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Finn Group

Computational metagenomics and analysis

The Finn research group focuses on developing computational approaches for the reconstruction of genomes from metagenomes, and investigates the distribution of microbes and functions in different environments.

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The Finn research group focuses on developing computational approaches for the reconstruction of genomes from metagenomes, and investigates the distribution of microbes and functions in different environments.

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What we do

We explore the entire microbiome, including the important yet understudied viral and eukaryotic (single-cell) fractions, to elucidate the functions of microbial communities, as well as their complex interplay and dynamics.

In doing this, we also consider the genomic plasticity and diversity generated by mobile genetic elements (MGE), which can create opportunistic pathogens and/or drug resistant microbes. 

Finally, we constantly evaluate and adopt new technologies (e.g. long-read sequencing) to overcome technical and analytical challenges, such as capturing microbial diversity from complex samples, obtaining high-quality genomes from low-yield environments, and reducing the computational overheads to achieve in-field, real-time surveillance. 

Achievements

Our large-scale studies have identified thousands of novel species, which are now driving new developments in the MGnify microbiome resource. We have:

  • Defined a new blueprint for the human gut microbiome by generating the Unified Human Gastrointestinal Genome (UHGG) collection based on large-scale metagenomic analysis. This represents nearly 5,000 species, 70% of which have never been experimentally cultured to date.
  • Developed and used the new VIRify tool to identify genomes of 142,000 viral species comprising the viral catalogue, generated by mining 28,000 globally distributed human gut metagenomes.
  • Developed the new EukCC tool to assess eukaryotic genome quality.
  • Produced the Skin Microbial Genome Collection (SMGC), spanning viruses, bacteria, and eukaryotes obtained from human skin.
  • Developed pipelines to enable the incorporation of long-read metagenomic sequences.

Future projects and goals 

Our overarching goal is to decode the role of microbial communities in health and disease. We will exploit these new and expanding genomic resources to elucidate compositional changes and to address key knowledge gaps, including uncharacterised human microbiomes from under-represented geographical regions. 

We will study the functional repertoire encoded by these newly discovered genomes to identify those with key roles in microbial adaptation to a particular ecological niche. 

We will also focus efforts on the detection, prevalence, and impact of MGE (e.g. plasmids, phages, and transposons) to facilitate insights into their roles in community function, and exploit their functions in applied settings, for example fuelling new greener approaches to industrial biotechnology. 

Finally, we will pursue real-world applications of metagenomics techniques, such as pathogen surveillance or the study of complex symbionts.

Phylogenetic tree showing the distribution of metagenome assembled genomes of novel species (green, inner)  we  recovered from human gut samples. The outer ring shows the different phyla.

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