Seasonal changes in the digesta-adherent rumen bacterial communities of dairy cattle grazing pasture

The complex microbiota that resides within the rumen is responsible for the break-down of plant fibre. Most studies examining the ecology of this important microbiome only offer a ‘snapshot’ in time. We monitored the diversity of rumen bacteria in four dairy cows grazing pasture over five consecutive seasons using denaturing gradient gel electrophoresis (DGGE) and high throughput pyrosequencing of bacterial 16S rRNA genes. Bacteria adhering to the digesta were compared to those that were free-living or only loosely-associated with the digesta. 16S rRNA gene sequencing showed a high level of bacterial diversity, totalling 1539 operational taxonomic units (OTUs, grouped at 96% sequence similarity) across all samples, and ranging from 653 to 926 OTUs per individual sample. DGGE and sequence analysis showed that, overall, the bacterial communities were broadly similar in different animals and in the two rumen fractions (adherent vs free-living/loosely associated). The adherent bacterial community was strongly dominated by members of Firmicutes (82.1%), followed by Bacteroidetes (11.8%). This community differed between the seasons, returning close to that observed in the same season one year later. These seasonal differences were only small, but were statistically significant (p < 0.001), and were probably due to seasonal differences in the diet. These results demonstrate a general invariability of the ruminal bacterial community structure in these grazing dairy cattle.