National survaliance of SARS-CoV-2 variants in Denmark
In March 2020 our group volunteered to set up national SARS-CoV-2 sequencing in Denmark and established the Danish Covid-19 Genome Consortium (DCGC). The mission of the DCGC is to assist public health authorities to monitor the spread of SARS-CoV-2. The project was established through the coordinated effort of Aalborg University, Statens Serum Institute, Hvidovre Hospital, and Aalborg University Hospital. Large-scale SARS-CoV-2 sequencing capacity was initially established at Aalborg University and local sequencing capacity at Statens Serum Institute and Hvidovre Hospital. Since June 2020, the consortium has established additional local sequencing nodes at Aalborg University Hospital, Aarhus University Hospital, Slagelse Hospital, Rigshospitalet, Sygehus Lillebælt, and Odense University Hospital.
The project was initially established by temporarily re-directing all personal and funding from Microflora Danica to SARS-CoV-2 sequencing. Subsequently the project received initial funding from the Grundfos foundation and Udannelses- og forsningsministeriet. After the summer of 2020 the project was established as a National program and funded directly by the Statens Serum Institute.
The team at Albertsen lab set up sequencing, coordinated metadata integration and deployed local sequencing and education to most hospitals in Denmark. From March 2020 to June 2021 we gradually scaled-up operation and reaching a capacity of sequencing 1000 SARS-CoV-2 positive samples pr. day in November 2020. In the first 6 months of 2021 we sequenced an average of 5000 SARS-CoV-2 samples pr. week. Since June 2021 the effort has been taken over by the State Serum Insitute. A national overview of the data produced by DCGC can be found in this overview.
Identification of life is essential to our understanding of the world. Traditionally, the focus has been on objects we can recognize with our eyes, such as plants and animals. However, in the last decades it has become evident that microorganisms, small cells invisible to the naked eye, are involved in all aspects of our lives. From making us sick or keeping us healthy, to climate change and sustainable biotechnology production.
Microflora Danica is aiming to describe the microbiome of Denmark. Our ambition is to discover and characterize the microbial diversity across all parts and habitats of Denmark through the analysis of 10.000 representative samples (AAU link, project link).
Data Science meets Microbial Dark Matter
In this project, we want to improve the rate of recovery of microbial genomes and ensure evidence-based analysis by leveraging, expanding, and combining state-of-the-art methods within several fields in exponential growth: DNA sequencing, machine learning, and graph-based analysis. This ambitious goal can only be achieved by the synergy of both data science and bioscience and will thus push the boundaries of both fields.
Collaborative project with Prof. Katja Hose and Prof. Thomas Dyhre Nielsen from AAU Computer Science (AAU project page).
Deciphering the role of microbial dark matter by novel DNA sequencing approaches
Microbial communities underpin all processes in the environment and have direct impact on human health. Despite their importance, only a tiny fraction of the millions of different microbes is known. This is mainly due to the immense difficulties of cultivating microbes from natural systems in the laboratory. This discrepancy is also known as the “microbial dark matter”.
For any microbe, the genome is the blueprint of its physiological properties. Having this in hand, it is possible to reconstruct its potential metabolism and establish hypotheses for evolution, function and ecology. Furthermore, it provides a foundation for further validating its function through a variety of in situ methods. However, genomes are extremely difficult to obtain from the microbial dark matter.
Currently, multiple metagenomes combined with bioinformatic approaches, is used to retrieve individual genomes from complex samples. This has let to numerous fundamental discoveries, including the discovery of bacteria cable of complete ammonia oxidation (Comammox), which radically change our view of the global nitrogen cycle and granted us the “Danish research result of the year, 2015”. However, we are still far from realizing the full potential of metagenomics to retrieve genomes. Mainly due to the complexity of nature, where multiple closely related strains co-exists, which renders the current approaches useless.
In this project, we want to use cutting-edge DNA sequencing related techniques to enable access to all genomes despite strain-complexity, link genomes, plasmids and phages, and enable direct measurements of in situ bacterial activity. The ability to readily obtain activity measurements of any bacteria, in any microbial ecosystem, will radically change microbial ecology and environmental biotechnology.