Understanding the functional and genomic architecture of the rumen microbiome affecting performance traits in bovines

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

By 2050, the human population will grow to over 9 billion people, and in the same time frame, global meat production is set to increase by 73%. There is a need to increase the efficiency and sustainability of animal production, reduce waste in the food chain and ensure safe and nutritious diets in order to address this challenge. Rumen microbes confers a unique ability to convert human inedible high-fibre forage into nutrients the animal can absorb to produce high-quality proteins as meat and milk. However, intensive food production puts a strain on the environment, and there is a need to produce more food ethically and in a way that does not harm the environment. The project addresses these challenges by unravelling the functional and genomic architecture of the ruminal microbiome affecting performance traits of cattle. This information will be used to identify fundamental associations between the microbiome or its genes with animal performance traits and methane emissions. In this study we will sequence all microbial genomes - the metagenome - to describe the composition of the microbial community and its functional genes. The analysis will be based on a unique dataset of 288 experimental beef cattle, with rumen DNA samples and a large array of performance information (e.g. feed conversion efficiency, growth, body composition and meat quality) available. These data are structured by breeds and sire progeny groups to estimate the animal host genetic effects on the microbiome and microbial genes. The experimental data have been the basis of numerous publications in which it was shown that at the animal performance level, and for methane emissions, there are large differences between breeds, sire progeny groups and diets. Preliminary analysis for 8 of these animals suggests that there is a link between the abundance of the microbial community or microbial genes and animal performance traits and methane emissions. However, to understand the function and genomic architecture of the ruminal microbiome, analysis of the full sample set is necessary. Algorithms will be developed to predict animal performance, e.g. feed conversion efficiency and methane emissions from the abundance of the microbial community and genes. These high value, but costly-to-measure traits could then be predicted by analysing the rumen microbiome (sampled via stomach tube on live animals or in the abattoir). However, to verify the associations between the rumen microbiome and performance traits, we need basic knowledge about the functional and genomic architecture of the microbiome. Additionally, microbial biomarkers to predict e.g. feed conversion efficiency could be identified. Due to the unique structure of the data in sire progeny groups and diets, we will be able to predict the host genetic and nutritional effect on the microbial community and microbial genes. This structure can also be used in the network analysis to identify animal genetic effects on the functional and genomic architecture of the microbiome. The project will provide unprecedented new knowledge of the genomic and functional architecture of the microbiome and its impact on performance traits and methane emissions as well as the interaction with animal genetics and nutrition. We will compare the functional and genetic architecture of the microbiome in beef cattle with that of other species to provide insights about the microbiome of different species, in particular humans. By understanding host genetic effects on the rumen microbiota and associations with body composition, we expect to provide new insights for human personalised medicine approaches to reduce obesity.

Technical Summary

Rumen microbial fermentation confers a unique ability to efficiently convert human inedible feed into foods with high nutritional value (e.g. meat, milk). However, there is a disadvantage from the environmental and energetic efficiency point of view, in that microbial fermentation also results in methane production. There is a large variation between animals in feed conversion efficiency and methane emissions, so that the substantial lack of knowledge about the functional and genomic architecture of the rumen microbiome has to be closed to efficiently breed and feed those animals. We will use deep metagenomic sequencing to gain insight into the functional and genomic architecture of the rumen microbiome, identifying the key microbial taxa and genes. Our approach will use highly-phenotyped beef cattle (n=288) to discover and prioritise putative links between the microbiome and phenotypic performance. Host genetic and nutritional effects on the microbiome will be estimated utilising the unique structure of experimental data, including different sire progeny groups and diets. Preliminary analysis suggests a link between the microbiome, phenotypic performance, animal genetics and nutrition, but was not able to provide detailed information about the functional and genomic architecture of the ruminal microbiome affecting performance traits and whether and how these interact with the host animal and nutrition. This study will provide substantial insight into the structure and function of the microbiome and identity novel microbial genes. Based on the abundance of the microbial community and genes, the research will provide novel functional and genetic networks to explain the link between the microbiome, phenotypic performance and host genetics or nutrition (e.g. the cross-talk between host and microbiome). Comparative functional genomics will broaden the potential applications of the research.

