PSLBII-7 - Meta-analysis of the whole-body microbiota in cattle

Abstract: Distinctive and self-sustainable microbial communities are present along the digestive, respiratory, and reproductive tracts, as well as in the mammary gland, and mucosal surfaces of the eye and hoof in cattle. Although the taxonomic and functional features of each of these communities have been relatively well characterized, this has been largely limited to the microbiome of an individual organ/site. However, recent developments suggest the presence of core taxa shared across the gut, respiratory, and reproductive microbiotas in cattle, and there is a need for a more holistic evaluation of microbial communities in and on cattle. Here, we performed a meta-analysis using all publicly available bovine 16S rRNA gene datasets deposited since 2019 to provide a holistic view of the whole-body microbiota. In total, we retrieved 16S rRNA gene sequences from 6,215 samples (53 studies originating from 29 different anatomical sites within beef and dairy cattle from Africa, Asia, Europe, South America, and North America. The 29 different anatomical sites including gut (ruminal fluid, ruminal tissues, feces, ileum, jejunum, cecum, colon and duodenum), respiratory (nasal cavity, deep nasopharynx, trachea and lung tissue), and reproductive tracts (female: vagina, endometrium and uterus; male: semen and prepuce), as well as the mammary gland (udder, teat apex, teat barrel, teat canal), eye (conjunctiva, ocular fluid and ocular surface swab), blood, hoof, joints and liver. Microbial community structure was distinct among different sample types (PERMANOVA, P < 0.05). Microbial richness differed by sample type (P < 0.0001) with mucosal surfaces (e.g. udder, eye and feet) having the greatest microbial richness followed by the gut. The lungs, liver, joints, semen and prepuce had the lowest microbial richness. Microbial diversity was highest in the microbiota of the colon, cecum, teat apex, ruminal tissue and duodenum (Shannon diversity index > 5) while the liver (1.5), joint (2.3), and prepuce microbiota (2.7) were the least diverse. Bacillota had the highest relative abundance among phyla in the majority of microbial communities except for in the blood, prepuce, trachea and nasal cavity (dominated by Pseudomonadota), and liver (dominated by Fusobacteriota). The relatively most abundant genera across all samples were Mycoplasma (12.9%), Prevotella (3.9%), Bacteroides (2.4%), Escherichia (2.1%), Fusobacterium (2.0%), Ruminococcaceae UCG-005 (1.9%), Streptococcus (1.8%), Rikenellaceae RC9 (1.6%), and Corynebacterium (1.4%). However, their relative abundance varied greatly by body site, with the ocular and respiratory system samples dominated by Mycoplasma. Fusobacterium was relatively most abundant in the liver and semen, Corynebacterium in the mammary gland-associated samples, Bacteroides in the gut, and Streptococcus in the lower reproductive tract microbiota. Overall, our meta-analysis provides a comprehensive evaluation of the multiple bacterial communities in and on cattle, which will be useful for harnessing the whole-body microbiome to improve animal health and productivity.