standOff, and the article is at its publisher via the link below. 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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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.| relation to other work | claim_relations | how this paper stands to another: agrees, contradicts, extends, qualifies |
| claim type | claim_type | the shape of the claim: existence, mechanism, method, critique, prediction, null |
| concept edge | concept_edges | an asserted relation between two concepts, with the sentence asserting it |
| concept | concepts | an idea the paper works with, quoted where the paper uses it |
| content tag | content_tags | a finding, definition, quantity, statistic or variable named in the paper |
| contribution | contribution | what the paper claims to add |
| control | controls | an experiment run to eliminate a rival explanation |
| limitation | limitations | what the paper says its evidence cannot support |
| mechanism | mechanisms | how the reported effect is said to come about |
| method | method | how the paper produced its evidence |
| object of study | object_of_study | what the paper is about — the thing it investigates |
| phenomenon | phenomenon | the effect or regularity under study |
| research question | research_question | the question the paper sets itself |
| sense | senses | a distinct use of a term, quoted where the paper fixes it |
| transfer | transfers | a method or concept carried in from another field |
Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; 5 of 5 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | the short-chain fatty acids bacteria make from dietary fibre - acetate, propionate and butyrate - and what they do to the intestinal epithelium and immune cells in inflammatory bowel disease Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | object_of_study | the paper's words | |
| research_question | whether the reduced SCFA levels seen in IBD are a mechanism of the disease and a possible therapy, or a consequence of it Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | research_question | the paper's words | |
| contribution | an overview of SCFA production, transport and receptor signalling in the gut, which states that fecal SCFA quantification measures a steady state and not production, and that whether dysbiosis causes IBD is unresolved Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | contribution | the paper's words | |
| claim_type | mechanism Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_type | the paper's words | |
| 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | phenomenon | the paper's words | |
| method | review Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: review | method | the paper's words | |
| mechanisms | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[2] | 0.95 | the tagger's words |
| mechanisms | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[3] | 0.95 | the tagger's words |
| mechanisms | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: oxygen as the intermediate | mechanisms[4] | 0.95 | the tagger's words |
| limitations | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[0] | 0.95 | the tagger's words |
| limitations | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[1] | 0.95 | the tagger's words |
| limitations | it remains unclear whether dysbiosis is a cause or a consequence of IBD Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[2] | 0.95 | the tagger's words |
| limitations | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[3] | 0.95 | the tagger's words |
| limitations | the mechanisms involved in IBD pathophysiology are still not resolved, nor how butyrate regulates inflammation and transcription in colonic mucosa Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[4] | 0.95 | the tagger's words |
| limitations | well-controlled randomised placebo-controlled trials are still needed before prebiotic supplementation can be said to produce clinical improvement Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[5] | 0.95 | the tagger's words |
| limitations | faecal microbiome transplantation has generated inconsistent results and is placed outside the scope of the review Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[6] | 0.95 | the tagger's words |
| limitations | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[7] | 0.95 | the tagger's words |
| transfers | resistant-starch feeding trials in pigs, carried into human gut physiology as a model for dietary regulation of SCFA transporters Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | transfers[0] | 0.95 | the tagger's words |
| transfers | the Codex Alimentarius definition of dietary fibre, a food-regulation standard used here to fix what counts as the substrate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | transfers[1] | 0.95 | the tagger's words |
| controls | SLC5A8 (SMCT1) mRNA measured alongside SLC16A1 (MCT1) in the same pigs on the same resistant-starch and digestible-starch diets Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a general effect of diet on monocarboxylate transport - SMCT1 does not move, so the MCT1 response is specific to that transporter · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | germ-free conditions applied in two different colitis models - chronic IL-10-deficient and acute chemically-induced Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a single-model answer standing for the microbiota's role - running both shows the sign reverses, which one model alone would have hidden · outcome: partial | controls[1] | 0.95 | the tagger's words |
| controls | SCFA levels measured in liver and blood as well as intestine Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: 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 · outcome: held | controls[2] | 0.95 | the tagger's words |
