Alvaro San Millan
@sanmillan.bsky.social
📤 1639
📥 641
📝 85
Plasmid biology, antimicrobial resistance plasmidlab.es
reposted by
Alvaro San Millan
Jerónimo Rodríguez-Beltrán
6 days ago
🚨 New preprint from the lab! 🚨 We show that multireplicon plasmids are true AMR "jack-of-all-trades": Widespread, highly mobile, broad host-range, and packed with resistance genes. Far from random, they form co-evolving associations driven & 𝘮𝘢𝘪𝘯𝘵𝘢𝘪𝘯𝘦𝘥 by IS elements. See Nacho's thread below!👇👇
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David Bikard
26 days ago
Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to
@seth-shipman.bsky.social
!
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Alvaro San Millan
Ilyas Alav
29 days ago
My main postdoc paper is now out in
@natureportfolio.nature.com
npj Antimicrobials and Resistance!
www.nature.com/articles/s44...
. Using flow cytometry, we show that the nucleoside analogues azidothymidine, didanosine, stavudine, and trifluridine reduced transfer of AMR plasmids pCT and pKpQIL (1/3)
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Mechanistic insights into plasmid transfer inhibition in Enterobacterales by nucleoside analogues - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Mechanistic insights into plasmid transfer inhibition in Enterobacterales by nucleoside analogues
https://www.nature.com/articles/s44259-026-00197-5#rightslink
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Alvaro San Millan
Centro Nacional de Biotecnología (CNB)
about 1 month ago
En
#AGolpeDeBit
#RTVE
,
@sanmillan.bsky.social
investigador del
#CNB
@csic.es
habla de este estudio liderado junto a Alfonso Santos López
@uam.es
y en colaboración con Ayari Fuentes
#UNAM_MX
centrado en el plásmido pOXA-48 de gran interés clínico 📻 ¡No te lo pierdas!
www.rtve.es/play/audios/...
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Resistencia a antibióticos: hallada nueva clave en plásmidos
Ponemos el foco en un estudio que identifica un nuevo mecanismo por el que los plásmidos pueden acelerar la aparición de resistencia a los antibióticos
https://www.rtve.es/play/audios/a-golpe-de-bit/golpe-bit-resistencia-antibioticos-hallada-nueva-clave-plasmidos/17015765/
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Alvaro San Millan
Vaughn Cooper
about 1 month ago
Now out in AEM
@asm.org
! 🎉🧪 *High school student-isolated mutants 👉🏻 novel genetic causes of biofilm-associated adaptations *We learn how diversity arises quickly and is maintained *EvolvingSTEM enables scalable research in classrooms & promotes scientific literacy
journals.asm.org/eprint/FBU9M...
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Alvaro San Millan
Teresa M. Coque
about 2 months ago
We are pleased to share our last article
rdcu.be/fabhM
. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇
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The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the “robust-yet-fragile” architecture ...
https://rdcu.be/fabhM
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Alvaro San Millan
Will Smith
about 2 months ago
Here’s the latest preprint from my work on evolved resistance to Type VI Secretion system (T6SS) weaponry, funded by a
@wellcometrust.bsky.social
Sir Henry Wellcome Fellowship. So happy to see this out!
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.03.17.712380v1
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Alvaro San Millan
Filipa Trigo da Roza
about 2 months ago
New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms. If you want to know more, here is a thread 🧵
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.03.17.712381v1
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Craig MacLean
3 months ago
New
#AMR
pre-print Combining antibiotics with genotoxins can efficiently suppress bacterial in high throughput experimental models.
www.biorxiv.org/content/10.6...
Fun collaboration with Nassos Typas lab led by
@mulkern.bsky.social
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https://www.biorxiv.org/content/10.64898/2026.02.20.706947v1
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Final version of our last paper is out!
www.nature.com/articles/s41...
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Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology
Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
https://www.nature.com/articles/s41564-026-02290-x
2 months ago
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Alvaro San Millan
Centro Nacional de Biotecnología (CNB)
2 months ago
Identifican un nuevo mecanismo utilizado por plásmidos para acelerar la aparición de resistencia a los antibióticos.
@sanmillan.bsky.social
@uam.es
@csic.es
Más info en nuestra web: https://f.mtr.cool/pmappovlkt Artículo en: https://f.mtr.cool/yvxpgzaraz
@natureportfolio.nature.com
@erc.europa.eu
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Alvaro San Millan
Alvaro Sanchez
2 months ago
New preprint on the limits of detecting higher-order interactions in microbial communities.
www.biorxiv.org/content/10.6...
