Periodic Reporting for period 1 - HoloRuminant (Understanding microbiomes of the ruminant holobiont)
Reporting period: 2021-10-01 to 2023-03-31
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.
A living document with Standard Operating Procedures has been generated. Existing ruminant-associated microbiome data has been identified for consolidation; and computational workflows and resources are being developed. Generation of novel genomic data from poorly sampled microbes has begun and a priority list of species for sequencing has been developed; Novel computational workflows and algorithms are in development to allow consolidation of the existing and novel data.
The microbiomes of calves born naturally and by caesarean section have been compared. The results highlighted the potential to promote early establishment of beneficial microbes in the GIT of young ruminants and confirmed that many microbial species colonise the host early in life.
A study has been performed to examine the incidence of diarrhoea in early life and its effect on the faecal microbiome in calves. In other study, the effect of birthing protocols (remain with the dam or snatched at birth) and milk replacer feeding levels (Conventional or Intensive) and their role on health, performance and multi-site microbiomes is currently being analysed.
A transportation study (whereby calves were transported from their farm of origin in France to a commercial farm in Northern Spain) has been completed.
To investigate maternal-calf bonding, a study with triplet lambs is on-going. Following birth, lambs were divided into 3 groups; 1) maternal, 2) artificial without adult contact and 3) artificial with occasional adult contact.
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 genetic response of the host in the presence of the pathogen.
The role of gastrointestinal microbiomes on dietary transition is being investigated in both dairy cows and beef during the transition period. Sample collection has been completed and analysis is underway. Also, the role of the microbiome on feed efficiency is currently being assessed using samples originated from steers, divergent for residual feed intake, offered either a zero grazed grass or concentrate diet.
Methane mitigation studies analysing the effects of dietary supplementation with oils and fats on methane production across a range of basal diets, breeds of cattle and geographical location have been completed.
An Outreach, Dissemination and Training Plan was developed, including the design of the website, a communications package with the project identity, and the launch of HoloRuminant social media channels. A Joint Dissemination Network has been established, bringing together various projects working in the field of microbiomes and epigenetics.
The microbiomes of calves born naturally and by caesarean section have been compared. The results highlighted the potential to promote early establishment of beneficial microbes in the GIT of young ruminants and confirmed that many microbial species colonise the host early in life.
A study has been performed to examine the incidence of diarrhoea in early life and its effect on the faecal microbiome in calves. In other study, the effect of birthing protocols (remain with the dam or snatched at birth) and milk replacer feeding levels (Conventional or Intensive) and their role on health, performance and multi-site microbiomes is currently being analysed.
A transportation study (whereby calves were transported from their farm of origin in France to a commercial farm in Northern Spain) has been completed.
To investigate maternal-calf bonding, a study with triplet lambs is on-going. Following birth, lambs were divided into 3 groups; 1) maternal, 2) artificial without adult contact and 3) artificial with occasional adult contact.
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 genetic response of the host in the presence of the pathogen.
The role of gastrointestinal microbiomes on dietary transition is being investigated in both dairy cows and beef during the transition period. Sample collection has been completed and analysis is underway. Also, the role of the microbiome on feed efficiency is currently being assessed using samples originated from steers, divergent for residual feed intake, offered either a zero grazed grass or concentrate diet.
Methane mitigation studies analysing the effects of dietary supplementation with oils and fats on methane production across a range of basal diets, breeds of cattle and geographical location have been completed.
An Outreach, Dissemination and Training Plan was developed, including the design of the website, a communications package with the project identity, and the launch of HoloRuminant social media channels. A Joint Dissemination Network has been established, bringing together various projects working in the field of microbiomes and epigenetics.
Technical progress allowed the generation of over 200 Metagenomically Assembled Genomes (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 and developments 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. The importance of early establishment of a “good” microbiota in young animals was well understood and innovations in this field, were considered very interesting. The stakeholders expected solid scientific evidence on whether practices have an effect on production parameters and health, product quality and safety, the environment and sustainability of ecosystems. For farmers, the promotion of innovations such as microbiome modulation, must consider economic incentives, farmer knowledge and attitudes, and the influences of peers and advisors.
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 and developments 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. The importance of early establishment of a “good” microbiota in young animals was well understood and innovations in this field, were considered very interesting. The stakeholders expected solid scientific evidence on whether practices have an effect on production parameters and health, product quality and safety, the environment and sustainability of ecosystems. For farmers, the promotion of innovations such as microbiome modulation, must consider economic incentives, farmer knowledge and attitudes, and the influences of peers and advisors.