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Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals.

Whitfield-Cargile CM, Cohen ND, Suchodolski J, Chaffin MK, McQueen CM, Arnold CE, Dowd SE, Blodgett GP - PLoS ONE (2015)

Bottom Line: We thus hypothesized that varying composition or reduced diversity of the intestinal microbiome of neonatal foals would contribute to increased susceptibility of their developing R. equi pneumonia.No significant differences were found among groups at either sampling time, indicating absence of evidence of an influence of composition or diversity of the fecal microbiome, or predicted fecal metagenome, on susceptibility to subsequent R. equi pneumonia.A marked and significant difference identified between a relatively short interval of time appeared to reflect ongoing adaptation to transition from a milk diet to a diet including available forage (including hay) and access to concentrate fed to the mare.

View Article: PubMed Central - PubMed

Affiliation: Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America.

ABSTRACT
In equids, susceptibility to disease caused by Rhodococcus equi occurs almost exclusively in foals. This distribution might be attributable to the age-dependent maturation of immunity following birth undergone by mammalian neonates that renders them especially susceptible to infectious diseases. Expansion and diversification of the neonatal microbiome contribute to development of immunity in the gut. Moreover, diminished diversity of the gastrointestinal microbiome has been associated with risk of infections and immune dysregulation. We thus hypothesized that varying composition or reduced diversity of the intestinal microbiome of neonatal foals would contribute to increased susceptibility of their developing R. equi pneumonia. The composition and diversity indices of the fecal microbiota at 3 and 5 weeks of age were compared among 3 groups of foals: 1) foals that subsequently developed R. equi pneumonia after sampling; 2) foals that subsequently developed ultrasonographic evidence of pulmonary abscess formation or consolidation but not clinical signs (subclinical group); and, 3) foals that developed neither clinical signs nor ultrasonographic evidence of pulmonary abscess formation or consolidation. No significant differences were found among groups at either sampling time, indicating absence of evidence of an influence of composition or diversity of the fecal microbiome, or predicted fecal metagenome, on susceptibility to subsequent R. equi pneumonia. A marked and significant difference identified between a relatively short interval of time appeared to reflect ongoing adaptation to transition from a milk diet to a diet including available forage (including hay) and access to concentrate fed to the mare.

No MeSH data available.


Related in: MedlinePlus

The composition of the predicted metagenome changes between time 1 and time 2.(A) Principal coordinate analysis of the Bray Curtis dissimilarity metric of the predicted metagenome for time 1 (red) and time 2 (blue). There was obvious visual clustering of the predicted metagenome at time 1 and time 2. B) Pie chart showing the predicted functional pathways that were significantly (Mann Whitney U test FDR P value < 0.05) decreased >2 fold between time 1 and time 2. The figure legend accompanying the figure explains which pathways are represented by which colors. C) Pie chart showing the predicted functional pathways that were significantly (Mann Whitney U test FDR P value < 0.05) increased >2 fold between time 1 and time 2. The figure legend accompanying the figure explains which pathways are represented by which colors.
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pone.0136586.g008: The composition of the predicted metagenome changes between time 1 and time 2.(A) Principal coordinate analysis of the Bray Curtis dissimilarity metric of the predicted metagenome for time 1 (red) and time 2 (blue). There was obvious visual clustering of the predicted metagenome at time 1 and time 2. B) Pie chart showing the predicted functional pathways that were significantly (Mann Whitney U test FDR P value < 0.05) decreased >2 fold between time 1 and time 2. The figure legend accompanying the figure explains which pathways are represented by which colors. C) Pie chart showing the predicted functional pathways that were significantly (Mann Whitney U test FDR P value < 0.05) increased >2 fold between time 1 and time 2. The figure legend accompanying the figure explains which pathways are represented by which colors.

Mentions: As expected from the observed time-dependent fecal microbiota differences, there also were time-dependent differences in the predicted metagenome revealed by PCoA of the Bray Curtis dissimilarity metric (Fig 8A). ANOSIM results calculated on the Bray Curtis dissimilarity metric revealed significant differences of the predicted metagenome at time 1 and time 2 (R = 0.2376; P = 0.001). There were 367 KEGG orthologies that were significantly (adjusted P < 0.05) decreased more than 2-fold between time 1 and time 2, and 486 KEGG orthologs were significantly (adjusted P < 0.05) increased by more than 2-fold between time 1 and time 2 (S3 Table). The different pathways to which these KEGG orthologies belong are represented as pie charts (Fig 8B and 8C). Approximately half (13) of the top 25 predicted functional pathways that were decreased by 2-fold or more between 3 and 5 weeks were related to metabolism. Moreover, the majority of these decreased metabolic pathways were related to metabolism of simple sugars (sucrose, glucose, fructose, and mannose) and amino acids (tyrosine, arginine, and proline). Predicted functional pathways that were increased more than 2-fold over the same time period were evenly distributed among metabolic pathways, transcriptional pathways, and a myriad of unclassified or unknown pathways.


Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals.

