Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations

From BugSigDB
Reviewed Marked as Reviewed by KateRasheed on 2025-6-12
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Otani S, Louise Jespersen M, Brinch C, Duus Møller F, Pilgaard B, Egholm Bruun Jensen E, Leekitcharoenphon P, Aaby Svendsen C, Aarestrup AH, Sonda T, Sylvina TJ, Leach J, Piel A, Stewart F, Sapountzis P, Kazyoba PE, Kumburu H, Aarestrup FM
Journal
Gut microbes
Year
2025
Keywords:
African hominidae, Microbiome, evolution, host adaptation
In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.

Experiment 1


Reviewed Marked as Reviewed by KateRasheed on 2025-6-12

Curated date: 2025/04/24

Curator: Joiejoie

Revision editor(s): Joiejoie, Victoria

Subjects

Location of subjects
United Republic of Tanzania
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Lifestyle measurement Lifestyle measurement,lifestyle measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Chimpanzees (combined Issa Valley + Mahale chimpanzees)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Humans (combined Hadza + non-indigenous adults + non-indigenous children)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group is a combined cohort of indigenous Hadza hunter-gatherers and non-indigenous urban and rural Tanzanian adults and children.
Group 0 sample size Number of subjects in the control (unexposed) group
90
Group 1 sample size Number of subjects in the case (exposed) group
456

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
Statistical test
Welch's T-Test
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes


Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-6-12

Curated date: 2025/04/29

Curator: Joiejoie

Revision editor(s): Joiejoie, Victoria

Source: Fig. 3D & Supplementary Figure S3

Description: Statistically significant MAGs between human and chimpanzee gut microbiomes

Abundance in Group 1: increased abundance in Humans (combined Hadza + non-indigenous adults + non-indigenous children)

NCBI Quality ControlLinks
Agathobacter
Blautia
Dorea
Faecalibacterium
Faecalicatena
Firmicutes bacterium CAG:83
Fusicatenibacter
Gemmiger
Oscillibacter
Oscillibacter sp. ER4
Prevotella
Ruminiclostridium
UBA11524UBA11524

Revision editor(s): Joiejoie, Victoria

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-12

Curated date: 2025/04/29

Curator: Joiejoie

Revision editor(s): Joiejoie, Victoria

Source: Fig. 3D & Supplementary Figure S3

Description: Statistically significant MAGs between human and chimpanzee gut microbiomes

Abundance in Group 1: decreased abundance in Humans (combined Hadza + non-indigenous adults + non-indigenous children)

NCBI Quality ControlLinks
Blautia
Collinsella
Dialister
Dorea
Eubacterium
Firmicutes bacterium CAG:791
Mogibacterium
Parasporobacterium
Prevotella
Prevotellaceae bacterium UBA6398
Senegalimassilia
Solobacterium
Unassigned MAG 2256Unassigned MAG 2256
Unassigned MAG 3218Unassigned MAG 3218
UBA7160UBA7160
UBA636UBA636

Revision editor(s): Joiejoie, Victoria

Experiment 2


Reviewed Marked as Reviewed by KateRasheed on 2025-6-12

Curated date: 2025/04/27

Curator: Joiejoie

Revision editor(s): Joiejoie, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Hadza humans (indigenous hunter-gatherers)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Non-indigenous humans (urban/rural Tanzanian adults and children)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This group comprises of Non-indigenous Tanzanian adults and children living in urban and rural settings.
Group 0 sample size Number of subjects in the control (unexposed) group
48
Group 1 sample size Number of subjects in the case (exposed) group
408

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-6-12

Curated date: 2025/04/29

Curator: Joiejoie

Revision editor(s): Joiejoie, Victoria

Source: Fig. 3E & Supplementary Figure S3

Description: Statistically significant genera

Abundance in Group 1: increased abundance in Non-indigenous humans (urban/rural Tanzanian adults and children)

NCBI Quality ControlLinks
Acetatifactor
Agathobacter
Alistipes
Bacteroides
Coprococcus
Dialister
Dorea
Eisenbergiella
Eubacterium
Eubacterium sp. CAG:180
Faecalibacterium
Holdemanella
Parabacteroides
Prevotella
Roseburia
Unassigned MAG 7092Unassigned MAG 7092

Revision editor(s): Joiejoie, Victoria

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-12

Curated date: 2025/04/29

Curator: Joiejoie

Revision editor(s): Joiejoie, Victoria

Source: Fig. 3E & Supplementary Figure S3

Description: Statistically significant genera.

Abundance in Group 1: decreased abundance in Non-indigenous humans (urban/rural Tanzanian adults and children)

NCBI Quality ControlLinks
Brachyspira
Campylobacter
Collinsella
Firmicutes bacterium CAG:110
Mogibacterium
Olsenella
Parabacteroides
Prevotella
Ruminiclostridium
Slackia
Solobacterium
Solobacterium sp. UBA636
UBA9475UBA9475
Unassigned MAG 3879Unassigned MAG 3879
Unassigned MAG 2673Unassigned MAG 2673
UBA3624UBA3624

Revision editor(s): Joiejoie, Victoria