PT - JOURNAL ARTICLE AU - Carolyn Elya AU - Vivian Zhang AU - Will Ludington AU - Michael B Eisen TI - Stable host gene expression in the gut of adult <em>Drosophila melanogaster</em> with different bacterial mono-associations AID - 10.1101/053512 DP - 2016 Jan 01 TA - bioRxiv PG - 053512 4099 - http://biorxiv.org/content/early/2016/05/15/053512.short 4100 - http://biorxiv.org/content/early/2016/05/15/053512.full AB - There is growing evidence that the microbes found in the digestive tracts of animals influence host biology, but we still do not understand how this comes about. Here, we evaluated how different microbial species commonly associated with laboratory-reared Drosophila melanogaster impact host biology at the level of gene expression in the dissected adult gut or the entire adult organism. We observed that guts from gnotobiotic animals associated from the embryonic stage with either zero, one or three bacterial species demonstrated indistinguishable transcriptional profiles. Additionally, we found that the gut transcriptional profiles of animals reared in the presence of the yeast Saccharomyces cerevisiae alone or in combination with bacteria could recapitulate those of conventionally-reared animals. In contrast, we found whole body transcriptional profiles of conventionally-reared animals were distinct from all of the gnotobiotic treatments tested. Our data suggest that adult flies are insensitive to the ingestion of different bacterial species but that prior to adulthood, different microbes impact the host in ways that lead to global transcriptional differences observable across the whole adult body.