Leading microbiome research excellence to understand the role that microorganisms play in health and diseases.

Microbial bioinformatics research projects

Strain-resolved community profiling of metagenomic datasets and identification of novel metabolites using high resolution mass spectrometry

Mr. Rhys Newell

Metagenomics has so far been limited to studying microbial communities at best at the species level with little understanding of what metabolites are currently being produced by the community. However, the ability to investigate communities beyond the species level has arrived with the advent of long read sequencing. Additionally, the arrival of high-resolution ion cyclotron resonance mass spectrometry has allowed us to investigate the metabolic landscape of microbial communities.

We have been developing bioinformatics techniques that will allow researchers to harness the information from long read sequencing and bulk metabolomic samples. We have been using metagenomic data collected from Stordalen mire and Abisko Scientific Research Station (Sweden) and multiple long running bioreactors in the form of long and short read sequences, as well as mass spectrometry profiles from samples taken from one of the bioreactors.

This research has resulted in the development of Lorikeet, a strain-resolved genotyping tool that harnesses both long and short reads to produce likely microbial strains. Additionally, we have applied Lorikeet and other tools to a community of enriched anaerobic methanotrophic archaea in hopes of investigating what mechanism is responsible for the different observable phenotypes present in the community. This analysis resulted in the recovery of the first circular ANME-2d metagenome-assembled genome (MAG) to date. Although the analysis of metabolomic datasets identifying novel metabolites is still underway, we anticipate that we should soon be able to describe potential metabolites with estimated quantities within microbial communities.

Being able to analyse the potential genotypes associated with a MAG will allow future researchers to better describe what the metabolic capabilities of a particular community is, as certain strains lose or gain the ability to harness certain pathways. Additionally, being able to ascertain quantitatively which metabolites are present within a community will allow researchers to better understand what the ecological functions a community is responsible for.