Microbiome 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 the environment.

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The Pandhal group are using top-down engineering (complex to simplified consortia) and bottom-up (synthetic mixing of isolates) to generate microbial consortia that are able to out-perform existing communities but also enable them to recover resources, such as nutrients, metals and plastics. We use tools such as metaproteomics and our in-house constructed AMEn (Automated Microbial EvolutioN) machine pictured above.

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Background

Historically, humans have exploited microbial communities for a variety of processes e.g. beer and wine fermentation, and more recently biomanufacturing and bioremediation. Consortia hold several major advantages over monoculture: (i) Perform tasks which are metabolically incompatible within one strain e.g. lignocellulose breakdown (ii) Increased resilience to environmental fluctuations (typical of wastewaters) (iii) Parallel pathways for substrate processing and hence a more resilient system (iv) Lower cultivation costs (i.e. knowledge and capital), particularly at large-scale. For example, within waste treatment, microorganisms are often sourced locally and these naturally diverse assemblages are stable, benefitting from years of adaptation. Engineering these microbial consortia could further advance treatment rates (e.g. select for “high performing” species by removing functional redundancy) but also incorporate the bio-manufacture of green chemicals. Only now is the technology to perform the experiments rapidly and controllably being developed, as well as advanced modelling approaches.

We are also entering the era of microbiome engineering There has been a surge of interest in recent years to understand the composition of microbiomes, be it in humans/animals or in the environment and relate these to physiology and psychology of the host, or productivity of agriculture, respectively. With recent advances in genome sequencing and meta-omics (metaproteomics, metagenomics), microbiome research has led to the exciting prospect of controlling the functionality of microbiomes. Some would argue that it has already begun, through administration of probiotics and faecal microbiota transplants. However, the real challenge is whether we can design functionally desirable microbial consortia by applying engineering principles.

Industry need to exploit biodiversity with better control and prediction Optimising the performance or increasing the functionality of an industrially relevant microorganism depends on incorporating multiple genes within a consolidated bioprocessing strain. This is largely undertaken under the banner of ‘synthetic biology’. However, this often leads to metabolic burden with reduced process efficiencies. Utilising microbial consortia is an attractive alternative, adding stability and lowering costs, and designing optimal communities is often considered a goal of ‘synthetic ecology.’ However, optimising these uncharacterised and non-cultivatable microbial species for industry is a considerable multi-disciplinary challenge.