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. 👇

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 5d ago

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics https://www.biorxiv.org/content/10.64898/2026.07.30.741866v1

🦠 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

📣 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...

📢 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

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...

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

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

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: https://go.nature.com/4a8YZzr

🚨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...

A new method for inference and tracking the transmission of strains in metagenomes #MicroSky #MicroEco www.nature.com/articles/s41...

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.

nature.com

Out Now! Unravelling bacterial complexity at high resolution with single-cell transcriptomics #MicroSky

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 🤩

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...

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.

gizmodo.com

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...

Have you developed a new #bioinformatics tool to understand #phage or #virus? Make sure you add it to #awesome-virome github.com/shandley/awe...

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.

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.

publichealth.jhu.edu

ICYMI: New online! Diet–microbiome associations

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...

Katalin Karikó will be @jhu.edu's 2026 commencement speaker. Excellent choice! www.jhunewsletter.com/article/2026...

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...

jhunewsletter.com

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...

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...

cell.com

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...

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

🚨 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...

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...

nature.com

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...

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...

link.springer.com

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...

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

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...

nature.com

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

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...

science.org

Nitzan Tal@nitzantal.bsky.social · last yr.

📢Preprint out! Excited to share my final work from the @soreklab.bsky.social! We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery. Found 3 new families targeting immune signaling!

"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

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.

sciencenews.org

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...

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 ...

doi.org

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