Microbiota and its contribution to brain function and diseases has become a hot topic in neuroscience. In this article in the Journal of Cerebral Blood Flow and Metabolism we discuss the emerging role of commensal bacteria in the course of stroke. Further, we review potential pitfalls in microbiota research and their impact on how we interpret the available evidence, emerging results, and on how we design future studies

The recent availability of powerful and inexpensive sequencing methods that allow the characterization of individual metagenomes and the use of GF animals and experimental fecal transplant approaches have led to a surge in insights into the role of gut microbiota in health and disease. In neuroscience, commensal microbiota has been incorporated into the concept of brain–gut signaling. Several groups have provided experimental evidence that intestinal microbiota is involved in the development of neurological diseases. Although as yet, little is known about the role of gut microbiota in stroke, it is highly plausible that microbiota affect outcome after stroke, and a number of groups worldwide are pursuing research into this relevant topic. However, we should learn from other fields of biomedicine, in which microbiota research is more advanced, to avoid overconfidence and overenthusiasm in interpreting our results. Cognizant of the many pitfalls and limitations of the emerging field of gut microbiome research, we will successfully elucidate the highly complex interactions of the trillions of foreign organisms we harbor in our guts with our immune and nervous systems and drawing from this knowledge we will be able to develop novel therapeutic strategies against CNS disorders.Read full article.