Planned Impact

The beneficiaries of this research will include academic scientists, farmers, the livestock breeding and feed industries, national governments, climate scientists, environmentalists and the general public. The FAO predicts that by 2050, the human population will grow to over 9 billion people, and in the same time frame, global meat consumption is projected to increase by 73%. In order to address food security, as well as economic and environmental impacts of food production, sustainable intensification has been suggested by Godfray et al. (2010) - with genetic improvement of feed conversion efficiency of highest importance in farm animals. Rumen microbial fermentation confers a unique ability to efficiently convert human inedible feed (e.g. high-fibre forage) into food products, such as meat and milk, of high nutritional value. Performance traits, such as feed efficiency, vary substantially between cattle so that genetic improvement and nutritional intervention could have a substantial effect on the efficiency of using limited feed resources, as well as a major financial impact since feed is the largest variable cost in production. Furthermore, rumen fermentation contributes to greenhouse gas (GHG) emissions, in particular methane. Any marginal reduction in GHG emissions, achieved through genetic improvement, has the potential to contribute significantly to UK Climate Change Act commitments, including the need for an 11% reduction in agricultural emissions by 2020. Using animal breeding and nutritional interventions to alter the rumen microbiome is expected to improve feed efficiency, growth, body composition, meat quality or animal health and thus contribute to address the overall economic and environmental challenges. The academic partners (SRUC and Roslin Institute) have excellent links to the cattle breeding and feed industries, farmers and the entire food chain. They will ensure that any immediate impacts can be passed on, once IP has been suitably protected.
Overall, the research will deliver substantial contributions to fundamental understanding of the functional and genomic architecture of the rumen microbiome in bovines, whilst also offering insights for other ruminant species or monogastric species including humans. In particular, it will provide unprecedented new knowledge about the genomic and functional architecture of the microbiome and its impact on performance traits and methane emissions that will set the direction for animal breeding programmes and novel animal feeding strategies.
Comparative functional genomics will be used to uncover differences and similarities in functional and genetic architecture between species, providing unprecedented knowledge about the microbiome and host-microbiome interactions across species. In particular, we foresee longer-term benefits for research on host genetic effects on the rumen microbiota and its association with body composition (e.g. for human personalised medicine approaches to reduce obesity).
We will realise academic impact by publication of papers in high-impact peer-reviewed journals (open-access where possible), by presentations at scientific meetings and through deposition of datasets in public databases. We will also publish articles in trade journals to ensure that our findings are communicated to our stakeholders. SRUC and RI will present the project at public science events, such as the Roslin Open Doors Day, ensuring the general public are aware of our research and its importance. We will keep policy makers aware of the research findings and our appraisal of potential to help meet climate change targets in the medium- and longer-term. Significant findings will be communicated to the industry and general public through press releases and information on a specific project website hosted by SRUC.

Publications

10 25 50

 
Description • From the rumen of 43 Scottish cattle spanning 4 different breeds and multiple diets, we have assembled 913 novel microbial genomes, representing novel strains, species and genera of bacteria and archaea that live in the rumen and contribute to the breakdown of complex carbohydrates.
• Identified that diet has a large effect on the prevalence of AMR genes in cattle. Specifically, that the diversity and abundance of 204 AMR genes are significantly higher in abundance in concentrate-fed animals
• From 50 cattle and the associated rumen metagenome, we have defined a set of robust microbiome markers for methane emissions. 37 genes from the rumen microbiome, as part of our model including breed and diet, can explain 62% of the variance in methane emissions
• We have published MAGpy, a reproducible pipeline for the analysis of metagenome-assembled genomes (MAGs). This is an open source implementation that is available for anyone in industry and academia to use
• We have comprehensively reviewed the complex literature around biases in microbiome studies and have published a "consensus best practice" review which provides advice at every stage of the experimental process
Exploitation Route • We believe the 913 genomes we have published from the rumen microbiome will form the basis of hundreds of future studies into the structure and function of the rumen microbiome and how it contributes to beef and dairy production, and animal health and welfare.
• Our robust methane markers may be used as an intermediary phenotype in selective breeding for lower methane cattle
• Our AMR work may be used to adjust diets in cattle to help reduce the incidence of anti-microbial resistance genes in the human food chain
• Our software could be used by scientists throughout the biological sciences who wish to discover and annotate novel microbial genomes
Sectors Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology

 
Description We use the latest tools to assemble the genomes of important pathogens and commensal organisms; and we use metagenomics to study the structure and function of the rumen microbiome. These studies have resulted in the discovery of thousands of novel proteins which are of interest to our commercial partner Ingenza, a biofuels and biotechnology company. More widely, by making large datasets such as these available and demonstrating their novelty, we are pushing back the boundaries of human knowledge and enabling others to make similar discoveries. We have associated components of the rumen microbiome with methane emissions and feed-conversion-ratio, and demonstrated the microbiome is under host-genetic control. This will enable breeders and farmers to breed for both production (FCR) and environmental (lower methane emissions) traits.
Sector Agriculture, Food and Drink,Environment
Impact Types Economic

 
Description GCRF Data and Resources round 2
Amount £220,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 07/2018
 
Description Microbiome and metagenomic study of the rumen microbial population and their microbial enzyme genes
Amount £90,000 (GBP)
Organisation Government of Scotland 
Sector Public
Country United Kingdom
Start 09/2016 
End 09/2019
 
Title Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen 
Description This dataset represents 913 draft bacterial and archaeal genomes assembled from over 800 gigabases of rumen metagenomic sequence data derived from 43 Scottish cattle, using both metagenomic binning and Hi-C-based proximity-guided assembly. Most of these genomes represent previously unsequenced strains and species. The draft genomes contain over 1.2 million predicted protein sequences, and 69,000 proteins predicted to be involved in carbohydrate metabolism. ## Relation to earlier versions ## This data is referenced by Watson et al. (In Submission). A previous paper, in bioRXiv, referenced the earlier dataset "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2772. This in turn was superseded by the more recent version Hi-C genomes from "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" https://datashare.is.ed.ac.uk/handle/10283/2911. The paper underwent many rounds of review, the first-round revised paper referenced the second (Hi-C) dataset and the final, accepted version will reference the DOI of this dataset. The datasets changed in nature and in name during this process. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact The dataset is expected to underpin global rumen microbiome research in the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/3009
 
Title Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism 
Description The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of huge industrial interest. Despite this, rumen microbes are under-represented in the public databases. Here we present 220 high quality bacterial and archaeal genomes assembled directly from 768 gigabases of rumen metagenomic sequence data. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 13,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in the public databases. Inclusion of the 220 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a hugely valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact This dataset is expected to underpin research in rumen microbiomes over the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/2772
 
Title Hi-C genomes from "Assembly of hundreds of microbial genomes from the cow rumen reveals novel microbial species encoding enzymes with roles in carbohydrate metabolism" 
Description The cow rumen is a specialised organ adapted for the efficient breakdown of plant material into energy and nutrients, and it is largely the rumen microbiome that encodes the enzymes responsible. Many of these enzymes are of significant industrial interest. Despite this, rumen microbes are under-represented in public databases. Here we present 283 draft bacterial and archaeal genomes assembled directly from over 800 gigabases of rumen metagenomic sequence data and 43 samples, using both metagenomic binning and Hi-C-based Proximity-Guided Assembly. Comparative analysis with current publicly available genomes reveals that the majority of these represent previously unsequenced strains and species of bacteria and archaea. The genomes contain over 16,000 proteins predicted to be involved in carbohydrate metabolism, over 90% of which do not have a good match in public databases. Inclusion of the 283 genomes presented here improves metagenomic read classification by 2-3-fold, both in our data and in other publicly available rumen datasets. This release improves the coverage of rumen microbes in the public databases, and represents a highly valuable resource for biomass-degrading enzyme discovery and studies of the rumen microbiome. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
 
Title PRJEB21624 
Description This is one of the largest rumen metagenomics datasets ever released and represents 43 Scottish cattle from diverse breeds, different in methane emissions and feed conversion ratio. These data were used to assemble over 913 novel rumen microbial genomes. 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact These data were used to assemble over 913 novel rumen microbial genomes, which are expected to impact global rumen microbiome research over the next 5-10 years 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB21624
 
