominantly in the colon. This involves multiple steps and typically begins with the initial deconjugation of glycine or taurine, followed by dehydroxylation (Ridlon et al., 2006).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Ridlon et al., 2006 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
“the combined knockout of Nr1i2 and the gene encoding the LPS sensor toll-like receptor 4 (Tlr4) can rescue the phenotype of Nr1i2−/− mice, possibly because it counteracts the accelerated cell death of inflammatory monocytes observed in NR1I2-deficient mice (Z. Qiu et al., 2016; Venkatesh et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
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.
It may state two separate claims as one.
In the paper
“After passage through the small intestine, about 95% of bile acids are reabsorbed in the terminal ileum by active transport, mostly in their conjugated form, and recycled by the host.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Martinez-Augustin and Sanchez de Medina, 2008
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
“Bile acids have also been reported to function as agonists to additional receptors, but the physiological relevance of these pathways remains incompletely understood (Thomas et al., 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Thomas et al., 2008 source
hedgedconditional- 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
“Arginine itself is an important modulator of the immunometabolism of macrophages and T cells and thus affects their effector functions (O'Neill et al., 2016).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites O'Neill et al., 2016
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
“Extraneous spermine is taken up by monocytes and macrophages and selectively inhibits the LPS-induced expression of pro-inflammatory cytokines (M. Zhang et al., 1999; 1997).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
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.
None of the sources cited for this claim have been checked yet.
In the paper
“GPBAR1, as the name suggests, is a Gs-protein-coupled receptor. Binding by bile acids triggers an increase in intracellular cAMP levels and the activation of ERK (Kawamata et al., 2003; Maruyama et al., 2002).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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
“Primary bile acids are more readily absorbed in the small intestine, whereas secondary bile acids are more hydrophobic and can thus be taken up more efficiently in the colon (Martinez-Augustin and Sanchez de Medina, 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Martinez-Augustin and Sanchez de Medina, 2008
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
“treatment with a synthetic agonist of BAR has protective effects in mouse models of colitis, whereas BAR-deficient (Nr1h4−/−) mice exhibit exacerbated pathology (Gadaleta et al., 2011; Vavassori et al., 2009).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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
“taurine, another microbial metabolite that derives from host-produced bile acids (see below), counteracts the effects of spermine and histamine, indicating a finely tuned balance of opposing bacterial stimuli (Levy et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Levy et al., 2015 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.
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
“Primary bile acids, such as cholic acid and chenodeoxycholic acid, are synthesized in the liver from cholesterol and conjugated to glycine or taurine prior to secretion.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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
“Polyamines are present in every living cell and fulfill important roles in gene expression and proliferation; therefore their endogenous production in eukaryotic cells is strictly regulated (Miller-Fleming et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are produced by bacteria from dietary components
What the sources say
- Not checked yetcites Miller-Fleming et al., 2015 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.
In the paper
“About half of the remaining bile acids are taken up in the colon by passive absorption, the rest is excreted with the feces (Martinez-Augustin and Sanchez de Medina, 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Martinez-Augustin and Sanchez de Medina, 2008
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
“mice deficient for the epithelial ATP-degrading enzyme ectonucleoside triphosphate diphosphohydrolase 7 (ENTPD7) exhibit higher levels of luminal ATP and an increase in TH17 cells in the lamina propria of the small-intestinal epithelium (Kusu et al., 2013).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Kusu et al., 2013 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.
None of the sources cited for this claim have been checked yet.
In the paper
“This has been linked to direct inhibition of NF-κB activation, but is also consistent with a model of transcriptional competition between NF-κB and the cAMP-activated transcription factor cAMP response element binding protein (CREB) (C. Guo et al., 2015; Kawamata et al., 2003; Keitel et al., 2008; Pols et al., 2011; Y.-D. Wang et al., 2011; Wen et al., 2010).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
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.
