Miss Salmonella

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...

Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this
www.biorxiv.org/content/10.6...

Genome Science UK 2026 - SAVE THE DATE 📅
Manchester 14th-16th September 🧬🧬
#Genomics

I can log in... I can check for you...

sometimes there are training datasets in the Illumina BaseSpace, i.e., focused on some diseases like breast cancer. You can download the fastq files for free.

“What is true for E. coli is also true for the elephant.”
— Jacques Monod, quoted in the latest highlight by @relenski.bsky.social. A line we all love if we’ve worked (or still work) in bacterial evolution. It’s Friday… have fun 🧬

Murcia incorpora a los veterinarios voluntarios en casos de emergencias de protección civil El Gobierno de la Región de Murcia y el Colegio Oficial de Veterinarios colaborarán para integrar la participación voluntaria del colectivo en situaciones de emergencias de protección civil ...

La Región de Murcia ha dado un paso adelante en la gestión de emergencias al incorporar de forma oficial a los #veterinarios voluntarios en los planes de protección civil

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.

academic.oup.com/nar/advance-...

Por qué creo que es tan grave lo de los historiales de Andalucía? Porque atenta contra la confianza básica en las instituciones, poniendo en duda sus cimientos. Mañana alguien puede borrar mi enfermedad por lo que sea. O inventarse una nueva y "filtrarla" para perjudicarme. O cambiar datos

Residuos agrícolas como solución verde: cáscaras de pistacho, almendra y nuez para capturar CO₂ Los cultivos de frutos secos, cada más extendidos a escala global, generan grandes cantidades de residuos que pueden ser aprovechados para desarrollar materiales sostenibles con múltiples aplicaciones

Los cultivos de frutos secos generan grandes cantidades de residuos que pueden ser aprovechados para desarrollar materiales sostenibles con múltiples aplicaciones.

Mañana Mary-Claire King recibirá premio Princesa de Asturias. Donará el importe a una organización médica palestina 👏👏

Publicó el artículo que identificaba el gen del cáncer de mama. Trabajó con las Abuelas de la Plaza de Mayo usando ADN para identificar a niñas/os robados durante la dictadura.

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes academic.oup.com/nar/advance-... #jcampubs

Preocupante lo que está pasando en el #NIH y que impacta en nuestro trabajo diario con las bases de datos de NCBI, SRA, GEO…
Hora de reevaluar nuestros procesos y de planificar un sistema más resiliente ante cambios externos y que nada tienen que ver con la ciencia y la #Bioinfo

Comparative analysis of illumina and oxford nanopore sequencing platforms for 16S rRNA profiling of respiratory microbial communities - Scientific Reports Scientific Reports - Comparative analysis of illumina and oxford nanopore sequencing platforms for 16S rRNA profiling of respiratory microbial communities

Do we see the same respiratory microbiome with #Illumina and #Nanopore? Macip et al. (2025, Sci Rep) show we don’t — Illumina captures higher richness, Nanopore better species resolution. Perhaps the future is an hybrid approach?
#metataxonomy
doi.org/10.1038/s415...

How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study | Applied and Environmental Microbiology Accurate characterization of microbial communities and their functional traits, such as antibiotic resistance, is essential for evaluating water quality and associated public health risks. However, th...

How does the sequencing technology we choose shape what we see in a microbiome? Hu et al. (2025, AEM) show that Illumina, 16S, and Nanopore tell different microbial stories — from native taxa to ARGs and pathogens #Microbiome #AMR
🔗 doi.org/10.1128/aem....

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

🧬 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...

A teal flyer for a PhD opportunity to investigate how warming may change antimicrobial resistance. The project will use experiments on Klebsiella bacteria to answer questions about how temperature affects their response to antibiotics, plasmid transfer, and fitness costs. The research involves microbiology lab work, bioinformatics, and mathematical modeling. The flyer includes contact details for Dr. Daniel Padfield and the logos of the sponsoring institutions.

