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Evaluation of full-length 16S rRNA amplicon sequencing using Oxford Nanopore Technologies for diversity surveys of understudied microbiomes

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Reposted by Anna Maria Niewiadomska

Mónica Medina @momedinamunoz.bsky.social · 2d

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

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...

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Reposted by Anna Maria Niewiadomska

medRxivpreprint @medrxivpreprint.bsky.social · 7d

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

Nanopore metagenomics: from sample to analysis 2026

Reposted by Anna Maria Niewiadomska

Zymo Research @zymoresearch.bsky.social · 5d

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...

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Reposted by Anna Maria Niewiadomska

Earlham Institute @earlhaminst.bsky.social · 5d

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

buff.ly/tCB0Zeu

#MAGS #nanopore #eDNA 🧬💻

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

Surveying Tropical Faunal Diversity via Airborne DNA Analyses

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Reposted by Anna Maria Niewiadomska

Ewan Birney @ewanbirney.bsky.social · 7d

(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)

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Reposted by Anna Maria Niewiadomska

Dorottya Nagy @dotnagy.bsky.social · 10d

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.

Figure 2 from my recently pre-printed manuscript on the completeness and accuracy of Nanopore long-read only bacterial genome assembly for Enterobacterales. a) tile plot of chromosome circularisation, with assembler on the x-axis and sample on the y-axis, shows that the consensus long-read only assembler, Autocycler, circularised more chromosomes at 95% (87/92) than any other long-read or hybrid assembler. b) complex upset plot of plasmid reconstruction, showing that the best plasmid reconstruction was achieved by long-read assemblers incorporating the separate plasmid assembly tool, Plassembler, namely Autocycler and Hybracter, reconstructing >96% of plasmids.

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Reposted by Anna Maria Niewiadomska

Physalia-courses@Online @physaliacourses.bsky.social · 9d

🚀 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🧬

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Reposted by Anna Maria Niewiadomska

Earlham Institute @earlhaminst.bsky.social · 11d

💬 "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 🧬💻

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.

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Anna Maria Niewiadomska @amnbio.bsky.social · 13d

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

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…

Comparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus Mycetohabitans

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Anna Maria Niewiadomska @amnbio.bsky.social · 17d

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

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…

Nanopore metagenomics: from sample to analysis 2026

Reposted by Anna Maria Niewiadomska

Earlham Institute @earlhaminst.bsky.social · 22d

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

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

Nanopore long-read only genome assembly of clinical Enterobacterales isolates is complete and accurate

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Reposted by Anna Maria Niewiadomska

UK Health Security Agency @ukhsa.bsky.social · 20d

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.

Sam Lipworth @samlipworth.bsky.social · 21d

Great new work from #DotNagy @modmedmicro.bsky.social - she tool 96 clinical isolates from the NEKSUS study and sequenced with both Illumina and Nanopore - question was, can we do away with hybrid sequencing for the rest of the study?
www.biorxiv.org/content/10.1...

Whole bacterial genome sequence reconstruction using Oxford Nanopore Technologies ('Nanopore') long-read only sequencing may offer a lower-cost, higher-throughput alternative for pathogen surveillance...

Nanopore metagenomics: from sample to analysis 2026

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Reposted by Anna Maria Niewiadomska

Earlham Institute @earlhaminst.bsky.social · Sep 8

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

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

Which assembly should be chosed `hifiasm HiFi+HiC+ONT->Cphasing Pore-C` or `hifiasm ONT` · Issue #874 · chhylp123/hifiasm

Reposted by Anna Maria Niewiadomska

Albert Vilella, PhD. @albertvilella.bsky.social · 24d

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...

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...

github.com

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Reposted by Anna Maria Niewiadomska

Xiu Jia @xiujia.bsky.social · 23d

💧🌊 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

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...

Benchmarking three ONT-based workflows for untargeted sequencing of RNA viruses in wastewater

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Reposted by Anna Maria Niewiadomska

SecureBio, Inc. @securebio.org · 22d

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.

At the NAO, we use short-read Illumina technology as the gold standard for untargeted sequencing of RNA viruses in wastewater because it provide...

naobservatory.org

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Reposted by Anna Maria Niewiadomska

Jim Shaw @jimshaw.bsky.social · Sep 7

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

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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Anna Maria Niewiadomska @amnbio.bsky.social · 29d

#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...

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…

www.researchsquare.com

Anna Maria Niewiadomska @amnbio.bsky.social · Sep 8

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

Anna Maria Niewiadomska @amnbio.bsky.social · Sep 5

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

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

epi2me.nanoporetech.com

Oropouche virus: a rapid evidence gap map

Reposted by Anna Maria Niewiadomska

Stephen Graham's Lab @atomicvirology.bsky.social · Aug 14

#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

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

www.gov.uk

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Anna Maria Niewiadomska @amnbio.bsky.social · Aug 11

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-...

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…

virological.org

Anna Maria Niewiadomska @amnbio.bsky.social · Aug 6

"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