CeMbio - The Caenorhabditis elegans Microbiome Resource
Abstract
The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.
- Authors:
-
- Christian-Albrechts University, Kiel (Germany)
- Baylor College of Medicine, Houston, TX (United States)
- University Medical Center Schleswig-Holstein, Kiel (Germany)
- Institute of Biology of the Ecole Normale Supérieure, Paris (France)
- Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH)
- OSTI Identifier:
- 1816499
- Grant/Contract Number:
- AC02-05CH11231; DP2DK116645; R01OD024780; R01AG061302; CSP-503338; P40 OD010440
- Resource Type:
- Accepted Manuscript
- Journal Name:
- G3
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 2160-1836
- Publisher:
- Genetics Society of America
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; C. elegans; microbiome resource; host-microbe interactions; synthetic communities; metabolic networks
Citation Formats
Dirksen, Philipp, Assié, Adrien, Zimmermann, Johannes, Zhang, Fan, Tietje, Adina-Malin, Marsh, Sarah Arnaud, Félix, Marie-Anne, Shapira, Michael, Kaleta, Christoph, Schulenburg, Hinrich, and Samuel, Buck S. CeMbio - The Caenorhabditis elegans Microbiome Resource. United States: N. p., 2020.
Web. doi:10.1534/g3.120.401309.
Dirksen, Philipp, Assié, Adrien, Zimmermann, Johannes, Zhang, Fan, Tietje, Adina-Malin, Marsh, Sarah Arnaud, Félix, Marie-Anne, Shapira, Michael, Kaleta, Christoph, Schulenburg, Hinrich, & Samuel, Buck S. CeMbio - The Caenorhabditis elegans Microbiome Resource. United States. https://doi.org/10.1534/g3.120.401309
Dirksen, Philipp, Assié, Adrien, Zimmermann, Johannes, Zhang, Fan, Tietje, Adina-Malin, Marsh, Sarah Arnaud, Félix, Marie-Anne, Shapira, Michael, Kaleta, Christoph, Schulenburg, Hinrich, and Samuel, Buck S. Tue .
"CeMbio - The Caenorhabditis elegans Microbiome Resource". United States. https://doi.org/10.1534/g3.120.401309. https://www.osti.gov/servlets/purl/1816499.
@article{osti_1816499,
title = {CeMbio - The Caenorhabditis elegans Microbiome Resource},
author = {Dirksen, Philipp and Assié, Adrien and Zimmermann, Johannes and Zhang, Fan and Tietje, Adina-Malin and Marsh, Sarah Arnaud and Félix, Marie-Anne and Shapira, Michael and Kaleta, Christoph and Schulenburg, Hinrich and Samuel, Buck S.},
abstractNote = {The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.},
doi = {10.1534/g3.120.401309},
journal = {G3},
number = 9,
volume = 10,
place = {United States},
year = {Tue Sep 01 00:00:00 EDT 2020},
month = {Tue Sep 01 00:00:00 EDT 2020}
}
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