Metagenomics detects a minimal disruption in the bovine abomasal microbiota by the parasitic nematode Ostertagia ostertagi in immune animals

Ostertagia ostertagi infections in ruminants result in impaired gastrointestinal function. Partially immune animals were developed after multiple experimental infections. These animals displayed reduced worn burdens and a slightly elevated abomasal pH upon reinfection. In this study, we characterized the abomasal microbiota in response to reinfection using metagenomic tools. Compared to control animals, reinfection did not seem to induce a conspicuous change in microbial community composition. Phylogenetic analysis identified 33 phyla in the bovine abomasal microbiota with Bacteroidetes, Firmicutes, Proteobacteria, Fibrobacteres, and Spirochates being the most predominant, in this order. Among the 294 genera identified in the abomasal microbiota, Prevotella, Bacteroides, Fibrobacter, Clostridium and Ruminococcus were the most abundant. Infection did not seem to impact the abomasal microbial diversity at a genus level. Up to 36% of the DNA sequences were unknown, suggesting that a substantial portion of bovine abomasal microbial diversity remained unexplored. Proteins predicted from DNA sequences were assigned to 5,408 Pfam protein families, demonstrating dazzling arrays of functional diversity in bovine abomasal microbial communities. Metagenome plasticity in the abomasum was evident. Sixty nine protein families were significantly impacted by reinfection. Our results demonstrated that immune animals developed abilities to maintain proper stability of their abomasal microbial ecosystem. A minimal disruption in the bovine abomasal microbiota by reinfection may contribute equally to the restoration of gastric function in immune animals.