Léonard Dubois
@leonardubois.bsky.social
Researcher (bioinformatics and microbiome) and martial arts teacher (aikido).
Post-doc at Sorbonne Université in Pr. Harry Sokol's team. Previously PhD in Trento University with Pr. Nicola Segata
Post-doc at Sorbonne Université in Pr. Harry Sokol's team. Previously PhD in Trento University with Pr. Nicola Segata
Reposted by Léonard Dubois
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Léonard Dubois
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 8:39 AM
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Reposted by Léonard Dubois
Cool application of microbiome in food science
Using metagenomics on Colombian cacao, they mapped how microbes influence chocolate flavors. Then they built a defined microbial consortium that replicates premium chocolate flavors -- validated by trained tasters!
www.nature.com/articles/s41...
Using metagenomics on Colombian cacao, they mapped how microbes influence chocolate flavors. Then they built a defined microbial consortium that replicates premium chocolate flavors -- validated by trained tasters!
www.nature.com/articles/s41...
A defined microbial community reproduces attributes of fine flavour chocolate fermentation - Nature Microbiology
An in-depth microbiological and metagenomic analysis of Colombian farm and fermentation facilities resulted in the design of a defined microbial community that can reproduce the flavour of fine chocol...
www.nature.com
August 19, 2025 at 8:07 PM
Cool application of microbiome in food science
Using metagenomics on Colombian cacao, they mapped how microbes influence chocolate flavors. Then they built a defined microbial consortium that replicates premium chocolate flavors -- validated by trained tasters!
www.nature.com/articles/s41...
Using metagenomics on Colombian cacao, they mapped how microbes influence chocolate flavors. Then they built a defined microbial consortium that replicates premium chocolate flavors -- validated by trained tasters!
www.nature.com/articles/s41...
Reposted by Léonard Dubois
Fun fact: In reference 28 here, I used the word strain to mean something similar to the lineage level because a reviewer refused to let me use the word lineage.
There is still a lot of confusion in this space, and I strongly recommend defining whatever terminology you use.
There is still a lot of confusion in this space, and I strongly recommend defining whatever terminology you use.
I love this diagram
August 18, 2025 at 6:03 PM
Fun fact: In reference 28 here, I used the word strain to mean something similar to the lineage level because a reviewer refused to let me use the word lineage.
There is still a lot of confusion in this space, and I strongly recommend defining whatever terminology you use.
There is still a lot of confusion in this space, and I strongly recommend defining whatever terminology you use.
Reposted by Léonard Dubois
🧬🖥️ Postdoc positions available SOON!!
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics
July 4, 2025 at 9:11 AM
🧬🖥️ Postdoc positions available SOON!!
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics
Looking for researchers with strong computational skills (programming essential) to work on microbiome & phylogenetics projects.
📅 Start on Nov 1, 2025 (flexible)
📍 Trento, Italy
DM me for details or share!
#postdocjobs #microbiome #metagenomics #phylogenetics
Reposted by Léonard Dubois
Today I will be attending a conference at Stanford University, in honor of Susan Holmes, who is retiring. She has been an essential driving force for our microbiome research.
Bridging Biology and Statistics: Insights and Innovations for Modern Biology
www.eventcreate.com/e/stats4mode...
Bridging Biology and Statistics: Insights and Innovations for Modern Biology
www.eventcreate.com/e/stats4mode...
Bridging Biology and Statistics: Insights and Innovations for Modern Biology | June 03, 2025
Join us on June 03
www.eventcreate.com
June 3, 2025 at 3:24 PM
Today I will be attending a conference at Stanford University, in honor of Susan Holmes, who is retiring. She has been an essential driving force for our microbiome research.
Bridging Biology and Statistics: Insights and Innovations for Modern Biology
www.eventcreate.com/e/stats4mode...
Bridging Biology and Statistics: Insights and Innovations for Modern Biology
www.eventcreate.com/e/stats4mode...
Reposted by Léonard Dubois
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine
An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...
www.nature.com
June 3, 2025 at 10:43 AM
🥁NEW publication from our lab:
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
the largest meta-analysis of gut microbiome associations with CRC!
www.nature.com/articles/s41...
