GitHub - iLivius/cFMDbench: ML classification benchmarks on cFMD with mlr3. Quarto-driven, Conda-based, TabPFN-ready, GPU optional. Built for teaching and testing. ML classification benchmarks on cFMD with mlr3. Quarto-driven, Conda-based, TabPFN-ready, GPU optional. Built for teaching and testing. - iLivius/cFMDbench

Just released cFMDbench: a repository where I pulled together methods I’ve been using for #ML classification on #metagenomic data with #mlr3, benchmarked on the #cFMD dataset. More a structured workflow than a “product”, but maybe useful to others. github.com/iLivius/cFMD...

Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of or...

📢 new paper alert! 📢
Do we find the same #bacteria in the mouth and in the gut of stunded children?

Go find out: doi.org/10.1080/1949...

#microbiome #gut #gutmicrobes #metagenomic

With @vonaeschlab.bsky.social at @dmf-unil.bsky.social

PhD A matter of gut instinct: from mucus to microbiome (LANGRIDGE_Q26MMBiCASE) 2026/27 | UEA PhD A matter of gut instinct: from mucus to microbiome (LANGRIDGE_Q26MMBiCASE) 2026/27 | UEA

This is no April fools!!!

🚨 @langridgelab.bsky.social has a funded #PhD for UK candidates

Do you love #microbiomes, #bioinformatics & translational science?

Come & join us, & @andrewjpage.bsky.social at @originsciences.bsky.social & get stuck into a ton of #metagenomic data🧬

Apply by 8 April

Deep untargeted #wastewater #metagenomic #sequencing from #sewersheds across the #USA

Deep untargeted #wastewater #metagenomic #sequencing from #sewersheds across the #USA, etidiohnew.blogspot.com/2026/03/deep...

Explore microbial functionality with #metagenomic analysis. Learn strategies for integrating taxonomic & functional insights to reveal biological mechanisms and advance #microbiome research.

#FunctionalGenomics #Bioinformatics #MicrobialResearch #LifeSciences #Genomics https://tinyurl.com/44c6zvzf

🔬✨ Tool of the week: #Metagenomic data analysis made easy!
🚀 The Metagenomics-Toolkit offers a complete workflow: from raw Illumina or Nanopore reads 📈 to taxonomic 🦠 and functional 🧬 insights.
📊 Reproducible, publish-ready results.
Ready to boost your research? 🌍📝
www.denbi.de/services-acc...

🔬The latest shotgun #metagenomic data from #seawater and #sediment #microbial #communities is finally here!

🧬This work is part of the #European #Marine Omics #Biodiversity Observation Network (EMO BON), a long-term initiative launched in 2021 by @embrc-eu.bsky.social

📖 doi.org/10.3897/BDJ....

In this new technical blog, Postdoc Researcher Ned Peel shares with you his guide and advice on using the recently published MARTi software for real-time #taxonomic classification and visualisation of #metagenomic data. @nanoporetech.com

➡️ buff.ly/ymybUeq

💻🧬

It integrates over 306,000 representative genomes—more than doubling the number included in the GTDB—and provides standardized #taxonomy, functional annotations, and resources for #metagenomic profiling and #comparativegenomics.

New software tool MARTi fast-tracks identification and response to microbial threats. Scientists at the Earlham Institute introduce MARTi, a powerful new tool for the real-time analysis of nanopore metagenomics.

MARTi is a new #opensource software tool developed by @richardmleggett.bsky.social and team to power rapid identification, analysis and visualisation of #metagenomic #data. 🧬💻

Read more below 👇

Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2 - Microbiome Background The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms...

