The risk of respiratory disease in the transported horse can increase as a consequence of immunosuppression and stress associated primarily with opportunistic bacterial proliferation and viral reactivation. This study examines the ecology of equid herpesviruses (EHV) in these horses, exploring reactivation and changes in infection and shedding associated with transport, and any potential contributions to transport-related respiratory disease. Twelve horses were subjected to an 8-h road-transport event. Antibodies to EHV-1 and EHV-4 were detected by ELISA in serum collected prior to, immediately after and 2 weeks post transport. Respiratory tract endoscopy and tracheal washes were collected prior to and 5 days after transportation. Nasal swabs collected prior to, immediately after, 1 and 5 days following transport were screened for EHV-1,-2,-4,-5 using qPCR. Six horses had persistent neutrophilic airway infiltrates post transportation, indicative of subclinical respiratory disease. No horses were qPCR positive for either of the alphaherpesviruses (i.e., EHV-1/-4) nor did any seroconvert to either virus. Four out of nine horses positive for either EHV-2 or EHV-5 on qPCR prior to transport developed neutrophilic airway inflammation. Five horses showed increasingly positive readings on qPCR (i.e., reduced Cq) for EHV-2 after transportation and seven out of eleven horses positive for EHV-2 after transport shared strains of high sequence similarity with other horses in the study. One EHV-2 virus detected in one horse after transport was genetically different which may be due to reactivation. The clinical significance of EHV-2 and EHV-5 remains in question. However these results indicate that transportation may lead to increased shedding, transmission and reactivation of EHV-2 and EHV-5 but not EHV-1/-4. Unlike previous work focusing on the role of alphaherpesviruses, this research suggests that investigation of the gammaherpesviruses (i.e., EHV-2/-5) in transport-related disease should not be dismissed, particularly given that these viruses can encode suppressive immunomodulators that may affect host health.

Background: A foal undergoes considerable growth and development from birth to weaning, progressing from a milk-based diet to complete herbivory. The symbiotic relationships between bacteria, archaea and fungi substantiate this energy demand by colonising the hindgut and remaining flexible throughout the diet transitions. Methods: A total of 70 faecal samples were collected from 14 mares and their foals across five studs in NSW as they aged from 0 to 5 months old. DNA was extracted from faecal samples and underwent amplification and sequencing of the 16S rRNA gene V4 hypervariable region of archaea and bacteria, and the fungal internal transcribed spacer-1 (ITS1) region. The fungal and bacterial community structure was assessed using Bray-Curtis dissimilarities, and the effect of age at sampling and location was determined using PERMANOVA. Results: Age at sampling had a substantial effect on the foal's archaeal and bacterial faecal microbiota (PERMANOVA: R 2 = 0.16; p < 0.01), while the effect of geographical location was smaller but still significant (PERMANOVA: R 2 = 0.07; p < 0.01). The overall abundance, diversity and richness of bacterial and archaeal populations increased (p < 0.01) as foals aged, most noticeably rising between foals 1 to 2 and 2 to 3 months of age. The 15 most relatively abundant fungal species were all environmental saprophytes, most strongly affected by geographical location (p < 0.01) rather than age at sampling. There was an effect of location on Preussia Africana (p = 0.02) and a location × age interaction for fungal species Preussia persica (p < 0.01), Acremonium furcatum (p = 0.04), and Podospora pseudocomata (p = 0.01). There was no effect of age, location, or location × age interaction on the relative abundance of the remaining fungal species. Conclusions: The faecal microbiome appeared to stabilise for most bacterial and archaeal genera by 2 to 3 months of age, resembling an adult mare. Bacterial genera isolated from faecal samples belonged mainly to the Firmicutes phylum. Age at sampling more strongly affected the archaeal and bacterial faecal microbiota than the effect of the geographical location where the horse was sampled. The lack of effect of location on microbe populations suggests that although environmental factors may influence population structure, there are distinct differences at each stage of foal maturation.

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