The last time you took an antibiotic course for a bacterial infection, you would likely not have known that you were consuming a number of biochemicals that are commonly referred to as ‘metabolites’. Metabolites — such as glucose and amino acids — are a critical part of therapeutic sciences.

Metabolites are produced in the cells of living organisms. However, as global populations expand, and the demand for food and medicine too increases, there is a rising need for metabolites. Scientific research is focused on making the industrial production of metabolites less expensive and more efficient.

Since metabolites are biochemicals, you would need to use living organisms to produce them in labs or factories. Metabolites are produced and exchanged when microbes interact. So, you would need at least one microbe to produce a particular metabolite. Now, there are thousands of microbes — which one works best for a metabolite? It was phenomenally costly to work out the answer through trial and error — until a new branch of science emerged: computational biology.

Two by two

Research in labs usually involves two microbes at a time, popularly known as ‘two-species’, or ‘co-culture’ communitiesAnd why two species? Because the more the number of microbes, the less the burden of production on each microbe. In a lab environment, it is practical to study two-species communities.

Computational biosciences helps estimate which two species of microbes can best interact with each other to yield the most metabolite.

In one research project, Karthik Raman, Associate Professor, Bhupat & Jyoti Mehta School of Biosciences, IIT-Madras, and his team formed a strategy ‘for the selection of suitable microbial communities for target metabolite production’, using what they call a ‘workflow for co-culture/community analyses for metabolite production (CAMP)’.

They used computational biosciences to identify the best pairs of bacteria to produce high yields of a metabolite called ‘lactate’, showing the way for similarly choosing relevant species to produce other metabolites.

The findings were published in a paper titled ‘Two-species community design of lactic acid bacteria for optimal production of lactate’ in the Computational and Structural Biotechnology Journal in November 2021.

Helpful genes

Raman and his team brought in genomic models that had the whole genome sequence for lactate. Given that each species’ properties are known, the computational model helped determine where the highest yield was possible.

The team selected 49 microbial species and generated all possible combinations to yield 1,176 pairs of bacterial candidates to produce lactate.

Next, the team analysed the flow of metabolites through the metabolic network, which is a set of processes that determine the physical property of a cell — in this instance, the lactate yield. The higher the flow, the greater the metabolite yield. Communities with a 10-fold increase in yield of metabolite are regarded as candidate communities for optimal production, says Prof Raman.

Earlier research too found that some genes in species either inhibit or help enhance metabolite production.

‘Knockout’ factor

Says Prof Raman, “Knockouts of genes or enzymes involve engineering the microbial strain such that it no longer produces the particular enzyme. This helps to eliminate other by-products… This would improve the yield of lactate.”

The team was able to predict reaction knockouts for improved lactate flux. Specifically, knockouts of acetate kinase, phosphate acetyltransferase, and fumarate reductase in the communities helped enhance lactate production, he says.

Of the 1,176 pairs, 822 were found non-viable — that is, one of the two species showed no growth.

Finally, wouldn’t the next step be to actually get into ‘wet lab’ experiments to check whether the pairs picked by the computational study actually worked as desired? “We have conducted preliminary experiments in collaboration with the Department of Biotechnology at our institute to validate our predictions. They have shown promising results with one particular microbial community of L. casei and L. plantarum showing higher lactate yields in experiments as well, compared to five other co-cultures tested.” These findings are yet to be published or peer-reviewed.