The exploitation of metagenomics and meta-omics approaches in life science research; community network in metagenomics

Lead Research Organisation: University of Warwick
Department Name: School of Life Sciences

Abstract

Microrganisms play a vital role in our environment they occupy a wide range of habitats from our onw gut and body surfaces all the way to hot vents under the sea, they are critical in the soil for recycling of nutrients and plant health and responsible for the essential digestion of cellulose from grass being broken down in the specialised stomach of the cow termed the rumen to the global cycling of carbon in the oceans via harvesting of sunlight as many bacteria can photosynthesize and thus harvest light energy to fix carbon dioxide. A major problem exists in our ability to study the physiology and overall activities of these microbes due to the fact that we cannot isolate and cultivate (yet) the vast majority (probably over 98%) of them in the laboratory. We know they exist because we have used methods similar to DNA forensic approaches to detect them solely based on their DNA using signature genes which allow us to identify and group them. Most of this diversity is bacterial but there are also several groups of fungi. New methods are being developed for the study of these microbial populations and this is called metagenomics so that we study the microbial community as a population of many genomes rather than trying to isolate and study one. We can study this population in our guts or in the soil by extracting and analysing DNA for diversity analysis, RNA for gene expression and protein for confirmation of activities and metabolites to determine physiology. In addition we can extract DNA and express it in other bacteria which are culturable. This allows us to capture the DNA and express it thus gaining an insight into some functions such as specific enzymes or pigments with special properties. The imof the proposed work is to establish a network of academic partners to build capacity in this important area of science to ensure that we are able to study and exploit all the interesting and exciting attributes of bacterial populations and harness them for a sustainable future.

Technical Summary

The microbial populations existing in nature can be viewed as a community and their genomes considered as polygenomes which is the approach of metagenomics. The aim of the proposed community network is to improve our ability to use metagenomic techniques to undertake a range of research activities and within the network we aim to consider three main approaches embodied in the work packages A, B and C as follows: WPA Metagenome exploitation- expression tools; WPB Metagenomic population structure and function- pipeline tools; WPC Integration of data sets; meta-omic analysis. As a network we aim to improve existing capacity and build new and in additional develop new research tools to enable statistical and modelling analysis. The three areas will also be the subject of three main workshops held one per year over three years. Other activities will be a web site and online research tools hosted by Warwick University together with a virtual learning environment which will allow members of the network to improve their skills in analysing the complex data produced by studying metagenomic populations. The workshops will consider both statistical approaches for the in depth analysis of metagenomic DNA, RNA and protein/metabolites but also focus on the technical difficulties of the experimental work. For the full exploitation of biodiversity we need to gain access to the properties of microbial populations hence the focus on metagenomic library construction and screening for novel properties. International experts will be invited to the workshops and scientists will also be encourage to network with them and each other to build capacity. Technology transfer will also be achieved by short exchanges of personnel between universities in the network.

Planned Impact

This research will benefit the scientific community by providing tools and guidance to how we can study uncultured biodiversity in microbial communities, and how it is possible for us to exploit these biologically diverse bacterial communities in a wide range of environments. The outputs of the network will facilitate study of microbial communities as a whole and the web site will provide guidance on how to deal with the significant diversity when working with metagenomic DNA, RNA and proteins and or metabolites.
Meta-omics is in its infancy and has only very recently been applied to the study of microbial communities but promises to be a valuable complement to the latest extraction and analysis of metagenomic DNA. Guidance, online tools and capacity building for the development and application of these cutting-edge techniques will provide important information for other life scientists trying to disentangle the relationship between members of microbial communities and also their interactions with their hosts or other members of the environment such as plant roots, insects and other eukaryotes.
Guidance on new approaches to exploiting metagenomic libraries and Identification of novel genes and enzymes will be of interest to biotechnology companies. The general public have an interest in their gut microbiota, but also in microbial interactions with plants and animals. Synthetic biology approaches will seek to exploit and manipulate these communities to reduce our dependence on chemicals, drugs and make a more sustainable future.
Outreach activities from the project will provide answers to the way in which we can study the uncultured majority of bacteria and exploit their diversity.

