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

There are shared microbial properties between meconium and rumen fluid at birth and these samples are also compositionally similar to the mature rumen microbiome providing potential evidence for the timing of gastrointestinal tract colonization. Lay Summary Developmental programming has highlighted important influences of maternal factors on offspring development. Recent research indicates a programming potential of the rumen microbiome and understanding this role as well as how inoculation occurs may allow beef producers to optimize management practices of gestating cows such that offspring performance is improved via the rumen microbiome. To investigate this, rumen fluid samples were collected from mature cows immediately prior to calving, from their calf immediately after calving with a meconium sample, day 2, and day 28 as well as collected from both dam and calf at weaning. The rumen and meconium microbiome of the newborn calf were similar to each other as well as to the cow rumen microbiome at weaning, although not to the cow rumen microbiome immediately prior to calving. The shared microbiome of the early calf gut highlight a common source of inoculation. The similarities with the cow rumen at weaning could indicate initiation of colonization occurs early in gestation. Results indicate there are shared microbial properties between the cow and calf rumen microbiome. This further supports the opportunity to alter the calf rumen microbiome to improve productivity through the management of the cow during gestation. 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.