Environmental control of gene expression in commensal protozoa

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The gastrointestinal tract is the body's largest mucosal surface and an essential organ for the generation and absorption of vitamins and the metabolism of nutrients. An instrumental tool in this process is the intestinal microbiome (the collection of all microbes in our intestine), finding its home in our digestive tract. It is one of the largest and most diverse community of microbes vastly outnumbering the genetic information encoded by our body. These microbial communities are considered an additional vital organ within our body and are thus an integral part of the mammalian physiology. Interestingly the diversity of the microbiome has only recently begun to be uncovered and most strikingly, bacteria (unlike often anticipated) are not the only microbial kingdom in our intestines. Fungi, viruses, worms and protozoa are additional members of the microbiome and are parts of unique and distinct phylogenetic kingdoms. Our advancement in molecular DNA sequencing technologies opened the possibility to simultaneously analyze the composition of viral, bacterial, protozoan and fungal genomes within these complex communities. Cutting edge next-generation sequencing is not only able to uncover the identity of individual microbial members within this highly complex assembly of microorganism, but further to this enable the characterization of genes actively expressed within individual members. Based on these very informative data sets, functional adaptations can be extrapolated ranging from whole communities to even individual members therein. We recently identified Trichomonas musculis (T.mu), a new protozoan species, as a permanent inhabitant of the healthy mouse intestine. T.mu, much like its closest human relative Dientameba fragilis have a reportedly high abundance an colonization efficiency in mice and humans (ranging from 4-40%, depending on the community). Uptake of as little as 1000 purified T.mu results in a live-long colonization and horizontal transmission in mice. Changes in the bacterial microbiome are the result of changing diets, increase in age, infections, the environment and life style, often accomplished through direct impact of these factors on the bacterial community. The transcriptome of T.mu is currently unknown. Determining the gene expression profile of T.mu within the intestinal environment could inform about mechanisms and pathways, utilized to stably colonize our gut and become a member of the intestinal microbiome. Within this project, we aim to understand how environmental factors like the intestinal bacterial microflora and the mucosal immune system control the gene expression of T.mu to allow stable adaptation of T.mu in the context of a changing environment.