We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.
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https://www.biorxiv.org/content/10.64898/2026.03.05.709494v1
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Alberto HCA
2 months ago
Excited to share our latest work! 📝 We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬 Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them. Learn more 👇🏼
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Pedro Dorado-Morales
3 months ago
New preprint out on bioRxiv!
www.biorxiv.org/content/10.6...
Can conjugative plasmids be used to control plasmid and pathogen spread? Follow me down the rabbit hole that led to this story 🧵
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https://www.biorxiv.org/content/10.64898/2026.02.25.707879v1
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Great news!! Really looking forward to starting this collaboration
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3 months ago
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Jesse Shapiro
3 months ago
Now out & nicely formatted in
@isme-microbes.bsky.social
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs,
@gmdouglas.bsky.social
&
@cyanophage.bsky.social
along with co-PIs
@lbobay.bsky.social
& Samuel Chaffron. A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
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Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny
Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring
https://doi.org/10.1093/ismejo/wraf275
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So great to finally have such a clear answer to this question!! Well done guys!
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4 months ago
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Alvaro San Millan
Allison Lopatkin, PhD
4 months ago
Big week: welcomed a new baby boy Harris Lopatkin, AND our PlasAnn paper is finally out:
academic.oup.com/nar/article/...
(obviously the first more important than the second 🥰). Currently on leave but if anyone has the need to annotate large plasmids, go check it out!
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PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis
Abstract. Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse micro
https://academic.oup.com/nar/article/54/3/gkaf1507/8442276?guestAccessKey=bed9ef95-96ab-485e-82af-431dd6c97f13&utm_source=authortollfreelink&utm_campaign=nar&utm_medium=email
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Alvaro San Millan
Paula Ramiro-Martínez
4 months ago
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story
www.pnas.org/doi/10.1073/...
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Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...
https://www.pnas.org/doi/10.1073/pnas.2526088123
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Alvaro San Millan
Jerónimo Rodríguez-Beltrán
4 months ago
New paper out in
@pnas.org
, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿
www.pnas.org/doi/10.1073/...
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Alvaro San Millan
bioRxiv Evolutionary Biology
4 months ago
Novel genes arise from genomic deletions across the bacterial tree of life
https://www.biorxiv.org/content/10.64898/2026.01.05.697752v1
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Alvaro San Millan
Angel Goñi-Moreno
5 months ago
Preprint out! By controlling growth, via RNAP, we control the entire cellular machinery, and tune the cellular context into distinct, stable states. See how NOT gates behave! Kudos to
@angeles-hg.bsky.social
and
@mirobueno.bsky.social
🔗https://www.biorxiv.org/content/10.64898/2025.12.19.695408v1
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Growth control as a central regulator for tuning the cellular context
The cellular context interacts with genetic circuits, decisively defining their performance. However, contextual dependencies (the interplay between the host and the circuit) are often difficult to en...
https://www.biorxiv.org/content/10.64898/2025.12.19.695408v1
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Alvaro San Millan
Tatiana Dimitriu
5 months ago
Our story on plasmid streamlining is now published in PLoS Biology! With
@andrewmatthews.bsky.social
and
@sonjalehtinen.bsky.social
#MicroSky
#Mevosky
journals.plos.org/plosbiology/...
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Plasmid streamlining drives the extinction of antibiotic resistance plasmids under selection for horizontal transmission
Conjugative plasmids play an important role in the spread of antimicrobial resistance (AMR) genes among pathogenic bacteria. This study shows that AMR loss in evolving populations is associated with t...
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003564
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Alvaro San Millan
Centro Nacional de Biotecnología (CNB)
5 months ago
Last week, we hosted the XXXIII CNB Scientific Workshop. We are delighted to announce this year’s award winners: 🏆 Best Postdoctoral Talk: Alicia Calvo-Villamañán 🏆 Best PhD Talk: Silvia López Borrego 🏆 Best Poster: Jorge Sastre Domínguez Congratulations to all!
#CNB_CSIC
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Alvaro San Millan
Teresa M. Coque
6 months ago
A pleasure and an honour to have received this prestigious grant with my admired colleagues and friends
@sanmillan.bsky.social
and
@asanchezlab.bsky.social
. More about AMR under plasmid lens!. My sincere gratitude to
@caixaresearch.bsky.social
@microryc.bsky.social
@esgem-sg.bsky.social
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Alvaro San Millan
Michael Baym
6 months ago
Hot off the press! Our latest paper led by
@fernpizza.bsky.social
, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
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Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
https://www.science.org/doi/10.1126/science.adx0665
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Alvaro San Millan
Centro Nacional de Biotecnología (CNB)
6 months ago
👏 Dos proyectos del
#CNB
seleccionados en la convocatoria de Investigación en Salud 2025 de la
@caixaresearch.bsky.social
Ambos abordan un gran reto global: la resistencia a los antimicrobianos.
