🚀 TaxSEA v1.2 is now live in #Bioconductor release 3.22! TaxSEA brings enrichment testing to #metagenomics data. Just like GSEA does for transcriptomics making #microbiome & #microbiota results biologically interpretable, fast, and reproducible. We've added new DBs & features in 1.2 👇 🧵

Dear community, Bakta needs your help! To further improve the functional annotation of "hypothetical" CDS, me and @gbouras13.bsky.social, we are looking for the worst Bakta-annotated bacterial genomes ;-) (1/2)

📣 Speakers announced for the Oral Tissue Collaborative (OTC) Symposium Register now to join either in person or online for the event on the future of oral tissue biorepositories 🗓️ 10 October Register by 3 October ⤵️

Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data. @ruoshiz.bsky.social @milot.bsky.social www.nature.com/articles/s41...

Finding microbes in cancer sequencing data has been controversial. Are we seeing real biology… or just contamination + batch effects?

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

About 18 months ago we held a @microbiologysociety.org meeting in Glasgow to discuss the thorny topic of #microbial #taxonomy and #nomenclature - and now you can read what we talked about :D #microbiology #controversy doi.org/10.1099/ijse...

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata www.microbiologyresearch.org/content/jour... 🧬🖥️ Nextflow code: github.com/ag-computati...

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

The human pangenome continues to grow and improve! Release 2 is here! Click through for the details, but this is a pretty amazing dataset including not just the phased assemblies, but PacBio HiFi, ONT Ultralong, Dovetail/Illumina Hi-C, PacBio Kinnex, and Illumina WGS for all samples

This is important work for the exciting next stage of metagenomics #MicroSky

Very compelling study showing the association between herpes zoster vaccination and dementia prevention. The authors leveraged a unique cohort for this natural experiment which shows a reduction in dementia risk of 20% in vaccinated individuals. #MedSky #IDSky 🧪 www.nature.com/articles/s41...

If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!

🧫🧪 "Ten species comprise half of the bacteriology literature, leaving most species unstudied." 'Model' gram - and gram + (Escherichia coli and Bacillus subtitles) + human pathogens www.biorxiv.org/content/10.1...

1/9 🚨 New preprint alert! Frustrated by strange results with your metagenomic data? Meet CroCoDeEL, an accurate, easy-to-use tool to detect and quantify cross-sample contamination—no need for negative controls or sample positions! 🔗 doi.org/10.1101/2025...

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

This seems odd. A cancer microbiome machine learning paper that uses data from the retracted Poore et al. 2020 Nature paper has been published just last week in mSystems. Some of the claims seem very strong. Also, it seems to have been accepted four days after submission. 🧬 & 🖥️ #microbiome

This has been a long journey and I think it's the correct outcome. Thanks to everyone that has been involved, especially @abrahamgihawi.bsky.social who has been investigating this since his PhD days, and Steven Salzberg for really raising the analysis and awareness to another level. 🧬🖥️

Great PhD opportunity available with us. Bacteria, bioinformatics, lab work, ancestry, and prostate cancer. Fully funded for those eligible for UK fees. Deadline 15th April. buff.ly/43AZD4k @ueamedical.bsky.social 🧬🖥️🩺 #microbiome Contact me or @abrahamgihawi.bsky.social for more details.

New review paper out today in Journal of Medical Biology "Cancer invasion and anaerobic bacteria: new insights into mechanisms". Great work by Rachel Hurst, with @abrahamgihawi.bsky.social, John Wain, and Colin Cooper. doi.org/10.1099/jmm....

New paper by Pat Schloss about rarefaction is definitely worth a read for microbiome aficionados journals.asm.org/doi/10.1128/...

Come and join our group as a PhD student using computational methods to investigate bacteria and viruses in aggressive prostate cancer. Applications are now open! @danbrewer.bsky.social www.findaphd.com/phds/project...

If you discovered a novel microbial strain or species, please check out abon - a new program in the zol suite, which lets you easily check the conservation of your sample's BGC-ome (from antiSMASH & GECCO predictions) across target genomes: github.com/Kalan-Lab/zo... #secmet #bgc

Ryan Wick has tested out the latest kits and basecalling for bacterial genome assembly: rrwick.github.io/2023/10/24/o... At assembly error rates like this I start to begin wondering what is "ground truth"

Important paper on microbiome heritability microbiomejournal.biomedcentral.com/articles/10....

🧪🔬🧫🦠🖥🧬 Methods matter. Stats matter. Specially when running microbiome analyses. Contact your statistician AND ecologist early in your project. Before experimental design. journals.asm.org/doi/10.1128/...

Our paper examining critical errors in a cancer metagenomics study is now live in mbio. Work carried out with Steven Salzberg, @danbrewer.bsky.social and others. Errors in bioinformatics can be subtle but incredibly important! doi.org/10.1128/mbio...

Pleased to see that our next paper examining the problematic 2020 cancer microbiome results is now published in ASM journal mBio. With Steven Salzberg and @abrahamgihawi.bsky.social. 🧬🖥️ #microbiome doi.org/10.1128/mbio...

Microbiome twitter, we are looking for negative control samples from as many sources and kits as possible. If you've included blanks in your 16S or ITS amplicon seq project and the data is publicly available, drop a link in the thread! RTs appreciated!

And today in #ClosedAcess irony