Biology subjects

Sorensen, E. A.

Publications and source records attributed to Sorensen, E. A..

4 recordsLinked to original sources

bioRxiv2025

Nanoscale precise stamping of biomolecule patterns using DNA origami

Understanding the importance of ligand patterning in biological processes requires precise control over molecular positioning and spacing. While DNA origami structures offer nanoscale precision in biomolecule arrangement, their biological applications are limited by challenges related to their structural stability, scalability, and surface area. Here, we present a straightforward and rapid DNA origami stamping technique for transferring nanoscale oligonucleotide patterns onto surfaces, visualized using DNA-PAINT super-resolution microscopy to quantitatively assess the stamping efficiency and precision across different stamp types. Unlike traditional top-down methods that require specialized equipment, our technique provides an accessible, self-assembled platform for surface patterning, with versatility across various substrates via modifiable pattern-transfer oligonucleotides. We demonstrate reliable, efficient, and precise pattern transfer at single-molecule resolution, enabling new opportunities to study distance-dependent biological processes, including receptor activation, multivalent binding, and enzymatic cascades across broader spatial scales and different detection techniques. The use of the passivated surface limits non-specific interactions with unpatterned areas and enables control over the interaction between the biological target and the patterned biomolecules. Our method advances surface patterning by combining DNA nanotechnology with single-molecule imaging techniques, expanding access to cost-effective analytical approaches and potentially enabling multiplexed detection and live measurements.

bioengineering↗

bioRxiv2024

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

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 microbial genome catalogue of soils and sediments has been challenging due to the enormous complexity of these environments. Here, we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected across Denmark and through an optimised bioinformatics pipeline, we recovered genomes of 15,314 novel microbial species, including 4,757 high-quality genomes. The recovered microbial genomes span 1,086 novel genera and provide the first high-quality reference genomes for 612 previously known genera, expanding the phylogenetic diversity of the prokaryotic tree of life by 8 %. The long-read assemblies also enabled the recovery of thousands of complete rRNA operons, biosynthetic gene clusters and CRISPR-Cas systems, all of which were underrepresented and highly fragmented in previous terrestrial genome catalogues. Furthermore, the incorporation of the recovered MAGs into public genome databases significantly improved species-level classification rates for soil and sediment metagenomic datasets, thereby enhancing terrestrial microbiome characterization. With this study, we demonstrate that long-read sequencing and optimised bioinformatics, allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain the largest untapped source of biodiversity for expanding genome databases and filling in the gaps of the tree of life.

bioinformatics↗

bioRxiv2024

Microflora Danica: the atlas of Danish environmental microbiomes

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 microbial life in the oceans1, wastewater2, human gut3,4, and earth5,6, with compilations encompassing thousands of public datasets7-13. So far, large-scale microbiome studies either miss functional information or consistency in sample processing, and although they may cover thousands of locations, these are missing resolution, sparsely located, or lacking metadata. Here, we present Microflora Danica, an atlas of Danish environmental microbiomes, encompassing 10,686 shotgun metagenomes and 449 full-length 16S and 18S rRNA datasets linked to a detailed 5 level habitat classification scheme. We determine that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.

microbiology↗

bioRxiv2021

Assessing long-read sequencing with Nanopore R9, R10, and PacBio CCS to obtain high-quality metagenome assembled genomes from complex microbial communities

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 to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-perfect microbial genomes from isolates or metagenomes without shortread or reference polishing.

microbiology↗