Microbiome
Human body microbiome biogeography
Open access · cc by · source: Europe PMC
Healthy human body sites host distinct bacterial communities across a massive 16S survey.
Study at a glance
- Design
- Cross-sectional — Multi-habitat 16S analysis of HMP and related healthy cohorts
- N
- N=236 · 2,983 specimens from 236 HMP subjects (plus smaller urine/penis, preterm stool, conjunctiva sets); >24 million reads
- Population
- Healthy Human Microbiome Project subjects across body habitats
- Outcome
- Taxonomic biogeography of the healthy human microbiome
Structured fields used in claim comparison tables when every cited study has a complete layer.
Key findings
30 phyla to 929 genera detected; habitats differ strongly; average V3–V5 depth ~8,167 reads.
Methodology
Analyzed >24 million 16S reads from 2,983 specimens spanning HMP and related healthy cohorts across many body habitats.
Limitations
Does not define disease causality for any taxon.
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.
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.
Scope note — different scale — body-site biogeography, not within-species gene content
Limits the claim's scope: a different population, assay, or outcome.
Body habitat dominates taxonomy in healthy humans. Analysis of more than 24 million 16S reads from 2,983 specimens detected 30 phyla to 929 genera; habitats differed strongly, with average V3–V5 depth around 8,167 reads. The map is biogeography, not a disease mechanism.
Evidence for the claim as stated.
Marker-gene 16S and shotgun metagenomes answer different questions in this set. HMP biogeography and the bee pesticide paper are amplicon community maps (the bee paper adds ITS); the infant diet paper sequences stool metagenomes and host mRNA. Treating every 'microbiome sequencing' paper as 16S genus tables hides the extra functional genes the infant paper actually uses.
Evidence for the claim as stated.
Healthy-body biogeography analysed more than 24 million 16S reads from 2,983 specimens across HMP and related cohorts: 30 phyla to 929 genera, strong habitat differences, average V3–V5 depth about 8,167 reads. This is amplicon biogeography, not shotgun gene content, and it does not define disease causality for any taxon.
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.
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.
Marker-gene 16S and shotgun metagenomes answer different questions in this set. HMP biogeography and the bee pesticide paper are amplicon community maps (the bee paper adds ITS); the infant diet paper sequences stool metagenomes and host mRNA. Treating every 'microbiome sequencing' paper as 16S genus tables hides the extra functional genes the infant paper actually uses.
- Supports · Infant diet shapes gut–host immunity
- Supports · Pesticides reshape honey bee gut microbes
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 · How much do gut bacterial gene contents differ?
- 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.
Placed as a scope qualifier 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.