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deemteam.bsky.social
DEEMteam_Orsay
@deemteam.bsky.social
990 followers 220 following 89 posts

Diversity, Ecology and Evolution of Microbes (DEEM) team. Posts by David Moreira. #treeoflife #evolution
Paris, France
https://www.deemteam.fr/en/

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Biology 37%
Environmental science 34%
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Reposted by David Moreira

natmicrobiol.nature.com
Nature Microbiology @natmicrobiol.nature.com · 7d
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...

Reposted by David Moreira

genomebiolevol.bsky.social
Genome Biology and Evolution @genomebiolevol.bsky.social · 7d
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
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

Reposted by Mart Krupovìč, Maria Faticov

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · 8d
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

Reposted by George A. O’Toole, David Moreira, Nicole Dubilier

asm.org
ASM @asm.org · 12d
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

Reposted by David Moreira

waynemaddison.bsky.social
Wayne Maddison @waynemaddison.bsky.social · 17d
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
Mesquite's two icons, one against a black background, and one against a sun on a sky blue background.

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · 17d
Maybe because it is a private organization. Have you tried DSMZ, CCAP, etc.? (depending on what you are looking for)

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · 18d
Congrats!

Reposted by Simon Roux, David Moreira

ace-gtdb.bsky.social
ace-gtdb.bsky.social @ace-gtdb.bsky.social · 20d
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-...
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

Reposted by Mart Krupovìč, David Moreira

natmicrobiol.nature.com
Nature Microbiology @natmicrobiol.nature.com · 21d
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...
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

Reposted by David Moreira

mkrupovic.bsky.social
Mart Krupovic @mkrupovic.bsky.social · 22d
A nice N&V article by Mike Dyall-Smith on our recent paper
( 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

Reposted by Simon Roux, David Moreira

mkrupovic.bsky.social
Mart Krupovic @mkrupovic.bsky.social · 25d
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 👇

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · 27d
Congrats!

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · 29d
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...

Reposted by David Moreira

molbioevol.bsky.social
Molecular Biology and Evolution @molbioevol.bsky.social · Sep 8
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
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

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Aug 31
Enjoying the mountains that forams built for us (with some help from plate tectonics) long ago.

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Aug 26
Thank you very much for teaching her this amazing technique!

Reposted by David Moreira

kristina-prokina.bsky.social
Kristina Prokina @kristina-prokina.bsky.social · Aug 26
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....

Reposted by Simon Roux, David Moreira, Jason Stajich

biocs.bsky.social
Michael Kuhn @biocs.bsky.social · Aug 15
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
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Aug 14
Congratulations!

Reposted by David Moreira

andrewjroger.bsky.social
Andrew Roger @andrewjroger.bsky.social · Aug 12
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...
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

Reposted by Simon Roux

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Aug 7
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....

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Aug 4
Gloeomargarita lithophora, it has many interesting metabolic and evolutionary stories to tell.

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Jul 27
This could have been avoided if Science had requested a second round of reviews when the deluge of criticisms arrived following the paper’s pre-publication. Publishing it along with all the criticisms, and then retracting it now -and only this paper- after so many years, seems odd.

Reposted by David Moreira

matthewcobb.bsky.social
Matthew Cobb @matthewcobb.bsky.social · Jun 26
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

Reposted by Jonathan A. Eisen, Simon Roux, David Moreira , and 1 more

benjwoodcroft.bsky.social
Ben J Woodcroft @benjwoodcroft.bsky.social · Jul 16
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 🧵
Logo for the Sandpiper website

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Jul 23
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/...

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Jul 23
🚨 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/...
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

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Jul 15
Some ceramic protists from our talented friend Anabel López-Archilla. Do you recognize them?

Reposted by David Moreira

univparissaclay.bsky.social
Université Paris-Saclay @univparissaclay.bsky.social · Jul 10
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

deemteam.bsky.social
DEEMteam_Orsay @deemteam.bsky.social · Jul 9
Joachim Hämmerling experiments in the 50’s using giant unicellular algae (Acetabularia) to demonstrate that the genetic information is contained in the nucleus.

www.sciencedirect.com/science/arti...
Nucleo-cytoplasmic Relationships in the Development of Acetabularia
The Acetabulariae are green marine algae of subtropical and tropical waters (class Siphonocladales, family Dasycladaceae, subfamily Acetabulariae). Th…
www.sciencedirect.com