Evaluation of rumen bacterial composition in Holstein and Jersey cows under similar dietary conditions using different sampling methods

Abstract Text:

This study utilized 16S rRNA gene amplicon sequencing to describe the rumen bacterial community composition in Holstein and Jersey cows fed an identical diet by sampling the rumen microbiota via the rumen cannula or esophageal tubing. Five ruminally cannulated Holstein cows and 4 Jersey cows (not cannulated) were fed a diet composed of 51% forage and 49% concentrate during 4 weeks. On the 28^th day, rumen samples were collected from both Holstein and Jersey cows using the esophageal tubing, and an additional rumen sample was collected from Holstein cows via the cannula. After collection of the rumen sample via esophageal tubing, particles attached to the metal strainer were added to the sample to better represent whole rumen content and to include particle associated bacteria. Total rumen DNA was extracted using the PowerMag^TM Soil DNA Isolation Kit, and the V3 region of the bacterial 16S rRNA was amplified and then sequenced using the Ion Torrent^TM Personal Genome Machine. The resulting sequences were quality filtered and operational taxonomic units (OTUs) were generated at 97% similarity. Taxonomy assignment was performed using the Greengenes database. The 2 main phyla identified regardless of breed or sampling method, were Firmicutes and Bacteroidetes, which accounted for 44.3 and 42.9 % of the sequences. Alpha diversity metrics, observed OTUs and Chao1 estimates, displayed higher (P < 0.01) bacterial richness in Holstein compared to Jersey cows. However, between the samples collected via the cannula and stomach tubing in Holstein cows, no difference in species richness was detected (P > 0.40). Principal coordinate analysis using the unweighted UniFrac displayed clustering by breed suggesting that Holstein and Jersey cows may harbor distinct rumen bacterial communities. Non-parametric multivariate analysis of variance supported the significant effect of breed (P = 0.01). No significant difference in bacterial community structure was detected by sampling method (P = 0.18). Linear discriminant analysis of effect size was used to identify OTUs that differ between breeds. Family level classification of most abundant differential OTUs identified OTUs from the bacterial families Lachnospiraceae, Veillonellaceae, Ruminococcaceae, and Fibrobacteraceae to be more predominant in Holstein compared to Jersey cows whereas an OTU from the family Prevotellaceae was more predominant in Jersey compared to Holstein cows. Overall, results suggest that the bacterial community between Holstein and Jersey cows differ and that esophageal tubing with collection of feed particles associated with the strainer provides an adequate sampling method for rumen bacterial community studies.

Keywords: Holstein cow, Jersey cow, rumen bacterial community composition