"Tell me who your friends are, and I’ll tell you who you are." It turns out, microbes follow the same rule!
Very proud to share our lab's new paper in @natmicrobiol.nature.com showing that bacteria don't just respond to their environment, they respond to each other.
www.nature.com/articles/s41...
New paper out! 🔈
Genomic Characterization of the RyC collection: 50 Multidrug Resistant Clinical Isolates of Escherichia coli and Klebsiella spp.
50 MDR gut isolates, 2 sequencing platforms, 4 “omes,” and 1 mission: provide a resource to decode AMR and MGE dynamics
www.biorxiv.org/content/10.6...
Biotic interactions modulate protein abundance, reducing functional redundancy and increasing productivity in complex bacterial communities.
The version of record of our revised preprint is finally out today. In it, we introduce a fast and reliable methdology for the full factorial design of microbial communities, i.e. constructing every monoculture, pair, trio, four-member,... n-member co-culture of N strains.
doi.org/10.7554/eLif...
Mizrahi Lab
A rapid, inexpensive, and easy to implement experimental protocol enables the construction of combinatorially complete sets of microbial consortia.
Interested in predicting the dynamics of antibiotic resistance? Come work with us! We're looking for two postdocs to develop predictive models of resistance. We're interested in a range of approaches (mathematical & statistical modelling, causal inference, machine learning).
tinyurl.com/6c4y3jke
🚨 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!👇👇
Final version of our last paper is out!
www.nature.com/articles/s41...
Plasmids are DNA molecules that replicate independently of the bacterial chromosome and are typically associated with the spread of antimicrobial resistance (AMR) and virulence determinants, among other relevant traits. Fusion events between plasmids generate larger, complex backbones that carry two or more replication systems, known as multireplicon plasmids. Despite decades of study, we are still far from understanding how multireplicon plasmids arise, persist, and shape the evolution of AMR. Here, we analyzed 24,000 non-redundant plasmids across bacterial genera and found that more than 30% of them encoded multiple replicons. Compared to single-replicon plasmids, multireplicon plasmids were larger, were enriched in genes encoding antimicrobial, metal, and biocide resistance as well as virulence factors, and showed higher mobility and a broader host range. We also found that multireplicon assembly is not random. Some replicon pairs repeatedly merge into stable multireplicon plasmids, while other pairs rarely fuse even when they commonly coexist intracellularly. We also show that replicon pairs tend to be localized either in close proximity to one another or on opposite poles of the plasmid. We further highlight that multireplicon plasmids can be broadly classified into two groups: long-term coevolving replicon pairs and transient associations that lack a shared evolutionary history. Finally, we reveal the molecular mechanisms underlying multireplicon formation and highlight the role of insertion sequences in their formation and maintenance. Together, our work sheds light on the abundance, gene content, evolutionary patterns, and formation dynamics of multireplicon plasmids and pinpoints their relevance to bacterial evolution and human health. ### Competing Interest Statement The authors have declared no competing interest. Instituto de Salud Carlos III, https://ror.org/00ca2c886, PI23/01945, PFIS - FI22/00265, Miguel Servet - CP22/00164 European Research Council, https://ror.org/0472cxd90, HorizonGT, 101077809 Fundación Ramón Areces, "Ayudas Fundación Ramón Areces para la realización de Tesis Doctorales en Ciencias de la Vida y de la Materia 2025" Coordenação de Aperfeicoamento de Pessoal de Nível Superior, https://ror.org/00x0ma614, 88881.128025/2025-01
Really happy to see this out! Great work led by @mboum.bsky.social
A nice example of how microbiome-specific ecological constraints can shape E. coli growth www.pnas.org/doi/10.1073/... @pnas.org
Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
New paper: mechanisms that maintain diversity in bacterial genomes also play a role in organising it.
This paper combines two of my favourite topics in bacterial evolution: NFDS and strain structure.
journals.plos.org/ploscompbiol...
What if multireplicon plasmids are not an oddity, but an evolutionary strategy?
We found that they are common, more mobile, broader-host-range, and enriched in AMR.
Even more interesting: their assembly doesn’t look random. 👀
Paper preprint: www.biorxiv.org/content/10.6...
Thread below!🧵👇
www.biorxiv.org
New paper out in @pnas.org 🎆!
Across healthy humans, the same bacterium encounters markedly different gut microbiomes.
How does this shape the ecological interactions it experiences?
We explored this focusing on commensal E. coli.
www.pnas.org/doi/10.1073/...
Image: @illuzation.bsky.social
