The establishment of the intestinal microbiota is critical for the digestive and immune systems. We studied the early development of the microbiota in horse, a hindgut fermenter, from birth until 7 days of age, by qPCR and 16S rRNA gene amplicon sequencing. To evaluate initial sources of foal microbiota, we characterized dam fecal, vaginal and oral microbiotas. We utilised an amplicon sequence variant (ASV) based pipeline to maximize resolution and reproducibility. Stringent ASV filtering based on prevalence and abundance in samples and controls purged reagent contaminants while preserving intestinal taxa. The newborn rectum contained small amounts of diverse bacterial DNA, with a profile closer to mare feces and vagina than mouth. 24 hours after birth, the intestine was colonized by Firmicutes and Proteobacteria, some foals dominated by a single genus. At day 7, the phylum-level composition resembled adult feces but genera were different. The mare vaginal microbiota contributed to 24 h and 7 day microbiotas. It contained few lactobacilli, with Corynebacterium, Porphyromonas, Campylobacter and Helcococcus as the most abundant genera. In the oral mucosa, Gemella was extremely abundant. Our observations suggest that bacteria or bacterial components translocate to the equine fetus, but the intestinal microbiota changes rapidly after birth.
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