Animalcules

@nitzantal.bsky.social @romihadary.bsky.social @soreklab.bsky.social use structure prediction and in silico binding site analysis to discover viral immune evasion proteins! Exciting for our lab @reneechang.bsky.social @riveralopz.bsky.social to help with this project.
www.science.org/doi/10.1126/...

#PhageSky is curious to learn more about this fancy phage 👋

It’s not me, it’s you: Anti-phage nuclease specificity inside a bacterium

Very timely review; thank Alex Hong and @jbdsf.bsky.social for putting this together
journals.plos.org/plospathogen...

Structure-guided generative design of peptides targeting the FtsQBL divisome complex inhibit Escherichia coli cell division. https://www.biorxiv.org/content/10.64898/2026.02.27.708549v1

Common mouth bacteria may fuel stomach cancer growth Evidence suggests a common oral bacterium could increase stomach cancer risk by feeding tumors methionine.

Common mouth bacteria may fuel stomach cancer growth #EarthDotCom #EarthSnap #Earth

Photo of PCR plate with chemical extracts

First extracts went out for antibiotic testing this week. Still waiting for some additional pipettes from Thermo Fisher (to the point they are sending loaners in the meantime) at which point we can finally start our anticancer and immune modulator assays.

🔬 Calcium triggers natural transformation in 𝐴𝑐𝑖𝑛𝑒𝑡𝑜𝑏𝑎𝑐𝑡𝑒𝑟 𝑏𝑎𝑢𝑚𝑎𝑛𝑛𝑖𝑖, boosting DNA uptake and resistance acquisition, reports the Charpentier Lab. Opens new doors for genetic engineering.

✍️ @labxc.bsky.social & coll.
📖 shorturl.at/F2GGl

#MicroSky #AntibioticResistance #NaturalTransformation

🔬 New work from the Mazel Lab engineers programmable conjugative plasmids to selectively target MDR bacteria and the resistance plasmid pOXA-48, blocking its spread in complex communities.

✍️ @amazeld.bsky.social & coll. @pasteur.fr
📖 shorturl.at/GZdJu

#MicroSky #AntibioticResistance #Conjugation

Stale Bread and E. Coli Could Transform How We Make Drugs and Plastics Somewhere in a sealed flask at the University of Edinburgh, a colony of E. coli is doing something rather useful with its lunch. Fed sugars extracted from

Stale #Bread and E. Coli Could Transform How We Make #Drugs and #Plastics ...

| #Ecoli | #fermentation | #Hydrogenation | #Carbon | Via @scienceblog.com

A symbiotic origin of the ribosome? Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b

academic.oup.com/pnasnexus/ar...

Mechanistic basis of teichoic acid transport by a gatekeeper flippase www.biorxiv.org/content/10.6...

Beating cancer by eating cancer A research team led by the University of Waterloo is developing a novel tool to treat cancer by engineering hungry bacteria to literally eat tumours from the inside out. Bacteria spores enter the...

Beating cancer by eating cancer | EurekAlert! www.eurekalert.org/news-release...

#microsky

Anoxia-adapted cyanobacteria in a marine blue hole | Applied and Environmental Microbiology We report metabolically active cyanobacteria thriving in darkness and oxygen deprivation at 250 m depth in the ocean. Genomics results show these microbes share evolutionary roots with sponge cyanobacterial symbionts but developed unique adaptations for anoxic and sulfidic environments. Strikingly, they retain photosynthesis genes as genomic remnants (with no detected transcription) while losing genes critical for environmental stress responses, including DNA repair, osmotic regulation, and circadian control, suggesting a potential evolutionary connection to symbiotic relatives. Crucially, they maintain metabolic autonomy via phenylalanine biosynthesis and light-independent serine biosynthesis, exhibiting traits absent in most symbionts. This demonstrates how cyanobacteria adapt to anoxic environments through targeted genome reduction, revealing novel survival strategies in oxygen-depleted oceans and providing a research case for microbial resilience during marine deoxygenation.

Anoxia-adapted cyanobacteria in a marine blue hole | Applied and Environmental Microbiology https://journals.asm.org/doi/full/10.1128/aem.02576-25?af=R

The Origins of Agar First introduced into laboratories in 1881, agar remains indispensable as a culture medium.

The Origins of Agar
open.substack.com/pub/cell/p/a...

#microsky

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health Silva et al. perform a global analysis of over 11,000 gut microbiomes and reveal that uncultured bacteria are key markers of gut health. The uncultured genus CAG-170 is strongly linked to low gut dysb...

#NatMicroPicks

A microbial signature of health! 🦠⚕️

A large meta-analysis highlights the importance of previously unknown and uncultured gut bacteria in maintaining human health

#MicroSky

www.cell.com/cell-host-mi...

