phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| phenomenon | a bacterial metabolite acting as fuel, as a barrier signal and as an immunomodulator at once, whose measured concentration is the small fraction the mucosa did not absorb— “Bacteroidetes (gram-negative) and Firmicutes (gram-positi ve) are the most abundant phyla in the intestine, with members of the Bacteroidetes mainly producing acetate and propionate, while Firmicutes mostly produce butyrate in the human gut” | |
| claim-type | mechanism— “Bacteroidetes (gram-negative) and Firmicutes (gram-positi ve) are the most abundant phyla in the intestine, with members of the Bacteroidetes mainly producing acetate and propionate, while Firmicutes mostly produce butyrate in the human gut” | |
| method — evidence | — “Here, we aim to provide an overview of microbial SCFAs production in the intestine and their effect on intestinal cells and the immune response. Moreover, gut microbiome changes in IBD are reviewed and how they are related to impaired intestinal SCFAs production and associate to cell metabolism and signaling pathways controlling mucosal… | |
| object of study — evidence | — “Here, we aim to provide an overview of microbial SCFAs production in the intestine and their effect on intestinal cells and the immune response. Moreover, gut microbiome changes in IBD are reviewed and how they are related to impaired intestinal SCFAs production and associate to cell metabolism and signaling pathways controlling mucosal… | |
| research question — evidence | — “However, it remains unclear whether dysbiosis is a cause or a consequence of IBD” | |
| contribution — evidence | — “Quantification of human intestinal SCFAs only provides steady state levels and may not accurately reflect the level of bacterial production as most SCFAs produced in the colonic lumen (90–95%) are absorbed by the gut mucosa” | |
| transfer | from animal science: resistant-starch feeding trials in pigs, carried into human gut physiology as a model for dietary regulation of SCFA transporters— “Similar observations were made in pigs, where SLC16A1 mRNA levels increased in cecal and colonic mucosa after dietary supplementation with RS compared to digestible starch (DS) ( 41). In contrast, SLC5A8 mRNA levels (encoding SMCT1) were not affected by RS or DS diet ( 41), showing a specific regulation of MCT1 expression by RS in comparison… | transfers[0] |
| transfer | from food regulation: the Codex Alimentarius definition of dietary fibre, a food-regulation standard used here to fix what counts as the substrate— “Here, we aim to provide an overview of microbial SCFAs production in the intestine and their effect on intestinal cells and the immune response. Moreover, gut microbiome changes in IBD are reviewed and how they are related to impaired intestinal SCFAs production and associate to cell metabolism and signaling pathways controlling mucosal… | transfers[1] |
| mechanism | the measurement is what absorption left behind 90 to 95 per cent of the SCFAs produced in the colonic lumen are taken up by the mucosa before anything is collected. A fecal SCFA concentration is therefore the small remainder, and a difference between patients and controls could be a difference in production, in absorption, or in transit - the number cannot distinguish them— “Quantification of human intestinal SCFAs only provides steady state levels and may not accurately reflect the level of bacterial production as most SCFAs produced in the colonic lumen (90–95%) are absorbed by the gut mucosa” | mechanisms[0] |
| mechanism | an intervention whose sign is a property of the model germ-free conditions make IL-10-deficient chronic colitis less severe and acute chemically-induced colitis worse. Any statement of the form 'the microbiota protects against colitis' is therefore incomplete without naming the model, and two papers reporting opposite results may both be right— “This may go either way, e.g., IL-10 deficient mice show less severe chronic bowel inflammation in germfree (GF) conditions ( 13, 14), while acute chemically-induced colitis is exacerbated in GF mice compared to mice with a normal microbiome” | mechanisms[1] |
| mechanism | a null result whose treatment lacked the active ingredient probiotics showed no significant effect in Crohn's disease - and the review notes in the next sentence that the probiotics evaluated in those studies were not butyrate-producing bacteria. The hypothesis being tested was about butyrate and the intervention did not contain any— “So far, probiotic treatments have not shown a significant effect in inducing or maintaining remission of active or quiescent CD, or in preventing relapse of CD after surgically-induced remission (146, 147). However, probiotics evaluated in these studies were not butyrate-producing bacteria.” | mechanisms[2] |
