Engineering Microbial Consortia for Industry

Lead Research Organisation: University of Sheffield
Department Name: Chemical & Biological Engineering


Microbial communities inhabit our entire planet and play a vital role in biogeochemical processes through to human health. Although we have exploited these consortia for a variety of biotechnology processes, rapid technological advances have led to the emerging field of 'microbiome engineering', ripe for exploitation across a plethora of industries, and play a major role in facing grand challenges in health, food, energy and environment. This travel grant is focussed on translating knowledge of natural microbial diversity data, and combining this with expertise in microfluidic screening platforms, quantitative omics technologies and mathematical models to describe mixed-culture interactions for generating synthetic microbial consortia for industry.

Our previous work has revealed fundamental mechanisms by which microbes work together and we have translated this for industry at pilot scale. However, we have also encountered many unknowns to advance the field into more complex systems, particularly where we can recover multiple resources from waste, rather than just detoxify it.

To enable us to move into more design led approaches for constructing microbial communities, I have identified global leaders in their field, and the goal is to exchange knowledge and data and generate new exciting and ambitious grant proposals in engineering microbial consortia for industry.

Planned Impact

The UK currently has limited research groups looking to engineer microbial communities. Contrarily, the USA is putting more resources and emphasis on developing the area, largely for healthcare and agriculture. This overseas travel grant will enable Dr. Pandhal to better understand the emerging techniques and approaches being employed, impacting on UK competitiveness in this engineering field.

The impact of this research is wide as any industry currently utilising microbial communities will have a tool box to engineer them for high performance or stronger resilience. For example- industrial biotechnology, food/beverage, bioremediation, waste management, resource recovery etc. The specific focus of our previous research and therefore more immediate for this proposal is waste treatment and resource recovery, which represents an exemplar application for knowledge and data exchange. From a technology perspective, the synthetic ecology/biology community will benefit from a methodology to create synthetic consortia, as well as analytical processing to screen co-cultures with associated omics analyses.

Impact will be seen across existing industries who have increasingly stringent regulations to meet in terms of waste treatment (e.g. EU Urban Waste Water Directive 91/271/EEC), industries with a desire to be more sustainable and use biological methods over chemical/physical approaches, and recover resources (circular economy). Engineering microbial communities has significant potential in more recently emerging industries too, including human health (gut microbiome) and agriculture (soil microbiome).

Due to the sustainability aspect of exploiting microbial communities, the more long term impacts on reducing resource use and waste production, as part of a circular economy, would have profound impact on ecosystem health, improving human-associated uses such as recreational water use (e.g. fishing, water sports, swimming, boat clubs etc.) and industry (fisheries etc.), as well as benefit to the natural environment (e.g. wildlife), and increase the opportunity to achieve "good ecological status" (National UK Ecosystem Assessment by Defra).

The interaction with World leading groups would be invaluable for Dr. Pandhals career progression. As well as generating new ideas and sharing knowledge, he is expected to generate further grant proposals to help understand rules governing the presence of specific microbes and the interactions between them. e.g. UKRI, Industry Challenge Strategy Fund.
Description This was a networking grant where I visited various labs around the World to learn new tools on how to engineer microbial consortia. These included new experimental approaches through to modelling type analyses to infer rules on how to create synthetic microbial consortia.

The contacts I have made have led to several collaborations 1. B. Dutilh with a shared student 2. S. Mayfield and mapping glycosylation of therapeutic proteins expressed in algae

My research proposal based on this grant for £1m was ranked 6th in responsive mode, sadly only the top 5 were funded. This gave me sleepless nights for a while but now has motivated me to re-submit with a few changes.
Exploitation Route We aim to publish approaches used which can assist others in advancing and improving processes where microbial communities are exploited e.g. waste management, resource recovery, decarbonising systems.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Energy,Environment,Manufacturing, including Industrial Biotechology,Transport

Description So far, I have increased my global network in this research. Although academic impact has already been realised, increased contacts has been useful for communicating with new industry partners. A new grant submission to the Sheffield Innovation Partnership has been completed with Matsya Technologies.
First Year Of Impact 2022
Sector Manufacturing, including Industrial Biotechology
Impact Types Economic

Description Defence and Security Accelerator (DASA)
Amount £300,000 (GBP)
Organisation Ministry of Defence (MOD) 
Sector Public
Country United Kingdom
Start 03/2021 
End 03/2021
Description Developing, understanding, and harnessing modular carbon/nitrogen-fixing tripartite microbial consortia for versatile production of biofuel and platform chemicals
Amount $1,500,000 (USD)
Funding ID DE-SC0022136 
Organisation U.S. Department of Energy 
Sector Public
Country United States
Start 03/2022 
End 11/2023
Description UKRI Interdisciplinary Centre for Circular Chemical Economy
Amount £4,436,401 (GBP)
Funding ID EP/V011863/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 01/2021 
End 12/2024
Description DASA Ministry of Defence 
Organisation Ministry of Defence (MOD)
Country United Kingdom 
Sector Public 
PI Contribution We will create a microbial community to degrade MoD waste. We will also perform a TEA of the process.
Collaborator Contribution Provision of waste, guidance for objectives.
Impact The grant has just started
Start Year 2020
Description Synthetic microbial tri-culture 
Organisation University of Michigan
Country United States 
Sector Academic/University 
PI Contribution We have undertaken experiments to generate preliminary data for quantitative proteomics in the trial-culture.
Collaborator Contribution Our partner, Dr. Nina Lin at the University of Michigan has submitted a grant for engineering this consortium. We are a member of this team
Impact We have submitted a grant to the NSF and are waiting for reviews.
Start Year 2020