Sign in

Louis-Marie Bobay

@lbobay.bsky.social
263 followers 253 following 12 posts

Associate Professor. NC State. Microbial Genomics, Evolution, Bioinformatics.

PostsRepliesMedia
Reposted by Louis-Marie Bobay
Simonetta Gribaldo @sgribaldo.bsky.social · 23/09/2026
Interested in #archaea, #methane, #cell-envelopes? New paper out @nature.com ! We discovered an enzyme that specifically cleaves the cell wall of methanogens, revealing a new chemical structure of archaeal peptidoglycan, 50 yrs after its first description www.nature.com/articles/s41... #MicroSky 🧵👇
nature.com
1412374
Reposted by Louis-Marie Bobay
Ben Parker @ben-parker.bsky.social · 21/09/2026
Excited that our new paper with @henrylabsymbio.bsky.social and Kerry Oliver is out @pnas.org! We show that mobile genetic elements can spread adaptive host-benefiting traits across heritable insect symbionts on eco-evolutionary timescales.🧵 www.pnas.org/doi/10.1073/...
pnas.org
Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont | PNAS
Heritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont s...
29345
Reposted by Louis-Marie Bobay
David Bikard @dbikard.bsky.social · 21/09/2026
New paper from the lab, out in Nature Microbiology. We ran CRISPRi screens to ask what genes E. coli needs in order to live in a gut and what this can tell us about the gut environment itself. doi.org/10.1038/s41564-026-02471-8
311154
Reposted by Louis-Marie Bobay
Vaughn Cooper @vscooper.micropopbio.org · 20/09/2026
Now published from a fun collaboration, please see 🧵 academic.oup.com/ismecommun/a...
academic.oup.com
Mixed-species interactions constrain diversification and shape biofilm evolution
Abstract. Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Kle
03921
Reposted by Louis-Marie Bobay
Didier Mazel @amazeld.bsky.social · 18/09/2026
Dear all, I have the pleasure to inform you that the online course "Resistance to Antibacterial Agents", produced by the Institut Pasteur, will start on November 3, 2026. How does ABR emerge and spread? ... 🔗 www.fun-mooc.fr/en/courses/r...
fun-mooc.fr
Resistance to antibacterial agents
The origin, risks, diagnosis, epidemiology of resistance to antibacterial agents in man and livestock worldwide, as well as preventive and countermeasures, in a « one health » perspective.
12018
Reposted by Louis-Marie Bobay
Will Ratcliff @wcratcliff.bsky.social · 15/09/2026
1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...
310369
Reposted by Louis-Marie Bobay
Diversify Microbiology @diversifymicro.bsky.social · 11/09/2026
UNC Greensboro Department of Biology is hiring for three positions this year including one in microbiology! spartantalent.uncg.edu/postings/35918
spartantalent.uncg.edu
Assistant Professor Microbiology
The Department of Biology at UNC Greensboro (UNCG) seeks an individual with a strong record of accomplishment in microbiology broadly defined for a tenure-track faculty position at the rank of Assista...
05585
Reposted by Louis-Marie Bobay
Nancy Moran @nancy-moran.bsky.social · 24/08/2026
Insights into the role of a genotoxin in nature, through the lens of a honeybee gut. Colibactin stabilizes a symbiont community and keeps out invaders... Congratulations to Yulin Song and other authors! rdcu.be/fBIeq or (subscription) www.nature.com/articles/s41...
rdcu.be
14512
Reposted by Louis-Marie Bobay
Jesse Shapiro @bjesseshapiro.bsky.social · 24/08/2026
Now published in @asm.org mSystems! journals.asm.org/doi/10.1128/...
journals.asm.org
Species-specific prophage induction by ciprofloxacin in human gut metagenomes | mSystems
Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses ...
0248
Reposted by Louis-Marie Bobay
Cameron Thrash @jcamthrash.bsky.social · 13/07/2026
Characterizing the ecological niche of insertion sequences within prokaryotic genomes academic.oup.com/ismej/advanc... #jcampubs
academic.oup.com
Characterizing the ecological niche of insertion sequences within prokaryotic genomes
Abstract. Insertion sequences (ISs) are widespread prokaryotic transposable elements, often regarded as genomic parasites that primarily cause deleterious
03216
Reposted by Louis-Marie Bobay
Nancy Moran @nancy-moran.bsky.social · 02/07/2026
A step forward in discovering Buchnera's key to the aphid's heart, published today! Thanks to Jerry Maeda and other authors--a great team -- and to the helpful reviewers #SymbioSky doi: doi.org/10.1038/s415...
doi.org
A secreted endosymbiont protein essential for colonizing host cells - Nature
SyeA was present in the Buchnera ancestor, is secreted into the host cytoplasm, is homologous to secreted effectors of bacterial pathogens and is essential for Buchnera transmission.
