H2020 HoloRuminant Project: Understanding the microbiomes of the ruminant holobiont
- Type Project
- Status Firmado
- Execution 2021 -2026
- Assigned Budget 9.724.763,75 €
- Scope Europeo
- Main source of financing H2020
- Project website Proyecto HoloRuminant
Ruminant livestock species, such as cattle, sheep, and goats, depend on their body microbes for essential functions and interactions with the environment. The association between the ruminant host microbiome, the holobiont, is the biological unit that influences ruminant development, growth, health, and environmental footprint.
The primary objective of the EU-funded HoloRuminant project is to study the role of the microbiome in animal health and production efficiency. Researchers will adopt a multi-omics approach to analyze the microbiome and host, as well as the impact of their interaction at key life stages in ruminants. The ultimate goal is to characterize and identify ruminant-associated microbiomes that are associated with increased production efficiency, health, and well-being.
A dynamic document with standard operating procedures has been generated. Existing data on the ruminant-associated microbiome have been identified for consolidation; and workflows and computational resources are being developed. Generation of new genomic data from poorly sampled microbes has begun, and a prioritized list of species for sequencing has been developed. New workflows and computational algorithms are being developed to enable consolidation of existing and new data. The microbiomes of calves born naturally and by cesarean section have been compared. The results highlighted the potential to promote the early establishment of beneficial microbes in the gastrointestinal tract of young ruminants and confirmed that many microbial species colonize the host early in life. A study was conducted to examine the incidence of diarrhea early in life and its effect on the fecal microbiome in calves. In another study, the effect of birth protocols (staying with the mother or being removed at birth) and levels of milk replacer feeding (conventional or intensive) on the health, performance, and microbiomes of multiple sites is currently being analyzed.
A transport study has been completed (in which calves were transported from their farm of origin in France to a commercial farm in northern Spain). To investigate the mother-calf bond, a study with triplet lambs is underway.
After birth, the lambs were divided into 3 groups:
- Maternal.
- Artificial without contact with adults.
- Artificial with occasional contact with adults.
Sampling of calves challenged with two Bovine Respiratory Disease challenge studies has been completed. In mastitis studies, LAB strains are being tested for their protective properties when cells are challenged with the pathogen Staphylococcus aureus. This will examine whether the presence of LAB changes the host's genetic response in the presence of the pathogen. The role of gastrointestinal microbiomes in dietary transition is being investigated in both dairy and beef cattle during this period. Sample collection has been completed, and analysis is ongoing. Additionally, the role of the microbiome in feed efficiency is being evaluated using samples from steers with divergent residual feed intake, which were offered either a grazed-free diet or a concentrate diet.
Methane mitigation studies have been completed, analyzing the effects of dietary supplementation with oils and fats on methane production across a variety of basal diets, livestock breeds, and geographic locations. An Outreach, Dissemination, and Training Plan was developed, including website design, a communications package with the project identity, and the launch of HoloRuminant's social media channels. A Joint Dissemination Network has been established, bringing together diverse projects in the field of microbiomes and epigenetics.
The sustainability of ruminant production is of concern to society due to its environmental, economic, and food security implications. The host-associated microbiome plays a key role in the health, well-being, 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 interconnectedness and communication between animals and their different microbiomes have never been studied in such a deep and integrated way. The project's goal is to elucidate the role of ruminant-associated microbiomes and their interaction with the host in early life and throughout key life events. HoloRuminant will use a holistic multi-omics approach to characterize the acquisition and evolution of microbiomes from different body sites, their heritability, and their influence on host disease resistance and environmental efficiency of production.
Specifically, we will determine the functions of microbiomes by combining multilevel information on microbes, host, and their interactions; we will define the role of microbiomes during challenging life stages, such as the perinatal stage, weaning, and post-pathogen exposure; and we will evaluate the impact of ruminant microbiomes on phenotypes critical to sustainable production, health, and well-being. This will enable the identification of novel microbial markers for monitoring, predicting, and selecting phenotypes of interest.
By engaging stakeholders in the livestock value chain, we will assess the socioeconomic impact and acceptability of the proposed innovations among stakeholders and the public. HoloRuminant will provide highly innovative and standardized methodologies that will radically advance our understanding of the ruminant holobiont. This knowledge and the tools created will enable the use of microbiome-based diagnostics and solutions to improve ruminant sustainability.
The sustainability of ruminant production is a matter of concern for society due to its implications for the environment, the economy, and food security. Host-associated microbiomes play a key role in health, well-being, and environmental efficiency in 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 interconnectedness and communication between the animal and its different microbiomes has never been studied in an in-depth and integrated way.
The project aims to elucidate the role of ruminant-associated microbiomes and their interaction with the host in early life stages and throughout fundamental life events. HoloRuminant will use a holistic multi-omics approach to characterize the acquisition and evolution of microbiomes from different body parts, their heritability, and their influence on host disease resistance and environmental production efficiency. Specifically, we will: determine microbiome functions by combining multi-level information on microbes, the host, and their interaction; define microbiome functions during challenging life periods, such as the perinatal period, weaning, and after pathogen exposure; and assess the effect of ruminant microbiomes on phenotypes critical for sustainable production, health, and welfare.
This will enable the identification of new microbial markers for monitoring, predicting, and selecting phenotypes of interest. By engaging actors across the livestock value chain, we will assess the socioeconomic impact and acceptability of the proposed innovations among stakeholders and the public. HoloRuminant will provide highly innovative, standardized methodologies that will radically improve our understanding of the ruminant holobiont. This knowledge and the tools created will enable the use of microbiome-based diagnostics and solutions to improve ruminant sustainability.
Technical progress has enabled the generation of more than 200 Metagenomically Assembled Genomes (MAGs) with complete rrn operons for organisms not yet cultivated. These connected high-quality (HQ) MAGs constitute a significant outcome and, promisingly, allow us to link these HQ-MAGs with publicly available 16S inventories. Furthermore, they will allow us to link the functional genomic information from our HQ-MAG inventories with larger and more comprehensive studies from previous European projects, thus contributing to the functional characterization of the heritable microbiota in ruminants. A first version of a novel computational algorithm was developed that allows for stable (taxonomy-free) and scalable consolidation of multiple datasets from different amplicon targets and their association with cross-referencing of genomic data with microbiome data (16S, cultivated genomes, and MAGs).
A large longitudinal study to understand the colonization of ruminants by microbial communities, their temporal stability, and their associations with disease incidence and productivity traits is underway in several countries.
Investigating these data will enable the identification of microbial biomarkers for different developmental stages and health traits, and potentially the development of probiotics. The results of the first completed study evaluating the role of microbiomes in health and disease show that calf challenges with Bovine Respiratory Syncytial Virus (BRSV) resulted in differences in major microbial genera between infected and uninfected calves, suggesting that BRSV infection causes nasal microbiome dysbiosis.
All of these results and developments have the potential to enable a greater understanding of the societal concerns driven by the microbiome of ruminant agriculture, including greenhouse gas emissions, resource use, and overall production efficiency.
Significant feedback was collected from stakeholders who had a real interest in the microbiome and were eager to receive research results as soon as possible. The importance of establishing an appropriate microbiota early in young animals was well understood, and innovations in this field were considered highly interesting. Stakeholders expected robust scientific evidence on the impact of practices on production parameters and health, product quality and safety, and environmental and ecosystem sustainability. For livestock producers, promoting innovations such as microbiome modulation must consider economic incentives, their knowledge and attitudes, and the influence of their peers and advisors.
- INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT (INRAE)
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