Protocol for microbiota analysis of a murine stroke model

Investigations on the microbiota in neurological diseases such as stroke are increasingly common; however, stroke researchers may have limited experience with designing such studies. Here, we describe a protocol to conduct a stroke microbiota study in mice, from experimental stroke surgery and sample collection to data analysis. We provide details on sample processing and sequencing and provide a reproducible data analysis pipeline. In doing so, we hope to enable researchers to conduct robust studies and facilitate identification of stroke-associated microbial signatures. For complete details on the use and execution of this protocol, please refer to Sorbie et al. (2022).¹.