Abstract
Simple SummaryPrevotella is an abundant genus which plays an important role for lignocellulose digestion in goat rumen and is significant to the yield and quality of milk and meat in cows. In a previous study, we sequenced bacterial metagenome from Vietnamese native goat rumen to get 8.4 GB clean data and found very diverse genes related to lignocellulose degradation. However, due to the limitation in the metagenomic size, low amount of complete lignocellulase genes, and high bacterial diversity, further analysis was restricted. In this study, metagenomic deep sequencing was used to obtain 48.66 GB of reliable data, thus some lignocellulolytic enzymes were first seen and a picture of bacterial enzymes involved in lignocellulose digestion in the goat rumen was drawn. The loci for galactan-, xylan-, and arabinan-processing in Prevotella were observed for the first time. We confirm that Prevotella plays pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin conversion in the goat rumen. A gene coding endoxylanase was expressed in E. coli. The recombinant enzyme was tolerant with some salts, detergents, and had high activity, thus is a good candidate for lignocellulose processing and as an animal feed food additive to effectively improve xylooligosaccharide production.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.
Highlights
Microorganism composition in the rumen of ruminants is diverse and plays essential roles in the digestion of complex of fibrous substrates, mostly lignocellulose, into fermentable sugars [1,2]
By analysing of genes clusters in the eleven contigs, we found nine contigs related to hemicellulose degradation, all belonging to Prevotella, and two contig that contributed for cellulose degradation belonging to Bacteroides and Prevotella (Figure 5)
In the present study, using deep sequencing to sequence metagenomic DNA of bacteria in Vietnamese native goats’ rumen, we identified for the first time 10 kinds of enzymes coded by genes from bacteria of the goats’ rumen
Summary
Microorganism composition in the rumen of ruminants is diverse and plays essential roles in the digestion of complex of fibrous substrates, mostly lignocellulose, into fermentable sugars [1,2]. The sugars were fermented by bacteria to produce volatile fatty acids (VFA). VFAs are the major energy source (70%) for ruminants. The majority (90%) of VFAs are acetate, butyrate, and propionate that are absorbed into the blood through the rumen wall and immigrate into the liver. VFAs are converted into other energies for synthesis of, e.g., lipids, lipoproteins, and lactose, for body growth and development, pregnancy, and milk production [3]. The genus Prevotella is found to be effective in the digestion of xylans and pectins because it has gene clusters coding for many kinds of enzymes especially xylanase GH10, beta-xylosidase
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