Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic
- PDF / 1,551,834 Bytes
- 13 Pages / 595.276 x 790.866 pts Page_size
- 102 Downloads / 165 Views
ORIGINAL PAPER
Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach Varsha Bohra1 · Nishant A. Dafale1 · Hemant J. Purohit1 Received: 27 May 2019 / Revised: 2 July 2019 / Accepted: 11 July 2019 © Springer-Verlag GmbH Germany, part of Springer Nature 2019
Abstract Rumen microbial community harbors a distinct genetic reservoir of potent carbohydrate-active enzymes (CAZyme) that functions efficiently for the deconstruction of plant biomass. Based on this premise, metagenomics approach was applied to characterize the rumen microbial community and identify carbohydrate-active genes of Bos taurus (cow) and Bubalus bubalis (buffalo) fed on green or dry roughage. Metadata was generated from the samples: green roughage-fed cow (NDC_GR), buffalo (NDB_GR) and dry roughage-fed cow (NDC_DR), buffalo (NDB_DR). Phylogenetic analysis revealed the dominance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria and Fibrobacter in all the four samples, covering 90–96% of the total bacterial population. On finer resolution, higher abundance of bacterial genera Fibrobacter, Bacteroides, Clostridium, Prevotella and Ruminococcus involved in plant biomass hydrolysis was observed in NDB_DR. Functional annotation using dbCAN annotation algorithm identified 28.13%, 8.08% 10.93% and 12.53% of the total contigs as putatively carbohydrateactive against NDC_GR, NDB_GR, NDC_DR and NDB_DR, respectively. Additional profiling of CAZymes revealed an over representation and diversity of putative glycoside hydrolases (GHs) in the animals fed on dry roughage with substantial enrichments of genes encoding GHs from families GH2, GH3, GH13 and GH43. GHs of families GH45, GH12, GH113, GH128, GH54 and GH27 were observed exclusively in NDB_DR metagenome. A higher abundance of cellulases, hemicellulases, debranching and oligosaccharide hydrolyzing enzymes was revealed in NDB_DR metagenome. Accordingly, it can be concluded that buffalo rumen microbiome are more efficient in plant biomass hydrolysis. The present study provides a deep understanding of the shifts in microbial community and plant polysaccharide deconstructing capabilities of rumen microbiome in response to changes in the feed type and host animal. Activity-specific microbial consortia procured from these animals can be used further for efficient plant biomass hydrolysis. The study also establishes the utility of rumen microbiome as a unique resource for mining diverse lignocellulolytic enzymes. Keywords Glycoside hydrolase · MG-RAST · dbCAN · CAZyme · Microbial community · Biomass hydrolysis
Introduction
Communicated by Erko Stackebrandt. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00203-019-01706-z) contains supplementary material, which is available to authorized users. * Nishant A. Dafale [email protected] 1
CSIR - National Environmental Engineering Research Institute, Nagpur, India
The rumen chamber in ruminant digestive tract has evolved into
Data Loading...