In the paper
“Within the host, ATP is released passively from necrotic cells and actively from stressed or stimulated cells, e.g. during an inflammatory response.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Faas et al., 2017
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
“ENTPD1 converts ATP to AMP, which is then quickly metabolized to the anti-inflammatory adenosine by 5’-nucleotidase (also known as CD73) (Allard et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Allard et al., 2017 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
“changes in the composition of the bile acid pool, an increase in colonic expression of GPBAR1 and a decrease in ileal activity of BAR have all been detected in patients suffering from IBD (Cipriani et al., 2011; Duboc et al., 2013; Lenz et al., 1976; Nijmeijer et al., 2011; Rutgeerts et al., 1979).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
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
“The efficiency of bile-acid recycling depends on their biotransformation by the microbiome; however, the de novo synthesis of bile acids is subject to a strict feedback mechanism, which may limit the effect of increased excretion of bile acids in the absence of a fully functional microbiota (Martinot et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Bile acids: metabolites produced by the host and biochemically modified by gut bacteria
What the sources say
- Not checked yetcites Martinot et al., 2017 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.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“some, but not all, intestinal bacteria actively secrete ATP, and germ-free mice have lower ATP concentrations in their gut than controls (Atarashi et al., 2008; Hironaka et al., 2013; Iwase et al., 2010).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
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.
None of the sources cited for this claim have been checked yet.
In the paper
“P2rx7−/− mice were protected against experimental induction of colitis, as were rats treated prophylactically with a chemical P2X7 antagonist (Marques et al., 2014; Neves et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“The production of IL-10 is primarily mediated by DCs, which internalize PSA and present fragments to CD4+ T cells in conjunction with the major histocompatibility complex class II (MHC-II), thus stimulating activation and clonal expansion of T cells.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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
“Mice deficient for P2X7 (P2rx7−/−) have elevated Tfh cell numbers in the intestinal mucosa, presumably because they are resistant to ATP-induced cell death.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Proietti et al., 2014 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.
It may state two separate claims as one.
In the paper
“Germ-free mice show a severe reduction of TH17 lymphocytes in the lamina propria of the colonic epithelium, which can be rescued by the direct administration of ATP.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Atarashi et al., 2008 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
“extracellular ATP is the sole agonist for receptors of the P2X family, which are ligand-activated ion channels expressed by a variety of tissues including innate and adaptive immune cells (Faas et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Faas et al., 2017
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
“segmented filamentous bacteria (SFB), which have been shown to induce TH17 cells in the lamina propria of the murine small intestine, do not produce high levels of ATP (Ivanov et al., 2009).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Ivanov et al., 2009 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
“PSA induces secretion of the potent anti-inflammatory cytokine IL-10 by CD4+ T cells and promotes the differentiation of naive CD4+ T cells into TH1 cells over TH2 cells.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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.
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
“intestinal ATP has also been implicated in the development of IBD, likely due to the generally pro-inflammatory properties of ATP.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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.
It may state two separate claims as one.
- Rests on an assumption: Extracellular ATP primarily has pro-inflammatory properties.
None of the sources cited for this claim have been checked yet.
In the paper
“this has been shown to elicit activation of the NLRP3 inflammasome in LPS-stimulated macrophages, which causes secretion of IL-18 (but also of the pro-inflammatory cytokine IL-1β) and may thus promote maintenance and function of the epithelial barrier (Mariathasan et al., 2006; Sutterwala et al., 2014; 2006; Yaron et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
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.
In the paper
“As such, it serves as an endogenous danger-associated molecular pattern (DAMP) that can drive chemotaxis of and cytokine release by immune cells (interestingly, low concentrations of ATP tend to have the opposite effect) (Faas et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Faas et al., 2017
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
“In humans, polymorphisms of ENTPD1 were shown to be associated with IBD, and expression of P2X7 was increased in the intestinal epithelium and lamina propria of IBD patients (Friedman et al., 2009; Neves et al., 2014).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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.
In the paper
“This results in an increase in high-affinity IgA specific for intestinal bacteria secreted into the intestinal lumen and thereby a depletion of the gut microbiota.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Proietti et al., 2014 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
“Geva-Zatorsky et al. monocolonized germ-free mice separately with 53 different bacterial species resident in the human intestine (less than five percent of the estimated total!) and found that each one of them had some sort of immunomodulatory effect on the host (Geva-Zatorsky et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Concluding remarks
What the sources say
- Not checked yetcites Geva-Zatorsky et al., 2017 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
“Virtually all functional studies of the microbiome have been limited to single bacterial species or metabolites.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Concluding remarks
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.
None of the sources cited for this claim have been checked yet.
In the paper
“The PSA-induced production of IL-10 inhibits the activity of mucosal effector T cells, in particular of TH17 cells, and thereby protects mice in experimental models of colitis (Dasgupta et al., 2014; Mazmanian et al., 2008).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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
“Jiang et al. recently reported that fetal enterocytes exposed to PSA produce lower levels of the IL-1β-induced, pro-inflammatory cytokine IL-8, which may play a role in the development of necrotizing enterocolitis in prematurely born infants (Jiang et al., 2017).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Jiang et al., 2017 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.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Importantly, PSA also activates toll-like receptor (TLR) 2 expressed on the surface of DCs, which triggers the release of cytokines that promote IL-10 production by T cells (Cobb et al., 2004; Dasgupta et al., 2014; Johnson et al., 2015; Mazmanian et al., 2005; 2008; Telesford et al., 2015; Q. Wang et al., 2006).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
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
“PSA exposure increases expression of ENTPD1 on FoxP3+ Tregs, thus suggesting a potential intersection between PSA and (microbially derived) extracellular ATP in the regulation of the immune system (Telesford et al., 2015).”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Microbiome-Associated Metabolites that Shape the Immune System > Metabolites that are synthesized de novo by gut microbes
What the sources say
- Not checked yetcites Telesford et al., 2015 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
“most of the known bacterially derived metabolites in the intestinal tract remain functionally uncharacterized, and it is unclear how many other, hitherto unidentified metabolites are yet to be discovered.”
§ Understanding the Holobiont: How microbial metabolites affect human health and shape the immune system > Concluding remarks
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.
Probably not a substantial claim. It may state two separate claims as one.
The paper relies on this without support.
Extracellular ATP primarily has pro-inflammatory properties.
“Unlike the other microbiota-derived compounds discussed so far, extracellular ATP primarily exhibits pro-inflammatory properties.”
The paper relies on this without support.
IL-22 supports intestinal mucosa integrity by inducing antimicrobial peptide secretion from epithelial cells, mucin production, and intestinal goblet cell proliferation.
“Protection against these pathologies is mediated by expression of IL-22, a cytokine that supports the integrity of the intestinal mucosa by inducing the secretion of antimicrobial peptides from epithelial cells, production of mucins and proliferation of intestinal goblet cells.”
The paper relies on this without support.
Protection against the immunological pathologies of AhR deficiency is mediated by IL-22 expression.
“Protection against these pathologies is mediated by expression of IL-22”
The paper relies on this without support.
T follicular helper cells in Peyer's patches foster development of B cells that produce immunoglobulins specific for intestinal bacteria, which can be secreted across the epithelium as IgA.
“T follicular helper (Tfh) cells in the Peyer’s patches foster the development of B cells that produce immunoglobulins with specificity for intestinal bacteria, which can be secreted across the epithelium as IgA.”
The paper relies on this without support.
The human intestinal tract is believed to contain up to 1,150 bacterial species, with at least 160 present in any given individual.
“Considering that up to 1,150 different bacterial species are believed to reside in the human intestinal tract, and at least 160 of them are present in any given individual”
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
“Considering that bile acids regulate metabolism and anti-inflammatory signals 40 and that they are depleted in Lmna G609G/G609G mice 28 , the restoration of secondary bile acidsand other metabolites (arabinose, ribose, inosine)by FMT might contribute to extend healthspan and lifespan in progeroid mice (Fig. 4g).”
From Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice (2019) · cites this paper as [40]
Citations
Cites
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444 · cited 1×
“Crucially, the transfer of the microbiota from obese mice to germ-free animals results in a significantly larger weight increase than an equivalent transfer from lean mice, clearly demonstrating that body weight is in part controlled by the microbiome (Turnbaugh et al., 2006, 2008).”
BackgroundStructure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Diet rapidly and reproducibly alters the human gut microbiome
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100 · cited 1×
“Conversely, a plant-based diet promotes the enrichment of microbial species that efficiently ferment fiber (Bacteroidetes) (De Filippo et al., 2010; Wu et al., 2011).”
