The recent explosion in marine microbiome research has generated extensive unassembled short-read datasets, which have limited use for biodiscovery. To overcome this, BlueRemediomics is developing a Discovery Platform that integrates informatics tools/pipelines/data (MGnify microbiome resource is the focal point) with wet-lab experimental validation. The platform employs state-of-the-art informatics tools to process short-read data into larger genomic fragments to derive metagenome assembled genomes (MAGs), generating biologically meaningful information, such as proteins, pathways, and biosynthetic gene clusters (BGCs) they encode. This facilitates analysis of a whole organism, but can also help establish synthetic communities. We aim to provide greater connectivity of this data to the marine culture collections and concomitantly develop innovative high throughput screening methods suitable for diverse use cases to enhance biodiscovery of novel products and processes of societal benefit.
To evaluate platform functionality, we have chosen use cases that vary in complexity (from single enzymes to whole communities) and developmental maturity. This includes potential cosmeceutical and antimicrobial candidates produced by BGCs, while other approaches will investigate the use of fermentation extracts and products as potential phytostimulants. The project will also focus efforts on fermentation scale-up methodologies to meet evolving biotechnological demands.
In response to the EU initiative to reduce fish meal in aquaculture feeds, we will explore alternative sustainable feed sources. To address salmon survival issues when fish are transferred from controlled systems to sea cages, the project will dissect mechanisms underpinning the resilience of surviving fish by investigating whether there are specific microbiome members that confer resilience/mortality . Another approach aims to increase sustainability of the aquaculture industry by reducing fish bone waste by discovering improved bone degrading enzymes from MGnify. Similar approaches will be used to identify potential plastic degrading enzymes to address plastic pollution in the marine ecosystem. In parallel, we will investigate microbial bioremediation of UV blockers found in sunscreens, an emerging marine pollutant.
Based on the burgeoning datasets, we intend to link observations of different communities, microbes, genes, and even variants associated with ocean health or stress. The resulting Ocean Health Microbiome Index (OMHI) can potentially inform efforts to restore healthy oceans and link human activities with ocean stress. Data driven approaches will be coupled with the use of “sensor” organisms that could also represent other ecosystem monitoring services.
Underpinning BlueRemediomics is the need to improve awareness of access and benefit sharing (ABS), while ensuring the appropriate levels of intellectual property (IP) protection. By improving legal frameworks and enhancing ABS knowledge/decisions by policy stakeholders, the project aspires to sensibly balance ABS and IP obligations. Another key objective is to understand society’s appetite for biobased solutions for carbon capture, combating climate change, or using viruses to combat algal blooms in the context of the “do no significant harm” principle through Town Hall meetings.
