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Background   Mycobacterium avium  subsp.  paratuberculosis  (MAP), the etiologic agent of Johne’s disease is spread between cattle via the fecal-oral route, yet the functional changes in the salivary gland associated with infection remain uncharacterized. In this study, we hypothesized that experimental challenge with MAP would induce stable changes in gene expression patterns in the salivary gland that may shed light on the mucosal immune response as well as the regional variation in immune capacity of this extensive gland. Holstein-Friesian cattle were euthanized 33 months’ post oral challenge with MAP strain  CIT003  and both the parotid and mandibular salivary glands were collected from healthy control ( n  = 5) and MAP exposed cattle ( n  = 5) for histopathological and transcriptomic analysis.    Results  A total of 205, 21, 61, and 135 genes were significantly differentially expressed between control and MAP exposed cattle in dorsal mandibular (M1), ventral mandibular (M2), dorsal parotid (P1) and ventral parotid salivary glands (P2), respectively. Expression profiles varied between the structurally divergent parotid and mandibular gland sections which was also reflected in the enriched biological pathways identified. Changes in gene expression associated with MAP exposure were detected with significantly elevated expression of  BoLA DR-ALPHA ,  BOLA-DRB3  and complement factors in MAP exposed cattle. In contrast, reduced expression of genes such as polymeric immunoglobin receptor ( PIGR ),  TNFSF13 , and the antimicrobial genes lactoferrin ( LF ) and lactoperoxidase ( LPO ) was detected in MAP exposed animals.    Conclusions  This first analysis of the transcriptomic profile of salivary glands in cattle adds an important layer to our understanding of salivary gland immune function. Transcriptomic changes associated with MAP exposure have been identified including reduced LF and LPO. These critical antimicrobial and immunoregulatory proteins are known to be secreted into saliva and their downregulation may contribute to disease susceptibility. Future work will focus on the validation of their expression levels in saliva from additional cattle of known infection status as a potential strategy to augment disease diagnosis.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5845-4) contains supplementary material, which is available to authorized users.

Characterization of the bovine salivary gland transcriptome associated with Mycobacterium avium subsp. paratuberculosis experimental challenge