BackgroundHuman 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 · cited 5×
“The composition of the microbiome differs between obese and lean individuals in humans and in animal models: obesity is associated with a relative increase in Firmicutes at the expense of Bacteroidetes (Ley et al., 2005, 2006).”
BackgroundInfluentialDiversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · cited 1×
“Members of the phylum Proteobacteria are also represented frequently but far less prominently (Eckburg et al., 2005; Hold et al., 2002; Human Microbiome Project Consortium, 2012).”
BackgroundA core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823 · cited 1×
“Obese individuals share a functionally similar gut microbiome between them, with reduced but still considerable species diversity (Human Microbiome Project Consortium, 2012; Kurokawa et al., 2007; Qin et al., 2010; Turnbaugh et al., 2009).”
BackgroundFrom Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites
Koh, A., De Vadder, F., Kovatcheva-Datchary, P., & Bäckhed, F. (2016) · Cell · doi:10.1016/j.cell.2016.05.041 · Cited by 7,070
A metagenome-wide association study of gut microbiota in type 2 diabetes
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762
Metabolic Endotoxemia Initiates Obesity and Insulin Resistance
Cani, P. D., Amar, J., Iglesias, M. A., Poggi, M., Knauf, C., Bastelica, D., Neyrinck, A. M., Fava, F., Tuohy, K. M., Chabo, C., et al. (2007) · Diabetes · doi:10.2337/db06-1491 · Cited by 6,638 · cited 1×
“Interestingly, mice chronically exposed to low levels of LPS for 4 weeks gained weight and became resistant to insulin (Cani et al., 2007).”
Background
Cited by
Sorted by citations
Short-chain fatty acids: Linking diet, the microbiome and immunity
Mann, E. R., Lam, Y. K., & Uhlig, H. H. (2024) · Nature reviews. Immunology · doi:10.1038/s41577-024-01014-8 · Cited by 1,595
Human gut microbiome: Hopes, threats and promises
Cani, P. D. (2018) · Gut · doi:10.1136/gutjnl-2018-316723 · Cited by 1,386
Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis
Song, X., Sun, X., Oh, S. F., Wu, M., Zhang, Y., Zheng, W., Geva-Zatorsky, N., Jupp, R., Mathis, D., Benoist, C., et al. (2020) · Nature · doi:10.1038/s41586-019-1865-0 · Cited by 1,024
Probiotics Mechanism of Action on Immune Cells and Beneficial Effects on Human Health
Mazziotta, C., Tognon, M., Martini, F., Torreggiani, E., & Rotondo, J. C. (2023) · Cells · doi:10.3390/cells12010184 · Cited by 889
Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation
Sinha, S. R., Haileselassie, Y., Nguyen, L. P., Tropini, C., Wang, M., Becker, L. S., Sim, D., Jarr, K. J., Bishop, E. S., Singh, G., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2020.01.021 · Cited by 880
Metadata
- Authors
- Postler, T. S., & Ghosh, S.
- Affiliations
- Columbia University (US)
- Columbia University Irving Medical Center (US)
- Corresponding author
- Ghosh, Sankar
- Venue
- Cell Metabolism
- Publisher
- Elsevier BV
- Published
- 2017-07
- Volume
- 26
- Issue
- 1
- Pages
- 110-130
- ISSN
- 1550-4131 (ISSN-L)
- PMC
- PMC5535818
- OpenAlex
- W2625068954
- Semantic Scholar
- 75cf85d5fe820ba74946018ee4d760637d128aae
- Cited by
- 876
- References
- 252
- Citations by year
- 2026: 89 · 2025: 91 · 2024: 120 · 2023: 113 · 2022: 97 · 2021: 102 · 2020: 106 · 2019: 92 · 2018: 52 · 2017: 14
- FWCI
- 6.78
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell Metabolism (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK102180)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Keywords
- gut microbiota, microbial metabolites, host-microbe interactions, gut-immune axis, immune system development, metabolic disorders, inflammatory bowel disease, cancer, mood and behavior, dietary metabolites
- MeSH terms
- Gastrointestinal Microbiome, Animals, Bacteria, Humans, Immune System, Inflammation, Metabolic Diseases, Inflammatory Bowel Diseases, Metabolome
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 2026-10-07, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-07 (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 ›
Are you an author, or do you see a problem with this page? Request a review