Evaluation of microbial communities associated with the liquid and solid phases of the rumen of cattle offered a diet of perennial ryegrass or white clover

Rumen microbiota plays an important role in animal productivity, methane production and health. Several different locations have been used to obtain rumen samples (i.e.,liquid-phase samples, solid-phase samples, buccal swabs) in previous studies. Here we assess differences in the rumen microbiota between solid- and liquid-phases of the rumen under differing dietary conditions (white clover vs. perennial ryegrass); there were 4 sample types: liquid-associated/grass (LG), solid-associated/grass (SG), liquid associated/clover (LC), and solid-associated/clover (SC). Four Holstein-Friesian cows were strip grazed on pure stands of perennial ryegrass or white clover in a change over design experiment with 3 periods (each lasting for 3 weeks). Solid- and liquid phase microbes were obtained following total rumen evacuation on the penultimate day of each period. DNA was extracted and multiplexed libraries sequenced using16S next generation sequencing (Illumina MiSeq). Demultiplexed sequences underwentquality control and taxonomic profiles were generated for each sample. Statisticalanalysis for the effects of diet and phase was conducted both overall [using nonmetricmultidimensional scaling (NMDS) and diversity indices] and for individual taxa.Separation of both diet and phase was observed NMDS, with significant effects of diet(P < 0.001) and phase (P < 0.001) being observed. Regardless of diet, Prevotella wasmost abundant in the liquid samples. When assessing differences between phases,the majority of statistically significant taxa (predominantly from Archaea and the orderClostridiales) were found at higher relative abundances in solid-phase samples. Diversity(Shannon Index) was lower in the liquid-phase samples, possibly because of the higherrelative abundance of Prevotella. A presence vs. absence approach, followed by Chisquaredtesting, was adopted. Differences between phases (LG vs. LC, LC vs. LG, SGvs. SC, and SC vs. SG) and differences between phases for the clover diet (LC vs.SC and SC vs. LC) were significant (P < 0.001); differences between phases for thegrass diet were non-significant. Sampling technique has a profound impact on reportedmicrobial communities, which must be taken into consideration, particularly as archaeamay be underestimated in the liquid-phase.