Led by Dr Kim Handley, (University of Auckland)
The metagenomics approach is rapidly transitioning into a mainstream tool in microbial ecology. However, there is a need for approaches to reconstruct and analyse challenging mixtures of prokaryotic (bacterial and archaeal) community sequence data along with the genomes of other understudied organisms (viruses and microeukaryotes). The Environmental Microbiomes project looks to meet this need by providing clear methods and guidelines.
The Environmental Microbiomes project encompasses three work streams: (1) virome, (2) microbial strain heterogeneity, and (3) microeukaryote (tiny multicellular organisms) analyses.
The project will develop best practice guidelines for DNA and RNA virome analysis, and an approach for viral genome fragment dereplication in multisample datasets. This work capitalises on the virus genomes generated from the Environmental Metagenomics project. Additionally, two model systems will be used to explore microbial strain heterogeneity, improving assemblies using data subsampling to reduce sequence complexity and using chromatin-based sequencing. Finally, a new protocol will be developed to generate microeukaryote genomes from metagenomic data.
The project aligns with key objectives for Genomics Aotearoa capability building and advanced genomics research, through the contribution of step-by-step workflows and hands-on-training, and research at the leading edge of microbial ecology