Finally out! 🎉 After 3 years of postdoc in London, here is my main work, now published in Nature Comm. (and as co-corresponding author!) Using a combination of bioinformatic and experimental approaches, we propose a model of plasmid evolution in Staphylococcus. www.nature.com/articles/s41... ⬇️ 1/4

1/ Excited to share the newest tool in the pangenome MUMiverse: Shredtools! Shredtools enables a user to navigate the pangenome coordinate system with multi-MUMs. More in the thread🧵 Code: github.com/vikshiv/shredtools Interactive tool for querying HPRC assemblies: vikshiv.github.io/shredtools

Navigating the pangenome coordinate system with Shredtools

Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...

biorxiv.org

Our Pectobacterium story continues. This one shows the conservation of tailocin and localized HGT of the tail fiber locus across the Pectobacterium genus.

Genome Biology and Evolution@genomebiolevol.bsky.social · 4mo ago

@lakhanp01.bsky.social @annecmg.bsky.social et al. characterized the genomic diversity of a tailocin and discovered that diversity is maintained through exchange of the tail fiber locus DNA across Pectobacterium, a pathogen causing soft rot. 🔗 doi.org/10.1093/gbe/evag106 #genome #evolution

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity! www.nature.com/articles/s41...

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology

The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

nature.com

A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41... How bacteria evolved thousands of precision nanoinjectors? Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).

Merry X-SMASH! My first first author paper is out on bioRxiv! 🖥 We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫 1/8

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 10mo ago

epsSMASH uncovers exopolysaccharide biosynthetic gene clusters in environmental and human microbiomes https://www.biorxiv.org/content/10.64898/2025.12.21.693542v1

Thrilled to share our new review online with @scottvedwards.bsky.social in @Trends Ecol & Evo! “pangenomics is rapidly transforming our ability to dissect the genetic basis of ecological and evolutionary change in natural systems.”

Trends in Ecology & Evolution@cp-trendsecolevo.bsky.social · 10mo ago

Online now: Pangenomes: new tools for ecological and evolutionary genomics

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

Life Identification Numbers: A bacterial strain nomenclature approach

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

doi.org

Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0 Code: github.com/vikshiv/mume... Very efficient pangenome visualization tool, revealing synteny and variations!

Hi everyone, a few years ago, we started a list of labs studying bacterial immunty for students, editors, conference organizers... (currently n=79). Update time ! Send me a message to 1) add your lab or others 2) Correct info docs.google.com/spreadsheets... #Phagesky #Microsky

Labs in bacterial immunity

docs.google.com

Do plasmids really move around that much? Well, maybe not always Thrilled to have contributed to this story with two of my favourite microbiologists: @jrpenades.bsky.social & @sanmillan.bsky.social This great work was led by Akshay Sabnis & @wfigueroac3.bsky.social www.cell.com/cell-reports...

Non-conjugative plasmids limit their mobility to persist in nature

Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

cell.com

Movi 2: Fast and Space-Efficient Queries on Pangenomes. #Pangenomes #SequenceQueries #Genomics #Bioinformatics @biorxiv-genomic.bsky.social 🧬 🖥️ www.biorxiv.org/content/10.1...

Between 2018–2023, antibiotic resistance increased in over 40% of the pathogen–antibiotic combinations monitored, with an average annual rise of 5–15%. Resistance is highest in the WHO South-East Asian & Eastern Mediterranean Regions, where 1 in 3 reported infections were resistant 👉 bit.ly/438Ta1u

🧬 What if #plasmids weren’t competitors, but cooperators? A new study in npj Antimicrobials & Resistance shows that many plasmids coexist within the same bacterium — and that non-resistant ones survive thanks to those carrying #AMR genes. #AMR #Plasmids #OneHealth 🔗 doi.org/10.1038/s442...

Communities of plasmids as strategies for antimicrobial resistance gene survival in wastewater treatment plant effluent - npj Antimicrobials and Resistance

npj Antimicrobials and Resistance - Communities of plasmids as strategies for antimicrobial resistance gene survival in wastewater treatment plant effluent

doi.org

Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky www.nature.com/articles/s41...

Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications

Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.

nature.com

#MicroSky

Dave Baltrus 🦦@surtlab.bsky.social · last yr.

Here’s published version of our manuscript using GWAS to investigate tailocin sensitivity in Pseudomonas syringae. TL:DR pretty clear LPS is tailocin receptor but also that P.syringae often completely swaps out its entire O antigen biosynth pathway w/ recombination academic.oup.com/g3journal/ad...

Sassy is out now! Ever need to search for approximate matches of short DNA strings? Sassy is the tool to use! Available now wherever you get your code With @rickbitloo.bsky.social curiouscoding.nl/papers/sassy... github.com/ragnarGrootK...

In this great new paper, the authors use metagenomic Hi-C to show that #phage with broad host range are fairly common, contrary to the prevailing view on their biology. Cutting edge methods like Hi-C are shedding light on our blind spots in the microbial world.

Phages with a broad host range are common across ecosystems - Nature Microbiology

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

nature.com

New pre-print from my lab! Plasmids link antibiotic resistance and phage defense. E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!! #microsky#AMR#phage www.biorxiv.org/content/10.1....

Plasmids link antibiotic resistance genes and phage defense systems in E. coli

Phage therapy has been proposed as an alternative to antibiotics to treat resistant infections. However, we have a limited understanding of how antibiotic resistance genes (ARGs) associate with bacter...

biorxiv.org

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

Super paper from the mighty Mia Winkler, @genomarit.bsky.social and Iren Lohr. "We have previously shown that there were relatively few strain-sharing events across ecological niches...plasmid-sharing is considerably more common across niches than strain-sharing. " www.biorxiv.org/content/10.1...

A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome

Plasmids play a pivotal role in the horizontal gene transfer of antimicrobial resistance (AMR) and virulence determinants among bacteria. Members of the Klebsiella pneumoniae species complex (KpSC) ca...

biorxiv.org

CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. #MicrobialGenomes #Bioinformatics 🧬 🖥️ academic.oup.com/bioinformati...

Identification and Functional Insights into New Phage Tail-Like Bacteriocins (PTLBs) Targeting Pseudomonas aeruginosa as new antimicrobials https://www.biorxiv.org/content/10.1101/2025.08.20.671207v1

Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice. #TransposableElements #TE #Pangenomes #RiceGenomes @natcomms.nature.com www.nature.com/articles/s41...

This is very cool. @sanmillan.bsky.social I wonder to what extend these non-random IS-dynamics are naturally selected for. Could it be the result of a long co-evolutionary history of ISs and bacteria? Are there differences in natural/non-natural antimicrobials? www.biorxiv.org/content/10.1...

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation

Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...

biorxiv.org

"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude." www.biorxiv.org/content/10.1...

Protein structure alignment significance is often exaggerated

Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...

biorxiv.org

Mumemto: efficient maximal matching across pangenomes. #Pangenomes #VisualizationTool #PangenomeDiagnostic #Bioinformatics #Genomics #GenomeBiology genomebiology.biomedcentral.com/articles/10....

Mumemto: efficient maximal matching across pangenomes - Genome Biology

Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the…

genomebiology.biomedcentral.com