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Jotham Suez (SuezLab@JHU)

@suez.bsky.social
1.9K followers 302 following 51 posts

Microbiome enthusiast 🦠 || Assistant Professor for Molecular Microbiology and Immunology at Johns Hopkins University || He/Him 🏳️‍🌈🏳️‍⚧️ www.suezlab.org

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Reposted by Jotham Suez (SuezLab@JHU)
David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
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Reposted by Jotham Suez (SuezLab@JHU)
Matthias C. Rillig @mrillig.bsky.social · 20/08/2026
Twenty-two easy ways to power up your lab meetings | Nature by Hannah Docter-Loeb in Nature Careers Scientists share help and advice on how they got their research discussions flowing (including a contribution from our lab) www.nature.com/articles/d41...
nature.com
Twenty-two easy ways to power up your lab meetings
Scientists share help and advice on how they got their research discussions flowing.
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Reposted by Jotham Suez (SuezLab@JHU)
Nature Portfolio @natureportfolio.nature.com · 22/08/2026
In a small case series, combined phage therapy and faecal microbiota transplantation was safe and led to sustained reductions in recurrence, severity and antibiotic use in women with recurrent urinary tract infections, according to a paper in Nature Microbiology. go.nature.com/4gh0yyS #microsky 🧪
This is figure 1, which shows the treatment overview.
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Reposted by Jotham Suez (SuezLab@JHU)
Dept of Molecular Microbiology & Immunology at Johns Hopkins @johnshopkinsmmi.bsky.social · 11/08/2026
A new lab study suggests some sweeteners may affect gut bacteria. Jotham Suez, PhD, of Johns Hopkins, explains why human trials are needed to understand what this means for health. Read more in www.verywellhealth.com/common-sweet...
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Reposted by Jotham Suez (SuezLab@JHU)
Sean Gibbons 🦠💩 @gibbological.bsky.social · 02/08/2026
Exciting collaboration with @annabiosys.bsky.social's lab just went online. @isbscience.org metaSPLiT: a fast, efficient, and relatively low-cost method for single-cell transcriptomics in the human gut microbiome. 👇
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Reposted by Jotham Suez (SuezLab@JHU)
3rd Edition: Global Microbiome Congress & Exhibition 2027 @microbiomecongress.bsky.social · 08/07/2026
🦠 The Skin Microbiome: From History to Therapeutic Frontiers From early microscopy to AI-driven microbiome engineering, skin microbiome research is transforming the future of dermatology. 📝: microbiomecongress.org/abstract-sub... #SkinMicrobiome #Microbiome #Dermatology #MicrobiomeResearch
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Reposted by Jotham Suez (SuezLab@JHU)
Clinical Microbiology and Infection @cmijournal.bsky.social · 08/07/2026
📣 New Supplement publication in CMI The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the #EUCAST Subcommittee @escmid.bsky.social Read here: www.clinicalmicrobiologyandinfection.org/article/S119...
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Reposted by Jotham Suez (SuezLab@JHU)
Laura K. Jennings @laurakjennings.bsky.social · 29/06/2026
📢 We're hiring! The Department of Microbiology & Cell Biology at Montana State University is hiring an Assistant Professor of Microbiology. We welcome applicants working in microbial pathogenesis, immunology, genetics, microbial evolution, and related areas. Apply: jobs.montana.edu/postings/52009
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Reposted by Jotham Suez (SuezLab@JHU)
Tim Donohue @timdonohue1283.bsky.social · 30/06/2026
Openings in cell and community synthetic biology at UW-Madison!! Some are at any level, so tell colleagues and yourselves. Information below, more to appear here & on campus sites soon. Great colleagues, facilities, place to live, succeed. What more could you ask for!! bact.wisc.edu/bacteriology...
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Reposted by Jotham Suez (SuezLab@JHU)
ASM @asm.org · 01/06/2026
As we kick off #PrideMonth, ASM proudly honors the achievements & contributions of 2SLGBTQIA+ scientists to the microbial sciences. Diverse identities, lived experiences & perspectives catalyze transformative scientific progress. Explore our resources: asm.social/2Xr
Test tubes in front of a rainbow background
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Reposted by Jotham Suez (SuezLab@JHU)
Cell Press @cellpress.bsky.social · 01/06/2026
Cell Host & Microbe Focus Issue: The Virome www.cell.com/issue/S1931-... This focus issue offers a collection of articles that deliver cutting-edge insights and forward-looking perspectives on the virome's influence. @cp-cellhostmicrobe.bsky.social
On the cover: A bacteriophage illuminates a bacterial host in the gut microenvironment, capturing the intimate and consequential relationship between phages and their bacterial targets—one that can provide beneficial or detrimental functions, sustaining microbial balance or tipping the ecosystem toward dysbiosis depending on context. 

