Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Carbohydrate-Active enZYmes (CAZy), and HMMER database, and taxonomically classified by MEGAN. As a result, 65,554 genes encoding for 30 enzymes/proteins related to lignocellulose conversion were exploited, in which nine enzymes were seen for the first time in goat rumen. Prevotella was the most abundant genus, contributing 30% hemicellulases and 36% enzymes/proteins for lignocellulose pretreatment, and supporting 98.8% of feruloyl esterases and 71.7% acetylxylan esterases. In addition, 18 of the 22 most lignocellulose digesting- potential contigs belonged to Prevotella. Besides, Prevotella possessed many genes coding for amylolytic enzymes. One gene encoding for endoxylanase was successfully expressed in E. coli. The recombinant enzyme had high Vmax, was tolerant to some salts and detergents, worked better at pH 5.5–6.5, temperature 40–50 °C, and was capable to be used in practices. Based on these findings, we confirm that Prevotella plays a pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin digestion in the goat rumen.

We aimed to investigate the microbial diversity, mine lignocellulose-degrading enzymes/proteins, and analyze the domain structures of the mined enzymes/proteins in humus samples collected from the Cuc Phuong National Park, Vietnam. Using a high-throughput Illumina sequencer, 52 Gbs of microbial DNA were assembled in 2,611,883 contigs, from which 4,104,872 open reading frames (ORFs) were identified. Among the total microbiome analyzed, bacteria occupied 99.69%; the five ubiquitous bacterial phyla included Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Acidobacteria, which accounted for 92.59%. Proteobacteria (75.68%), the most dominant, was 5.77 folds higher than the second abundant phylum Bacteroidetes (13.11%). Considering the enzymes/proteins involved in lignocellulose degradation, 22,226 ORFs were obtained from the annotation analysis using a KEGG database. The estimated ratio of Proteobacteria/Bacteroidetes was approximately 1:1 for pretreatment and hemicellulases groups and 2.4:1 for cellulases. Furthermore, analysis of domain structures revealed their diversity in lignocellulose-degrading enzymes. CE and PL were two main families in pretreatment; GH1 and GH3-FN3 were the highest domains in the cellulase group, whereas GH2 and GH43 represented the hemicellulase group. These results validate that natural tropical forest soil could be considered as an important source to explore bacteria and novel enzymes/proteins for the degradation of lignocellulose.