1. A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
- Author
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Bisanz, Jordan E, Soto-Perez, Paola, Noecker, Cecilia, Aksenov, Alexander A, Lam, Kathy N, Kenney, Grace E, Bess, Elizabeth N, Haiser, Henry J, Kyaw, Than S, Yu, Feiqiao B, Rekdal, Vayu M, Ha, Connie WY, Devkota, Suzanne, Balskus, Emily P, Dorrestein, Pieter C, Allen-Vercoe, Emma, and Turnbaugh, Peter J
- Subjects
Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Microbiome ,Infection ,Good Health and Well Being ,Actinobacteria ,Animals ,Anti-Bacterial Agents ,Bacteria ,Dissection ,Gastrointestinal Microbiome ,Gastrointestinal Tract ,Genes ,Bacterial ,Genomics ,Germ-Free Life ,Humans ,Metagenome ,Metagenomics ,Mice ,Microbial Sensitivity Tests ,Multigene Family ,Phenotype ,Polymorphism ,Genetic ,Coriobacteriia ,Eggerthella lenta ,colonization ,comparative genomics ,fitness ,human gut microbiome ,metabolism ,metabolomics ,Medical Microbiology ,Immunology ,Biochemistry and cell biology ,Medical microbiology - Abstract
Despite the remarkable microbial diversity found within humans, our ability to link genes to phenotypes is based upon a handful of model microorganisms. We report a comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease. We uncover extensive genetic and metabolic diversity and validate a tool for mapping phenotypes to genes and sequence variants. We also present a tool for the quantification of strains from metagenomic sequencing data, enabling the identification of genes that predict bacterial fitness. Competitive growth is reproducible under laboratory conditions and attributable to intrinsic growth rates and resource utilization. Unique signatures of in vivo competition in gnotobiotic mice include an adhesin enriched in poor colonizers. Together, these computational and experimental resources represent a strong foundation for the continued mechanistic dissection of the Coriobacteriia and a template that can be applied to study other genetically intractable taxa.
- Published
- 2020