| mechanism | a division of labour that makes composition into chemistry Bacteroidetes make acetate and propionate; Firmicutes make butyrate. A shift in phylum ratio is therefore automatically a shift in which metabolite the colon receives, which is why a compositional 16S result can be read as a functional claim and why that reading is only as good as the division— “Bacteroidetes (gram-negative) and Firmicutes (gram-positi ve) are the most abundant phyla in the intestine, with members of the Bacteroidetes mainly producing acetate and propionate, while Firmicutes mostly produce butyrate in the human gut” | mechanisms[3] |
| mechanism | oxygen as the intermediate butyrate absorbed and oxidised by the epithelium consumes local oxygen. Deplete the anaerobes with antibiotics, butyrate falls, the mucosa stops consuming oxygen, and the colon becomes hospitable to aerobes such as Salmonella - a chain in which the metabolite acts by changing the physical environment rather than by signalling— “The susceptibility due to the depletion of anaerobic bacteria (induced by antibiotics ) is associated to a reduction in butyrate levels, thus promoting an aerobic environment and the expansion of aerobic bacteria suc h as Salmonella typhimurium” | mechanisms[4] |
| qualifies | the literature's use of fecal SCFA concentration as a measure of bacterial production, since 90-95% is absorbed before collection— “Quantification of human intestinal SCFAs only provides steady state levels and may not accurately reflect the level of bacterial production as most SCFAs produced in the colonic lumen (90–95%) are absorbed by the gut mucosa” | claim_relations[0] |
| qualifies | the causal reading of dysbiosis in IBD - the review states it remains unclear whether dysbiosis is cause or consequence— “However, it remains unclear whether dysbiosis is a cause or a consequence of IBD” | claim_relations[1] |
| critiques | the probiotic trials in Crohn's disease, whose null result is reported alongside the observation that the probiotics tested were not butyrate producers— “So far, probiotic treatments have not shown a significant effect in inducing or maintaining remission of active or quiescent CD, or in preventing relapse of CD after surgically-induced remission (146, 147). However, probiotics evaluated in these studies were not butyrate-producing bacteria.” | claim_relations[2] |
| builds-on | germ-free and gnotobiotic colitis models, while reporting that they answer in opposite directions— “This may go either way, e.g., IL-10 deficient mice show less severe chronic bowel inflammation in germfree (GF) conditions ( 13, 14), while acute chemically-induced colitis is exacerbated in GF mice compared to mice with a normal microbiome” | claim_relations[3] |
| extends | the metabolic account of SCFAs as colonocyte fuel, by adding transporter regulation and GPCR signalling as immunomodulatory routes— “Here, we aim to provide an overview of microbial SCFAs production in the intestine and their effect on intestinal cells and the immune response. Moreover, gut microbiome changes in IBD are reviewed and how they are related to impaired intestinal SCFAs production and associate to cell metabolism and signaling pathways controlling mucosal… | claim_relations[4] |
| sense | SCFA level - AS MEASURED IN FECES: a steady state, and 5 to 10 per cent of what was produced, because the mucosa absorbs 90-95% of the colonic lumen's SCFAs before anything is collected— “Quantification of human intestinal SCFAs only provides steady state levels and may not accurately reflect the level of bacterial production as most SCFAs produced in the colonic lumen (90–95%) are absorbed by the gut mucosa” | senses[0] |
| sense | SCFA level - AS INTENDED: the rate of bacterial production, which the authors say the fecal measurement may not accurately reflect and which is inferred from its association with resistant-starch diets— “Nevertheless, the analysis of SCFAs in fecal samples is used as an approximation of gut levels, since excreted SCFA concentrati ons are associated with RS enriched diets (substrates of SCFAsproducing bacteria), inferring the relationship between in testinal SCFAs production and fecal levels” | senses[1] |
| sense | removing the microbiota - IN IL-10-DEFICIENT MICE: protective, giving less severe chronic bowel inflammation under germ-free conditions— “This may go either way, e.g., IL-10 deficient mice show less severe chronic bowel inflammation in germfree (GF) conditions ( 13, 14), while acute chemically-induced colitis is exacerbated in GF mice compared to mice with a normal microbiome” | senses[2] |
| sense | removing the microbiota - IN CHEMICALLY-INDUCED COLITIS: harmful, with the acute disease exacerbated in germ-free mice against animals with a normal microbiome— “This may go either way, e.g., IL-10 deficient mice show less severe chronic bowel inflammation in germfree (GF) conditions ( 13, 14), while acute chemically-induced colitis is exacerbated in GF mice compared to mice with a normal microbiome” | senses[3] |
| sense | SCFAs acting on the epithelium - IN HEALTH: fuel and proliferation for colonocytes | senses[4] |
| sense | SCFAs acting on the epithelium - IN CANCER: suppression of proliferation and induction of apoptosis, the opposite sign in the same tissue | senses[5] |
