Anna Maria Niewiadomska

Hope you had a chance to chat with Max at @nanoporetech.com Biopharma Day Philadelphia. We had a great time discussing:
- Plasmid EZ: Easy as 1, 2, 3
- Nanopore Technology Applications at Azenta Life Sciences
- Benefits of mixed platform multiomics

#BiopharmaDay #Nanopore #NGS #ONT

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…

"near-complete de novo assembly of chromosomes and plasmids by long-read nanopore sequencing allowed for high-resolution strain identification, plasmid profiling, and antibiotic resistance gene detection"
www.biorxiv.org/content/10.1...
#AMR #Nanopore #PublicHealth #GenomicSurveillance

Microbial isolation at Kalk Bay and the value of DNA sequencing. Careers in Marine Sciences Academic Talk: "Microbial isolation at Kalk Bay and the value of DNA sequencing." Speaker: Dr Lonnie van Zyl, Chief Officer – IMBM

Cool talk on microbial isolation and metagenomics at Kalk Bay in S. Africa, to screen previously uncharacterised genomes to search for novel antimicrobial compounds
📺 You can watch here: www.youtube.com/watch?v=t5cQ...
#LongReads #AMR #antimicrobial #metagenomics #microbiome #nanopore

Just under 6 weeks until the metagenomic virus discovery workshop kicks off in Stellenbosch, South Africa. We're excited to be bringing together a fantastic group of speakers and teachers with expertise in all aspects of virus discovery from around the world.

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…

New TB genomics study! Culture-free Mycobacterium tuberculosis WGS using nanopore sequencing directly from sputum. Faster, simpler, and actionable for public health.
biorxiv.org/content/10.1101/2025.09.23.678181v1

#NanoporeSequencing #Genomics #TB

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 yet...

We examined Oxford Nanopore 16S amplicon sequencing as a tool for recovering marine microbial communities and we are pleased with the results! Check out our preprint 🌎🧪🧬🌊🖥️🦠https://www.biorxiv.org/content/10.1101/2025.09.20.676612v2.abstract

16S rRNA gene and rpoB Nanopore Sequencing for Bacterial Detection and Identification in Clinical Samples https://www.medrxiv.org/content/10.1101/2025.09.30.25336965v1

Webinar: Squiggles to the Rescue: Nanopore Sequencing and AI for Rapid One Health Surveillance

Join us as Dr. Lara Urban explores how nanopore sequencing and AI can empower rapid One Health strategies.

Thursday, Oct. 23, 2025, 11:00 AM PT

Register Now: www.zymoresearch.com/pages/squigg...

Nanopore metagenomics: from sample to analysis 2026 In this in-person workshop, learn how to extract DNA from metagenomic samples, prepare libraries, carry out nanopore sequencing and analyse data.

Limited places now remaining for our #nanopore #metagenomics workshop!

buff.ly/tCB0Zeu

#MAGS #nanopore #eDNA 🧬💻

(For people who don’t know - I’m a long established consultant to Oxford Nanopore and a shareholder. No company vets my social media posts)

To summarise our recent pre-print: Autocycler, the automated consensus assembler, when used with Nanopore long-read only Enterobacterales assemblies, produces more complete chromosomes and plasmids, with an accuracy comparable to hybrid assemblies.

🚀 We’ve just kicked off the 4th edition of our Genome Assembly course with the fantastic team at @nanoporetech.com
For the next few days, participants from all over the world will dive into the latest strategies, tools, and hands-on practice for assembling and polishing genomes with #Nanopore data🧬

Dr Darren Heavens leads course delegates in the lab practicals during the nanopore metagenomics course.

Dr Richard Leggett guides participants through the data analysis and visualisation sessions.

Nanopore Metagenomics course attendant during one of the lab practicals at the Earlham Institute.

💬 "This course provided me great detail of general aspects that are crucial to understanding #metagenomics covering technical aspects of the use of #ONT platform and interface."

Keen to learn about lab and in-field @nanoporetech.com metagenomics?
👉 buff.ly/tCB0Zeu

#MAGS #nanopore #eDNA 🧬💻

Surveying Tropical Faunal Diversity via Airborne DNA Analyses Here, we assess the potential of airborne eDNA (airDNA) metabarcoding to characterize arthropod and vertebrate assemblages in a tropical forest. We deployed 28 high-flow air samplers across a 1.5 km2…

You can't just pull data out of thin air. Or can you...?
That's exactly what Craine et al. did in Panama, through air sampling and airDNA metabarcoding, detecting ~1800 arthropod and vertebrate OTUs.
www.biorxiv.org/content/10.1...
#nanopore #airsampling #metabarcoding #biodiversity

Comparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus Mycetohabitans Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they become more host-restricted in lifestyle. Understanding…

TIL about endofungal bacteria! Mycetohabitans spp. are bacterial endosymbionts of the fungus Rhizopus microsporus. Abbot et al. assembled 28 complete genomes including chromosomes, chromids and mobilome-rich plasmids.
www.biorxiv.org/content/10.1...
#nanopore #plasmidsaurus

Nanopore metagenomics: from sample to analysis 2026 In this in-person workshop, learn how to extract DNA from metagenomic samples, prepare libraries, carry out nanopore sequencing and analyse data.