Whitfield-Cargile CM, Cohen ND, Suchodolski J, Chaffin MK, McQueen CM, Arnold CE, Dowd SE, Blodgett GP - PLoS ONE (2015)

The composition of the predicted metagenome changes between time 1 and time 2.(A) Principal coordinate analysis of the Bray Curtis dissimilarity metric of the predicted metagenome for time 1 (red) and time 2 (blue). There was obvious visual clustering of the predicted metagenome at time 1 and time 2. B) Pie chart showing the predicted functional pathways that were significantly (Mann Whitney U test FDR P value < 0.05) decreased >2 fold between time 1 and time 2. The figure legend accompanying the figure explains which pathways are represented by which colors. C) Pie chart showing the predicted functional pathways that were significantly (Mann Whitney U test FDR P value < 0.05) increased >2 fold between time 1 and time 2. The figure legend accompanying the figure explains which pathways are represented by which colors.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4549325&req=5

pone.0136586.g008: The composition of the predicted metagenome changes between time 1 and time 2.(A) Principal coordinate analysis of the Bray Curtis dissimilarity metric of the predicted metagenome for time 1 (red) and time 2 (blue). There was obvious visual clustering of the predicted metagenome at time 1 and time 2. B) Pie chart showing the predicted functional pathways that were significantly (Mann Whitney U test FDR P value < 0.05) decreased >2 fold between time 1 and time 2. The figure legend accompanying the figure explains which pathways are represented by which colors. C) Pie chart showing the predicted functional pathways that were significantly (Mann Whitney U test FDR P value < 0.05) increased >2 fold between time 1 and time 2. The figure legend accompanying the figure explains which pathways are represented by which colors.
Mentions: As expected from the observed time-dependent fecal microbiota differences, there also were time-dependent differences in the predicted metagenome revealed by PCoA of the Bray Curtis dissimilarity metric (Fig 8A). ANOSIM results calculated on the Bray Curtis dissimilarity metric revealed significant differences of the predicted metagenome at time 1 and time 2 (R = 0.2376; P = 0.001). There were 367 KEGG orthologies that were significantly (adjusted P < 0.05) decreased more than 2-fold between time 1 and time 2, and 486 KEGG orthologs were significantly (adjusted P < 0.05) increased by more than 2-fold between time 1 and time 2 (S3 Table). The different pathways to which these KEGG orthologies belong are represented as pie charts (Fig 8B and 8C). Approximately half (13) of the top 25 predicted functional pathways that were decreased by 2-fold or more between 3 and 5 weeks were related to metabolism. Moreover, the majority of these decreased metabolic pathways were related to metabolism of simple sugars (sucrose, glucose, fructose, and mannose) and amino acids (tyrosine, arginine, and proline). Predicted functional pathways that were increased more than 2-fold over the same time period were evenly distributed among metabolic pathways, transcriptional pathways, and a myriad of unclassified or unknown pathways.

Bottom Line: We thus hypothesized that varying composition or reduced diversity of the intestinal microbiome of neonatal foals would contribute to increased susceptibility of their developing R. equi pneumonia.No significant differences were found among groups at either sampling time, indicating absence of evidence of an influence of composition or diversity of the fecal microbiome, or predicted fecal metagenome, on susceptibility to subsequent R. equi pneumonia.A marked and significant difference identified between a relatively short interval of time appeared to reflect ongoing adaptation to transition from a milk diet to a diet including available forage (including hay) and access to concentrate fed to the mare.

View Article: PubMed Central - PubMed

Affiliation: Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America.

ABSTRACT
In equids, susceptibility to disease caused by Rhodococcus equi occurs almost exclusively in foals. This distribution might be attributable to the age-dependent maturation of immunity following birth undergone by mammalian neonates that renders them especially susceptible to infectious diseases. Expansion and diversification of the neonatal microbiome contribute to development of immunity in the gut. Moreover, diminished diversity of the gastrointestinal microbiome has been associated with risk of infections and immune dysregulation. We thus hypothesized that varying composition or reduced diversity of the intestinal microbiome of neonatal foals would contribute to increased susceptibility of their developing R. equi pneumonia. The composition and diversity indices of the fecal microbiota at 3 and 5 weeks of age were compared among 3 groups of foals: 1) foals that subsequently developed R. equi pneumonia after sampling; 2) foals that subsequently developed ultrasonographic evidence of pulmonary abscess formation or consolidation but not clinical signs (subclinical group); and, 3) foals that developed neither clinical signs nor ultrasonographic evidence of pulmonary abscess formation or consolidation. No significant differences were found among groups at either sampling time, indicating absence of evidence of an influence of composition or diversity of the fecal microbiome, or predicted fecal metagenome, on susceptibility to subsequent R. equi pneumonia. A marked and significant difference identified between a relatively short interval of time appeared to reflect ongoing adaptation to transition from a milk diet to a diet including available forage (including hay) and access to concentrate fed to the mare.

No MeSH data available.


Related in: MedlinePlus