phenomenon · claim-type · cross-domain-transfer · mechanism · claim-relation · replication-status · limitation — grounded in the full text| 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— “Indeed, current evidence from animal models indicates a bidirectional relationship to exist between microbiome perturbation and immune dysregulation. As such, distinct microbiota and metabolites drive immune activation, and chronic in flammation conversely may shape the dysbiotic con figuration and functions of microbial communities. However… | |
| claim-type | critique— “Here, we review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs. We highlight aspects of the current knowledge, challenges and limitations in achieving causal understanding of host… | |
| method — evidence | — “As the large body of evidence related to host immune-microbiome interactions cannot be summarized by a single review, we aim to provide key concepts and examples of such interactions and their potential effects on human health and disease risk, while referring throughout the review to multiple other recent reviews 14–16 focusing on distinct… | |
| object of study — evidence | — “Here, we review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs. We highlight aspects of the current knowledge, challenges and limitations in achieving causal understanding of host… | |
| research question — evidence | — “Indeed, current evidence from animal models indicates a bidirectional relationship to exist between microbiome perturbation and immune dysregulation. As such, distinct microbiota and metabolites drive immune activation, and chronic in flammation conversely may shape the dysbiotic con figuration and functions of microbial communities. However… | |
| contribution — evidence | — “More importantly, the causal effect of the microbiome on immune dysregulation in most human disorders listed above remains to be proven.” | |
| transfer | from machine learning: machine learning, proposed for decoding individualised microbiome patterns - a response to inter-individual variance being larger than the disease signal— “Finally, the microbiome configuration and immune responses are both increasingly appreciated to be highly variable among human individuals, with more variances typically explained by inter-individual variation than by disease state.” | transfers[0] |
| transfer | from genomics: shotgun metagenomic sequencing and the wider multi-omics stack, carried from genomics into immunology to replace a genus-level instrument— “In addition, many studies focusing on microbiome-immunity interaction have utilized 16S rRNA sequencing to characterize the microbiome, but this modality is limited by its genus-level and purely compositional resolution. Given that strain level resolution and functional insights are better served by shotgun metagenomic sequencing, the field… | transfers[1] |
| mechanism | an instrument that is an extreme, not a control 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— “The study of mechanistic causal relationships between commensal microbiota and host immunity is strongly informed by the use of germ-free (GF) animal models. Early studies on GF animals demonstrated that absence of commensal microbes is associated with profound intestinal defects of lymphoid tissue architecture and immune functions.” | mechanisms[0] |
| mechanism | bidirectionality defeats observation 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— “Indeed, current evidence from animal models indicates a bidirectional relationship to exist between microbiome perturbation and immune dysregulation. As such, distinct microbiota and metabolites drive immune activation, and chronic in flammation conversely may shape the dysbiotic con figuration and functions of microbial communities. However… | mechanisms[1] |
| mechanism | the resolution decides the finding 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— “In addition, many studies focusing on microbiome-immunity interaction have utilized 16S rRNA sequencing to characterize the microbiome, but this modality is limited by its genus-level and purely compositional resolution. Given that strain level resolution and functional insights are better served by shotgun metagenomic sequencing, the field… | mechanisms[2] |
| mechanism | the phenotype belongs partly to the building 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— “Importantly, the impact of NLRP6 on microbiota community structure is dependent on the background microbiota in the vivarium, with dysbiosis occurring in mice lacking NLRP6 only in the presence of distinct microbiome configuration containing pathobionts such as Helicobacter spp” | mechanisms[3] |
| mechanism | a target with no definition 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— “For example, in an aim to restore a healthy microbiome configuration in patients suffering from dysbiosis linked to immune-mediated disease, fecal microbiome transplantation (FMT), which has so far been widely used in Clostridium dif ficile infections, is considered also as potential treatment in this clinical context. However, there is still… | mechanisms[4] |
| 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— “Indeed, current evidence from animal models indicates a bidirectional relationship to exist between microbiome perturbation and immune dysregulation. As such, distinct microbiota and metabolites drive immune activation, and chronic in flammation conversely may shape the dysbiotic con figuration and functions of microbial communities. However… | claim_relations[0] |
| critiques | the reliance on laboratory mice, whose microbiota is divergent from wild animals and humans and whose translational potential is therefore limited— “Importantly in all of these efforts, the microbiome research community massively uses laboratory mice that harbor a divergent microbiota from ‘wild’ animals and humans, thereby featuring a limited translational potential and reproducibility as compared to ‘real-life’ settings.” | claim_relations[1] |
| critiques | 16S rRNA sequencing as the field's default instrument, on the grounds that its genus-level compositional resolution cannot register strain or function— “In addition, many studies focusing on microbiome-immunity interaction have utilized 16S rRNA sequencing to characterize the microbiome, but this modality is limited by its genus-level and purely compositional resolution. Given that strain level resolution and functional insights are better served by shotgun metagenomic sequencing, the field… | claim_relations[2] |
| qualifies | microbiome-targeted therapy, by noting that there is no consensus definition of the healthy configuration such therapy aims to restore— “For example, in an aim to restore a healthy microbiome configuration in patients suffering from dysbiosis linked to immune-mediated disease, fecal microbiome transplantation (FMT), which has so far been widely used in Clostridium dif ficile infections, is considered also as potential treatment in this clinical context. However, there is still… | claim_relations[3] |
