Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing

Abstract

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.

Comparison of rumen bacterial communities between yaks (Bos grunniens) and Qaidam cattle (Bos taurus) fed a low protein diet with different energy levels

“…Prevotella was the most dominant genus, which is in agreement with previous studies in steers (Xin et al, 2019), dairy cows (Wei et al, 2021), goats (Dao et al, 2021), and sheep (Huang et al, 2022). In the present study, Prevotella contained a number of metabolic versatile species, which secrete enzymes to degrade protein, starch, peptides, hemicellulose, and pectin into VFAs and amino acids (Stevenson and Weimer, 2007;Dao et al, 2021).…”

The gastrointestinal microbiome of browsing goats (Capra hircus)

“…Indeed, members of this genus were typically observed in higher numbers in stomachs (26.7–49.9%) than in other regions of the GIT of ruminants [ 25 , 37 , 39 ]. Different members of the genus Prevotella are known for their capability to degrade non-cellulolytic polysaccharides (hemicelluloses, mainly xylans, pectin, starch, lignans) and proteins, although some cellulolytic enzymes may also be produced [ 45 – 47 ]. Prevotella dominance in rumen bacterial communities is thought to be related to their genetic and functional diversity [ 48 , 49 ], the reason why they may be indispensable players in the transformation of the ingested feed by ruminants.…”

Prevotella: A Key Player in Ruminal Metabolism

“…Prevotella is ubiquitous. For example, it is found in various body environments (oral cavity, urogenital and gastrointestinal tracts) [ 3 , 6 , 7 , 8 , 9 , 10 ] and across multiple species of animals, including humans, livestock, rodents and insects [ 1 , 2 , 3 , 4 , 11 , 12 , 13 , 14 , 15 , 16 ]. In the phylum Bacteroidetes, the phylogenetic and biological distinction between the genera Bacteroides and Prevotella is rather unclear [ 17 , 18 ], and this explains apparent controversies found in the early literature.…”