Sign in

Benjamin Guinet

@benjaminguinet.bsky.social
208 followers 229 following 29 posts

Postdoctoral researcher at Helmholtz Institute for One Health | Interested in the evolution of microbes-host interactions across time. Paleovirology, metagenomic, evolutionary genomics 🧬🦣 🐄 🐝🦠

PostsRepliesMedia
Reposted by Benjamin Guinet
Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 27/06/2026
#gbdraw v0.12.1 is now live with a massive update! Powerful new features are now available in your local environment: ​You can now generate circular comparisons (homology rings) and interactive SVG files directly on your machine 🧬 #bioinformatics #genomics
2104
Benjamin Guinet @benjaminguinet.bsky.social · 22/06/2026
www.lemonde.fr/sciences/art...
lemonde.fr
La recherche française déstabilisée par une crise multiforme
Affaiblissement financier et humain, montée des attaques idéologiques, émergence de l’intelligence artificielle… La communauté scientifique est confrontée à de nombreux défis, à l’image du CNRS, victi...
000
Reposted by Benjamin Guinet
Felix M Key @keyfm.bsky.social · 18/06/2026
Wrote a short piece about the opportunities and challenges of pushing ancient pathogen genomics into a new frontier: the zooarchaeological record. Pretty excited about what is going to come. www.science.org/eprint/MSG3Z...
science.org
Tracking the roots of zoonoses
Ancient pathogen DNA from animals elucidates the origin and evolution of infectious diseases
13314
Reposted by Benjamin Guinet
Mahan Ghafari @mghafari.bsky.social · 21/05/2026
Our two-part analysis of the current MV Hondius Andes virus outbreak is now live, including reconstruction of the outbreak molecular clock dating of the closest known ancestors of the outbreak lineage. Part 1: outbreak sequence reconstruction and rooting virological.org/t/molecular-...
virological.org
Molecular evolutionary analysis of the current MV Hondius Andes virus outbreak
Preliminary reconstruction of the current MV Hondius Andes virus outbreak sequences Note on data use This is an informal analysis of currently available consensus sequences and is not intended as a fo...
12113
Reposted by Benjamin Guinet
Ernst Johnson @officialernst.bsky.social · 08/05/2026
The biggest challenge during my PhD within sedimentary ancient DNA was to figure out how to bioinformatically process several hundreds of sequenced samples. This workflow is optimised for identification of eukaryotes from metagenomic shotgun data. Let me introduce the preprint of metaJAM! 1/6
1124
Benjamin Guinet @benjaminguinet.bsky.social · 27/04/2026
Measles Is Back. What Comes Next Will Be Worse. www.nytimes.com/2026/04/25/o...
nytimes.com
Opinion | Measles Is Back. What Comes Next Will Be Worse.
010
Reposted by Benjamin Guinet
Ernst Johnson @officialernst.bsky.social · 14/04/2026
Very excited to share our study of an ancient environmental genome extracted from lake sediment! It originates from a brown bear that lived around 9,600 years ago close to the last ice-sheet remains in northern Sweden, and has an unexpected mitochondrial haplogroup. 1/7 www.pnas.org/doi/10.1073/...
pnas.org
Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia | PNAS
After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two direc...
15225
Reposted by Benjamin Guinet
Rosemonde Power @rosepower.bsky.social · 21/01/2026
🔔 New paper from the Vet Para lab @sydney.edu.au 🪱 In @commsbio.nature.com, our global analyses of 100+ heartworm genomes uncover the unexpected evolutionary history and population structure of this canine parasite 🧬🌏 Read the full paper here: doi.org/10.1038/s420... Key findings in the 🧵 below 👇
doi.org
Population genomics reveals an ancient origin of heartworms in canids - Communications Biology
Genomic analyses of heartworms from multiple continents suggest a deeper evolutionary origin in canids than previously recognised, with evidence of both ancient dispersal events and more recent introd...
