"Microbe at play" 👇 Our “microbiome epigenetic bet-hedging” paper made the cover of @cp-cellhostmicrobe.bsky.social! Creative work by @Lily Armstrong-Davies! Congrats to Mi Ni @fannimi2001.bsky.social and the team! Link to post: bsky.app/profile/gang... Link to paper: www.cell.com/cell-host-mi...

Cell Host & Microbe@cp-cellhostmicrobe.bsky.social · 2mo ago

Our June issue is now live. The cover image puts microbes at play. Have your own fun and enjoyment reading the content within: www.cell.com/cell-host-mi...

New #MicrobiomeDigest is OUT microbiomedigest.com/2026/05/29/m... • root microbiome/ @algazuccaro.bsky.social   • gut microbiome-epigenetics/ @gangfang.bsky.social   • resistome annotation/ @bigdatabiology.bsky.social   • invitation for #MVIF 50🎂 / @microbiomevif.bsky.social & more. Happy Friday!

May 29, 2026

See you next week at MVIF! Global microbiome Advancing microbial ecology, microbiomes, and One Health in Africa: From regional initiatives to pan-African flagship programs – Mohamed Hijri – The ISM…

microbiomedigest.com

Glad that our paper is out today in @cp-cellhostmicrobe.bsky.social A baby received a routine course of amoxicillin. In that infant's #gut 💩, we could see something remarkable, already present **before** the antibiotic arriveda single strain 🦠 of #Akkermansia muciniphila was already running 1/n

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

Ni et al. show that epigenetic phase variation (ePV)—gene expression changes mediated by bacterial DNA methylation—is prevalent in the human gut microbiome and associated with fluctuating environments...

cell.com

First genome sequence from Andes hantavirus strain from ongoing ship outbreak posted on Virological: virological.org/t/complete-s... courtesy Swiss National Reference Centre for Emerging Viral Infections, Geneva University Hospitals, University of Zurich

Complete sequence of Orthohantavirus andesense virus: Swiss resident 2026

Posted on behalf of the Swiss National Reference Center for Emerging Viral Infections, Geneva University Hospitals and the Institute of Medical Virology, University of Zurich (Partner Laboratory Natio...

virological.org

Further details on the meningococcal genome and genomic epidemiology including data release info from the recent explosive Kent outbreak: www.gov.uk/government/p...

Invasive Meningococcal Disease outbreak 2026: technical briefing 1

gov.uk

Paper 🚨: in this Narrative Review we describe the challenges and opportunity of a microbiome research facility, based on our experiences at LUMC with Center for Microbiome Analyses and Therapeutics (CMAT) www.sciencedirect.com/science/arti... #ESGHAMI @escmid.bsky.social @cmijournal.bsky.social

How to set up and manage a microbiome research facility

The increasing number of therapeutic intervention studies in the microbiome field has sparked broad interest among clinicians and scientists to incorp…

sciencedirect.com

🎆Very excited to share our perspective piece calling for higher standards in reports on microbial detection in cancers! It was great to put this together with some of the leaders in the field including @stevensalzberg.bsky.social @rafalab.bsky.social Barry Marshall and Eske Willerslev: rdcu.be/e4IaU

Setting higher standards for reports of microbial species in human cancers

Nature Cancer - Nagarajan and colleagues overview the current challenges in microbiome analyses from human cancer samples and discuss the optimal practices for improving the standards of reporting...

rdcu.be

Five years after the rollout of Covid-19 vaccines started, it seems the mystery of why the Astra-Zeneca and J&J vaccines led to a rare but deadly side effect of unusual blood clots and bleeding has finally been solved. 
 It's a fascinating case of molecular mimicry that may help make vaccine safer.🧪

Rare, dangerous side effects of some COVID-19 vaccines explained

“Groundbreaking” study uncovers why adenovirus-based shots caused life-threatening blood clots and bleeding in some people

science.org

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data www.nature.com/articles/s41... (thread 1/n)

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

nature.com

Data duplication reported in influential Nature paper on gut microbiome-brain axis pubpeer.com/publications...

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/

New discovery in ulcerative colitis: a bacterial toxin that kills macrophages and increases inflammation, which could be the foundation for a new treatment science.org/doi/10.1126/... science.org/doi/10.1126/... @science.org

A bacterial toxin disarms gut defenses against inflammation

Macrophage-toxic bacteria from patients with ulcerative colitis worsen gut inflammation in mice

science.org

OUT NOW - Long-read metagenomics method for strain tracking after FMT #microsky www.nature.com/articles/s41...

Long-read metagenomics for strain tracking after faecal microbiota transplant - Nature Microbiology

A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains and revealing genomic ch...

nature.com

Excited to share our LongTrack study out in @natmicrobiol.nature.com today! Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/ 📄 rdcu.be/eL8mR

Long-read metagenomics for strain tracking after faecal microbiota transplant

Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...

rdcu.be

Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇

Frédérique Le Roux@fredoleroux.bsky.social · 10mo ago

Phages evolve fast, or do they? In oysters, some stay identical for years. With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements. Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

I'm thrilled to share that our study is now published in Cell: Extensive N4 cytosine methylation is essential for Marchantia sperm function. www.cell.com/cell/fulltex... This paper confirms our 4mC discovery in Marchantia sperm and takes it much further. A thread: 0/13

Extensive N4 cytosine methylation is essential for Marchantia sperm function

Global N4 cytosine methylation in Marchantia polymorpha sperm regulates gene expression and promotes sperm fertility.

cell.com

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut. Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals. doi.org/10.1101/2025...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

doi.org

⚠️ New preprint ⚠️: Two new antibiotics are likely coming for gonorrhea 💊. How should we deploy them in the US to minimize drug resistance? @kroster.bsky.social @dhelekal.bsky.social Eva Rumpler @yhgrad.bsky.social [1/10] www.medrxiv.org/content/10.1...

