Mads Albertsen

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

Nanopore metagenomic sequencing links clinically relevant resistance determinants to pathogens

This paper develops a method to link plasmid-encoded AMR genes to their bacterial hosts using nanopore sequencing methylation data, achieving high accuracy in clinical samples.

The MiDAS global genome catalog: 53,501 long-read MAGs representing all core prokaryotic genera in the global activated sludge microbiome

The paper constructs a global genome catalog of 53,501 long-read MAGs from activated sludge, representing 12,047 prokaryotic species and enabling analysis of functional traits and ecological roles in wastewater treatment systems.

From soil to sea: unravelling the metabolic versatility and social dynamics of Myxococcota bacteria from different Danish environments

The paper investigates the distribution, diversity, and metabolic potential of Myxococcota bacteria across Danish environments using metagenomic data, revealing their ecological roles and biotechnological potential.

Ecological specificity and interconnectivity in Danish environmental resistomes

This study characterizes the Danish environmental resistome across 7,000 samples, identifying core and habitat-specific ARGs and their connectivity across ecosystems.

A national baseline for methane sink habitats and methanotroph diversity

The paper presents a national study of methanotroph diversity and distribution in Denmark, revealing uncharacterised species as dominant in natural ecosystems and highlighting potential targets for methane mitigation.

Microflora Danica: the atlas of Danish environmental microbiomes

Microflora Danica compiles 10,686 shotgun metagenomes and 449 rRNA datasets to create an atlas of Danish environmental microbiomes, revealing hidden homogeneity and novel nitrifiers.

Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment

The paper identifies candidate flocking bacteria in freshwater sediments that express extracellular electron transfer genes, suggesting they facilitate electron transfer to cable bacteria and influence element cycling.

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

This study uses long-read sequencing and optimized bioinformatics to recover high-quality microbial genomes from soil and sediment samples, revealing over 15,000 novel prokaryotic species and expanding microbial community characterization.

Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. nov.

This paper proposes a new genus and species, Patescibacterium danicum, to provide nomenclatural stability for the phylum Ca. Patescibacteria.

Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities

Nanomotif uses DNA methylation motifs to improve MAG recovery and plasmid host association from metagenomic data.

Greengenes2 enables a shared data universe for microbiome studies

Greengenes2 aligns 16S rRNA and shotgun metagenomic data using a whole-genome phylogeny, showing agreement in principal coordinates, taxonomy, and phenotype effect size.

Metagenomic binning with assembly graph embeddings

This paper introduces GraphMB, a deep learning method for metagenomic binning that integrates assembly graph structures with contig features, improving the number of high-quality genome bins obtained.

Enabling high-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

Dual patterned unique molecular identifiers (UMIs) turn Nanopore or PacBio CCS reads of ~4400 bp rRNA operons into single-molecule consensus sequences with 0.0049% (ONT) or 0.0006% (PacBio) mean error.

ampvis2: an R package to analyse and visualise 16S rRNA amplicon data

ampvis2 unifies 16S amplicon count tables, taxonomy, and sample metadata in one R object, feeding ggplot2 heatmaps at any taxonomic rank and single-call ordination (seven methods).

mmgenome: a toolbox for reproducible genome extraction from metagenomes

The paper introduces mmgenome, a toolbox for reproducible genome extraction from metagenomes, integrating binning strategies, visualization, validation, and full reproducibility through Rmarkdown.