MetaExplore Partners

Project:  Metagenomic screening and directed evolution of plastic-degrading enzymes in microdroplets. 

Secondments: Drop-Tech Ltd (Cambridge, UK), Janssen (J&J, Beerse, Belgium), AstraZeneca (Cambridge, UK) EMBL-EBI (Hinxton, UK) and Evoralis Ltd (Cambridge, UK).

Project: Ultra-high throughput screening and characterization of glycoside utilization pathways involved in host-microbiota interactions 

Secondments: Prozomix Ltd (Haltwhistle, UK) and NTNU (Trondheim, Norway)

Project 1: Functional metagenomics screening for novel enzymes from waste-water using previously unexplored environmental bacteria 

PhD degree: The HUN-REN BRC doctoral candidate will receive their diploma from the University of Szeged, Hungary.

Secondments: University of Cambridge (Cambridge, UK) and Seqomics Biotechnology Ltd (Morahalom, Hungary)

Project 2: Genome-centric monitoring of anaerobic degradation processes linked to urban sewage systems

Anaerobic sludge digestion (ASD) has the capability as effective technology for the treatment of residual sewage sludge containing hardly degradable materials including hazardous wastes like various dyes, toxins, drug residues or even highly prevalent and mobile antibiotic resistance genes (ARGs). A combination of cutting-edge metagenomic and metatranscriptomic approaches will be applied to generate metagenome-assembled genomes (MAGs) and to functionally characterize them. Minimum standards will be defined for the generation, deposition, and publication of MAGs derived from uncultivated pathogens and to capture the appropriate metadata in a consistent and standardized manner. Current standards of Minimum Information of Metagenome Assembled Genomes (MIMAG) will be followed. Shotgun metatranscriptome data will be used for mapping the active members of the microbial community and to link specific functions to the MAGs and to specific genes within MAGs. 

PhD degree: The HUN-REN BRC doctoral candidate will receive their diploma from the University of Szeged, Hungary.

Secondments: University of Alicante (Alicante, Spain) and Seqomics Biotechnology Ltd (Morahalom, Hungary)

Required skills: molecular biology techniques (PCR, DNA/RNA isolation, manipulation, NGS libraries), bioinformatics experience (R programming language for statistical computing and data visualization).

Project: Harvesting and evolving proteases for medical applications 

PhD degree: The Astrazeneca doctoral candidate will be enrolled at the University of Cambridge.

Secondments: Drop-Tech Ltd (Cambridge, UK), University of Cambridge (Cambridge, UK) and EMBL-EBI (Hinxton, UK)

Project: Computational strategies for detecting novel bacteriocins in the metagenomes and experimental verification.

PhD degree: The EMBL-EBI doctoral candidate will be enrolled at the University of Cambridge.

Secondments: Drop-Tech Ltd (Cambridge, UK), University of CAmbridge (Cambridge, UK) and University of College London (London, UK).

Project: High-throughput LC-MS screening of metagenomic expression libraries to identify novel enzymes for xenobiotic biotransformation reactions.

PhD degree: The EMBL doctoral candidate will be enrolled at the University of Tübingen

Secondments: University of Tübingen (Germany), HUN-REN (Szeged, Hungary) and AstraZeneca (Cambridge, UK).

Project: Novel cold-adapted enzymes from the polar regions. 

The aim of this project is to characterise novel cold-adapted enzymes from samples of water, sediment and soil from the polar regions, with an emphasis on phosphatases, hydrolases and sulphatases. Identification of enzyme activities will be carried out using microfluidic bioassays, with directed evolution used to improve kinetic activities.

PhD degree: The BAS doctoral candidate will be enrolled at the University of Cambridge.

Secondments: Drop-Tech Ltd (Cambridge, UK) and the University of Cambridge (Cambridge, UK).

Required skills: wet lab skills (molecular biology) and bioinformatics.

Project 2: Screening in microfluidics droplets of biofilm inhibitors from microbial communities of extreme environments

This project will address the identification of biofilm inhibitors using Functional Metagenomics and High Throughput Screening. The researcher will be particularly focused on the discovery of inhibitors of queuosine (Q), a tRNA modification that controls biofilm formation and virulence in bacteria and represents a promising new target to prevent infections or biofouling. Using a patented Q reporter strain and developing multiplate and microfluidic workflows, Q inhibitors will be screened in large metagenomic libraries from different microbial communities, from gut microbiome to extreme environments. Identified anti-Q genes and compounds will be characterized, and their anti-biofilm activities will be tested. 

Secondments: Drop-Tech Ltd (Cambridge, UK) and SINTEF (Trondheim, Norway)

Required skills: Microbiology, Molecular Biology, Bioinformatics

Project: Gene transfer in the urban water cycle – implications for the human health and the environment 

Secondments: Universidad Autónoma de Madrid (Madrid, Spain) or University of Cambridge (Cambridge, UK), and Labaqua (Alicante, Spain)

Project: Identification of biocatalyst for C-C-bond forming transformations & the build-up of tertiary stereocenters 

Secondments: Vlaams Instituut voor Biotechnologie (Ghent, Belgium) and University of Cambridge (Cambridge, UK)

Project: Computational screening of metagenome samples for novel plastic degrading enzymes and experimental verification.

This project aims to identify novel plastic degrading enzymes (e.g PETases) in large scale metagenome data using a range of bioinformatic strategies and AI-based machine-learning tools, to obtain a detailed classification of PETase-like enzymes with subfamilies likely to have different activities.

Secondments: EMBL-EBI (Hinxton, UK) and University of Cambridge, (Cambridge, UK)

Required skills: Protein structure analysis, AI-based deep learning methods, python programming