論文

査読有り 国際誌
2020年1月23日

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
開始ページ
5
終了ページ
5
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

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. Video abstract.

リンク情報
DOI
https://doi.org/10.1186/s40168-019-0779-2
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/31969191
PubMed Central
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977353
ID情報
  • DOI : 10.1186/s40168-019-0779-2
  • PubMed ID : 31969191
  • PubMed Central 記事ID : PMC6977353

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