GALBA2 walks into the arena. We rewrote our protein-based genome annotation pipeline in Snakemake.
Give it a genome + proteins from close relatives → get gene predictions. No RNA-Seq, no GeneMark needed.
miniprot → AUGUSTUS, fully containerised, HPC-ready.
github.com/Gaius-Augustus/GALBA2
Long-reads exposed plasmid-driven carbapenem resistance transmission missed by routine diagnostics
📌Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing
www.doi.org/10.1099/mgen.0.001644
🖥️🧬💻
#AcademicSky
#MicroSky
#IDSky
🧪🧫🦠
Wildlife trade drives animal-to-human pathogen transmission over 40 years
New in @science.org ‼️ In the most comprehensive study to date, we show that wildlife trade is driving animal-to-human zoonotic spillover at a planetary scale, with +1 spillover per host every 10 years. Live animal markets and illegal trade pose even greater risks. 🔓 www.science.org/doi/10.1126/...
Host read removal sounds simple. It's not. 🧫
Ep. 151 of #microbinfie: we talk with @bede.im about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2.
#metagenomics
on.soundcloud.com/gEm7QyaTauvd...
“Antibiotic stewardship-induced syncope. It's a new diagnosis.”
The latest video in our partnership with @glaucomflecken.bsky.social summarizes a recent trial investigating whether a single dose or multiple doses of benzathine penicillin G is needed for early syphilis. 👉 nej.md/DrG28
Pleased to share our new preprint on genomic epi of #treponema www.medrxiv.org/content/10.6... focusing on genomic diversity and transmission of #syphilis in Africa with @drmichaelmarks.bsky.social @sangerinstitute.bsky.social @thruzim.bsky.social and many others
🔬 50 years of electron microscopy (EM) at VIDRL, from Australia’s first HIV ultrastructural images in the 1980s to the first local images of SARS‑CoV‑2. EM is a vital tool for detecting and characterising pathogens during outbreaks.
Find out more 🔗 https://bit.ly/4sLZOoK
12 years in the making - we are finally scaling up our “universal diagnostics” platform. m.youtube.com/watch?v=gbeg...
Read about the global program here: news.stanford.edu/stories/2026...
If you are passionate about bringing cutting edge tools to work for “everyone” - reach out and engage.
🚨vConTACT3 now in Nature Biotechnology:
- >95% agreement with ICTV for known viruses
- Classifies both prokaryotic and eukaryotic viruses
- Extends beyond genus → subfamily, family & order
- Systematically assigns taxonomy to tens of thousands of previously unclassified viruses
The long-held belief that only female mosquitoes bite may not be true after all.
Very excited to have had the opportunity to contribute to this study showing that male mosquitoes can also bite and feed on blood.
www.biorxiv.org/content/10.1...
Navigating multiple analysis tools shouldn't be a project in itself 🧬💻️
Introducing BioCommons Access: a new SSO ecosystem launching 26 March! Seamlessly connect & transition between #GalaxyAustralia & the @bioplatformsaus.bsky.social Data Portal with just one login.
Read more:
The're also doing untargeted deep sequencing of wastewater RNA. Cool project! naobservatory.org/casper/
There's a preprint out: www.medrxiv.org/content/10.6...
I’m please to announce that our research on a faecal mNGS assay has been published. Our findings highlight the potential for mNGS to improve clinical diagnostics by providing a high-resolution view of rare pathogens and AMR genes in a single test.
www.frontiersin.org/journals/cel...
🧬🖥️ I’m building an open-source framework for easily compiling #bioinformatics pipeline results into pdf/html/xlsx reports. It will have built-in parsers for popular CLI tools
Now looking for a few bioinformaticians for a brief usability feedback interview 👩💻
DM me or respond here if interested 👋
We’ve published a wee pilot study assessing the utility of metagenomics & full-length 16S sequencing for the detection of seasonal pathogens (and AMR) in our local urban recreational swimming hot-spot
Check it out if you’re into that stuff :)
www.microbiologyresearch.org/content/jour...
We're thrilled to announce the Ctrl-Z Award, a US$2,500 prize for researchers “who discover substantial errors in their published work and take meaningful steps to correct the scientific record."
Covered by @nature.com today; read more here: centerforscientificintegrity.org/2026/03/10/a...
🐄🧬 The Bioplatforms Animal Disease Genomics Initiative is now an official project supporting DAFF Animalplan 2022–2027, Australia’s first national action plan for production animal health. 🦠🔬 #NCRISimpact
👉 Read more: www.agriculture.gov.au/agriculture-...
