Metagenomic analysis of bacterial community structure and diversity of lignocellulolytic bacteria in Vietnamese native goat rumen

Abstract

ObjectiveIn a previous study, analysis of Illumina sequenced metagenomic DNA data of bacteria in Vietnamese goats’ rumen showed a high diversity of putative lignocellulolytic genes. In this study, taxonomy speculation of microbial community and lignocellulolytic bacteria population in the rumen was conducted to elucidate a role of bacterial structure for effective degradation of plant materials.MethodsThe metagenomic data had been subjected into Basic Local Alignment Search Tool (BLASTX) algorithm and the National Center for Biotechnology Information non-redundant sequence database. Here the BLASTX hits were further processed by the Metagenome Analyzer program to statistically analyze the abundance of taxa.ResultsMicrobial community in the rumen is defined by dominance of Bacteroidetes compared to Firmicutes. The ratio of Firmicutes versus Bacteroidetes was 0.36:1. An abundance of Synergistetes was uniquely identified in the goat microbiome may be formed by host genotype. With regard to bacterial lignocellulose degraders, the ratio of lignocellulolytic genes affiliated with Firmicutes compared to the genes linked to Bacteroidetes was 0.11:1, in which the genes encoding putative hemicellulases, carbohydrate esterases, polysaccharide lyases originated from Bacteroidetes were 14 to 20 times higher than from Firmicutes. Firmicutes seem to possess more cellulose hydrolysis capacity showing a Firmicutes/Bacteroidetes ratio of 0.35:1. Analysis of lignocellulolytic potential degraders shows that four species belonged to Bacteroidetes phylum, while two species belonged to Firmicutes phylum harbouring at least 12 different catalytic domains for all lignocellulose pretreatment, cellulose, as well as hemicellulose saccharification.ConclusionBased on these findings, we speculate that increasing the members of Bacteroidetes to keep a low ratio of Firmicutes versus Bacteroidetes in goat rumen has resulted most likely in an increased lignocellulose digestion.

High‐production dairy cattle exhibit different rumen and fecal bacterial community and rumen metabolite profile than low‐production cattle

“…It was known that the fiber content in the rumen was far higher than that in the hindgut; thus, we inferred the extra Bacteroidetes present in rumen fluid may be enriched for cellulolytic bacteria. Analogous differences were observed in a recent study on goat (Do et al., ). The study indicated that increasing the members of Bacteroidetes to keep low ratio of Firmicutes versus Bacteroidetes in goat rumen resulted an increased lignocellulose digestion.…”

“…It was known that the fiber content in the rumen was far higher than that in the hindgut; thus, we inferred the extra Bacteroidetes present in rumen fluid may be enriched for cellulolytic bacteria. Analogous differences were observed in a recent study on goat (Do et al, 2018).…”

Evaluation of the digestibility of steam-exploded wheat straw by ruminal fermentation, sugar yield and microbial structurein vitro

“…45,49 Reports showed that the genera Butyrivibrio and Clostridium belong to the phylum Firmicutes and these genera were associated with oligosaccharide-degrading and bre-degrading processes; 47,50 the genus Clostridium could produce abundant cellulases in the rumen. 42 Therefore, the elevated relative abundance of Butyrivibrio and Clostridium in the TRT group revealed that SE promoted the colonization of brolytic bacteria. Given that wheat straw might consist low content of starch in TRT group, while starch was a basic nutrient for the growth of Succiniclasticum, 51 the abundance of the Succiniclasticum genus significantly decreased in the TRT group.…”

“…This difference in the relative abundance changes of Firmicutes and Bacteroidetes was most likely due to SE treatment could increase the digestibility of lignocellulose, while the Firmicutes contain more microorganisms that could digest lignocellulose than the Bacteroidetes. 42 In addition, Bacteroidetes performed great capability of digesting small organic molecules. 43 In the present study, eighteen genera that accounted for more than 0.1% of the total sequences were identied.…”

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

“…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.…”