Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota
Abstract 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...
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | Microbiome |
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| Online Access: | https://doi.org/10.1186/s40168-019-0779-2 |
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| author | Rieka Chijiiwa Masahito Hosokawa Masato Kogawa Yohei Nishikawa Keigo Ide Chikako Sakanashi Kai Takahashi Haruko Takeyama |
| author_facet | Rieka Chijiiwa Masahito Hosokawa Masato Kogawa Yohei Nishikawa Keigo Ide Chikako Sakanashi Kai Takahashi Haruko Takeyama |
| author_sort | Rieka Chijiiwa |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-14T05:44:50Z |
| format | Article |
| id | doaj.art-5258188bd12c4d318738d79d49cb11f6 |
| institution | Directory Open Access Journal |
| issn | 2049-2618 |
| language | English |
| last_indexed | 2024-12-14T05:44:50Z |
| publishDate | 2020-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Microbiome |
| spelling | doaj.art-5258188bd12c4d318738d79d49cb11f62022-12-21T23:14:54ZengBMCMicrobiome2049-26182020-01-018111410.1186/s40168-019-0779-2Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiotaRieka Chijiiwa0Masahito Hosokawa1Masato Kogawa2Yohei Nishikawa3Keigo Ide4Chikako Sakanashi5Kai Takahashi6Haruko Takeyama7Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and EngineeringResearch Organization for Nano and Life Innovation, Waseda UniversityDepartment of Life Science and Medical Bioscience, Graduate School of Advanced Science and EngineeringDepartment of Life Science and Medical Bioscience, Graduate School of Advanced Science and EngineeringDepartment of Life Science and Medical Bioscience, Graduate School of Advanced Science and EngineeringResearch Organization for Nano and Life Innovation, Waseda UniversityDepartment of Life Science and Medical Bioscience, Graduate School of Advanced Science and EngineeringDepartment of Life Science and Medical Bioscience, Graduate School of Advanced Science and EngineeringAbstract 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.https://doi.org/10.1186/s40168-019-0779-2Single-cell genomicsGut microbiomeUncultured bacteriaMouseInulinBacteroides |
| spellingShingle | Rieka Chijiiwa Masahito Hosokawa Masato Kogawa Yohei Nishikawa Keigo Ide Chikako Sakanashi Kai Takahashi Haruko Takeyama Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota Microbiome Single-cell genomics Gut microbiome Uncultured bacteria Mouse Inulin Bacteroides |
| title | Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota |
| title_full | Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota |
| title_fullStr | Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota |
| title_full_unstemmed | Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota |
| title_short | Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota |
| title_sort | single cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota |
| topic | Single-cell genomics Gut microbiome Uncultured bacteria Mouse Inulin Bacteroides |
| url | https://doi.org/10.1186/s40168-019-0779-2 |
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