Ruminal bacterial community structure of dairy cows fed conventional and reduced-fat dried distillers grains with solubles
Four lactating, ruminally cannulated Holstein cows with (mean ± SD) 98 ± 11 DIM and 603 ± 52 kg BW were used in a Latin square design to test the effects of feeding regular dried distillers grains with solubles (DDGS) or reduced-fat DDGS (RF-DDGS) combined with rumen inert fat (RIF, as Ca-salts of long chain fatty acids) on ruminal bacterial community structure using a DNA pyrosequencing approach. Cows were housed in a tie-stall barn, fed once daily, and milked twice daily. In each 21-d period, cows were randomly assigned to 1 of 4 dietary treatments (values expressed on a DM basis): control diet (CON) was a conventional dairy ration (no corn ethanol by-products); a second diet (DG) contained 30% DDGS; a third diet (RF) contained 30% LF-DDGS and; a fourth diet (COMBO) contained 30% LF-DDGS supplemented with 1.9% RIF. Ruminal digesta was collected at 0, 8 and 23 h post-feeding on d 21 of each period and was immediately frozen (-20°C) for later analysis of the bacterial community. The rumen bacterial community was evaluated from frozen samples using the Roche 454 pyrosequencing platform. The sequences generated were analyzed using established MOTHUR and QIIME (Quantitative Insights Into Microbial Ecology) pipelines. Diet did not affect bacterial community composition at phylum level. The most abundant phyla were Firmicutes (46 ± 4.78%) and Bacteroidetes (51 ± 4.87%). The phylum TM7 accounted for 2.25 ± 0.41%. The Tenericutes, SR1, and Spirochaetes phyla were grouped as “Others” and accounted for 0.58 ± 0.10%. Time post-feeding had an effect (P= 0.02) on phyla distribution; the proportion of Firmicutes decreased from 52 to 39 ± 4% by 9 h post-feeding and increased to 46 ± 4% by 23 h; conversely Bacteroidetes increased from 45 to 58 ± 4% at 9 h post-feeding and decreased to 51 ± 4% by 23 h post-feeding. The results from this experiment demonstrate that phyla distribution is relatively stable across diets; nonetheless diurnal patterns in ruminal bacterial phyla relative to time post-feeding were observed. To our knowledge, this is the first study in dairy cattle that utilizes high throughput sequencing to analyze bacterial community structure in order to evaluate diurnal variation of the rumen bacterial community.
Keywords: microbial community, bacteria, sequencing