Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis

Abstract

Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40–50%), Bacteroidetes (~15–25%) and Proteobacteria (~5–25%), in addition to ~10–20% of non-classified bacteria. 45–55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vaginal microbiota in cattle. Archaeal samples were dominated by the Methanobrevibacter genus (Euryarchaeota, ~55–70%). Ascomycota was the main fungal phylum (~80–95%) and Mycosphaerella the most abundant genus (~70–85%). Hormonal influence was not clear, but a tendency for the reduction of bacterial and increase of archaeal populations in pregnant animals was observed. Eukaryotes did not vary significantly between pregnant and non-pregnant animals, but tended to be more abundant on cows than on heifers. The present work describes a great microbial variability in the vaginal community among the evaluated animals and groups (heifers and cows, pregnant and non-pregnant), which is significantly different from the findings previously reported using culture dependent methods, pointing out the need for further studies on this issue. The microbiome found also indicates that the vaginal colonization appears to be influenced by the gastrointestinal community.

Unravelling vaginal microbial genetic diversity and abundance between Holstein and Fleckvieh cattle

“…The results of the bacterial composition are comparable to the study conducted by Laguardia-Nascimento et al 20 The group evaluated vaginal microbiota composition in Nellore cattle and found that rmicutes (40-50%) was predominant in the vaginal microbiota, followed by bacteroidetes (15-25%) and proteobacteria (5-25%). Swarts et al…”

Microbiomes in ruminant protein production and food security.

“…The dominance of relative abundances compared with other genera and the great functional diversity of Prevotella may lead to decreased FE in cattle. It has been demonstrated that the increased diversity within species can lead to deleterious health outcomes [45][46][47][48]. However, little is still known about the contributions of Prevotella or its intra-species diversity towards divergences in FE in cattle, and the studies presented provide only correlation, not causation, of taxa-level associations with FE.…”

“…In the same study by Shabat et al, it was observed that less-FE animals did not have any taxa that dominated in phylogenetic annotations of genes, suggesting that greater diversity or lack of dominant functionality results in decreased FE [43]. Microbial phylogenetic diversity variations have often been implicated in deleterious phenotypes, such as health outcomes [45][46][47][48]. As the power of FE microbiome studies in ruminants beings to increase with the reduction in sequencing costs and availability of larger study populations, microbial phylogenetic diversity may further prove to be an important indicator in FE and animal health.…”

“…Lactobacillus appears to be important for human reproductive health, however, Lactobacilli are present in very low abundances in the vagina of cattle and other ruminants, suggesting that other vaginal microbiota may fulfill the function of protecting the host from pathogenic microbiota [90]. Similar to humans, ruminants possess unique uterine and vaginal microbiomes [46,90,91]. In cattle, vaginal bacterial communities are dominated by Firmicutes, Bacteroidetes and Proteobacteria, not unlike the rumen and lower gastrointestinal tract microbiomes [46,90,91].…”

“…Similar to humans, ruminants possess unique uterine and vaginal microbiomes [46,90,91]. In cattle, vaginal bacterial communities are dominated by Firmicutes, Bacteroidetes and Proteobacteria, not unlike the rumen and lower gastrointestinal tract microbiomes [46,90,91]. The role of the uterine microbiome is much less explored or understood.…”