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Journal of veterinary internal medicine2026; 40(4); aalag137; doi: 10.1093/jvimsj/aalag137

Clinical and microbiota alterations in performance horses undergoing long-distance transport.

Abstract: Transport-associated pneumonia contributes substantially to morbidity, impaired welfare, and economic loss in high-performance horses and may be associated with alterations in the respiratory microbiota. Objective: Examine the effect of long-distance transport on the respiratory microbiota and correlate changes in microbiota diversity and composition with systemic and airway inflammation. Methods: Seventeen client-owned performance horses transported from New England to Florida under optimized trailering conditions, and 12 non-traveling horses. Methods: Physical examination, blood testing, nasopharyngeal wash, endoscopy, tracheal aspirates, and thoracic ultrasonography were performed 48 h before, and 24 and 72 h after transport (T1-T3). Upper and lower respiratory microbiota were characterized using high-throughput 16S rRNA sequencing and correlated with clinical variables using constrained ordination. Transport effects were evaluated using repeated measures analysis of variance (ANOVA). Results: Cortisol concentrations decreased post-transport (P = .02), whereas ultrasound scores (P = .01) and serum amyloid A concentrations (P = .03) increased from T1 to T3. Timepoint explained a small but significant portion of microbiota variability (P < .001). Upper and lower airway microbiota differed, with the lower airway showing more β diversity (lower stability; P < .001). Together, timepoint and ultrasound scores explained 19% and 10%, respectively, of nasal and tracheal bacterial microbiota variability. Operational taxonomic units with the highest fit to timepoint and ultrasound were enriched for plant-associated bacterial taxa, mainly Hyphomicrobiales. Conclusions: Even under standardized, optimized transport conditions, respiratory microbiota alterations occurred in healthy, athletic horses, correlating with ultrasonographic evidence of pulmonary inflammation. Inclusion of the fungal mycobiome may further improve our understanding of transport-associated respiratory disease.
© The Author(s) 2026. Published by Oxford University Press on behalf of the American College of Veterinary Internal Medicine.
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Publication Date: 2026-07-14 PubMed ID: 42442368PubMed Central: PMC13362966DOI: 10.1093/jvimsj/aalag137Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

  • This study investigates how long-distance transport affects the respiratory microbiota and inflammation in high-performance horses, potentially contributing to transport-associated pneumonia.
  • It examines changes in respiratory bacterial communities and inflammation markers before and after transport under optimized conditions.

Background and Importance

  • Transport-associated pneumonia is a significant health problem in performance horses, causing illness, welfare issues, and economic losses.
  • Previous research suggests that alterations in the respiratory microbiota may play a role in the development of pneumonia during transport.
  • This study aims to clarify how long-distance transport alters the respiratory microbiota and whether these changes are linked to inflammation and clinical signs of respiratory disease.

Study Design and Methods

  • Subjects: Seventeen client-owned performance horses were transported from New England to Florida, and 12 horses served as non-transport control subjects.
  • Transport conditions: Horses underwent transport under optimized trailer conditions designed to reduce stress and disease risk.
  • Sample collection: Measurements were taken at three time points:
    • 48 hours before transport (T1)
    • 24 hours after transport (T2)
    • 72 hours after transport (T3)
  • Clinical assessments included:
    • Physical examination
    • Blood testing (including cortisol and serum amyloid A levels)
    • Nasopharyngeal wash (upper airway sampling)
    • Endoscopy
    • Tracheal aspirates (lower airway sampling)
    • Thoracic ultrasonography to detect lung inflammation
  • Microbiota analysis:
    • 16S rRNA gene sequencing characterized bacterial communities in both upper and lower respiratory tracts.
    • Statistical analyses, including constrained ordination and repeated measures ANOVA, evaluated the relationship between microbiota changes and clinical variables over time.

Key Findings

  • Inflammation markers and clinical changes:
    • Cortisol levels decreased after transport, indicating a possible reduction in acute stress response.
    • Ultrasound scores, which reflect pulmonary inflammation, increased after transport, suggesting lung involvement.
    • Serum amyloid A, an acute phase protein indicating systemic inflammation, also increased post-transport.
  • Microbiota dynamics:
    • Time after transport explained a small but statistically significant amount of variation in respiratory microbiota composition, meaning transport influenced bacterial communities.
    • Upper (nasal) and lower (tracheal) airway microbiota were distinctly different, with the lower airway microbiota exhibiting higher beta diversity, indicating less stability in this region.
    • The combination of time and ultrasound scores explained 19% of nasal and 10% of tracheal bacterial variability, linking microbiota changes to inflammation severity.
    • Specific bacterial taxa associated with plant material (mainly Hyphomicrobiales) increased following transport, which could relate to environmental exposure during transit or altered airway conditions.

Conclusions and Implications

  • Even under carefully controlled and optimized transport conditions, healthy athletic horses experienced changes in their respiratory microbiota after long-distance transport.
  • These microbiota shifts correlated with ultrasonographic findings of pulmonary inflammation, implicating microbiota alterations as a component of transport-associated respiratory disease.
  • The study suggests that monitoring both clinical signs and microbiota changes could improve detection and prevention of transport-associated pneumonia.
  • Future research including analysis of fungal communities (mycobiome) is recommended to build a more comprehensive understanding of respiratory microbiota and the pathogenesis of transport-associated respiratory diseases in horses.

Cite This Article

APA
Mahalingam-Dhingra A, Bedenice D, da Silva DRR, Mazan M, Hall T, Tenney W, Widmer G. (2026). Clinical and microbiota alterations in performance horses undergoing long-distance transport. J Vet Intern Med, 40(4), aalag137. https://doi.org/10.1093/jvimsj/aalag137

Publication

Journal of veterinary internal medicine
ISSN: 1939-1676
NlmUniqueID: 8708660
Country: England
Language: English
Volume: 40
Issue: 4
PII: aalag137

Researcher Affiliations

Mahalingam-Dhingra, Ananya
  • Department of Large Animal Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA 01536, United States.
Bedenice, Daniela
  • Department of Large Animal Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA 01536, United States.
da Silva, Debora Regina Romualdo
  • Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA 01536, United States.
Mazan, Melissa
  • Department of Large Animal Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA 01536, United States.
Hall, Tiffany
  • Hagyard Medical Institute, Lexington, KY 40511, United States.
Tenney, Wade
  • Department of Large Animal Clinical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA 01536, United States.
Widmer, Giovanni
  • Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA 01536, United States.

MeSH Terms

  • Animals
  • Horses / microbiology
  • Microbiota
  • Transportation
  • Horse Diseases / microbiology
  • Male
  • RNA, Ribosomal, 16S / genetics
  • Female
  • Hydrocortisone / blood
  • Serum Amyloid A Protein / analysis

Grant Funding

  • Dorothy Russell Havemeyer Foundation
  • Companion Animal Health Fund
  • R21AI173461 / National Institute of Allergy and Infectious Diseases

Conflict of Interest Statement

The authors declare no conflicts of interest.

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