To address uncertainty in model choice for reconstructing population history, Xu, @alexeidrummond.bsky.social et al. introduce a new Bayesian model averaging (BMA) framework. 🔗 doi.org/10.1093/molbev/msaf297 #evobio #molbio #compbio

Get excited :) PhyloSpec is coming! A shared standard + modelling language for phylogenetic models. Write a model once, run it across engines like BEAST X, BEAST 2.8 & RevBayes. Easy and reproducible. Built by @tochsner.bsky.social & collaborators (ETH Zürich, Auckland, LMU). phylospec.com

my first 'data descriptor'! hoping this one will be useful for folks interested in tracing the distribution of genomes/genes/proteins over physicochemical gradients in the (deep) marine water column.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2w ago

Deeply-sequenced metagenomes and over 1000 draft genomes from the epipelagic to bathypelagic Northeast Pacific Ocean https://www.biorxiv.org/content/10.64898/2026.07.18.739368v1

Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans www.nature.com/articles/s41... #jcampubs 🌊

We first took a broad comparative-genomics approach, updating the map of ERs across bacterial diversity by analyzing >40,000 complete genomes. Large ERs tend to converge in GC content toward their host chromosome, recur independently, and are often conserved at the genus level.

Nature research paper: Decade-long warming accelerates antibiotic resistance in grassland soils go.nature.com/4cCPhG1

Decade-long warming accelerates antibiotic resistance in grassland soils - Nature

Decade-long warming increased soil antibiotic-resistance genes by about 24%, enriching resistant microbes and gene transfer, driven by selection for thermal tolerance and linked traits, with implications for public health.

go.nature.com

📣 New publication: the 2026 Europe report of the Lancet Countdown is out! The report shows how climate change is already harming health across Europe, how fossil fuel dependence is slowing progress, and why stronger leadership is urgently needed. Read the full report: doi.org/10.1016/S246...

🧬 New in Bioinformatics Advances: "Memod-s: A standardised workflow to explore and analyse prokaryotic methylation patterns for Nanopore sequencing data"  Explore the study: https://doi.org/10.1093/bioadv/vbag072  Authors include: @alessiome.bsky.social, @jaimemurtaza.bsky.social

Bacteria swap DNA far more than we thought. This study shows recombination between species can blur genetic boundaries, with up to 95% of diversity coming from hybrid DNA in some microbes.

Remixing the gene pool

Microbes might behave less like distinct species and more like constantly interbreeding communities.

buff.ly

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

Strain displacement in microbiomes via ecological competition #microbes #ecology #microSky www.nature.com/articles/s41...

Strain displacement in microbiomes via ecological competition - Nature Microbiology

Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

nature.com

Hybridisation breaks species barriers in long-term coevolution of a cyanobacterial population. buff.ly/EaJskBA

New online! From clonality to complexity: a journey through microbial ecology and evolution

From clonality to complexity: a journey through microbial ecology and evolution

Nature Reviews Genetics, Published online: 30 October 2025; doi:10.1038/s41576-025-00910-6Jaime Martinez-Urtaza reflects on two papers by Smith et al., who found that bacteria exist along a continuum from clonal to recombining populations, and introduced the concept of an ‘epidemic’ microbial population structure.

nature.com

🚨 JUST PUBLISHED 🚨 ⚠️ The 2025 @lancetcountdown.bsky.social report reveals climate change inaction is costing lives and livelihoods, and harming the economy. ❤️‍🩹 Protecting people’s health demands all hands on deck. Read more: www.lancetcountdown.org/2025-report/ #LancetClimate25

Bacteria undergo rapid genetic changes that are selected by alterations in the human gut environment. Learn more in a new #SciencePerspective: https://scim.ag/4qaRWNh

Natural directed evolution in gut microbiota

Bacteria undergo rapid genetic changes that are selected by alterations in the human gut environment

scim.ag

please read this thread - even if you don;t get time to read the paper!!!!! just the best - great work, really really great.

Zamin Iqbal@zaminiqbal.bsky.social · 10mo ago

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

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...

Vibrio2026: The International Meeting on the Biology of Vibrios

Fourwaves - Vibrio2026: The International Meeting on the Biology of Vibrios

event.fourwaves.com

🚨 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

Nature Ecology & Evolution@natecoevo.nature.com · 11mo ago

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...

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...

Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss - Nature Ecology & Evolution

A combination of large-scale phylogenomic analysis, mouse lethality experiments and bacterial growth assays shows that gene loss in the putrescine utilization pathway has enhanced biofilm formation an...

nature.com

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

Nature Ecology & Evolution@natecoevo.nature.com · 11mo ago

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...

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...

Evolution of hunt, kill, devour in a Vibrio ecospecies

Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Using coadaptation analysis as a foundation for laboratory experime...

biorxiv.org

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

Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer - Nature Medicine

An analysis of 18 metagenomic datasets of individuals with colorectal cancer, adenomas and healthy controls yields improved cancer prediction accuracy based solely on gut metagenomics, as well as the ...

nature.com

🚨 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...

Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain - Nature Microbiology

ChronoStrain accurately profiles low-abundance strains in longitudinal samples by jointly modelling nucleotide sequencing errors, strain presence/absence and the temporal information associated with e...

nature.com

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...

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution - Nature Biotechnology

The evolution of microbial strains is revealed by analyzing structural variation.

nature.com

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/...

Release RAxML-NG v2.0-beta2 · amkozlov/raxml-ng

Main new features Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024) Multiple fast branch support measures Integrated model testing Full Changelog: 1.2.2...2.0-beta2

github.com