Microbial biodiversity of the liquid fraction of rumen content from lactating cows

Abstract

Host and dietary interactions with the rumen microbiome can affect the efficacy of supplements, and their effect on the composition of the bacterial population is still unknown. A 16S rRNA metagenomic approach and Next-Generation Sequencing (NGS) technology were used to investigate the bacterial microbiome composition in the liquid fraction of the rumen content collected via stomach tubing. To investigate biodiversity, samples were taken from three groups of four lactating dairy cows given a supplement of either 50 g of potato protein (Ctrl group), or 50 g of lyophilized Saccharomyces cerevisiae (LY group) or 50 g of dried S. cerevisiae (DY group) in a potato protein support. Rumen samples were collected after 15 days of dietary treatments and milk production was similar between the three groups. Taxonomic distribution analysis revealed a prevalence of the Firmicutes phylum in all cows (79.76%) and a significantly (P < 0.05) higher presence of the genus Bacillus in the DY group. Volatile fattyacid concentration was not significantly different between groups, possibly because of relatively high inter-animal variability or limited effect of the treatments or both, and the correlation analysis with bacterial taxa showed significant associations, in particular between many Firmicutes genera and butyrate. Limited differences were observed between dietary treatments, but the lack of microbiome data before yeast administration does not allow to draw firm conclusions on the effect of dietary treatments.Keywords: rumen bacteria community, Saccharomyces cerevisiae, Next-Generation Sequencing, 16S rRNA, dairy cows Implications Next-Generation Sequencing technology offers the opportunity to gather information regarding the rumen microbiome by comparing repository databases of rumen bacteria 16S rRNA gene sequences generated through different experiments. The high extent of sequencing attained through this research provides valuable information on the microbial biodiversity of the liquid phase of the rumen and represents a contribution to research in rumen microbiology and dairy feed supplements. However, the effectiveness of yeast supplements to modify the rumen bacterial microbiome requires further investigation.

Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding

“…For example, an unclassified genus of Veillonellaceae was negatively correlated with propionate concentrations in lambs fed a linseed oil-supplemented diet [69]. Sandri et al reported that Veillonellaceae was negatively correlated with butyrate in lactating cows [70]. Furthermore, the acetate concentration was negatively related to Succiniclasticum in dairy cows fed high-grain diets [71], which was consistent with our findings in goats under indoor feeding.…”

Variations in methane yield and microbial community profiles in the rumen of dairy cows as they pass through stages of first lactation

“…The predominately negative correlations observed may indicate that these bacterial genera are using the SCFA or competing for nutrients with acetate, butyrate, and propionate producers. Although some studies have proposed roles for specific bacteria based on observed correlations (Sandri et al, 2014), it is difficult to draw conclusions based on correlations given the complex nature of the rumen microbial community and the lack of information concerning metabolic pathways employed by particular microbes. Furthermore, rumen fungi and ciliate protozoa also produce acetate, butyrate, and propionate during anaerobic digestion of feed (Martin et al, 2010).…”

Investigation of rumen metagenome in Italian Simmental and Italian Holstein cows using a whole-genome shotgun sequencing technique

“…In the present study, we sampled rumen contents from commercial farms and, although the rations were similar in terms of ingredients and contents of nutrients (Table 2), the different environments of the stable can have exerted some influence on rumen microbial communities. A considerable individual variability has been widely shown in rumen microbial profile (Ross et al 2012;Sandri et al 2014), independently from the diet and environment. On the other hand, Ross et al (2013) after repeated samples from the same cows taken several weeks apart, observed a high repeatability of microbiome composition within the animal.…”