ArticleMicrobiome2020
Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota.
Article in Microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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85 citing papers in PubMed, 152 citations in OpenAlex.
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- Mining Microbial Dark Matter: Advanced Cultivation Techniques for Bioactive Compound Discovery.Pharmaceuticals (Basel, Switzerland) · 2025Review
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- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Microbiome Landscape and Association with Response to Immune Checkpoint Inhibitors in Advanced Solid Tumors: A SCRUM-Japan MONSTAR-SCREEN Study.Cancer research communications · 2025Article
- Assessing the relationship between the gut microbiota and growth traits in Chinese indigenous pig breeds.BMC veterinary research · 2025Article
- Inulin Diet Alleviates Abdominal Aortic Aneurysm by Increasing Akkermansia and Improving Intestinal Barrier.Biomedicines · 2025Article
- Cecal microbial composition and serum concentration of short-chain fatty acids in laying hens fed different fiber sources.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Microbial function in food fermentations: Current research and future directions.Current research in microbial sciences · 2025Article
- Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism.Frontiers in microbiology · 2025Article
25 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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. Video abstract.
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