Characterization of the microbiota associated with 12-week-old bovine fetuses exposed to divergent in utero nutrition

Abstract

A recent study reported the existence of a diverse microbiota in 5-to-7-month-old calf fetuses, suggesting that colonization of the bovine gut with so-called 'pioneer' microbiota may begin during mid-gestation. In the present study, we investigated 1) the presence of microbiota in bovine fetuses at early gestation (12 weeks), and 2) whether the fetal microbiota is influenced by the maternal rate of gain or dietary supplementation with vitamins and minerals (VTM) during early gestation. Amniotic and allantoic fluids, and intestinal and placental (cotyledon) tissue samples obtained from fetuses (n = 33) on day 83 of gestation were processed for the assessment of fetal microbiota using 16S rRNA gene sequencing. The sequencing results revealed that a diverse and complex microbial community was present in each of these fetal compartments evaluated. Allantoic and amniotic fluids, and fetal intestinal and placenta microbiota each had distinctly different (0.047 ≥ R2 ≥ 0.019, P ≤ 0.031) microbial community structures. Allantoic fluid had a greater (P < 0.05) microbial richness (number of OTUs) (Mean 122) compared to amniotic fluid (84), intestine (63) and placenta (66). Microbial diversity (Shannon index) was similar for the intestinal and placental samples, and both were less diverse compared with fetal fluid microbiota (P < 0.05). Thirty-nine different archaeal and bacterial phyla were detected across all fetal samples, with Proteobacteria (55%), Firmicutes (16.2%), Acidobacteriota (13.6%) and Bacteroidota (5%) predominating. Among the 20 most relatively abundant bacterial genera, Acidovorax, Acinetobacter, Brucella, Corynebacterium, Enterococcus, Exiguobacterium and Stenotrophomonas differed by fetal sample type (P < 0.05). A total of 55 taxa were shared among the four different microbial communities. qPCR of bacteria in the intestine and placenta samples as well as scanning electron microscopy imaging of fetal fluids provided additional evidence for the presence of a microbiota in these samples. Minor effects of maternal rate of gain and VTM supplementation, and their interactions on microbial richness and composition were detected. Overall, the results of this study indicate that colonization with pioneer microbiota may occur during early gestation in bovine fetuses, and that that the maternal nutritional regime during gestation may influence the early fetal microbiota.

The Nasopharyngeal, Ruminal, and Vaginal Microbiota and the Core Taxa Shared across These Microbiomes in Virgin Yearling Heifers Exposed to Divergent In Utero Nutrition during Their First Trimester of Gestation and in Pregnant Beef Heifers in Response to Mineral Supplementation

“…A recent study by Guzman and colleagues [13], however, provided sequencing and culture-based evidence indicating that the intestine of calf fetus is not sterile and colonization by so-called "pioneer" microbes may occur during gestation. This is further supported by our preliminary data which suggested that colonization of the fetal intestine by archaea and bacteria may take place within the first 12 weeks of gestation in cattle [14]. These observations highlight the potential and extended role of the maternal microbiome in calf ruminal microbiome development.…”

“…Regardless of animal group and diet, these OTUs were shared by a high proportion of the nasopharyngeal, ruminal fluid, and vaginal samples, suggesting that these taxa may be so-called "core taxa" among these anatomical locations. Methanogenic archaea, and in particular members of the Methanobrevibacter genus, have been reported to colonize the intestine of 83-day-old [14], and 5-to 7-month-old calf fetuses [13], as well as newborn calves [40,41]. In addition, we identified here two Methanobrevibacter OTUs (OTU8 and OTU23) that were shared by a relatively high portion (≥65%) of all samples collected from both virgin yearling and pregnant heifers (Table S1).…”