This goes on next week’s reading list! #MicroSky (and cc to @c-cornbill.bsky.social 🙂)

Genetic basis of cefiderocol resistance in Acinetobacter baumannii: insights from functional genomics and clinical isolates | Microbiology Spectrum Cefiderocol (CFDC) is one of the few remaining antibiotics with activity against carbapenem-resistant Acinetobacter baumannii (CRAB), an urgent global health threat. Yet, resistance to CFDC is increas...

Genetic basis of cefiderocol resistance in Acinetobacter baumannii: insights from functional genomics and clinical isolates | Microbiology Spectrum journals.asm.org/doi/10.1128/...

#microsky

Genomic diversity in the critical priority pathogen Klebsiella pneumoniae: global and regional perspectives - BMC Microbiology BMC Microbiology - Klebsiella pneumoniae (Kpn) is a hospital-acquired pathogen of critical importance due to extensive resistance to last-resort antibiotics like carbapenems and colistin. The...

link.springer.com/article/10.1...

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

youtu.be/0Og4p0xUtzc?...

Two cartoon images of children with plasmids for faces about to fight. Commentators are saying "Plasmid-borne CRISPR-Cas systems provide significant defensive benefits" and "Yes, but toxin-antitoxin systems on competitor plasmids constrain the offensive CRISPR-Cas benefit"

Out now in @plosbiology.org : our big joint effort on the role of #CRISPR in plasmid competition. Read on for a really fun (I’m biased ok) analysis of how a defence system has new selective pressures when it’s mobile
journals.plos.org/plosbiology/... 1/6

💙🌊 Saccharomonospora cyanea isolated from the Clarion-Clipperton Zone (CCZ) by @zmaw.bsky.social #actinomycete #deepsea #secmet

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...

Generative AI for synthetic biology: Designing biological parts, circuits, and genomes The convergence of generative AI and synthetic biology is transforming biological design, enabling the de novo creation of biological parts and systems with predictable, programmable function. Kim et ...

*Very* interested to see this, for all sorts of reasons.
www.cell.com/cell-systems...

Regulatory rewiring drives intraspecies competition in Bacillus subtilis Author summary Microbial competition and cooperation are key in shaping the structure and evolution of microbial communities. Our study on Bacillus subtilis, a model for microbial social interactions,...

journals.plos.org/plosgenetics...

#microsky

Four graphs, showing the response of PA14 and an isogenic pel mutant, and PAO1 and an isogenic pel psl double mutant, to meropenem and colistin. There is no difference between the response of mutants and WTs.

During her PhD, Jenny found something unexpected: biofilm-deficient P. aeruginosa mutants were just as tolerant to antibiotics as the WT when grown in our cystic fibrosis lung model. But why? #MicroSky 1/n

Bacterial metabolic remodeling by convergent evolution unlocks nutrient availability after a host switch Staphylococcus aureus has undergone metabolic remodeling to adapt to the dairy niche.

Insights into how #Staph aureus adapts to the bovine host by unlocking nutrients from the dairy niche. Great work by Amy Pickering, Jamie Gorzynski and others in the group. Bacterial metabolic remodeling by convergent evolution after a host switch.|Science Advances www.science.org/doi/10.1126/...

The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization | mSystems Most soil microbes are dormant, so they must exit dormancy to have the potential to carry out plant-beneficial functions. It is unclear if dormant microbes revive in proximity to plant-produced resources and if overcoming dormancy in the soil is important for successful plant colonization. We use a novel microbial activity probing technique for the first time on and in plant roots, and with it, we observe microbes increased in activity 10× inside plant tissues compared to the soil, likely in response to plant-produced resources. In complex, native microbial communities, we observe that microbes that are active and abundant are more likely to colonize plant roots successfully than just abundant microbes. Our research shows that plants could be leveraged to promote a distinct active microbial community from the native soil, a discovery that has the potential to improve sustainability in agriculture.

The activity of soil microbial taxa in the rhizosphere predicts the success of root colonization | mSystems journals.asm.org/doi/10.1128/...

#microsky

Probing the active fraction of soil microbiomes using BONCAT-FACS - Nature Communications Standard DNA-based analyses of microbial communities cannot distinguish between active microbes and dead or dormant cells. Here, Couradeau et al. use BONCAT (bioorthogonal non-canonical amino acid tag...

www.nature.com/articles/s41...

#microsky

Frontiers | Exploration of Chemical Biology Approaches to Facilitate the Discovery and Development of Novel Antibiotics Approximately 2.8 million people worldwide are infected with bacteria that are deemed resistant to clinically relevant antibiotics. This accounts for 700,000...

www.frontiersin.org/journals/tro...