| sense | SCFA concentration - AS A SINGLE NUMBER: misleading, because proximal colon runs 70-140 mM and distal colon 20-70 mM and both vary with fibre intake Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | senses[6] |
| control | SLC5A8 (SMCT1) mRNA measured alongside SLC16A1 (MCT1) in the same pigs on the same resistant-starch and digestible-starch diets — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out a general effect of diet on monocarboxylate transport - SMCT1 does not move, so the MCT1 response is specific to that transporter Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| control | germ-free conditions applied in two different colitis models - chronic IL-10-deficient and acute chemically-induced — partial Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out a single-model answer standing for the microbiota's role - running both shows the sign reverses, which one model alone would have hidden Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[1] |
| control | SCFA levels measured in liver and blood as well as intestine — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out the assumption that SCFA action is systemic - levels elsewhere are much lower, placing signalling and uptake at the mucosa, while their detectability still supports systemic function Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[2] |
| control | SCFA-producing bacteria and SCFA levels both measured in IBD patients, rather than inferring the metabolite from the taxon — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out a taxonomic shift being reported as a metabolic one - here both the producers and the product are shown to be reduced Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[3] |
| control | probiotic trials in Crohn's disease, reported as showing no significant effect on inducing or maintaining remission — failed Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. — rules out nothing about butyrate, and the review says so in the next sentence - the probiotics tested were not butyrate-producing bacteria, so the null result does not test the mechanism it appears to test Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[4] |
| control | well-controlled randomised placebo-controlled trials of prebiotic supplementation, named as needed and not yet done — absent-declared-unreported — rules out placebo response and spontaneous remission in IBD - the randomised placebo-controlled trials that would rule them out are named as needed and not yet done Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[5] |
| control | faecal microbiome transplantation, named as producing inconsistent results and excluded from the review's scope — absent-stated-about-other — rules out the possibility that the SCFA effects are reproduced by wholesale microbiota transfer - excluded from the review's scope rather than resolved Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[6] |
| weight | the literature's use of fecal SCFA concentration as a measure of bacterial production, since 90-95% is absorbed before collection — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[0] |
| weight | the causal reading of dysbiosis in IBD - the review states it remains unclear whether dysbiosis is cause or consequence — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[1] |
| weight | the probiotic trials in Crohn's disease, whose null result is reported alongside the observation that the probiotics tested were not butyrate producers — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[2] |
| weight | germ-free and gnotobiotic colitis models, while reporting that they answer in opposite directions — 0.9 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[3] |
| weight | the metabolic account of SCFAs as colonocyte fuel, by adding transporter regulation and GPCR signalling as immunomodulatory routes — 0.9 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | claim_relations[4] |
| differs in (stated by the tagger, no quotation) | steady state levels —distinct-from→ bacterial production — whether the number is a rate of production or the residue left after absorption | concept_edges[0] |
| relation | steady state levels —distinct-from→ bacterial production — quantifying SCFAs returns a standing concentration after the mucosa has absorbed 90-95% of what the lumen contained, which is not the production rate the field means Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| weight | steady state levels —distinct-from→ bacterial production — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[0] |
| audit | IL-10 deficient mice —distinct-from→ chemically-induced colitis — Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says the effect 'may go either way' in the two models; distinct-from is loose. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| differs in (stated by the tagger, no quotation) | IL-10 deficient mice —distinct-from→ chemically-induced colitis — which direction removing the microbiota moves the disease | concept_edges[1] |
