The oyster’s invisible architects

@harvard.edu just launched a cool new website about research across campus and, lo and behold, there's a bit about our latest publication in @pnas.org about oyster-microbial interactions. I'm very proud to be working with Andrea and the whole team!

current.fas.harvard.edu/stories/oyst...

Great summary by @philipcball.bsky.social! Our findings certainly don’t invalidate the central dogma, but rather demonstrate an unexpected (and cool!) structural mechanism by which a sequence-specific DNA is created in a cell. (1/6)

A series of spontaneously blinking dyes for super-resolution microscopy - Nature Methods A series of spontaneously blinking dyes in the far-red range facilitate single-molecule localization microscopy. These dyes vary in their blinking properties and can be matched to the applications and...

Out in @natmethods.nature.com: More dyes. They work. Quite well. And blink. Pick the one that fits your target, your technique, and your labeling density. With too many collaborators and institutes to list, but anchored at @hhmijanelia.bsky.social www.nature.com/articles/s41...

Living together: evolutionary and ecological dimensions of protist endosymbiosis From symbionts to organelles: evolutionary integration of microbial partners into eukaryotic cells.

academic.oup.com/microlife/ar...
#protistsonsky

Enantiomer sensing enables social avoidance by bacterial spores
(of Bacillus subtilis)

@cp-iscience.bsky.social from Gürol Süel

www.cell.com/iscience/ful...

Why scientists are nervous about fungi They can pose a threat to human health — yeast infections are but one example. Scientists say not enough attention is paid to their ability to develop resistance to medications that treat them.

They can pose a threat to human health — yeast infections are but one example. Scientists say not enough attention is paid to their ability to develop resistance to medications that treat them.

Deaths of migrants in ICE custody hit record high under Trump Twenty-nine people have died in ICE custody since October, the start of the federal government's fiscal year, already surpassing 2004's toll of 28, the previous record, according to government data.

Twenty-nine people have died in ICE custody since October, the start of the federal government's fiscal year, already surpassing 2004's toll of 28, the previous record, according to government data. n.pr/4sLetjV

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 !

Cognition without brains? Learning and memory in microorganisms Memory and learning are cognitive abilities typically associated with animals that possess a complex nervous system. Interestingly, recent studies suggest that microorganisms might also display learning-like behaviours. However, a factor limiting progress in this field is the lack of shared, microbe-specific frameworks that allow microbiologists to easily compare discoveries with concepts developed in cognitive sciences. In this review, we aim to bridge this gap by providing a conceptual overview of the definitional requirements for memory and learning to classify microbial behaviours and capabilities. Additionally, we identify and address problems that cause conceptual ambiguity in the microbial cognition literature, thereby facilitating more productive debates on the topic. Finally, we provide a novel perspective on how microbes might ‘learn’ from each other.

Cognition without brains? Learning and memory in microorganisms: Trends in Microbiology www.cell.com/trends/microbiology/full...

Nutrient availability shapes the diversity and structure of microbial communities | bioRxiv www.biorxiv.org/content/10.64898/2026.04...

The correct link: lh3.github.io/2026/04/17/t...

This is WILD
(& microbes rock 🎸)
“These findings […] revealing a protein-templated mechanism for sequence-specific DNA synthesis.”

Take that, central dogma! 🧪

“Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase”
www.science.org/doi/10.1126/...

A bacterial CARD–NLR-like immune system controls the release of gene transfer agents - Nature Microbiology An immunity-like system functions as a lysis control hub to promote gene transfer agent particle release from host bacterial cells, suggesting that bacterial immune systems may be co-opted to promote ...

Delighted to share our latest work on gene transfer agents (GTAs). We found a lysis control hub which allows GTAs to escape their bacterial host cells and transfer DNA 🧬 between bacteria. Thanks to @tunglejic.bsky.social, all co-authors, and our amazing collaborators!
www.nature.com/articles/s41...

Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology Diversity-generating retroelements are engineered for directed evolution in E.coli.

#synbiosky #microsky #phagesky

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

‘Without them there is no life’: the race to understand the mysterious world of Africa’s fungi Amid growing evidence of fungi’s key role in ecosystems and storing carbon, African scientists are championing the need to preserve ‘funga’ as much as flora and fauna

www.theguardian.com/environment/...

Absolute banger:

"find that metaSPAdes consistently outperforms MEGAHIT"

"Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance"

"We further show that CheckM2 systematically overestimates completeness and underestimates contamination"

Membrane structural properties in Staphylococcus aureus are tuned by the carotenoid 4,4′-diaponeurosporenoic acid www.biorxiv.org/content/10.6...

