DEEMteam_Orsay
@deemteam.bsky.social
Diversity, Ecology and Evolution of Microbes (DEEM) team. Posts by David Moreira. #treeoflife #evolution
Paris, France
https://www.deemteam.fr/en/
Paris, France
https://www.deemteam.fr/en/
Reposted by DEEMteam_Orsay
Bernabeu, @microbiobits.bsky.social and @tonigabaldon.bsky.social use simulations to test for the robustness of inferred relative timings of gene transfers in the lineage leading to the ancestor of eukaryotes
🔗 doi.org/10.1093/gbe/evaf190
#genome #evolution
🔗 doi.org/10.1093/gbe/evaf190
#genome #evolution
Phylogeny-aware Simulations Suggest a Low Impact of Unsampled Lineages in the Inference of Gene Flow During Eukaryogenesis
Abstract. The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners
doi.org
November 3, 2025 at 4:23 PM
Bernabeu, @microbiobits.bsky.social and @tonigabaldon.bsky.social use simulations to test for the robustness of inferred relative timings of gene transfers in the lineage leading to the ancestor of eukaryotes
🔗 doi.org/10.1093/gbe/evaf190
#genome #evolution
🔗 doi.org/10.1093/gbe/evaf190
#genome #evolution
Reposted by DEEMteam_Orsay
Dive into our November issue featuring:
🪆nested archaeal symbioses
🌱microbiota driven drought responses in plants
🏗️ BAM complex in Bacteroidota
💨microbial fermentative growth in the gut
🍸hospital-specific phage therapy cocktail
and much more..!
www.nature.com/nmicrobiol/v...
🪆nested archaeal symbioses
🌱microbiota driven drought responses in plants
🏗️ BAM complex in Bacteroidota
💨microbial fermentative growth in the gut
🍸hospital-specific phage therapy cocktail
and much more..!
www.nature.com/nmicrobiol/v...
November 3, 2025 at 4:31 PM
Dive into our November issue featuring:
🪆nested archaeal symbioses
🌱microbiota driven drought responses in plants
🏗️ BAM complex in Bacteroidota
💨microbial fermentative growth in the gut
🍸hospital-specific phage therapy cocktail
and much more..!
www.nature.com/nmicrobiol/v...
🪆nested archaeal symbioses
🌱microbiota driven drought responses in plants
🏗️ BAM complex in Bacteroidota
💨microbial fermentative growth in the gut
🍸hospital-specific phage therapy cocktail
and much more..!
www.nature.com/nmicrobiol/v...
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com
rdcu.be/eLtCH
rdcu.be/eLtCH
November 2, 2025 at 5:52 PM
This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com
rdcu.be/eLtCH
rdcu.be/eLtCH
Reposted by DEEMteam_Orsay
How did life begin, and why does it matter? Scientists are tracing early microbial life–from LUCA to multicellularity–to unlock insights for biotech, climate science and even space exploration. Read the article: asm.org/articles/202...
Early Microbial Evolution | ASM.org
How did life begin, and why does it matter? Scientists are tracing early microbial life—from LUCA to multicellularity—to unlock insights for biotech, climate science and even space exploration.
asm.org
October 30, 2025 at 2:09 PM
How did life begin, and why does it matter? Scientists are tracing early microbial life–from LUCA to multicellularity–to unlock insights for biotech, climate science and even space exploration. Read the article: asm.org/articles/202...
Reposted by DEEMteam_Orsay
Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio
@bembidion.bsky.social
@bembidion.bsky.social
October 25, 2025 at 12:37 AM
Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio
@bembidion.bsky.social
@bembidion.bsky.social
Reposted by DEEMteam_Orsay
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 by DEEMteam_Orsay
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions
Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues.
@mkrupovic.bsky.social
@yifanzhou.bsky.social
@deemteam.bsky.social
www.nature.com/articles/s41...
Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues.
@mkrupovic.bsky.social
@yifanzhou.bsky.social
@deemteam.bsky.social
www.nature.com/articles/s41...
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
www.nature.com
October 20, 2025 at 7:46 PM
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions
Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues.
@mkrupovic.bsky.social
@yifanzhou.bsky.social
@deemteam.bsky.social
www.nature.com/articles/s41...
Out now in Nature Microbiology, by Yifan Zhou, Mart Krupovic & colleagues.
@mkrupovic.bsky.social
@yifanzhou.bsky.social
@deemteam.bsky.social
www.nature.com/articles/s41...