Interested in @nanoporetech.com for #metagenomics?

Register for our January workshop which will guide you through the #nanopore metagenomics workflow from sample through to analysis.

buff.ly/VfiprRP

🖥️ 🧬 #MAGs #MicroSky

This new paper from @ukhsa.bsky.social scientists including @smhopkins.bsky.social and @cstewartb.bsky.social - and @ox.ac.uk academics like @samlipworth.bsky.social - looks at possible improvements to pathogen surveillance through the use of Oxford Nanopore Technologies.

Nanopore metagenomics: from sample to analysis 2026 In this in-person workshop, learn how to extract DNA from metagenomic samples, prepare libraries, carry out nanopore sequencing and analyse data.

Join our #nanopore #metagenomics course to learn more about different approaches to sample preparation and options for comprehensive and rapid data analysis.

buff.ly/hOI2AfN

@nanoporetech.com @richardmleggett.bsky.social

Which assembly should be chosed `hifiasm HiFi+HiC+ONT->Cphasing Pore-C` or `hifiasm ONT` · Issue #874 · chhylp123/hifiasm Hi, I used two assemble strategy, first version is hifiasm with HiFi+HiC+ONT data, then Cphasing scaffold with Pore-C data, second version is hifiasm with ONT data. However, first version genome ha...

Genome assembly is a software+data problem, and since the latest version of hifiasm, the best data is Oxford @nanopore data. github.com/chhylp123/hi...

Bacterial community adaptation after freshwater and seawater coalescence Microbial community coalescence, the merging of entire microbial communities, is common across ecosystems, particularly in estuaries where freshwater and seawater mix. The complexity of these habitats...

💧🌊 What happens when freshwater bacteria meet their salty counterparts?
Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social

At the Nucleic Acid Observatory, we usually rely on Illumina technology for wastewater viral sequencing.

Recently we benchmarked different Oxford Nanopore sequencing workflows.

In a new post, we examine these workflows in detail and explain why one emerges as our top choice.

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

Characterising the microbial and antimicrobial resistance signatures of hospital-acquired pneumonia using nanopore metagenomic sequencing Hospital-acquired pneumonia (HAP) is a significant burden in nosocomial settings, yet its microbial underpinnings remain poorly understood. Here, we leverage shotgun nanopore sequencing to…

#Nanopore #metagenomics reveals the hidden microbial & resistance landscape of hospital-acquired pneumonia, from overlooked fungi to previously unknown #AMR reservoirs. www.researchsquare.com/article/rs-7...

Another study showing that Oxford Nanopore beats short reads in genus-level 16S rRNA taxonomy accuracy.
Database choice matters even more than platform.
Long reads + smart pipelines = better microbial profiling.
🔗 buff.ly/m28Tu7q
#Microbiome #Nanopore #16S #Metagenomics

Metagenomic sequencing for pathogen surveillance The Oxford Nanopore Technologies' dual-arm rapid metagenomic sequencing method can be used for…

🦠 New #nanopore open dataset alert!
⚡ Rapid mNGS for pathogen surveillance (bacteria, fungi, viruses).
Check it out 👉 epi2me.nanoporetech.com/pathogen_surveillance_2025.09

Oropouche virus: a rapid evidence gap map This rapid evidence gap map identifies and categorises the available evidence on Oropouche virus to inform research prioritisation.

#Oropouche virus news!! @ukhsa.bsky.social has mapped the evidence for Oropouche virus epidemiology, vectors and ecology, virology, pathogenesis, medical countermeasures and public health:
www.gov.uk/government/p...

An incredibly useful resource to guide future research and funding

Detection of Mpox virus clade IIb from whole genome sequencing in Guinea, June 2025 Mpox_A2.PDF (423.7 KB) On 13 June 2025, CERFIG (Centre de Recherche et de Formation en Infectiologie de Guinée confirmed Mpox infection in a 53‑year‑old patient attending the Dermatology Department…

A Clade IIb, lineage A.2.2 mpox virus was detected for the first time in Conakry, Guinee, highlighting the continued evolution and spread of Clade IIa viruses in West Africa.
#nanopore #mpox #CERFIG
virological.org/t/detection-...

"Continental-scale genomic surveillance of Plasmodium falciparum malaria with rapid nanopore sequencing". A low-cost (<$25/sample), rapid (~5 hours), and portable assay, enabling on-site sequencing & analysis in resource-limited settings, without the need for internet connectivity.
buff.ly/yxNIzCD

A recent study reconstructed the spatiotemporal spread of the North American Influenza A (H5N1) outbreak, sequencing ~3,000 H5N1 genomes from birds and mammals across Canada and the US with real-time, field-deployable nanopore sequencing.
www.science.org/doi/10.1126/...
#H5N1 #influenza #Nanopore

A deep amplicon sequencing approach for detection of filarial nematodes in mosquitoes. This paper also discusses potential applications as a molecular xenomonitoring tool for public health and veterinary medicine. www.biorxiv.org/content/10.1...

#nanopore #pathogensurveillance #filariasis #NTD