| controls | SCFA-producing bacteria and SCFA levels both measured in IBD patients, rather than inferring the metabolite from the taxon Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a taxonomic shift being reported as a metabolic one - here both the producers and the product are shown to be reduced · outcome: held | controls[3] | 0.95 | the tagger's words |
| controls | probiotic trials in Crohn's disease, reported as showing no significant effect on inducing or maintaining remission Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: 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 · outcome: failed | controls[4] | 0.95 | the tagger's words |
| controls | well-controlled randomised placebo-controlled trials of prebiotic supplementation, named as needed and not yet done Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: 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 · outcome (stated by the tagger, no quotation): absent-declared-unreported | controls[5] | 0.95 | the tagger's words |
| controls | faecal microbiome transplantation, named as producing inconsistent results and excluded from the review's scope Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the possibility that the SCFA effects are reproduced by wholesale microbiota transfer - excluded from the review's scope rather than resolved · outcome (stated by the tagger, no quotation): absent-stated-about-other | controls[6] | 0.95 | the tagger's words |
| concepts | SCFAs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: SCFAs | concepts[0] | 0.95 | the paper's words |
| concepts | steady state levels Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: steady state levels | concepts[1] | 0.95 | the paper's words |
| concepts | bacterial production Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: bacterial production | concepts[2] | 0.95 | the paper's words |
| concepts | butyrate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: butyrate | concepts[3] | 0.95 | the paper's words |
| concepts | Bacteroidetes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Bacteroidetes | concepts[4] | 0.95 | the paper's words |
| concepts | Firmicutes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Firmicutes | concepts[5] | 0.95 | the paper's words |
| concepts | germfree Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: germfree | concepts[6] | 0.95 | the paper's words |
| concepts | IL-10 deficient mice Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: IL-10 deficient mice | concepts[7] | 0.95 | the paper's words |
| concepts | chemically-induced colitis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: chemically-induced colitis | concepts[8] | 0.95 | the paper's words |
| concepts | dysbiosis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: dysbiosis | concepts[9] | 0.95 | the paper's words |
| concepts | IBD Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: IBD | concepts[10] | 0.95 | the paper's words |
| concepts | MCT1 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: MCT1 | concepts[11] | 0.95 | the paper's words |
| concepts | SMCT1 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: SMCT1 | concepts[12] | 0.95 | the paper's words |
| concepts | IECs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: IECs | concepts[13] | 0.95 | the paper's words |
| concepts | antibiotics Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: antibiotics | concepts[14] | 0.95 | the paper's words |
| concepts | Salmonella typhimurium Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Salmonella typhimurium | concepts[15] | 0.95 | the paper's words |
| concepts | probiotic Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: probiotic | concepts[16] | 0.95 | the paper's words |
| senses | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[0] | 0.95 | the tagger's words |
| senses | 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 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[1] | 0.95 | the tagger's words |
| senses | removing the microbiota - IN IL-10-DEFICIENT MICE: protective, giving less severe chronic bowel inflammation under germ-free conditions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[2] | 0.95 | the tagger's words |
| senses | removing the microbiota - IN CHEMICALLY-INDUCED COLITIS: harmful, with the acute disease exacerbated in germ-free mice against animals with a normal microbiome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[3] | 0.95 | the tagger's words |
| senses | SCFAs acting on the epithelium - IN HEALTH: fuel and proliferation for colonocytes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[4] | 0.95 | the tagger's words |
| senses | SCFAs acting on the epithelium - IN CANCER: suppression of proliferation and induction of apoptosis, the opposite sign in the same tissue Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[5] | 0.95 | the tagger's words |
| senses | 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 record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[6] | 0.95 | the tagger's words |
| claim_relations | qualifies → the literature's use of fecal SCFA concentration as a measure of bacterial production, since 90-95% is absorbed before collection Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | qualifies → the causal reading of dysbiosis in IBD - the review states it remains unclear whether dysbiosis is cause or consequence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[1] | 0.95 | the tagger's words |
| claim_relations | critiques → the probiotic trials in Crohn's disease, whose null result is reported alongside the observation that the probiotics tested were not butyrate producers Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[2] | 0.95 | the tagger's words |
| claim_relations | builds-on → germ-free and gnotobiotic colitis models, while reporting that they answer in opposite directions Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[3] | 0.95 | the tagger's words |
| claim_relations | extends → the metabolic account of SCFAs as colonocyte fuel, by adding transporter regulation and GPCR signalling as immunomodulatory routes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[4] | 0.95 | the tagger's words |