Reposted by DEEMteam_Orsay
A nice N&V article by Mike Dyall-Smith on our recent paper
( www.nature.com/articles/s41... ):
www.nature.com/articles/s41...
( www.nature.com/articles/s41... ):
www.nature.com/articles/s41...
Archaeal symbioses all the way down - Nature Microbiology
Ethiopian salt lakes feature unique microbial communities with nesting layers of symbioses, where haloarchaea and their ultra-small archaeal symbionts are prey to viruses, which are in turn hijacked b...
www.nature.com
October 20, 2025 at 11:51 AM
A nice N&V article by Mike Dyall-Smith on our recent paper
( www.nature.com/articles/s41... ):
www.nature.com/articles/s41...
( www.nature.com/articles/s41... ):
www.nature.com/articles/s41...
Reposted by DEEMteam_Orsay
Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
www.nature.com
October 17, 2025 at 10:28 AM
Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇
A proposal for journal accreditation systems to counter predatory practices. If funding agencies enforced these accreditations, predatory journals would quickly vanish.
doi.org/10.1093/fems...
doi.org/10.1093/fems...
October 12, 2025 at 5:15 PM
A proposal for journal accreditation systems to counter predatory practices. If funding agencies enforced these accreditations, predatory journals would quickly vanish.
doi.org/10.1093/fems...
doi.org/10.1093/fems...
Reposted by DEEMteam_Orsay
Ponce-Toledo et al. confirm the presence, homology, and monophyletic origin of the SELMA protein complex in Cryptophyta, Alveolata, Stramenopiles, and Haptophyta, shedding light on the evolution of photosynthetic eukaryotes.
🔗 doi.org/10.1093/molbev/msaf167
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf167
#evobio #molbio
Molecular Phylogeny of the SELMA Translocation Machinery Recounts the Evolution of Complex Photosynthetic Eukaryotes
Abstract. Photosynthetic eukaryotes and their relatives are the result of an intricate evolutionary history involving a series of plastid acquisitions thro
doi.org
September 8, 2025 at 4:57 PM
Ponce-Toledo et al. confirm the presence, homology, and monophyletic origin of the SELMA protein complex in Cryptophyta, Alveolata, Stramenopiles, and Haptophyta, shedding light on the evolution of photosynthetic eukaryotes.
🔗 doi.org/10.1093/molbev/msaf167
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf167
#evobio #molbio
Enjoying the mountains that forams built for us (with some help from plate tectonics) long ago.
August 31, 2025 at 4:16 PM
Enjoying the mountains that forams built for us (with some help from plate tectonics) long ago.
Reposted by DEEMteam_Orsay
New paper is out! We have studied the cute tiny Discocelia plataet sp. n. to obtain the first molecular data of the order Discocelida and clarify its cell structure. All this for a better understanding of the evolution of Cercozoa.
onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com/doi/epdf/10....
August 26, 2025 at 4:54 PM
New paper is out! We have studied the cute tiny Discocelia plataet sp. n. to obtain the first molecular data of the order Discocelida and clarify its cell structure. All this for a better understanding of the evolution of Cercozoa.
onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com/doi/epdf/10....
Reposted by DEEMteam_Orsay
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7
#microsky
#microsky
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de
August 15, 2025 at 8:07 AM
We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7
#microsky
#microsky
Reposted by DEEMteam_Orsay
Our paper describing our new improved GFmix models for phylogenetic inference that capture site-and-branch heterogeneity in amino acid composition.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Modeling site-and-branch-heterogeneity with GFmix
Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino acid sequences may be heterogeneous across both sites an...
www.biorxiv.org
August 12, 2025 at 12:53 PM
Our paper describing our new improved GFmix models for phylogenetic inference that capture site-and-branch heterogeneity in amino acid composition.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
In our ongoing saga of description of new protists, we are happy to introduce Multisulcus malaysiensis, a deep-branching heterolobosean that forms highly unusual multiflagellated cells with multiple ventral grooves. Great work by @kristina-prokina.bsky.social
onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com/doi/epdf/10....
August 7, 2025 at 12:26 PM
In our ongoing saga of description of new protists, we are happy to introduce Multisulcus malaysiensis, a deep-branching heterolobosean that forms highly unusual multiflagellated cells with multiple ventral grooves. Great work by @kristina-prokina.bsky.social
onlinelibrary.wiley.com/doi/epdf/10....
onlinelibrary.wiley.com/doi/epdf/10....
