In 2016-2017, the Australian beef industry gross value was $A16.85 billion, which is 20% of the total farm production in Australia ($62b). Overall beef production is dependent on the lifetime reproductive efficiency of the cow, as the relative cost of raising a breeding female decreases with increased calving. It has been estimated that neonatal calf mortalities, pestivirus and bovine genital campylobacteriosis (vibriosis) collectively contribute to ~$236m in production losses in Australian cattle industries each year. Genital tract microbiome has a direct impact on bovine reproductive health and susceptibility to infectious diseases which may be associated with infertility and pregnancy losses.
16S ribosomal DNA amplicon sequencing has been utilized to characterize both human and bovine vaginal microbiomes and has generated confident characterization of representative microorganisms for different gynaecological and obstetric conditions. However, it is accepted that there is an underlying bias in 16S metagenomic sequencing. Hence, shotgun whole-metagenome sequencing (WMS) is proposed for this study to overcome this bias. Additionally, shotgun WGS is able to generate more valuable insights into the phylogenetic composition, metabolic capacity and functional diversity. The major challenge in using WGS from clinical samples is the large amount of host genetic material present in these samples.
We conducted a preliminary study to examine the effects of four host depletion and microbial enrichment methods on cattle genital tract samples. Soft-spinning and benzonase extraction were shown to be the most efficient host elimination methods, yielding more comprehensive taxonomic and functional profiles for the microbiome in bovine genital tracts than the other depletion methods evaluated.