Microbiome
How much do gut bacterial gene contents differ?
Open access · cc by · source: Europe PMC
Same gut bacterial species can differ widely in gene content across people, shaping functional individuality.
Study at a glance
- Design
- Cross-sectional — Metagenomic gene-deletion detection quantifying within-species gene content across gut communities
- N
- N=207 · 252 fecal metagenomes from 207 individuals (HMP and European MetaHIT)
- Population
- Human gut metagenomes from public cohorts
- Outcome
- Inter-individual within-species gene-content variation
Structured fields used in claim comparison tables when every cited study has a complete layer.
Key findings
Strain-level gene content varies substantially among individuals for the same species in natural habitats.
Methodology
Developed metagenomic gene-deletion detection and quantified within-species gene-content differences in human gut communities.
Limitations
Presence/absence is not full phenotype; sample sizes remain limited.
How this study connects
Role on claims
Each row is a claim on a concept or method page where this paper supports, challenges, or qualifies the statement. Roles are hand-checked — not a model guess.
Bacterial bile-salt enzymes can change host bile acids and weight-related phenotypes in models.
Selective bacterial bile-salt hydrolases can change host bile-acid chemistry and weight-related phenotypes in colonization models—evidence that specific microbial enzymes, not only community membership lists, can matter for host physiology.
Scope note — different question — strain gene-content variation across people
Limits the claim's scope: a different population, assay, or outcome.
Strain-level gene content varies a lot within the same gut species — species labels are coarse.
Even within the same named gut species, strain-level gene content varies substantially among healthy people—so species labels alone understate functional diversity.
Evidence for the claim as stated.
A gene-deletion detection method on human gut metagenomes found that strain-level gene content for the same species varies substantially among individuals in natural habitats. Presence/absence is not a full phenotype, and sample sizes remain limited.
Evidence for the claim as stated.
Shotgun gene-content metagenomics (within-species deletions across people; infant diet genes plus 459/660 host transcripts; B. dorei before seroconversion) is not the same experiment as HMP-style 16S biogeography (>24 million reads, 2,983 specimens, ~8,167 V3–V5 reads). A 16S habitat map cannot report accessory genes; a gene-deletion call cannot replace body-wide taxonomy.
Evidence for the claim as stated.
Even among shotgun studies, claims differ in strength. Infant diet work is n=6 versus 6 with host-transcript correlations; DIPP is 76 children and 947 samples but still does not prove B. dorei causes autoimmunity; within-species gene content varies without assigning a disease. Pooling them as 'the microbiome causes immunity' overreads every design.
Evidence for the claim as stated.
Open questions
Tensions this paper is part of
From concept pages' “where studies disagree.” Disagreement means the same question; scope means different assays, populations, or outcomes.
Shotgun gene-content metagenomics (within-species deletions across people; infant diet genes plus 459/660 host transcripts; B. dorei before seroconversion) is not the same experiment as HMP-style 16S biogeography (>24 million reads, 2,983 specimens, ~8,167 V3–V5 reads). A 16S habitat map cannot report accessory genes; a gene-deletion call cannot replace body-wide taxonomy.
- Supports · Infant diet shapes gut–host immunity
- Supports · B. dorei rises before T1D autoimmunity
- Supports · Human body microbiome biogeography
Even among shotgun studies, claims differ in strength. Infant diet work is n=6 versus 6 with host-transcript correlations; DIPP is 76 children and 947 samples but still does not prove B. dorei causes autoimmunity; within-species gene content varies without assigning a disease. Pooling them as 'the microbiome causes immunity' overreads every design.
- Supports · Infant diet shapes gut–host immunity
- Supports · B. dorei rises before T1D autoimmunity
History
When this study was placed
Dated entries from the concept change log — when this paper was added or removed as support, challenge, or qualifier on a claim.
Removed as supporting evidence on Microbiome
Selective bacterial bile-salt hydrolases can change host bile-acid chemistry and weight-related phenotypes in colonization models—evidence that specific microbial enzymes, not only community membership lists, can matter for host physiology.
Placed as a scope qualifier on Microbiome
Selective bacterial bile-salt hydrolases can change host bile-acid chemistry and weight-related phenotypes in colonization models—evidence that specific microbial enzymes, not only community membership lists, can matter for host physiology.
Placed as supporting evidence on Microbiome
Even within the same named gut species, strain-level gene content varies substantially among healthy people—so species labels alone understate functional diversity.
Related papers in this topic
Same topic cluster — not a recommendation engine.