Winter Summit 2025 | The Future of Microbiome Future of the Microbiome2025 Winter Summit Join us November 18-20, 2025! REGISTER NOW The Future of the Microbiome Winter Summit explores what’s next for the microbiome industry, bringing together bri...

Dr. Nick Quinn-Bohmann will present a Keynote Talk at this year's Future of the Microbiome Winter Summit (Nov. 18-20).

He'll talk about his work on using community-scale metabolic modeling to design personalized, microbiome-informed interventions. futureofmicrobiome.com/winter-summi...

GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.

academic.oup.com/nar/advance-...

A periodic table of bacteria?: Mapping bacterial diversity in trait space Bacterial diversity can be overwhelming. There is an ever-expanding number of bacterial taxa being discovered, but many of these taxa remain uncharacterized with unknown traits and environmental prefe...

New pre-print from my group - project led by PhD student Michael Hoffert. We set out on a daunting mission to generate a 'periodic table' of bacterial diversity (1/6) www.biorxiv.org/content/10.1...

Genome Sciences is looking for a Director of Departmental Computing. This is a rare opportunity for someone interested in leading our excellent IT team, building and maintaining computational infrastructure, and working closely with our faculty and labs uwhires.admin.washington.edu/ENG/candidat...

Guidelines for preventing and reporting contamination in low-biomass microbiome studies Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

Microbe with bizarrely tiny genome may be evolving into a virus With DNA focused almost entirely on replication, newly discovered organism blurs the line between cells and viruses

STORY ABOUT A BACTERIA GOING VIRAL

Genome of 𝘚𝘶𝘬𝘶𝘯𝘢𝘢𝘳𝘤𝘩𝘢𝘦𝘶𝘮 𝘮𝘪𝘳𝘢𝘣𝘪𝘭𝘦 is so stripped down— just 238,000 bp—that it blurs the line between cell and virus

Encodes just DNA replication, transcription, and translation—no metabolism, no cellular independence

Begs the question: WhAt Is CeLLuLaR LiFe?

The timeline shows clinical development and regulatory milestones for VOWST, a microbial product used to treat rCDI.

In a review led by @gilbertjacka.bsky.social in @natmedicine.bsky.social we highlight the state of clinical translation in microbiome research. We have gone from basic discoveries to FDA-approved therapies in <20 years, on par with the pace of mRNA vaccine development.
www.nature.com/articles/s41...

Moving from genome-scale to community-scale metabolic models for the human gut microbiome - Nature Microbiology In this Perspective, Deiner, Gibbons and colleagues describe the current strengths and limitations of microbial community-scale metabolic models in microbiome research.

Microbial community-scale metabolic models (MCMMs) map gut microbiome composition & dietary context to functional outputs, at scale.

Here, we describe these emerging tools & their utility to both basic & translational microbiome research. @natmicrobiol.nature.com

www.nature.com/articles/s41...

Human microbiome acquisition and transmission Nature Reviews Microbiology, Published online: 21 March 2025; doi:10.1038/s41579-025-01166-xEach human hosts a unique microbiome, but only recently have we started to uncover how such uniqueness can arise. In this Review, Heidrich, Valles-Colomer and Segata highlight studies that surveyed how we acquire and transmit our microbiome strains through interactions with other humans and the environment.

New online! Nature Reviews Microbiology, Published online: 21 March 2025; doi:10.1038/s41579-025-01166-xEach human hosts a unique microbiome, but only recently have we started to uncover how such uniqueness can arise. In this Review, Heidrich, Valles-Colomer and Segata highlight studies that…

Capsule-Based Single-Cell Genome Sequencing https://www.biorxiv.org/content/10.1101/2025.03.14.643253v1

A screenshot of the release notes for radEmu v2. Text available at https://github.com/statdivlab/radEmu/releases

We've just released radEmu v2.0.0 🥳🦤😻

`remotes::install_github("statdivlab/radEmu")`

A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!

Release notes: github.com/statdivlab/r...

I am restarting the StatDivLab blog! Goal is rigorous but accessible statistics for microbiome science. Here's the new scope & welcome: 😽✉️📝

statdivlab.github.io/blog/index.h...

PS. I see you, friends. What a disaster. Please keep resisting, and encourage those around you to do the same.

Tomorrow, 1:30pm. AADOCR in NYC.

Honored to be a speaker alongside @jmarkwelch.bsky.social and @mbio.bsky.social Editor in Chief Marvin Whiteley.
#microbiology #dentistry

SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome - Nature Microbiology Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.

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...

Highly multiplexed spatial transcriptomics in bacteria Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...

🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈

“Bacterial-MERFISH” provides ~1000-fold volumetric expansion of individual cells, charts gene expression in hundreds of thousands of cells, deciphering bacterial single-cell heterogeneity, intracellular transcriptome organization, and bacterial adaptation to µm-scale niches in vivo

Some bacterial toxins enter hosts through skin and mucus membranes. This new article dives into how scientists are harnessing these toxins and repurposing them as vaccine delivery tools. asm.org/Articles/202... #microsky

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)

Excited to share our new preprint on the detailed investigation of Type 4 pili in epibiont oral Saccharibacteria! Led by Alex Grossman from our lab, and with Jun Liu (Yale), Jeff McLean (UW) and Xuesong He. Check it out: biorxiv.org/content/10.1...

I'm so thankful for @amazonwebservices.bsky.social's support in bringing our My Digital Gut prototype to life! 🎉

The future of microbiome-informed precision nutrition will be coming to a clinical trial near you, hopefully in the next year or two 🤞

Appreciate the effort to generate this list. I would be grateful if you could add me to this list as well. thank you.

Saccharibacteria deploy two distinct Type IV pili, driving episymbiosis, host competition, and twitching motility https://www.biorxiv.org/content/10.1101/2024.11.25.624915v1 All cultivated Patescibacteria, or CPR, exist as obligate episymbionts on other microbes. Despite be

Saccharibacteria deploy two distinct Type IV pili, driving episymbiosis, host competition, and twitching motility https://www.biorxiv.org/content/10.1101/2024.11.25.624915v1

Excited to share our latest, "Biofilm dispersal patterns revealed using far-red fluorogenic probes." @plos.bsky.social We developed a cell-labeling strategy using far-red dyes to image dense microbial communities (where fluorescent proteins often do not work well) journals.plos.org/plosbiology/...

Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov Abstract. Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metaboli

Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov academic.oup.com/ismecommun/a...

Just wanted to share the link to the awesome Thematic Issue on Biofilms that was recently published by #FEMS, academic.oup.com/femsre/pages.... Looking forward to another one on Biofilms in time for the 10th ASM conference on Biofilms #ASMBiofilms

Evo, a genomic foundation model. Source: https://pubmed.ncbi.nlm.nih.gov/39541441/

Genomes by AI

by Roberto — Two years ago I played, simultaneously amused and bemused, with ChatGPT. It was clear artificial intelligence (AI) had taken a quantum leap. While I did not get to play with it, reading about Evo last...

Read more > schaechter.asmblog.org/schaechter/2...
#MicroSky

lab website
Jsmcleanlab.com