Sourik Dey

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge.

Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...

Goodbye colonoscopy? Simple stool test detects 90% of colorectal cancers Scientists at the University of Geneva have created the first detailed catalogue of gut bacteria at the subspecies level, unlocking powerful new ways to detect colorectal cancer. By applying machine l...

www.sciencedaily.com/releases/202...

Being a better version of yourself: genetically engineered probiotic bacteria as host defense enhancers in the control of intestinal pathogens Intestinal pathogens pose a significant global health burden, and traditional antibiotic treatments often disrupt the beneficial gut microbiota that plays a crucial role in maintaining host health ...

Very interesting read!
#synbio

www.tandfonline.com/doi/full/10....

Excited to launch my postdoc at the Cleveland Clinic Lerner Research Institute! 🧪 In Prof. Dwidar’s lab, I’m harnessing bacterial synthetic biology 🦠to pioneer new therapeutics and shape the future of precision medicine. Let’s do this! 🚀#synbio #PostdocJourney #ClevelandClinic

A biocompatible Lossen rearrangement in Escherichia coli - Nature Chemistry Biocompatible chemistry merges chemo-catalytic reactions with cellular metabolism for sustainable small-molecule synthesis. Now a biocompatible Lossen rearrangement has been demonstrated to control ba...

Wow: Plastic → Tylenol? 🧪♻️💊

A biocompatible Lossen rearrangement—a reaction never seen in nature—occurring INSIDE E. coli

Bacteria engineered to convert PET plastic → Tylenol in <24h, with 92% yield + low emissions

Stunning blend of chemistry and synthetic biology

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

When academics say industries were running after them for recruitment, but they chose a path of passion instead!

The 'Oscar' of food prizes goes to a Brazilian who harnessed the power of bacteria This year's $500,000 World Food Prize, for advances in agriculture and nutrition, goes to a Brazilian who boosted the country's farming revolution, turning it into a soybean superpower.

The 'Oscar' of food prizes goes to a Brazilian who harnessed the power of bacteria

Mariangela Hungria found microbes that were good at capturing nitrogen from the air and turning it into fertilizer for crops.

www.npr.org/2025/05/14/n...

Adaptations of Gram-Negative and Gram-Positive Probiotic Bacteria in Engineered Living Materials Encapsulation of microbes in natural or synthetic matrices is a key aspect of engineered living materials, although the influence of such confinement on microbial behavior is poorly understood. A few ...

Excited to share our latest work, published in a peer-reviewed journal. We studied how Gram +/- probiotic bacteria would adapt in mechanical confinements - key part in understanding the fundamentals of Engineered living materials. Read it here:

pubs.acs.org/doi/10.1021/...

Finally, access to a pichia pastoris strain. Time to adapt it enough to become a truly open strain, without the $5000 buy in of the current "open" version. Worst case $20/stab and zero MTA. Evolved with love. Big thanks to @koeng101 off Twitter for sourcing! 💚

#harvard #budgetcut

Article (paywalled) about our pre-print discussing Bioengineered journal’s paper mill problem: www.nature.com/articles/d41...

arxiv.org/abs/2503.21267

Thanks to @deadneanderthals.bsky.social @mortenoxe.bsky.social @elisabethbik.bsky.social @smutclyde.bsky.social
for letting me tag along!

Lol I have A LOT of work to do before I get even remotely close to the level of protein expression a well designed plasmid can generate. This is pCambia2300 expressing the same RFP circuit (albeit in Agrobacterium; left) and my single copy transposon integration in BL21 Ecoli (right).

From the hasty lab:

Evolved microbial diversity enables combinatoric biosensing in complex environments
doi.org/10.1101/2025...

There’s a New Generation of Probiotics Coming to a Store Near You - SynBioBeta

"In other words, traditional probiotics don’t really work, but you should give these new ones a try and keep an eye out for more evidence-based probiotics in the future!"

#synbio #probiotics

Researchers at @mitchemistry.bsky.social have developed a new system for delivering peptide-based drugs, like GLP-1, by “painting” them on antibodies to improve and prolong their therapeutic effects. They report their results today at #ACSSpring2025: buff.ly/f6oHqxb

Happy to share our genetic toolkit designed to make your gene editing (life) easier, faster and very efficient!

Also suitable to build saturated chromosomal variant libraries using oligo-recombineering with extra short homology arms!

www.biorxiv.org/content/10.1...

When you grow yeast on yeast extract medium

Synthetic Biology runs on plasmids and we've got some for engineering lactobacilli that are in high demand!
So, we finally did the sensible thing and deposited them with Addgene to make them easily accessible - www.addgene.org/Shrikrishnan...

Thanks @sourikdey.bsky.social & @marcblanch.bsky.social

Europe struggles to fund many of their good projects at times. Therefore, a huge influx would be mostly unsustainable!

Protein-based molecular imprinting: gelatin nanotraps for interleukin-6 sequestration in inflammation cell models Gelatin methacryloyl (GelMA) was harnessed to create nanotraps via molecular imprinting that were specifically designed to scavenge interleukin-6 (IL-6) in inflammation models. This innovative approach leverages safe and biocompatible protein-based…

Online now: Protein-based molecular imprinting: gelatin nanotraps for interleukin-6 sequestration in inflammation cell models

Good branding

It's hard to express how lucky I feel to have a team that self-organizes a vibrant lunch together on a Saturday and are happy to have their boss there 🤓

We even got to celebrate our wonderful women in science on Women's Day! 👩‍🔬

#womensday

A woolly mouse (left) next to an ordinary one. CREDIT: Colossal Biosciences

Genetically altered 'woolly mice' express several mammoth-like traits, including the animal's iconic coat. The cuteness, meanwhile, is a complete coincidence. That and more of the best in @science.org and science in this edition of #ScienceAdviser: www.science.org/content/arti... 🧪

I think it is working again.

They might recover it by replacing Verizon's contract with Starlink at the FAA. Thats a lot of money.

Exploring the principles behind antibiotics with limited resistance - Nature Communications This study shows that only those dual-targeting antibiotics limit resistance in Gram-negative pathogens that also target the membrane of the bacteria. This mechanism provides a basis for designing fut...

Exploring the principles behind antibiotics with limited resistance
www.nature.com/articles/s41...

The first night ended in a burial ritual on the beach, symbolically burying our presumptions and assumptions that we brought with us from all over the world, to start the first day of work with an open mind.

The Men Who Stare At Mice “Do Cohen’s colleagues and superiors know or care that he hosts wizards in his lab? Or perhaps this is simply common place, wizards roam throughout MD Anderson free range, blasting the …

These kind of research are one of the reasons why people lose their trust in science! #cancer #ridiculous

forbetterscience.com/2025/02/26/t...

A former Stanford employee was convicted of altering data used in a breast cancer study after she was fired, according to the United States Department of Justice.

www.kron4.com/news/bay-are...

DOCTORAL RESEARCHER POSITION IN MICROBIAL CO-CULTURES (F/M/D) at INM - Leibniz-Institut für Neue Materialien gGmbH We're looking for: DOCTORAL RESEARCHER POSITION IN MICROBIAL CO-CULTURES (F/M/D) (Full Time) • Campus, 66123 Saarbrücken, Deutschland

In the bubbling world of bioreactors, lonely Lactobacilli are searching for a perfect partner. Will it be strong and stable Cyanobacteria or resourceful Microalgae?

We're seeking a PhD candidate to turn microbial matchmaking into productive co-cultures! - tinyurl.com/Alacto
@leibnizinm.bsky.social