Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

Yaung, Stephanie J.; Deng, Luxue; Li, Ning; Braff, Jonathan L.; Church, George M.; Bry, Lynn; Wang, Harris H.; Gerber, Georg K.

doi:10.15252/msb.20145866

Title: Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

Journal Article · Wed Mar 11 00:00:00 EDT 2015 · Molecular Systems Biology

DOI:https://doi.org/10.15252/msb.20145866· OSTI ID:1546862

Yaung, Stephanie J. ^[1]; Deng, Luxue ^[2]; Li, Ning ^[2]; Braff, Jonathan L. ^[3]; Church, George M. ^[4]; Bry, Lynn ^[2]; Wang, Harris H. ^[5]; Gerber, Georg K. ^[2]

Program in Medical Engineering and Medical Physics Harvard‐MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge MA USA, Department of Genetics Harvard Medical School Boston MA USA, Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA USA
Center for Clinical and Translational Metagenomics Department of Pathology Brigham &, Women's Hospital Harvard Medical School Boston MA USA
Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA USA
Department of Genetics Harvard Medical School Boston MA USA, Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA USA
Department of Systems Biology Columbia Initiative in Systems Biology Columbia University New York NY USA, Department of Pathology and Cell Biology Columbia University Medical Center New York NY USA

Elucidating functions of commensal microbial genes in the mammalian gut is challenging because many commensals are recalcitrant to laboratory cultivation and genetic manipulation. We present Temporal FUnctional Metagenomics sequencing (TFUMseq), a platform to functionally mine bacterial genomes for genes that contribute to fitness of commensal bacteria in vivo. Our approach uses metagenomic DNA to construct large-scale heterologous expression libraries that are tracked over time in vivo by deep sequencing and computational methods. To demonstrate our approach, we built a TFUMseq plasmid library using the gut commensal Bacteroides thetaiotaomicron (Bt) and introduced Escherichia coli carrying this library into germfree mice. Population dynamics of library clones revealed Bt genes conferring significant fitness advantages in E. coli over time, including carbohydrate utilization genes, with a Bt galactokinase central to early colonization, and subsequent dominance by a Bt glycoside hydrolase enabling sucrose metabolism coupled with co-evolution of the plasmid library and E. coli genome driving increased galactose utilization. Here, our findings highlight the utility of functional metagenomics for engineering commensal bacteria with improved properties, including expanded colonization capabilities in vivo.

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Research Organization:: Harvard Univ., Cambridge, MA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: DE‐FG02‐02ER63445; FG02-02ER63445

OSTI ID:: 1546862

Alternate ID(s):: OSTI ID: 1312902; OSTI ID: 1546863

Journal Information:: Molecular Systems Biology, Journal Name: Molecular Systems Biology Vol. 11 Journal Issue: 3; ISSN 1744-4292

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 22 works

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Title: Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

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