Inducible CRISPR-targeted “knockdown” of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies

Author:

Beller Zachary W.12ORCID,Wesener Darryl A.12,Seebeck Timothy R.123,Guruge Janaki L.12,Byrne Alexandra E.12,Henrissat Suzanne124,Terrapon Nicolas4,Henrissat Bernard56,Rodionov Dmitry A.7,Osterman Andrei L.7,Suarez Chris8,Bacalzo Nikita P.8,Chen Ye8,Couture Garret8,Lebrilla Carlito B.8ORCID,Zhang Zhigang3,Eastlund Erik R.3,McCann Caitlin H.3,Davis Gregory D.3,Gordon Jeffrey I.12

Affiliation:

1. Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110

2. Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110

3. Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO 63103

4. Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288 Marseille, France

5. Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark

6. Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia

7. Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037

8. Department of Chemistry, University of California, Davis, CA 95616

Abstract

Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these “alternate consumers” was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus , a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.

Funder

HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3