210541
Reposted by Louis-Marie Bobay
Gavin Douglas @gmdouglas.bsky.social · 17/06/2026
Scott Gilbert made a useful critique of our preprint, which we have replied to: doi.org/10.32942/X2W...
doi.org
The holobiont is not a useful model for most host-microbiome interactions
041
Reposted by Louis-Marie Bobay
Benoit Nabholz @benoitevol.bsky.social · 15/06/2026
Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them academic.oup.com/gbe/article/...
academic.oup.com
A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi
0149
Reposted by Louis-Marie Bobay
Seema Sheth @seemasheth.bsky.social · 09/06/2026
Amy Angert and I are recruiting 2 temporary field technicians to assist with demographic surveys across the range of scarlet monkeyflower in California and Oregon. Perfect for recent graduates who are considering applying for grad school. Apply here: jobs.ncsu.edu/postings/231.... Please share!
jobs.ncsu.edu
Temporary Plant Ecology Field Technician - CA/OR
The Sheth evolutionary ecology lab in the Department of Plant and Microbial Biology at North Carolina State University (Raleigh, North Carolina; USA) and the Angert Lab in the Departments of Botany an...
02843
Reposted by Louis-Marie Bobay
Parul Johri @johriparul.bsky.social · 08/06/2026
We are actively searching for a postdoc to join the lab! Details provided here - johrilab.org/join Please share. I will be at PEQG and will be happy to chat if you're interested!
johrilab.org
Join | JohriLab
01818
Reposted by Louis-Marie Bobay
Claus Wilke @clauswilke.com · 08/06/2026
New paper about zero-shot predictions of mutational effects. There's a lot of misunderstanding about what such predictions can and cannot do. In brief, they're good at identifying deleterious mutations but bad at predicting fitness improvements. 1/ www.biorxiv.org/content/10.6...
biorxiv.org
Overestimating zero-shot fitness prediction: Broad benchmarks mask local failures and practical limitations
Deep learning models have emerged as promising tools for navigating mutational landscapes in protein engineering. These models can be used to predict mutation fitness without the need for task-specifi...
1158
Reposted by Louis-Marie Bobay
Parul Johri @johriparul.bsky.social · 04/06/2026
Our preprint, where we infer the fitness effects of new mutations in regulatory regions of the D. melanogaster genome. We find an abundance of weakly deleterious effects - www.biorxiv.org/content/10.6... Led by @adaigle.bsky.social .
biorxiv.org
0187
Reposted by Louis-Marie Bobay
Matthew Hahn @3rdreviewer.bsky.social · 02/06/2026
Very happy to announce a big new paper from the lab, led by grad students @smishra677.bsky.social and Laia Pomar-Pallarès (in collaboration with @roblanfear.bsky.social). We introduce a new way to study introgression, with accompanying software (DAFT) 1/n 🧵 www.biorxiv.org/content/10.6...
biorxiv.org
49467
Reposted by Louis-Marie Bobay
Dan Schrider @samurscicop.bsky.social · 31/05/2026
Andy Kern, who doesn't (really) have an account here, would like to share his group's new tool for speeding up pop gen summary stat calculations using GPUs. Check it out here: www.biorxiv.org/content/10.6... And see his thread over at the other place: x.com/pastramimach...
biorxiv.org
23914
Reposted by Louis-Marie Bobay
Gordon Bennett @symboevo.bsky.social · 29/05/2026
I’m excited to share a new paper out today led by Dr. Younghwan Kwak. Cool story on symbiont genomic variation within individual hosts. (And, also, just an impressive display of -omics skill). academic.oup.com/mbe/advance-...
academic.oup.com
Intrahost mutational dynamics parallel long-term genome evolution in endosymbionts
Abstract. Obligate endosymbionts of insects undergo extreme genome evolution, marked by accelerated molecular evolution, severe base-pair compositional bia
094
Reposted by Louis-Marie Bobay
Alex Wild @alexwild.bsky.social · 29/05/2026
If you would like the government to know what you think about their proposal to put federal science funding, communication, and travel under strict political control, you can tell them in the public comment section here: www.regulations.gov/commenton/OM...
