Less than 1% of the microorganisms can be cultivated and studied in the lab. With the advent of low-cost high-throughput DNA sequencing technologies, it has become possible to explore the genetic material from entire microbial communities directly without the need of culturing the organisms under study. This emerging field, known as Metagenomics, utilizes a huge genetic reservoir of non-culturable organisms as a resource for biotechnological and medical products and processes.
The Metagenomics group collects samples from all-over the world and develop tools that will address many of the unique challenges of metagenomics data sets.
The majority of our projects are based on the Who, What, How approach:
- Who is there?
- What is made?
- How is it made?
Genome and metagenome assembly
Through years of experience in assembly of Next Generation Sequencing (NGS) data into genes, genomes and communities, our group has developed in-depth knowledge on best practise in genome and metagenome assembly. We work in collaborations with scientific groups with widely different interests and experience in bioinformatics from all over the world. Our group is constantly exploring challenges and possibilities within the areas of NGS, Omics, Big Data and Artificial Intelligence. We also collect samples from all branches of the tree of life and engage in expeditions across the globe including India, the Amazon rainforest, Australian bush, Arabian desert, Greenland wilderness, Polar seas and the Southeast Asian rainforests.
A major focus of the group is on animal (everything from human, koalas, vultures to vampires) microbiomes, hologenomes and the development of novel strategies for microbiome analysis. We are also involved in the Center for Genomic Epidemiology for the analysis of metagenomic samples from sewage, urine, feces, lungs, blood for surveillance and diagnostics and outbreak detection and visualisation e.g. global disease tracking using long-distance flights
Solutions to industrial challenges
A substantial part of our research is to support the biotech industry and find novel solution to industrial challenges. That ranges from using ‘omics tools to identify the pathways responsible for the production of the natural colours in insects and plants, to improving the taste of wine by identifying microbial communities and their importance during anaerobic fermentation and aerobic processes.
Biodiversity in the Amazon
Recently we embarked into plant biosynthesis pathways discovery by combining Omics, Big Data and Machine Learning. A promising new endeavour is our newly established Amazon Genomics Consortium, where we are moving into the area of biodiversity in the Amazon Rainforest with the mission of tapping into the biological, medical and scientific potential of the Amazon biodiversity.
The following topics are suggestions for projects to bachelor, master or Ph.D students.
(This is not a definitive list so if you have an idea of a project you would like to work on, please contact group leader Thomas Sicheritz-Pontén )
- Artificial Intelligence / Machine Learning solutions for Metagenomic Data
- Big Data in Metagenomics, Biotechnology Informatics and Health Informatics
- Large Scale Phylogenies
- Horizontal Gene Transfers