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 WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below.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 An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason.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 two-way traffic between the commensal microbiota and the mammalian immune system - how microbes train immunity and how immunity in turn shapes which microbes persist 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 | which microbiome-immunity interactions are mechanistically established, and what still stands between association and a causal claim in human disease 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 | a review that organises the mechanisms by compartment and by disease and then states plainly that a direct causal relationship has not been established in most medical conditions - the negative claim is the contribution 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 | critique 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 | host-microbe mutualism and its breakdown - a relationship in which each side regulates the other, so that neither perturbation nor dysregulation can be read as the cause of the other from observation alone 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 | the causal claims of this field rest on germ-free animals - raised with no commensals at all. That is the cleanest possible contrast and it is also a state no animal is ever in outside a facility, so what it establishes is that commensals matter, not which ones do what at natural abundance 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 | microbiota drive immune activation and inflammation conversely reshapes the microbial community. When each side changes the other, an observed association in a diseased human carries no direction, which is exactly why the authors say the causal relationship before onset has not been established Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: bidirectionality defeats observation | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | 16S rRNA sequencing reports genus and composition. Every strain-level and every functional difference in the reviewed literature was therefore not measured rather than not present - and the recommendation to move to shotgun metagenomics is a statement about what the existing corpus of findings could not have seen Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: the resolution decides the finding | mechanisms[2] | 0.95 | the tagger's words |
| mechanisms | NLRP6's effect on microbiota structure appears only where the background microbiota contains particular pathobionts such as Helicobacter. A knockout phenotype that depends on the vivarium is a joint property of gene and facility, and two labs reporting different 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[3] | 0.95 | the tagger's words |
| mechanisms | faecal microbiome transplantation aims to restore a healthy microbiome configuration, and the authors state there is no general consensus on which features constitute a healthy microbiome. The therapy is specified by its mechanism and not by its endpoint Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: a target with no definition | mechanisms[4] | 0.95 | the tagger's words |
| limitations | a direct causal relationship between the microbiome and immunity before onset or in early disease has not been established in most medical conditions 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 causal effect of the microbiome on immune dysregulation in most human disorders remains to be proven 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 | the field runs on laboratory mice whose microbiota is divergent from wild animals and humans, limiting translational potential and reproducibility 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 | most of the reviewed work used 16S rRNA sequencing, which resolves genus and composition only and cannot see strain-level or functional differences 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 | inter-individual variation typically explains more variance in both microbiome and immune response than disease state does 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 | there is no general consensus on which features constitute a healthy microbiome, so FMT efficacy in IBD remains under evaluation 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 | the prophylactic and therapeutic efficacy of traditional individual probiotics in promoting human health is limited Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. about this quote: PAGE FURNITURE IS SPLICED INTO THE 'evidence' QUOTE - the journal's running head and a page number, 'Review Article 501 Cell Research…', between 'potentially' and 'may provide'. The words on either side of it were never continuous on the page; read the quote with it deleted. | limitations[6] | 0.95 | the tagger's words |
| limitations | the review does not claim coverage - it states that the evidence cannot be summarised in one review and refers out to others 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 | machine learning, proposed for decoding individualised microbiome patterns - a response to inter-individual variance being larger than the disease signal 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 | shotgun metagenomic sequencing and the wider multi-omics stack, carried from genomics into immunology to replace a genus-level instrument 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 | germ-free animals, raised with no commensal microbes at all, used as the reference state for every claim that a commensal is required for an immune structure Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the possibility that the lymphoid and immune defects are produced by something other than the absence of commensals - there are none to confound with · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | Th17 cells scored in germ-free mice and again after defined colonisation, with SFB and with other commensals separately Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the Th17 population being a fixed host trait - it is absent without microbes and returns on colonisation, so the microbe is doing the work · outcome: held | controls[1] | 0.85 | the tagger's words |
