High resolution flow cytometry of the intestinal microbiota

The intestinal microbiota is an important component of the mammalian organism critical for nutrient metabolism and immune homeostasis. Pathological changes within the microbiota, known as dysbiosis, have been implicated in the pathogenesis of chronic inflammatory disorders like inflammatory bowel disease (IBD). Currently, analysis of the microbiota is done primarily by qPCR- or next generation sequencing approaches. These methods are not only laborious and time-consuming but are also biased towards more abundant bacterial strains.

We present here a novel, fast and inexpensive flow cytometry-based approach to characterize the complexity of the intestinal microbiota. High resolution measurement of forward and side scatter of the microbes as well as their DNA content, allowed the discrimination of over 35 different bacterial subpopulations from formaldehyde-fixed murine stool samples. Using this method, we could discriminate the microbiota of mice derived from different facilities and could monitor the adaptation of the intestinal microbiota in individual mice upon co-housing. In addition, we tracked the dynamic changes of the microbiota in two mouse models for IBD, i.e. T cell transfer colitis and DSS-induced colitis. By our flow cytometry-based analysis we could confirm the previously described loss of microbial complexity upon intestinal inflammation. Taken together, we have established an inexpensive and fast, flow cytometry-based method to monitor changes in the intestinal microbiota. We will now translate this approach to the human intestinal microbiota to test the feasibility of defining specific microbiota changes as biomarkers for the diagnosis and prognosis of IBD.

*/° = equal contribution