Bacterial communities in pika stomachs

Mammalian stomach acts as an important barrier against ingested pathogens into the entire gastrointestinal tract (GIT), thereby playing a key role in host health. However, little is known regarding to the stomach microbiota composition of wild mammals and factors that influence the community composition. Using high-throughput sequencing of 16Sr RNA gene, we characterized the stomach bacterial community composition, diversity and interactions in two common pika (Ochotona spp.) species in China, including Plateau pikas (O. curzoniae) living in the Qinghai-Tibet Plateau and Daurian pikas (O. daurica) inhabiting the Inner Mongolia Grassland. The bacterial communities can be divided into two distinct phylogenetic clusters. The most dominant bacteria in Cluster I were unclassified bacteria. Cluster II was more diverse, with predominantly Bacteroidetes, followed by unclassified bacteria, Firmicutes, Proteobacteria. Three dominant genera (Prevotella, Oscillospira and Ruminococcus) in pika stomachs were significantly enriched in Cluster II. Helicobacter sp. sequences were not detected in our samples. Most individuals in Daurian pikas belonged to Cluster I, while a majority of individuals in Plateau pikas was affiliated with Cluster II. In addition, seasons, host species and sampling sites as well as body weight and sex almost had no significant impacts in shaping the composition and diversity of pika stomach communities. Interestingly, Plateau pikas harbored a more complex bacterial network than Daurian pikas, while these two pika species showed different co-occurrence patterns. These results suggested that pika stomach harbors a diverse but relatively stable bacterial community, which may steadily maintain the function of the GIT.