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Loïs Maignien, PhD.

@loimai.bsky.social
172 followers 325 following 15 posts

PI Microbial Ecogenomics Group at Brest Univ. 🇫🇷 maignienlab.github.io

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Reposted by Loïs Maignien, PhD.
Thomas Mock @thomasmock.bsky.social · 28/07/2026
Our new MSCA-Doctoral Network project ML4Plankton will kick off soon. 14 PhD students will start in March 2027 to work on plankton big data, i.e., machine learning. Get in touch if you are interested. Coordinator: Sakina-Dorothée Ayata @norwichmicro.bsky.social www.normalesup.org/~ayata/DN_ML...
normalesup.org
ML4Plankton Doctoral Network
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Reposted by Loïs Maignien, PhD.
Pierre Peterlongo @pierrepeterlongo.bsky.social · 03/06/2026
🌎 🧬 🖥️ logan-search.org the tool to query all SRA sequences (Dec 2023 snapshot) — just got major updates. Here's what's new. 🧵 1/12
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Dr Emma Hodcroft @firefoxx66.bsky.social · 10/05/2026
My ANDV #Hantavirus @nextstrain.org phylogenies now pull directly from @pathoplexus.org to incorporate all seqs I'll continue to improve them, & will keep them updated Change the Tip Labels in the left-hand menu. You can see links to all builds, plus tanglegrams at: nextstrain.org/groups/hodcr...
A phylogenetic tree showing linked sequences from the S and L segment of ANDV virus (Andes Hantavirus)
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Gaëtan Benoit @gaetanbenoit.bsky.social · 20/04/2026
I was investigating the genomes that I didn't manage to convert to near-complete MAGs in my assembly graph (the components in gray). The circle on top left is actually a complete genome but with 40% completeness (both in metaMDBG and myloasm)
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Reposted by Loïs Maignien, PhD.
ace-gtdb.bsky.social @ace-gtdb.bsky.social · 15/04/2026
GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.
gtdb.ecogenomic.org
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
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Loïs Maignien, PhD. @loimai.bsky.social · 10/04/2026
www.nature.com/articles/s41...
nature.com
Advancing microbiology through foundational science - Nature Microbiology
Microorganisms have tremendous potential to impact humanity, but such revelations are only possible in the light of foundational, discovery-based microbiology research.
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Reposted by Loïs Maignien, PhD.
Steven Salzberg @stevensalzberg.bsky.social · 30/03/2026
In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...
stevensalzberg.substack.com
AI is starting to look like pseudoscience
Not all of it, but some scientists are too eager to believe their own hype
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Loïs Maignien, PhD. @loimai.bsky.social · 29/03/2026
www.lemonde.fr/planete/arti...
lemonde.fr
Des pôles aux abysses, les nouveaux explorateurs scientifiques font rêver mais irritent le monde de la recherche
Les expéditions mêlant aventure, sport et recherche se multiplient dans les zones extrêmes du globe. Très médiatisées, elles suscitent pourtant des réserves chez les chercheurs académiques, qui dénonc...
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Reposted by Loïs Maignien, PhD.
Nature Communications @natcomms.nature.com · 28/03/2026
Researchers Uncover Hidden Genetic World in Antarctic Waters "at least a third of the genes identified are missing from existing marine gene catalogs" @loimai.bsky.social #microbiome #oceans
dlvr.it
Researchers Uncover Hidden Genetic World in Antarctic Waters
The discovery of vast numbers of previously unknown microbial genes in Antarctic waters could improve understanding of how the ocean shapes Earth’s climate.
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Reposted by Loïs Maignien, PhD.
Mike Jetten @msmjetten.bsky.social · 21/03/2026
Exciting new methane research: Huge credit to @annajwallenius.bsky.social & Andy Leu for using nifty bioinformatics to disentangle 8 novel MAGs of 'Candidatus Methanoborealis' This is version 1 of our #bioRxiv preprint. Aanalysis is ongoing & we welcome your feedback! doi.org/10.64898/202...
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DEEMteam_Orsay @deemteam.bsky.social · 17/03/2026
Living patescibacterial (CPR) cells are a rare sight! Meet Strigamonas methylophilicida, a parasite of methylotrophic proteobacteria we just described in our latest paper: doi.org/10.1128/mbio...
