Limits...
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

Phylogenetic comparisons of ileal mucosa-associated (MAM) and fecal microbiota in control and MAP-infected animals. LEfSe was used to determine differentially abundant genera in (A) fecal microbiota, and (B) ileal MAM of MAP-infected and control animals. Color code represents the class of treatment (red indicates variables that were significantly enriched in response to MAP infection, whereas green indicates variables that were significantly enriched in the control group).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4814471&req=5

Figure 4: Phylogenetic comparisons of ileal mucosa-associated (MAM) and fecal microbiota in control and MAP-infected animals. LEfSe was used to determine differentially abundant genera in (A) fecal microbiota, and (B) ileal MAM of MAP-infected and control animals. Color code represents the class of treatment (red indicates variables that were significantly enriched in response to MAP infection, whereas green indicates variables that were significantly enriched in the control group).

Mentions: Statistical analyses regarding relative abundances of bacterial taxa at different phylogenetic levels between MAP-infected and control calves were performed using Linear Discriminant Analysis Effective Size (LEfSe; Segata et al., 2011), software principally developed to discover metagenomics biomarkers. This included the non-parametric factorial Kruskal–Wallis (KW) sum rank test (Kruskal and Wallis, 1952) to test whether the values (the relative abundances of the OTUs summarized at the genus level) in different classes (MAP-infected vs. control) were differentially distributed, then the pairwise Wilcoxon test was used to determine whether all pairwise comparisons between subclasses (experimental years 1 and 2) within different classes agreed with the class level trend. Finally, linear discriminant analysis (LDA) was done to estimate the effect size of each differentially abundant feature. The threshold on the logarithmic LDA score for discriminative features was set at 2.0, so that features with at least 2.0 log-fold changes were considered significant (Figures 4, 7). The relative abundances of the genera showing the highest LDA scores (revealed by LEfSe analysis) were entered into a logistic regression model and their ability to discriminate group classification was evaluated using area under the receiver operator characteristic (ROC) curve (Figure 5; Delong et al., 1988).


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)

Phylogenetic comparisons of ileal mucosa-associated (MAM) and fecal microbiota in control and MAP-infected animals. LEfSe was used to determine differentially abundant genera in (A) fecal microbiota, and (B) ileal MAM of MAP-infected and control animals. Color code represents the class of treatment (red indicates variables that were significantly enriched in response to MAP infection, whereas green indicates variables that were significantly enriched in the control group).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 4: Phylogenetic comparisons of ileal mucosa-associated (MAM) and fecal microbiota in control and MAP-infected animals. LEfSe was used to determine differentially abundant genera in (A) fecal microbiota, and (B) ileal MAM of MAP-infected and control animals. Color code represents the class of treatment (red indicates variables that were significantly enriched in response to MAP infection, whereas green indicates variables that were significantly enriched in the control group).
Mentions: Statistical analyses regarding relative abundances of bacterial taxa at different phylogenetic levels between MAP-infected and control calves were performed using Linear Discriminant Analysis Effective Size (LEfSe; Segata et al., 2011), software principally developed to discover metagenomics biomarkers. This included the non-parametric factorial Kruskal–Wallis (KW) sum rank test (Kruskal and Wallis, 1952) to test whether the values (the relative abundances of the OTUs summarized at the genus level) in different classes (MAP-infected vs. control) were differentially distributed, then the pairwise Wilcoxon test was used to determine whether all pairwise comparisons between subclasses (experimental years 1 and 2) within different classes agreed with the class level trend. Finally, linear discriminant analysis (LDA) was done to estimate the effect size of each differentially abundant feature. The threshold on the logarithmic LDA score for discriminative features was set at 2.0, so that features with at least 2.0 log-fold changes were considered significant (Figures 4, 7). The relative abundances of the genera showing the highest LDA scores (revealed by LEfSe analysis) were entered into a logistic regression model and their ability to discriminate group classification was evaluated using area under the receiver operator characteristic (ROC) curve (Figure 5; Delong et al., 1988).

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