| builds-on | germ-free and gnotobiotic animal work as the basis for every mechanistic claim in the review— “The study of mechanistic causal relationships between commensal microbiota and host immunity is strongly informed by the use of germ-free (GF) animal models. Early studies on GF animals demonstrated that absence of commensal microbes is associated with profound intestinal defects of lymphoid tissue architecture and immune functions.” | claim_relations[4] |
| sense | the microbiome-immunity relationship - AS ESTABLISHED: a bidirectional relationship in animal models, where microbiota drive immune activation and inflammation conversely reshapes the community— “Indeed, current evidence from animal models indicates a bidirectional relationship to exist between microbiome perturbation and immune dysregulation. As such, distinct microbiota and metabolites drive immune activation, and chronic in flammation conversely may shape the dysbiotic con figuration and functions of microbial communities. However… | senses[0] |
| sense | 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— “Indeed, current evidence from animal models indicates a bidirectional relationship to exist between microbiome perturbation and immune dysregulation. As such, distinct microbiota and metabolites drive immune activation, and chronic in flammation conversely may shape the dysbiotic con figuration and functions of microbial communities. However… | senses[1] |
| sense | 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— “In addition, many studies focusing on microbiome-immunity interaction have utilized 16S rRNA sequencing to characterize the microbiome, but this modality is limited by its genus-level and purely compositional resolution. Given that strain level resolution and functional insights are better… | senses[2] |
| sense | the microbiome - AS MEASURED BY SHOTGUN METAGENOMICS: strain-level and functional, the resolution the authors say the field must move to | senses[3] |
| sense | 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 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[4] |
| sense | the mouse microbiota - IN THE LABORATORY: divergent from wild animals and humans, with limited translational potential 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[5] |
| sense | 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 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 | 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 — 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 possibility that the lymphoid and immune defects are produced by something other than the absence of commensals - there are none to confound with 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 | Th17 cells scored in germ-free mice and again after defined colonisation, with SFB and with other commensals separately — 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 Th17 population being a fixed host trait - it is absent without microbes and returns on colonisation, so the microbe is doing the work 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 | laboratory mice given a wild microbiota, then challenged with influenza virus and with colitis-induced tumorigenesis — 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 host genotype explaining the difference - the same laboratory animal changes phenotype when only the microbiota is swapped 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 | microbiome depletion by broad-spectrum antibiotics in humans, followed by seasonal influenza vaccination and plasma metabolome profiling — 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 reverse causation from immune state to microbiome - here the microbiome was depleted deliberately and the antibody response followed 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 | NLRP6-deficient mice compared across vivaria with different background microbiota, rather than in one facility — 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 gene effect that is really a facility effect - and the comparison shows the phenotype appears ONLY where particular pathobionts are 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. | controls[4] |
| control | 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 — absent-declared-unreported — rules out 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 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 in IBD, named as under evaluation with fecal processing and patient safety unresolved — absent-declared-unreported — rules out whether restoring the microbiome restores the immune phenotype - named as under evaluation, with faecal processing and patient safety 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. | controls[6] |
| weight | its own field's causal language about the microbiome, by stating that a direct causal relationship has not been established in most medical conditions — 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 reliance on laboratory mice, whose microbiota is divergent from wild animals and humans and whose translational potential is therefore limited — 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 | 16S rRNA sequencing as the field's default instrument, on the grounds that its genus-level compositional resolution cannot register strain or function — 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 | microbiome-targeted therapy, by noting that there is no consensus definition of the healthy configuration such therapy aims to restore — 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[3] |
| weight | germ-free and gnotobiotic animal work as the basis for every mechanistic claim in the review — 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] |
| audit | laboratory mice —distinct-from→ humans — Audit 2026-09-28: DOUBTFUL - read against its span and kept, but laboratory mice carry a divergent microbiota; 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[0] |
| differs in (stated by the tagger, no quotation) | laboratory mice —distinct-from→ humans — whether the microbiota is the one the conclusion is meant to be about | concept_edges[0] |
| relation | laboratory mice —distinct-from→ humans — 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 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[0] |
| weight | laboratory mice —distinct-from→ humans — 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 | inter-individual variation —distinct-from→ disease state — 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. 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) | inter-individual variation —distinct-from→ disease state — which source of variance a case-control comparison is actually measuring | concept_edges[1] |
| relation | inter-individual variation —distinct-from→ disease state — in both microbiome configuration and immune response, more variance is typically explained by who the person is than by whether they are ill 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 | inter-individual variation —distinct-from→ disease state — 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] |
| effect direction (stated by the tagger, no quotation) | segmented filamentous bacteria —causes→ Th17 — increases | concept_edges[2] |
| relation | segmented filamentous bacteria —causes→ Th17 — 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 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 | segmented filamentous bacteria —causes→ Th17 — 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] |
