Hominid gut microbiome across lifestyles in Tanzania

Host microbiome interactions are complex and often select for traits that benefit one or both mutualistic partners. Co-adaptive responses emerge from these interactions to increase the fitness of the host, microbiome or both. Here we investigated the evolutionary signature impact on hominidae-microbiome composition and functions that explain host-microbiome co-evolutionary adaptation to different lifestyles (e.g., dietary breakdown, pathogens and antimicrobial resistance). 586 microbiomes from five hominid populations that span different evolutionary steps and lifestyles in Tanzania were characterised using deep-sequencing metagenomics: two urban human populations, hunter-gatherer (Hadza), and two chimpanzee populations. Our results showed host evolutionary trait signatures onto gut microbiome bacteria, viruses, parasites, CAZyme genes, antimicrobial resistance genes and metabolic pathways. Different populations harboured differently abundant bacterial taxa, even at strain phylogenies, and mirrored the host adaptive fitness in the environment to serve the host physiological demands, e.g., pectin degrading bacteria were more abundant in chimpanzee guts compared to others, and fructose fermenting bacteria were more abundant in Hadza guts. Hominid microbiomes also showed varying dietary-derived eukaryotic signals that correspond to the varying bacterial loads to target those dietary intakes (increased fruits and plants in Hadza and chimpanzee guts, respectively). Antimicrobial resistant genes were also more abundant in urban populations where modern medicine (e.g., antibiotics) are more practiced compared to chimpanzees and Hadza populations. Our results show that hominid microbiomes form a tight mutualistic relationship with their hosts that uniformly enhances both partner fitness in nature, and serves the function demands that surfaced during the co-evolutionary course of the association.

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. Assay shotgun_dna.

• host study.description · “586 microbiomes from five hominid populations”
• host study.description · “two urban human populations, hunter-gatherer (Hadza)”
• body site run.scientific_name · “feces metagenome”
• body site study.description · “pectin degrading bacteria were more abundant in chimpanzee guts”

587 runs over 481 samples · mean 15.82 Gbp per run (median 14.90 Gbp, total 9,287.77 Gbp; 587 runs with a base count) · layout PAIRED 587 · platform ILLUMINA 587 · models Illumina NovaSeq 6000 (587) · 89% of runs with a Sandpiper profile · first public 2022-12-20 – 2023-01-09

Otani S first · 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 last · Kjærgaard Munk K · Fjermedal S · Meyer AS

3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata

PRJEB58441.csv.gz (12.1 KB) · parquet (86.5 KB) — all 481 samples, every field with route and confidence · PRJEB58441_determinations.csv.gz (7.9 KB) — 1,443 evidence rows