論文

2020年1月

Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota

MICROBIOME
  • Rieka Chijiiwa
  • ,
  • Masahito Hosokawa
  • ,
  • Masato Kogawa
  • ,
  • Yohei Nishikawa
  • ,
  • Keigo Ide
  • ,
  • Chikako Sakanashi
  • ,
  • Kai Takahashi
  • ,
  • Haruko Takeyama

8
1
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1186/s40168-019-0779-2
出版者・発行元
BMC

Background The gut microbiota can have dramatic effects on host metabolism; however, current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabolic changes in the microbiota. In this study, we describe a novel single-cell genomic sequencing technique that can identify metabolic responders at the species level without the need for reference genomes, and apply this method to identify bacterial responders to an inulin-based diet in the mouse gut microbiota. Results Inulin-feeding changed the mouse fecal microbiome composition to increase Bacteroides spp., resulting in the production of abundant succinate in the mouse intestine. Using our massively parallel single-cell genome sequencing technique, named SAG-gel platform, we obtained 346 single-amplified genomes (SAGs) from mouse gut microbes before and after dietary inulin supplementation. After quality control, the SAGs were classified as 267 bacteria, spanning 2 phyla, 4 classes, 7 orders, and 14 families, and 31 different strains of SAGs were graded as high- and medium-quality draft genomes. From these, we have successfully obtained the genomes of the dominant inulin-responders, Bacteroides spp., and identified their polysaccharide utilization loci and their specific metabolic pathways for succinate production. Conclusions Our single-cell genomics approach generated a massive amount of SAGs, enabling a functional analysis of uncultured bacteria in the intestinal microbiome. This enabled us to estimate metabolic lineages involved in the bacterial fermentation of dietary fiber and metabolic outcomes such as short-chain fatty acid production in the intestinal environment based on the fibers ingested. The technique allows the in-depth isolation and characterization of uncultured bacteria with specific functions in the microbiota and could be exploited to improve human and animal health.

Web of Science ® 被引用回数 : 37

リンク情報
DOI
https://doi.org/10.1186/s40168-019-0779-2
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000513559600001&DestApp=WOS_CPL
ID情報
  • DOI : 10.1186/s40168-019-0779-2
  • ISSN : 2049-2618
  • Web of Science ID : WOS:000513559600001

エクスポート
BibTeX RIS