🧬📸 Calling all eDNA enthusiasts, researchers, students & practitioners!
We want to see eDNA through your lens 👀
The #eDNAinFocus Photo Competition celebrates the creativity, diversity & real-world impact of environmental DNA research across Australia, New Zealand & beyond 🌏
🧵👇
🦉 New publication! 🦆
BirT: A Novel Primer Pair for Avian Environmental DNA Metabarcoding
onlinelibrary.wiley.com/doi/10.1002/...
Want to amplify birds from #eDNA samples? This new primer pair is the way to go!
@dirch3.bsky.social, Rachel Empey, Megan Cowperthwaite, Katerina Coveny #metabarcoding
Due March 31, 2026. Microgrant for 10 people from historically underfunded geographies/institutions to attend the Global eDNA Conference, Seattle, WA Oct 28-30. Covers 4 nights hotel and conference registration; does NOT cover travel and other expenses. #eDNA #grant forms.gle/99jEZj6K8cD7...
Check out this list of awesome #virome tools and be sure to add yours!
github.com/shandley/awe...
#phagesky #microsky
See you this Wedneday 😀
Join us for an evening of cutting-edge microbiology, industry insights, and great conversation!
📅 Wednesday, 25 February 2026
⏰ 6:00–7:30pm
📍 The Burrow (Beer Garden Room), West End
🍕 Free pizza provided!
👉 Register via the QR code on the poster.
Tool of the week: Comparing microbial #genomes just got easier. EDGAR – comparative genomics without the headaches. Publication-ready figures, genome similarity analyses, phylogenetic trees. All in one platform. 🧬
edgar3.computational.bio.uni-giessen.de
EMBL International PhD Programme - summer recruitment 2026! 👀
Research groups across EMBL are recruiting now! www.embl.org/about/info/e...
Don’t miss this opportunity to receive dedicated mentoring while doing interdisciplinary research.
Left: Probiotic strain abundance quantification in two probiotic intervention trials. Top left: Based on qPCR data, there was a significant enrichment in Akkermansia muciniphila and Bifidobacterium infantis probiotics in Validation Study A at Week 12 compared to Week 0. There was no enrichment of Clostridium beijerinckii, Clostridium butyricum, and Anaerobutyricum hallii probiotics. Bottom left: Based on shotgun metagenomic data, there was significant enrichment in Enterocloster bolteae, Flavonifractor plautii, Sellimonas intestinalis, and Clostridium symbiosum in Validation Study B at Week 12 compared to Week 0. Only E. bolteae and F. plautii showed notable enrichment above the relative abundance threshold of 0.005. Right: Switching from a low- to high-fiber diet in the Arivale cohort causes non-uniform shifts in MCMM-predicted butyrate production. Simulating a dietary shift from a low-fiber standard European diet (blue points) to a high-fiber diet (red points) results in a non-uniform increase in butyrate production across the study population (N = 1,786). Points from the same individual are connected by a horizontal gray line.
#Prebiotic & probiotic interventions can induce therapeutically relevant shifts in your #microbiome, but their effects vary. @gibbological.bsky.social &co show that metabolic models can predict #probiotic engraftment & shifts in SCFA production after intervention @plosbiology.org 🧪 plos.io/4asmMuV
Reminder: We are accepting nominations for the 2026 Microbiome Medal Laureate, honoring excellence in research, mentorship, and service!
🗓 Deadline: April 10
📩 Submit nominations to microbiomecenter@psu.edu
🔗 www.psu.edu/news/researc...
We would love to host a #postdoctoral fellow in Data-Driven Life Science!
If you have expertise in #microbiome analyses, #multi-omics studies and/or #machinelearning, please get in touch to discuss potential projects.
More infos:
www.scilifelab.se/data-driven/...
#bioinformatics #datascience
You gotta be kidding me
gift link
www.wsj.com/tech/persona...
The 'but I like this meme'. Top panel: 'The public' referring to Jeremy Clarkson standing between two cars. The red car on the right says: 'Antimicrobial resistance (AMR). Jeremy says: "This is brilliant" Bottom panel: Jeremy points to the silver car which is captioned: 'Antibiotic resistance' and says: "But I like this"
The language we use in science is important.
Repeatedly, the public understands 'antibiotic resistance' over 'antimicrobial resistance'
Clarity > correctness. #AMR will continue until messaging improves
#AntibioticResistance #SciComm
www.nature.com/articles/s43...
www.nature.com/articles/s43...
The surge of HPAI in cattle has had an intersting side effect - way more research, and detections, of influenza D virus.
👉 www.science.org/content/arti...