| relation | IL-10 deficient mice —distinct-from→ chemically-induced colitis — germ-free conditions reduce inflammation in the chronic IL-10-deficient model and worsen acute chemically-induced colitis - one intervention, two signs Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| weight | IL-10 deficient mice —distinct-from→ chemically-induced colitis — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[1] |
| differs in (stated by the tagger, no quotation) | Bacteroidetes —distinct-from→ Firmicutes — which short-chain fatty acid the organism produces | concept_edges[2] |
| relation | Bacteroidetes —distinct-from→ Firmicutes — the two dominant phyla make different SCFAs - acetate and propionate against butyrate - so the metabolite profile is a readout of which phylum is present Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[2] |
| weight | Bacteroidetes —distinct-from→ Firmicutes — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[2] |
| differs in (stated by the tagger, no quotation) | MCT1 —distinct-from→ SMCT1 — whether dietary substrate regulates the transporter's expression | concept_edges[3] |
| relation | MCT1 —distinct-from→ SMCT1 — resistant starch raises SLC16A1 mRNA (MCT1) in pig cecal and colonic mucosa while SLC5A8 (SMCT1) is unaffected by the same diets Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[3] |
| weight | MCT1 —distinct-from→ SMCT1 — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[3] |
| audit | antibiotics —causes→ butyrate — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but antibiotics deplete anaerobes, which is associated with lower butyrate; causes is indirect. Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| effect direction (stated by the tagger, no quotation) | antibiotics —causes→ butyrate — reduces | concept_edges[5] |
| relation | antibiotics —causes→ butyrate — depleting anaerobic bacteria with antibiotics lowers butyrate, which makes the colon aerobic and lets Salmonella typhimurium expand Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| weight | antibiotics —causes→ butyrate — 0.95 Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concept_edges[5] |
| outcome | control — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[0] |
| outcome | control — partial Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[1] |
| outcome | control — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[2] |
| outcome | control — held Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[3] |
| outcome | control — failed Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[4] |
| outcome (stated by the tagger, no quotation) | control — absent-declared-unreported Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[5] |
| outcome (stated by the tagger, no quotation) | control — absent-stated-about-other Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | controls[6] |
| limitation | fecal and tissue SCFA quantification gives steady state levels and may not accurately reflect bacterial production, since 90-95% is absorbed by the mucosa Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[0] |
| limitation | the fecal measurement is used as an approximation of gut levels, justified by association with resistant-starch diets rather than by direct comparison Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[1] |
| limitation | it remains unclear whether dysbiosis is a cause or a consequence of IBD Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[2] |
| limitation | the molecular mechanism by which SCFAs suppress pro-inflammatory mediators has not been completely determined in human or mouse mononuclear cell models Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[3] |
| limitation | the mechanisms involved in IBD pathophysiology are still not resolved, nor how butyrate regulates inflammation and transcription in colonic mucosa Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[4] |
| limitation | well-controlled randomised placebo-controlled trials are still needed before prebiotic supplementation can be said to produce clinical improvement Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[5] |
| limitation | faecal microbiome transplantation has generated inconsistent results and is placed outside the scope of the review Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[6] |
| limitation | SCFA concentration is not one number - proximal colon runs 70-140 mM against 20-70 mM distally, and both depend on fibre intake Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | limitations[7] |
finding · quantity · variable · definition · key-term — grounded in the full text| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[0] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[1] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[2] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[3] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[4] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[5] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[6] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[7] |
| finding | Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.findings[8] |
| quantity | to 95 per cent of colonic-lumen SCFAs are absorbed by the mucosa before any measurement is taken Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.quantities[0] |
