Searching for green chemistry in culture collections

As society seeks to cut pollution and tackle climate change by phasing out fossil fuels, the issue of sustainable chemical production becomes ever more important. It is essential, and indeed paramount, that new sustainable ways of producing commodity and speciality chemicals are found.

Biotechnology offers a route to sustainable manufacturing through harnessing the biochemical pathways of microorganisms to produce high-value chemicals, with less energy usage and waste than traditional manufacturing approaches. The National Collection of Industrial, Food and Marine Bacteria (NCIMB) has a focus on strains with industrial applications and so is well placed to play a central role in this new era, providing solutions to this and other pressing issues. However, while there are many examples of bacteria in this culture collection that have been studied with respect to their ability to carry out chemical transformations, such as the production of acetone or butanol, the full potential of the collection as an industrial biotechnology resource has yet to be realised.

While advances in gene sequencing facilitate more rapid microbial screening for specific, industrially relevant metabolic functions than was historically possible, there are still barriers. Most notably, in order to do that screening, it is necessary to first find an organism that carries out that function and then identify the gene sequence that is associated with it. This basic work still needs to be done for many biochemical pathways, and this has held back efforts to identify new microbes with industrial potential. NCIMB’s culture collection started in the 1950s and since then has acceded over 10,000 strains. Unfortunately, many special properties of these strains remain unknown, and therefore a significant programme of work will be required in order to meet the needs of industry in a post-fossil fuel era.

In an effort to address this, a collaborative project involving NCIMB and the University of Edinburgh kicked off earlier this year to screen microorganisms from the NCIMB collection for their ability to perform new chemical transformations of interest to the UK’s industrial biotechnology and chemical manufacturing sectors. The project is a great example of how we can start to accelerate efforts to discover new sustainable solutions to the biological production of high-value chemicals by accessing the untapped potential held within culture collections. The project has the ultimate aim of replacing current energy- and waste-intensive petrochemical transformations with renewable bio-based alternatives that can be applied to high-value manufacturing.

Discussions with the chemical industry provided the starting point for the work, highlighting two chemical reactions for which there are currently no sustainable or biological alternatives available. The first is an important reaction within pharmaceutical manufacture and is an enabling reaction in organic chemistry. Despite mechanistic similarities to reactions in nature, no enzyme has been identified that can replicate this chemistry. This limits what can be achieved by searching microbial genomes in silico for homologues to known enzyme families. This is important as the future availability, overuse and high cost of chemical catalysts in manufacturing is a limitation of existing approaches and the sector’s ambitious future net-zero sustainability targets.

The second reaction included in this project is applicable to the recycling of the persistent waste products from existing chemical manufacturing processes. Building new, microbiological initiatives to these problems may reduce emissions through reducing the amount of new stock required to keep fundamental synthetic chemical reactions running – ultimately improving the greenness of these processes and allowing their continued use in the future, without the need to overhaul large parts of established infrastructure, the technology for which often still lags behind.

The first step in the project was to put together a shortlist of candidate strains for each pathway using, for example, attributes such as known tolerances to organic habitats, salinity and high temperatures. The next step was to capitalise on the diverse range of pre-existing information about the collection, gathering examples of sequenced and unsequenced genomes, explored and unexplored, recently identified and historic strains alike. This allows us to investigate strains that may have been untouched since being deposited, but also enables us to re-explore other microbes through the lens of applied microbiology. Through doing so, we mirror the first modern biocatalytic discoveries by Louis Pasteur, and may identify chemistries previously missed by bioinformatics.

Culture collections are fantastic genetic resources that have often grown over many decades, preserving microorganisms that have been isolated over the course of all kinds of research programmes, and the NCIMB collection includes strains isolated from some of the most extreme environments on earth. Over millions of years, microbes have evolved to develop the diversity of biochemical pathways that allow them to survive, compete and thrive in these environments. The scientists who preserved some of the earlier deposits could never have foreseen what the future requirements of the bio-manufacturing sector would be, but the information recorded in the catalogue entries with respect to observed characteristics, isolation site and growth requirements can often indicate strains that might be a good starting point for new areas of research.

To date, we have had some promising initial results that validate the concept that culture collections are reservoirs of untapped and sometimes unpredictable chemistry that could provide a solution to the sustainable manufacture of essential products such as pharmaceuticals. We hope that when complete, this work will demonstrate the benefit of screening large microbial collections to identify novel functionalities for bio-manufacturing, and drive new industrial collaborations.

The project has been funded by The High Value Biorenewables Network – a BBSRC Network in Industrial Biotechnology and Bioenergy – and supported through a UKRI Future Leaders Fellowship to Stephen Wallace.