🧵⬇️
1/6
Reposted by Léonard Dubois
Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw
Large-scale skin metagenomics reveals extensive prevalence, coordination, and functional adaptation of skin microbiome dermotypes across body sites
The human skin microbiome is increasingly recognized to influence skin health, immune function and disease susceptibility. However, large-scale, multi-site metagenomic studies in the general populatio...
www.biorxiv.org
April 28, 2025 at 4:52 AM
Super thrilled to share our labor of love from the Asian Skin Microbiome Program! We collected >3,500 skin samples, built metagenomic libraries w/ >70 billion reads and >10TB of data to study heterogeneity of the skin microbiome in the general population (200 adults, 18 sites) t.co/ZylbJMpvpw
Reposted by Léonard Dubois
🥁
We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD)
🔗 Get it here: github.com/SegataLab/cFMD
🧵👇
1/5
We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD)
🔗 Get it here: github.com/SegataLab/cFMD
🧵👇
1/5
GitHub - SegataLab/cFMD: Public repository for cFMD - curatedFoodMetagenomicData
Public repository for cFMD - curatedFoodMetagenomicData - SegataLab/cFMD
github.com
March 12, 2025 at 1:56 PM
🥁
We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD)
🔗 Get it here: github.com/SegataLab/cFMD
🧵👇
1/5
We are happy to announce the release of a new version of curatedFoodMetagenomicData (cFMD)
🔗 Get it here: github.com/SegataLab/cFMD
🧵👇
1/5
Reposted by Léonard Dubois
It's Friday!
...and a new #MVIF program is out! 🤩
Registration here:
cassyni.com/s/mvif-36
⭐️ MicroTalks:
🇯🇵 Nodoka Chiba
🇮🇩 Patsy Tasyana Fitri
⭐️ Keynote:
🇯🇵 Ruixin Liu
⭐️ Selected talks:
🇦🇺 @aroneys.bsky.social
🇬🇧 Maria Kardakova
🇦🇺 Theo Portlock
...and a new #MVIF program is out! 🤩
Registration here:
cassyni.com/s/mvif-36
⭐️ MicroTalks:
🇯🇵 Nodoka Chiba
🇮🇩 Patsy Tasyana Fitri
⭐️ Keynote:
🇯🇵 Ruixin Liu
⭐️ Selected talks:
🇦🇺 @aroneys.bsky.social
🇬🇧 Maria Kardakova
🇦🇺 Theo Portlock
February 7, 2025 at 12:39 PM
It's Friday!
...and a new #MVIF program is out! 🤩
Registration here:
cassyni.com/s/mvif-36
⭐️ MicroTalks:
🇯🇵 Nodoka Chiba
🇮🇩 Patsy Tasyana Fitri
⭐️ Keynote:
🇯🇵 Ruixin Liu
⭐️ Selected talks:
🇦🇺 @aroneys.bsky.social
🇬🇧 Maria Kardakova
🇦🇺 Theo Portlock
...and a new #MVIF program is out! 🤩
Registration here:
cassyni.com/s/mvif-36
⭐️ MicroTalks:
🇯🇵 Nodoka Chiba
🇮🇩 Patsy Tasyana Fitri
⭐️ Keynote:
🇯🇵 Ruixin Liu
⭐️ Selected talks:
🇦🇺 @aroneys.bsky.social
🇬🇧 Maria Kardakova
🇦🇺 Theo Portlock
Reposted by Léonard Dubois
EDITORIAL: Ensuring rigour of low-biomass microbiome research
Read it here: www.nature.com/articles/s41...
#microsky #microbiomesky 🧪
Read it here: www.nature.com/articles/s41...
#microsky #microbiomesky 🧪
Ensuring rigour of low-biomass microbiome research - Nature Microbiology
Determining whether human organs house a resident microbiome is challenging and the findings can be controversial. However, forging collaborations and careful study design can help overcome these issu...
www.nature.com
February 4, 2025 at 5:48 PM
EDITORIAL: Ensuring rigour of low-biomass microbiome research
Read it here: www.nature.com/articles/s41...
