Dynamic Changes in Fecal Bacterial Microbiota of Dairy Cattle across the Production Line

Abstract

Bacteria play important roles in the gastrointestinal tract (GIT) of dairy cattle as the communities are responsible for host health, growth and production performance. However, a systematic characterization and comparison of microbial communities in the GIT of cattle housed in different management units on a modern dairy are still lacking. In this study, we used 16S rRNA sequencing to evaluate the fecal bacterial communities of 90 dairy cattle raised and housed in 12 clearly defined management units on a modern dairy farm. We found that -diversity differed between several pairs of management units, especially between the hutch calves (management unit 1) and the other units except post weaned heifers (management unit 2). Although {beta}-diversity revealed that most of the samples did not cluster according to their management unit membership except management unit 1, in which the samples grouped and separated from others, we observed three major clusters. Besides the hutch calves (management unit 1), most samples from the other 11 units formed two distinct clusters and the relative abundance of Patescibacteria might be the reason for the separation. Moreover, we identified 212 amplicon sequence variants (ASVs) with relative abundances > 0.1% in more than 10% of the total samples that had significantly different abundances in these units. Furthermore, we found that, as the calves aged, 19 ASVs that were exclusively detected in unit 1, gradually degraded and never reoccurred in other management units. Lastly, we recognized 181 pairs of interactions between 61 ASVs with possibly strong synergistic or antagonistic relationships. These results suggest the enteric microbial communities of dairy cattle housed in different management units are quite dynamic. IMPORTANCEBacterial communities of GIT are crucial for ruminants, such as dairy cattle since they contribute to not only the cattles physiology and health but also milk production and food safety that are closely related to human health. Both scientifically and agriculturally, it is necessary to have deep insights into the composition and changes of the bacteria on modern dairy farms. In this study, we provided the profiles of fecal bacterial communities of dairy cattle in each management unit on a modern dairy and described how the enteric microbial communities changed across these management units. The findings have implications for improving animal health, dairy production, farm management, and food safety.