Rasmus Hansen Kirkegaard
YOU?
Author Swipe
View article: The Microflora Danica atlas of Danish environmental microbiomes
The Microflora Danica atlas of Danish environmental microbiomes Open
View article: Secondary Metabolite Biosynthesis Potential of <i>Streptomyces</i> Spp. from the Rhizosphere of <i>Leontopodium nivale</i> Subsp. <i>alpinum</i>
Secondary Metabolite Biosynthesis Potential of <i>Streptomyces</i> Spp. from the Rhizosphere of <i>Leontopodium nivale</i> Subsp. <i>alpinum</i> Open
Bacteria of the phylum Actinomycetota, particularly those of the genus Streptomyces, are prolific producers of secondary metabolites (SMs), many of which have been developed into antibiotics, immunosuppressants, and cancer therapeut…
View article: The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration Open
Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, s…
View article: Gut microbiota genome features associated with brain injury in extremely premature infants
Gut microbiota genome features associated with brain injury in extremely premature infants Open
Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbi…
View article: Niche and spatial partitioning restrain ecological equivalence among microbes along aquatic redox gradient
Niche and spatial partitioning restrain ecological equivalence among microbes along aquatic redox gradient Open
Microbial metabolic capabilities and interactions shape their niche hypervolume that in turn governs their ecological strategies and ecosystem services. In the context of functional redundancy or ecological equivalence, the focus has been …
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: Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum
Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum Open
Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces…
View article: Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities
Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities Open
DNA methylation is found across all domains of life but is a rarely used feature in recovery of metagenome-assembled genomes (MAGs). Recently, Oxford Nanopore introduced all context methylation detection models. We leveraged this to develo…
View article: The Parkinson’s drug entacapone disrupts gut microbiome homeostasis via iron sequestration
The Parkinson’s drug entacapone disrupts gut microbiome homeostasis via iron sequestration Open
Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbia…
View article: Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the <i>Nitrospirales</i>
Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the <i>Nitrospirales</i> Open
Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital role…
View article: Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer
Correction: Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer Open
View article: Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris
Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris Open
A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received …
View article: Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing Open
Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary …
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: Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load
Increased transmissibility of SARS-CoV-2 lineage B.1.1.7 by age and viral load Open
View article: Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing
Oxford Nanopore R10.4 long-read sequencing enables near-perfect bacterial genomes from pure cultures and metagenomes without short-read or reference polishing Open
Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-perfect genomes it has been necessary t…
View article: Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing
Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing Open
View article: Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers
Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers Open
Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive datas…
View article: FISH RAW Tiff images and metadata for images in the study
FISH RAW Tiff images and metadata for images in the study Open
The RAW Tiff images of the FISH images presented in this study.
View article: Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting
Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting Open
Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospina…
View article: Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting
Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting Open
Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospina…
View article: Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers
Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers Open
Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive data sets have hi…
View article: Connecting structure to function with the recovery of over 1000 high-quality activated sludge metagenome-assembled genomes encoding full-length rRNA genes using long-read sequencing
Connecting structure to function with the recovery of over 1000 high-quality activated sludge metagenome-assembled genomes encoding full-length rRNA genes using long-read sequencing Open
Microorganisms are critical to water recycling, pollution removal and resource recovery processes in the wastewater industry. While the structure of this complex community is increasingly understood based on 16S rRNA gene studies, this str…
View article: 3733 HQ and MQ metagenome-assembled genomes from 23 Danish WWTP
3733 HQ and MQ metagenome-assembled genomes from 23 Danish WWTP Open
This is the data associated with the HQ MAGs recovered from the activated sludge of Danish wastewater treatment plants. Here we include the medium quality as well as high quality MAGs for quick and easy download. The HQ MAGs and metagenome…
View article: The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities
The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities Open
This study systematically evaluated the global patterns of microbial antisense expression across various environments and provides a bird’s-eye view of general patterns observed across data sets, which can provide guidelines in our underst…
View article: Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics
Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics Open
Short-chain fatty acid (SCFA) degradation is an important process in methanogenic ecosystems, and is usually catalyzed by SCFA-oxidizing bacteria in syntrophy with methanogens. Current knowledge of this functional guild is mainly based on …
View article: Ecoli K12 MG1655 R10.3 HAC
Ecoli K12 MG1655 R10.3 HAC Open
Ecoli K12 MG1655 DNA sequencedPlatform: Nanopore MinIONLibrary kit: LSK109Flowcelltype: R10.3Basecaller: Guppy v. 3.4.5Basecallermode: HACmd5sum: 14ae7c31805ab048e0b413261857d82fOriginal fast5 data https://www.ebi.ac.uk/ena/data/view/PRJEB…
View article: Unlinked rRNA genes are widespread among bacteria and archaea
Unlinked rRNA genes are widespread among bacteria and archaea Open
Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought …
View article: The signal and the noise - characteristics of antisense RNA in complex microbial communities
The signal and the noise - characteristics of antisense RNA in complex microbial communities Open
High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With the onset of metatranscriptomics, it is now possible to interrogate the transcriptome of multiple organis…
View article: Unlinked rRNA genes are widespread among Bacteria and Archaea
Unlinked rRNA genes are widespread among Bacteria and Archaea Open
Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in Bacteria and Archaea. These ribosomal rRNA genes are typically organized into a single operon, an arrangement t…