Complex microbial communities inhabiting natural Cordyceps militaris and the habitat soil and their predicted functions.

Cordyceps militaris is a traditional Chinese medicinal food that is challenging to quality maintaining while mass cultivation. Many studies have found that abundant microbes inhabit Ophiocordyceps sinensis and perform important functions for their host. In this study, our objective was to reveal the microbial communities that inhabit C. militaris and analyze their potential functions. High-throughput sequencing of 16S rRNA and ITS genes was used to compare the diversity and composition of the bacterial and fungal communities associated with naturally occurring C. militaris collected from Yunnan Province, southwestern China. The diversity and richness of the microbial communities and the number of function genes of the bacteria were significantly higher in the habitat soil than in the fruiting body. The sclerotia and stromata samples shared the same microbiota and functions. The main bacterial phyla were Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria, and Ascomycota was the main fungal phylum. The growth-promoting bacteria Herbaspirillum and the plant probiotic Phyllobacterium, which may enhance C. militaris quality and facilitate its cultivation, were detected in the fruiting body samples. Genes related to metabolism were more abundant in the soil bacteria, while membrane transport genes were more abundant in the endophytic bacteria of C. militaris. Our study is the first to reveal the unexpectedly high diversity of the microbial communities and the bacterial functions inhabiting the natural C. militaris using high-throughput sequencing, and our results provide insights into mining the functions of microorganisms in the development and quality of C. militaris.