Jotham Suez (SuezLab@JHU)

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes

www.science.org/doi/10.1126/...

Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration!

Linking below previous thread on our findings

Can you trust the results from gut microbiome tests? Maybe not Seven firms reported inconsistent results on the same sample, some over multiple tests. These gut microbe discrepancies could have health consequences.

"Can you trust the results from gut microbiome tests? Maybe not." www.sciencenews.org/article/resu...

I understand why the authors didn't disclose the different company IDs...but I'm very curious to know which is which

Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...

Our latest is out today in @plosbiology.org:

"Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials"

@isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social

doi.org/10.1371/jour...

Panel A: The weekly Gravitrap Aedes aegypti index (GAI), which measures the abundance of adult A. aegypti mosquitoes, in the intervention and control clusters before and during the release of wolbachia-infected male mosquitoes. Panel B: A spatial visualization of the intervention (red) and control (teal) clusters.

In this report from Singapore, the release of wolbachia-infected, irradiated male 𝘈𝘦𝘥𝘦𝘴 𝘢𝘦𝘨𝘺𝘱𝘵𝘪 mosquitoes resulted in a reduction in the vector population and in the risk of dengue infection. Full report: nej.md/4atd2iN

#MedSky #IDSky

Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial - Nature Medicine In a phase 2 trial evaluating healthy donor fecal microbial transplantation plus either anti-PD-1 in patients with non-small cell lung cancer or anti-PD-1 and anti-CTLA-4 in patients with melanoma, en...

#NatMicroPicks

FMT for cancers in clinic! 💩🦠🦀⚕️

Three different clinical trials report activity of faecal microbiota transplant against cancer

#MicroSky #CancerSky

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

Human and bacterial genetic variation shape oral microbiomes and health - Nature Human genetic loci that associate with composition of the oral microbiome are identified using saliva-derived DNA, where the same host genetics also shapes oral health and genetic varia...

Largest oral microbiome GWAS (n=12519; SPARK): 11 host loci (incl FUT2 and AMY1 CNV) shape oral community composition and even bacterial genomes. Signals colocalize with dentures/tooth-loss risk in UKB, suggesting specific host–microbe interactions in cariogenesis
www.nature.com/articles/s41...

More and more cool work looks at the role of human archaea in health outcomes. In this preprint, authors suggest protective role & show that colonisation of mice with M. smithii or M. stadtmanae thickens mucus, boosts reg. T cells & protects vs DSS colitis.
www.biorxiv.org/content/10.6...

The Government Wants You to Kick Your Diet Soda Habit New recommendations advise limiting foods and drinks with nonsugar sweeteners, but industry groups maintain the products are safe.

Jothan Suez, PhD, @suez.bsky.social, who studies sweeteners @jhu.edu @johnshopkinssph.bsky.social, comments on @wsj.com article

www.wsj.com/health/new-d...

Tools and approaches to study the human gut virome: from the bench to bioinformatics | mSystems The human gut microbiome is a complex community of bacteria, archaea, fungi, protozoa, and viruses that reside within the gastrointestinal (GI) tract (1). Notably, much of the literature regarding the...

Super excited to share my latest publication with Justin Malogan and @suez.bsky.social , my love letter to viromics! 🦠 Here, we discuss computational and wet lab methods to study the gut virome and how they can be used together

But why is this synergy so important?
journals.asm.org/doi/10.1128/...

Cluster dispersal shapes microbial diversity during community assembly Author summary Microbial communities, such as those living in the gut, play important roles in host health, yet we still do not fully understand how their diversity is established. In many cases, thes...

🦠 How do microbes arrive together, and why does it matter for #microbial #diversity?
👉 Read the paper: journals.plos.org/ploscompbiol...
Published in @plos.org Computational Biology

🎉 Congratulations to authors Loïc Marrec & Sonja Lehtinen @sonjalehtinen.bsky.social @unil.bsky.social @sib.swiss

So proud of all the hard work by our @johnshopkinssph.bsky.social @johnshopkinsmmi.bsky.social postdoc Dr. Haley Hallowell @haleybiont.bsky.social and graduate student Justin Malogan on this! 👏

+ a genuine gratitude to the reviewers for their highly valuable feedback! 🙏

A figure from the paper that provides an overview of available culture-dependent and culture-independent approaches for characterizing the human gut virome. Both culture-dependent and culture-independent approaches should be used to study the gut virome. At the bench, many protocols have been adapted to enrich viruses in a sample and isolate them using a sensitive host. Once a virus is isolated, various assays can be used to characterize how the virus interacts with its bacterial host. On the command line, viral genomes can be predicted and viral taxonomy can be identified within a sample. Once procured, multiple tools can be used to annotate viral genomes for predicted gene content and viral lifestyle and predict bacterial host taxonomy.

