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Derakhshani H, De Buck J, Mortier R, et al. The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis. Front Microbiol. 2016;7:426doi: 10.3389/fmicb.2016.00426.
Derakhshani, H., De Buck, J., Mortier, R., Barkema, H. W., Krause, D. O., & Khafipour, E. (2016). The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis. Frontiers in microbiology, 7426. https://doi.org/10.3389/fmicb.2016.00426
Derakhshani, Hooman, et al. "The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis." Frontiers in microbiology vol. 7 (2016): 426. doi: https://doi.org/10.3389/fmicb.2016.00426
Derakhshani H, De Buck J, Mortier R, Barkema HW, Krause DO, Khafipour E. The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis. Front Microbiol. 2016 Mar 31;7:426. doi: 10.3389/fmicb.2016.00426. eCollection 2016. PMID: 27065983; PMCID: PMC4814471.
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Front Microbiol. 2016 Mar 31;7:426. doi: 10.3389/fmicb.2016.00426. eCollection 2016.

The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis.

Frontiers in microbiology

Hooman Derakhshani, Jeroen De Buck, Rienske Mortier, Herman W Barkema, Denis O Krause, Ehsan Khafipour

Affiliations

  1. Department of Animal Science, University of Manitoba Winnipeg, MB, Canada.
  2. Department of Production Animal Health, University of Calgary Calgary, AB, Canada.
  3. Department of Animal Science, University of ManitobaWinnipeg, MB, Canada; Department of Medical Microbiology, University of ManitobaWinnipeg, MB, Canada.

PMID: 27065983 PMCID: PMC4814471 DOI: 10.3389/fmicb.2016.00426

Abstract

Current diagnostic tests for Johne's disease (JD), a chronic granulomatous inflammation of the gastrointestinal tract of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP), lack the sensitivity to identify infected animals at early (asymptomatic) stages of the disease. The objective was to determine the pattern of MAP-associated dysbiosis of intestinal microbiota as a potential biomarker for early detection of infected cattle. To that end, genomic DNA was extracted from ileal mucosa and fecal samples collected from 28 MAP-positive and five control calves. High-throughput Illumina sequencing of the V4 hypervariable region of the 16S rRNA gene was used for community profiling of ileal mucosa-associated (MAM) or fecal microbiota. The PERMANOVA analysis of unweighted UniFrac distances revealed distinct clustering of ileal MAM (P = 0.049) and fecal microbiota (P = 0.068) in MAP-infected vs. control cattle. Microbiota profile of MAP-infected animals was further investigated by linear discriminant analysis effective size (LEfSe); several bacterial taxa within the phylum Proteobacteria were overrepresented in ileal MAM of control calves. Moreover, based on reconstructed metagenomes (PICRUSt) of ileal MAM, functional pathways associated with MAP infection were inferred. Enrichment of lysine and histidine metabolism pathways, and underrepresentation of glutathione metabolism and leucine and isoleucine degradation pathways in MAP-infected calves suggested potential contributions of ileal MAM in development of intestinal inflammation. Finally, simultaneous overrepresentation of families Planococcaceae and Paraprevotellaceae, as well as underrepresentation of genera Faecalibacterium and Akkermansia in the fecal microbiota of infected cattle, served as potential biomarker for identifying infected cattle during subclinical stages of JD. Collectively, based on compositional and functional shifts in intestinal microbiota of infected cattle, we inferred that this dynamic network of microorganisms had an active role in intestinal homeostasis.

Keywords: Johne's disease (JD); Mycobacterium avium subspecies paratuberculosis (MAP); dysbiosis; gut inflammation; microbiota

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