MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes. #MAGs #Metagenomics #MetagenomeAssembly #GenomeBiology genomebiology.biomedcentral.com/articles/10....

Cool result: Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii "Exposure of a transposon insertion mutant library to extended weak antibiotic selection ... revealed genes that indirectly increased fitness due to elevated general mutation rates"

What determines who a phage can infect? We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort. 👇 A thread!

Another paper from the lab, trying to look at in vitro biological relevant phenotypes in essential genomes www.microbiologyresearch.org/content/jour...

New preprint up on the changes in the bovine virome though different life stages led by @milja001.bsky.social @ryancook94.bsky.social www.biorxiv.org/content/10.1...

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight) interpretamr.github.io/AMRrules

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace. Check out the course objectives below and sign up before June 9th to join us! www.futurelearn.com/courses/anti...

New paper where we suggest bacteria in the honeybee stomach may be more interesting to study than generally thought. doi.org/10.1007/s002...

Interesting paper on novel bacteria isolated from the Phoenix Space Mission microbiomejournal.biomedcentral.com/articles/10....

Super cool #bioinformatics tool alert: @widdowquinn.bsky.social group releases PyANI-plus, a flexible tool for exploring whole-genome similarity on large AND detailed scales. Walkthrough available below!

Autocycler: long-read consensus assembly for bacterial genomes https://www.biorxiv.org/content/10.1101/2025.05.12.653612v1

I've spent some time updating my two Nextflow-based bacterial QC pipelines (bacQC and bacQC-ONT). It'd be great to get some feedback. github.com/avantonder/b... github.com/avantonder/b...

New awesome Rust bioinformatics tool just dropped!

I'm really excited to share the postdoc I completed before joining PHG. It combines two great passions - bacteria and horses!! Read more here: www.linkedin.com/posts/hayley... or go straight to the paper here: www.microbiologyresearch.org/content/jour...

Worth a read about a new antibiotic: pubmed.ncbi.nlm.nih.gov/39372947/

New work showing that multidrug-resistant 𝘈𝘤𝘪𝘯𝘦𝘵𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘣𝘢𝘶𝘮𝘢𝘯𝘯𝘪𝘪 isn’t a scattered threat—it’s a structured epidemic! A dominant super-lineage and a rising clade (2.5.6) are spreading worldwide, fueled by gene exchange. Li et al. Nat Commun #AMR #bacterialgenomics www.nature.com/articles/s41...

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 https://buff.ly/4gyYCzx We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling

This is very important - shortening antibiotic treatment duration is a good way to reduce consumption

An ICE, a PICI, and a phage walk into a cell… and start crosstalking. Interesting read on how MGEs juggle interactions like pros! 🦠 academic.oup.com/ismej/articl...

Latest publication with @virologyvet.bsky.social trying to make sense of viral/bacterial interactions in co-infections www.mdpi.com/2076-0817/14...

PredCMB: Predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data academic.oup.com/bioinformati... #jcampubs

CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes bmcbioinformatics.biomedcentral.com/articles/10.... #jcampubs

I thoroughly enjoyed this read. It put into words my own thought well. Definitely going to take up some of the suggestions.

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)

DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems https://www.biorxiv.org/content/10.1101/2025.01.08.631726v1

Evolution of antibiotic resistance #AMR can lead to collateral resistance/sensitivity to other drugs; @jeffmaltas.bsky.social &co show that these effects can fluctuate over time, needing precise timing & stochastic control models to optimize treatment strategies 🧪 @plosbiology.org plos.io/3C2Ao1y

Orthology inference across thousands of genomes within a day‽ that sounds incredible

Are there virulent phages hiding in your bacterial culture? Here we find hundreds of virulent phage genomes in bacterial genome assemblies. Bioinformatic and experimental evidence indicate these are not contaminations, but represent persistent infections. www.biorxiv.org/content/10.1...

Potentially new components of the microbiome www.cell.com/cell/abstrac...

Important paper by @henrikstrahl.bsky.social and colleagues

New release of host decontamination tool Hostile: - Much faster long read decontamination - Full support for streaming via stdin and stdout - Full support for interleaved input/output github.com/bede/hostile...

We're thrilled to introduce LexicMap v0.5.0🎉 It's more accurate and slightly faster! LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes! We'll provide an index for ATB on AWS later. github.com/shenwei356/L...

"Over a decade of research indicates that contamination, typically from laboratory reagents, is the most plausible explanation for such findings, particularly when even supposedly ultrapure water has been shown to harbour DNA signatures and culturable microbes." www.theguardian.com/science/2024...

Microbial functional diversity and redundancy: moving forward academic.oup.com/femsre/advan... #jcampubs

Pod5Viewer: a GUI for inspecting raw nanopore sequencing data. #Nanopore #SequencingData #Bioinformatics #Genomics @nanoporetech.com 🧬 🖥️ academic.oup.com/bioinformati...

Panacus: fast and exact pangenome growth and core size estimation. #Pangenomes #PangenomeAnalysis #Bioinformatics #Genomics 🧬 🖥️ academic.oup.com/bioinformati...

Protein sequencing with nanopores? The latest review on the subject dropped yesterday 🤓 www.nature.com/articles/s44...

High accuracy meets high throughput for near full-length 16S ribosomal RNA amplicon sequencing on the #Nanopore platform #microbiome

Two important papers on the gut microbiome and disease —The fecal microbial load is a key determinant confounding prior reports of association with diseases cell.com/cell/fulltex... —Innovative approaches to establish causality and mechanisms science.org/doi/10.1126/...

Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index www.biorxiv.org/content/10.1...

New academic position coming up here at Nottingham Vet School Microbiology/Computational Biology and AMR One Health focused. Please share! jobs.nottingham.ac.uk/Vacancy.aspx...

Multi-pass, single-molecule nanopore reading of long protein strands https://www.nature.com/articles/s41586-024-07935-7 🧬🖥️ https://github.com/uwmisl/PASTOR-sequencing

Mapping cellular interactions from spatially resolved transcriptomics data https://www.nature.com/articles/s41592-024-02408-1 (read free: https://rdcu.be/dSTC5) Spacia software: https://github.com/yunguan-wang/Spacia 🧬🖥️

Amazing piece of work from Lars Barquist this journals.asm.org/doi/10.1128/...

NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs genomebiology.biomedcentral.com/articles/10.... #jcampubs

LexicMap: efficient sequence alignment against millions of prokaryotic genomes https://www.biorxiv.org/content/10.1101/2024.08.30.610459v1

I'm looking for 2 Postdocs & a Technician to join my team in Edinburgh, investigating #mucosal #immunity & #inflammation during #schistosome #infection. If this sounds exciting to you, pls apply! (by 19th Sep)🪱🔬🏴󠁧󠁢󠁳󠁣󠁴󠁿 elxw.fa.em3.oraclecloud.com/hcmUI/Candid... elxw.fa.em3.oraclecloud.com/hcmUI/Candid...

Using Glittr.org to find, compare and re-use online bioinformatics training materials https://www.biorxiv.org/content/10.1101/2024.08.20.608021v1 🧬🖥️

Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03363-y 🧬🖥️ https://github.com/xinehc/melon

New web-interface for the interrogation of TIS data from us! Turn long boring tables into shorter boring tables with some pretty pictures!