New publication🧬 𝐌𝐞𝐭𝐞𝐨𝐫𝟐 𝐢𝐬 𝐚𝐧 𝐨𝐩𝐞𝐧-𝐬𝐨𝐮𝐫𝐜𝐞 𝐭𝐨𝐨𝐥 𝐟𝐨𝐫 𝐭𝐚𝐱𝐨𝐧𝐨𝐦𝐢𝐜, 𝐟𝐮𝐧𝐜𝐭𝐢𝐨𝐧𝐚𝐥, 𝐚𝐧𝐝 𝐬𝐭𝐫𝐚𝐢𝐧-𝐥𝐞𝐯𝐞𝐥 𝐩𝐫𝐨𝐟𝐢𝐥𝐢𝐧𝐠 𝐨𝐟 𝐦𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐢𝐜 𝐬𝐚𝐦𝐩𝐥𝐞𝐬. 𝐟𝐨𝐫 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐦𝐞 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡
microbiomejournal.biomedcentral.com/articles/10....
#metagenomic #science #data #lefrenchgut
@inrae-france.bsky.social @institutpasteur.bsky.social

New software tool MARTi fast-tracks identification and response to microbial threats. Scientists at the Earlham Institute introduce MARTi, a powerful new tool for the real-time analysis of nanopore metagenomics.

Scientists at Earlham Institute have developed MARTi - an open-source software tool that powers real-time analysis and visualisation of #metagenomic #data.

buff.ly/iIPUpty

@nanoporetech.com

.. @kguschan.bsky.social, and me and my lab group.

Tasks consist of bioinformatic analyses of #metagenomic data from chironomid gut #microbiomes, incl identifying AMR genes.🧬 And running lab experiments of chironomids, testing horizontal and vertical transmission patterns of bacteria and #AMR.🦠 3/3

Metagenomic mining reveals novel Cas12 subtypes and their evolutionary diversification We identified 4112 Cas12 Proteins and 6 new Cas12 subtypes, revealed their significant diversity in N-terminal regions, repeat sequences, and sequences motifs. We developed an AI-driven algorithm, Ca...

🧬 New insights into the diversity of #CRISPR–Cas systems!
#Metagenomic analyses uncovered 4,112 Cas12 proteins and 6 novel subtypes.
🤖 #AI-based Cas12fam annotates 18 domains.
🌿 Cas12 subtypes show habitat-specific enrichment.
🔗 doi.org/10.1002/imo2...
#microbiome #metagenomics #bioinformatics

Overview of the project.

Adaptive #sampling with Oxford Nanopore offers a simple way to improve the efficiency of #plant #metagenomic studies

A #Letter by Verhoeven et al. 👇

📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

#LatestIssue #PlantScience @nanoporetech.com

ganon2 offers scalable, up-to-date #metagenomic classification with fast incremental indexing and accurate taxonomic binning, designed to keep pace with exploding public sequence repositories. #PathogenSurveillance #Bioinformatics 🚀🧬🔎
📄https://doi.org/10.1093/nargab/lqaf094
👤EVBC: Knut Reinert

TIPP-SD: A New Method for Species Detection in Microbiomes In this study, we present TIPP-SD (i.e., TIPP for Species Detection), a new technique for species detection in a microbiome sample. TIPP-SD uses a modified version of TIPP3, which is a recently develo...

This could be a neat method for species detection in #metagenomic datasets, but why on earth are we simulating PacBio and ONT error rates at >10%? 🫣🤔🫠

PacBio HiFi has had >99% accuracy since 2019.

Very hard to interpret the results based on 90% accuracy.

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

🧬 Keeping the #guthealth trend going is Marwan Majzoub with our final medium talk for #MicroSeq2025! Take a look at this #metagenomic approach to characterise gut #bacteriophages. Could the phageome help us identify disease determinants and treatment outcome? #virology #microbiome

💩 @gazollavolpiano.bsky.social starts us off with a comprehensive study of archaeal diversity and clinical associations in faecal #metagenomic data. Check out what kind of role these strange microbes play in human health! #MicroSeq2025 #archaea #guthealth

Metagenomic Analysis of Tick-Borne Viruses in Hulunbuir, Inner Mongolia, China: Epidemiological Risk of Potential Novel Pathogenic Viruses Relevant to Public Health Inner Mongolia, with its vast grasslands providing ideal habitats for ticks, has recently emerged as a hotspot of novel Tick-Borne virus (TBV) prevalence. However, the diversity of TBVs and their potential spillover risks remain to be elucidated.

