Calf rumen microbiome from birth to weaning and shared microbial properties to the maternal rumen microbiome

Abstract

Optimization of host performance in cattle may be achieved through programming of the rumen microbiome. Thus, understanding maternal influences on the development of the calf rumen microbiome is critical. We hypothesized that there exists a shared microbial profile between the cow and calf rumen microbiomes from birth through weaning. Specifically, our objective was to relate the calf's meconium and rumen fluid microbiomes in early life to that of the cow rumen fluid prior to parturition and at weaning. Rumen fluid was collected from multiparous Angus crossbred cows (n = 10) prior to parturition and at weaning. Immediately following the parturition, meconium and rumen fluid were collected from the calf. Rumen fluid was collected again from the calf on day 2, day 28, and at weaning. The rumen fluid microbial profile and subsequent volatile fatty acid (VFA) profile were characterized using 16S rRNA sequencing and gas liquid chromatography, respectively. Microbial data was analyzed using QIIME2 and the GLM procedure of SAS was used to analyze the VFA profile. Alpha diversity was similar in the early gut microbiome (meconium, rumen fluid at birth and day 2; q ≥ 0.12) and between the cow and calf at weaning (q ≥ 0.06). Microbial composition, determined by beta diversity, differed in the early rumen microbiome (rumen fluid at birth, day 2, and day 28; q ≤ 0.04), and VFA profiles complimented these results. There were similarities in composition between meconium, rumen fluid at birth, and rumen fluid from the cow at weaning (q ≥ 0.09). These data indicate successive development of the rumen microbiome and stabilization over time. Similarities between meconium and rumen fluid at birth potentially indicates in utero colonization of the calf gastrointestinal tract. Similarities in composition between the early calf rumen microbiome and the cow at weaning prompt an interesting comparison and area for future consideration in terms of identifying at what stage of gestation might colonization begin. Overall, this study provides insight into similarities between the cow and calf microbiomes and may be helpful in developing hypotheses for the pathway of colonization and programming potential in the early gut.

Keywords: meconium; programming; rumen microbiome.

Figure 1.

Taxonomy bar graph at the phylum level (with inclusion of the domain Archaea) for meconium (M), calf rumen fluid at birth (RFd1), calf rumen fluid 24 hr post-parturition (RFd2), calf rumen fluid 28 d post-parturition (RFd28), calf rumen fluid at weaning (RFNw), cow rumen fluid prior to parturition (RFC), and cow rumen fluid at weaning (RFCw).

Figure 2.

Alpha diversity box plots showing Shannon richness for meconium (M), calf rumen fluid at birth (RFd1), calf rumen fluid 24 hr post-parturition (RFd2), calf rumen fluid 28 d post-parturition (RFd28), calf rumen fluid at weaning (RFNw), cow rumen fluid prior to parturition (RFC), and cow rumen fluid at weaning (RFCw). Significant differences (q ≤ 0.05) are denoted by letters a, b, c, d, e.

Figure 3.

Alpha diversity box plots showing Evenness for meconium (M), calf rumen fluid at birth (RFd1), calf rumen fluid 24 hr post-parturition (RFd2), calf rumen fluid 28 d post-parturition (RFd28), calf rumen fluid at weaning (RFNw), cow rumen fluid prior to parturition (RFC), and cow rumen fluid at weaning (RFCw). Significant differences (q ≤ 0.05) are denoted by letters a, b, c, d.

Figure 4.

Alpha diversity box plots showing Faith’s phylogeny for meconium (M), calf rumen fluid at birth (RFd1), calf rumen fluid 24 hr post-parturition (RFd2), calf rumen fluid 28 d post-parturition (RFd28), calf rumen fluid at weaning (RFNw), cow rumen fluid prior to parturition (RFC), and cow rumen fluid at weaning (RFCw). Significant differences (q ≤ 0.05) are denoted by letters a, b, c.

Figure 5.

Beta diversity by sample type and date. Principal coordinate analysis plot based on Bray-Curtis dissimilarity matrix for meconium (M), calf rumen fluid at birth (RFd1), calf rumen fluid 24 hr post-parturition (RFd2), calf rumen fluid 28 d post-parturition (RFd28), calf rumen fluid at weaning (RFNw), cow rumen fluid prior to parturition (RFC), and cow rumen fluid at weaning (RFCw).

Figure 6.

Beta diversity by sample type and date. Principal coordinate analysis plot based on unweighted UniFrac matrix for meconium (M), calf rumen fluid at birth (RFd1), calf rumen fluid 24 hr post-parturition (RFd2), calf rumen fluid 28 d post-parturition (RFd28), calf rumen fluid at weaning (RFNw), cow rumen fluid prior to parturition (RFC), and cow rumen fluid at weaning (RFCw).

Figure 7.

Beta diversity by sample type and date. Principal coordinate analysis plot based on weighted UniFrac matrix for meconium (M), calf rumen fluid at birth (RFd1), calf rumen fluid 24 hr post-parturition (RFd2), calf rumen fluid 28 d post-parturition (RFd28), calf rumen fluid at weaning (RFNw), cow rumen fluid prior to parturition (RFC), and cow rumen fluid at weaning (RFCw).