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

Abstract

In the present study, we evaluated whether the nasopharyngeal, ruminal, and vaginal microbiota would diverge (1) in virgin yearling beef heifers (9 months old) due to the maternal restricted gain during the first trimester of gestation; and (2) in pregnant beef heifers in response to the vitamin and mineral (VTM) supplementation during the first 6 months of pregnancy. As a secondary objective, using the microbiota data obtained from these two cohorts of beef heifers managed at the same location and sampled at the same time, we performed a holistic assessment of the microbial ecology residing within the respiratory, gastrointestinal, and reproductive tract of cattle. Our 16S rRNA gene sequencing results revealed that both α and β-diversity of the nasopharyngeal, ruminal and vaginal microbiota did not differ between virgin heifers raised from dams exposed to either a low gain (targeted average daily gain of 0.28 kg/d, n = 22) or a moderate gain treatment (0.79 kg/d, n = 23) during the first 84 days of gestation. Only in the vaginal microbiota were there relatively abundant genera that were affected by maternal rate of gain during early gestation. Whilst there was no significant difference in community structure and diversity in any of the three microbiota between pregnant heifers received no VTM (n = 15) and VTM supplemented (n = 17) diets, the VTM supplementation resulted in subtle compositional alterations in the nasopharyngeal and ruminal microbiota. Although the nasopharyngeal, ruminal, and vaginal microbiota were clearly distinct, a total of 41 OTUs, including methanogenic archaea, were identified as core taxa shared across the respiratory, gastrointestinal, and reproductive tracts of both virgin and pregnant heifers.

Keywords: beef heifers; core taxa; maternal nutrition; nasopharyngeal microbiota; offspring; ruminal microbiota; vaginal microbiota.

Figure 1

Beta and alpha diversity of the nasopharyngeal, ruminal and vaginal microbiota of virgin yearling heifers from low gain (LG) or moderate gain (MG) dams as determined during the first trimester of gestation. (A) Non-metric multidimensional scaling (NMDS) plots of the Bray–Curtis dissimilarities, (B) number of operational taxonomic units (OTUs), and Shannon (C) and inverse Simpson’s diversity index (D) of each microbial community.

Figure 2

Beta and alpha diversity of the nasopharyngeal, ruminal and vaginal microbiota of pregnant heifers that received a vitamin and mineral supplement (VTM) or a control diet (Control) during the first six months of gestation. (A) Non-metric multidimensional scaling (NMDS) plots of the Bray–Curtis dissimilarities, (B) number of operational taxonomic units (OTUs), and Shannon (C) and inverse Simpson’s diversity index (D) of each microbial community.

Figure 3

Percent relative abundance of the eight most relatively abundant phyla in the nasopharyngeal, ruminal and vaginal microbiota of (A) virgin yearling heifers from low gain (LG) or moderate gain (MG) dams and (B) pregnant heifers that received a vitamin and mineral supplement (VTM) or a control diet (Control) during the first 6 six months of gestation.

Figure 4

Non-metric multidimensional scaling (NMDS) plots of the Bray–Curtis dissimilarities of the nasopharyngeal, ruminal and vaginal microbiota of (A) virgin yearling and (B) pregnant heifers.

Figure 5

Heat map showing the 100 most abundant OTUs (log₄) overall by sample type within each animal group (Pregnant and virgin heifers).

Figure 6

Overall relative abundance of Methanobrevibacter in nasopharyngeal, ruminal and vaginal microbiota by sample types (A) and by animal groups (B–D).

Figure 7

Correlations between the 25 most relatively abundant genera in the ruminal (A) and vaginal (B) microbiota of virgin yearling heifers. Spearman’s rank correlation coefficients (r). Bold correlation coefficients with 0.01 ≤ p < 0.05, and underlined bold correlation coefficients with p < 0.01.

Figure 8

Correlations between the 25 most relatively abundant genera in the ruminal (A) and vaginal (B) microbiota of pregnant heifers. Spearman’s rank correlation coefficients (r). Bold correlation coefficients with 0.01 ≤ p < 0.05, and underlined bold correlation coefficients with p < 0.01.