The composition of the perinatal intestinal microbiota in cattle

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.

The composition of the perinatal intestinal microbiota in horse

“…Almost all of the Firmicutes genera observed in our newborns, as well as the most prevalent genera of other phyla, represented typical mucosal taxa and were shared with the core vaginal and/or fecal microbiota of the mares. Several of these genera were reported in the previous analysis of newborn foal microbiota and many were also observed by us in newborn calf rectum 24,27 . The prevalent ASVs with species-level classification by our analysis pipeline showed sequence matches to equine-associated species.…”

“…In order to maximize the reliability of the microbiota analyses, we applied several types of negative controls and performed a stringent filtering of the sequencing data to remove potential contaminants. Our data decontamination protocol was based on a previously published logic, comparing the prevalence and relative abundance of each taxon in samples and negative controls 27,31,32 . We performed filtering on the amplicon sequence variants (ASVs), which provides maximum resolution of the 16S rRNA gene sequencing data 29,30 .…”

“…We compared the foal microbiota to the fecal, vaginal and oral microbiotas of their dams. These locations have been regarded as potential initial sources of the early microbiota 9,27,28 . We used 16S rRNA gene amplicon sequencing and quantitative PCR to characterize the composition and abundance of the various microbiotas.…”

Influence of Colostrum and Vitamins A, D3, and E on Early Intestinal Colonization of Neonatal Holstein Calves Infected with Mycobacterium avium subsp. paratuberculosis

“…reported by Derakhshani et al [49] despite the abbreviated 14-day study period and lack of lesions noted in the intestinal tissues. Additionally, the general microbiome also aligned with results observed for rectal swabs from calves collected at 7 days of age [50], suggesting that commonalities shared in the gut microbiome were likely due to normal populations in the gut of young calves.…”

Feeding modes shape the acquisition and structure of the initial gut microbiota in newborn lambs

“…The mother's oral cavity is another important source of the suckled lamb gut microbiota, which is consistent with previous studies on humans (Mackie et al ., ;Dominguez‐Bello et al ., ; Ferretti et al ., ). A recent study showed that the faecal microbiota of neonatal and 1‐day calves were more similar to their mother's oral microbiota, as compared to the vaginal or faecal microbiota, indicating that the mother's oral cavity is an important source of early gut microbiota (Alipour et al ., ). After birth, the mother's oral cavity microbes were mechanically transferred to the newborns by licking the suckled lambs.…”