Image credit: Concept by Naama Geva-Zatorsky and Tomm Blum Barzilai. Illustration by Tomm Blum Barzilai
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Reposted by Jotham Suez (SuezLab@JHU)
Immunology Podcast @immunologypodcast.com · 26/05/2026
Be sure to catch next week's episode featuring Dr. Samuel Nobs from @irbbellinzona.bsky.social! His research interests focus on the interplay between the microbiome and the lung immune system, in health and during disease. 🥼 Check out his research: go.nature.com/4a8YZzr
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Reposted by Jotham Suez (SuezLab@JHU)
Lauren Palmer @laurenpalmer.bsky.social · 07/05/2026
🚨Faculty job search: University of Illinois Chicago Micro & Immuno department is hiring! Open rank and open area within host-pathogen interactions. Apply by May 31 to join us in UI College of Medicine in the heart of Chicago! uic.csod.com/ux/ats/caree...
Image of UIC sculpture, recreation center, and Medical Sciences Building
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Reposted by Jotham Suez (SuezLab@JHU)
Taylor priest @taylorpriest.bsky.social · 04/05/2026
A new method for inference and tracking the transmission of strains in metagenomes #MicroSky #MicroEco www.nature.com/articles/s41...
nature.com
Strain-level transmission inference across multi-kingdom metagenomic data using TRACS - Nature Microbiology
The TRACS algorithm tracks bacteria, viruses and parasites in metagenomic or population sequencing data, detecting microbial transmission even when multiple strains coexist within a host.
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Reposted by Jotham Suez (SuezLab@JHU)
Nature Microbiology @natmicrobiol.nature.com · 01/05/2026
Out Now! Unravelling bacterial complexity at high resolution with single-cell transcriptomics #MicroSky
go.nature.com
Unravelling bacterial complexity at high resolution with single-cell transcriptomics
Nature Microbiology, Published online: 01 May 2026; doi:10.1038/s41564-026-02333-3This Review summarizes recent advances in bacterial single-cell transcriptomics approaches, while also discussing technological and computational challenges remaining to be met and the need for standardization going forwards.
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Jotham Suez (SuezLab@JHU) @suez.bsky.social · 02/05/2026
If you’re at #DDW2026, come say hi! Started the meeting strong co-moderating a session with Long Nguyen, a full room came at 8AM to listen to Gautam Dantas, David Underhill & Megan Baldridge sharing exciting unpublished data on gut phages 🦠 fungi 🍄 & eukaryotic RNA viruses 🤩
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Reposted by Jotham Suez (SuezLab@JHU)
Dept of Molecular Microbiology & Immunology at Johns Hopkins @johnshopkinsmmi.bsky.social · 28/04/2026
Check out science writer Ed Cara's @edcara.bsky.social piece 'Should We Finally Ditch Artificial Sweeteners?' Ed talks to @johnshopkinssph.bsky.social & @jhu.edu molecular microbiologist & microbiome expert Jotham Suez @suez.bsky.social gizmodo.com/should-we-fi...
gizmodo.com
Should We Finally Ditch Artificial Sweeteners for Good?
Recent studies have suggested that sugar substitutes might not be the free lunch they're advertised as. We asked experts what they thought.
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Reposted by Jotham Suez (SuezLab@JHU)
Joe Bondy-Denomy @jbdsf.bsky.social · 24/04/2026
Phage community: our plasmids for executing phage transposon mutagenesis are now on AddGene and I would love for you to try it out! It is powerful for ID'ing all essential genes and knocking out all non-essentials in a single experiment :) New exp here: www.addgene.org/browse/artic...
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Reposted by Jotham Suez (SuezLab@JHU)
Rob Edwards @linsalrob.bsky.social · 08/04/2026
Have you developed a new #bioinformatics tool to understand #phage or #virus? Make sure you add it to #awesome-virome github.com/shandley/awe...