| variable | butyrate Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[0] |
| variable | dysbiosis Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.variables[1] |
| definition | steady state levels Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[0] |
| definition | probiotic Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | content_tags.definitions[1] |
| concept | SCFAs — not defined in this paper's own words; acetate, propionate and butyrate from anaerobic fermentation of dietary fibre - the review's object, and a quantity whose fecal measurement is the fraction the gut failed to absorb Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[0] |
| concept | steady state levels — not defined in this paper's own words; what SCFA quantification actually returns - a standing concentration after absorption, not a rate Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[1] |
| concept | bacterial production — not defined in this paper's own words; the quantity the field means when it says SCFA level, and the one the authors say the measurement may not accurately reflect Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[2] |
| concept | butyrate — not defined in this paper's own words; the SCFA made mainly by Firmicutes, the colonocyte's primary fuel, and the one whose loss the IBD literature is built on Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[3] |
| concept | Bacteroidetes — not defined in this paper's own words; gram-negative phylum producing mainly acetate and propionate - one half of a division of labour that makes the SCFA profile a readout of community composition Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[4] |
| concept | Firmicutes — not defined in this paper's own words; the phylum producing most human gut butyrate, so a shift in phylum ratio is a shift in which metabolite is available Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[5] |
| concept | germfree — not defined in this paper's own words; the field's instrument for asking what the microbiota does - and one whose answer changes sign between two colitis models in a single sentence of this review Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[6] |
| concept | IL-10 deficient mice — not defined in this paper's own words; the chronic colitis model in which germ-free conditions make the disease LESS severe Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[7] |
| concept | chemically-induced colitis — not defined in this paper's own words; the acute model in which germ-free conditions make the disease WORSE - the same intervention, the opposite direction Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[8] |
| concept | dysbiosis — not defined in this paper's own words; an imbalanced intestinal microbiota; whether it is a cause or a consequence of IBD is stated here as unresolved Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[9] |
| concept | IBD — not defined in this paper's own words; inflammatory bowel disease - ulcerative colitis and Crohn's disease, the setting in which every SCFA finding here is meant to apply Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[10] |
| concept | MCT1 — not defined in this paper's own words; the monocarboxylate transporter whose mRNA rises with resistant starch - the regulated half of a transporter pair Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[11] |
| concept | SMCT1 — not defined in this paper's own words; the sodium-coupled transporter whose mRNA does NOT respond to the same diet - the control that makes the MCT1 result specific Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[12] |
| concept | IECs — not defined in this paper's own words; intestinal epithelial cells - where SCFAs support proliferation in health, against the opposite effect on cancer cells Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[13] |
| concept | antibiotics — not defined in this paper's own words; the perturbation that depletes anaerobes and butyrate together, creating an aerobic niche - so its effect is attributable to the pair, not to either alone Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[14] |
| concept | Salmonella typhimurium — not defined in this paper's own words; the aerobe that expands once butyrate falls and the colon's oxygen rises - the endpoint of the antibiotic chain Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[15] |
| concept | probiotic — not defined in this paper's own words; live microorganisms given as therapy - and in the Crohn's trials that found no effect, ones that were not butyrate producers Quotation withheld — this paper is not ours to reproduce, and the page has already quoted as much of it as the rights layer allows. The tag, its field and its confidence stand; the sentence is at the publisher. | concepts[16] |
When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.
Tag layer © the Meta-Tagging Project, CC BY 4.0. The paper text is © its authors/publisher
and is linked, not reproduced. Excerpts shown are short quotations for identification and verification.
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