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 α-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 β-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

Rumen Sampling Methods Bias Bacterial Communities Observed

“…However, they found no difference in the abundance of Lachnospiraceae. A recent preprint found strikingly similar relative abundances of top three most abundant families in feces from dairy cattle: Ruminococcaceae (34.9% compared to our 40.7%), and Rikenellaceae (11.6% compared to our 15.7%) and Lachnospiraceae (6.8% compared to our 7.7%) [71]. These data show that Ruminococcaceae is typically found in higher abundance in feces, while fecal Lachnospiraceae will have lower abundance than the rumen population.…”