I have an MRC-funded PhD project available (www.exeter.ac.uk/study/fundin...) on how warming will change the problem of AMR. Join a small and friendly group (padpadpadpad.netlify.app/about) in (sometimes) sunny Cornwall. 🧪🦠 #microsky

Please share the ad below with anyone who may be interested.

Capturing 100 years of antibiotic resistance evolution Researchers dive into the pre-antibiotic history of bacterial plasmids to understand the spread of treatment-resistant infections worldwide.

Capturing 100 years of antibiotic resistance evolution
www.ebi.ac.uk/about/news/r...

Lo hace todo…

🚧 “Closed for training” this week — learning to fly our new PromethION P2i @nanoporetech.com 🧬🚀
Metagenomes, big genomes, epigenetics, transcriptomics… here we come!
We generate data. We analyze data. We generate knowledge. 💥

📢 Join us for the next ECDC Lighthouse webinar
“The public as partners: unlocking the potential of citizen science in disease prevention and control”.

What happens when science opens its doors to the public?
🗓️ Monday 22/09/2025
🕕 13.00-14.00 CET
💻 Online

#ECDCLighthouse

Alucino escuchando a @perestupinya.bsky.social en @avivirser.bsky.social anunciando la cancelación de El cazador de cerebros y @orbitalaika.bsky.social en @rtvecom.bsky.social cuya nueva dirección no parece tener interés en que la sociedad sepa de ciencia de forma cercana/rigurosa. Un despropósito.

Ancient host-associated microbes obtained from mammoth remains Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we a…

New record set! Scientists have sequenced the oldest host-associated microbial DNA ever found, from mammoths. This groundbreaking work opens the door for deeper study of the bacterial communities that existed over a million years ago. #AncientDNA #NGS

www.sciencedirect.com/science/arti...

UCL – University College London UCL is consistently ranked as one of the top ten universities in the world (QS World University Rankings 2010-2022) and is No.2 in the UK for research power (Research Excellence Framework 2021).

Excited to say we’re hiring 😊. We’re looking for a post-doc in ancient pathogen genomics to join our friendly supportive team in London at @ugiatucl.bsky.social. Start date January 2026.

www.ucl.ac.uk/work-at-ucl/...

Breaking News: Read three top CDC officials' resignation emails. The end of an era.

Enough is enough. The health of the country is in danger. Read our resignation letters: insidemedicine.substack.com/p/breaking-n...

Viromics approaches for the study of viral diversity and ecology in microbiomes Nature Reviews Genetics, Published online: 21 July 2025; doi:10.1038/s41576-025-00871-wIn this Review, Roux and Coclet outline current viromics approaches and discuss how they have contributed to our growing understanding of viral genomic diversity, focusing on uncultivated viruses of microorganisms.

New online! Viromics approaches for the study of viral diversity and ecology in microbiomes

suele estar bien cotejar con el artículo original: bsky.app/profile/serg...

Postdoctoral position - Uppsala University Postdoctoral position, Department of Immunology, Genetics and Pathology, Uppsala University

A postdoc position in genomics available at our infrastructure in Uppsala, Sweden! An interesting R&D role a bit outside the traditional academic environment, great colleagues, work at the forefront of (long-read) sequencing.

www.uu.se/en/about-uu/...

To truly understand health in a global sense, we need to integrate #genomics with #exposome. This recent paper highlights how this integrated vision can drive a more realistic #PrecisionMedicine. The future of precision health will be genomic… but also environmental.
www.nature.com/articles/s41...

Accurate and reproducible whole-genome genotyping for bacterial genomic surveillance with Nanopore sequencing data | Journal of Clinical Microbiology ONT sequencing methodology is especially attractive for small and medium-sized laboratories due to its relatively low capital investment and price per sample consumable costs. However, until recently, it lacked accuracy and reproducibility for bacterial ...

link to the paper: journals.asm.org/doi/10.1128/...