Two community types occur in gut microbiota of large-sample wild plateau pikas (Ochotona curzoniae).

Studies on large-sample gut microbial sequencing data indicate that gut microbiota can be divided into multiple community types; different community types may influence the community function and ecosystem service. However, the knowledge on the classification, diversity, interaction, and assembling of microbial community types in the gut of wild animals is still insufficient. Here, we used pika gut microbiota data as an example to study the microbial community types in large-sample sequencing dataset. Cecal microbial communities from 118 wild plateau pika (Ochotona curzoniae) individuals at 5 elevational regions on the Qinghai-Tibet Plateau were analyzed. Our results show that pika gut microbiota can be separated into 2 community types (Cluster I and Cluster II). Cluster I was mainly distributed on the high-elevation regions with more than 3694 m and was most dominated by Firmicutes. Cluster II was from the low-elevation areas (lower than 3580 m), and was predominated by Bacteroidetes. Cluster I had a higher community alpha-diversity and predicted functional diversity than Cluster II, and the beta-diversity and predicted functional profiles of these 2 clusters were significantly different. Network analysis revealed that there were more complex interactions between Cluster I, which had enhanced influence on the co-occurrences of other microbes in the bacterial community when compared to Cluster II. Phylogenetic analysis found that the environmental filtering in the Cluster I was stronger than Cluster II. The assemblages of pika gut bacterial communities were determined mainly by deterministic processes, while the relative importance of deterministic processes accounted for more percentages in the Cluster I than Cluster II. Our results demonstrated that 2 gut microbial community types in pikas had distinct diversity patterns and ecological functions. Current methods are also helpful for identifying gut community types and the related mechanisms behind gut microbiota types in large-sample sequencing data of wild animals.