Anna Maria Niewiadomska

Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this
www.biorxiv.org/content/10.6...

A webpage section listing three resources related to measles virus genomic epidemiology. The first item shows an icon and the heading ‘Measles virus genomic epidemiology’ with a subheading ‘A primer on measles virus genomic epidemiology and why we do it.’ The second item shows an icon and the heading ‘artic-measles/400/v1.0.0 Primer Scheme’ with a description of the ARTIC-network primer scheme for sequencing measles virus. The third item shows an icon and the heading ‘ARTIC-network MEV wet-lab protocol’ with a description of the wet-lab protocol for sequencing MEV using the artic-measles/400/v1.0.0 primer scheme.

A webpage section titled ‘User‑interface pipelines using Epi2me,’ displaying four items. The first item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME’ and describes using EPI2ME to run the ARTIC amplicon‑nf pipeline without the command line. The second item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME for Illumina Data,’ again describing use of EPI2ME to run the amplicon‑nf pipeline without the command line. The third item shows an icon with the heading ‘amplicon‑nf: Running the pipeline in EPI2ME for Oxford Nanopore Data,’ with the same description. The fourth item shows an icon with the heading ‘amplicon‑nf: Viewing outputs of the pipeline in EPI2ME,’ describing how to view outputs of the amplicon‑nf pipeline within EPI2ME.

A webpage section titled ‘Command line interface pipeline SOPs.’ The first item shows an icon with the heading ‘Fieldbioinformatics: viral amplicon sequencing bioinformatics SOP’ and labels indicating ‘Nanopore | bioinformatics.’ A second section titled ‘Phylogenetics and Interpretation’ includes an icon with the heading ‘MeV Phylogenetics’ and a description stating it contains resources and protocols for measles virus alignment and phylogenetics.

ARTIC 2 measles resources are live!

As part of the Wellcome Trust funded ARTIC 2 project we have developed a collection of measles virus resources that are now openly available at artic.network/viruses/mev

Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing The growing resistance of Enterobacterales to last-resort antibiotics such as carbapenems puts a significant burden on healthcare systems, also due to plasmids driving a rapid spread of carbapenem res...

Long-reads exposed plasmid-driven carbapenem resistance transmission missed by routine diagnostics

📌Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing

www.doi.org/10.1099/mgen.0.001644

🖥️🧬💻
#AcademicSky
#MicroSky
#IDSky
🧪🧫🦠

Happy our preprint is out🦠:

"Evaluation of an Oxford Nanopore sequencing workflow for mycobacteria from primary MGIT culture"

We developed and tested a workflow for long-read sequencing of #mycobacteria, including optimising DNA extraction and assessing how #ONT performs compared with #Illumina.

"Our findings underscore the importance of GuFi phages with broad host ranges in the gut microbiome, and the utility of long-read sequencing for viral discovery, paving the way for deeper insights into the role of bacteriophages in human health and disease."
www.biorxiv.org/content/10.6...

Application of Nanopore sequencing to intact caspid-packaged DNA reveals that bacterial DNA encapsulation is widespread in the human gut #microbiome

www.nature.com/articles/s41...

GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont

Announcing a new tool for "denoising" long-read amplicon sequences: savont.

Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.

1/4

github.com/bluenote-157...

Epitranscriptomic signatures of m5C, m6A, and pseudouridine in COVID-19 reveal host RNA modifications involved in viral pathogenesis | Microbiology Spectrum RNA modifications are increasingly recognized as critical regulators of host-virus interactions, yet their specific roles in human viral infections remain largely unexplored. Here, we provide the firs...

End of an era! 🧬 Our latest paper is out now in Microbiology Spectrum.
This marks our final study utilizing the @nanoporetech.com RNA002 chemistry before we transition to RNA004. It’s been a wild ride with those flow cells! 🧪📖
Read it here: journals.asm.org/doi/10.1128/...
#Nanopore #DRS #UWM

Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, design…

Interested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT.
www.sciencedirect.com/science/arti...
🧵1/7
🧪

We are on!

Air 🌬️
Sea spray 💦
Surface 🌊
3000 m deep ⚓

~1 million DNA molecules/hour
sequenced live in the middle of the Pacific Ocean!

Shout out to Aden and Rhonda,l who can extract DNA, PCR, and library prep without getting seasick ⛵️

From sample to data in less than 48 hrs.

#eDNA #nanopore #UW

Genotypic Technology invites you to an exclusive webinar on Oxford Nanopore RNA Sequencing, exploring how long-read and direct RNA sequencing overcome the limitations of short-read platforms.
Register now shorturl.at/uCc1Q

Need an excuse to visit Antwerp in April? You can register for our Flanders Nanopore Day. Research using @nanoporetech.com sequencing will be highlighted, throughout a variety of research fields. And for academia, registration is for free.

nanoporeflanders.be

@keygene.com 's @awngs.bsky.social will be a speaker during the Industry Workshop of Oxford Nanopore Technologies ( @nanoporetech.com ), presenting some recent results in technology development for single-nuclei transcriptomics at PAG33 in San Diego on January 12.

Latest #CDlab paper on nanopore protein sequencing now published in JACS: pubs.acs.org/doi/full/10....

Here, Justas Ritmejeris, Xiuqi Chen, collaborator Bauke Albada, and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!

Complex HPV-human DNA structures revealed by large-scale DNA analyses in an HPV-cancer derived cell line Most human papillomavirus (HPV)-associated cancers harbor viral DNA integrated into the human genome as extrachromosomal circles, intrachromosomal segments, or both. Distinguishing intrachromosomal…

Long-read Nanopore WGS can resolve large multi-kb integration events in HPV infected cells, that cause structural rearrangements, leading to oncogenesis.

