Abstract
Recent research suggests that the microbial colonization of the mammalian intestine may begin before birth, but the observations are controversial due to challenges in the reliable sampling and analysis of low-abundance microbiota. We studied the perinatal microbiota of calves by sampling them immediately at birth and during the first postnatal week. The large size of the bovine newborns allows sampling directly from rectum using contamination-shielded swabs. Our 16S rDNA data, purged of potential contaminant sequences shared with negative controls, indicates the existence of a diverse low-abundance microbiota in the newborn rectal meconium and mucosa. The newborn rectal microbiota was composed of Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. The microbial profile resembled dam oral rather than fecal or vaginal vestibular microbiota, but included typical intestinal taxa. During the first postnatal day, the rectum was invaded by Escherichia/Shigella and Clostridia, and the diversity collapsed. By 7 days, diversity was again increasing. In terms of relative abundance, Proteobacteria were replaced by Firmicutes, Bacteroidetes and Actinobacteria, including Faecalibacterium, Bacteroides, Lactobacillus, Butyricicoccus and Bifidobacterium. Our observations suggest that mammals are seeded before birth with a diverse microbiota, but the microbiota changes rapidly in the early postnatal life.
Highlights
Recent research suggests that the microbial colonization of the mammalian intestine may begin before birth, but the observations are controversial due to challenges in the reliable sampling and analysis of low-abundance microbiota
The total level of contaminating bacterial 16S rDNA was 1.3·105 ± 3.1·104 copies per swab, which includes the contamination in the ultra-pure water, DNA extraction and PCR reagents and in the sterile swab itself
We evaluated the similarity of the microbiota profiles in newborns, older calves and various adult cow locations by principal coordinates analysis (PCoA; Fig. 4a) and Spearman rank correlations (ρ; Fig. 4b,c)
Summary
Recent research suggests that the microbial colonization of the mammalian intestine may begin before birth, but the observations are controversial due to challenges in the reliable sampling and analysis of low-abundance microbiota. Our 16S rDNA data, purged of potential contaminant sequences shared with negative controls, indicates the existence of a diverse low-abundance microbiota in the newborn rectal meconium and mucosa. Microbe-derived compounds were elegantly shown to promote the differentiation of gut-specific innate lymphoid cells in the murine fetus[12]. Enterococci administered orally to pregnant mice could be detected in fetal meconium[25] These observations are still controversial due to technical challenges in reliable sampling and analysis of very low-abundance microbiota in these samples[26].
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