Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals.
Authors: Whitfield-Cargile Canaan M, Cohen Noah D, Suchodolski Jan, Chaffin M Keith, McQueen Cole M, Arnold Carolyn E, Dowd Scot E, Blodgett Glenn P
Journal: PloS one
Summary
Rhodococcus equi pneumonia predominantly affects foals during their first months of life, a period coinciding with critical immune system development and microbiome establishment. Researchers hypothesised that reduced microbial diversity or altered faecal composition at 3 and 5 weeks of age might predispose foals to subsequent R. equi infection, comparing three groups: those developing clinical pneumonia, those with subclinical ultrasonographic evidence of pulmonary lesions, and unaffected controls. Analysis of 16S rRNA gene sequencing and metagenomic prediction revealed no significant differences in microbiota composition, diversity indices or functional gene abundance between groups at either sampling timepoint—a finding that argues against the microbiome as a determining factor in R. equi susceptibility during early life. The most notable microbiota shift occurred between the two sampling intervals and reflected the foals' dietary transition from milk to forage and concentrates rather than any predisposition to disease. Whilst microbiome immaturity likely contributes to neonatal susceptibility to R. equi, this work suggests that other factors—including specific immune responses, management practices or environmental pathogen exposure—warrant greater investigative focus when evaluating pneumonia risk in young foals.
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Practical Takeaways
- •Early fecal microbiome assessment cannot be used to predict which foals will develop R. equi pneumonia, so clinicians must rely on other risk factors and clinical vigilance
- •Microbiome diversity in neonatal foals does not appear to be a protective factor against R. equi infection during the period when foals are most susceptible
- •Management focus should remain on established prevention strategies rather than microbiome-based risk stratification at 3-5 weeks of age
Key Findings
- •Fecal microbiome composition and diversity at 3 and 5 weeks of age showed no significant differences between foals that subsequently developed R. equi pneumonia and those that remained unaffected
- •Predicted fecal metagenome analysis did not identify differences associated with susceptibility to subsequent R. equi pneumonia development
- •Significant microbiome differences were detected between the 3 and 5 week sampling intervals, reflecting dietary transition from milk to forage and concentrate