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

Differentiation of functional metagenomes of ileal mucosa (MAM) and fecal microbiota in control and MAP-infected calves. A Statistical differences between KEGG pathways (explored at Levels 1–3, indicated as L1–L3) of ileal MAM metagenomes were evaluated by LEfSe, a metagenome analysis approach which performed the linear discriminant analysis following the Wilcoxon Mann–Whitney test to assess effect size of each differentially abundant variable. The length of the horizontal bars indicated log-fold changes for each variable. Color code represents the class of treatment (red indicates variables that were significantly altered in response to MAP infection, whereas green indicates variables that were significantly associated with the control group).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 7: Differentiation of functional metagenomes of ileal mucosa (MAM) and fecal microbiota in control and MAP-infected calves. A Statistical differences between KEGG pathways (explored at Levels 1–3, indicated as L1–L3) of ileal MAM metagenomes were evaluated by LEfSe, a metagenome analysis approach which performed the linear discriminant analysis following the Wilcoxon Mann–Whitney test to assess effect size of each differentially abundant variable. The length of the horizontal bars indicated log-fold changes for each variable. Color code represents the class of treatment (red indicates variables that were significantly altered in response to MAP infection, whereas green indicates variables that were significantly associated with the control group).

Mentions: The reference-based OTU picking resulted in 80.03% of the sequencing reads being mapped to the Greengenes database. Consequently, a high proportion of MAM were utilized for metagenomic predictions. Major KEGG pathways including valine, leucine, and isoleucine degradation, as well as glutathione and tryptophan metabolism exhibited more than 2.5 log-fold increase within the ileal MAM of control calves, whereas the proportion of fatty acid, lysine, thiamine, and histidine metabolism pathways were enriched in the ileal MAM of the MAP-infected group (Figure 7).


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)

Differentiation of functional metagenomes of ileal mucosa (MAM) and fecal microbiota in control and MAP-infected calves. A Statistical differences between KEGG pathways (explored at Levels 1–3, indicated as L1–L3) of ileal MAM metagenomes were evaluated by LEfSe, a metagenome analysis approach which performed the linear discriminant analysis following the Wilcoxon Mann–Whitney test to assess effect size of each differentially abundant variable. The length of the horizontal bars indicated log-fold changes for each variable. Color code represents the class of treatment (red indicates variables that were significantly altered in response to MAP infection, whereas green indicates variables that were significantly associated with the control group).
© Copyright Policy
Related In: Results  -  Collection

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

Figure 7: Differentiation of functional metagenomes of ileal mucosa (MAM) and fecal microbiota in control and MAP-infected calves. A Statistical differences between KEGG pathways (explored at Levels 1–3, indicated as L1–L3) of ileal MAM metagenomes were evaluated by LEfSe, a metagenome analysis approach which performed the linear discriminant analysis following the Wilcoxon Mann–Whitney test to assess effect size of each differentially abundant variable. The length of the horizontal bars indicated log-fold changes for each variable. Color code represents the class of treatment (red indicates variables that were significantly altered in response to MAP infection, whereas green indicates variables that were significantly associated with the control group).
Mentions: The reference-based OTU picking resulted in 80.03% of the sequencing reads being mapped to the Greengenes database. Consequently, a high proportion of MAM were utilized for metagenomic predictions. Major KEGG pathways including valine, leucine, and isoleucine degradation, as well as glutathione and tryptophan metabolism exhibited more than 2.5 log-fold increase within the ileal MAM of control calves, whereas the proportion of fatty acid, lysine, thiamine, and histidine metabolism pathways were enriched in the ileal MAM of the MAP-infected group (Figure 7).

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