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

Derakhshani H, De Buck J, Mortier R, Barkema HW, Krause DO, Khafipour E - Front Microbiol (2016)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Science, University of Manitoba Winnipeg, MB, Canada.

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.

No MeSH data available.


Related in: MedlinePlus

Spearman's correlation coefficient analysis. The correlation matrix was based on the relationship of the abundant ileal mucosa-associated bacterial genera (>0.1% of community) with the severity of macroscopic and histological lesions. The strength of the correlation between each pair of variables is indicated by the size and color intensity of the squares. A color code of dark blue indicates a positive correlation coefficient close to +1, whereas dark red indicates a negative correlation coefficient close to –1. All pairwise correlations with a P < 0.05 were considered significant and indicated by “*”. The last row of the matrix was included to explore the correlation between the proportion of genus Mycobacterium and other abundant members of the mucosa-associated microbiota (MAM).
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Figure 6: Spearman's correlation coefficient analysis. The correlation matrix was based on the relationship of the abundant ileal mucosa-associated bacterial genera (>0.1% of community) with the severity of macroscopic and histological lesions. The strength of the correlation between each pair of variables is indicated by the size and color intensity of the squares. A color code of dark blue indicates a positive correlation coefficient close to +1, whereas dark red indicates a negative correlation coefficient close to –1. All pairwise correlations with a P < 0.05 were considered significant and indicated by “*”. The last row of the matrix was included to explore the correlation between the proportion of genus Mycobacterium and other abundant members of the mucosa-associated microbiota (MAM).

Mentions: There were significant correlations between the ileal MAM and occurrence of macroscopic and histological lesions. Within the p. Firmicutes, members of the g. Clostridium (Spearman's ρ = +0.48 and P = 0.008) and Turicibacter (Spearman's ρ = +0.46 and P = 0.012), and f. Peptostreptococcaceae (Spearman's ρ = +0.42 and P < 0.022) had strong positive correlations with severity of histological lesions, whereas g. Pseudomonas (within p. Proteobacteria) were negatively correlated (Spearman's ρ = −0.38 and P = 0.041) with severity. The g. Lysinibacillus (p. Firmicutes) were the only member of the ileal MAM positively correlated (Spearman's ρ = +0.42 and P = 0.023) with occurrence and severity of macroscopic lesions. Exploring co-occurrence of the g. Mycobacterium with other abundant members of the ileal MAM also suggested a strong negative correlation between members of this genus and those of the g. Streptococcus (p. Firmicutes; Figure 6).


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

Derakhshani H, De Buck J, Mortier R, Barkema HW, Krause DO, Khafipour E - Front Microbiol (2016)

Spearman's correlation coefficient analysis. The correlation matrix was based on the relationship of the abundant ileal mucosa-associated bacterial genera (>0.1% of community) with the severity of macroscopic and histological lesions. The strength of the correlation between each pair of variables is indicated by the size and color intensity of the squares. A color code of dark blue indicates a positive correlation coefficient close to +1, whereas dark red indicates a negative correlation coefficient close to –1. All pairwise correlations with a P < 0.05 were considered significant and indicated by “*”. The last row of the matrix was included to explore the correlation between the proportion of genus Mycobacterium and other abundant members of the mucosa-associated microbiota (MAM).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814471&req=5

Figure 6: Spearman's correlation coefficient analysis. The correlation matrix was based on the relationship of the abundant ileal mucosa-associated bacterial genera (>0.1% of community) with the severity of macroscopic and histological lesions. The strength of the correlation between each pair of variables is indicated by the size and color intensity of the squares. A color code of dark blue indicates a positive correlation coefficient close to +1, whereas dark red indicates a negative correlation coefficient close to –1. All pairwise correlations with a P < 0.05 were considered significant and indicated by “*”. The last row of the matrix was included to explore the correlation between the proportion of genus Mycobacterium and other abundant members of the mucosa-associated microbiota (MAM).
Mentions: There were significant correlations between the ileal MAM and occurrence of macroscopic and histological lesions. Within the p. Firmicutes, members of the g. Clostridium (Spearman's ρ = +0.48 and P = 0.008) and Turicibacter (Spearman's ρ = +0.46 and P = 0.012), and f. Peptostreptococcaceae (Spearman's ρ = +0.42 and P < 0.022) had strong positive correlations with severity of histological lesions, whereas g. Pseudomonas (within p. Proteobacteria) were negatively correlated (Spearman's ρ = −0.38 and P = 0.041) with severity. The g. Lysinibacillus (p. Firmicutes) were the only member of the ileal MAM positively correlated (Spearman's ρ = +0.42 and P = 0.023) with occurrence and severity of macroscopic lesions. Exploring co-occurrence of the g. Mycobacterium with other abundant members of the ileal MAM also suggested a strong negative correlation between members of this genus and those of the g. Streptococcus (p. Firmicutes; Figure 6).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal Science, University of Manitoba Winnipeg, MB, Canada.

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.

No MeSH data available.


Related in: MedlinePlus