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

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 cultiv...

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Autores principales: Merrill, Bryan D., Carter, Matthew M., Olm, Matthew R., Dahan, Dylan, Tripathi, Surya, Spencer, Sean P., Yu, Brian, Jain, Sunit, Neff, Norma, Jha, Aashish R., Sonnenburg, Erica D., Sonnenburg, Justin L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9558438/
https://www.ncbi.nlm.nih.gov/pubmed/36238714
http://dx.doi.org/10.1101/2022.03.30.486478
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author Merrill, Bryan D.
Carter, Matthew M.
Olm, Matthew R.
Dahan, Dylan
Tripathi, Surya
Spencer, Sean P.
Yu, Brian
Jain, Sunit
Neff, Norma
Jha, Aashish R.
Sonnenburg, Erica D.
Sonnenburg, Justin L.
author_facet Merrill, Bryan D.
Carter, Matthew M.
Olm, Matthew R.
Dahan, Dylan
Tripathi, Surya
Spencer, Sean P.
Yu, Brian
Jain, Sunit
Neff, Norma
Jha, Aashish R.
Sonnenburg, Erica D.
Sonnenburg, Justin L.
author_sort Merrill, Bryan D.
collection PubMed
description 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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spelling pubmed-95584382022-10-14 Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes Merrill, Bryan D. Carter, Matthew M. Olm, Matthew R. Dahan, Dylan Tripathi, Surya Spencer, Sean P. Yu, Brian Jain, Sunit Neff, Norma Jha, Aashish R. Sonnenburg, Erica D. Sonnenburg, Justin L. bioRxiv Article 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. Cold Spring Harbor Laboratory 2022-10-06 /pmc/articles/PMC9558438/ /pubmed/36238714 http://dx.doi.org/10.1101/2022.03.30.486478 Text en https://creativecommons.org/licenses/by-nd/4.0/This work is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, and only so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Merrill, Bryan D.
Carter, Matthew M.
Olm, Matthew R.
Dahan, Dylan
Tripathi, Surya
Spencer, Sean P.
Yu, Brian
Jain, Sunit
Neff, Norma
Jha, Aashish R.
Sonnenburg, Erica D.
Sonnenburg, Justin L.
Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
title Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
title_full Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
title_fullStr Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
title_full_unstemmed Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
title_short Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes
title_sort ultra-deep sequencing of hadza hunter-gatherers recovers vanishing gut microbes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9558438/
https://www.ncbi.nlm.nih.gov/pubmed/36238714
http://dx.doi.org/10.1101/2022.03.30.486478
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