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

Nathani NM, Patel AK, Mootapally CS, Reddy B, Shah SV, Lunagaria PM, Kothari RK, Joshi CG - BMC Genomics (2015)

Bottom Line: The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids.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.Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India. neelam.nathani@yahoo.com.

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.

No MeSH data available.


Related in: MedlinePlus

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]
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Fig3: 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]

Mentions: Functional analysis at level 1 using the SEED database in MG-RAST revealed that the highest coding sequences were present for the protein metabolism followed by carbohydrate metabolism category. At level 1, about ten categories including secondary metabolite; nitrogen metabolism; DNA metabolism; protein metabolism; carbohydrates; amino acids and derivatives; sulfur metabolism; cofactors, motility and Chemotaxis; and miscellaneous were observed to be significantly different between the liquid and solid fractions (Fig. 3a). Among these, the abundance of all categories was more in the solid fraction except the carbohydrate and protein metabolism which was higher in the liquid portion, which clearly indicated the difference in the microbial diversity of both the fractions. Three of the categories viz. carbohydrates; amino acids and its derivatives; and miscellaneous differed significantly across the J1, J2 and J3 dietary treatments, wherein the coding sequences related to the Carbohydrate subsystem increased with the increase in roughage concentration (Fig. 3b).Fig. 3


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

Nathani NM, Patel AK, Mootapally CS, Reddy B, Shah SV, Lunagaria PM, Kothari RK, Joshi CG - BMC Genomics (2015)

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]
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696265&req=5

Fig3: 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]
Mentions: Functional analysis at level 1 using the SEED database in MG-RAST revealed that the highest coding sequences were present for the protein metabolism followed by carbohydrate metabolism category. At level 1, about ten categories including secondary metabolite; nitrogen metabolism; DNA metabolism; protein metabolism; carbohydrates; amino acids and derivatives; sulfur metabolism; cofactors, motility and Chemotaxis; and miscellaneous were observed to be significantly different between the liquid and solid fractions (Fig. 3a). Among these, the abundance of all categories was more in the solid fraction except the carbohydrate and protein metabolism which was higher in the liquid portion, which clearly indicated the difference in the microbial diversity of both the fractions. Three of the categories viz. carbohydrates; amino acids and its derivatives; and miscellaneous differed significantly across the J1, J2 and J3 dietary treatments, wherein the coding sequences related to the Carbohydrate subsystem increased with the increase in roughage concentration (Fig. 3b).Fig. 3

Bottom Line: The rumen microbiota functions as an effective system for conversion of dietary feed to microbial proteins and volatile fatty acids.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.Results reveals that high roughage diet feed improved microbial protein synthesis and reduces methane emission.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand, Gujarat, 388 001, India. neelam.nathani@yahoo.com.

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.

No MeSH data available.


Related in: MedlinePlus