195
Reposted by Benjamin Guinet
Daniel Blanco-Melo @dbm003.bsky.social · 31/01/2026
Excited to share our work on #AncientRNA from alcohol-preserved lungs, recovering the oldest human RNA virus genome (an 18th-century rhinovirus). Our study shows that viral RNA remnants persist in centuries-old tissue, opening new ways to study virus evolution and historical disease #Paleovirology🫁🦠
biorxiv.org
27221
Reposted by Benjamin Guinet
Katharina Hoff @katharinahoff.bsky.social · 19/12/2025
My dear colleagues @tjorven-hinzke.bsky.social and others put together a cool manuscript on viruses in ancient penguin mummies. Pleasure to have been involved! doi.org/10.64898/202...
doi.org
RNA virus genomes from centuries- to millennia-old Adelie penguin mummies
Direct studies of long-term RNA virus evolution are largely limited to chemically-fixed specimens from natural history and pathology museums collected over the past two centuries. Detecting genomic tr...
052
Reposted by Benjamin Guinet
Aris Katzourakis @ariskatzourakis.bsky.social · 15/09/2025
Termite genomes shed light on the enigmatic deltaviruses, their ancient origins, and an intriguing example of co-option of viral genes by a host. www.cell.com/cell-reports...
cell.com
Endogenous viral elements in termite genomes reveal extensive diversity of deltaviruses and provide insights into their origins
Barreat et al. describe the discovery of deltavirus genomic fossils (ẟEVEs) in multiple species of termites. The wide expression of ẟEVEs in termites and a host gene fusion indicate that some ẟEVEs ma...
02811
Reposted by Benjamin Guinet
CNRS @cnrs.fr · 09/09/2025
To rehabilitate the general view of women's contributions to the history of science, the CNRS is part of a commission that aims to inscribe the names of 72 female scientists on the Eiffel Tower. 🗼 #WomenInScience
cnrs.fr
Women scientists to be showcased on the Eiffel Tower soon
To rehabilitate the general view of women's contributions to the history of science, the CNRS is part of a commission that aims to inscribe
0359
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
🔚 Together, these findings pave the way for exploring the microbiota of extinct species and offer deeper insights into the dynamics of their microbial ecosystems, contributing to a broader understanding of the biology of species that are no longer with us. #Mammoths #aDNA #Paleomicrobiology #Cell
Mammoth tusk (photo by Love Dalén)
040
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
⑧ 𝐖𝐡𝐚𝐭 𝐢𝐭 𝐭𝐞𝐥𝐥𝐬 𝐮𝐬 𝐚𝐛𝐨𝐮𝐭 𝐦𝐚𝐦𝐦𝐨𝐭𝐡 𝐡𝐞𝐚𝐥𝐭𝐡 Most microbes were harmless commensals, but some were related to modern pathogens. Although mammoths were likely exposed to infections, there is no evidence so far that diseases caused their extinction.
120
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
⑦ An 𝘌𝘳𝘺𝘴𝘪𝘱𝘦𝘭𝘰𝘵𝘩𝘳𝘪𝘹 species was recovered from a tooth of a Steppe mammoth that lived 1.1 million years ago in Adycha, Russia. This finding provides a unique opportunity to study how bacterial DNA can be preserved over such vast timescales, dating all the way back to the Early Pleistocene.
 Mammuthus trogontherii. (Creator:Dmitry Bogdanov)
110
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
⑥ A bacterium linked to an African elephant pathogen 𝘗𝘢𝘴𝘵𝘦𝘶𝘳𝘦𝘭𝘭𝘢 → closely related to the strain behind fatal septicemia in Zimbabwe elephants (2020). It may have caused similar disease in mammoths, even if this cannot be established with certainty.
