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

Molecular Systems Biology

Stephanie J Yaung¹  Luxue Deng⁴  Ning Li⁴  Jonathan L Braff²  George M Church⁵  Lynn Bry⁴  Harris H Wang³ 

[1] Program in Medical Engineering and Medical Physics, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, 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;Center for Clinical and Translational Metagenomics, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA;Department of Genetics, Harvard Medical School, Boston, MA, USA

关键词: commensal fitness;    functional metagenomics;    microbiota;    next‐generation sequencing;    synthetic biology;   

DOI  :  10.15252/msb.20145866

来源: Wiley

【 摘 要 】

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. Our findings highlight the utility of functional metagenomics for engineering commensal bacteria with improved properties, including expanded colonization capabilities in vivo.

Synopsis

A platform for mining metagenomic DNA for genes contributing to fitness of commensal bacteriain vivo is presented. TFUMseq (Temporal FUnctional Metagenomics sequencing) uses shotgun libraries cloned into a recipient bacterial species, tracked over time in gnotobiotic mice by deep sequencing and computational methods.

• TFUMseq highlights the utility of functional metagenomics for engineering commensal bacteria with improved properties, including expanded colonization capabilities in vivo.
• Genes from a donor commensal bacterial species, Bacteroides thetaiotaomicron, confer fitness advantages to E. coli growing in the mouse gut.
• Analyses of population dynamics of E. coli clones harboring Bacteroides thetaiotaomicron genes reveals a galactokinase central to early colonization of the mouse gut, and subsequent dominance of a glycoside hydrolase enabling sucrose metabolism in E. coli.
• Co-evolution of the donor plasmid library and the E. coli genome occurs, driving increased galactose utilization in E. coli.

【 授权许可】

CC BY   
© 2015 The Authors. Published under the terms of the CC BY 4.0 license

Creative Commons Attribution 4.0 License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.