Researchers at University of Toronto’s Department of Chemical Engineering & Applied Chemistry have made a key discovery about how certain bacterial strains produce a set of economically valuable chemicals — opening the door to new, more sustainable production methods.
The finding, published in Nature Microbiology , shows how a family of molecules used in everything from cleaning products to cosmetics to nutritional supplements could be made via bacterial fermentation instead of from palm oil, as they are today.
“The chemicals we are targeting here are known as medium-chain carboxylic acids (MCCAs) or medium-chain fatty acids (MCFAs),” says Professor Chris Lawson, who led the team.
“They are six to twelve carbon atoms long, and they are used in all kinds of things: agricultural feeds, cosmetics, antimicrobials, surfactants and much more. The global market for them is on the order of $3 billion.”
Lawson says that currently, MCFAs are mainly produced from palm kernel oil, made from the seeds of the palm fruit. Palm oil, in general, has a poor reputation: its production is widely associated with deforestation, biodiversity loss and other environmental problems.
Furthermore, because palm kernel oil is traded as a bulk commodity, Lawson says it can be difficult to trace whether it originates from sustainably managed plantations.
Lawson and his team are among many groups around the world that aim to develop alternative methods for MCFA production.
“Some groups have tried to produce MCFAs using model industrial microbes, for example, genetically modified E. coli or yeast,” says Lawson.
“But this process is expensive and typically requires refined sugars, derived from plants and starch. What we want to do is take advantage of strains of bacteria that produce MCFAs naturally, via a simple fermentation process. It’s similar to how yeast metabolize sugar into ethanol in the beer-brewing industry.”
The bacterial species that Lawson and his team are focusing on are known as chain-elongating bacteria, or CEBs. They are anaerobic, meaning that they thrive only in oxygen-free conditions, such as deep underground or even in the human digestive system.
CEBs are capable of producing MCFAs up to eight carbons in length, in partnership with other bacteria that help breakdown complex organic waste. Because they don’t need highly refined food such as corn starch, they enable the possibility of producing high-value MCFAs from materials that might otherwise be discarded as waste.
For example, Lawson and his team are looking at feeding them food waste, such as that collected via Toronto’s Green Bin program, and byproducts from the agri-food sector such as dairy waste.
But first, the team has to overcome a key limitation: while CEBs can produce high-value MCFAs, they don’t always do so.
“What we want them to produce is octanoic acid, which is eight carbons long and one of the most high-value MCFAs, especially because palm kernel oil doesn’t contain that much of it,” says Lawson.
“But what we often find when we grow these CEBs is that they instead produce a less-valuable four-carbon molecule called butyrate. Which product they produce depends on the conditions they find themselves in and until now, it has been generally not possible to predict.”
In the new paper, Lawson and his team — including PhD student Ian Gois, recent graduate Connor Bowers, postdoctoral fellow Byung-Chul (Roy) Kim and research scientist Rob Flick — describe in detail the metabolic and biochemical mechanisms that favour production of octanoic acid over butyrate.
The paper presents a metabolic model and biochemical evidence for how the ratio of lactate to acetate — two of the organic molecules that the CEBs feed on — controls the carbon chain length of the products they create.
Another key contribution that the team makes is to explain the role of an enzyme known as CoA transferase (CoAT) in the fermentation process.
“While some bacteria can naturally produce MCFAs up to eight carbons long, most microbes stop at four-carbon molecules,” says Lawson.
“What we’ve shown is that in the bacteria that make the longer molecules, their CoA transferase is different. It can act on precursors that are already six or eight carbons long, whereas those organisms that only make four-carbon molecules like butyrate have a different version of the enzyme that can’t do this.”
Lawson says that the improved understanding of the factors and mechanisms that influence which product the CEBs make will enable researchers to design systems that optimize their production for high-value products over low-value ones.
In fact, he and his team are already at work on this, and the latest study is just one of their many recent publications about CEBs.
In another paper, published in ACS SynBio together with PhD student Ethan Agena, Lawson and his team describe new genetic tools that could be used to manipulate CEBs and enable them to produce even longer MCFAs, in the nine-to-twelve carbon range.
A third paper, which the team has submitted for publication and posted to bioRxiv , focuses on scaling up the system to industrial levels by proposing a new bioprocess system to grow the bacteria and harvest the products from them. This paper was led by ChemE PhD students Diana Dyussekenova and Jasmeen Parmar and was carried out in collaboration with Professor Jay Werber.
Three members of Lawson’s team, Bowers, Agena, and PhD student Joel Howard have teamed up to create a startup, SymBL Innovations , to help commercialize their discoveries and innovations. The company recently received support from Genome Canada and Ontario Genomics through a Regional Genomic Applications Partnership Program (GAPP) award to further advance this work.
Lawson and his collaborators are also part of the Waste to Chemicals (W2C) Alliance , a multidisciplinary collaboration supported by the Ontario Water Consortium, NSERC and Mitacs.
“If we want to sell these chemicals on the open market, we need to show that we can deploy these microbes in a fully integrated bioreactor process producing MCFAs at scale, and at a competitive price,” says Lawson.
“We think these discoveries show that we can do that. There’s also the fact that our process is much more sustainable, which is a great selling point, especially with customers who are focused on ethically sourced ingredients. We’re very excited about the potential of this new pathway.”
Nature Microbiology