Julien Tap
@julientap.bsky.social
food and gut #microbionaut | #microbiota #microbiome | research scientist
@INRAE_France
| https://fme.micalis.fr
@INRAE_France
| https://fme.micalis.fr
Reposted by Julien Tap
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
www.nature.com
December 17, 2025 at 6:53 PM
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
I presented new data from the French Gut project during the last Food System #Microbiomes congress in Wageningen
fme.micalis.fr/congress/202...
fme.micalis.fr/congress/202...
The FME lab communicates about the links between the microbiome, nutrition and health.
The FME lab communicates about the links between the microbiome, nutrition and health in Food System Microbiome conference.
fme.micalis.fr
December 3, 2025 at 5:05 PM
I presented new data from the French Gut project during the last Food System #Microbiomes congress in Wageningen
fme.micalis.fr/congress/202...
fme.micalis.fr/congress/202...
A new article, “𝘼 𝙨𝙘𝙤𝙥𝙞𝙣𝙜 𝙧𝙚𝙫𝙞𝙚𝙬 𝙤𝙛 𝙩𝙝𝙚 𝙝𝙚𝙖𝙡𝙩𝙝 𝙚𝙛𝙛𝙚𝙘𝙩𝙨 𝙤𝙛 𝙛𝙚𝙧𝙢𝙚𝙣𝙩𝙚𝙙 𝙛𝙤𝙤𝙙𝙨 𝙞𝙣 𝙨𝙥𝙚𝙘𝙞𝙛𝙞𝙘 𝙝𝙪𝙢𝙖𝙣 𝙥𝙤𝙥𝙪𝙡𝙖𝙩𝙞𝙤𝙣𝙨 𝙖𝙣𝙙 𝙩𝙝𝙚𝙞𝙧 𝙥𝙤𝙩𝙚𝙣𝙩𝙞𝙖𝙡 𝙧𝙤𝙡𝙚 𝙞𝙣 𝙥𝙧𝙚𝙘𝙞𝙨𝙞𝙤𝙣 𝙣𝙪𝙩𝙧𝙞𝙩𝙞𝙤𝙣” has been published in Frontiers in Nutrition as part of the COST Action PIMENTO.
fme.micalis.fr/article/2025...
fme.micalis.fr/article/2025...
Understanding How Fermented Foods Shape Health Insights From a New PIMENTO Review
A scoping review of the health effects of fermented foods in specific human populations and their potential role in precision nutrition: current knowledge and gaps
fme.micalis.fr
December 3, 2025 at 5:03 PM
A new article, “𝘼 𝙨𝙘𝙤𝙥𝙞𝙣𝙜 𝙧𝙚𝙫𝙞𝙚𝙬 𝙤𝙛 𝙩𝙝𝙚 𝙝𝙚𝙖𝙡𝙩𝙝 𝙚𝙛𝙛𝙚𝙘𝙩𝙨 𝙤𝙛 𝙛𝙚𝙧𝙢𝙚𝙣𝙩𝙚𝙙 𝙛𝙤𝙤𝙙𝙨 𝙞𝙣 𝙨𝙥𝙚𝙘𝙞𝙛𝙞𝙘 𝙝𝙪𝙢𝙖𝙣 𝙥𝙤𝙥𝙪𝙡𝙖𝙩𝙞𝙤𝙣𝙨 𝙖𝙣𝙙 𝙩𝙝𝙚𝙞𝙧 𝙥𝙤𝙩𝙚𝙣𝙩𝙞𝙖𝙡 𝙧𝙤𝙡𝙚 𝙞𝙣 𝙥𝙧𝙚𝙘𝙞𝙨𝙞𝙤𝙣 𝙣𝙪𝙩𝙧𝙞𝙩𝙞𝙤𝙣” has been published in Frontiers in Nutrition as part of the COST Action PIMENTO.
fme.micalis.fr/article/2025...
fme.micalis.fr/article/2025...
Reposted by Julien Tap
cFMD v1.3.0 is here! 🚀
We're thrilled to announce the release of the latest version of the curatedFoodMetagenomicData (cFMD) github.com/SegataLab/cFMD
While we're keeping the same core datasets & samples, we've packed this release w/ significant improvements under the hood.
1/4
We're thrilled to announce the release of the latest version of the curatedFoodMetagenomicData (cFMD) github.com/SegataLab/cFMD
While we're keeping the same core datasets & samples, we've packed this release w/ significant improvements under the hood.
