Identification and characterization of a skin microbiome on Caenorhabditis elegans suggests environmental microbes confer cuticle protection
[1];
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[4];
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA, University of California San Diego, La Jolla, California, USA
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USA, Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA, Biology, University of Portland, Portland, Oregon, USA
ABSTRACT In the wild, C. elegans are emersed in environments teeming with a veritable menagerie of microorganisms. The C. elegans cuticular surface serves as a barrier and first point of contact with their microbial environments. In this study, we identify microbes from C. elegans natural habitats that associate with its cuticle, constituting a simple “skin microbiome.” We rear our animals on a modified CeMbio, mCeMbio, a consortium of ecologically relevant microbes. We first combine standard microbiological methods with an adapted micro skin-swabbing tool to describe the skin-resident bacteria on the C. elegans surface. Furthermore, we conduct 16S rRNA gene sequencing studies to identify relative shifts in the proportion of mCeMbio bacteria upon surface-sterilization, implying distinct skin- and gut-microbiomes. We find that some strains of bacteria, including Enterobacter sp. JUb101 , are primarily found on the nematode skin, while others like Stenotrophomonas indicatrix JUb19 and Ochrobactrum vermis MYb71 are predominantly found in the animal’s gut. Finally, we show that this skin microbiome promotes host cuticle integrity in harsh environments. Together, we identify a skin microbiome for the well-studied nematode model and propose its value in conferring host fitness advantages in naturalized contexts. IMPORTANCE The genetic model organism C. elegans has recently emerged as a tool for understanding host–microbiome interactions. Nearly all of these studies either focus on pathogenic or gut-resident microbes. Little is known about the existence of native, nonpathogenic skin microbes or their function. We demonstrate that members of a modified C. elegans model microbiome, mCeMbio, can adhere to the animal's cuticle and confer protection from noxious environments. We combine a novel micro-swab tool, the first 16S microbial sequencing data from relatively unperturbed C. elegans , and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wild C. elegans skin microbiomes and use C. elegans as a model for skin research.
- Research Organization:
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Sponsoring Organization:
- HHS | National Institutes of Health (NIH); National Aeronautics and Space Administration (NASA); National Science Foundation (NSF); USDOE
- Grant/Contract Number:
- AC02-05CH11231
- OSTI ID:
- 2396398
- Journal Information:
- Microbiology Spectrum, Journal Name: Microbiology Spectrum Journal Issue: 8 Vol. 12; ISSN 2165-0497
- Publisher:
- American Society for MicrobiologyCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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