| effect direction (stated by the tagger, no quotation) | Broad-spectrum antibiotic —causes→ SCFAs — reduces | concept_edges[3] |
| relation | Broad-spectrum antibiotic —causes→ SCFAs — 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 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 | Broad-spectrum antibiotic —causes→ SCFAs — 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] |
| effect direction (stated by the tagger, no quotation) | Bilophila wadsworthia —causes→ colitis — increases | concept_edges[4] |
| relation | Bilophila wadsworthia —causes→ colitis — 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 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[4] |
| weight | Bilophila wadsworthia —causes→ 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[4] |
| 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 — 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[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 — 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[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-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[6] |
| evidence status note | limitation — 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. 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 | 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 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 causal effect of the microbiome on immune dysregulation in most human disorders remains to be proven 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 | the field runs on laboratory mice whose microbiota is divergent from wild animals and humans, limiting translational potential and reproducibility 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 | 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 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 | inter-individual variation typically explains more variance in both microbiome and immune response than disease state does 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 | there is no general consensus on which features constitute a healthy microbiome, so FMT efficacy in IBD remains under evaluation 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 | the prophylactic and therapeutic efficacy of traditional individual probiotics in promoting human health is limited 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 | 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 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] |
| variable | microbiome 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 | disease state 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 | germ-free 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 | 16S rRNA sequencing 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 | microbiome — not defined in this paper's own words; the collective genomes of the bacteria, fungi, viruses and parasites colonising the host - a term whose extension in practice is whatever the sequencing modality could resolve 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 | germ-free — not defined in this paper's own words; an animal raised with no commensals at all - the field's instrument for causal claims, and an extreme rather than a control for any natural state 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 | segmented filamentous bacteria — not defined in this paper's own words; the commensal whose colonisation induces Th17 cells in mice that have none - the single clearest microbe-to-immune-cell link in 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. | concepts[2] |
| concept | Th17 — not defined in this paper's own words; IL-17-producing CD4+ effector T cells, absent in germ-free mice and inducible by colonisation - so their presence is a readout of the microbiota, not only of the host 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 | Broad-spectrum antibiotic — not defined in this paper's own words; the field's blunt perturbation - it depletes the microbiota and its SCFAs together, so what follows is attributable to the pair and 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[4] |
| concept | SCFAs — not defined in this paper's own words; short-chain fatty acids produced by the microbiota; their depletion by broad-spectrum antibiotics is the mechanism linking antibiotic use to immune hyperactivation 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 | 16S rRNA sequencing — not defined in this paper's own words; the modality most of this literature was produced with - genus-level and purely compositional, so a strain difference and a functional difference are both invisible to it 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 | shotgun metagenomic sequencing — not defined in this paper's own words; strain-level and functional resolution - the instrument the authors say the field is expected to move to, which is a statement about what the existing findings could not have seen 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 | laboratory mice — not defined in this paper's own words; the animal nearly all of this evidence comes from, carrying a microbiota the authors describe as divergent from wild animals and humans 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 | wild mice — not defined in this paper's own words; the comparison animal whose microbiota, transferred into laboratory mice, makes them less susceptible to influenza and to colitis-induced tumorigenesis 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 | inter-individual variation — not defined in this paper's own words; the source of variance that typically exceeds disease state in both microbiome configuration and immune response - which decides what a case-control design can detect 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 | disease state — not defined in this paper's own words; the contrast the field's studies are designed around, and the smaller of the two variance components 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 | Bilophila wadsworthia — not defined in this paper's own words; a pathobiont expanded by saturated fat via taurocholic acid - a named organism standing in a full dietary causal 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[12] |
| concept | NLRP6 — not defined in this paper's own words; an inflammasome sensor whose effect on microbiota structure appears only against certain background microbiota - so the phenotype belongs partly to the animal facility 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 | humans — not defined in this paper's own words; the population every one of these findings is meant to be about, and the one the laboratory mouse's microbiota is said to diverge from 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 | colitis — not defined in this paper's own words; the intestinal inflammation used throughout as the disease readout - here the endpoint of a fully specified dietary chain running through a named pathobiont 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 | vivarium — not defined in this paper's own words; the animal facility, and here an explicit determinant of whether a knockout shows a phenotype at all 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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