Proud to share our single-cell transcriptomics approach for the microbiome by instrument-free split-pool barcoding - metaSPLiT, developed by the incredible @monochamussutor.bsky.social together with @gibbological.bsky.social, @cdiener.com, et al. at @isbscience.org

Dmitry Sutormin@monochamussutor.bsky.social · 2d ago

🚀 Thrilled to share our first metaSPLiT preprint from @annabiosys.bsky.social's lab in collaboration with @gibbological.bsky.social! Explore hidden bacterial phenotypic heterogeneity in the human gut microbiome and discover the concept of "physiological guilds": www.biorxiv.org/content/10.6...

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

ISB@isbscience.org · 5mo ago

In the gut microbiome, bacteria are constantly under attack from viruses, but not all cells respond the same way. A new study uses single-cell sequencing to reveal hidden differences that determine whether bacteria survive or succumb to infection. isbscience.org/news/health/...

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...

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...

His Harvard Lab Was Thriving. Then Came the Cuts.

nytimes.com

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

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...

biorxiv.org

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

ISB@isbscience.org · 11mo ago

It’s #PostdocAppreciation Week! @isbscience.org Postdoc Dr. Dmitry Sutormin found gut bacteria form 3 guilds: Stressors Metabolizers Growers A survival “bet-hedging” strategy that helps them adapt. 🎥 Watch Dmitry explain: youtu.be/5LG_Ae0SiFg

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

ISB@isbscience.org · 10mo ago

This morning, @isbscience.org's Dr. Mary Brunkow was awarded the 2025 Nobel Prize in Physiology or Medicine! Dr. Brunkow shares the award with Fred Ramsdell and Shimon Sakaguchi. Read the press release here: www.nobelprize.org/.../medicine.... What a tremendous honor! Congratulations!

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

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...

biorxiv.org

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

Cress Lab@cresslab.bsky.social · last yr.

Dive into our lab’s first peer-reviewed publication—co-led with our friends @benadler.bsky.social and Muntathar Al-Shimary from the @doudna lab! If you’ve already read the preprint, don’t miss the new updates: doi.org/10.1038/s415... @naturemicrobiol.bsky.social

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

Scientists Develop First Stool-Based Test for Tracking Diet and Disease Risk

YouTube video by Institute for Systems Biology

youtu.be

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

Christian Diener@cdiener.com · last yr.

Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42... #metagenomics #microbiome #microbiomesky So what is MEDI? A combination of two things:

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?!

Apoorva Mandavilli@apoorvanyt.bsky.social · 2y ago

BREAKING: The Trump administration has instructed organizations in other countries to stop disbursing HIV medications purchased with U.S. aid, even if the drugs have already been obtained and are sitting in local clinics. www.nytimes.com/2025/01/27/h...

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.

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.

washingtonpost.com

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...

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...

biorxiv.org

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-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.

isbscience.org

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...

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.

isbscience.org

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...

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.

nature.com

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...