#HealthResearch
#FundaciónlaCaixa
@sanmillan.bsky.social
@jaescudero.bsky.social
f.mtr.cool/jejatlbssz
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Alvaro San Millan
6 months ago
1/ Antibiotic resistance causes ➕ than 1 M deaths each year and understanding why this happens is key to stopping it. With #HealthResearch support,
@sanmillan.bsky.social
#HealthResearch
is investigating how different plasmids (DNA fragments) coexist in bacteria and confer resistance.
https://tinyurl.com/3bysv6cr
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Alvaro San Millan
Connor Sharp
6 months ago
So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae.
www.nature.com/articles/s41...
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Bacterial warfare is associated with virulence and antimicrobial resistance - Nature Communications
Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...
https://www.nature.com/articles/s41467-025-64363-5
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Alvaro San Millan
Pablo Laborda
7 months ago
New preprint out! 📣🚨 We found that loss-of-function mutations in the carbapenem entry porin OprD of Pseudomonas aeruginosa do more than confer
#AntibioticResistance
: they reshape the bacterial membrane and interaction with the host, enhancing epithelial colonization capacity 🦠
#Microsky
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Alvaro San Millan
José Aguilar-Rodríguez
7 months ago
One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.
www.biorxiv.org/content/10.1...
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Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation
The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
https://www.biorxiv.org/content/10.1101/2024.10.30.621178
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Wendy Figueroa
7 months ago
✨New paper from
@jrpenades.bsky.social
and
@sanmillan.bsky.social
labs. We found that non-conjugative plasmids 🧬 tend to have low mobility to promote functional diversity ⚔️💊 in bacterial communities🦠🦠. Brilliant work by Akshay,
@asantoslopez.bsky.social
and others.
www.cell.com/cell-reports...
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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...
https://www.cell.com/cell-reports/fulltext/S2211-1247%2825%2901227-6
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New paper with my (amazing) friend and mentor
@jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!! With
@asantoslopez.bsky.social
@wfigueroac3.bsky.social
Akshay Sabins and others
www.cell.com/cell-reports...
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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...
https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01227-6
7 months ago
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Alvaro San Millan
Imperial Life Sciences
7 months ago
New paper just out from
#OurImperial
@tcostalab.bsky.social
The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain.
www.nature.com/articles/s41...
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The assembly of a hybrid type IV secretion system by a Crohn’s disease-associated Escherichia coli strain - Nature Communications
Adherent-invasive strains of E. coli are commonly isolated from patients with Crohn’s disease. Here, the authors show that an AIEC harbours a hybrid Type IV secretion system (T4SS) that mediates pilin...
https://www.nature.com/articles/s41467-025-63859-4
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Alvaro San Millan
Nature Communications
7 months ago
Dissecting the fitness effects of a carbapenem resistance plasmid in clinical Enterobacterales using plasmid-wide CRISPRi screens
@aliciapcv.bsky.social
@jorgesastred.bsky.social
@sanmillan.bsky.social
@cnb-csic.bsky.social
#bacteria
#plasmids
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Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens - Nature Communications
This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the carbapenemase OXA-48 has a role in the plasmid-associated fitness costs.
https://bit.ly/42KaCJA
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Alvaro San Millan
Vaughn Cooper
7 months ago
DYK most P. aeruginosa carry filamentous phage(s) that don't need to kill the cell to reproduce? We 👉🏻@nanamikubota.bsky.social show that these Pf phages can go ROGUE. "Filamentous cheater phages drive bacterial and phage populations to lower fitness" 🔗
authors.elsevier.com/c/1lt5I3QW8S...
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Alvaro San Millan
Centro Nacional de Biotecnología (CNB)
7 months ago
Nuestro compañero Álvaro San Millán (
@sanmillan.bsky.social
), investigador en el
#CNB_CSIC
ha recibido el Premio María Moliner, que reconoce la labor de quienes se inician en la dirección de tesis doctorales, destacando su compromiso en el acompañamiento del talento emergente. ¡Enhorabuena!👏
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Craig MacLean
7 months ago
New pre-print
www.biorxiv.org/content/10.1...
