Delighted to announce that The International Meeting on the Biology of Vibrios will be back next year! Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists! event.fourwaves.com/vibrio2026/p...

🚨 NEW: Climate change is already causing 30,000 deaths per year - a global annual economic loss of $100-350B USD - but the true damage is probably 10x higher. Out TODAY in Nature Climate Change: the first systematic look at the science of "health impact attribution" 🔓 www.nature.com/articles/s41...

Our “Less is more” story is out! 🚀 We reveal how gene loss shaped the adaptive evolution of pandemic Vibrio parahaemolyticus, highlight a potentially general mechanism across bacteria. Huge thanks @danielfalush.bsky.social @campy-bara.bsky.social @jaimemurtaza.bsky.social & all coauthors

Combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows sheds light on how a pandemic clone of Vibrio parahaemolyticus was able to spread worldwide www.nature.com/articles/s41...

Beautiful work on the emergence of the pandemic clone of V. parahaemolyticus

How to get introgressed fragments in genomic data? Everything you always wanted to know you find in our review in @cp-trendsgenetics.bsky.social, led by Xin Huang: doi.org/10.1016/j.ti...

Really excited to share the first paper from my PhD - it’s all about assumptions in modelling and the history of early population genetics… 🧵 doi.org/10.1111/ahg....

Long et al. integrate population genomics, experimental evolution, and environmental modeling to elucidate the evolutionary responses to climate change in Populus lasiocarpa. This study has made the July cover of MBE. 🔗 doi.org/10.1093/molbev/msaf116 #evobio #molbio

Happy to share the preprint from here in Shanghai, together with @danielfalush.bsky.social, as well as with team Zhizhou Jia, Huqi Wen, and Zhe Xie! www.biorxiv.org/content/10.1...

Cleanifier: A fast and lightweight k-mer based tool to remove contamination in microbial sequence data. #MicrobialSequences #ContaminationRemoval #Kmers #Genomics #Bioinformatics @biorxivpreprint www.biorxiv.org/content/10.1...

🥁NEW publication from our lab: the largest meta-analysis of gut microbiome associations with CRC! www.nature.com/articles/s41... 🧵⬇️ 1/6

🚨 Out now! Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻 @travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org #MicroSky 🦠 #MicrobiomeSky www.nature.com/articles/s41...

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution @natbiotech.nature.com from @microbiome.bsky.social www.nature.com/articles/s41...

RAxML-NG v2.0 beta is here github.com/amkozlov/rax... Features 1. Difficulty prediction academic.oup.com/mbe/article/... 2. Adaptive search academic.oup.com/mbe/article/... 3. Early Stop www.biorxiv.org/content/10.1... 4. Model selection 5. Rapid bootstrapping academic.oup.com/mbe/article/...

Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes - @lauraluebbert.com @lpachter.bsky.social go.nature.com/4lGrSY3

New genomic & genetic insights into Mendel’s pea genes, including previously uncharacterised alleles 159 years after Mendel published his work, this is a real delight (especially for a geneticist) 🧪 @nature.com www.nature.com/articles/s41...

This new Hifiasm --ont option is amazing. It worked like a charm for us in the nanopore adaptive sampling based assembly paradigm we introduced in a preprint recently. www.biorxiv.org/content/10.1...

Our rising seas. This is only going to get harder to ignore. This NASA visualization was created by svs.gsfc.nasa.gov/5520/

Ocean heat content (OHC) in 2024 Global full-depth OHC gain since 1960 reached a record 452 ± 77 zetajoules (ZJ) in 2024. OHC was 15 ± 9 ZJ higher than in 2023, primarily associated with warming in the Atlantic and Indian Oceans 1 ZJ = 1,000,000,000,000,000,000,000 J www.nature.com/articles/s43...

Experiments in bacteria test the 50-year-old Ohno’s hypothesis that having duplicates of a gene (true for about 50% of them) allows evolution to accelerate. #EvoBio #Evolution

A project five years in the making, we've now published complete "T2T" genomes for six additional ape species! It turns out that finishing (and analyzing) six genomes is slightly more work than one... doi.org/10.1038/s415...

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

It's finally out!!!! Our review on long-reads transcriptomics was published in @natrevgenet.bsky.social!! You can have a look at the paper here rdcu.be/efugl! We hope you like it 😀

Anthropogenic activity and climate change exacerbate the spread of pathogenic bacteria in the environment | Science Advances www.science.org/doi/10.1126/...

It is hard to determine habitat adaptations in host-associated bacteria, e.g. because strains might be allochthonous or mislabeled. Here we present aurora, a gwas tool that identifies autochthonous strains and the genes associated with their habitats. doi.org/10.1186/s130...