Publications

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Quince C (2017) Shotgun metagenomics, from sampling to analysis. in Nature biotechnology

 
Title Methods manual for schools to do microbial community analysis 
Description Resources for workshops to run at primary schools have been developed and been run at local schools. These can be differentiated to suit different age ranges. The first workshop was 'Yeastie Beasties' exploring the use of yeast in food and biotechnology, and considering growth requirements, whilst inflating yeast balloons with the CO2 generated. The second workshop was 'Marvellous Microbes' which explores the microscopic world around us. It considered microbes as not only pathogens, but also essential for human health and present all around in great numbers and diversity. Brightly coloured EM images of bacteria (http://ngm.nationalgeographic.com/2013/01/125-microbes/wolfe-text) beautifully illustrated these concepts (Figure 4) as well as providing inspiration for the creation of colourful play-dough models. 
Type Of Art Artwork 
Year Produced 2016 
Impact Children motivated to read more about microbiomes and metagenomes 
URL http://www.metagenomics.uk
 
Description A network of scientists was established to promote exchange of expertise and encourage interest in the topic of metagenomics and the study of whole community genomes collectively with the emphasis on microbial communities. The aim of disseminating methods, bioinformatic tools and analytical approaches was achieved by holding a series of workshops, coupled with development of a website and exchange of personnel across labs within the UK.
Exploitation Route Improved web tools and better communication between academics to collaborate and combine expertise.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

URL http://www.metagenomics.uk
 
Description Improved awareness of the value microbial communities have in areas such as human health and the gut microbiome, with the increased economic interest in exploring and exploiting microbial communities. Metagenomics has facilitated the exploration of microbial community diversity as many species have never been obtained in pure culture and there has been development of a new way of defining host-microbe interactions in terms of benefits and mutualism.
First Year Of Impact 2016
Sector Agriculture, Food and Drink,Environment,Healthcare,Leisure Activities, including Sports, Recreation and Tourism,Government, Democracy and Justice,Pharmaceuticals and Medical Biotechnology
Impact Types Cultural,Societal

 
Title Novel enzymes 
Description Novel enzyme assay and enzyme activity relating to phosphate solubilisation 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2017 
Provided To Others? No  
Impact Important for commercial exploitation of bacteria in the rhizosphere of plant for improved supply of inorganic phosphate 
 
Description Collaboration with Prof Chris Quince on recovering genomes from metagenomes 
Organisation University of Warwick
Department Warwick Medical School
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of data and metagenomes, experimental and field work expertise.
Collaborator Contribution Expertise in bioinformatics
Impact Data base of metagenomes to be added to EBI metagenomes portal and also for use with workshops on analysis of metagenomes in ComMet workshop
Start Year 2016
 
Description Environmental reservoirs of microbial pathogens 
Organisation National University of Sciences and Technology
Department Institute of Environmental Sciences and Engineering (IESE)
Country Pakistan 
Sector Academic/University 
PI Contribution Working on developing bids for GCRF and other funding agencies to halt the spread of microbial pathogens and AMR in the environment
Collaborator Contribution Hosted a workshop and paid our team's expenses to visit and work in a collaborative pilot study in addition to talks and visits to field sites
Impact The collaboration resulted in the analysis of field sites to consider the environmental reservoirs of microbial pathogens and understanding transmission pathways through water and food chain routes.
Start Year 2019
 
Description Environmental reservoirs of microbial pathogens 
Organisation University College of Islamabad
Country Pakistan 
Sector Academic/University 
PI Contribution Working on developing bids for GCRF and other funding agencies to halt the spread of microbial pathogens and AMR in the environment
Collaborator Contribution Hosted a workshop and paid our team's expenses to visit and work in a collaborative pilot study in addition to talks and visits to field sites
Impact The collaboration resulted in the analysis of field sites to consider the environmental reservoirs of microbial pathogens and understanding transmission pathways through water and food chain routes.
Start Year 2019
 
