iiinova — where your digital self keeps evolving

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Cameron Thrash @jcamthrash.bsky.social · 01/05/2026

MetaMAG Explorer: A Database-Augmenting Pipeline for Genome-Resolved Metagenomics and Enhanced Microbial Classification www.biorxiv.org/content/10.6... #jcampubs

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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 08/03/2026

Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics

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Reposted by Adam Blanchard

Giacomo Donati @giacomodonatijd.bsky.social · 09/01/2026

Check out our review on epithelial–microbiome interactions and their disruption in inflammatory skin disorders. + computational tools to study host–microbe crosstalk + ecological memory (epithelial and microbial memories) in barrier tissues. www.nature.com/articles/s41...

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Ben J Woodcroft @benjwoodcroft.bsky.social · 23/03/2026

New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows. We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠 Here's what we found 👇 doi.org/10.1128/msystems.01062-25

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Javier Santoyo @jsantoyo.bsky.social · 14/09/2025

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

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Alex Crits-Christoph @acritschristoph.bsky.social · 29/06/2025

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"

journals.asm.org

Transposon insertion sequencing reveals novel hypermutator genes in Acinetobacter baumannii | mBio

All organisms have the capacity for evolution through mutation. Bacteria with high mutation rates have a survival advantage in some stressful environments because they generate beneficial mutations mo...

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Rafal Mostowy @rafalmostowy.bsky.social · 26/06/2025

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!

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Kat Holt @katholt.bsky.social · 22/05/2025

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

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Conor (Conchúr) Meehan @conmeehan.bsky.social · 22/05/2025

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...

futurelearn.com

Antimicrobial Databases and Genotype Prediction - Online Course - FutureLearn

Transform your understanding of antimicrobial resistance (AMR) and elevate your research or clinical practice with Wellcome Connecting Science.

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Titus Brown @titus.idyll.org · 15/05/2025

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!

pyani-plus.github.io

pyANI-plus walkthrough – pyANI-plus

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Reposted by Adam Blanchard

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 15/05/2025

Autocycler: long-read consensus assembly for bacterial genomes www.biorxiv.org/content/10.1101/202…

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Andries van Tonder @andriesvt.bsky.social · 06/03/2025

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...

github.com

GitHub - avantonder/bacQC-ONT: QC pipeline for ONT data

QC pipeline for ONT data. Contribute to avantonder/bacQC-ONT development by creating an account on GitHub.

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Reposted by Adam Blanchard

Rob Patro @robp.bsky.social · 09/04/2025

New awesome Rust bioinformatics tool just dropped!

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Hayley Wilson @thehjbrod.bsky.social · 31/03/2025

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...

linkedin.com

Progressive evolution of Streptococcus equi from Streptococcus equi subsp.… | Hayley Wilson

I'm really excited to share this work with the world! As we know, academic research work will follow you even after you've left. So this is my post-doc project…

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ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ @nizet.bsky.social · 23/03/2025

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...

nature.com

Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii - Nature Communications

In this study, authors conduct a genomic analysis of 15,000 Acinetobacter baumannii isolates, revealing a dominant multidrug-resistant super-lineage (accounting for approximately 70% global isolates),...

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Reposted by Adam Blanchard

Noémie Lefrancq @noemielefrancq.bsky.social · 02/01/2025

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 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

buff.ly

Learning the fitness dynamics of pathogens from phylogenies - Nature

Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of…

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Craig MacLean @craigmaclean.bsky.social · 30/01/2025

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

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Cameron Thrash @jcamthrash.bsky.social · 16/01/2025

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

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Evelien Adriaenssens @evelienadri.bsky.social · 15/01/2025

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

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Ryan Wick @rrwick.bsky.social · 31/12/2024

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)

github.com

Home

A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 09/01/2025

DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems www.biorxiv.org/content/10.1101/202…

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PLOS Biology @plosbiology.org · 09/01/2025

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

Success of switching to a second antibiotic is contingent on temporally dynamic collateral effects. Top: Twenty replicate populations of E. faecalis V583 were exposed to increasing concentrations of the antibiotic ceftriaxone over the course of 14 days via serial passage. At the end of each day, a sample of the population was isolated and cultured in a range of doxycycline concentrations for 24 h. Middle: Density (OD) after 24 h versus drug (DOX) concentration for all 20 populations (light gray), and the mean over the 20 populations (dark black) at different days of the evolution experiment. Bottom left: Average sensitivity over 20 populations (error bar standard error of the mean) at different time points. Bottom right: Collateral effects; dashed region highlights a transient six-day window where collateral sensitivity is more pronounced.

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Dr Mark D. Scherz @markscherz.bsky.social · 03/01/2025

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

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Peter Dougherty @peterdoug.bsky.social · 02/01/2025

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...

biorxiv.org

Persistent virulent phages exist in bacterial isolates

Despite the immense diversity of tailed bacteriophages, they are traditionally classified as either virulent or temperate, with only the latter thought capable of long-term persistence in bacterial ce...

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Willem van Schaik @wvschaik.bsky.social · 21/12/2024

Important paper by @henrikstrahl.bsky.social and colleagues

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Bede Constantinides @bede.im · 20/12/2024

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...

github.com

Release 2.0.0 · bede/hostile

A major release with faster long read decontamination and support for stdin and stdout for both single and paired reads. Interleaved paired reads are now supported via stdin and stdout. A breaking ...

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Wei Shen 沈伟 @shenwei356.bsky.social · 19/12/2024

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...

One-page introduction of LexicMap, a sequence alignment tool scalable to millions of prokaryotic genomes.

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Onisillos @onisillos.bsky.social · 20/12/2024

"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...

theguardian.com

There’s little evidence of a ‘brain microbiome’ | Letter

Letters: Prof Mark Pallen, Dr Aimee Parker, Prof Nick Loman and Prof Alan Walker take issue with an article that discussed the existence of a brain microbiome and its impact on diseases

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Cameron Thrash @jcamthrash.bsky.social · 18/12/2024

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

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Javier Santoyo @jsantoyo.bsky.social · 04/12/2024

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

Source
https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae665/60938432/btae665.pdf

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Javier Santoyo @jsantoyo.bsky.social · 04/12/2024

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

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Eric Topol @erictopol.bsky.social · 15/11/2024

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/...

cell.com

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

A machine-learning approach enables the quantification of microbial load (microbial cells per gram) in fecal samples based on the relative microbiome profile. The predicted microbial load emerged as a...

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Zamin Iqbal @zaminiqbal.bsky.social · 15/11/2024

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...

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Stephen Turner @stephenturner.us · 12/09/2024

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

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Stephen Turner @stephenturner.us · 04/09/2024

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

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