PSXIII-30 - The bovine microbiome: A holistic view on different bacterial communities in cattle

Abstract: The bovine body is home to trillions of microbial cells that are residing and establishing self-sustaining microbial communities along the digestive, respiratory, and reproductive tracts, mammary gland, and mucosal surfaces of the eye and hoof. Although the taxonomic and functional features of each of these communities and their potential association with site-specific nutrient or infectious/metabolic disease phenotypes have been relatively well characterized, the approaches employed are largely limited to individualistic views. This is based on a notion that the microbiome associated with a particular organ/site is regarded as a separate entity. Increasing evidence suggests the presence of a core taxa shared across the gut, respiratory, and reproductive microbiotas in cattle, and increased appreciation of the involvement of the gut microbiome in gut-organ (lung/brain/liver/skin) axis together highlight the necessity of establishing a holistic perspective on how all different microbial communities shape systemic animal health and development. Holistic understanding of the interactive effects of microbiome on different body sites is critical to develop strategies aiming to harness whole-body microbiota for improved cattle health and productivity. In the present study, we evaluated the similarity of bacterial communities associated with 11 different anatomical sites in cattle to provide a holistic view on the composition of bacterial microbiota. For this, we performed a comprehensive analysis on 16S rRNA gene sequencing data (N=1430 samples) our lab has created, as well as publicly available data originating from 7 different studies. Sequencing samples originated from 10 different anatomical sites spanning from gastrointestinal (ruminal fluid), respiratory (nasal and deep nasopharyngeal swabs, and lung tissue), and reproductive (vaginal and uterine swabs) tracts, as well as oral and ocular swabs, liver tissue and semen of beef cattle. As expected, microbial community structure was distinct among different sample types (PERMANOVA, P < 0.05). Microbial richness (Observed ASVs) was also different in different anatomical sites (P < 0.0001), with the rumen harboring richest microbial community (1121±22), followed by uterus (816) and vagina (636). Total observed ASVs did not differ among seminal, oral, nasal, and nasopharyngeal and liver microbiota (189-279; P>0.05), but liver and ocular microbiota had the least species richness (P < 0.05). Similar community diversity (Shannon and Inverse Simpson) was observed between ruminal fluid, uterine, oral, and nasal microbiota. Overall, Firmicutes, Proteobacteria, Fusobacteriota, Bacteroidota and Actinobacteriota were the most predominant phyla. However, their abundance varied highly by body sites, with Fusobacteriota being the main colonizer in liver (75.0%), semen (36.3%) and oral cavity (34.1%). Firmicutes dominated vagina (53.1%), uterus (62.5%), lung (48%) and upper airway while Proteobacteria and Bacteroidota were the most abundant in ocular surface and rumen, respectively. Core genera and taxa shared by these 10 different body sites were identified. Overall, our results provide holistic insights into 10 different bacterial communities in cattle.