120
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
⑤ 𝐂𝐨𝐦𝐦𝐞𝐧𝐬𝐚𝐥 𝐛𝐚𝐜𝐭𝐞𝐫𝐢𝐚 𝐢𝐬𝐨𝐥𝐚𝐭𝐞𝐝 𝐟𝐫𝐨𝐦 🦷 • 𝘚𝘵𝘳𝘦𝘱𝘵𝘰𝘤𝘰𝘤𝘤𝘶𝘴 → oral microbe related to modern strains causing cavities in many other animals 🪥 • 𝘈𝘤𝘵𝘪𝘯𝘰𝘣𝘢𝘤𝘪𝘭𝘭𝘶𝘴 → probably from an oral bacteria found in 9 woolly mammoths, showing lineage continuity from the Late Pleistocene to Wrangel Island extinction ⌛
Mammoth tooth (photo by Peter Mortensen)
110
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
③ 𝐇𝐨𝐰 𝐰𝐞 𝐝𝐢𝐝 𝐢𝐭? • Compared sequences with soil and lab contaminants • Checked for signs of ancient DNA degradation • Used phylogeny to trace evolutionary relationships compared to other animal bacteria. This let us focus on microbes truly associated with living mammoths. What did we found ? ⬇️
110
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
② 𝐓𝐡𝐞 𝐦𝐚𝐢𝐧 𝐜𝐡𝐚𝐥𝐥𝐞𝐧𝐠𝐞 Most bacteria found on ancient remains are 𝘱𝘰𝘴𝘵-𝘮𝘰𝘳𝘵𝘦𝘮 contaminants, originating either from the surrounding environment where mammoth were excavated or from laboratory contamination. Our goal was to identify the microbes that truly inhabited the mammoths during their lifetime.
110
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
① 𝐖𝐡𝐚𝐭 𝐰𝐞 𝐝𝐢𝐝? We analyzed 483 mammoth specimens from North America and Britain to Siberia, and date from the Early Pleistocene — around one million years ago — to the extinction of the last mammoths on Wrangel Island (a remote island off the coast of Siberia) during the Holocene, 4,000 years ago.
110
Benjamin Guinet @benjaminguinet.bsky.social · 03/09/2025
🧵 Exciting news from our lab #CpgSthlm! 🥳 Thousands of years ago, mammoths roamed, and so did their fascinating microbial companions. Our latest study, published in 𝘊𝘦𝘭𝘭, brings them to light 🦣🦠🧬 Read the full paper here 👉 doi.org/10.1016/j.ce...
Mammoth tusk emerging from the permafrost on Wrangel Island (Siberia) in 2017 (photo by Love Dalén)
24516
Benjamin Guinet @benjaminguinet.bsky.social · 21/08/2025
Please share this Global South survey 🙏 #ESEB2025
021
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
Sources : - www.microbiologyresearch.org/content/jour... - academic.oup.com/ve/article/1... - www.science.org/doi/10.1126/... - elifesciences.org/articles/85993 - royalsocietypublishing.org/doi/full/10....
elifesciences.org
Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
The propensity to endogenize and domesticate dsDNA viruses depends on lifestyle in Hymenoptera.
000
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
𝐂𝐨𝐧𝐜𝐥𝐮𝐬𝐢𝐨𝐧 : Pretty fascinating, isn’t it? This kind of viral domestication has evolved multiple times, independently, across different wasp lineages and viral families. As more genomes get sequenced, we’re likely just scratching the surface. Who knows what other viral hitchhikers we’ll find next?
100
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
7) Yes, I said domesticated! After viral DNA accidentally integrates into the host genome, it can sometimes be co-opted to boost the host’s survival. In wasps, this means using viral genes to produce virus-like particles injected with the egg, helping suppress the host insect’s immune system.
110
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
6) This virus–wasp relationship isn’t new, it’s been going on for millions of years. Over such long timescales viral DNA can accidentally integrate the wasp’s genome. This is not rare, take mammals for instance, part of the placenta is the result of a retrovirus domesticated gene (𝘴𝘺𝘯𝘤𝘪𝘵𝘪𝘯).
110
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
5) In this red queen race, some wasps have fought back too, evolving ways to shut down the host’s immune response and protect their eggs. That’s where the 𝘍𝘪𝘭𝘢𝘮𝘦𝘯𝘵𝘰𝘷𝘪𝘳𝘶𝘴𝘦𝘴 come in, but not into their free-living forms.
100
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
4) To understand this, let’s zoom in on the wasp’s lifestyle. For the unlucky host insect, getting injected with wasp eggs is a death sentence, unless its immune system fights back. Over time, insects have evolved smart defenses, like encapsulating the eggs to block and kill them before they hatch.
