Our keynote speaker Franziska Faber on sRNAs in #Cdiff #sporulation @3cdf.bsky.social #3CdF2026

Offering 1 PhD position under the call in the link

Helmholtz-Zentrum für Infektionsforschung (HZI)@helmholtzhzi.bsky.social · 2d ago

🚨 We're recruiting! The HZI is offering 16 fully funded PhD positions to tackle pressing challenges in infection research — from basic science to translational innovation. 📍 Braunschweig, Würzburg, Hannover or Saarbrücken 📅 Apply by September 11 Learn more: jobs.helmholtz-hzi.de/job/Braunsch...

Preprint alert! Work from my postdoc in the lab of @roi1avraham.bsky.social In a collaboration with @danielschraivogel.bsky.social and Lars Steinmetz www.biorxiv.org/content/10.6...

Image-based transposon screening reveals a flavin reductase that restrains intracellular Salmonella replication in macrophages

Intracellular bacterial pathogens can survive and replicate within host cells, yet an isogenic population follows divergent fates: some bacteria are killed, some arrest growth, and others replicate to...

biorxiv.org

Congrats to NUCLEATE PIs Jörg Vogel & Alexander Westermann on their new paper in PNAS! 👏 Alongside partners at Uni Marburg, they identified SAILR, a long non-coding RNA that acts as an apoptosis regulator. Read more: www.pnas.org/doi/10.1073/... #NUCLEATECluster

Helmholtz-Zentrum für Infektionsforschung (HZI)@helmholtzhzi.bsky.social · 2w ago

#Makrophagen sind die „Fresszellen“ des #Immunsystems, doch manche Erreger machen sich gerade diese Zellen als Versteck zunutze. Ein Team des @helmholtz-hiri.bsky.social hat mit Partnern eine #RNA gefunden, die ein "Notausschalter" für infizierte Immunzellen ist. www.helmholtz-hzi.de/media-center...

NCBI Hidden Markov Models (HMM) Release 20.0 18,950 prokaryotic protein HMMs maintained by @ncbi ncbiinsights.ncbi.nlm.nih.gov/2026/07/01/h... #microbiology #bioinforbioinformatics #genomics

Now Available! NCBI Hidden Markov Models (HMM) Release 20.0 - NCBI Insights

Download release 20.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryoti...

ncbiinsights.ncbi.nlm.nih.gov

Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk

Why do some bacteria evolve antibiotic resistance more readily than others? Loved writing this one with @craigmaclean.bsky.social and Liam.

Craig MacLean@craigmaclean.bsky.social · 4w ago

New Essay: 'Resistance potentiators: Evolutionary catalysts of antibiotic resistance' To understand the evolutionary drivers of #AMR we need to move beyond resistance genes to thinking about the ability of genomes to generate AMR variants. #microsky journals.plos.org/plosbiology/...

The @qedscience.bsky.social "impact" score generated a lot of discussion on ranking preprints, including ideas on multi-dimensional rankings that are user specific. Besides describing the ideas, we can now prototype them (with Claude in this case). Here is Salient salient-sgeu6fs5ua-uc.a.run.app

New! R-scape version v2.6.11 github.com/EddyRivasLab... with drawings of R-scape annotated RNA consensus structures with many fewer overlaps!! Using RFview github.com/dincarnato/R... Shout out to @incarnatolab.bsky.social for displaying R-scape's covariation outputs + CaCoFold-R3D structures.

New study by Alexander Henoch (@ahenoch.bsky.social), a PhD student in our group @hifmb.de and @awi.de, shows what it takes to bring gene synteny into microbial pangenomes, and what we learn about the variability landscape of genomes when we do that. See the pre-print here: doi.org/10.64898/202...

"How to give a bad talk". Great commentary on how not to do this! www.nature.com/articles/s41...

Rough day, so have a poem about the Jar of Moles in the Grant Zoology Museum in London that everyone has regarded as too thoroughly batshit to publish

Congratulations to @nanopat.bsky.social on receiving the @rnasociety.bsky.social’s Eclipse Award for Innovation in High Throughput Biology! 🎉 The award recognizes the #RNA research methods he developed during his doctoral studies in #HIRI’s Smyth lab. Read more: www.helmholtz-hiri.de/en/newsroom/...

Award-winning novel methods in RNA research

Patrick Bohn receives RNA Society Eclipse Award for Innovation in High Throughput Biology

helmholtz-hiri.de

Latest research from the lab out now. We examined the role and expression of fimbriae during UPEC bloodstream infection. A real team effort and brilliant collaboration with Mark Schembri’s lab in Brisbane. Thanks to the MRC and BBSRC for supporting our research @ukri.org

Yad fimbriae are triggered by host cues and enhance extraintestinal pathogenic Escherichia coli tissue colonisation during bloodstream infection

Author summary Extraintestinal pathogenic Escherichia coli (ExPEC) colonise the human gut without causing disease but can disseminate to the urinary tract and bloodstream. Understanding the mechanisms...

journals.plos.org

Introducing nail - a Rust implementation of profile HMM sequence alignment for proteins. Near-HMMER sensitivity, but a lot faster: www.biorxiv.org/content/10.1... github.com/TravisWheele...

