The composition of the perinatal intestinal microbiota in horse

Abstract

The establishment of the intestinal microbiota is critical for the digestive and immune systems. We studied the early development of the rectal 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 the foal microbiota, we characterised dam fecal, vaginal and oral microbiotas. We utilised an amplicon sequence variant (ASV) pipeline to maximise resolution and reproducibility. Stringent ASV filtering based on prevalence and abundance in samples and controls purged contaminants while preserving intestinal taxa. Sampled within 20 minutes after birth, rectal meconium contained small amounts of diverse bacterial DNA, with a profile closer to mare feces than mouth. 24 hours after birth, rectum was colonised by Firmicutes and Proteobacteria, some foals dominated by single genera. At day 7, the rectal genera were still different from adult feces. 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 indicate that bacteria or bacterial components are present in the intestine immediately after birth, but the newborn microbiota changes rapidly.

The composition of the microbiota in the full-term fetal gut and amniotic fluid: a bovine caesarean section study

“…This is consistent with previous studies in cattle, in which calves born at term per vias naturales, were sampled (Mayer et al, 2012;Alipour et al, 2018;Klein-Jöbstl et al, 2019). A profile dominated by the phyla Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria was identified in the meconium, in agreement with previous studies using 16S rRNA gene amplicon sequencing (Alipour et al, 2018;Yeoman et al, 2018;Klein-Jöbstl et al, 2019;Husso et al, 2020;Guzman et al, 2020). Additionally, some of the most prevalent genera observed in meconium in our study, such as Sphingomonas, Acinetobacter, Pseudomonas, Ruminococcus…”

“…DNA from the meconium samples (N = 25) and corresponding negative controls (N = 11) were extracted using ZymoBIOMICS DNA Miniprep Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer's instructions, with minor modifications to the protocol as described previously (Alipour et al, 2018;Husso et al, 2020). ZymoBIOMICS™ Microbial Community Standard and an in-house fecal standard were processed with the meconium samples and no-template-controls were included in every batch.…”

“…The bacterial 16S rRNA gene copy numbers in the meconium, amnion and negative control samples were determined using quantitative PCR. The analyses were performed as described previously (Alipour et al, 2018;Husso et al, 2020), with the exception that the PCR master mix was first treated using a dsDNAse based decontamination kit (Enzo Life Sciences, Farmingdale, New York). The amplification was performed using the Bio-Rad CFX96 instrument (Bio-Rad, Hercules, California) and universal eubacteria probe and primers (Nadkarni et al, 2002).…”

“…The V3-V4 region of the 16S rRNA gene amplicons was sequenced using the Illumina MiSeq platform in the DNA core facility of the University of Helsinki, as described previously (Alipour et al, 2018;Husso et al, 2020). In total, 23 amniotic fluid samples and 23 meconium samples of the same cow-calf couple were sequenced.…”

“…The processed data was in silico filtered to remove ASVs which represented probable contaminants, as described previously (Husso et al, 2020). Briefly, an ASV was removed if its prevalence in actual samples was ≤2× its prevalence in instrument controls (DNA extracted from empty sampling instruments only handled aseptically in a laminar flood cabinet) or its prevalence in field controls (empty sampling instruments exposed to the surgery room environment), and if its mean relative abundance in actual samples was ≤10× its mean abundance in instrument controls or its mean abundance in field controls.…”