We sat down with Anika & Dmitry to discuss the new paper where we use bacterial scRNA-seq for studying bacterial phage infection and defenses. It turns out that bacteria use pre-existing variation in multiple layers of traits to protect themselves from unpredictable phages @isbscience.org

Paper out: Profiling of lytic phage infection in individual B. fragilis cells with bacterial scRNA-seq. Congratulations Anika Gupta, Norma Morella, @monochamussutor.bsky.social Dmitry Sutormin et al, in collaboration with Georg Seelig (UW) and Neel Dey (Fred Hutch). www.nature.com/articles/s41...

His Harvard Lab Was Thriving. Then Came the Cuts.

NYT feature on their website's front page about our local C. elegans colleague Will Mair and NIH funding
www.nytimes.com/2026/03/13/u...

We are excited for mapSPLiT to enable genome-scale genetic screens with transcriptomic readouts for bacteria in the future (just like eukaryotes). Amazing work Jacob Brandner, Quoc Tran, Yujia Huang, Dmitry Sutormin and Karl Gaisser from @isbscience.org and UW. 4/4

mapSPLiT also uncovered the genetic interactions between multiple genes via a combinatorial screen of double and triple perturbations. Finally, we show that mapSPLiT can be ported to a less studied bacterium P. putida, revealing new responses to a perturbation of a carbon metabolism regulator. 3/4

mapSPLiT works by detecting a barcode construct specific to the perturbation alongside the transcripts in each single cell using microSPLiT, a bacterial scRNA-seq method. We used mapSPLiT to map gene expression responses to 118 perturbations in a single experiment in E. coli. 2/4

Pooled single-cell CRISPRa/i screens for functional genomics in bacteria at scale Pooled CRISPR screens using single-cell RNA sequencing (scRNA-seq) have emerged as powerful tools to uncover gene function, map regulatory networks, and identify genetic interactions. However, the inh...

Pooled CRISPR screens with transcriptomics readout arrived for bacteria. We introduce mapSPLiT, an approach to profiling transcriptional responses to CRISPR perturbations at scale. Collaborative work with Carothers, Zalatan, and Seelig groups at UW&@isbscience.org www.biorxiv.org/content/10.6... 1/4

Home The Kuchina Lab at ISB uses advanced technologies to study microbial communities down to a single-cell level.

We're moving in that direction! kuchina.isbscience.org

Left to right: Sean Gibbons, Naeha Subramanian, Mary Brunkow, Anna Kuchina, and Sid Venkatesh

Rubbing shoulders with a @nobelprize.bsky.social laureate! 🤩What a week!

Couldn’t have happened to a nicer person: isbscience.org/news/press-r...

@isbscience.org @naehasubramanian.bsky.social @flash-point.bsky.social @annabiosys.bsky.social

Dmitry explains how surprisingly universal functional patterns emerge once you look closer into a bacterial community. @isbscience.org

What an astonishing achievement, congratulations Mary! @isbscience.org

Multiomic clocks to predict phenotypic age in mice Biological age refers to a person's overall health in aging, as distinct from their chronological age. Diverse measures of biological age, referred to as clocks, have been developed in recent years an...

Check out our latest preprint on the development of clocks to predict PhenoAge in mice! www.biorxiv.org/content/10.1...

Huge work from @benadler.bsky.social et al @cresslab.bsky.social; Glad to be part of this super cool work.

Scientists Develop First Stool-Based Test for Tracking Diet and Disease Risk YouTube video by Institute for Systems Biology

I sat down with @isbscience.org president Jim Heath, to chat about our work, which you can watch here: youtu.be/ZwMDqp5n1S4?...

Estimation of diet from the metagenomics data is now possible! Curious to see how this can be applied for reanalyzing existing datasets to link the diet information with the data

What a stupid, petty move (rising to the top of the many many stupid, petty moves by this administration so far).

Dispersing free HIV medication is one of the greatest unequivocally 'good' things the US does for the world. This program has saved 25 million lives. Why the fuck would you cut it?!

White House pauses all federal grants, sparking confusion The Trump administration has put a hold on all federal financial grants and loans, affecting tens of billions of dollars in payments.

I think some people hear “grants” and think that without them, scientists and government workers just have less stuff to play with at work. But grants fund salaries for students, academics, researchers, and people who work in all areas of public service.

“Pausing” grants means people don’t eat.

Combinatorial phenotypic landscape enables bacterial resistance to phage infection Success of phage therapies is limited by bacterial defenses against phages. While a large variety of anti-phage defense mechanisms has been characterized, how expression of these systems is distribute...

How can single-cell transcriptomics profile phage infection in individual microbial cells? Check out our preprint with Anika Gupta, Norma Morella, Dmitry Sutormin & other authors, in collaboration with Georg Seelig (UW) and Neel Dey (Fred Hutch). www.biorxiv.org/content/10.1...

ISB-Developed MetaboCore Offers Precision Cancer Care Faster Than Ever ISB's MetaboCore is a diagnostic tool that can help physicians quickly select the most effective systemic therapy for each cancer patient.

ISB Associate Professor Dr. Wei Wei has developed a promising new companion diagnostic tool called MetaboCore to help physicians quickly select the most effective systemic therapy for each cancer patient. Learn more: isbscience.org/news/2024/11...

ISB Named Winner of 2024-2025 Amazon Web Services IMAGINE Grant for Nonprofits ISB was selected as a winner of the 2024 Amazon Web Services (AWS) IMAGINE Grant, which will support continued development of My Digital Gut.

Warm congratulations to my @isbscience.org colleagues @gibbological.bsky.social, Andrew Magis, and team for winning a 2024 Amazon Web Services IMAGINE grant for developing "My Digital Gut", an online platform for personalized, predictive, and preventive healthcare!

isbscience.org/news/2024/12...

Diverse viral cas genes antagonize CRISPR immunity - Nature We demonstrate that phages have co-opted cas genes from CRISPR defence systems, which subsequently evolved anti-defence functions.

Finally caught up with some beautiful work from Alex Meeske in Nature! His lab has identified proteins in Listeria that either substitute for Cas in Cascade complexes (anti-type I-B CRISPR immunity) or degrade crRNA (anti-type VI-A CRISPR immunity). Inspiring stuff!

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

Great highlight by Chandra and @pipethero.bsky.social on recently published work by my colleague @flash-point.bsky.social (from his postdoc work) on endocannabanoids produced by specific members of the gut microbiota that likely impact host satiety/appetite. @isbscience.org

doi.org/10.1016/j.ch...