Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes

Merrill, B. D.; Carter, M. M.; Olm, M. R.; Dahan, D.; Tripathi, S.; Spencer, S. P.; Yu, F. B.; Jain, S.; Neff, N.; Jha, A. R.; Sonnenburg, E. D.; Sonnenburg, J. L.

doi:10.1101/2022.03.30.486478

bioRxiv · 10.1101/2022.03.30.486478

Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes

Merrill, B. D.·Carter, M. M.·Olm, M. R.·Dahan, D.·Tripathi, S.·Spencer, S. P.·Yu, F. B.·Jain, S.·Neff, N.·Jha, A. R.·Sonnenburg, E. D.·Sonnenburg, J. L.

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Abstract

The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.

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Merrill, B. D., Carter, M. M., Olm, M. R., Dahan, D., Tripathi, S., Spencer, S. P., Yu, F. B., Jain, S., Neff, N., Jha, A. R., Sonnenburg, E. D., Sonnenburg, J. L.. 2022-03-31. Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes. https://doi.org/10.1101/2022.03.30.486478

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