دورية أكاديمية
A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria.
| العنوان: | A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria. |
|---|---|
| المؤلفون: | Bisanz JE; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA., Soto-Perez P; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA., Noecker C; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA., Aksenov AA; Collaborative Mass Spectrometry Innovation Center, Department of Pediatrics, Center for Microbiome Innovation, Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, CA 92093, USA., Lam KN; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA., Kenney GE; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA., Bess EN; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA., Haiser HJ; Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA., Kyaw TS; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA., Yu FB; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA., Rekdal VM; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA., Ha CWY; Department of Medicine, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA., Devkota S; Department of Medicine, Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA., Balskus EP; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA., Dorrestein PC; Collaborative Mass Spectrometry Innovation Center, Department of Pediatrics, Center for Microbiome Innovation, Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, San Diego, CA 92093, USA., Allen-Vercoe E; Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada., Turnbaugh PJ; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address: peter.turnbaugh@ucsf.edu. |
| المصدر: | Cell host & microbe [Cell Host Microbe] 2020 Jun 10; Vol. 27 (6), pp. 1001-1013.e9. Date of Electronic Publication: 2020 Apr 28. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Cell Press Country of Publication: United States NLM ID: 101302316 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1934-6069 (Electronic) Linking ISSN: 19313128 NLM ISO Abbreviation: Cell Host Microbe Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Cambridge, Mass. : Cell Press |
| مواضيع طبية MeSH: | Genomics*, Bacteria/*genetics , Bacteria/*isolation & purification , Dissection/*methods , Gastrointestinal Microbiome/*genetics, Actinobacteria/classification ; Actinobacteria/drug effects ; Actinobacteria/genetics ; Actinobacteria/isolation & purification ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification ; Bacteria/drug effects ; Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; Genes, Bacterial/genetics ; Germ-Free Life ; Humans ; Metagenome ; Metagenomics ; Mice ; Microbial Sensitivity Tests ; Multigene Family ; Phenotype ; Polymorphism, Genetic |
| مستخلص: | 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. Competing Interests: Declaration of Interests P.J.T. is on the scientific advisory boards for Kaleido, Pendulum, Seres, and SNIPRbiome. E.A.V. is co-founder and CSO of NuBiyota. All other authors declare no competing interests. (Copyright © 2020 Elsevier Inc. All rights reserved.) |
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| معلومات مُعتمدة: | T32 GM007810 United States GM NIGMS NIH HHS; T32 AI060537 United States AI NIAID NIH HHS; R21 CA227232 United States CA NCI NIH HHS; T32 GM007618 United States GM NIGMS NIH HHS; M01 RR001271 United States RR NCRR NIH HHS; P30 DK098722 United States DK NIDDK NIH HHS; R01 HL122593 United States HL NHLBI NIH HHS; R01 AR074500 United States AR NIAMS NIH HHS |
| فهرسة مساهمة: | Keywords: Coriobacteriia; Eggerthella lenta; colonization; comparative genomics; fitness; human gut microbiome; metabolism; metabolomics |
| المشرفين على المادة: | 0 (Anti-Bacterial Agents) |
| SCR Organism: | Eggerthella lenta |
| تواريخ الأحداث: | Date Created: 20200430 Date Completed: 20210119 Latest Revision: 20240329 |
| رمز التحديث: | 20240329 |
| مُعرف محوري في PubMed: | PMC7292766 |
| DOI: | 10.1016/j.chom.2020.04.006 |
| PMID: | 32348781 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1934-6069 |
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| DOI: | 10.1016/j.chom.2020.04.006 |