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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 diversity or richness of the fecal microbiota between time 1 and time 2 but the composition of the fecal microbiota is different between time 1 and time 2.A) Scatter dot plot of Shannon diversity index for time 1 (dots) and time 2 (squares). Horizontal line represents mean and error bars represent the standard deviation. There were no statistical differences between the groups. B) Scatter dot plot of Simpson diversity index for time 1 (dots) and time 2 (squares). Horizontal line represents mean and error bars represent the standard deviation. There were no statistical differences between the groups. C) Alpha rarefication curves for time 1 (red) and time 2 (blue) 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 time 1 (red) and time 2 (blue). There was obvious clustering of the time 1 samples and the time 2 samples.
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pone.0136586.g007: No differences in the diversity or richness of the fecal microbiota between time 1 and time 2 but the composition of the fecal microbiota is different between time 1 and time 2.A) Scatter dot plot of Shannon diversity index for time 1 (dots) and time 2 (squares). Horizontal line represents mean and error bars represent the standard deviation. There were no statistical differences between the groups. B) Scatter dot plot of Simpson diversity index for time 1 (dots) and time 2 (squares). Horizontal line represents mean and error bars represent the standard deviation. There were no statistical differences between the groups. C) Alpha rarefication curves for time 1 (red) and time 2 (blue) 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 time 1 (red) and time 2 (blue). There was obvious clustering of the time 1 samples and the time 2 samples.

Mentions: The distribution of the major (frequency > 1%) families of microbes present at time 1 and time 2 were plotted as pie charts (Fig 6). There were no differences in the diversity indices or richness calculated for horses at times 1 or 2 irrespective of health status (Fig 7A–7C). The PCoA plots of the first 3 principal coordinates based on the unweighted UniFrac distance metric revealed obvious visual clustering of the health groups by time (Fig 7D). ANOSIM revealed significant differences of both the unweighted Unifrac distance metric (R = 0.6945; P = 0.001) and weighted Unifrac distance metric (R = 0.2566; P = 0.001). In order to identify bacterial taxa that contributed to the difference between times, we performed SIMPER analysis at the levels of both the phyla and family. Mean change in abundance with time and percent contribution to differences in the Bray Curtis dissimilarity metric were tabulated (Table 1 for Phyla and S1 Table for Family). Mann-Whitney U tests on the proportion of OTUs per sample revealed many differences in the abundance of OTUs between time 1 and time 2 samples (S2 Table).


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 diversity or richness of the fecal microbiota between time 1 and time 2 but the composition of the fecal microbiota is different between time 1 and time 2.A) Scatter dot plot of Shannon diversity index for time 1 (dots) and time 2 (squares). Horizontal line represents mean and error bars represent the standard deviation. There were no statistical differences between the groups. B) Scatter dot plot of Simpson diversity index for time 1 (dots) and time 2 (squares). Horizontal line represents mean and error bars represent the standard deviation. There were no statistical differences between the groups. C) Alpha rarefication curves for time 1 (red) and time 2 (blue) 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 time 1 (red) and time 2 (blue). There was obvious clustering of the time 1 samples and the time 2 samples.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0136586.g007: No differences in the diversity or richness of the fecal microbiota between time 1 and time 2 but the composition of the fecal microbiota is different between time 1 and time 2.A) Scatter dot plot of Shannon diversity index for time 1 (dots) and time 2 (squares). Horizontal line represents mean and error bars represent the standard deviation. There were no statistical differences between the groups. B) Scatter dot plot of Simpson diversity index for time 1 (dots) and time 2 (squares). Horizontal line represents mean and error bars represent the standard deviation. There were no statistical differences between the groups. C) Alpha rarefication curves for time 1 (red) and time 2 (blue) 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 time 1 (red) and time 2 (blue). There was obvious clustering of the time 1 samples and the time 2 samples.
Mentions: The distribution of the major (frequency > 1%) families of microbes present at time 1 and time 2 were plotted as pie charts (Fig 6). There were no differences in the diversity indices or richness calculated for horses at times 1 or 2 irrespective of health status (Fig 7A–7C). The PCoA plots of the first 3 principal coordinates based on the unweighted UniFrac distance metric revealed obvious visual clustering of the health groups by time (Fig 7D). ANOSIM revealed significant differences of both the unweighted Unifrac distance metric (R = 0.6945; P = 0.001) and weighted Unifrac distance metric (R = 0.2566; P = 0.001). In order to identify bacterial taxa that contributed to the difference between times, we performed SIMPER analysis at the levels of both the phyla and family. Mean change in abundance with time and percent contribution to differences in the Bray Curtis dissimilarity metric were tabulated (Table 1 for Phyla and S1 Table for Family). Mann-Whitney U tests on the proportion of OTUs per sample revealed many differences in the abundance of OTUs between time 1 and time 2 samples (S2 Table).

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