The awesome virome logo of a phage above a strand of DNA

Have you developed a new #bioinformatics tool to understand #phage or #virus? Make sure you add it to #awesome-virome

github.com/shandley/awe...

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.

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.

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...

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...

Katalin Karikó will be @jhu.edu's 2026 commencement speaker. Excellent choice!

www.jhunewsletter.com/article/2026...

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...

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...

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

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...

🚨 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...

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...

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 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...

Super impressed by the scope of this study - would love to see this replicated in other countries, and I wonder if there are datasets that would be able to address the impact of probiotics or different diets on preventing the lasting impacts of antibiotics on the microbiome.

From a research perspective, we need more causal evidence that these disruptions affect health, especially for antibiotics administered to younger children whose microbiomes are still developing.

"What should patients do with this?"

And my take is that patients should trust that their clinicians weigh risks/benefits when prescribing antibiotics. This expands our understanding of the risks, and patients can discuss those risks/benefits with their doctors.

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...

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

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.