Rumen Bacterial Community Composition in Holstein and Jersey Cows Is Different under Same Dietary Condition and Is Not Affected by Sampling Method

Abstract

The rumen microbial community in dairy cows plays a critical role in efficient milk production. However, there is a lack of data comparing the composition of the rumen bacterial community of the main dairy breeds. This study utilizes 16S rRNA gene sequencing to describe the rumen bacterial community composition in Holstein and Jersey cows fed the same diet by sampling the rumen microbiota via the rumen cannula (Holstein cows) or esophageal tubing (both Holstein and Jersey cows). After collection of the rumen sample via esophageal tubing, particles attached to the strainer were added to the sample to ensure representative sampling of both the liquid and solid fraction of the rumen contents. Alpha diversity metrics, Chao1 and observed OTUs estimates, displayed higher (P = 0.02) bacterial richness in Holstein compared to Jersey cows and no difference (P > 0.70) in bacterial community richness due to sampling method. The principal coordinate analysis displayed distinct clustering of bacterial communities by breed suggesting that Holstein and Jersey cows harbor different rumen bacterial communities. Family level classification of most abundant (>1%) differential OTUs displayed that OTUs from the bacterial families Lachnospiraceae and p-2534-18B5 to be predominant in Holstein cows compared to Jersey cows. Additionally, OTUs belonging to family Prevotellaceae were differentially abundant in the two breeds. Overall, the results from this study 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 a representative rumen sample similar to a sample collected via the rumen cannula. Thus, in future studies esophageal tubing with addition of retained particles can be used to collect rumen samples reducing the cost of cannulation and increasing the number of animals used in microbiome investigations, thus increasing the statistical power of rumen microbial community evaluations.

Effect of partially replacing a barley-based concentrate with flaxseed-based products on the rumen bacterial population of lactating Holstein dairy cows

“…The amplicon library was subjected to high‐throughput DNA sequencing at the Department of Animal Science of University of Nebraska‐Lincoln according to the protocol utilized by Paz et al . () and Xie et al . ().…”

“…() and Paz et al . (). The PCR reactions were performed in 20 μ l volumes and contained 0·5 U of Terra DNA polymerase (Clontech Laboratories, Mountain view, CA), 200 nmol l −1 of each primer, 50 ng of nucleic acid template or nontemplate control, 10 μ l of Terra PCR buffer and 6·5 μ l of PCR water.…”

“…; Paz et al . ; Xie et al . ) according to manufacturer's instructions at the Department of Animal Science of University of Nebraska‐Lincoln.…”

“…The resulting amplicons from targeted hypervariable region have been shown to be effective for describing the rumen bacterial communities (Paz et al . ; Xie et al . ).…”

The Type of Forage Substrate Preparation Included as Substrate in a RUSITEC System Affects the Ruminal Microbiota and Fermentation Characteristics

“…Reducing methane (CH 4 ) emissions from anthropogenic activities is of considerable interest since enteric fermentation from ruminants accounts for 25% of the 40% derived from agriculture (Olivier et al, 1999; Steinfeld et al, 2006). Ruminants are considered economically important due to their capacity to digest low-quality forages (Flint, 1997) and their ability to convert these substrates into energy is largely dependent on the rumen microbiota (i.e., bacteria, anaerobic fungi, protozoa, and methanogenic archaea) which converts indigestible plant material into usable energy for the host.…”