1/4
GitHub - SegataLab/cFMD: Public repository for cFMD - curatedFoodMetagenomicData
Public repository for cFMD - curatedFoodMetagenomicData - SegataLab/cFMD
github.com
November 26, 2025 at 1:09 PM
cFMD v1.3.0 is here! 🚀
We're thrilled to announce the release of the latest version of the curatedFoodMetagenomicData (cFMD) github.com/SegataLab/cFMD
While we're keeping the same core datasets & samples, we've packed this release w/ significant improvements under the hood.
1/4
We're thrilled to announce the release of the latest version of the curatedFoodMetagenomicData (cFMD) github.com/SegataLab/cFMD
While we're keeping the same core datasets & samples, we've packed this release w/ significant improvements under the hood.
1/4
November 22, 2025 at 4:43 PM
Reposted by Julien Tap
📢 [𝐍𝐞𝐰 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧] 𝐀𝐧𝐭𝐢𝐛𝐢𝐨𝐭𝐢𝐜𝐬 𝐚𝐧𝐝 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐭𝐚: 𝐩𝐡𝐚𝐠𝐞𝐬, 𝐚𝐥𝐥𝐢𝐞𝐬 𝐨𝐟 𝐫𝐞𝐬𝐢𝐥𝐢𝐞𝐧𝐜𝐞.
@metagenopolis.bsky.social @inrae-france.bsky.social with @inserm.fr @institutpasteur.bsky.social
#microbiome #science #antibiotics #phages #research #health
@eugenpfeifer.bsky.social
www.cell.com/cell-reports...
@metagenopolis.bsky.social @inrae-france.bsky.social with @inserm.fr @institutpasteur.bsky.social
#microbiome #science #antibiotics #phages #research #health
@eugenpfeifer.bsky.social
www.cell.com/cell-reports...
Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages
Antibiotic-induced disruption of the gut microbiome leads to a transient loss of microbiome
diversity (bacterial and viral) and causes blooms of bacteria and their viruses. Our
analysis suggests that ...
www.cell.com
October 22, 2025 at 12:30 PM
📢 [𝐍𝐞𝐰 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧] 𝐀𝐧𝐭𝐢𝐛𝐢𝐨𝐭𝐢𝐜𝐬 𝐚𝐧𝐝 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐭𝐚: 𝐩𝐡𝐚𝐠𝐞𝐬, 𝐚𝐥𝐥𝐢𝐞𝐬 𝐨𝐟 𝐫𝐞𝐬𝐢𝐥𝐢𝐞𝐧𝐜𝐞.
@metagenopolis.bsky.social @inrae-france.bsky.social with @inserm.fr @institutpasteur.bsky.social
#microbiome #science #antibiotics #phages #research #health
@eugenpfeifer.bsky.social
www.cell.com/cell-reports...
@metagenopolis.bsky.social @inrae-france.bsky.social with @inserm.fr @institutpasteur.bsky.social
#microbiome #science #antibiotics #phages #research #health
@eugenpfeifer.bsky.social
www.cell.com/cell-reports...
Reposted by Julien Tap
New publication🧬 𝐌𝐞𝐭𝐞𝐨𝐫𝟐 𝐢𝐬 𝐚𝐧 𝐨𝐩𝐞𝐧-𝐬𝐨𝐮𝐫𝐜𝐞 𝐭𝐨𝐨𝐥 𝐟𝐨𝐫 𝐭𝐚𝐱𝐨𝐧𝐨𝐦𝐢𝐜, 𝐟𝐮𝐧𝐜𝐭𝐢𝐨𝐧𝐚𝐥, 𝐚𝐧𝐝 𝐬𝐭𝐫𝐚𝐢𝐧-𝐥𝐞𝐯𝐞𝐥 𝐩𝐫𝐨𝐟𝐢𝐥𝐢𝐧𝐠 𝐨𝐟 𝐦𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐢𝐜 𝐬𝐚𝐦𝐩𝐥𝐞𝐬. 𝐟𝐨𝐫 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐦𝐞 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡
microbiomejournal.biomedcentral.com/articles/10....
#metagenomic #science #data #lefrenchgut
@inrae-france.bsky.social @institutpasteur.bsky.social
microbiomejournal.biomedcentral.com/articles/10....
