Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review

Abstract

Undesirable microbial infiltration into the female bovine reproductive tracts, for example during calving or mating, is likely to disturb the commensal microflora. Persistent establishment and overgrowth of certain pathogens induce reproductive diseases, render the female bovine reproductive tract unfavourable for pregnancy or can result in transmission to the foetus, leading to death and abortion or birth abnormalities. This review of culture-independent metagenomics studies revealed that normal microflora in the female bovine reproductive tract is reasonably consistently dominated by bacteria from the phyla Bacteroidetes, Firmicutes, Proteobacteria, following by Actinobacteria, Fusobacteria and Tenericutes. Reproductive disease development in the female bovine reproductive tract was demonstrated across multiple studies to be associated with high relative abundances of bacteria from the phyla Bacteroidetes and Fusobacteria. Reduced bacterial diversity in the reproductive tract microbiome in some studies of cows diagnosed with reproductive diseases also indicated an association between dysbiosis and bovine reproductive health. Nonetheless, the bovine genital tract microbiome remains underexplored, and this is especially true for the male genital tract. Future research should focus on the functional aspects of the bovine reproductive tract microbiomes, for example their contributions to cattle fertility and susceptibility towards reproductive diseases.

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing

“…Histophilus was described as an obligate commensal member in bovine genital mucosal surfaces as well as an opportunistic pathogen under favorable conditions ( Bisgaard, 1995 ; Sandal and Inzana, 2010 ). On the other hand, genus Brucella and Ochrobactrum were not reported as the top abundant genera in other bovine vaginal metagenomic studies ( Jeon and Galvão, 2018 ; Ong et al, 2021 ). Genus Burkholderia in bovine vaginal metagenome was identified as the indicator of exposure to toxic fescue, which is associated with reduced reproductive success ( Ratton et al, 2018 ).…”

Core Microbiome of Slovak Holstein Friesian Breeding Bulls’ Semen

“…Only a few information from metagenomic bacterial characterizations are reported, if any. Most metagenomic studies on the bovine reproductive tract are relevant for vaginal or uterine specimens [ 25 ]. The commonly identified bacterial phyla in bovine female reproductive tracts are represented by Bacteroidetes, Firmicutes and Proteobacteria, followed by Actinobacteria and Fusobacteria.…”

“…Some of them correspond to the phyla that were detected in our study on bovine semen. Bacteria from these phyla were reported to be present regardless of the breed, farm, gender, geographical location, sampling site, reproductive status or reproductive health [ 25 ].…”

“…An accurate and effective prediction of the fertility of bulls is of high importance, as it determines the economic parameters and the sustainability of the cattle industry [ 20 ] as the bacterial contamination of extended semen is reported to be a reason for sperm agglutination, acrosomal damage, decreased sperm motility or viability [ 21 , 22 , 23 , 24 ]. Currently, the bovine urogenital microbiome is has not been fully described or understood, especially in the case of males [ 25 ]. A previous study on the identification of bacterial presence in the semen of Holstein Friesian bulls used blood agars, Gassner agars and Tryptic soy agars, identifying the following bacteria: Bacillus cereus, Staphylococcus cohnii, Staphylococcus klosii, Micrococcus luteus, Bacillus licheniformis, Staphylococcus xylosus, Staphylococcus aureus, Staphylococcus warneri, Staphylococcus lentus, Staphylococcus epidermidis, Bacillus mycoides and Staphylococcus haemolyticus [ 26 ].…”

Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples

“…In most of the bovine vaginal metagenomic studies, DNeasy Blood and Tissue extraction kit (DNeasy) was incorporated for metagenome DNA extraction ( 41 ). However, the benefits of effective host depletion for metagenomic studies were reported, primarily for human clinical samples ( 42 – 45 ).…”