The awesome virome logo of a phage above a strand of DNA
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Reposted by Jotham Suez (SuezLab@JHU)
Johns Hopkins Bloomberg School of Public Health @johnshopkinssph.bsky.social · 07/04/2026
We are proud to again be recognized by our peer schools and programs as the #1 public health school in the nation, as reported by U.S. News & World Report. The Bloomberg School is grateful to partner closely with our peers on our shared commitment to improving health for people everywhere.
publichealth.jhu.edu
Johns Hopkins Bloomberg School of Public Health Again Rated #1 by Peers in U.S. News & World Report | Johns Hopkins Bloomberg School of Public Health
The School has held the #1 spot since the rankings began in 1994. The School has also been named by peers as a leader in five specialty areas within public health this year.
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Reposted by Jotham Suez (SuezLab@JHU)
Nature Reviews Gastroenterology & Hepatology @natrevgastrohep.nature.com · 10/04/2026
ICYMI: New online! Diet–microbiome associations
dlvr.it
Diet–microbiome associations
Nature Reviews Gastroenterology & Hepatology, Published online: 09 April 2026; doi:10.1038/s41575-026-01205-9Diet–microbiome associations
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Reposted by Jotham Suez (SuezLab@JHU)
Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 10/04/2026
Microbes impact peanut allergy Mouth & gut contain peanut-degrading bacteria(Rothia) that metabolize PN allergens. Mice colonized w/Rothia show decreased anaphylaxis & allergic patients w/better PN tolerance have higher abundance of these bacteria www.cell.com/cell-host-mi...
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Reposted by Jotham Suez (SuezLab@JHU)
Sean Carroll @seanmcarroll.bsky.social · 08/04/2026
Katalin Karikó will be @jhu.edu's 2026 commencement speaker. Excellent choice! www.jhunewsletter.com/article/2026...
jhunewsletter.com
Nobel Prize winner Katalin Karikó to be 2026 Commencement speaker
On Tuesday, April 7 a leaked University video announced that Katalin Karikó will deliver the commencement speech for the Class of 2026. Karikó is a Hungarian-American biochemist and the 2023 winner of...
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Reposted by Jotham Suez (SuezLab@JHU)
Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 08/04/2026
Female urogenital microbiome: Review by Sarah Lebeer & Co In urogenital tract, dominant lactobacilli shape vaginal immunity & community stability. Review examines molecular strategies & rational design of next-generation microbiome-based therapies www.cell.com/cell-host-mi...
cell.com
The female urogenital microbiome: Ecological insights, therapeutic strategies, and molecular mechanisms
In the urogenital tract, dominant lactobacilli shape vaginal immunity and community stability. In this review, Dillen and Dricot et al. integrate clinical and mechanistic evidence on their molecular s...
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Reposted by Jotham Suez (SuezLab@JHU)
Journal of Clinical Investigation @jci.org · 24/03/2026
Gut microbes sound the alarm during sleep loss Leone et al. find short-term sleep loss in healthy humans alters 24-hr rhythmic profiles of circulating microbially derived metabolites, including butyric acid & tryptophan catabolites, relative to habitual sleep: doi.org/10.1172/JCI1...
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Reposted by Jotham Suez (SuezLab@JHU)
Ben J Woodcroft @benjwoodcroft.bsky.social · 23/03/2026
New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows. We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠 Here's what we found 👇 doi.org/10.1128/msystems.01062-25
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Reposted by Jotham Suez (SuezLab@JHU)
Chris Stewart @stewartlab.bsky.social · 18/03/2026
🚨 A new piece of the preterm gut microbiome puzzle just fell into place! Bifidobacterium metabolise human milk oligosaccharides (HMOs) in early life — shaping immunity, supporting gut development, and protecting against diseases like necrotising enterocolitis (NEC). www.nature.com/articles/s41...
nature.com
Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids - Nature Microbiology
Clostridium perfringens lacking perfringolysin O toxin isolated from preterm infants metabolizes human milk oligosaccharide disialyllacto-N-tetraose to produce metabolites that promote the growth of c...
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Reposted by Jotham Suez (SuezLab@JHU)
Jack A Gilbert @gilbertjacka.bsky.social · 15/03/2026
Our new study shows that a human-derived Bacteroides salyersiae can reverse depressive-like behavior in a chronic stress model, with effects comparable to ketamine. The talented @philstrandwitz.bsky.social to creating microbiome-based antidepressant therapeutics. link.springer.com/article/10.1...
link.springer.com
A human-derived Bacteroides strain attenuates depressive-like behavior in a rat model of social defeat-induced stress - BMC Medicine
Background The gut microbiome has been linked to mood disorders via communication along the gut-brain axis. We previously found levels of fecal Bacteroides were inversely associated with brain signatu...