Direct nanopore sequencing of M. tuberculosis on sputa and rescue of suboptimal results to enhance transmission surveillance Whole-genome sequencing (WGS) enhances precision in predicting antimicrobial resistance and tracking Mycobacterium tuberculosis (MTB) transmission. Due to MTB’s slow-growing nature, genomic results…

A new study shows MTB surveillance and transmission can be resolved without culture or capture-based enrichment, using nanopore WGS directly from sputum.
www.biorxiv.org/content/10.1...

Long-read single-cell RNA sequencing uncovers cell-type specific transcript regulation in COVID-19 SARS-CoV-2 infection leads to extensive host transcriptomic changes, but the role of alternative splicing in shaping the immune response remains underexplored. Here, we present the first application…

Long-read single-cell RNA sequencing on nasopharyngeal swabs from COVID-19 patients; authors were able to identify differences in splice isoforms for genes that modulate immune signaling and apoptosis.

The tiny germline chromosomes of Paramecium aurelia have an exceptionally high recombination rate and are capped by a new class of Helitrons Background Paramecia belong to the ciliate phylum of unicellular eukaryotes characterized by nuclear dimorphism. A diploid germline micronucleus (MIC) transmits genetic information across sexual…

Interesting news in the world of transposable elements. Discovery of "a novel clade of Helitrons, with 9-10 kb transposase ORFs under purifying selection, that have remained active" in Paramecium aurelia.
www.biorxiv.org/content/10.1...

Telomeric assemblies of Paracoccidioides genomes Paracoccidioides is a genus of dimorphic fungal pathogens endemic to Latin America. We generated long-read de novo assemblies for 11 isolates representing four species of the brasiliensis complex (…

Long-read de novo assemblies for 5 paracoccidioides fungal pathogen species endemic to Latin America. (P. brasiliensis, P. americana, P. restrepiensis, P. venezuelensis and P. lutzii)
www.biorxiv.org/content/10.1...

Evaluation of full-length 16S rRNA amplicon sequencing using Oxford Nanopore Technologies for diversity surveys of understudied microbiomes 1. The use of long-read sequencing using portable Oxford Nanopore Technologies (ONT) is becoming increasingly popular in the study of host-associated microbiomes. However, its application has not…

"This work validates ONT long-read sequencing as a powerful tool for marine microbiome studies to catalyze advancements in the fields of ecology and evolution, resource management, and conservation"
www.biorxiv.org/content/10.1...

Terminal conjugation enables nanopore sequencing of peptides Nanopore sequencing of peptides holds great promise for single-molecule proteomics, but robust conjugation strategies to adapt native peptides for motor-enzyme–driven translocation have yet to be…

Very cool to see the early results of nanopore sequencing of PEPTIDES!
The ability to perform genomics, transcriptomics and proteomics on a single platform is incredibly exciting, and the potential for future applications is massive.

www.biorxiv.org/content/10.1...

Tick Genome Assemblies: Overcoming biological limitations through advances in sequencing technologies Ticks are blood-feeding arthropods with approximately 1,000 species, however, only 24 species currently have a genome assembly. These genome assemblies are important resources to advance tick biology…

Not sure which tick reference genome to use for your analysis?
This paper provides a very nice assessment of 34 high-quality tick genome assemblies from 21 species.
www.biorxiv.org/content/10.1...

Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains Telomeres gradually shorten at each cell division and telomerase counteracts this shortening by elongating telomere sequences. This dynamic balance between elongation and shortening results in a…

Using long reads that can span the length of telomeric regions, researchers developed a method to measure telomere length in S. cerevisiae, and found wide variation in telomere length, ploidy, and subtelomere structure.
buff.ly/hGM08qS

Insights on genomic profiles of drug resistance and virulence in a cohort of Leishmania infantum isolates from the Mediterranean area Background Drug-resistant strains of Leishmania infantum challenge the effectiveness of treatments for clinical leishmaniosis and may lead to more frequent relapses. Copy number variation (CNV) at…

Long-read WGS of 48 L. infantum identified drug-resistance biomarkers in 80% of the isolates!
"Leveraging WGS, our approach provides a methodological advantage by complementing CNV analysis with detailed read sequence profiling "
buff.ly/LRIDrOr

COATswga: A Coverage Optimizing and Accurate Toolkit for fast primer design in selective whole genome amplification Background Despite the transformative nature of next-generation sequencing in genomics, efficiently capturing underrepresented microbial DNA from complex biological mixtures, such as pathogens from…

Potentially useful new tool for targeted microbial genomics.
- Toolkit to design selective WGA (sWGA) primers
- ~99% on-target reads + strong genome coverage when tested with P. falciparum samples
- Validated with long read Oxofrd Nanopore sequencing

🧬 Now published in Bioinformatics Advances: "Snappy: Fast identification of DNA methylation motifs based on Oxford Nanopore reads"  

Full article available: https://doi.org/10.1093/bioadv/vbaf296

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years

#phagesky

www.nature.com/articles/s41...

Very pleased to have been able to participate in this, and looking forward to hearing more about the participants' future work!

🔬 L’équipe de Sciensano dirigée par Margo Maex remporte le #BSFM2025PosterAward 🏆 pour ses travaux sur l’usage d’Oxford Nanopore Technologies dans la surveillance de Salmonella.

Une avancée vers une #surveillance plus rapide et intégrée en #microbiologie !