HoloRuminant has generated a living document of standard operation protocols for the project, identified keystone species associated with ruminants, identified ruminant-associated microbes that are linked to host phenotypes, compiled published ruminant-associated metataxonomic studies for consolidation, created novel taxonomy-free classification tools for amplicon data and applied them to the Greengenes2 database. Participants have also consolidated all available ruminant associated microbial isolate genomes and high quality-Metagenom assembled genomes (HQ-MAGs) and combined them with novel data generated by other tasks to create a new interoperable functional annotation for use in the HoloR Tools database.
The project worked with earlier studies and sample sets focused on the early establishment of microbiomes in cattle, The work showed that the maternal vaginal microbiota significantly impacts the rumen microbiome colonization in offspring. This study enhances the understanding of microbiome development in neonatal calves and the potential to influence it for better health and productivity outcomes.
The main objectives of the large longitudinal study are to identify patterns of microbiome colonization, persistence, and effects, as well as any genetic control of microbiomes by the animals. The relationship between microbiomes and disease incidence, is also being explored. Beneficiaries have recorded major disease incidences to investigate if certain microbiomes are protective against disease. This research is expected to provide valuable insights into the early establishment of microbiomes and their impact on health and productivity in cattle and sheep.
Another objective of the project is to establish the link between host-associated multi-site microbiomes and phenotypes related to health/disease/welfare and environmental sustainability in ruminant production. It has focused on critical time points during animals’ life with special interest in (i) early life farm management practices related to maternal-calf bonding, adult companionship or early life transportation influence on calf health. Later in the animal’s life the focus shifts to (ii) transition period induced adjustments in dairy cows metabolism or dietary transitions in beef cattle and disease events such as and mastitis. In addition, we also address (iii) environmental challenges animals face in terms of need to reduce methane emissions and the negative environmental effect of heat stress. For most interventions examined, animal studies have occurred, multi-site sampling has been completed and sequencing data analysis using bioinformatic tools is underway.
Another objective was to improve understanding of rumen microorganisms. The project is developing approaches to build HQ-genomes and interpret functional roles for native populations. This involves using 3rd generation metagenomic technologies and integrating eukaryotic genomes into computational workflows. These improvements have impacted how we interpret microbial interactions across the entire rumen system and their contribution to the host animals health and nutrition.
International Stakeholder Platform (ISP) community was established. Consumer opinions regarding innovative management practices and the role of microbiomes in ruminant production were analysed through consumer focus group discussions and an online survey. The financial impact of innovative feeding, health, early-life management and genetic selection at farm level was assessed using simulation models.