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Reposted by Jotham Suez (SuezLab@JHU)
Eric Topol @erictopol.bsky.social · 11/03/2026
A single course of antibiotics can have lasting effects on your gut microbiome, with changes that last well beyond 4 years. Three types of antibiotics stood out for their long term disruptive impact (3 at left, Figure) nature.com/articles/s41...
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Jotham Suez (SuezLab@JHU) @suez.bsky.social · 11/03/2026
Impressive new study by @tovefall.bsky.social showing some antibiotics impact the gut microbiome >4 years www.nature.com/articles/s41... I shared some thoughts with Scientific American: www.scientificamerican.com/article/a-si... Sadly, they did not include my answer to the question... 1/2
nature.com
Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals - Nature Medicine
Using individual-level data from the Swedish Prescribed Drug Register and fecal metagenomes of 14,979 individuals in Sweden, the authors examined the association between oral antibiotic use over 8 yea...
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Reposted by Jotham Suez (SuezLab@JHU)
Sorek Lab @soreklab.bsky.social · 05/03/2026
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
science.org
Structural modeling reveals phage proteins that manipulate bacterial immune signaling
Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and bioph...
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Reposted by Jotham Suez (SuezLab@JHU)
Sean Gibbons 🦠💩 @gibbological.bsky.social · 26/02/2026
"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
sciencenews.org
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.
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Reposted by Jotham Suez (SuezLab@JHU)
Sean Gibbons 🦠💩 @gibbological.bsky.social · 19/02/2026
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...
doi.org
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 ...
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Reposted by Jotham Suez (SuezLab@JHU)
NEJM.org @nejm.org · 11/02/2026
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
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.
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Nature Microbiology @natmicrobiol.nature.com · 07/02/2026
#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...
nature.com
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...
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Reposted by Jotham Suez (SuezLab@JHU)
Guillaume Méric @gmeric.bsky.social · 04/02/2026
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...
nature.com
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...
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Reposted by Jotham Suez (SuezLab@JHU)
Guillaume Méric @gmeric.bsky.social · 04/02/2026
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...
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Reposted by Jotham Suez (SuezLab@JHU)
Dept of Molecular Microbiology & Immunology at Johns Hopkins @johnshopkinsmmi.bsky.social · 29/01/2026
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...
wsj.com
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.
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Reposted by Jotham Suez (SuezLab@JHU)
Dr. Haley Hallowell @haleybiont.bsky.social · 04/02/2026
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/...
journals.asm.org
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...
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Reposted by Jotham Suez (SuezLab@JHU)
fbm-unil.bsky.social @fbm-unil.bsky.social · 04/02/2026
🦠 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
journals.plos.org
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...
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Jotham Suez (SuezLab@JHU) @suez.bsky.social · 04/02/2026
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
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.
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Ran Blekhman @blekhman.bsky.social · 04/02/2026
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...
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eLife @elife.bsky.social · 09/12/2025
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
The commitments in the SAFE Labs Handbook.
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Tal Korem @tkorem.bsky.social · 28/11/2025
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.
science.org
Distributional bias compromises leave-one-out cross-validation
Leave-one-out cross-validation, a common machine learning evaluation method, has a pernicious flaw; a practical fix is presented.
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 26/11/2025
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-...
isbscience.org
2025 ISB Virtual Microbiome Symposium - Institute for Systems Biology (ISB)
The gut’s microbial ecosystem produces diverse metabolites that actively shape neural, immune, and endocrine function. Join leading researchers on December 12 as they share new discoveries into these ...
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Jotham Suez (SuezLab@JHU) @suez.bsky.social · 18/10/2025
Campus friends @ Homewood
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Reposted by Jotham Suez (SuezLab@JHU)
Oded Rechavi @odedrechavi.bsky.social · 15/10/2025
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 👇)
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Hutlab @hutlab.bsky.social · 17/10/2025
Congrats to Yancong, Amrisha, Xochitl, Eric and all co-authors!!!
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Jotham Suez (SuezLab@JHU) @suez.bsky.social · 15/10/2025
Love this approach!
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Reposted by Jotham Suez (SuezLab@JHU)
Nature Microbiology @natmicrobiol.nature.com · 15/08/2025
#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...
nature.com
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.
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