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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: 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.

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

No differences in the fecal microbiota among the health groups at time 2.A) Scatter dot plot of Shannon diversity index for all health groups; healthy (dots), subclinical (squares), and clinical (triangles) at time 2. Horizontal lines represent the mean for each group and error bars represent the standard deviation. There were no statistical differences among the groups. B) Scatter dot plot of Simpson diversity index for all health groups; healthy (dots), subclinical (squares), and clinical (triangles) at time 2. Horizontal lines represent the mean for each group and error bars represent the standard deviation. There were no statistical differences among the groups. C) Alpha rarefication curves for each of the health groups; healthy (red), clinical (blue), subclinical (orange) at time 2 showing numbers of observed species at each sampling depth on the y-axis and sequences/sample on the x-axis up to 10,800 sequences/sample. Error bars represent standard deviations of each group at the specified sampling depth. D) Principal coordinate analysis of unweighted Unifrac distance metric for all heath groups; healthy (red), clinical (blue), subclinical (orange) at time 2. There were no differences among the groups.
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pone.0136586.g004: No differences in the fecal microbiota among the health groups at time 2.A) Scatter dot plot of Shannon diversity index for all health groups; healthy (dots), subclinical (squares), and clinical (triangles) at time 2. Horizontal lines represent the mean for each group and error bars represent the standard deviation. There were no statistical differences among the groups. B) Scatter dot plot of Simpson diversity index for all health groups; healthy (dots), subclinical (squares), and clinical (triangles) at time 2. Horizontal lines represent the mean for each group and error bars represent the standard deviation. There were no statistical differences among the groups. C) Alpha rarefication curves for each of the health groups; healthy (red), clinical (blue), subclinical (orange) at time 2 showing numbers of observed species at each sampling depth on the y-axis and sequences/sample on the x-axis up to 10,800 sequences/sample. Error bars represent standard deviations of each group at the specified sampling depth. D) Principal coordinate analysis of unweighted Unifrac distance metric for all heath groups; healthy (red), clinical (blue), subclinical (orange) at time 2. There were no differences among the groups.

Mentions: There were no differences in the diversity indices or richness calculated for the health groups at time 2 (Fig 4A–4C). Moreover, principal coordinate analysis (PCoA) plots based on the unweighted UniFrac distance metric revealed no apparent clustering of the health groups at time 2 (Fig 4D). The unweighted Unifrac distance metric was small but significantly different than 0 using ANOSIM analysis of the distance metric at time 2 (R = 0.072; P = 0.005). When using the weighted distance metric, however, the distance metric was small and there was no significant difference among the groups at time 2 (R = 0.0303; P = 0.083). Kruskal-Wallis tests revealed no significant differences in abundances of any OTUs among the health groups at time 2 (data not shown).


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)

No differences in the fecal microbiota among the health groups at time 2.A) Scatter dot plot of Shannon diversity index for all health groups; healthy (dots), subclinical (squares), and clinical (triangles) at time 2. Horizontal lines represent the mean for each group and error bars represent the standard deviation. There were no statistical differences among the groups. B) Scatter dot plot of Simpson diversity index for all health groups; healthy (dots), subclinical (squares), and clinical (triangles) at time 2. Horizontal lines represent the mean for each group and error bars represent the standard deviation. There were no statistical differences among the groups. C) Alpha rarefication curves for each of the health groups; healthy (red), clinical (blue), subclinical (orange) at time 2 showing numbers of observed species at each sampling depth on the y-axis and sequences/sample on the x-axis up to 10,800 sequences/sample. Error bars represent standard deviations of each group at the specified sampling depth. D) Principal coordinate analysis of unweighted Unifrac distance metric for all heath groups; healthy (red), clinical (blue), subclinical (orange) at time 2. There were no differences among the groups.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0136586.g004: No differences in the fecal microbiota among the health groups at time 2.A) Scatter dot plot of Shannon diversity index for all health groups; healthy (dots), subclinical (squares), and clinical (triangles) at time 2. Horizontal lines represent the mean for each group and error bars represent the standard deviation. There were no statistical differences among the groups. B) Scatter dot plot of Simpson diversity index for all health groups; healthy (dots), subclinical (squares), and clinical (triangles) at time 2. Horizontal lines represent the mean for each group and error bars represent the standard deviation. There were no statistical differences among the groups. C) Alpha rarefication curves for each of the health groups; healthy (red), clinical (blue), subclinical (orange) at time 2 showing numbers of observed species at each sampling depth on the y-axis and sequences/sample on the x-axis up to 10,800 sequences/sample. Error bars represent standard deviations of each group at the specified sampling depth. D) Principal coordinate analysis of unweighted Unifrac distance metric for all heath groups; healthy (red), clinical (blue), subclinical (orange) at time 2. There were no differences among the groups.
Mentions: There were no differences in the diversity indices or richness calculated for the health groups at time 2 (Fig 4A–4C). Moreover, principal coordinate analysis (PCoA) plots based on the unweighted UniFrac distance metric revealed no apparent clustering of the health groups at time 2 (Fig 4D). The unweighted Unifrac distance metric was small but significantly different than 0 using ANOSIM analysis of the distance metric at time 2 (R = 0.072; P = 0.005). When using the weighted distance metric, however, the distance metric was small and there was no significant difference among the groups at time 2 (R = 0.0303; P = 0.083). Kruskal-Wallis tests revealed no significant differences in abundances of any OTUs among the health groups at time 2 (data not shown).

Bottom Line: 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.

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