Thomas Bygh Nymann Jensen
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View article: Ecophysiology and niche differentiation of three genera of polyphosphate-accumulating bacteria in a full-scale wastewater treatment plant
Ecophysiology and niche differentiation of three genera of polyphosphate-accumulating bacteria in a full-scale wastewater treatment plant Open
Polyphosphate-accumulating organisms (PAOs) are the main bacteria responsible for phosphorus removal and recovery in full-scale wastewater treatment plants (WWTPs). They encompass members of the genera Candidatus Accumulibacter, Azonexus (…
View article: Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats Open
The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormou…
View article: Recovery of highly contiguous genomes from complex terrestrial habitats reveals over 15,000 novel prokaryotic species and expands characterization of soil and sediment microbial communities
Recovery of highly contiguous genomes from complex terrestrial habitats reveals over 15,000 novel prokaryotic species and expands characterization of soil and sediment microbial communities Open
Genomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the micr…
View article: High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark
High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark Open
Vast amounts of pathogen genomic, demographic and spatial data are transforming our understanding of SARS-CoV-2 emergence and spread. We examined the drivers of molecular evolution and spread of 291,791 SARS-CoV-2 genomes from Denmark in 2…
View article: Microflora Danica: the atlas of Danish environmental microbiomes
Microflora Danica: the atlas of Danish environmental microbiomes Open
Summary The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes in natural and human associated environments. Recent large-scale metagenome surveys record the variety of microbi…
View article: High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing
High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing Open
Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by th…
View article: Soil microbial communities in Danish lowlands are shaped by soil pH 
Soil microbial communities in Danish lowlands are shaped by soil pH  Open
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 lowlands might result in a change in microbial community composition…
View article: Taxonomic and environmental distribution of bacterial amino acid auxotrophies
Taxonomic and environmental distribution of bacterial amino acid auxotrophies Open
Many microorganisms are auxotrophic—unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino…
View article: High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing
High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing Open
Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by th…
View article: Closed genomes uncover a saltwater species of <i>Candidatus</i> Electronema and shed new light on the boundary between marine and freshwater cable bacteria
Closed genomes uncover a saltwater species of <i>Candidatus</i> Electronema and shed new light on the boundary between marine and freshwater cable bacteria Open
Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Ele…
View article: Closed genomes uncover a saltwater species of<i>Candidatus</i>Electronema and shed new light on the boundary between marine and freshwater cable bacteria
Closed genomes uncover a saltwater species of<i>Candidatus</i>Electronema and shed new light on the boundary between marine and freshwater cable bacteria Open
Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Ele…
View article: Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark Open
Background In early 2021, the SARS-CoV-2 lineage B.1.1.7 (Alpha variant) became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemi…
View article: Additional file 2 of Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark
Additional file 2 of Introduction and transmission of SARS-CoV-2 lineage B.1.1.7, Alpha variant, in Denmark Open
Additional file 2. GISAID accession numbers and acknowledgement table for sequences used in this study.
View article: Introduction and transmission of SARS-CoV-2 B.1.1.7 in Denmark
Introduction and transmission of SARS-CoV-2 B.1.1.7 in Denmark Open
In early 2021, the SARS-CoV-2 lineage B.1.1.7 became dominant across large parts of the world. In Denmark, comprehensive and real-time test, contact-tracing, and sequencing efforts were applied to sustain epidemic control. Here, we use the…