14340
Reposted by Louis-Marie Bobay
Erol Akcay @akcay.theoretical.bio · 28/05/2026
Check out this exciting new paper in @currentbiology.bsky.social from my friend and collaborator @stephaniesimone.bsky.social’s lab on the genomics of novel rhizobium endosymbiosis www.cell.com/current-biol...
cell.com
The evolutionary genomics of novel endosymbiosis in wild rhizobia bacteria
Resolving early steps in how hosts and microbes unite in novel endosymbiosis is critical for understanding key evolutionary innovations and ecosystem functions. Montoya et al. reveal how mobile geneti...
23814
Reposted by Louis-Marie Bobay
ERGA - European Reference Genome Atlas @ergabiodiv.bsky.social · 27/05/2026
#ERGAReads | How Did Evolution Halve Genome Size During an Oceanic Island Colonization? 🏝️ 🧬 🕷️ academic.oup.com/mbe/article/... #genomes #evolution #islandevolution #biology @molbioevol.bsky.social @ub.edu @jrozasub.bsky.social
academic.oup.com
How Did Evolution Halve Genome Size During an Oceanic Island Colonization?
Abstract. Red devil spiders of the genus Dysdera colonized the Canary Islands and underwent an extraordinary diversification. Notably, their genomes are ne
0218
Louis-Marie Bobay @lbobay.bsky.social · 25/05/2026
Check out this very nice piece by @gmdouglas.bsky.social and S. Andrew Inkpen. ecoevorxiv.org/repository/v...
ecoevorxiv.org
The holobiont is not a useful model for most host-microbiome interactions
071
Reposted by Louis-Marie Bobay
Jonathan Eisen @phylogenomics.bsky.social · 25/05/2026
A very important preprint to check out: The holobiont is not a useful model for most host-microbiome interactions By Gavin M Douglas an S. Andrew Inkpen ecoevorxiv.org/repository/v...
ecoevorxiv.org
The holobiont is not a useful model for most host-microbiome interactions
26220
Reposted by Louis-Marie Bobay
Martin Polz @polzlab.bsky.social · 06/05/2026
Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...
nature.com
Genome-wide sweeps create ecological units in the human gut microbiome - Nature
Genome-wide selective sweeps commonly occur in the human gut microbiome and can spread across the world within decades to produce epidemic-like population structures.
28243
Reposted by Louis-Marie Bobay
Andrew Roger @andrewjroger.bsky.social · 06/05/2026
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
academic.oup.com
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
2210105
Reposted by Louis-Marie Bobay
Caiti Smukowski Heil @caitismuheil.bsky.social · 04/05/2026
Super excited to share our lab's work led by PhD student Margot Ruffieux on domestication of Saccharomyces cerevisiae, with a focus on sourdough and baking associated yeast! 🍞
biorxiv.org
12711
Reposted by Louis-Marie Bobay
Dan Schrider @samurscicop.bsky.social · 28/04/2026
Please circulate: I will have a postdoc opening soon, ideally with a start date sometime this summer or fall. If you're interested in empirical population genetics, computational methods development, and/or evolutionary modeling via simulation, don't hesitate to reach out. For more info on the lab:
12031
Reposted by Louis-Marie Bobay
Nature Biotechnology @natbiotech.nature.com · 16/04/2026
Diversity-generating retroelements for programmable targeted hypermutagenesis - @dbikard.bsky.social @institutpasteur.bsky.social go.nature.com/3OG2nKN
go.nature.com
Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology
Diversity-generating retroelements are engineered for directed evolution in E.coli.
084
Reposted by Louis-Marie Bobay
François Rousset @francoisrousset.bsky.social · 03/04/2026
Machine learning models by the Bernheim and Laub labs vastly expand the predicted space of bacterial immunity, demonstrating that we are still at the beginning of our exploration 🔎 Congrats @mdmlab.bsky.social and @pdeweirdt.bsky.social et al!
0183
Reposted by Louis-Marie Bobay
Nandita Garud @nanditagarud.bsky.social · 31/03/2026
I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)
27032
Reposted by Louis-Marie Bobay
Eduardo Rocha @epcrocha.bsky.social · 17/03/2026
Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky
ecoevorxiv.org
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
19042
Reposted by Louis-Marie Bobay
Gavin Douglas @gmdouglas.bsky.social · 16/03/2026
New preprint where @lbobay.bsky.social and I were motivated by the fact that non-synonymous substitutions are commonly analyzed in molecular evolution studies, but the similarity of the amino acids being substituted is an understudied area. doi.org/10.64898/202...
doi.org
173
Reposted by Louis-Marie Bobay
Claus Wilke @clauswilke.com · 11/03/2026
New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/ www.biorxiv.org/content/10.6...
biorxiv.org
617972
Reposted by Louis-Marie Bobay
Jorge Moura de Sousa @jmouradesousa.bsky.social · 02/03/2026
➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇
biorxiv.org
17747
Reposted by Louis-Marie Bobay
Manuel Kleiner @manuelkleiner.bsky.social · 15/02/2026
If you are interested in investigating horizontal gene transfer by phages and virus-like particles using computational approaches, this postdoc position in the Callahan Lab could be for you jobs.ncsu.edu/postings/226...
jobs.ncsu.edu
Postdoctoral Research Scholar
The Callahan Lab at NC State University (https://callahanlab.cvm.ncsu.edu/team/) is seeking a postdoctoral scholar to study the transfer of DNA between bacteria (horizontal gene transfer;HGT) by virus...
