@jeffmclean.bsky.social
University of Washington Professor, Adj UW Micro
Jsmcleanlab.com
#saccharibacteria #patescibacteria #oralmicrobiome #microbiome
#metagenomics
Jsmcleanlab.com
#saccharibacteria #patescibacteria #oralmicrobiome #microbiome
#metagenomics
Pinned
The McLean Lab
Jsmcleanlab.com
lab website
Jsmcleanlab.com
Jsmcleanlab.com
Reposted
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...
He'll talk about his work on using community-scale metabolic modeling to design personalized, microbiome-informed interventions. futureofmicrobiome.com/winter-summi...
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...
futureofmicrobiome.com
November 11, 2025 at 9:55 PM
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...
He'll talk about his work on using community-scale metabolic modeling to design personalized, microbiome-informed interventions. futureofmicrobiome.com/winter-summi...
Reposted
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-...
academic.oup.com/nar/advance-...
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
academic.oup.com
October 22, 2025 at 2:20 PM
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-...
academic.oup.com/nar/advance-...
Reposted
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...
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...
www.biorxiv.org
July 18, 2025 at 4:44 PM
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...
Reposted
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...
UW Human Resources
University of Washington Human Resources
uwhires.admin.washington.edu
July 11, 2025 at 9:54 PM
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...
Reposted
Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io
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...
rdcu.be
June 21, 2025 at 7:59 PM
Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io
Reposted
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?
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?
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
www.science.org
June 17, 2025 at 5:22 AM
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?
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?
Reposted
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...
www.nature.com/articles/s41...
April 11, 2025 at 2:24 PM
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...
www.nature.com/articles/s41...
Reposted
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...
Here, we describe these emerging tools & their utility to both basic & translational microbiome research. @natmicrobiol.nature.com
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.
www.nature.com
April 11, 2025 at 2:38 PM
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...
Here, we describe these emerging tools & their utility to both basic & translational microbiome research. @natmicrobiol.nature.com
www.nature.com/articles/s41...
Reposted
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…
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.
www.nature.com
March 21, 2025 at 5:46 PM
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…
Reposted
Capsule-Based Single-Cell Genome Sequencing https://www.biorxiv.org/content/10.1101/2025.03.14.643253v1
March 17, 2025 at 8:33 PM
Capsule-Based Single-Cell Genome Sequencing https://www.biorxiv.org/content/10.1101/2025.03.14.643253v1
Reposted
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...
`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...
March 14, 2025 at 10:47 AM
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...
`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...
Reposted
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.
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.
StatDivLab Blog
This is a way to host a blog for the Statistical Diversity Lab.
statdivlab.github.io
February 19, 2025 at 3:49 PM
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.
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.
Reposted
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
Honored to be a speaker alongside @jmarkwelch.bsky.social and @mbio.bsky.social Editor in Chief Marvin Whiteley.
#microbiology #dentistry
March 11, 2025 at 3:26 PM
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
Honored to be a speaker alongside @jmarkwelch.bsky.social and @mbio.bsky.social Editor in Chief Marvin Whiteley.
#microbiology #dentistry
Reposted
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...
www.nature.com/articles/s41...
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.
www.nature.com
February 3, 2025 at 2:46 PM
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...
www.nature.com/articles/s41...
Reposted
🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈
“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
“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
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...
www.science.org
January 25, 2025 at 5:33 PM
🅲🅾🅾🅻 🆃🅴🅲🅷🅽🅾🅻🅾🅶🆈
“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
“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
Reposted
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
From Toxin to Taxi: Repurposing Bacterial Weapons | ASM.org
Some bacterial toxins enter hosts through skin and mucus membranes. Scientists are harnessing those toxins and repurposing them as vaccine delivery tools.
asm.org
January 10, 2025 at 7:05 PM
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
Reposted
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)
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)
Home
A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler
github.com
December 31, 2024 at 11:43 PM
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)
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)
Reposted
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...
December 4, 2024 at 11:09 AM
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...
Reposted
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 🤞
The future of microbiome-informed precision nutrition will be coming to a clinical trial near you, hopefully in the next year or two 🤞
Congratulations to @isbscience.org's @gibbological.bsky.social and colleagues, who were named a winner of a 2024-25 @amazonwebservices.bsky.social IMAGINE Grant for Nonprofits. isbscience.org/news/2024/12...
ISB Named Winner of 2024-2025 Amazon Web Services IMAGINE Grant for Nonprofits
ISB was selected as a winner of the 2024 Amazon Web Services (AWS) IMAGINE Grant, which will support continued development of My Digital Gut.
isbscience.org
December 3, 2024 at 9:05 PM
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 🤞
The future of microbiome-informed precision nutrition will be coming to a clinical trial near you, hopefully in the next year or two 🤞
Reposted
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
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
www.biorxiv.org
November 26, 2024 at 5:19 AM
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
Reposted
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/...
November 26, 2024 at 2:47 PM
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 academic.oup.com/ismecommun/a...
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
academic.oup.com
November 27, 2024 at 1:46 AM
Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov academic.oup.com/ismecommun/a...
Reposted
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
academic.oup.com
November 22, 2024 at 4:19 PM
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
Reposted
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
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
November 21, 2024 at 9:28 AM
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
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
Jsmcleanlab.com
The McLean Lab
Jsmcleanlab.com
November 16, 2024 at 1:38 AM
lab website
Jsmcleanlab.com
Jsmcleanlab.com