Description Korean partnering on metagenomics and microbiome analysis 
Organisation Chung-Ang University
Country Korea, Republic of 
Sector Academic/University 
PI Contribution Understanding the risk posed by the widespread dissemination of antimicrobial resistant bacteria (AMRB) and pathogenic variants (AMRP) in the environment depends on persistence of the bacteria and the resistance genes (ARGs). ARGs can move into indigenous environmental bacteria but risks of infection will be reduced or removed. What has been observed is the high diversity of resistance genotypes in waste water polluted environments coupled with the expansive diversity of the environmental resistome and so the extensive mixing of human and animal wastes with environmental bacteria particularly in the presence of antibiotics could produce AMRP capable of extensive resistance phenotypes. Uncertainty exists over the longevity and activity of AMRP in the environment outside of their hosts and to what extent they may participate in gene exchange so current work in both the Cha and Wellington groups is focused on this aspect and finding new ways of monitoring AMRP and their activities. Thus we identified two major challenges in understanding risk in environmental exposure to AMRP which relates to viability and ARG acquisition. In the form of two workshops and exchange of personnel the Wellington group members Dr Chiara Borsetto and Dr Robert James demonstrated their methods for using long read sequencing to gain an improved analysis of resistance genes in the environmental resistome, Chiara Borsetto talked about using mesocosms to establish if sublethal levels of antibiotics in the environment select for resistance phenotypes or are simply collocated with already resistant bacteria in waste water effluent. By characterizing the host genome it is possible to establish if the resistant bacteria are human adapted or environmental bacteria. From our work on river flumes used to model impact of waste water effluent in UK rivers it appears that sublethal antibiotic has a distinct impact on the prevalence of the relevant resistance genes.
Collaborator Contribution Professor Chang-Jun Cha's group have expertise in bioinformatics and hold a resistance gene database in addition to having a WaferGen SmartChip machine and the arrays which can detect very sensitively over 300 types of resistance genes using PCR conducted in hundreds of minicells.We were given access to this machine and were able to compare results and also establish diversity and new combinations of various mobile genetic elements. We aim to write a position paper comparing our results on anthropogenic impacts on Thames riverine microbiome compared with the study they are conducting on the Han river in South Korea. They provided access to databases and SmartChips plus shared sequences and databases.
Impact Two papers are in progress and one submitted currently: Submission no: ENVINT_2019_218, Submission title: A novel sulfonamide resistance mechanism by two-component flavin-dependent monooxygenase system in sulfonamide-degrading actinobacteria Corresponding author: Professor Chang-Jun Cha, Listed co-author(s): Dr Kihyun Lee, Dr Cung Nawl Thawng, Professor Elizabeth Wellington, Dr Dae-Wi Kim.
Start Year 2018
 
Description Public Science Evening 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation given at an evening event on the Microbiome event to inform the public about the importance of bacteria in the human gut, in the soil and in the bioremediation of polluted environments.
Year(s) Of Engagement Activity 2017
 
Description Public science evening 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact At the public science evening "The microbes on us and around us: We can't see them but can't live without them" hold at the university, the general public was introduced to the issue of AMR dissemination in the environment through oral and poster presentations followed by discussion in small groups with member of the team working on AMR. The Department reported an increased interest and understanding in the related subject area.
Year(s) Of Engagement Activity 2017
 
Description US-UK Microbiome Workshop San Diego and Los Angeles UK Science & Innovation Network British Consulate-General, Los Angeles 14th -18th March, 2016 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact • Statistical Training: Training for informaticians in microbiology and training for microbiologists in bioinformatics. Along with this, how to make sense of particular tool results.
• Having appropriate quality control standards. Researchers being aware and honest about the stability of certain bacterial classes. Along with this, how to tackle issues of sampling and faecal variability.
• Multi-meta-omic datasets. We are now beginning to see the different methods applied to study a single biome project. The data need to be archived systematically and analyses across the different datasets coupled.
• Informatics analysis is limited by the quality of reference databases. How can the community work together to strategically expand the repertoire of complete genomes and their interpretation?
• Data reusability. I.e., curation of the microbiome datasets, generated by everyone for diverse research purposes, such that they can readily be interrogated by the research community to answer very different questions, robustly into the long-term.
Year(s) Of Engagement Activity 2016
URL http://www.metagenomics.uk
 
Description Used method for part of a workshop on metagenomics network sponsored by BBSRC 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Training in methods needed for metagenomics and this included how analysis of habitat or sample total DNA, RNA and protein can be analysed for community functional studies. The primary focus was on bacteria and fungi but as proteins were analysed data was presented on total sample components including proteins from plants and animals. Purpose was to inform participants of the benefits of protein analysis and pitfalls when trying to identify proteins. Many attendees were motivated to try these new approaches.
Year(s) Of Engagement Activity 2009,2015,2016
URL http://www.metagenomics.uk