Abstract
BackgroundThe 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.ResultsInulin-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.ConclusionsOur 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.8L3gpTwLDKtEyhWyBHEX34Video abstract.
Highlights
The gut microbiota can have dramatic effects on host metabolism; current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabolic changes in the microbiota
* Correspondence: m.hosokawa@aoni.waseda.jp; haruko-takeyama@waseda.jp Rieka Chijiiwa and Masahito Hosokawa contributed to this work. 3Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan 1Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan Full list of author information is available at the end of the article. This dietary fiber metabolism is important for non-digestible inulin-type fructans classified as prebiotics, which are substrates that promote the growth of beneficial microorganisms in the gut [6,7,8,9,10,11,12]
To account for diurnal oscillations in gut microbiota composition [18, 19], feces were sampled in the morning and evening after 2 weeks of continuous inulin feeding
Summary
The gut microbiota can have dramatic effects on host metabolism; current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabolic changes in the microbiota. Many studies have demonstrated that dietary fiber supplementation can modulate gut microbiota composition and promote SCFA production [3,4,5]. This dietary fiber metabolism is important for non-digestible inulin-type fructans classified as prebiotics, which are substrates that promote the growth of beneficial microorganisms in the gut [6,7,8,9,10,11,12]. To enhance the benefits of dietary fiber to the host, it is important to identify inulin-responders in the complex microbiome community of the host intestine and (2020) 8:5 characterize their mechanisms of inulin fermentation and potential for SCFA production
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