A standardized way to describe phylogenetic model components, common assumptions, and best practices in the field of phylogenetics.

Marine bacteria Vibrio are emerging pathogens worldwide, yet their global dispersal is poorly understood. Combining metagenomic and ocean drifter data, authors show Vibrio dispersal across oceans, con...

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.

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

The future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...

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

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.

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

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

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...

ABSTRACT The panmictic population concept is at the heart of population, evolutionary and conservation genetics. However, in nature, true panmictic populations are vanishingly rare. As an idea conce...

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...

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 ...

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...

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

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

A workflow using conserved amino acid domains identifies viruses in sequence data at single-cell resolution.

Characterization of the genetic architecture underlying the 7 pairs of contrasting traits studied by Mendel and the over 70 additional agronomic traits in pea (Pisum sativum) reveals their m...

Recent advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals, plants and other eukaryotes. However, there...

Global full-depth ocean heat content (OHC) gain since 1960 reached a record 452 ± 77 ZJ in 2024. OHC was 15 ± 9 ZJ higher than in 2023, primarily associated with warming in the Atlantic and Indian Oce...

Experiments in bacteria test a 50-year-old hypothesis on how duplicate genes help living things evolve.

Climate change and human activity will increase global richness and abundance of pathogenic bacteria, threatening public health.

A primary goal of microbial genome-wide association studies is identifying genomic variants associated with a particular habitat. Existing tools fail to identify known causal variants if the analyzed ...

Nature Reviews Microbiology, Published online: 25 March 2025; doi:10.1038/s41579-025-01159-wIn this Review, Gagneux and colleagues discuss ecological and evolutionary concepts related to the biology and epidemiology of the Mycobacterium tuberculosis complex, including new phylogenetic lineages, host tropism among the various animal-adapted lineages, the evolutionary dynamics of antimicrobial resistance and transmission, as well as within-host diversity and structural genomic variation.

In the era of climate change, human societies face growing exposure to disasters and complex climate risks. This perspective explores the transformative potential of integrated Artificial Intelligence...

Withdrawing from the World Health Organization and the Paris Agreement (again), cutting climate, health and development funding, purging climate mentions from websites, muzzling the Centers for Diseas...

Here the authors show that lab mice have retained ancient gut bacterial symbionts that diversified in parallel with rodent species, but the genomes of these gut bugs have accumulated mutational burden...

Abstract. Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously m

Macrogenetics investigates the patterns and predictors of intraspecific genetic variation across diverse taxa, offering a framework to address longstanding evolutionary hypotheses. Here, we present a ...

Macrogenetics investigates the patterns and predictors of intraspecific genetic variation across diverse taxa, offering a framework to address longstanding evolutionary hypotheses. Here, we present a ...