New approaches to resolving community metaproteomes: ComProt

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

Abstract

Understanding interactions between organisms in an ecosystem is a critical part of ecological research and facilitates our understanding of how ecosystems function and this is particularly important for microorganisms and microarthropods as they are often difficult to study in situ in real time. Currently the natural environment faces many challenges and we need to be able to measure the impacts of changes in climate, pollutant levels, intensive farming and development of ley systems to understand how resilient communities are and how Carbon, nitrogen and phosphorous cycles are affected.
Microrganisms play a vital role in our environment they occupy a wide range of habitats from our 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 and we are focused in this projects on the proteins produced termed metaproteomic. Proteins equate with activity as all enzymes are proteins and act as catalysts for reactions. Therefore, we can use the metagenomes to help in identifying which proteins are present because there is a relationship between the DAN code and the sequence of peptides in a protein. Making this link is challenging so we aim to improve the understanding of how to translate a series of peptide sequences into functioning proteins and recognise both their origins and putative function.
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.

Planned Impact

The research has relevance to the study of the microbiome and interactions between microbes and their hosts which will be important in wildlife health and physiology to study host protein production in the gut, in humans for immune reactions or overreactions in gut pathologies and really put a strong focus on the interactions between microbiomes and their environment whether it is a river bed, waste water treatment plant or plant rhizosphere. The study of protein provides an opportunity to understand physiology and nutritional interactions important in biogeochemical cycles, soil fertility, decomposition and molecular ecology.
The new approach to directly uncovering enzyme diversity has very significant impact on the potential for exploitation of these enzymes for a wide range of applications. Academia as well as the biotechnology industry that is involved in food and waste management is continuously in search of novel enzymes able to degrade recalcitrant natural polymers such as chitins and lignins, and/or polluting man-made compounds such as halogenated aliphatic and aromatic compounds. In particular, biochemical transformations that bring novel opportunities to key industries involved in environmental sanitation and in the agricultural / pharmaceutical / chemical / food areas are of interest. Thus, a strong demand has developed concerning the production of novel enzymes of several classes. Although this project is supporting science it is providing the scientific community with the tools to exploit new ultra sensitive MS-MS systems to provide spectral analysis of minute quantities of peptides and this will facilitate take-up of the technology and encourage the study of metaproteomics and metaexoproteomics as a stepping stone towards significant improved understanding of microbial diversity. Funding this research will mean that in the long term we will have access to untapped enzyme biodiversity for exploitation for pollution control, clean energy generation and improved waste water effluent to name just a few of the applications. Metagenomics has become widely accepted in all parts of environmental research so it is now timely and important to take the next level of analysis to function thus achieving by the use of appropriate bioinformatics the link between structure and function.

Publications

10 25 50
 
Description This funding supported two workshops one held in Warwick and one in Sheffield. The first established a group of key workers based at both Warwick and Sheffield to prepare data for the second workshop to use as illustrations of work flows and extraction methods. We achieved the following activities:international exchanges and data analysis comparisons with key European and US groups, pipeline advice and improved information provided on website. Encouraged the development of a network of active researchers all interested in metaproteomics in relation to microbiome function and the optimal approaches to protein identification using metagenomic and MAG data.
Exploitation Route New freeware for analysis of metaproteomes with advice from a research technology platform (RTP) established at Warwick University with expertise in microbiome analysis and integration of metaomic data particularly for metaproteomics to enable activities of enzymes to be investigated
Sectors Agriculture, Food and Drink,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

URL http://www.metagenomics.uk
 
Description Increased the awareness and understanding of how microbial activities can be defined in situ and also new enzymes can be discovered, in particular enzymes involved in biodegradation and bioremediation in the environment. Allowed discovery of new enzymes involved in polymer degradation in soil which can be used for sustainable agriculture and recycling of organic phosphates. Microbial community degradation of toxic waste products, antibiotics and industrial effluents.
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Environment
Impact Types Economic

 
Description Development of point of care diagnostic test for pathogens in the Mycobacterium tuberculosis complex 
Organisation Bee Robotics Ltd
Country United Kingdom 
Sector Private 
PI Contribution Establish the molecular targets, design of the LAMP primers and establish the approaches to extraction procedures. Defined new loci for targeting detection of pathogen DNA in samples and beta tested specificity and sensitivity of the assay. Tried a range of extraction procedures, confirmed amplicon by minION long read sequencing.
Collaborator Contribution Provision of chemistry expertise, design of housing for the test and approaches to producing field based test.
Impact Multi-disciplinary collaboration still in progress
Start Year 2019
 
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 Antibiotic resistance in the environment- implications for human health 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentations during a partnering meeting with Thai University as part of a Symposium in the Faculty of Medical Sciences, Naresuan University, Thailand. The meeting focused on the problems of antibiotic resistance, new approaches to finding new antibiotics and new ways to treat bacterial infections. It involved excahnge of ideas with University of Warwick staff and those of Leicester and Nottingham Universities and the host University of Naresuan, Thailand.
Year(s) Of Engagement Activity 2019
 
Description CMI International Microbiome Meeting San Diego 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Workshop held at Scripps Centre as part of the Centre for Microbiome Innovation held a meeting on microbiomes and we presented on integration of metagenomics and metaproteomics related to antibiotic resistome in UK rivers.
Year(s) Of Engagement Activity 2019
 
Description Presentation of results regarding the impacts of antibiotic use in society on ecology of resistance in rivers 'What impacts do antibiotics have on environmental microbiomes?' 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation given on the way in which human waste is processed and discharged from Waste Water Treatment Plants (WWTPs) into rivers in the UK illustrated by the WWTPs on the Thames across the whole river catchment. Measuring the impact on the riverine microbiome provides evidence of ingression of resistance genes into the indigenous bacterial populations in the river in addition to demonstrating significant survival of pathogens in the river sediment. Also significant levels of drugs including antibiotics were detected in the river and were associated with high levels of resistance genes, which was correlative and not necessarily causative.
Year(s) Of Engagement Activity 2019
 
Description Prioritising the action on environmental AMR 
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 Hong Kong May 2019 meeting at part of the Wellcome Organisation host this initiative held at the EDAR International Meeting (Environmental Dimension of antimicrobial resistance)
Year(s) Of Engagement Activity 2019