Description Aviagen 
Organisation Aviagen Group
Country United States 
Sector Private 
PI Contribution We are working with Aviagen to explore the role of the chicken gut microbiome in performance of their chickens in diverse environments. So far this includes the placement of one of their staff members in my group for a short period of time for training and development
Collaborator Contribution Aviagen provide access to large commercial flocks of chickens under both controlled and natural environments
Impact No outputs so far
Start Year 2017
 
Description Charoen Pokphand (CP) group 
Organisation Charoen Pokphand Group
PI Contribution Charoen Pokphand (CP) group are a large Asian conglomerate with an interest in farming, food production and feed additives. They have placed one of their staff members with me for PhD training, fully funded by them. We are training the staff member in laboratory and bioinformatics techniques related to microbiome research in chickens.
Collaborator Contribution CP provide access to large chicken flocks both in at their farms and in their production facility. This enables us to study chicken breeds in the actual environments in which they live throughout Asia.
Impact This is a multi-disciplinary project involving both laboratory and computational techniques. The major outcome so far include a review paper (http://aem.asm.org/content/early/2018/01/29/AEM.02627-17.abstract) and the technology transfer from our group into the commercial partner.
Start Year 2017
 
Description SRUC - Rainer Roehe 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution We have collaborated with Rainer Roehe at SRUC since 2011, and we provide expertise in genomics, DNA sequencing, metagenomics and bioinformatics. We use this to investigate the role of the microbiome in methane emissions and feed conversion ratio.
Collaborator Contribution The SRUC partners provide expertise in rumen biology and function, alongside samples collected and measured for methane emissions and feed conversion ratio
Impact • Rumen metagenomics: we have sequenced the rumen metagenome of 8 cattle selected for high- and low- methane emissions, matched for breed and diet; and we have demonstrated that high methane emitters are enriched for (i) methanogenic Archaea and (ii) enzymes involved in the methane production pathway. Of the latter, we show that there exists over 5000 novel versions of known enzymes involved in methane production. We have made available a database of over 1.9 million proteins, the majority of them novel, as part of this study (10.1186/s12864-015-2032-0) • Host control of the microbiome: using the same dataset, we demonstrate that largely speaking the rumen microbiome structure and function if under genetic control; and can be significantly associated with both methane emissions and feed-conversion-ratio (FCR) (journal.pgen.1005846) • We have subsequently sequenced over 300 Scottish cattle rumens as part of a project funded by BBSRC. These ruminant metagenomes have resulted in the assembly and publication of several hundred novel rumen microbial genomes (10.1101/162578), publication of a novel pipeline for annotating such genomes (10.1101/233544), publication of robust methane markers in across multiple breeds (10.3389/fmicb.2017.02642) and associations between diet, rumen microbes and anti-microbial resistance (10.1186/s40168-017-0378-z)
Start Year 2011
 
Description The University of Aberdeen 
Organisation University of Aberdeen
Department Institute of Medical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution We have been working with Alan Walker and Tim Snelling in the field of rumen metagenomic profiling
Collaborator Contribution Alan and Tim are experts in rumen microbiology and 16S sequencing, whereas my group is expert in whole-genome-shotgun metagenomics and bioinformatics
Impact As part of a Scottish government project, we have sequenced 90 rumen metagenomes using whole genome sequencing, and almost 300 using 16S profiling. Data analysis is ongoing, but my team have assembled hundreds of microbial genomes from the rumen (10.1101/162578) and written a pipeline for analysiing such data(10.1101/233544)
Start Year 2016
 
Title MAGpy 
Description Recent advances in bioinformatics have enabled the rapid assembly of genomes from metagenomes (MAGs), and there is a need for reproducible pipelines that can annotate and characterise thousands of genomes simultaneously. Here we present MAGpy, a Snakemake pipeline that takes FASTA input and compares MAGs to several public databases, checks quality, assigns a taxonomy and draws a phylogenetic tree. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact This software was used to annotate 913 metagenome assembled genomes from the cattle rumen, a dataset which is expected to underpin rumen metagenomics research for the next 5-10 years 
URL https://datashare.is.ed.ac.uk/handle/10283/3009
 