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with
@brockhurstlab.bsky.social
!
#phagesky#microsky
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Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage
Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...
https://www.biorxiv.org/content/10.1101/2025.10.08.681082v1
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Alvaro San Millan
Centro Nacional de Biotecnología (CNB)
7 months ago
El proyecto "Descubrir actividades de resistencia antimicrobiana más allá de la resistencia" de
@sanmillan.bsky.social
(#CNB,
@csic.es
) y
@jaescudero.bsky.social
(
@ucm.es
) recibe una ayuda del Programa
#Fundamentos
de Fundación BBVA. ℹ️Lee la noticia aquí👇
bit.ly/48cvkp1
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Alvaro San Millan
Zamin Iqbal
8 months ago
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
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Michael Brockhurst
8 months ago
Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations
royalsocietypublishing.org/doi/epdf/10....
Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska
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Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections
https://royalsocietypublishing.org/doi/epdf/10.1098/rstb.2024.0080
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Craig MacLean
8 months ago
New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...
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Job Details
https://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form?p_company=10&p_internal_external=E&p_display_in_irish=N&p_process_type=&p_applicant_no=&p_form_profile_detail=&p_display_apply_ind=Y&p_refresh_search=Y&p_recruitment_id=179554
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Uli Klümper
8 months ago
Excited to share our new Perspective in npj Antimicrobials & Resistance: "Towards the integration of antibiotic resistance gene mobility into environmental surveillance and risk assessment.”
www.nature.com/articles/s44...
1/3
#AMR
#microsky
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Towards the integration of antibiotic resistance gene mobility into environmental surveillance and risk assessment - npj Antimicrobials and Resistance
npj Antimicrobials and Resistance - Towards the integration of antibiotic resistance gene mobility into environmental surveillance and risk assessment
https://www.nature.com/articles/s44259-025-00154-8
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Alvaro San Millan
Eduardo Rocha
8 months ago
How do loci for bacterial capsules (Klebsiella) manage to get swapped around despite their outstanding phenotypes? They just plug and play, having little impact on the rest of the genome. Kudos to
@julielebris.bsky.social
, check her thread below
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Alvaro San Millan
Mizrahi Lab
8 months ago
Continuing work on our exhibition
#microbes
🎨 Honored by a talk from Prof. Itzik Hen, director of The Institute for Advanced Studies Jerusalem and a researcher, followed by a food tour at Mahane Yehuda Market, and a recital by Ido Grinshpan and Shelly Jonathan.🎻 Stay tuned for
#exhibition
details! 🦠
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Zamin Iqbal
8 months ago
Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when
@shenwei356.bsky.social
joined our group for a year on an
@embl.org
sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
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Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
https://www.nature.com/articles/s41587-025-02812-8
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Alvaro San Millan
Olaya Rendueles
8 months ago
Check out
@julielebris.bsky.social
’s thread on our latest manuscript describing phenotypic heterogeneity in capsule production in Klebsiella & Acinetobacter
@klebclub.bsky.social
This work started when I was still in
@pasteur.fr
& got finished in
@cbitoulouse.bsky.social
#microsky
#phagesky
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José R Penadés
8 months ago
Thrilled to share our two latest papers with the
@tcostalab.bsky.social
lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species.
@imperialcollegeldn.bsky.social
www.cell.com/cell/fulltex...
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Chimeric infective particles expand species boundaries in phage-inducible chromosomal island mobilization
Capsid-forming PICIs (cf-PICIs) produce their own capsids and exploit phage tails from unrelated species to transfer their DNA across bacterial hosts. This tail piracy enables broad dissemination and ...
https://www.cell.com/cell/fulltext/S0092-8674%2825%2900974-2
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José R Penadés
8 months ago
Our second paper with
@tcostalab.bsky.social
and GoogleDeepMind reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...
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AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution
By solving a previously unsolved biological question, the AI co-scientist predicted a complex mechanism of gene transfer and generated hypotheses that opened new research directions, illustrating AI's...
https://www.cell.com/cell/fulltext/S0092-8674%2825%2900973-0
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Antimicrobial Resistance (AMR) could cause 10 million deaths by 2050. At PLAS-FIGHTER, we are working to change this! 🔎 We study how plasmids spread resistance to open up new avenues for future containment and diagnostic strategies. Find out more 👇
plasmidlab.es/project/
#AntibioticResistance
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Project - Plasmidlab
PLAS-FIGHTER Exploiting plasmid-bacteria interactions to fight
https://plasmidlab.es/project/
8 months ago
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