Thomas Bygh Nymann Jensen
A5018805892- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- COVID-19 epidemiological studies
- Lichen and fungal ecology
- Peatlands and Wetlands Ecology
- Soil Carbon and Nitrogen Dynamics
- Plant Virus Research Studies
- Soil and Water Nutrient Dynamics
- Environmental DNA in Biodiversity Studies
- Botany and Plant Ecology Studies
- Probiotics and Fermented Foods
- Animal Virus Infections Studies
- Microbial Fuel Cells and Bioremediation
- Historical and Archaeological Studies
- Virology and Viral Diseases
- Gut microbiota and health
- Bacteriophages and microbial interactions
- COVID-19 diagnosis using AI
- Protist diversity and phylogeny
Aalborg University
2021-2024
University of Colorado Boulder
2023
Cooperative Institute for Research in Environmental Sciences
2023
New lineages of SARS-CoV-2 are potential concern due to higher transmissibility, risk severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 (the Alpha variant) became dominant in early 2021, but the association between transmissibility and factors, such as age primary case viral load remains poorly understood. Here, we used comprehensive administrative data Denmark, comprising full population (January 11 February 7, 2021), estimate household transmissibility. This...
Abstract Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which capable conducting long-distance electron transfer. Currently, all cable classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Electrothrix, saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences metagenome-assembled genome (MAG) phylogenies. However, most currently available MAGs highly fragmented,...
Abstract Background In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of world. Denmark, comprehensive and real-time test, contact-tracing, sequencing efforts were applied to sustain epidemic control. Here, we use these data investigate transmissibility, introduction, onward transmission in Denmark. Methods We analyzed a set 60,178 genomes generated from high-throughput by Danish COVID-19 Genome Consortium, representing 34% all positive cases...
Many microorganisms are auxotrophic-unable to synthesize the compounds they require for growth. With this work, we quantify prevalence of amino acid auxotrophies across a broad diversity bacteria and habitats. We predicted biosynthetic capabilities 26,277 unique bacterial genomes spanning 12 phyla using metabolic pathway model validated with empirical data. Amino auxotrophy is widespread phyla, but conservatively estimate that majority taxa (78.4%) able all acids. Our estimates indicate more...
Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which drastically improved our understanding the microbial world. However, large projects are now hampered by cost library preparation low sample throughput, comparatively to actual costs. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead Kit, MP Biomedicals TM FastDNA -96 Soil Microbe DNeasy® PowerSoil® Pro QIAcube® HT Kit. The extractions were...
Summary The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes natural and human associated environments. Recent large-scale metagenome surveys record variety of microbial life oceans 1 , wastewater 2 gut 3,4 earth 5,6 with compilations encompassing thousands public datasets 7–13 . So far, microbiome studies either miss functional information or consistency sample processing, although they may cover locations, these are missing...
Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding SARS-CoV-2 emergence spread. We examined the drivers molecular evolution spread 291,791 genomes from Denmark in 2021. With a sequencing rate consistently exceeding 60%, up to 80% PCR-positive samples between March November, viral genome set is broadly whole-epidemic representative. identify consistent rise diversity over time, with notable spikes upon importation novel variants (e.g., Delta...
Abstract In early 2021, the SARS-CoV-2 lineage B.1.1.7 became dominant across large parts of world. Denmark, comprehensive and real-time test, contact-tracing, sequencing efforts were applied to sustain epidemic control. Here, we use these data investigate transmissibility, introduction, onward transmission in Denmark. a period with stable restrictions, estimated an increased transmissibility 58% (95% CI: [56%,60%]) relative other lineages. Epidemiological phylogenetic analyses revealed that...
Abstract Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which capable conducting long-distance electron transfer. Currently, all cable classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Electrothrix, saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences metagenome-assembled genome (MAG) phylogenies. However, most currently available MAGs highly fragmented,...
Agricultural activity on drained lowlands is a common practice in Denmark and there are suggestions to rewet some of them for climate mitigation purposes. Rewetting those might result change microbial community composition. This study investigates the current prokaryotic diversity composition soil samples from cultivated provide baseline monitoring changes after rewetting. Furthermore, variations properties between sites examined, driving differences identified. In total, 116 were collected...
Abstract Genomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery genomes from environmental samples at scale. However, expanding the genome catalogue soils sediments been challenging due enormous complexity these environments. Here, we performed deep, Nanopore 154 soil sediment collected across Denmark through an optimised bioinformatics pipeline, recovered 15,314 novel species, including 4,757...
Abstract Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which drastically improved our understanding the microbial world. However, large projects are now hampered by cost library preparation low sample throughput. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead Kit, MP Biomedicals TM FastDNA -96 Soil Microbe DNeasy® PowerSoil® Pro QIAcube® HT Kit. The extractions were evaluated based on...