Metagenomic sequencing of rumen microorganisms of cattle fed a corn stover-based diet

Abstract Worldwide, there is a need to discover new microorganisms that efficiently degrade lignocellulosic complexes that would help to improve the digestibility of low-quality agricultural byproducts. The aim of the study was to evaluate the effects of a corn stover-based diet (CSD) on rumen bacteria. Ruminal fluid of 6 Holstein cows (595 ± 96 kg) was collected during two periods. During first period, animals were consuming a diet based on corn silage and oat hay (DB), mineral premix and water ad libitum (50:50, DM). In second period, animals were provided a CSD (100% DM), mineral premix and water ad libitum for 45 days. Ruminal fluid was collected through esophageal tube, filtered and stored at -80°C until DNA extraction. Rumen microorganisms were identified by sequencing the 16SrRNA gene using the Illumina Miseq platform and primers for V3 and V4 regions. Data were analyzed by QIIME 1.9. Analysis of variance was performed for a completely randomized design using the MIXED procedure of SAS 9.1. The taxonomic affiliation showed that both populations were mainly composed of Firmicutes, Bacteroidetes and Proteobacteria. The most abundant bacteria species in both diets were Ruminococcus flavefaciens, Prevotella copri, Prevotella ruminicola, Fibrobacter succinogenes, Bacillus coagulans, Bacteroides uniformis and Selenomonas ruminantium. Feeding a CSD, increased the relative abundance of Prevotella ruminicola (from 6.1 to 20.9%, P < 0.01), Streptococcus luteciae (from 0.05 to 0.78%, P < 0.01), Clostridium aminophilum (0.45 to 3.1%, P < 0.01), Selenomonas ruminantium (5.2 to 21.8%, P < 0.02) and Pantoea agglomerans (0.7 to 3.9%, P < 0.01) and decreased Propionibacterium acnes (0.7 to 0.1%, P < 0.02) and Bacteroides ovatus (0.9 to 0.1%, P < 0.01). Feeding cattle with a diet with a more lignified forage like CSD led to the proliferation of bacteria such as Prevotella ruminicula, Streptococcus luteciae, Clostridium aminophilum, Selenomonas ruminantium and Pantoea agglomerans.