Anders Ogechi Hostrup Daugberg
@andersohd.bsky.social
PhD student at Aalborg University 🇩🇰
Using bioinformatics to understand how bacteria produce and secrete biopolymers (the backbone of biofilms!)🦠
Metagenomics/transcriptomics, gene cluster annotation, exopolysaccharides, functional amyloids, eDNA🧬
Using bioinformatics to understand how bacteria produce and secrete biopolymers (the backbone of biofilms!)🦠
Metagenomics/transcriptomics, gene cluster annotation, exopolysaccharides, functional amyloids, eDNA🧬
Realising the Eisenhofer study doesn't satisfy your request for a study using both Illumina and ONT, sorry
November 11, 2025 at 10:18 PM
Realising the Eisenhofer study doesn't satisfy your request for a study using both Illumina and ONT, sorry
Finally, Mantas Sereika performed long-read (ONT) metagenomic assembly on a subset of the Microflora Danica samples, while the main MFD paper performed short-read (Illumina) assembly on all the samples:
doi.org/10.1038/s415...
doi.org/10.1101/2024...
doi.org/10.1038/s415...
doi.org/10.1101/2024...
Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats - Nature Microbiology
Nanopore sequencing of Danish soils and sediments yields genomes from over 15,000 microbial species, expanding the phylogenetic diversity of prokaryotes by 8%.
doi.org
November 11, 2025 at 10:15 PM
Finally, Mantas Sereika performed long-read (ONT) metagenomic assembly on a subset of the Microflora Danica samples, while the main MFD paper performed short-read (Illumina) assembly on all the samples:
doi.org/10.1038/s415...
doi.org/10.1101/2024...
doi.org/10.1038/s415...
doi.org/10.1101/2024...
Eisenhofer et al. (2024) compares metagenome assembly of the microbiome in lab mouse feces using four approaches.
(i) 20 Gbp Illumina data
(ii) 40 Gbp Illumina data
(iii) 20 Gbp PacBio HiFi
(iv) 40 Gbp hybrid (20 Gbp Illumima + 20 Gbp PacBio)
doi.org/10.1128/spec...
(i) 20 Gbp Illumina data
(ii) 40 Gbp Illumina data
(iii) 20 Gbp PacBio HiFi
(iv) 40 Gbp hybrid (20 Gbp Illumima + 20 Gbp PacBio)
doi.org/10.1128/spec...
A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics | Microbiology Spectrum
Mice are an important model organism for understanding the gut microbiome. When studying
these gut microbiomes using DNA techniques, researchers can choose from technologies
that use short or long DNA...
doi.org
November 11, 2025 at 10:08 PM
Eisenhofer et al. (2024) compares metagenome assembly of the microbiome in lab mouse feces using four approaches.
(i) 20 Gbp Illumina data
(ii) 40 Gbp Illumina data
(iii) 20 Gbp PacBio HiFi
(iv) 40 Gbp hybrid (20 Gbp Illumima + 20 Gbp PacBio)
doi.org/10.1128/spec...
(i) 20 Gbp Illumina data
(ii) 40 Gbp Illumina data
(iii) 20 Gbp PacBio HiFi
(iv) 40 Gbp hybrid (20 Gbp Illumima + 20 Gbp PacBio)
doi.org/10.1128/spec...
I've got three! Needed them myself for comparing the effects of sequencing strategy on BGC detection.
The SPMP project uses both Illumina and Illumina+ONT sequencing on Singaporean stool samples: doi.org/10.1038/s414...
The SPMP project uses both Illumina and Illumina+ONT sequencing on Singaporean stool samples: doi.org/10.1038/s414...
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians - Nature Communications
Reference genomes for gut microbiomes help unravel microbial “dark matter” and serve as valuable resource for disease-focused studies. Here, the authors perform short and long read metagenomics and me...
doi.org
November 11, 2025 at 10:01 PM
I've got three! Needed them myself for comparing the effects of sequencing strategy on BGC detection.
The SPMP project uses both Illumina and Illumina+ONT sequencing on Singaporean stool samples: doi.org/10.1038/s414...
The SPMP project uses both Illumina and Illumina+ONT sequencing on Singaporean stool samples: doi.org/10.1038/s414...
Reposted by Anders Ogechi Hostrup Daugberg
note, gliding is not comparable to sliding
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
November 4, 2025 at 2:42 PM
note, gliding is not comparable to sliding
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant
the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant