Responses in the rumen microbiome of Bos taurus and indicus steers fed a low-quality rice straw diet and supplemented protein.

Bos indicus typically perform better than Bos taurus when consuming a low-quality diet; however, the response to supplementation is generally greater in B. taurus. The underlying mechanisms supporting these responses have not been fully elucidated. Characterization of differences in rumen prokaryotic populations and their functional role in the two subspecies may provide additional insight. Ten cannulated steers (5 Angus and 5 Brahman) were used in concurrent 5 × 5 Latin squares. Animals were offered ad libitum access to rice straw (4.7% CP). Treatments consisted of an unsupplemented control diet and two levels (50 or 120 mg N/kg BW) of isonitrogenous supplements (30% CP), that were either high (H; 74%) or low (L; 26%) in undegradable intake protein. Rumen samples were collected at 0 and 4 h postfeeding and separated into liquid and solid fractions. Rumen bacterial taxa were sequenced utilizing a Roche 454 platform based on the 16s rRNA gene. At 97% sequence similarity, 97,826 operational taxonomic units were identified, which included 24 phyla, 108 families, and 255 genera. Analysis included SAS PROC mixed model, QIIME, and PICRUSt. Across all samples, Bacteroidetes and Firmicutes accounted for 65% and 28% of total bacterial abundance, respectively. The families Prevotellaceae (P = 0.05) and Ruminococcaceae (P = 0.004) and the genera Prevotellaceae (family; P = 0.003) within the phyla Bacteroidetes differed significantly in relative abundance with added protein when compared to the control. Consistent differences in the relative abundance of family and genus taxa between B. indicus and B. taurus suggest roles the symbiotic rumen microbiome may have in the capacity of B. indicus to utilize low-quality forage over a range of supplement types and levels including (Prevotella, Ruminococcus [family], Sphingobacteriaceae [family], Bacteroidales [order], Pontibacter, Bacteroides, Succiclasticum, Barnesiella, and Xylanibacter). Overall bacterial community diversity differences across parameters were limited. Rice straw is recalcitrant to bacterial digestion because of high levels of silica in the epidermis making this straw more resistant to bacterial attachment. Thus, this analysis represents the bacterial diversity and function of the rumen under conditions depleted CP, recalcitrant fiber matrix and restricted digestibility which appear to limit the microbial population to those capable of attaching and digesting complexed structural carbohydrates, resulting in reduced plasticity, and more evenness in diversity across parameters.