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Lukas VF Novak @animalculum.bsky.social · 02/03/2026
New paper from my 2nd PostDoc is now published in The ISME Journal by @isme-microbes.bsky.social! #Sulfur disproportionation occurs globally across anoxic habitats & has multiple mechanisms of independent evolutionary origin academic.oup.com/ismej/advanc... #Bacteria #Microbes #Evolution #DeepSea
a figure from the linked paper which shows A) a world map and B) a schematic representation of various natural and artificial habitats, both annotated with information about which sulfur disproportionating bacteria have been found in the specific regions and environments
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James McInerney @jomcinerney.bsky.social · 11/03/2026
I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...
academic.oup.com
Genomic perplexity and the evolution of context-dependent function
Abstract. The fundamental principle that selection acts on a gene's function often assumes implicitly that this function is fixed and intrinsic. However, e
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Loïs Maignien, PhD. @loimai.bsky.social · 11/03/2026
Hello Ian, linking 'omics observations to ocean biogeochem is our grand challenge for all of us... Not there yet, but several smart ideas worth following: www.science.org/doi/full/10.... or www.primoscorwg.org Happy to talk more about the article data implications...
science.org
Unveiling the link between phytoplankton molecular physiology and biogeochemical cycling via genome-scale modeling
A genome-enabled ESM built on genomic data assesses physiological acclimation and biogeochemical effects through nutrient stress.
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
Since you arrived here, I want to share this: this article is a gem to me because this project could have failed at so many crossroads. Only with the contribution and trust of brilliant authors and friends could this happen! That what it takes ...10/10
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
Finally, this work brings a wealth of genomic data (218 metagenomes) associated with 50 environmental variables that will help putting the Southern Ocean at the center of the map… Code and data in the paper! More to come from visionary research programs like this one www.antarctica-insync.org 7/n
antarctica-insync.org
Antarctica InSync - Antarctica International Science & Infrastructure for Synchronous Observation - Antarctica Insync
Antarctica InSync Antarctica International Science & Infrastructure for Synchronous Observation Antarctica InSync is a global effort to synchronise research across Antarctica and the Southern Ocean, c...
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
DMSP lyase is one of the plankton functions that is most linked to environmental variations, suggesting a central role of sulfur compounds in this polar environment... 8/n
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
This microscopic world is structured by water mass, illustrating how ocean circulation controls marine life. Some ubiquitous bacteria (SAR11) adapt their genetic repertoires to thrive in all latitudes. 7/n
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
After a long bioinformatics journey, we found that about 1/3 of the plankton genes were never observed in any other ocean: this biome is unique! …6/n
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
To fill this important gap, we embarked on a fantastic Antarctic Circumnavigation Expedition to sample the different regions of the Southern Ocean and study plankton DNA. Take a deep dive in the Roaring Forties and the Furious Fifties with us: www.youtube.com/watch?v=lZkt... …5/n
youtube.com
Coup de chaud sur l'Antarctique ! Thalassa
YouTube video by Thalassa - France Télévisions
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
Due to low accessibility, we miss data and observations to understand and predict its evolution. Until recently, an extensive plankton genomic diversity survey of this ocean was still missing from global ocean data rdcu.be/e7Nep ...4/n
rdcu.be
Biosynthetic potential of the global ocean microbiome
Nature - Global ocean microbiome survey reveals the bacterial family ‘Candidatus Eudoremicrobiaceae’, which includes some of the most biosynthetically diverse microorganisms in the...
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
It is a fragile ecosystem with unique diversity of life and ecosystems and is the cradle of deep-water masses that feed the world’s Oceans. Now, the Southern Ocean seems to undergo abrupt changes, mostly visible in the last decade from strong sea ice cover anomalies. rdcu.be/e7M9R ... 3/n
rdcu.be
Emerging evidence of abrupt changes in the Antarctic environment
Nature - Abrupt changes are developing across Antarctica’s ice, ocean and biological systems; some of these changes are intensifying faster than equivalent Arctic changes, potentially...
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
It is rarely seen on a world map. Yet, the Southern Ocean is central for the functioning of our planet! It absorbs CO2 and heat like no other with respect to its surface. Let’s take a different view: rdcu.be/e7Nbh ... 2/n
rdcu.be
Carbon storage shifts around Antarctica
Nature Communications - Dense water production in the seas around Antarctica is a key process for century-scale carbon storage, slowing global warming. Results from an advanced new model reveal the...
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Loïs Maignien, PhD. @loimai.bsky.social · 10/03/2026
Very happy to share the latest paper of our group (et al.)! rdcu.be/e7zyX . This one has a special place… 1/n
rdcu.be
Water mass specific genes dominate the Southern Ocean microbiome
Nature Communications - Southern Ocean microbial communities are less well studied. Here, the authors generate a circumpolar-scale gene catalog from 218 metagenomics samples revealing broadscale...
