Reproductive Microbiomes in Domestic Livestock: Insights Utilizing 16S rRNA Gene Amplicon Community Sequencing

Abstract

Advancements in 16S rRNA gene amplicon community sequencing have vastly expanded our understanding of the reproductive microbiome and its role in fertility. In humans, Lactobacillus is the overwhelmingly dominant bacteria within reproductive tissues and is known to be commensal and an indicator of fertility in women and men. It is also known that Lactobacillus is not as largely abundant in the reproductive tissues of domestic livestock species. Thus, the objective of this review is to summarize the research to date on both female and male reproductive microbiomes in domestic livestock species (i.e., dairy cattle, beef cattle, swine, small ruminants, and horses). Having a comprehensive understanding of reproductive microbiota and its role in modulating physiological functions will aid in the development of management and therapeutic strategies to improve reproductive efficiency.

Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus

“…The three most abundant genera in the elk vaginal microbiota belonged to unclassified families belonging to the orders Lactobacillales , Bacteroidales , and Peptostreptococcales-Tissierellales . These orders all contain taxa previously documented in ruminant vaginal tracts ( 71 , 76 , 77 ). BLAST analysis indicated that OTUs 1, 2, and 3 were most similar to organisms in the genera Suicoccus , Anaerosphaera , and Porphyromonas , respectively.…”

“…Anaerosphaera has previously been identified in the vaginal tract of pigs but has also been identified in human feces and in a bioreactor ( 81–83 ). Finally, the genus Porphyromonas has been documented in multiple ruminant vaginal studies ( 71 , 72 , 75 ). While this genus can be found among the flora of the healthy bovine reproductive tract ( 74 , 75 , 84 ), multiple studies have found this genus to be positively correlated with cattle reproductive diseases including metritis, necrotic vulvovaginitis, and repeat breeder syndrome ( 73 , 76 , 85–91 ).…”

“…As discussed previously, Porphyromonas can colonize and invade ruminant uterine tissues and is associated with a number of reproductive tract diseases. The genus Trueperella and particularly the species T. pyogenes are often associated with metritis and purulent vaginal discharge in cattle; indeed, T. pyogenes is capable of causing a number of pathologies of the reproductive tract tissues in ruminants ( 71 , 84 , 90 , 91 , 119 ). However, the Trueperella isolate most abundant in this study (OTU 9) had less percent identity to T. pyogenes than to T. bialowiezensis , a proposed etiological agent of a necrotic disease of the penis of European bison ( 120 , 121 ).…”

Temporal changes in ewe vaginal microbiota throughout gestation

“…The sheep vaginal microbiota, like that of other livestock species, has been understudied ( Ong et al, 2021 ; Poole et al, 2023 ). Cultivation studies characterized the dynamics of ewe vaginal microbial communities when intravaginal sponges were used for synchronization of estrus, and researchers found that intravaginal sponges significantly increased the abundance of bacteria in the vagina.…”

Mammals’ sperm microbiome: current knowledge, challenges, and perspectives on metagenomics of seminal samples

“…Therefore, the percentage of bacterial-contaminated semen samples is usually high, which was reported to be up to 66.7% in the case of boars ( Schulze et al, 2015 ). Microbes have recently been shown to significantly affect males’ reproductive function and performance ( Alqawasmeh et al, 2022 ; Poole et al, 2023 ). Therefore, knowledge of the reproductive microbiome is fundamental to understanding the evolutionary ecology of reproductive strategies and sexual dynamics of host organisms.…”