02418
Reposted by Louis-Marie Bobay
Nandita Garud @nanditagarud.bsky.social · 12/02/2026
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.
05796
Reposted by Louis-Marie Bobay
Genome Biology and Evolution @genomebiolevol.bsky.social · 11/02/2026
@carolinamicro.bsky.social Huang & @lbobay.bsky.social investigated genomic rearrangements across 121 microbial species, showing that rearrangements occur at a variable pace across bacteria and archaea, pointing to different selective constraints. 🔗 doi.org/10.1093/gbe/evag002 #genome #evolution
doi.org
Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria
Abstract. The genetic material of bacteria and archaea is organized into various structures and setups, attesting that genome architecture is dynamic in th
0189
Reposted by Louis-Marie Bobay
Jesse Shapiro @bjesseshapiro.bsky.social · 09/02/2026
Now out & nicely formatted in @isme-microbes.bsky.social A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron. A few highlights... 🧵 (1/n) doi.org/10.1093/isme...
doi.org
Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny
Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring
27938
Reposted by Louis-Marie Bobay
Kranzusch Lab @kranzuschlab.bsky.social · 06/02/2026
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity! www.nature.com/articles/s41...
nature.com
The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
37940
Reposted by Louis-Marie Bobay
Gavin Conant @gavin-conant.bsky.social · 29/01/2026
My book is available for pre-order! www.routledge.com/Quantitative... Or you can request an inspection copy here: www.routledge.com/textbooks/ev...
011
Reposted by Louis-Marie Bobay
David Bikard @dbikard.bsky.social · 28/01/2026
🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...
research.pasteur.fr
Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research
The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...
07481
Louis-Marie Bobay @lbobay.bsky.social · 27/01/2026
Congrats to @carolinamicro.bsky.social for leading this study! We looked at genome rearrangements over short evolutionary timescales. Among other things, we found that genomes are highly syntenic within most species. However, several bacteria experienced sudden and massive genome rearrangements.
0145
Reposted by Louis-Marie Bobay
Segata Lab @cibiocm.bsky.social · 21/01/2026
🥁 NEW Our study on infant gut microbiome and #straintransmission is now published in @nature.com: doi.org/10.1038/s415... 1/10
doi.org
Baby-to-baby strain transmission shapes the developing gut microbiome - Nature
A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...
25934
Reposted by Louis-Marie Bobay
Gordon Bennett @symboevo.bsky.social · 09/01/2026
I’m excited to share a new paper by a super talented graduate-student-now-postdoc. Grateful to work with old and new collaborators! Characterizing a novel Symbiopectobacterium MEX strain at the early stages of establishing a symbiotic relationship url: academic.oup.com/gbe/article/...
academic.oup.com
Characterizing a novel Symbiopectobacterium purcellii MEX strain at the early stages of establishing a symbiotic relationship
Abstract. Insects ally with microbial symbionts for a diversity of services. The range of these interactions is wide, spanning from beneficial to pathogeni
1104
Reposted by Louis-Marie Bobay
David Bikard @dbikard.bsky.social · 19/01/2026
Deadline is approaching (Feb 9) to apply for a PI position at Institut Pasteur. Come join us and contribute to an amazing scientific environment!!!
11831
Reposted by Louis-Marie Bobay
Didier Mazel @amazeld.bsky.social · 18/01/2026
a quick reminder!
01511
Reposted by Louis-Marie Bobay
Xavier Charpentier @labxc.bsky.social · 13/01/2026
Une opportunité unique de former des étudiants talentueux à la biologie des bactéries à l'ENS Lyon et mener des recherches sur les phages, l'immunité bactérienne, le transfert génétique horizontal (HGT) et/ou les éléments génétiques mobiles au sein du département de bactériologie du CIRI.
0814
Reposted by Louis-Marie Bobay
Olivier Borkowski @oborkowski.bsky.social · 08/01/2026
Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change doi.org/10.64898/202...
11412