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About: BACKGROUND: MicroRNAs play key roles in host-pathogen-interactions and disease pathogenesis. Our aim was to characterize the differentially expressed miRNAs in the blood cells of diseased (Brucellosis-positive, Johne’s disease-positive) and healthy- water buffaloes. The pooled small-RNA samples of each group were sequenced on Ion Torrent Personal Genome Machine (PGM) sequencer and the data were analyzed for differential expression. RESULTS: Here we identified 274 known miRNAs with bovine homologs and 36 novel mature-star miRNAs from the sequnces of small RNA libraries. Overall 195 miRNAs were common to all the three groups. Certain miRNAs such as bta-miR-21-5p, −26a, −29a/b, −30d − 103, − 140, − 150, − 191, − 374, − 1434-5p,-1260b, − 2484 and let-7 members were abundantly expressed in diseased groups. Bta-miR-1434-5p, − 188, −200c were up-regulated (> 1.5 folds) while bta-miR-27a-5p, −34b and -2285x were down-regulated (> 100 folds) in Brucellosis group. In Johne’s Disease group, only 3 miRNAs (bta-miR-1434-5p, − 2340 and − 2484) were up-regulated (> 1.5 folds). The functional classification of miRNA target genes into gene ontology (GO) terms indicated their involvement in innate immunity and cellular process of disease pathogenesis. Expression profile of four differentially expressed miRNAs (bta-miR-9-5p, − 677, − 331-3p and − 2440) and eight predicted target-genes were validated through reverse transcriptase qPCR. CONCLUSION: This study provides a valuable frame of reference for elucidation of regulatory roles of miRNAs associated with disease pathogenesis in water buffaloes as well as identification of miRNA biomarkers for disease diagnosis and treatment.

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