New paper from the lab! Spoiler: data driven methods performed better for normalisation than spike in CUT&RUN (again). Congratulations especially to Krutika Ambani for most of the work here now embarking on a PhD.

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 2mo ago

Benchmarking normalisation methods for differential binding analysis in CUT&RUN https://www.biorxiv.org/content/10.64898/2026.05.24.727463v1

Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State in Enterococcus faecalis 🦠 queuosine Q again... (Q is also a japanese anime character) www.biorxiv.org/content/10.6...

More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form: "The elusive resistome: a global comparison reveals large discrepancies among detection pipelines" www.biorxiv.org/content/10.6...

Rugose coral video is done! Full video here: www.youtube.com/watch?v=dwkM... #SciArt #paleoart #3dAnimation #coral #reef

New paper out in @cp-cellhostmicrobe.bsky.social! Microbes evolving with modern lifestyles 🧬🦠 S. copri uses PerR to manage oxygen stress, but some strains acquired OxyR via HGT, boosting oxygen tolerance. These strains are enriched in industrialized populations. www.cell.com/cell-host-mi...

Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri

El Mouali and Tawk et al. characterize the oxygen-tolerance response in the human gut-residing bacterium Segatella copri. They identified a subset of strains that acquired an additional oxygen regulat...

cell.com

Are you frustrated by how arbitrary fixed SNPs thresholds "feel"? Are you wondering if there are genetic differences between "promiscuous" and "shy" pathogens? If yes, then read our latest preprint to see what @jburgaya.bsky.social has been up to! www.medrxiv.org/content/10.6...

Coupling time-aware SNP thresholds with genetic markers to define bacterial transmission chains in hospital surveillance

Hospital settings can act as reservoirs for pathogens, with many nosocomial bacteria surviving for extended periods of time and spreading via contaminated environments, healthcare workers, or medical ...

medrxiv.org

The Barrick & Lenski Labs in Dept of Microbiology, Genetics, & Immunology at Michigan State Univ seek a Research Assistant II to manage their research operations and participate in projects related to microbial evolution and synthetic biology. See details below. careers.msu.edu/jobs/researc...

Research Assistant II - East Lansing, Michigan, United States

Position Summary The Barrick and Lenski Labs in the Department of Microbiology, Genetics, & Immunology at Michigan State University are seeking a Research Assistant II to manage their research ope...

careers.msu.edu

🚨Another Langridge lab paper is hot off the press!🚨 We are excited to share the 1st paper from @nisbetalice.bsky.social, exploring the #genomic epidemiology of #entericfever in England & Wales (2004–23). But the hidden story is all about carriage... Now out in @plos.org Neglected Tropical Diseases!

The typhoid Mary legacy: Genomic epidemiology uncovers contemporary carriage dynamics across two decades of enteric fever surveillance in England and Wales

Author summary Enteric fever, caused by Salmonella enterica serovars Typhi and Paratyphi A/B, is a major global health issue. The burden of enteric fever is worsened by bacterial carriers – individual...

journals.plos.org

Microbial Primer: Bacterial energy metabolism www.microbiologyresearch.org/content/jour... #jcampubs

Microbial Primer: Bacterial energy metabolism

All cells need energy to perform their functions. This primer introduces energy metabolism in bacteria, with a focus on key pathways and examples from model organisms, while acknowledging that bacteri...

microbiologyresearch.org

New preprint from the lab. This has been a looong project -- checking how well do genome features (conservation, transcription, epigen, population var, repeats, sequence stats, etc) discriminate coding & noncoding genes from the genomic background.

bioRxivpreprint@biorxivpreprint.bsky.social · 4mo ago

Genomic indicators of gene function: A systematic assessment of the human genome https://www.biorxiv.org/content/10.64898/2026.04.08.717348v1

New tgv release! tgv now remembers your session by quitting with :wq. This release switches from rust-htslib to the native noodles library and reimplemented the S3 support through openDAL. The low-level API will enable finer optimization in the future. github.com/zeqianli/tgv

GitHub - zeqianli/tgv: Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion.

Explore genomes in the terminal. Light, blazing fast 🚀, vim-motion. - zeqianli/tgv

github.com

www.nature.com/articles/s41... #phage #phagesky #microsky

Evolution of pandemic cholera at its global source - Nature

The seventh cholera pandemic, driven by El Tor Vibrio cholerae, evolved separately in Bangladesh and India, with the Ganges Basin acting as the global source, and its evolution has been shaped by...

nature.com

Excited to share our new paper out today in @science.org 🎉 We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩 Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/ #microsky #phagesky www.science.org/doi/10.1126/...

My lab at Pitt is looking for a Research Scientist to help us make phage therapy for patients with antibiotic-resistant infections. Please share and apply! cfopitt.taleo.net/careersectio...

📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.