Metatranscriptomic analyses of gut bacterial and viral communities in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) under distinct environments

The Yangtze finless porpoise (YFP; Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean, but little is known about the microbiota and the influencing factors. Here, we performed metatranscriptomic sequencing on fecal samples collected from the YFPs under distinct environments to characterize the gut bacterial and viral communities, which consisted of 43 wild and 3 captive YFPs. Our analyses revealed that distinct environments of YFPs resulted in significant divergence in the gut microbiota. The captive adult YFPs inhabiting sanitized, stable environments exhibited consistent intestinal microbiota composition and structure, differing markedly from the wild adult YFPs. Notably, Romboutsia, a potential health-associated genus, was significantly prevalent in captive adult YFPs, whereas wild adult YFPs demonstrated higher relative abundances of known opportunistic pathogens. And the wild YFPs in a complex natural environment exhibited highly inter-individual variation with the absence of an age-specific pattern. High-abundance antibiotic resistance genes were prevalent in both captive and wild YFPs. Besides, less overlap in virus species between captive and wild populations was discovered, with one novel genus and two novel species identified. We aimed to comprehensively characterize the intestinal bacterial and viral communities of the YFP and to identify the influencing factors. Lifestyle differences were associated with distinct gut microbial compositions, while the individual specificity observed among the wild population may reflect environmental and host-specific influences.