Identification and characterization of a skin microbiome onCaenorhabditis eleganssuggests environmental microbes confer cuticle protection

Abstract

AbstractIn the wild,C. elegansare emersed in environments teeming with a veritable menagerie of microorganisms. TheC. eleganscuticular surface serves as a barrier and first point of contact with this microbial milieux. Here, we identify microbes fromC. elegansnatural 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 theC. eleganssurface. Further, 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, includingEnterobacter sp.JUb101, are primarily found on the nematode skin, while others likeStenotrophomonas indicatrixJUb19 andOchrobactrum vermisMYb71 are predominantly 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.ImportanceThe genetic model organismC. eleganshas 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, non-pathogenic skin microbes or their function. We show that members of a modifiedC. elegansmodel 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 unperturbedC. elegans, and physiological assays to demonstrate microbially mediated protection of the skin. This work serves as a foundation to explore wildC. elegansskin microbiomes and useC. elegansas a model for skin research.