Metagenomic insights into lignocellulose-degrading genes through Illumina-based <i>de novo</i> sequencing of the microbiome in Vietnamese native goats’ rumen

Abstract

The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats' rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes' modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.

Effects of Bacillus amyloliquefaciens and Bacillus pumilus on Rumen and Intestine Morphology and Microbiota in Weanling Jintang Black Goat

“…Adequate nutrients and a stable space environment are provided for the host for the microbiota in rumen and intestines, and the microorganisms contribute to nutrient absorption and digestion, as well as regulation of the host physiological functions. Recently, by developing the sequencing technology, the Illumina sequencing platform was utilized for the successful detection of the diversity of many animals digestive tract microbiota, including piglet, goat, and cow [ 17 , 18 , 19 ]. However, the precise roles of Bacillus in modulating the immune and microbiota response in goat rumen and intestines remain to be elucidated.…”

Some characters of bacterial cellulases in goats&apos; rumen elucidated by metagenomic DNA analysis and the role of fibronectin 3 module for endoglucanase function

“…In order to determine new cellulases for hydrolysis of cellulose biomass using modern technology, we sequenced the metagenomic DNA of bacteria in Vietnamese goats' rumen [11]. In total, 816 genes (297 complete genes) coding for cellulases were obtained.…”

“…In total, 816 genes (297 complete genes) coding for cellulases were obtained. The initial analysis has shown that the FN3 module was mainly found in the structure of beta-glucosidases (213 open reading frames [ORFs]) and endoglucanases (one ORF) structure while Ig module is only collocated in endoglucanases GH9 (30 ORFs) [11,12]. However modular structures and some characters such as pH, thermostablility of the putative enzymes containing FN3 and Ig were not illustrated.…”

Progress in Ameliorating Beneficial Characteristics of Microbial Cellulases by Genetic Engineering Approaches for Cellulose Saccharification

“…Metagenomics allows retrieval of genes encoding biocatalysts from culturable as well as non-cultural microbes. Many cellulase genes have been identified from environmental metagenomes ( Garg et al, 2016 ; Matsuzawa and Yaoi, 2016 ; Pandey et al, 2016 ; Zhou et al, 2016 ), hindgut contents of termites ( Duan et al, 2017 ; Tsegaye et al, 2018 ), rumen ( Ko et al, 2015 ; Song et al, 2016 ; Do et al, 2018 ), compost ( Lemos et al, 2017 ; Lee et al, 2018 ), oil reservoirs ( Lewin et al, 2017 ), and sludge from a biogas reactor ( Wei et al, 2015 ). Very few of them have, however, been characterized adequately ( Garg et al, 2016 ; Song et al, 2016 ; Lee et al, 2018 ).…”