Check out our paper to explore how the evolutionary history of SELMA supports or challenges various hypotheses on the origin of red complex plastids.
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
July 23, 2025 at 8:43 AM
Check out our paper to explore how the evolutionary history of SELMA supports or challenges various hypotheses on the origin of red complex plastids.
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
🚨 Fresh off the press! We have just published our paper on the evolution of the SELMA translocon of red secondary plastids. We analyze the phylogeny of each individual protein and the implications for the evolutionary history of the entire complex.
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
Molecular phylogeny of the SELMA translocation machinery recounts the evolution of complex photosynthetic eukaryotes
Abstract. Photosynthetic eukaryotes and their relatives are the result of an intricate evolutionary history involving a series of plastid acquisitions thro
academic.oup.com
July 23, 2025 at 8:33 AM
🚨 Fresh off the press! We have just published our paper on the evolution of the SELMA translocon of red secondary plastids. We analyze the phylogeny of each individual protein and the implications for the evolutionary history of the entire complex.
academic.oup.com/mbe/article/...
academic.oup.com/mbe/article/...
Reposted by DEEMteam_Orsay
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Some ceramic protists from our talented friend Anabel López-Archilla. Do you recognize them?
July 15, 2025 at 2:39 PM
Some ceramic protists from our talented friend Anabel López-Archilla. Do you recognize them?
Reposted by DEEMteam_Orsay
Partez à la quête des origines de la vie avec Puri Lopez-Garcia, naturaliste du monde microbien !
Puri López-García est chercheuse en biologie et directrice de recherche @cnrs.fr au laboratoire Écologie, société et évolution (ESE - Univ. Paris-Saclay/CNRS/AgroParisTech).
🔗 tinyurl.com/2cm7zn27
Puri López-García est chercheuse en biologie et directrice de recherche @cnrs.fr au laboratoire Écologie, société et évolution (ESE - Univ. Paris-Saclay/CNRS/AgroParisTech).
🔗 tinyurl.com/2cm7zn27
July 10, 2025 at 7:34 AM
Partez à la quête des origines de la vie avec Puri Lopez-Garcia, naturaliste du monde microbien !
Puri López-García est chercheuse en biologie et directrice de recherche @cnrs.fr au laboratoire Écologie, société et évolution (ESE - Univ. Paris-Saclay/CNRS/AgroParisTech).
🔗 tinyurl.com/2cm7zn27
Puri López-García est chercheuse en biologie et directrice de recherche @cnrs.fr au laboratoire Écologie, société et évolution (ESE - Univ. Paris-Saclay/CNRS/AgroParisTech).
🔗 tinyurl.com/2cm7zn27
Reposted by DEEMteam_Orsay
The cultivation of anaerobic microbes is essential in geomicrobiology and increasingly impactful in geosciences — yet remains underrepresented.🔬
New online! Using anaerobic cultivation chambers to decipher geomicrobiological processes
Using anaerobic cultivation chambers to decipher geomicrobiological processes
Nature Reviews Earth & Environment, Published online: 03 July 2025; doi:10.1038/s43017-025-00700-yLewen Liang explains how anaerobic cultivation chambers can be used to decipher geomicrobiological processes underlying key biogeochemical cycles.
www.nature.com
July 3, 2025 at 2:07 PM
The cultivation of anaerobic microbes is essential in geomicrobiology and increasingly impactful in geosciences — yet remains underrepresented.🔬
We are very happy to welcome Benjy Sedano @bencyano7.bsky.social , our new PhD student who will be working with some of our favorite cyanobacteria!
July 1, 2025 at 1:09 PM
We are very happy to welcome Benjy Sedano @bencyano7.bsky.social , our new PhD student who will be working with some of our favorite cyanobacteria!
The "most beautiful" but also the most intelligent experiment in biology.
Just learned that Frank Stahl (of the Meselson and Stahl DNA replication experiment ("the most beautiful experiment in biology") died at the beginning of April, to no fanfare. Here's a lovely video of them reminiscing: www.youtube.com/watch?v=7-tn...
The Most Beautiful Experiment: Meselson and Stahl
YouTube video by Science Communication Lab
www.youtube.com
June 26, 2025 at 11:06 AM
The "most beautiful" but also the most intelligent experiment in biology.
Reposted by DEEMteam_Orsay
Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA
June 22, 2025 at 12:15 AM
Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA
🔗: doi.org/10.1016/j.ce...
#Genomics #Evolution #CellBiology #LECA