100
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
3) However, this comes at a cost to the wasp: her egg now has to compete with others inside the same host. This is a situation they usually avoid by carefully probing their prey first. Nevertheless, these spaghetti-shaped viruses (see TEM image) also confer some mutual benefits on the wasp.
100
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
2) These DNA viruses have co-evolved with parasitoid wasps for millions of years, and they’ve learned a clever trick. They manipulate the behavior of infected female wasps to lay their eggs in hosts that are already infected with egg, increasing the chances for the virus to spread in the population.
110
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
1) Parasitoid wasps live a brutal life: they lay eggs inside other insects, and the larvae eat their hosts from the inside out. Think Alien, but real, and with bugs.
100
Benjamin Guinet @benjaminguinet.bsky.social · 28/07/2025
The viral family 𝘍𝘪𝘭𝘢𝘮𝘦𝘯𝘵𝘰𝘷𝘪𝘳𝘪𝘥𝘢𝘦 is now officially recognized by the ICTV! A perfect excuse to dive into their bizarre and fascinating partnership with parasitoid wasps, a story of evolution, genetic hijacking, insect horror and behavior manipulation. www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Animal DNA Viruses and Retroviruses Subcommittee, 2025
The International Committee on Taxonomy of Viruses (ICTV) holds a ratification vote annually after review of newly proposed taxa by ICTV Study Groups and members of the virology community. In March 20...
120
Benjamin Guinet @benjaminguinet.bsky.social · 21/07/2025
4) In contrast, damage intensity is driven by how genetically distant the reference genome is from the reads. This makes comparing damage curves between hosts and past symbionts or other microbes much trickier and needs to be taken into account by looking at the reference genome divergence distance.
010
Benjamin Guinet @benjaminguinet.bsky.social · 21/07/2025
3) This is partly because fewer reads map to distant references, but we show that this mostly affects the stochasticity (variability) of damage patterns.
110
Benjamin Guinet @benjaminguinet.bsky.social · 21/07/2025
2) In that context, when mapping aDNA reads to distant available reference genomes, we show that sequence divergence may obscure such C-to-T damage signals.
110
Benjamin Guinet @benjaminguinet.bsky.social · 21/07/2025
1) Microbial genomic databases often lack comprehensive representation, reducing the likelihood of having access to a closely related reference genome for many ancient microbial taxa.
110
Benjamin Guinet @benjaminguinet.bsky.social · 21/07/2025
New preprint 🎉! We explore the reliability of ancient DNA authentication, particularly cytosine deamination at fragment ends in metagenomic context. You can find the full results in our preprint: www.biorxiv.org/content/10.1...
biorxiv.org
The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts
The reliability of ancient DNA (aDNA) authentication depends on detecting characteristic damage patterns, particularly cytosine deamination at fragment ends. However, in ancient metagenomic studies, s...
141
Reposted by Benjamin Guinet
ICP2026 Stockholm @palaeogenomics.bsky.social · 27/05/2025
The FIRST International Conference on Palaeogenomics will happen in Stockholm, Sweden, June 23-26, 2026! Topics will encompass all corners of ancient DNA research, from humans to wildlife and sediments🧬🦣💀🦠 Save the dates ✅ Check the website icp2026.palaeogenomics.org and follow us for updates!
08149
Reposted by Benjamin Guinet
Centre for Palaeogenetics @cpgsthlm.bsky.social · 30/04/2025
NOBEL SYMPOSIA We are delighted to announce two exciting public talks on Ancient DNA at Aula Magna (Stockholm University) on May 30th, 10:00-12:30h. 🦣⬅️ ”Can we bring back the woolly mammoth?” by Beth Shapiro. 🐎✋”The taming of the horse” by Ludovic Orlando. Free entrance. All welcome!
12519
Benjamin Guinet @benjaminguinet.bsky.social · 07/03/2025
000
Benjamin Guinet @benjaminguinet.bsky.social · 22/01/2025
Our latest study uncovers a viral domestication event from ~75 million years ago, where viral genes enable parasitoid wasps to protect their eggs they lay within dipteran hosts! 🐝->🥚+🦠->🪰☠️ ->🐝🦠 Read more: royalsocietypublishing.org/doi/10.1098/... #paleovirology #parasitoid #evolution
0165