Usage of Cultured Human Fecal Microbiota for Colonization of Caenorhabditis elegans to Study Host–Microbe Interaction

Abstract

The role of the microbiota in health and disease is a research area receiving much attention in academia and industry. A person’s microbiota refers to a community of microorganisms found mainly in the gut. It is estimated that around 39 trillion bacteria can be found on and inside the human body and there is increasing evidence that they influence human health. Advances in sequencing techniques are revolutionizing characterization of the human microbiome. However, causality and underlying molecular mechanisms are still largely unknown due to the complexity of the human microbiome and its interaction with the host. Turning towards simpler host organisms and using well-defined microbiomes are two ways to strengthen studies of causality and mechanism. Here, we show that the nematode Caenorhabditis elegans can be used as host to study sub-microbiomes derived from human feces samples prepared for fecal microbiota transplantation following a simple feeding protocol. Approximately 200 amplicon sequence variants were identified in the worm gut following transplantation with human fecal microbiota samples. We find that the gut microbiome does not simply reflect the bacterial community initially fed to the worms. Hence, our experimental setup can be used to identify and characterize host genetic factors shaping the microbiota and improving our understanding of host–human microbiome interactions.

Feeding Drosophila gut microbiomes from young and old flies modifies the microbiome

“…Though the flies were supplied with quite different microbial feeds, they were observed to have very similar microbial compositions between the three feed regimens. This microbial selection/curation of the host seem to be a conserved trait and similar results have been found in humans and other model organisms 41 , 42 , 65 . Despite this selection revealing quite similar microbiomes across the feeding regimes, certain important age-related differences were observed among the microbiomes of flies fed with different microbial supplements.…”

“…Probing the complex interactions between microbiomes, host response, aging and environment in humans and wild living metazoans can prove wildly complex since it is hard to control for the many factors that can influence the delicate interactions 40 . For this reason, much of the research that is being performed in this field makes use of model organisms like C. elegans 18 , 41 , 42 or D. melanogaster 43 – 46 . Here we used D. melanogaster to investigate whether enriching the gut microbiome of flies by feeding them microbiomes from flies of different ages, altered the microbial composition and whether traits related to healthspan and lifespan were affected by the microbial enrichment.…”