Comparing Strategies to Introduce Two New Antibiotics for Gonorrhea: A Modeling Study

Introduction Drug resistance in Neisseria gonorrhoeae is an urgent public health threat. The anticipated approval of two new antimicrobials for gonorrhea prompts the need for evidence-based rollout st...

medrxiv.org

Important: if a bug does not make the WHO's priority list, this does not mean it is not relevant. We present arguments why investment in R&D for surveillance, control and treatment of C. difficile (CDI) is of critical importance: www.sciencedirect.com/science/arti...

Clostridioides difficile is a bacterial priority pathogen

sciencedirect.com

I am beyond thrilled to highlight @mbfneuro.bsky.social's thesis work! I've learned so much through his studies and am excited to take this project in new directions!

Michael Fernando, PhD@mbfneuro.bsky.social · last yr.

I’m so proud and beyond thrilled to share the final product of my thesis work from @sinaibrain.bsky.social , now published in @nature.com! Here, we explored the complex functional impact of rare neurexin-1 deletions across human glutamatergic and GABAergic neurons! www.nature.com/articles/s41...

I’m so proud and beyond thrilled to share the final product of my thesis work from @sinaibrain.bsky.social , now published in @nature.com! Here, we explored the complex functional impact of rare neurexin-1 deletions across human glutamatergic and GABAergic neurons! www.nature.com/articles/s41...

Phenotypic complexities of rare heterozygous neurexin-1 deletions - Nature

How NRXN1 variants affect multiple neuropsychiatric disorders is explored.

nature.com

Long reads such as @nanoporetech.com or @pacbio.bsky.social can provide insights into epigenetic. We @yileifu.bsky.social & @timp0.bsky.social )summarize the latest #Bioinformatics approaches & why this matters! Out now @natrevgenet.bsky.social at: bit.ly/4cjxUtl @bcmhouston.bsky.social @jhu.edu

I've been waiting for someone to do this: Phase variation via DNA methylation enables gut bacteria to adapt to environmental changes by regulating gene expression and enhancing phenotypic diversity. #microbiome www.biorxiv.org/content/10.1...

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase va...

biorxiv.org

ELGG paper has the following the statement about Bifidobacterium bifidum MAGs: "For instance, the MAGs from B. bifidum contain 27 CAZy families, 10 of which were not found in reference isolate genomes ... GH3, GH5, GH9, GH43, GH127, GH38, CE10, GH8, CBM6, and GH94" www.nature.com/articles/s41...

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome - Nature Communications

Here the authors present a large-scale resource of the early-life human gut microbiome from children under three years old, which comprises 32,277 metagenome-assembled gut genomes, representing 2172 s...

nature.com

Does anyone have examples of a (high profile?) paper that likely made an incorrect biological claim due to a contaminated genome from a metagenome? Don't worry, not a loaded question, because I think the answer should be.... yes! Just wondering what cases are out there.

Great new review @natrevgenet.bsky.social by @sedlazeck.bsky.social @timp0.bsky.social and @yileifu.bsky.social! 👇highlighting both the promise of long read DNA methylation analysis and remaining challenges such as the difficulty to benchmark 5hmC and non-CG 5mC given their low abundance👏

Yilei Fu@yileifu.bsky.social · last yr.

We summarized state-of-the-art computational methods for DNA methylation analysis using long-read sequencing, covering everything from base calling to sample-level, cell-type-level, and even population-scale analysis. Huge thanks to @sedlazeck.bsky.social and @timp0.bsky.social for this great work!

"As #longread sequencing is more often used in #microbiome studies, we anticipate that our findings will open new dimensions to characterize how gut bacteria adapt to various stress conditions and host interactions using #epigenetic mechanisms." #PacBio 🧵 1/5 www.biorxiv.org/content/10.1...

Epigenetic phase variation in the gut microbiome enhances bacterial adaptation

The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase va...

biorxiv.org

Phage satellites are now known to be very diverse, numerous and ancient. They pose many evolutionary, ecological and mechanistic questions. Lots of fun in perspective! Great pleasure to write this review to show it, with @jrpenades.bsky.social @dbikard.bsky.social Kim Seed & John Chen.

Nature Reviews Microbiology@natrevmicro.nature.com · last yr.

New online! Genetics, ecology and evolution of phage satellites

Preprint Alert 🧵Epigenetic phase variation in the gut microbiome enhances bacterial adaptation 🔎a hidden layer shaping gut microbiome. 👏5+ Yr journey by @fannimi2001.bsky.social in collab w/ @drvaldivia.bsky.social MartinBlaser WenyanJiang, LaurenDavey #Microbiome #Epigenetics bit.ly/43rX9at 👇 1/n

- What are the roles of m5C bases in bacterial genomes? - If a DNA methyltransferase is not genetically linked with a restriction enzyme (“solitary”), what is its role? - Are “solitary” Vsr-like proteins functional? --> Insights in our latest Preprint: doi.org/10.1101/2025...

Cytosine methylation by ScmA contributes to the fitness of Caulobacter crescentus cells naturally expressing a Vsr-like protein

While methylated cytosines are known to play important roles in eukaryotes, their significance in bacteria remains poorly understood especially when they are added on genomes by DNA methyltransferases...

doi.org