| controls | laboratory mice given a wild microbiota, then challenged with influenza virus and with colitis-induced tumorigenesis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the host genotype explaining the difference - the same laboratory animal changes phenotype when only the microbiota is swapped · outcome: held | controls[2] | 0.95 | the tagger's words |
| controls | microbiome depletion by broad-spectrum antibiotics in humans, followed by seasonal influenza vaccination and plasma metabolome profiling Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: reverse causation from immune state to microbiome - here the microbiome was depleted deliberately and the antibody response followed · outcome: held | controls[3] | 0.95 | the tagger's words |
| controls | NLRP6-deficient mice compared across vivaria with different background microbiota, rather than in one facility Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a gene effect that is really a facility effect - and the comparison shows the phenotype appears ONLY where particular pathobionts are present · outcome: partial | controls[4] | 0.95 | the tagger's words |
| controls | integration of multi-omics data sets - metagenomics, single-cell transcriptomics, epigenomics, proteomics and metabolomics - proposed for disentangling the interaction under host genetics and environmental triggers Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the direction of the microbiota-immune relationship, which the cited animal evidence shows to be bidirectional - the multi-omics integration that would separate cause from consequence is proposed, not done · outcome (stated by the tagger, no quotation): absent-declared-unreported | controls[5] | 0.95 | the tagger's words |
| controls | faecal microbiome transplantation in IBD, named as under evaluation with fecal processing and patient safety unresolved Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: whether restoring the microbiome restores the immune phenotype - named as under evaluation, with faecal processing and patient safety unresolved · outcome (stated by the tagger, no quotation): absent-declared-unreported | controls[6] | 0.95 | the tagger's words |
| concepts | microbiome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: microbiome | concepts[0] | 0.95 | the paper's words |
| concepts | germ-free Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: germ-free | concepts[1] | 0.95 | the paper's words |
| concepts | segmented filamentous bacteria Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: segmented filamentous bacteria | concepts[2] | 0.85 | the paper's words |
| concepts | Th17 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Th17 | concepts[3] | 0.85 | the paper's words |
| concepts | Broad-spectrum antibiotic Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Broad-spectrum antibiotic | concepts[4] | 0.95 | the paper'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[5] | 0.95 | the paper's words |
| concepts | 16S rRNA sequencing Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: 16S rRNA sequencing | concepts[6] | 0.95 | the paper's words |
| concepts | shotgun metagenomic sequencing Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: shotgun metagenomic sequencing | concepts[7] | 0.95 | the paper's words |
| concepts | laboratory mice Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: laboratory mice | concepts[8] | 0.95 | the paper's words |
| concepts | wild mice Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: wild mice | concepts[9] | 0.95 | the paper's words |
| concepts | inter-individual variation Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: inter-individual variation | concepts[10] | 0.95 | the paper's words |
| concepts | disease state Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: disease state | concepts[11] | 0.95 | the paper's words |
| concepts | Bilophila wadsworthia Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Bilophila wadsworthia | concepts[12] | 0.95 | the paper's words |
| concepts | NLRP6 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: NLRP6 | concepts[13] | 0.95 | the paper's words |
| concepts | humans Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: humans | concepts[14] | 0.95 | the paper's words |
| concepts | colitis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: colitis | concepts[15] | 0.95 | the paper's words |
| concepts | vivarium Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: vivarium | concepts[16] | 0.95 | the paper's words |
| senses | the microbiome-immunity relationship - AS ESTABLISHED: a bidirectional relationship in animal models, where microbiota drive immune activation and inflammation conversely reshapes the community 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 | the microbiome-immunity relationship - AS NOT ESTABLISHED: a direct causal relationship before onset or in early disease, which the authors say has not been shown in most medical conditions 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 | the microbiome - AS MEASURED BY 16S rRNA SEQUENCING: genus-level and purely compositional, which is the resolution most of the literature reviewed here was produced at 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 | the microbiome - AS MEASURED BY SHOTGUN METAGENOMICS: strain-level and functional, the resolution the authors say the field must move to 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 | a 'healthy' microbiome - AS A THERAPEUTIC TARGET: the configuration FMT aims to restore, and on which the authors say there is still no general consensus 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 | the mouse microbiota - IN THE LABORATORY: divergent from wild animals and humans, with limited translational potential 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 | the mouse microbiota - IN THE WILD: resilient, and shown to recapitulate human phenotypes better - laboratory mice receiving it become less susceptible to influenza and to colitis-induced tumorigenesis 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 → its own field's causal language about the microbiome, by stating that a direct causal relationship has not been established in most medical conditions 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 | critiques → the reliance on laboratory mice, whose microbiota is divergent from wild animals and humans and whose translational potential is therefore limited 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 → 16S rRNA sequencing as the field's default instrument, on the grounds that its genus-level compositional resolution cannot register strain or function 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 | qualifies → microbiome-targeted therapy, by noting that there is no consensus definition of the healthy configuration such therapy aims to restore 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 | builds-on → germ-free and gnotobiotic animal work as the basis for every mechanistic claim in the review 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 | laboratory mice —distinct-from→ humans Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: whether the microbiota is the one the conclusion is meant to be about · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): whether the microbiota is the one the conclusion is meant to be about · the relation stated: nearly all of this evidence comes from mice carrying a microbiota the authors call divergent from wild animals and from humans, which bounds what any of it translates to
Audit 2026-09-28: DOUBTFUL - read against its span and kept, but laboratory mice carry a divergent microbiota; distinct-from is loose. also in: laboratory mice · humans | concept_edges[0] | 0.95 | the tagger's words |
| concept_edges | inter-individual variation —distinct-from→ disease state Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. differs in: which source of variance a case-control comparison is actually measuring · the relation itself is separately evidenced · strength of the relation: 0.95 · differs in (stated by the tagger, no quotation): which source of variance a case-control comparison is actually measuring · the relation stated: in both microbiome configuration and immune response, more variance is typically explained by who the person is than by whether they are ill
Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but the span says more variance is explained by inter-individual variation than by disease state; distinct-from is loose. also in: inter-individual variation · disease state | concept_edges[1] | 0.95 | the tagger's words |
| concept_edges | segmented filamentous bacteria —causes→ Th17 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. direction on the measure: increases · the relation itself is separately evidenced · strength of the relation: 0.95 · direction on the measure (stated by the tagger, no quotation): increases · the relation stated: Th17 cells are absent in germ-free mice and are induced by colonisation, most notably with SFB - a single named commensal producing a defined immune cell population also in: segmented filamentous bacteria · Th17 | concept_edges[2] | 0.85 | the tagger's words |
| concept_edges | Broad-spectrum antibiotic —causes→ SCFAs 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: broad-spectrum antibiotics perturb the microbiota and deplete microbiota-derived SCFAs, and that depletion hyperactivates intestinal macrophages, expands pro-inflammatory T helper cells and raises susceptibility to infection also in: Broad-spectrum antibiotic · SCFAs | concept_edges[3] | 0.95 | the tagger's words |
| concept_edges | Bilophila wadsworthia —causes→ colitis Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. direction on the measure: increases · the relation itself is separately evidenced · strength of the relation: 0.95 · direction on the measure (stated by the tagger, no quotation): increases · the relation stated: saturated fat raises taurocholic acid, which expands this pathobiont, which promotes Th1 responses and raises colitis susceptibility - the review's most completely specified dietary chain also in: Bilophila wadsworthia · colitis | concept_edges[4] | 0.95 | the tagger's words |
| content_tags | a direct causal relationship between microbiome and immunity before disease onset has not been established in most medical conditions 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 | Th17 cells are absent in germ-free mice and are induced by colonisation, most notably with segmented filamentous bacteria Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[1] | 0.85 | the tagger's words |
| content_tags | broad-spectrum antibiotics deplete microbiota-derived SCFAs, hyperactivating intestinal macrophages and increasing susceptibility to infection 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 | microbiome depletion by antibiotics diminishes the antibody response to seasonal influenza vaccination in humans 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 | a diet high in saturated fats raises taurocholic acid, expands Bilophila wadsworthia and increases colitis susceptibility 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 | NLRP6's effect on microbiota structure appears only against a background microbiota containing particular pathobionts, so the phenotype depends on the vivarium 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 | more variance in microbiome configuration and immune response is explained by inter-individual variation than by disease state 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 | there is no general consensus on which features constitute a healthy microbiome 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 | an animal model raised without commensal microbes, used as the field's instrument for mechanistic causal relationships between microbiota and host immunity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: germ-free | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | a modality limited to genus-level and purely compositional resolution, as against shotgun metagenomics which resolves strain and function Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: 16S rRNA sequencing | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | microbiome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: microbiome | content_tags.variables[0] | 0.95 | the tagger's words |
| content_tags | disease state Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: disease state | 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.