Periodic Reporting for period 2 - HoloRuminant (Understanding microbiomes of the ruminant holobiont)
Reporting period: 2023-04-01 to 2024-09-30
The sustainability of ruminant production is of concern to society because of its environmental, economic and food security implications. The host-associated microbiome plays a key role in the health, welfare and environmental efficiency of ruminant production systems. However, despite the information already available, we lack the knowledge to precisely link the causes and mechanisms of microbial influence on ruminant phenotypes. This is because the interconnection and communication between the animal and its different microbiomes has never been studied in a deep, integrated way.
The goal of the project is to elucidate the role of ruminant-associated microbiomes and their interplay with the host in early life and throughout fundamental life events. HoloRuminant will use a holistic multi-omics approach to characterise the acquisition and evolution of microbiomes from different body sites, their inheritability and their influence on host resistance to disease and the environmental efficiency of production.
Specifically, we will: determine microbiomes’ functions by combining multi-level information for microbes, host and their interaction; define microbiomes’ roles during challenging life periods such as perinatal, weaning, and after exposure to pathogens; and evaluate the effect of ruminant microbiomes on critical phenotypes for sustainable production, health and welfare. This will allow the identification of novel microbial markers for monitoring, predicting and selecting phenotypes of interest. By engaging actors from the livestock value chain, we will evaluate the socio-economic impact and acceptability of the innovations proposed among stakeholders and the public. HoloRuminant will provide highly innovative, standardized methodologies that will radically advance our understanding of the ruminant holobiont. This knowledge and the tools created will allow the use of microbiome-based diagnostics and solutions for improving ruminant sustainability.
The goal of the project is to elucidate the role of ruminant-associated microbiomes and their interplay with the host in early life and throughout fundamental life events. HoloRuminant will use a holistic multi-omics approach to characterise the acquisition and evolution of microbiomes from different body sites, their inheritability and their influence on host resistance to disease and the environmental efficiency of production.
Specifically, we will: determine microbiomes’ functions by combining multi-level information for microbes, host and their interaction; define microbiomes’ roles during challenging life periods such as perinatal, weaning, and after exposure to pathogens; and evaluate the effect of ruminant microbiomes on critical phenotypes for sustainable production, health and welfare. This will allow the identification of novel microbial markers for monitoring, predicting and selecting phenotypes of interest. By engaging actors from the livestock value chain, we will evaluate the socio-economic impact and acceptability of the innovations proposed among stakeholders and the public. HoloRuminant will provide highly innovative, standardized methodologies that will radically advance our understanding of the ruminant holobiont. This knowledge and the tools created will allow the use of microbiome-based diagnostics and solutions for improving ruminant sustainability.
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.
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.
Technical progress allowed the generation of over 200 MAGs with complete rrn operons for organisms not yet in culture. These connected high-quality (HQ) MAGs is a significant result and excitingly means we can potentially link these HQ-MAGs to publicly available 16S inventories. Furthermore, it will allow to link the functional genomic information in our HQ-MAGs inventories to other larger comprehensive surveys from previous EU projects contributing thus towards functionally characterizing heritable microbiota in ruminants.
A first version of a novel computational algorithm that allows stable (taxonomy-free) and scalable consolidation of multiple datasets from different amplicon targets and their association with genomic data cross-linking of microbiome data (16S, cultured genomes and MAGs) was developed.
The large longitudinal study for understanding the colonization of ruminants by microbial communities, their temporal stability and associations with disease incidence and productivity traits is under way in several countries. Investigation of this data will allow for the identification of microbial biomarkers for different developmental stages and health traits, and potentially development of probiotics. Results from the first completed study evaluating the role of microbiomes in health and disease shows that calves challenges with Bovine Respiratory Syncytial Virus (BRSV) presented differences in the top microbial genera between infected and non-infected calves, suggesting that BRSV infection causes a dysbiosis of the nasal microbiome.
All these results have the potential to allow further insights into microbiome-driven societal concerns from ruminant agriculture, including greenhouse gas emissions, use of resources and overall efficiency of production.
Important feedback was collected from stakeholders that had a real interest in microbiome and were willing to receive research results as early as possible.
A first version of a novel computational algorithm that allows stable (taxonomy-free) and scalable consolidation of multiple datasets from different amplicon targets and their association with genomic data cross-linking of microbiome data (16S, cultured genomes and MAGs) was developed.
The large longitudinal study for understanding the colonization of ruminants by microbial communities, their temporal stability and associations with disease incidence and productivity traits is under way in several countries. Investigation of this data will allow for the identification of microbial biomarkers for different developmental stages and health traits, and potentially development of probiotics. Results from the first completed study evaluating the role of microbiomes in health and disease shows that calves challenges with Bovine Respiratory Syncytial Virus (BRSV) presented differences in the top microbial genera between infected and non-infected calves, suggesting that BRSV infection causes a dysbiosis of the nasal microbiome.
All these results have the potential to allow further insights into microbiome-driven societal concerns from ruminant agriculture, including greenhouse gas emissions, use of resources and overall efficiency of production.
Important feedback was collected from stakeholders that had a real interest in microbiome and were willing to receive research results as early as possible.