Abstract

The microbiome has emerged as an area of great promise for drug development, having benefited from recent advances in genome sequencing and data processing which have enabled the identification of candidate bacterial strains as interventions for eg. anti-ageing or anti-inflammatory applications. Robust models and methods are now required to investigate mode-of-actions and in vivo efficacy/profiles,  so that microbiome biotechs can take full advantage of their rich dataset of candidate strains.

C. elegans is a free-living nematode worm, 1mm long, transparent, with a lifespan of 3weeks, and which feeds on bacteria in the wild. It has long been adapted to laboratory culture conditions, where it is maintained on E. coli bacterial lawns. Because it can be be exposed to selected bacterial strains or extracts, C. elegans is a simple and fast model to test the effect of bacterial-host interactions in vivo on a whole organism. We successfully exemplified the utility of the C. elegans model for microbiome applications by maintaining C. elegans on each strain of a 1006-strain panel from the Keio collection. We identified several strains involved in lifespan extension, with further characterisation suggesting an involvement of the folate synthesis pathway. Disruption of the folate synthesis pathway in E. coli OP50, using the antibiotic sulfamethoxazole (SMX), replicated the lifespan extension. 

To demonstrate the predictivity of C. elegans compared to humans, we obtained a bacterial strain isolated from an obese human being (B29), and showed that maintaining C. elegans on B29 resulted in a decreased worm lifespan, thus offering a phenotype for wider screening.

To make this experimental strategy compatible with industrial processes, we developed an automated image acquisition and data analysis platform, involving an array of small cameras each controlled by a single board computer, allowing easy scaling to multiple plates. This system near-continuously tracks the movement of C. elegans on standard petri dishes, quantifying the rate of decay of movement over time using several parameters, including distribution of speeds. Other tractable endpoints include chemotaxis, exploration and paralysis, as well as increases in population size in fertile worms. Using our automated platform, we confirmed the role of SMX in reducing mobility decline with ageing. We have also developed strategies to evaluate the activity of bacterial extracts or fractions, for bacterial strains whose optical properties are incompatible with our imaging system.

We believe that the wider adoption of this assay platform by biotech and pharma companies can greatly aid the progress of microbiome therapeutics interventions at the junction between identification of a bacterial candidate strain from a genomics screen and its testing in rodent studies.