#Metagenomic analysis of tick-borne viruses (TBVs) in Hulunbuir, Mongolia, identified four novel viruses and highlighted the potential spillover risk of TBVs in humans, underscoring the need to monitor emerging TBVs at the tick-human-livestock interface.

#OpenAccess: tinyurl.com/2bemp4yq

@dportik.bsky.social and I wrote a book chapter on highly accurate #longread @pacbio.bsky.social HiFi sequencing for #microbiome and #metagenomic applications in "Metagenomics for Microbiology (Second Edition)" that is now published! Check it out here:
www.sciencedirect.com/science/arti...

Unveiling Origin Pitfalls in Metagenomic Surveillance for Emerging Infectious Diseases: Parvoviruses as a Model A diverse reagent-associated virome, including parvoviruses, misleads zoonotic surveillance. By leveraging large language models (ChatGPT-4o), we construct a virus discovery data framework (PVDDC) an...

Unveiling Origin Pitfalls in #Metagenomic Surveillance for Emerging Infectious Diseases: #Parvoviruses as a Model #iMetaMed onlinelibrary.wiley.com/doi/10.1002/... #mNGS #NGS #chatGPT #AI

HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly Recovering high-contiguity, circular bacterial genomes from complex microbiomes (e.g., gut) is challenged by limitations of short-read and error-prone long-read sequencing. This study comprehensively...

" @pacbio.bsky.social #HiFi #metagenomic assembly achieves a level of precision approaching that of isolated genomes derived from the same sample. This benchmarking establishes HiFi as a robust approach for generating #MAGs rivaling isolated genome quality."

onlinelibrary.wiley.com/doi/full/10....

Join us for our September #webinar, presented by Dr. Bilal Djeghout from @quadraminstitute.bsky.social, covering advanced #metagenomic methods for direct #Campylobacter detection/characterisation for surveillance/diagnostics, with #bioinformatics.

Register here: bit.ly/3URSw3O

#AMR #NGS #genomics

BugBuster is a modular, containerized workflow for #metagenomic analysis built with Nextflow DSL2. It supports read processing, taxonomic profiling, resistance gene prediction, assembly, binning, and functional annotation, enabling scalable and reproducible analysis of microbial communities.

January 2025
🥼After extracting the #sedDNA, we’re moving on to DNA library preparation—a key step in #metagenomic #shotgun-sequencing.🌋🧬
DNA libraries are sets of DNA fragments prepared with special adapters so they can be sequenced on the #Illumina platform.
#PRINVOLARE2022 #Laboratory #Research

Slacken paper published in NAR Genomics and Bioinformatics Our paper on Slacken, a metagenomic classifier based on the Kraken 2 method, was recently published in NAR Genomics and Bioinformatics. In this post I (Johan) would like to break down the main results...

Explaining in simple terms the two main results achieved by our #metagenomic classifier #Slacken - scaling independently of RAM, and sample-tailored libraries. jnpsolutions.io/2025/07/03/s...

Webinar time! #Microbiome and #metagenomic researchers come learn the power behind combining @zymoresearch.bsky.social ZymoBIOMICS workflow and #iconPCR for superior data and workflow innovation. Register now: hubs.ly/Q03st-vY0

GitHub - liusihang/ViOTUcluster: ViOTUcluster: A high-speed, all-in-one solution that streamlines the entire virome analysis workflow ViOTUcluster: A high-speed, all-in-one solution that streamlines the entire virome analysis workflow - liusihang/ViOTUcluster

ViOTUcluster: A high‐speed, All‐in‐one pipeline for viromic analysis of #metagenomic data, available on GitHub: github.com/liusihang/Vi... #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/...
#Bioinformatics #viruse #virome

🧬❓Can #metagenomic data offer superior assessments of benthic environmental impacts associated with #salmon #aquaculture compared to metabarcoding?

Don't miss this paper! 🔽🔽