| concept_edges | steady state levels —distinct-from→ bacterial production Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether the number is a rate of production or the residue left after absorption · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): whether the number is a rate of production or the residue left after absorption · the relation stated: 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 also in: steady state levels · bacterial production | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | IL-10 deficient mice —distinct-from→ chemically-induced colitis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: which direction removing the microbiota moves the disease · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): which direction removing the microbiota moves the disease · the relation stated: germ-free conditions reduce inflammation in the chronic IL-10-deficient model and worsen acute chemically-induced colitis - one intervention, two signs
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. also in: IL-10 deficient mice · chemically-induced colitis | concept_edges[1] | 0.95 | the tagger's words |
| concept_edges | Bacteroidetes —distinct-from→ Firmicutes Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: which short-chain fatty acid the organism produces · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): which short-chain fatty acid the organism produces · the relation stated: the two dominant phyla make different SCFAs - acetate and propionate against butyrate - so the metabolite profile is a readout of which phylum is present also in: Bacteroidetes · Firmicutes | concept_edges[2] | 0.95 | the tagger's words |
| concept_edges | MCT1 —distinct-from→ SMCT1 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether dietary substrate regulates the transporter's expression · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): whether dietary substrate regulates the transporter's expression · the relation stated: resistant starch raises SLC16A1 mRNA (MCT1) in pig cecal and colonic mucosa while SLC5A8 (SMCT1) is unaffected by the same diets | concept_edges[3] | 0.95 | the tagger's words |
| concept_edges | antibiotics —causes→ butyrate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. direction on the measure: reduces · the relation itself is separately evidenced · strength of the relation: 0.95 · direction on the measure (stated by the tagger, no quotation): reduces · the relation stated: depleting anaerobic bacteria with antibiotics lowers butyrate, which makes the colon aerobic and lets Salmonella typhimurium expand
Audit 2026-09-28: DOUBTFUL - read against its span and kept, but antibiotics deplete anaerobes, which is associated with lower butyrate; causes is indirect. also in: antibiotics · butyrate | concept_edges[5] | 0.95 | the tagger's words |
| content_tags | fecal SCFA quantification gives steady state levels and may not reflect bacterial production, because 90-95% of lumen SCFAs are absorbed by the mucosa Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[0] | 0.95 | the tagger's words |
| content_tags | germ-free conditions make IL-10-deficient colitis less severe and chemically-induced colitis worse - the same intervention with opposite signs Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[1] | 0.95 | the tagger's words |
| content_tags | it remains unclear whether dysbiosis is a cause or a consequence of IBD Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[2] | 0.95 | the tagger's words |
| content_tags | Bacteroidetes mainly produce acetate and propionate while Firmicutes mostly produce butyrate in the human gut Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | resistant starch raises MCT1 (SLC16A1) mRNA while SMCT1 (SLC5A8) is unaffected, making the regulation transporter-specific Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[4] | 0.95 | the tagger's words |
| content_tags | antibiotic depletion of anaerobes lowers butyrate, promotes an aerobic environment and expands Salmonella typhimurium Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[5] | 0.95 | the tagger's words |
| content_tags | probiotics showed no significant effect in Crohn's disease, and the probiotics evaluated were not butyrate-producing bacteria Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[6] | 0.95 | the tagger's words |
| content_tags | SCFAs suppress cancer cell proliferation and induce apoptosis, the opposite of their effect on healthy intestinal epithelial cells Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[7] | 0.95 | the tagger's words |
| content_tags | IBD patients show both reduced SCFA-producing bacteria and reduced SCFA levels compared with healthy controls Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[8] | 0.95 | the tagger's words |
| content_tags | what SCFA quantification returns - a standing concentration measured after the mucosa has absorbed 90-95% of what the lumen produced, and not the production rate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: steady state levels | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | live microorganisms that when administered in adequate amounts confer a health benefit on the host - and in the Crohn's trials, ones that were not butyrate producers Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: probiotic | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | to 95 per cent of colonic-lumen SCFAs are absorbed by the mucosa before any measurement is taken Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.quantities[0] | 0.95 | the tagger's words |
| content_tags | butyrate Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: butyrate | content_tags.variables[0] | 0.95 | the tagger's words |
| content_tags | dysbiosis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: dysbiosis | content_tags.variables[1] | 0.95 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.