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Loïs Maignien, PhD. @loimai.bsky.social · 16/02/2026
Interested in developing your skills in microbial 'omics? Consider joining us in Brest 🇫🇷, Oct. 10-24 for two weeks of intensive lectures an tutorial from top faculties and TA! maignienlab.gitlab.io/ebame/ Bonus: beautiful seascape and friendly spirit!
maignienlab.gitlab.io
EBAME workshop
EBAME - Computational Microbial Ecogenomics Workshop
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Reposted by Loïs Maignien, PhD.
Scientific Committee on Antarctic Research (SCAR) @scar-antarctic.bsky.social · 14/01/2026
Antarctica InSync will host two webinars, bringing together the science community to discuss the draft White Papers currently available on our website. · 20 January, 17:00–19:00 (CET) · 21 January, 09:00–11:00 (CET) 📌 Register: lnkd.in/epX4_JiA 📝 Provide input to the draft papers: lnkd.in/eYfJgTUV
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Reposted by Loïs Maignien, PhD.
Florian Trigodet @floriantrigodet.bsky.social · 06/01/2026
Now published in Nature Biotechnology: go.nature.com/44P7nSm If you missed it, the TL;DR is in my April thread below
go.nature.com
Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology
Long-read sequence assemblies from metagenomes contain frequent errors.
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Reposted by Loïs Maignien, PhD.
Australian Antarctic Program Partnership @antarctic.bsky.social · 11/12/2025
1/ The overturning circulation is a network of ocean currents transporting heat, carbon, oxygen and nutrients around the world. At the heart of this circulatory system is the global pumphouse of #Antarctica and the Southern Ocean. Animation: NASA-SVS
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Reposted by Loïs Maignien, PhD.
Evelien Adriaenssens @evelienadri.bsky.social · 11/12/2025
I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes. Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero link.springer.com/protocol/10....
link.springer.com
Virome Analysis
Viruses are omnipresent and the most abundant biological entities on the planet. They play a critical role in shaping the ecology and evolution of all life forms. This chapter provides methods to perf...
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Reposted by Loïs Maignien, PhD.
Sofia Medvedeva @sonaida.bsky.social · 28/11/2025
www.nature.com/articles/s41... Thrilled to share our new study! We show that mirusviruses include lineages packed with spliceosomal introns and likely replicating in the nucleus of unicellular eukaryotes—a sharp contrast to most large and giant eukaryotic viruses that replicate in the cytoplasm.
nature.com
Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
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Reposted by Loïs Maignien, PhD.
Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 26/11/2025
Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea
media.tenor.com
a man walking in a field with an umbrella
ALT: a man walking in a field with an umbrella
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Reposted by Loïs Maignien, PhD.
Christian Kost @kostchristian.bsky.social · 27/11/2025
I am very excited to announce that a fully funded PhD position is available in my group. Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia Please RT or forward this information to interested candidates. Deadline: 11.01.26 More info: shorturl.at/f1TuF
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GEOTRACES @geotraces.bsky.social · 27/11/2025
New GEOTRACES Science Highlight! 🌊 Long-range transport of iron via the #Agulhas Current and counter-current: a boon for the phytoplankton www.geotraces.org/long-range-t... Paper first authors: Eva Bucciarelli & Pierrick Penven, LEMAR #oceanscience #traceelements @scor-int.bsky.social
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Amy D Willis @amydwillis.bsky.social · 06/05/2025
Please, #microbiome and #sequencing data are NOT zero-inflated. Let's stop repeating this nonsense. Zero-inflated compared to what?? Those zeroes carry important information about abundance and sequencing depth, and are not "inflated" in any sense. 1/6
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Michael Brockhurst @brockhurstlab.bsky.social · 29/04/2025
This meeting will be great! Abstract submission open now See you 26-27 Nov in Liverpool microbiologysociety.org/event/societ...
microbiologysociety.org
Understanding and predicting microbial evolutionary dynamics - 2025 meeting
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Jesse Shapiro @bjesseshapiro.bsky.social · 24/04/2025
Come join us at @mcgill.ca as an assistant professor in virus-host interactions! Please share widely. mcgill.wd3.myworkdayjobs.com/en-US/McGill...
mcgill.wd3.myworkdayjobs.com
Assistant Professor (Research), Department of Microbiology & Immunology, (C2-240724)
Please refer to the How to Apply for a Job (for External Candidates) job aid for instructions on how to apply. If you are an active McGill employee (ie: currently in an active contract or position at ...
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Loïs Maignien, PhD. @loimai.bsky.social · 10/04/2025
#EBAME 10 Microbial Ecogenomics Workshop! Brest🇫🇷, Oct 11-25, 2025. A two-week workshop of lectures & tutorials to learn about omics data analysis for microbial ecology and evolution, all in the beautiful Brest Bay! Apply here until June 1: maignienlab.gitlab.io/ebame
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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024
🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience
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