Description Animal Microbiome Congress London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson presented his work on functional microbiome analysis at the Animal Microbiome Congress London. Attendees included industry/business, farmers, professional practitioners and academics
Year(s) Of Engagement Activity 2017
 
Description Aviagen / CP workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I presented our work on functional microbiome analysis during a one-day workshop which I set up and organised at The Roslin Institute. In attendance were employees of CP (a large Asian conglomerate) and Aviagen (one of the world's largest chicken breeding companies). The focus of the workshop was animal genetics and microbiome.
Year(s) Of Engagement Activity 2010,2017
 
Description Evonik research day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact I presented my work on precision analysis of microbiomes to Evonik, an international company with over 13000 employees and with interests in chemical and food production. This was part of a one day workshop with Evonik, hosted by Roslin and focused on microbiomes
Year(s) Of Engagement Activity 2018
 
Description ISAG 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson presented work on cutting edge techniques that can be used to analyse metagenomics sequence data. ISAG is the international society for animal genetics and this was the very first microbiome session. In attendance were industry practitioners and academics
Year(s) Of Engagement Activity 2017
URL http://www.isag.us/2017/
 
Description Mick Watson Roslin Industry Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Mick Watson presented on how genomic technologies are transforming biological research, to an audience of industry and professional practitioners invited to The Roslin Institute to discuss science and policy
Year(s) Of Engagement Activity 2016
 
Description PAG 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Mick Watson gave a talk at PAG 2017 on Comparison of Methods for Functional and Phylogenetic Characterisation of Rumen Metagenomic Data. Attendees include industry, professional practitioners and academics
Year(s) Of Engagement Activity 2017
 
Description PAG 2018 microbiome talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a talk on microbiome bioinformatics at PAG 2018 in San Diego in the microbiome session. PAG includes attendees from industry, farming and academia.
Year(s) Of Engagement Activity 2018
 
Description Rumen microbiome article in Farmer's Weekly 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Mick Watson was personally interviewed for an article in Farmer's weekly on the potential impact of our rumen microbiome work (doi:10.1038/s41467-018-03317-6) on breeding for production traits in beef and dairy cattle.
Year(s) Of Engagement Activity 2018
URL http://www.fwi.co.uk/livestock/rumen-genotyping-advances-enhance-cattle-breeding.htm
 
Description Rumen microbiome work in the national press (print editions) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Various articles about our rumen microbiome work appeared in the national press, including: Scottish Daily Express, Scottish Sun, The Scotsman and the Press and Journal
Year(s) Of Engagement Activity 2018
URL https://www.pressandjournal.co.uk/fp/business/farming/1427948/cow-digestion-discovery-could-boost-pr...
 
Description Rumen microbiome work on National Public Radio (NPR) in the USA 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Our rumen microbiome work was featured on NPR.org, (National Public Radio), a US news network that has over 7 million followers on Twitter and reaches millions of people online and via radio. The article was immediately syndicated across an additional ~40 NPR-associated websites
Year(s) Of Engagement Activity 2018
URL https://www.npr.org/sections/thesalt/2018/03/06/589997622/mysteries-of-the-moo-crobiome-could-tweaki...
 
Description Various articles on rumen microbiome work 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Various online websites picked up our press release on our rumen microbiome work (doi:10.1038/s41467-018-03317-6) including:
https://phys.org/news/2018-02-dna-cow-stomachs-aid-meat.html
https://www.sciencedaily.com/releases/2018/02/180228085347.htm
http://www.labmanager.com/news/2018/02/dna-study-of-cow-stomachs-could-aid-meat-and-dairy-production#.WpwhWOjFLZs
https://www.technologynetworks.com/genomics/news/cows-guts-could-hold-secrets-to-more-meat-and-milk-298080
http://www.sciencenewsline.com/news/2018030111510072.html
https://www.eurekalert.org/pub_releases/2018-02/uoe-dso022718.php
http://biofuelsdigest.com/nuudigest/2018/02/28/cow-stomach-microbes-could-hold-key-for-increased-food-and-biofuel-production/
Year(s) Of Engagement Activity 2018
URL https://www.sciencedaily.com/releases/2018/02/180228085347.htm