Exploring the Diversity of Active Ureolytic Bacteria in the Rumen by Comparison of cDNA and gDNA

• Main Authors: Sijia Liu, Nan Zheng, Shengguo Zhao, Jiaqi Wang
• Format: Article
• Language: English
• Published: MDPI AG 2020-11-01
• Series: Animals
• Subjects: rumen; ureolytic bacteria; active; diversity
• Online Access: https://www.mdpi.com/2076-2615/10/11/2162

In this study we revealed the diversity of active ureolytic bacteria in the rumen by compared <i>ureC</i> amplicons between gDNA and cDNA. Rumen fluid was collected from four Holstein dairy cows with rumen fistulas at 0, 2, and 6 h after morning feeding. Total microbial gDNA and RNA were isolated, and the RNA was reverse-transcribed into cDNA. The <i>ureC</i> gene amplicons of gDNA and cDNA were produced and sequenced by MiSeq. These results revealed that the sampling time had no significant difference on the alphssa and beta diversity indices of the ureolytic bacteria. The Shannon diversity of the <i>ureC</i> gene for cDNA was greater than that for gDNA (<i>p</i> < 0.05). There were significant difference in the beta diversity of ureolytic bacteria between gDNA and cDNA (<i>p</i> < 0.01), which indicates a shift in the community of active ureolytic bacteria. Approximately 67% of <i>ureC</i> sequences from cDNA could not be confidently classified at the genus level. The active ureolytic bacteria were mainly from <i>Helicobacter</i>, <i>Herbaspirillum</i>, <i>Clostridium</i>, <i>Paenibacillus</i>, <i>Synechococcus</i>, and <i>Sphingobacterium</i> sp. Changes in the operational taxonomic units revealed that the top abundant <i>ureC</i> genes were mostly consistent between gDNA and cDNA, and most differences occurred in the <i>ureC</i> genes with lower abundances. These results revealed distinct ureolytic bacteria community profiles based on gDNA and cDNA. The dominant ureolytic bacteria had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance.