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 = 0.16; p
0.01), while the effect of geographical location was smaller but still significant
(PERMANOVA: R = 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.