Molecular monitoring of the bacterial community structure in foal feces pre- and post-weaning

• The effect of age on the bacterial community structure in foal feces was studied.
• The meconium was not sterile.
• Significant age-related changes were detected from birth to one month of life.
• Weaning at 180 days of life did not affect the bacterial community structure.

This study assessed the time-scale variability of bacterial community structure in foal feces from birth to 365 days of age using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Fecal samples were collected from five foals 2 h after birth (meconium) and in the morning at days 1, 2, 5, 10, 30, 60, 120, 179, 183, 194 and 365. The ARISA profiles were compared using an analysis of similarity (ANOSIM). Although both the age effect and the foal effect were highly significant (P < 0.010), the R-ANOSIM value for the foal effect was very low (R-ANOSIM = 0.089), while that of the age effect was much higher (R-ANOSIM = 0.309). Significant age-related changes were detected between days 0 and 2 (R-ANOSIM = 0.500), days 2 and 10 (R-ANOSIM = 0.475) and days 10 and 30 (R-ANOSIM = 0.519). No further shifts between consecutive times of sampling were detected in the bacterial community after day 30 and no changes were observed at weaning (day 180). These results show that the establishment of the intestinal bacterial community in foals is a sequential process, which reaches its climax state at around one month of age. Further studies using new generation sequencing based methods could be conducted to identify which bacterial genera are establishing in foals during the first month of life.