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

Abstract

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.

Authors:
 [1];  [2];  [2];  [3];  [4];  [2];  [5];  [2]
  1. 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
  2. Center for Clinical and Translational Metagenomics Department of Pathology Brigham &, Women's Hospital Harvard Medical School Boston MA USA
  3. Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA USA
  4. Department of Genetics Harvard Medical School Boston MA USA, Wyss Institute for Biologically Inspired Engineering Harvard University Boston MA USA
  5. 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
Publication Date:
Research Org.:
Harvard Univ., Cambridge, MA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1546862
Alternate Identifier(s):
OSTI ID: 1312902; OSTI ID: 1546863
Grant/Contract Number:  
DE‐FG02‐02ER63445; FG02-02ER63445
Resource Type:
Published Article
Journal Name:
Molecular Systems Biology
Additional Journal Information:
Journal Name: Molecular Systems Biology Journal Volume: 11 Journal Issue: 3; Journal ID: ISSN 1744-4292
Publisher:
Nature Publishing Group
Country of Publication:
United Kingdom
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; commensal fitness; functional metagenomics; microbiota; next-generation sequencing; synthetic biology

Citation Formats

Yaung, Stephanie J., Deng, Luxue, Li, Ning, Braff, Jonathan L., Church, George M., Bry, Lynn, Wang, Harris H., and Gerber, Georg K. Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. United Kingdom: N. p., 2015. Web. doi:10.15252/msb.20145866.
Yaung, Stephanie J., Deng, Luxue, Li, Ning, Braff, Jonathan L., Church, George M., Bry, Lynn, Wang, Harris H., & Gerber, Georg K. Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. United Kingdom. https://doi.org/10.15252/msb.20145866
Yaung, Stephanie J., Deng, Luxue, Li, Ning, Braff, Jonathan L., Church, George M., Bry, Lynn, Wang, Harris H., and Gerber, Georg K. Wed . "Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics". United Kingdom. https://doi.org/10.15252/msb.20145866.
@article{osti_1546862,
title = {Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics},
author = {Yaung, Stephanie J. and Deng, Luxue and Li, Ning and Braff, Jonathan L. and Church, George M. and Bry, Lynn and Wang, Harris H. and Gerber, Georg K.},
abstractNote = {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.},
doi = {10.15252/msb.20145866},
journal = {Molecular Systems Biology},
number = 3,
volume = 11,
place = {United Kingdom},
year = {Wed Mar 11 00:00:00 EDT 2015},
month = {Wed Mar 11 00:00:00 EDT 2015}
}

Journal Article:
Free Publicly Available Full Text
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https://doi.org/10.15252/msb.20145866

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Cited by: 22 works
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