Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis)

Abstract

Background: The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids. In the present study, metagenomic approach was applied to elucidate the buffalo rumen microbiome of Jaffrabadi buffalo adapted to varied dietary treatments with the hypothesis that the microbial diversity and subsequent in the functional capacity will alter with diet change and enhance our knowledge of effect of microbe on host physiology. Eight adult animals were gradually adapted to an increasing roughage diet (4 animals each with green and dry roughage) containing 50:50 (J1), 75:25 (J2) and 100:0 (J3) roughage to concentrate proportion for 6 weeks. Metagenomic sequences of solid (fiber adherent microbiota) and liquid (fiber free microbiota) fractions obtained using Ion Torrent PGM platform were analyzed using MG-RAST server and CAZymes approach.

Results: Taxonomic analysis revealed that Bacteroidetes was the most abundant phylum followed by Firmicutes, Fibrobacter and Proteobacteria. Functional analysis revealed protein (25-30 %) and carbohydrate (15-20 %) metabolism as the dominant categories. Principal component analysis demonstrated that roughage proportion, fraction of rumen and type of forage affected rumen microbiome at taxonomic as well as functional level. Rumen metabolite study revealed that rumen fluid nitrogen content reduced in high roughage diet fed animals and pathway analysis showed reduction in the genes coding enzymes involved in methanogenesis pathway. CAZyme annotation revealed the abundance of genes encoding glycoside hydrolases (GH), with the GH3 family most abundant followed by GH2 and GH13 in all samples.

Conclusions: Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission. CAZyme analysis indicated the importance of microbiome in feed component digestion for fulfilling energy requirements of the host. The findings help determine the role of rumen microbes in plant polysaccharide breakdown and in developing strategies to maximize productivity in ruminants.

Fig. 1

a Taxonomic distribution of bacterial phyla based on predicted proteins and rRNA in the samples [Treatment vs Abundance in percentage] b Statistical analysis using STAMP based on genus level taxonomic assignments between treatments c Statistical analysis using STAMP based on genus level taxonomic assignments between liquid and solid fraction (*indicates p < 0.05, **indicate p < 0.01, ***indicate p < 0.001)

Fig. 2

Firmicutes/Bacteroidetes ratio during the three treatments

Fig. 3

a Statistical analysis using STAMP based on functional assignments at subsystem level 1 between treatments (p < 0.05) b Statistical analysis using STAMP based on functional assignments at subsystem level 1 between treatments (p < 0.05) between liquid and solid fraction (p < 0.05) c Distribution of Protein Metabolism subsystem at level 2 between treatments, diet and fractions [Sample type vs Abundance of categories in percentage] d Distribution of Carbohydrate Metabolism subsystem at level 2 between treatments, diet and fractions Metabolism [Sample type vs Abundance of categories in percentage]

Fig. 4

Principal component analysis based on taxonomic (phylum level) and functional distribution in each sample using PAST

Fig. 5

Glycosyl Hydrolase family distribution (Pooled de novo assembly of 4 animals maintained under same diet treatment was considered)

Fig. 6

Taxonomic distribution at genus level of microbes encoding genes for predicted CAZyme [Treatment vs Abundance in percentage] (a) Green roughage fed animals (b) Dry roughage fed animals