#microsky #microbiomesky 🧪
Read it here: www.nature.com/articles/s41...
#microsky #microbiomesky 🧪
Reposted by Léonard Dubois
🚨 New blog post! 🚨
If you want to learn about:
🎨 Monochrome colour palettes
📊 Designing better black & white visualisations
🛠️ Rethinking single-colour chart design
Read this ➡️ nrennie.rbind.io/blog/monochr...
#RStats #DataViz #ggplot2 #RLadies
If you want to learn about:
🎨 Monochrome colour palettes
📊 Designing better black & white visualisations
🛠️ Rethinking single-colour chart design
Read this ➡️ nrennie.rbind.io/blog/monochr...
#RStats #DataViz #ggplot2 #RLadies
Designing monochrome data visualisations | Nicola Rennie
In data visualisations, colours are often used to show values or categories of data. However, sometimes you might not be able to or want to use colour. This blog post discusses some tips for designing...
nrennie.rbind.io
February 5, 2025 at 9:45 AM
🚨 New blog post! 🚨
If you want to learn about:
🎨 Monochrome colour palettes
📊 Designing better black & white visualisations
🛠️ Rethinking single-colour chart design
Read this ➡️ nrennie.rbind.io/blog/monochr...
#RStats #DataViz #ggplot2 #RLadies
If you want to learn about:
🎨 Monochrome colour palettes
📊 Designing better black & white visualisations
🛠️ Rethinking single-colour chart design
Read this ➡️ nrennie.rbind.io/blog/monochr...
#RStats #DataViz #ggplot2 #RLadies
Reposted by Léonard Dubois
Hey #microbiome people,
Some time ago, I started compiling several lists (& still regularly updating them):
Bioinformatics learning github.com/SvetlanaUP/A...
Microbiome events github.com/SvetlanaUP/M...
Microbiome podcasts github.com/SvetlanaUP/M...
Pls add if I missed something!
Some time ago, I started compiling several lists (& still regularly updating them):
Bioinformatics learning github.com/SvetlanaUP/A...
Microbiome events github.com/SvetlanaUP/M...
Microbiome podcasts github.com/SvetlanaUP/M...
Pls add if I missed something!
GitHub - SvetlanaUP/A-microbiologist-wants-to-compute: This repo collects the list of learning online resources related to microbiome computational science and tools.
This repo collects the list of learning online resources related to microbiome computational science and tools. - SvetlanaUP/A-microbiologist-wants-to-compute
github.com
October 18, 2024 at 7:40 AM
Hey #microbiome people,
Some time ago, I started compiling several lists (& still regularly updating them):
Bioinformatics learning github.com/SvetlanaUP/A...
Microbiome events github.com/SvetlanaUP/M...
Microbiome podcasts github.com/SvetlanaUP/M...
Pls add if I missed something!
Some time ago, I started compiling several lists (& still regularly updating them):
Bioinformatics learning github.com/SvetlanaUP/A...
Microbiome events github.com/SvetlanaUP/M...
Microbiome podcasts github.com/SvetlanaUP/M...
Pls add if I missed something!
Reposted by Léonard Dubois
Our study @cellpress.bsky.social finds healthy Canadians that consume a non-industrialized-type #diet can modulate their #microbiome, boost beneficial metabolites and improve their health. In just 3 weeks:
LDL cholesterol ↓17%
fasting glucose ↓6%
CRP ↓ 14%
www.cell.com/cell/fulltex...
LDL cholesterol ↓17%
fasting glucose ↓6%
CRP ↓ 14%
www.cell.com/cell/fulltex...
Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation
Is it possible to restore the human gut microbiome in industrialized settings and
reintroduce microbial species that have been lost? In healthy adults, Li et al. found
that consuming a diet mimicking ...
www.cell.com
January 23, 2025 at 5:10 PM
Our study @cellpress.bsky.social finds healthy Canadians that consume a non-industrialized-type #diet can modulate their #microbiome, boost beneficial metabolites and improve their health. In just 3 weeks:
LDL cholesterol ↓17%
fasting glucose ↓6%
CRP ↓ 14%
www.cell.com/cell/fulltex...
