Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

Abstract

gThe bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for ϳ1% and ϳ0.1% of the total non-rRNAs, respectively. The majority (ϳ98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus and Fibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the genera Ruminococcus, Prevotella, and Fibrobacter. Most (ϳ82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the genera Ruminococcus, Fibrobacter, and Prevotella are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen. In nature, the cow rumen represents a highly specialized bioreactor wherein plant cell wall polysaccharides (PCWPs) are efficiently deconstructed. The extraordinary efficiency results from the concerted action of various enzymes produced by rumen-resident bacteria, archaea, fungi, and protozoa. Three rumen bacteria, i.e., Ruminococcus flavefaciens, Ruminococcus albus, and Fibrobacter succinogenes, which can be isolated and cultivated in the laboratory, have been thought to serve a predominant role in the degradation of cellulosic PCWPs in this niche (1, 2). However, metagenomic quantitations based on 16S rRNA gene analysis indicate that these three species of bacteria account for only less than 5% of the total rumen microorganisms (3). In addition, Koike et al. estimated that ϳ77% of the rumen microorganisms attached to solid fibers are uncultured, as their 16S rRNA gene sequences share less than 97% similarity with those of known isolates (4).To bypass the cultivation step, metagenomic approaches involving the direct analysis of total DNA sequences have been extensively used to investigate the PCWP-degrading gastrointestinal microbes in a variety of herbivores, such as termite hindguts (5); cow (6-8), yak (9), and Svalbard reindeer (10) ...

Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals

“…Two SRA datasets were identified that contained reads with similarity to statoviruses that could be assembled into contigs. The first contig was from a Bos taurus rumen sample from Beijing, China (SRA accession SRR1604865) (Dai et al, 2015). The assembled contig was 1,875 nt in length with > 3.8x average coverage and the translated amino acid sequence shared ≤33% amino acid identity to the ORF1 sequences of statovirus A1, B1 and C1 and thus was named “statovirus D1” (Fig.…”

Gene cloning and expression of fungal lignocellulolytic enzymes from the rumen of gayal (<i>Bos frontalis</i>)

“…Enzymes of the GH1 family are found in the intestine of many animals (Dai et al, 2015;Wang et al, 2011), and the majority of bglucosidases belong to the GH1 and GH3 families (Henrissat et al, 1995), which are important components of the cellulolytic enzyme system. Hong et al (2006) have found that an enzyme with both b-glucosidase and bxylosidase activity showed a better cellulolytic efficiency.…”

Recent biomedical applications of bio-sourced materials

“…A large number of microorganisms have the ability to oxidize and decompose complex organic matter and certain inorganic substances, and convert these substances into simple substances, or convert toxic substances into non-toxic substances [96,100]. Xu et al investigated the feasibility of using a bio-electrochemical system integrated with a capacitor deionization-microbial electrolytic desalination tank (MCDC) to treat the actual shale gas-produced water [101].…”