A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders; Weiwei Yan; Deus Mjungu; Elizabeth V. Lonsdorf; John A. Hart; Crickette M. Sanz; David B. Morgan; Martine Peeters; Beatrice H. Hahn; Andrew H. Moeller

doi:10.1186/s13059-022-02777-w

A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn, Andrew H. Moeller

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

Earth’s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.

Original language	English (US)
Article number	212
Journal	Genome biology
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s13059-022-02777-w
State	Published - Dec 2022
Externally published	Yes

All Science Journal Classification (ASJC) codes

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/s13059-022-02777-w

Cite this

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title = "A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes",

abstract = "Earth{\textquoteright}s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.",

author = "Sanders, {Jon G.} and Weiwei Yan and Deus Mjungu and Lonsdorf, {Elizabeth V.} and Hart, {John A.} and Sanz, {Crickette M.} and Morgan, {David B.} and Martine Peeters and Hahn, {Beatrice H.} and Moeller, {Andrew H.}",

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doi = "10.1186/s13059-022-02777-w",

language = "English (US)",

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T1 - A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

AU - Sanders, Jon G.

AU - Yan, Weiwei

AU - Mjungu, Deus

AU - Lonsdorf, Elizabeth V.

AU - Hart, John A.

AU - Sanz, Crickette M.

AU - Morgan, David B.

AU - Peeters, Martine

AU - Hahn, Beatrice H.

AU - Moeller, Andrew H.

PY - 2022/12

Y1 - 2022/12

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AB - Earth’s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.

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A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes

Abstract

All Science Journal Classification (ASJC) codes

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