LDL cholesterol ↓17%
fasting glucose ↓6%
CRP ↓ 14%
www.cell.com/cell/fulltex...
Reposted by Léonard Dubois
Today we report a new compendium of human gut microbiomes with >168,000 samples
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human
gut microbiome 16S samples, built with the integrated data from hundreds of independent
projects. The compendium is us...
www.cell.com
January 22, 2025 at 5:12 PM
Today we report a new compendium of human gut microbiomes with >168,000 samples
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria
Now out in Cell:
www.cell.com/cell/fulltex...
Reposted by Léonard Dubois
Microbiome science needs more microbiologists
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Microbiome science needs more microbiologists - Nature Microbiology
Microbiome science is a multi-disciplinary field, but classical microbiologists are needed to ensure advances are grounded in our understanding of basic microbiological concepts.
www.nature.com
January 22, 2025 at 6:12 PM
Microbiome science needs more microbiologists
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Léonard Dubois
Our new preprint "microGalaxy: A gateway to tools, workflows, and training for accessible, reproducible, and FAIR microbial data analysis" is live! 🎉
📝 Read it here: www.biorxiv.org/content/10.1...
#Microbiome #FAIRdata #usegalaxy @galaxyproject.bsky.social
📝 Read it here: www.biorxiv.org/content/10.1...
#Microbiome #FAIRdata #usegalaxy @galaxyproject.bsky.social
microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data
Microbial research generates vast and complex data from diverse omics technologies, necessitating innovative analytical solutions. microGalaxy (Galaxy for Microbiology) addresses these needs with a us...
www.biorxiv.org
January 8, 2025 at 12:16 PM
Our new preprint "microGalaxy: A gateway to tools, workflows, and training for accessible, reproducible, and FAIR microbial data analysis" is live! 🎉
📝 Read it here: www.biorxiv.org/content/10.1...
#Microbiome #FAIRdata #usegalaxy @galaxyproject.bsky.social
📝 Read it here: www.biorxiv.org/content/10.1...
#Microbiome #FAIRdata #usegalaxy @galaxyproject.bsky.social
Reposted by Léonard Dubois
Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social
Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology
Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...
www.nature.com
January 10, 2025 at 10:06 AM
Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social
Reposted by Léonard Dubois
🧵 How does being a #vegan, #vegetarian or omnivore impact your gut #microbiome? 🥦 Find out in our new paper on gut microbiome signatures of vegan, vegetarian & omnivore diets & associated health outcomes across 21,561 individuals in @naturemicrobiol.bsky.social!🎉 1/10
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals - Nature Microbiology
Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes.
www.nature.com
January 7, 2025 at 9:30 AM
🧵 How does being a #vegan, #vegetarian or omnivore impact your gut #microbiome? 🥦 Find out in our new paper on gut microbiome signatures of vegan, vegetarian & omnivore diets & associated health outcomes across 21,561 individuals in @naturemicrobiol.bsky.social!🎉 1/10
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Léonard Dubois
I encourage every young microbiologist to go to this conference
I was lucky to attend the last edition, the level of science is incredible (and I met my actual postdoc supervisor)
I was lucky to attend the last edition, the level of science is incredible (and I met my actual postdoc supervisor)
You want to learn about microbiology from a fantastic lineup of speakers on a beautiful Greek island? PhD students apply now for the @EMBO | @FEBSnews Lecture Course The New Microbiology!
Registration: 1 Apr 2025
Course: 03 – 11 Sep 2025 | Spetses, Greece
meetings.embo.org/event/25-new...
Registration: 1 Apr 2025
Course: 03 – 11 Sep 2025 | Spetses, Greece
meetings.embo.org/event/25-new...
December 16, 2024 at 1:37 PM
I encourage every young microbiologist to go to this conference
I was lucky to attend the last edition, the level of science is incredible (and I met my actual postdoc supervisor)
I was lucky to attend the last edition, the level of science is incredible (and I met my actual postdoc supervisor)