#metagenomic #science #data #lefrenchgut
@inrae-france.bsky.social @institutpasteur.bsky.social
Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2 - Microbiome
Background The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms...
microbiomejournal.biomedcentral.com
November 6, 2025 at 4:38 PM
New publication🧬 𝐌𝐞𝐭𝐞𝐨𝐫𝟐 𝐢𝐬 𝐚𝐧 𝐨𝐩𝐞𝐧-𝐬𝐨𝐮𝐫𝐜𝐞 𝐭𝐨𝐨𝐥 𝐟𝐨𝐫 𝐭𝐚𝐱𝐨𝐧𝐨𝐦𝐢𝐜, 𝐟𝐮𝐧𝐜𝐭𝐢𝐨𝐧𝐚𝐥, 𝐚𝐧𝐝 𝐬𝐭𝐫𝐚𝐢𝐧-𝐥𝐞𝐯𝐞𝐥 𝐩𝐫𝐨𝐟𝐢𝐥𝐢𝐧𝐠 𝐨𝐟 𝐦𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐢𝐜 𝐬𝐚𝐦𝐩𝐥𝐞𝐬. 𝐟𝐨𝐫 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐦𝐞 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡
microbiomejournal.biomedcentral.com/articles/10....
#metagenomic #science #data #lefrenchgut
@inrae-france.bsky.social @institutpasteur.bsky.social
microbiomejournal.biomedcentral.com/articles/10....
#metagenomic #science #data #lefrenchgut
@inrae-france.bsky.social @institutpasteur.bsky.social
Reposted by Julien Tap
Huge congratulations to our colleague @arnauvich.bsky.social for presenting his research on FODMAP restriction and gut microbiota in IBS patients at United European Gastroenterology Week 2025 in Berlin🇩🇪👏! #UEGWeek @myueg.bsky.social @vibmicrobes.bsky.social
October 6, 2025 at 11:54 AM
Huge congratulations to our colleague @arnauvich.bsky.social for presenting his research on FODMAP restriction and gut microbiota in IBS patients at United European Gastroenterology Week 2025 in Berlin🇩🇪👏! #UEGWeek @myueg.bsky.social @vibmicrobes.bsky.social
It was nice to have a chance to present few result from French Gut project.
fme.micalis.fr/congress/202...
#microbiome #EESMicrobiome
fme.micalis.fr/congress/202...
#microbiome #EESMicrobiome
The French Gut at EMBL Human Microbiome Symposium 2025
results from the French Gut project presented at the EMBL Human Microbiome Symposium
fme.micalis.fr
September 18, 2025 at 10:55 PM
It was nice to have a chance to present few result from French Gut project.
fme.micalis.fr/congress/202...
#microbiome #EESMicrobiome
fme.micalis.fr/congress/202...
#microbiome #EESMicrobiome
Reposted by Julien Tap
Starting my journey from Australia to Heidelberg 🇩🇪 to the @embl.org Human Microbiome conference
It’s not every day we get the chance of 4 days of human microbiome research 🤩🤩🤩 I’m so excited
Still chance to attend it online 👇
www.embl.org/about/info/c...
It’s not every day we get the chance of 4 days of human microbiome research 🤩🤩🤩 I’m so excited
Still chance to attend it online 👇
www.embl.org/about/info/c...
The human microbiome
www.embl.org
September 13, 2025 at 5:01 PM
Starting my journey from Australia to Heidelberg 🇩🇪 to the @embl.org Human Microbiome conference
It’s not every day we get the chance of 4 days of human microbiome research 🤩🤩🤩 I’m so excited
Still chance to attend it online 👇
www.embl.org/about/info/c...
It’s not every day we get the chance of 4 days of human microbiome research 🤩🤩🤩 I’m so excited
Still chance to attend it online 👇
www.embl.org/about/info/c...
Reposted by Julien Tap
Question: what’s one piece of advice you’d give to somebody starting out in quantitative ecology?
#QuantitativeEcology #Statistics #R
#QuantitativeEcology #Statistics #R
July 18, 2025 at 10:35 AM
Question: what’s one piece of advice you’d give to somebody starting out in quantitative ecology?
#QuantitativeEcology #Statistics #R
#QuantitativeEcology #Statistics #R
A three-country analysis of the gut #microbiome indicates taxon associations with diet vary by taxon resolution and population
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population | mSystems
An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why ...
journals.asm.org
July 2, 2025 at 4:47 PM
A three-country analysis of the gut #microbiome indicates taxon associations with diet vary by taxon resolution and population
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by Julien Tap
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances www.nature.com/articles/s41... #jcampubs
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances - Nature Microbiology
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances (PFAS), commonly known as forever chemicals, in intracellular aggregates. Colonization of gnotobiotic mice with bioaccumulating bac...
www.nature.com
July 1, 2025 at 1:38 PM
Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances www.nature.com/articles/s41... #jcampubs
One Health World #Microbiome Partnership Summit is coming soon!
