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

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

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👇

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

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...

⚠️ 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...

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...

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!

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...

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...

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...

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👏

"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...

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.

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...

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

Important note about this breakthrough: Literally would not exist without the kind of Federal support the current administration is slashing. Took 15+ years of research at a federal lab (Lawrence Berkeley) to get this to a point at which private enterprise could take over and make these at scale.

"Proteasome-cleaved peptides may have previously overlooked functions downstream of degradation. From a translational standpoint, identifying proteasome-derived defence peptides could provide an untapped source of natural antibiotics for biotechnological applications and therapeutic interventions"

Just one single gut bacteria is astonishingly sufficient to repress the antibiotic-resistant C. difficile infection. A real game changer from colleagues at the Center. AI and synthetic communities boiled it all down. Big vision by the trainees and faculty www.psu.edu/news/researc...

Ecstatic to see our paper "Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing" now published in @naturegenet.bsky.social with @trajnp.bsky.social and @panosroussos.bsky.social @sinaibrain.bsky.social www.nature.com/articles/s41...

Very interesting study "hyperglycemia plays a dominant role facilitating the expansion and takeover of resistant mutants in diabetic infections" | Science Advances www.science.org/doi/10.1126/...

Our mSCAPE project has been formally announced to the world by @smhopkins.bsky.social at #FOG2025 today: www.gov.uk/government/n... - a really exciting academic-public health collaboration to build a surveillance platform leveraging NHS metagenomic diagnostic data. @meerac.bsky.social

“the importance of quantifying antibiotic activity with real-time, single-cell assays under physiological conditions.”

Happy to share our new paper in @naturemicrobiol.bsky.social on mapping spatial relationships of the human gut microbiome. We identified distinct spatial hubs between gut bacteria that reflect sub-community assemblies at the micron-scale. Led by Miles Richardson & co. www.nature.com/articles/s41...

Great seeing this paper from Andrew Stergachis Lab published “Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition” www.nature.com/articles/s41...

I figured today was as good a day as any to introduce myself over here! My lab combines stem cell models and genome engineering to study how the interactions between genes and environments contributes to brain disease. The only thing I find more rewarding than scientific discovery is mentoring…

This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/... #microsky #microbial #microbiology #genomics #transcriptomic 🦠🧫

The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky

I'm incredibly honored by this opportunity to serve as President-Elect of @asm.org starting this summer. Looking forward to working with the Board, ASM leadership ,and staff to help advance the microbial sciences. I'm also glad to share my Vision statement, please join us! asm.org/Press-Releas...

Interested in predicting AMR in bacteria? We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. With @nwheeler443.bsky.social and former PhD student Yanying Yu. 🦠🧫🧬🖥️🧪 www.biorxiv.org/content/10.1...

Our paper on 🦠queuosine 34 modification of tRNA tyrosine and antibiotic response is finally out in its final form in @eLife ... and quite different from the preprint version. Many thanks to reviewers, editors and kudos to all authors🙏 elifesciences.org/articles/96317

Tracking bacterial ‘seeds’ in new soil reveals how they grow, adapt, and pave the way for next-gen microbiome therapies. @gangfang.bsky.social @biorxivpreprint.bsky.social t.co/QisGjqmInv #ImmunoSky 🧪

Please RT: Associate Professor position in my department at the University of Oxford. Broad search in molecular and cellular biology: my.corehr.com/pls/uoxrecru...

Our January 2025 issue is now live: go.nature.com/4gxO8jl Topics include: DNA methylation in mammalian development and disease; the molecular consequences of chromosomal instability (CIN) in cancer; ancestral recombination graphs; and the evolution and function of animal sex chromosomes

I’ve been out of the microbiome field field for a few years now but every time I see amazing work like this I’m impressed at how far we have come! Congrats @gangfang.bsky.social and @yufan01.bsky.social

Just saw this blog on @annaggreen.bsky.social 's paper on using CNNs to predict TB resistance. [Anna, mostly in case of interest to you!] medium.com/towards-data...

Glad to share our preprint 🏃 **LongTrack**: long read metagenomics-based precise tracking of bacterial strains (and their genomic changes!) after 💩 fecal microbiota transplantation. A 4+ years journey and tour de force by ** @yufan01.bsky.social ** & team. A long 🧵 www.biorxiv.org/content/10.1...

www.biorxiv.org/content/10.1... Our study published today on #bioRxiv describe the identification of a deaminase that converts 5mC to T, enabling direct sequencing of the human methylome and genome. This achievement was made possible through a collaborative effort across all departments at #NEB.

This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/

It's beginning to look a lot like Christmas!. Send us your own favourite #AgarArt so that we can add it to our album! 🦠🧫🎄🦌🎅🏻

My friend & colleague @micsysecolab.bsky.social Matthias has written this extremely insightful and fascinating perspective on bacterial collective metabolism, out now in @naturemicrobiol.bsky.social. So happy to see this out & super excited for proteome allocation! www.nature.com/articles/s41...

Exciting times! Our latest preprint is now live 🤩! After nearly 16 yrs of running my lab, I truly believe this is one of the most significant contributions we've made. It offers fresh hypotheses about how pandemic Vibrio cholerae spreads globally. Let’s dive in!🧵..1/n www.biorxiv.org/content/10.1...

Lots of activity in global genomics surveillance initiatives around AMR. These papers by @target-amr.bsky.social members @ksbakes.bsky.social @nwheeler443.bsky.social and many others give an excellent overview www.thelancet.com/journals/lan... and www.thelancet.com/journals/lan... #WAAW2024

Very much agreed. Positive controls are often clear. Negative controls sometimes have several layers of complexity, exactly the cautions needed in the detection of rare DNA (and RNA) modifications.

Thank u for this question. Worth another thread as it reflects common confusion that more data & better AI/ML is the solution (newer official @nanopore models & new customer methods are being developed/released). For abundant mods like 5mCpG in human, this strategy works. *BUT* for low abundance 1/5

Long-read special issue of GR is out, including our paper on T2T assembly using only Nanopore. Just in time for ONT to discontinue duplex cells on Nov 27 😅😂 Good thing Verkko also works great with HERRO-corrected simplex data! 📄 genome.cshlp.org/content/34/1... 📖 genome.cshlp.org/content/34/1...