Fun bit of trivia: the first photo of DNA's structure was from cow DNA.

Specifically, it's from 'calf thymus tissue', chosen because harvesting DNA from this tissue yields long continuous strands ("high MW DNA", in the parlance).

You're looking at what makes a cow a cow in this famous photograph.

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery - Nature Communications Benchmarking metagenomic binning tools with simulated and real datasets reveals factors affecting genome recovery and provides practical guidelines for improving metagenome assembled genome reconstruc...

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery www.nature.com/articles/s41... #jcampubs

Join us in Montreal for the Canada/US Northeast hub!

I will give a talk and @gmdouglas.bsky.social @nagissa.bsky.social & Tim Blower will surely give *great talks*

Opportunities for student talks and posters and a good time guaranteed!

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology FAMSA2 accurately aligns millions of protein sequences at high speed.

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration
www.nature.com/articles/s41...

Really happy to have played a small part in this cool piece of work led by @guido-valverde.bsky.social and @msabrysarhan.bsky.social. We characterised S. pyogenes in a pre-Columbian Bolivian mummy (suggesting circulation before European contact) #VivaBolivianMummies
www.nature.com/articles/s41...

Evolution of pandemic cholera at its global source - Nature The seventh cholera pandemic, driven by El Tor Vibrio cholerae, evolved separately in Bangladesh and India, with the Ganges Basin acting as the global source, and its evolution has been shaped by...

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

#phage #phagesky #microsky

Carbon monoxide metabolism in freshwater anaerobic methanotrophic archaea - Nature Communications Anaerobic methane-oxidizing archaea mitigate methane emissions in anoxic environments. Here, Egas et al. show that these microbes can also oxidize carbon monoxide, prompting re-evaluation of their cla...

Grab a coffee and enjoy reading up on CO metabolism in methanotrophs!

Freshwater ANME (own work):
www.nature.com/articles/s41...
Marine ANME (@Orphan lab):
www.nature.com/articles/s41...

Big thanks to our collaborators at QUT!
@sjmcilroy.bsky.social (Heyu/Andy/Gene!) @cuwelte.bsky.social

These Bacteria Digest Toxic Metals And Poop Out Tiny Gold Nuggets No other life form on our planet has infiltrated every environment as successfully as the minuscule single cells of bacteria.

www.sciencealert.com/bacteria-pro...

#microsky

🚨New paper from our lab!🚨
We show that disrupting mucin sugar utilization in Citrobacter rodentium causes the build-up of a sugar phosphate, which compromises bacterial growth, colonization, and pathogenesis. A metabolic bottleneck with big virulence consequences.
journals.asm.org/doi/10.1128/...

Convergent evolution of aerobic fermentation through divergent mechanisms acting on key shared glycolytic genes - The EMBO Journal As the tree of life becomes increasingly accessible to molecular investigations, describing mechanisms underlying evolutionary convergence and constraint will be crucial to understanding diversificati...

So pleased to share that this project identifying convergent evolution of aerobic fermentation in a poorly characterized genus of yeasts (Saturnispora) is now out in @embojournal.org

@hittingerlab.bsky.social @rokaslab.bsky.social @glbioenergy.bsky.social

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

Don’t Perish! A Step-by-Step Guide to Writing a Scientific Paper (2026 edition) Great science deserves to be read — not buried under unclear writing. This is the updated 2026 edition of your favorite guide to writing…

I just published Don’t Perish! A Step-by-Step Guide to Writing a Scientific Paper (2026 edition)

Great science deserves to be read—not buried under unclear writing. This is the updated 2026 edition of your favorite guide to writing scientific papers.

medium.com/p/dont-peris...

Reminds me of the journal Microbial Genomics

Rapid evolution of Klebsiella pneumoniae biofilms in vitro delineates adaptive changes selected during infection - Nature Communications Biofilm formation on implanted medical devices facilitates infection by the pathogen Klebsiella pneumoniae. Here, Zaborskytė et al. use experimental evolution to show that the bacteria rapidly evolve ...

🆒 new pub!
Rapid evolution of Klebsiella pneumoniae biofilms in vitro -> adaptations selected during infection by @gretazabo.bsky.social & Linus Sandegren
*hypermucoidy evolves via 📈c-di-GMP, overlaps w/ mutations in UTI and wound isolates.
*pleasure to advise this!

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