Agenda - World One Health Microbiome Summit
June 20, 2025 Académie Nationale de Médecine, Paris
Please note that this program could change.
wmp.symposium.inrae.fr
June 19, 2025 at 11:07 PM
One Health World #Microbiome Partnership Summit is coming soon!
Reposted by Julien Tap
Another review from my lab out this week, on analyzing gut microbiome data from global populations -- tackling computational challenges and providing practical frameworks and resources for the field
With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social
www.cell.com/trends/micro...
With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social
www.cell.com/trends/micro...
Analyzing human gut microbiome data from global populations: challenges and resources
Research on the human gut microbiome is expanding rapidly; yet, most published studies
focus on populations from high-income regions such as North America and Europe. Underrepresentation
of population...
www.cell.com
June 18, 2025 at 10:12 PM
Another review from my lab out this week, on analyzing gut microbiome data from global populations -- tackling computational challenges and providing practical frameworks and resources for the field
With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social
www.cell.com/trends/micro...
With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social
www.cell.com/trends/micro...
Reposted by Julien Tap
This is so cool - octopus can sense microbiomes: sending a gift link www.nytimes.com/2025/06/17/s...
Eight Arms to Taste Your Microbiome
www.nytimes.com
June 19, 2025 at 5:45 PM
This is so cool - octopus can sense microbiomes: sending a gift link www.nytimes.com/2025/06/17/s...
If you are an european citizen and you think we should ban conversion practices targeting LGBTQ+ citizens.
You should sign this.
Half of signature are from France, we need more countries!
eci.ec.europa.eu/043/public/#...
You should sign this.
Half of signature are from France, we need more countries!
eci.ec.europa.eu/043/public/#...
European Citizens' Initiative
Give your support !
eci.ec.europa.eu
May 16, 2025 at 5:25 PM
If you are an european citizen and you think we should ban conversion practices targeting LGBTQ+ citizens.
You should sign this.
Half of signature are from France, we need more countries!
eci.ec.europa.eu/043/public/#...
You should sign this.
Half of signature are from France, we need more countries!
eci.ec.europa.eu/043/public/#...
Reposted by Julien Tap
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
May 1, 2025 at 6:41 PM
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
🧵[1/10]
Reposted by Julien Tap
Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...
Global genetic structure of human gut microbiome species is related to geographic location and host health
The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…
www.sciencedirect.com
April 30, 2025 at 4:15 PM
Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...
Reposted by Julien Tap
Wow! Our paper in @natmicrobiol.nature.com has just surpassed 10,000 views in less than a month!! a rare feat for a #plant #microbiome study! We argue that seed-borne bacteria are the architects of the wheat rhizobiome. Thanks to everyone who’s been engaging with our work :) doi.org/10.1038/s415...
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation - Nature Microbiology
A sequential propagation strategy shows how the microbes initially on seeds are key to building complex, reproducible and heritable plant microbiomes.
doi.org
April 19, 2025 at 4:33 PM
Wow! Our paper in @natmicrobiol.nature.com has just surpassed 10,000 views in less than a month!! a rare feat for a #plant #microbiome study! We argue that seed-borne bacteria are the architects of the wheat rhizobiome. Thanks to everyone who’s been engaging with our work :) doi.org/10.1038/s415...
If you're a PhD student, Master's student or researcher interested in #artificial #intelligence applications to microbial ecosystems and in particular the gut #microbiome, we're organizing a researchers' school here:
ai-microbiome-school.onrender.com/speakers
ai-microbiome-school.onrender.com/speakers
Speakers | SCHOOL OF ARTIFICIAL INTELLIGENCE APPLIED TO MICROBIOMES
Meet the speakers at the School of AI Applied to Microbiomes
ai-microbiome-school.onrender.com
April 7, 2025 at 2:35 PM
If you're a PhD student, Master's student or researcher interested in #artificial #intelligence applications to microbial ecosystems and in particular the gut #microbiome, we're organizing a researchers' school here:
ai-microbiome-school.onrender.com/speakers
ai-microbiome-school.onrender.com/speakers