New online! Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex

In the era of #ClimateChange human societies face growing exposure to disasters and complex #climate risks. In this perspective, @reichstein-bgc.bsky.social, @vitusbenson.bsky.social, et al., explore the potential of integrated #ArtificialIntelligence in developing multi-hazard #EarlyWarningSystems

🔴⚠️🧊🌡️Dramatic conditions for the Arctic Circle as from the latest ERA5 data. It was hotter than the ref.per. 1991-2020 almost everywhere in the #Arctic with a max anomaly of +10.6°C for Feb.2025. Daily anomaly reached even +20°C in some areas, with seaice at their smallest extent ever for February

Europe's climate leadership in an ‘America first’ era - @lancetrh-europe.bsky.social Spain's 2024 simultaneous battle with deadly floods and severe droughts is a stark reminder that climate change already endangers lives in Europe. www.thelancet.com/journals/lan...

Lab mice (domesticated for >100y) have kept gut bacterial strains that codiversified w/ rodents for >25My. Here, authors show genetic drift occured in the lab, leading to loss of microb diversity+more deleterious mutations, impacting microbial fitness in lab vs wt mice www.nature.com/articles/s41...

Our review on k-mers + pop gen is now published! doi.org/10.1093/molb...

Just out - The first global ocean 3-Domain microbial survey where all organisms can be directly compared quantitatively. Unfractionated and amplified from just 2 primers (vetted with mock communities and metagenomics), so all with the same denominator. www.biorxiv.org/content/10.1...

Delighted to present our Macrogenetics atlas of prokaryotes. www.biorxiv.org/content/10.1... This is a herculean effort from Chao Yang, which has a previous existence as a preprint first posted in 2018 "why panmictic bacteria are rare?" www.biorxiv.org/content/10.1...

Very interesting new preprint from the Falush lab in Shanghai, describing an effort to parameterize a large number of microbial and population (phylo)genetic traits for >15k species, then examining their interactions. Loads to dig up & possibly quite impactful! 🔗 www.biorxiv.org/content/10.1...

I just posted "Some Experiments Work, and Some Don't." It features this new paper from Paul Rainey's group, along with a *failed* experiment that Paul Sniegowski and I ran in the 1990s trying to test the same idea. telliamedrevisited.wordpress.com/2025/02/21/s...

AI provides a universal framework that leverages data and compute at scale to uncover higher-order patterns Today, @arcinstitute.org in collaboration with Nvidia releases Evo 2—a fully open source biological foundation model trained on genomes spanning the entire tree of life.

Happy to announce that MEDI, our method to quantify dietary intake through metagenomics is out now. 🧬 🧪🧫🦠 www.nature.com/articles/s42... #metagenomics #microbiome #microbiomesky So what is MEDI? A combination of two things:

#MicroSky where diversity still thrives 👍

Huge analysis out as a preprint today! For every 9 years an animal spends in the wildlife trade, it shares an additional pathogen with humans. Clear long-term impacts based on 40 years of global trade data 🧪😷 biorxiv.org/content/earl...

Doge staffers enter Noaa headquarters and incite reports of cuts and threats Members reportedly sought access to IT systems at agency that Project 2025 has called ‘harmful to US prosperity’ www.theguardian.com/us-news/2025...

Documenting the life of his community in Panama, the Guna - one person’s evocative story:

Many of us, and especially early-career scientists, are facing huge challenges now. However, one of the joys of science is to delve into thinking about research. In that spirit, I offer this blog post on starting a microbial evolution experiment. telliamedrevisited.wordpress.com/2025/02/08/h...

Recently we have been doing lots of work on how modern #AI methods can be applied to studying virus evolution, so it felt like great timing to write a perspective about it! Very happy to see our paper as editor's pick in JVI!🥳🥳 doi.org/10.1128/jvi....

Trump orders USDA to take down websites referencing climate crisis www.theguardian.com/us-news/2025...

A University of Reading study confirms ocean warming is accelerating. phys.org/news/2025-01... #climatechange #oceans

My favourite papers yield more questions than answers. This one is like that. Fascinating! www.biorxiv.org/content/10.1...

Microbial species? OK, but... how? Ecological cohesiveness, coupled to unbiased horizontal gene flow, may account for the observed species and intraspecies clusters @ramonix.bsky.social @mpimarinemicrobio.bsky.social #microNatComms #microbiology 🦠 Read the paper: www.nature.com/articles/s41...

New research published today in Environmental Health Perspectives! 👩‍🔬 Forecasting climate-sensitive Vibrio vulnificus infections 🦠 (marine bacteria causing wound infections) using machine learning, environmental data 🌡️ (including EO 🛰️), and epi incidence data. Read here: doi.org/10.1289/EHP1...

Use the Human Microbiome Compendium data! We made the data and code available, & created a website and R package to navigate the compendium. Links: - Website: microbiomap.org - Data: zenodo.org/records/1373... - R package: blekhmanlab.github.io/MicroBioMap/ - Code: github.com/blekhmanlab/...

Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes ...BUT: they still don't capture a lot of the 🦠 species that are out there New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...