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A Double Humanized BLT-mice Model Featuring a Stable Human-Like Gut Microbiome and Human Immune System
Published on: August 30, 2019
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1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.
Yuanqiang Zou1,2,3, Wenbin Xue1,2, Guangwen Luo1,2,4
1BGI-Shenzhen, Shenzhen, China.
Nature Biotechnology
|February 6, 2019
Summary
A new collection of 1,520 human gut bacterial genomes, the Culturable Genome Reference (CGR), enhances metagenomic analysis. This resource improves read mapping rates, enabling deeper insights into the human gut microbiome composition and function.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Reference genomes are crucial for analyzing the human gut microbiome.
- Current reference catalogs lack comprehensive coverage of gut bacterial diversity.
Purpose of the Study:
- To present the Culturable Genome Reference (CGR), a novel collection of human gut bacterial genomes.
- To demonstrate the utility of CGR for improving metagenomic analysis and functional annotation.
Main Methods:
- Cultivation of >6,000 bacteria from human fecal samples.
- Generation of 1,520 high-quality draft genomes, ensuring broad phyla and genera coverage.
- Metagenomic read mapping and functional annotation using the CGR resource.
Main Results:
- The CGR includes 1,520 nonredundant genomes, with 264 novel entries not found in existing catalogs.
- Incorporating CGR improved metagenomic read mapping rates from 50% to over 70%.
- Functional annotation of 338 species and pan-genome analysis of 38 species were performed.
Conclusions:
- The CGR significantly enhances the resolution of human gut microbiome descriptions.
- This resource is valuable for both taxonomic and functional characterization of gut bacteria.
- Pan-genome analysis reveals functional diversity within gut bacterial species.
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