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Archives of Microbiology

, Volume 201, Issue 10, pp 1385–1397 | Cite as

Understanding the alteration in rumen microbiome and CAZymes profile with diet and host through comparative metagenomic approach

  • Varsha Bohra
  • Nishant A. DafaleEmail author
  • Hemant J. Purohit
Original Paper

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 carbohydrate-active 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 

Notes

Acknowledgements

Miss Varsha Bohra thanks the Department of Science and Technology (DST) of India for awarding Junior Research Fellowship (JRF). The funding from DBT project G-1-2282 is gratefully acknowledged for carrying out the work. The authors are thankful to Nagpur Veterinary Hospital and Gourakshan Kendra, Nagpur, for providing rumen samples from the animals. The manuscript has been checked for plagiarism by Knowledge Resource Centre, CSIR-NEERI, Nagpur, India, and assigned KRC No.: CSIR-NEERI/KRC/2019/MARCH/EBGD/1.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

203_2019_1706_MOESM1_ESM.doc (1.4 mb)
Supplementary material 1 (DOC 1402 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Varsha Bohra
    • 1
  • Nishant A. Dafale
    • 1
    Email author
  • Hemant J. Purohit
    • 1
  1. 1.CSIR - National Environmental Engineering Research InstituteNagpurIndia

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