It's increasingly clear that commensal viruses play important roles in human health, but how do you study them?

Our review "Tools and approaches to study the human gut virome: from the bench to bioinformatics" is out today in mSystems! journals.asm.org/doi/10.1128/...

@haleybiont.bsky.social

Our new paper, where we use metabolic modeling to show Fusobacterium grows faster in colorectal tumor vs normal tissue microenvironments, and use computational + experimental approach to find specific metabolic pathways driving host-microbiome interactions in cancer

www.biorxiv.org/content/10.6...

The commitments in the SAFE Labs Handbook.

A new community-driven lab handbook for reducing conflict and creating more positive and equitable work environments gets strong support from a survey of 200 researchers.
buff.ly/K7CGFLV

Out after peer-review: www.science.org/doi/full/10....

Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead!

We now also account for regression and nested cross-validation, with more extensive benchmarking.

We're at 735 registrants and counting! 🎉🦠

If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.

Please share with your networks. 🔗👇

isbscience.org/events/2025-...

Campus friends @ Homewood

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

Congrats to Yancong, Amrisha, Xochitl, Eric and all co-authors!!!

Love this approach!

Characterization of an amyloid-based antiphage defence system in Escherichia coli - Nature Microbiology Prion-like proteins in Escherichia coli trigger an abortive infection mechanism in response to phage infection—a process similar to amyloid-mediated immune signalling in fungi and animals.

#NewResearch

Prion-like proteins in Escherichia coli trigger an abortive infection mechanism in response to phage infection—a process similar to amyloid-mediated immune signalling in fungi and animals.

#MicroSky 🦠

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

Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut Carr et al. show how microbial community-scale metabolic models (MCMMs) predict personalized Clostridioides difficile colonization risk and probiotic efficacy. MCMMs reveal key metabolic strategies ex...

💥Personalized C. difficile colonization risk prediction and probiotic therapy assessment in the human gut💥

I'm very excited about this work, driven by Alex Carr & co-supervised by @cdiener.com

@cp-cellsystems.bsky.social @isbscience.org @nitinbaliga.bsky.social

www.cell.com/cell-systems...

🧵...

Korem Lab - Microbiome Systems Biology @ Columbia | New York, USA We apply systems biology approaches to decipher the metabolic interactions between the microbiome and its human host in diverse clinical settings, aiming towards personalized microbiome-based therapeu...

We are hiring a postdoc - come work with us (www.koremlab.science) at the intersection of #microbiome, data science, and women's health!
Message or email me if interested. 🖥️ 🧬

Excited 🥳 to share our latest work on gut phages!
Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌
Out in Cell Reports @cp-cellreports.bsky.social
doi.org/10.1016/j.ce...
Here's what we found 🤓

Really cool work, congrats!

Curious what this would say about our Cell 2018 data with humans taking antibiotics & probiotics 🙂

Really cool work, congrats Gechlang, Sean, and team! 👏🏽

We need more studies causally linking sucralose-altered human microbiomes to immunotherapy efficacy to guide clinical decision-making.

But there are already good reasons to consider reducing the intake of artificial sweeteners (and sugar!).

Congrats on an important and interesting work!

fin/🧵

Their data in humans are observational and extend to other non-nutritive sweeteners as well. These observations are supported by extensive preclinical work, including microbiome transplants to establish a causal role for the sucralose-altered microbiome in disrupting cancer immunotherapy.

3/🧵

We've shown before that sucralose alters the human microbiome (tinyurl.com/SuezCell22), and we know that the microbiome can impact responsiveness to cancer immunotherapy.

1+1=...? Yes!

The authors show that sucralose-elicited changes can disrupt immunotherapy efficacy.

2/🧵

AI-rendered illustration of the article's title: Sucralose consumption ablates cancer immunotherapy response through microbiome disruption

Sucralose may interfere with cancer immunotherapy - exciting and important new research from @overacrelab.bsky.social in @theaacr.bsky.social!

aacrjournals.org/cancerdiscov...

(AI-rendered illustration of the article's title)

1/🧵