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MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant

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Abstract

The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.

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Data Availability

Sequencing data is submitted in Sequence Read Archive at NCBI and can be accessed as a part of BioProject PRJNA603439 with SRA accession numbers SRR10987805-SRR10987900.

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Acknowledgements

The authors are thankful to the staff at Livestock Research Station, Navsari Agricultural University for their help and support in maintenance of animals and sample collection.

Funding

This study was funded by the Indian Council of Agricultural Research (ICAR), New Delhi, India under the Niche area of Excellence program entitled “Metagenomic Analysis of Ruminal Microbes” [10/(2)/2011-ecd date 21/10/2011 (AAU#203020)]. The funding agency had no role in sample collection, conducting experiment, data analysis and manuscript writing.

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  1. Ankit T. Hinsu and Ramesh J. Pandit have equally contributed to the manuscript.

Authors and Affiliations

  1. Department of Animal Genetics & Breeding, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India

    Ankit T. Hinsu & Avani B. Patel

  2. Department of Animal Biotechnology, College of Veterinary Sciences & A.H, Anand Agricultural University, Anand, Gujarat, India

    Ramesh J. Pandit, Jalpa R. Thakkar, Ravi K. Shah, Subhash J. Jakhesara, Prakash G. Koringa & Chaitanya G. Joshi

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  1. Ankit T. Hinsu
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Contributions

ATH and RKS were involved in sample collection. ATH, ABP, RJP and JRT were involved in processing of samples, extraction of nucleic acids and its sequencing. ATH and RJP did the data analysis and manuscript writing with inputs from CGJ. SJJ, PGK and CGJ conceptualised the study, acquired the funding and corrected the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Chaitanya G. Joshi.

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Present study was conducted with the prior approval of the Institutional Animal Ethics Committee (IAEC) of Veterinary College, Anand Agricultural University (No. AAU/GVC/CPCSEA-IAEC/108/2013 dated 05/10/2013). All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted.

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The animals used in the study are part of Livestock Research Station of Navsari Agricultural University and hence, no consent needs to be taken from owner.

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Hinsu, A.T., Patel, A.B., Pandit, R.J. et al. MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant. Mol Biol Rep 47, 5101–5114 (2020). https://doi.org/10.1007/s11033-020-05581-6

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