Invasive Meningococcal Disease outbreak 2026: technical briefing 1

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

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…

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

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...

🎆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

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

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.🧪

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.

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)

Data duplication reported in influential Nature paper on gut microbiome-brain axis

pubpeer.com/publications...

Link to preprint: www.biorxiv.org/content/10.6...

We’d love your thoughts!

#longread
@pacbio.bsky.social
@nanoporetech.com

#metagenomics #pacbio #nanopore 12/

Grateful to all collaborators who contributed valuable samples and feedback: @fannimi2001.bsky.social, @magdalenaksi.bsky.social, Lei Cao,
@lazu20.bsky.social, Gintaras Deikus, Robert Sebra, Rachel Brody, Raymund Yong, Ketan Badani,
Xue-Song Zhang. @sinaigenetics.bsky.social 11/

current consensus that most signals reflect background contamination, with true positives mainly expected during active infection.

Long story short, but this was a 4+ years effort led by @yanchunzhang93.bsky.social and Andy Mead. 10/

The new metric also helps #unify earlier debates about microbiomes reported in #placenta and #blood. When we reanalyzed long-read data from those settings using the same read length-based approach, we found no evidence for a stable resident microbiome under normal conditions, consistent with the 9/

One finding that stood out to us was the #lung, it is constantly exposed to microbes (breathe), yet in our analysis, the microbial signal appeared mostly as short DNA, which is more consistent with transient exposure and rapid clearance than with stable resident microbes in deep lung tissue. 8/

Outside those settings, most microbial signals look more like fragmented, and the occasional long fragments often match well-known #contaminant organisms. 7/

Across multiple tumor types and tissues (public + new data), we find that long microbial reads are mainly seen in tissues with natural microbial exposure (such as #gut, #stomach, #skin, #vagina and #cervix, etc). 6/

Positive #controls: bacteria spike-in, and importantly, GI tumors with well established bacteria: e.g. #Helicobacter #pylori in #gastric cancer, #Fusobacterium in #colorectal cancer. 5/

Negative #controls: germ-free mice and human cell culture datasets, where true resident microbes are not expected and any microbial signal is most likely introduced during workflows (i.e. contaminations). 4/

distributions, not mostly short broken (degraded) pieces. Long-read data lets us distinguish those two cases! To make this more robust across datasets, we developed a #metric that normalizes microbial DNA fragment lengths to human DNA fragment lengths within the same sample. 3/

of the microbial signal is real ❓ and how much is background noise from the lab or the environment ❓

We tackle this with a simple idea: look at DNA fragment sizes using #longread sequencing. If microbes are truly present as intact cells, their DNA should show up as long, genome-like fragment 2/

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/

A bacterial toxin disarms gut defenses against inflammation Macrophage-toxic bacteria from patients with ulcerative colitis worsen gut inflammation in mice

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

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...

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

📄 Link to paper: rdcu.be/eL8mR

🧵Link to a long thread: bsky.app/profile/gang...

#Microbiome #FMT #cdiff #IBD #PrecisionMedicine #NatureMicrobiology #MountSinai #FecalMicrobiotaTransplantation #Gastroenterology #MicrobiotaTherapeutics n/ END

👏 Congrats to first author
@yufan01.bsky.social, with nearly 5-year effort and innovation, thanks to *Jeremiah Faith*, our wonderful collaborator, @fannimi2001.bsky.social, @magdalenaksi.bsky.social and the entire team! @sinaigenetics.bsky.social @sinaiimmuno.bsky.social @mountsinaigi.bsky.social 5/

We’re excited because this study has important implications on the design of defined bacterial cocktails that are safer, more effective, more robust, and more consistent than whole-stool FMT. 4/

separating very similar strains that coexist in donors' or patients' gut. Our approach—building on long-read DNA sequencing—can tell highly similar strains apart, and importantly, detect their genomic changes that may reflect how bacteria 🦠 adapt to patients' gut after transplantation. 3/

We developed a precise way to track which donor bacteria successfully colonize after FMT and how they change over time—by identifying a unique genetic “fingerprint” in each bacterial strain. Previous studies have yielded great insights into FMT, but faced challenges 2/

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...

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

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👇

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.

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

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...

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...