The use of whole-genome sequencing for classification and surveillance of the pathogen Chlamydia trachomatis is limited due to the lack of standardized typing frameworks. Here, the authors present a c...

In this study, the authors demonstrate that trimeric autotransporter adhesins drive bacterial chain-like adhesion, expanding the surface colonization strategies of Shiga toxin-producing Escherichia co...

Plague, caused by the pathogen Yersinia pestis, has affected human societies for millennia. Here, the authors screened 1,400 ancient human remains from eastern Eurasia and recovered three prehistoric ...

Bacteria of the genus Gardnerella are associated with bacterial vaginosis. Here, the authors compile and analyse a reference set of high-quality Gardnerella genomes, revealing previously hidden specie...

Purine bias is critical for gene expression in bacteria, preventing premature transcription in species that exhibit runaway transcription.

Scientific Data - High-Quality Genome Assembly, Metabolome, Pangenome, and Metabolic Models of Megasphaera hexanoica KCCM 43214T

Antibiotics have been used to treat tuberculosis for over 80 years. Here, Chen et al. analyze over 18,000 Mycobacterium tuberculosis genomes to reconstruct the temporal and spatial evolution of drug r...

Coppens & Ledesma-Amaro present a transformer-based computational model trained on 9 million bacterial sequences from over 3,000 species, which enables automated identification of diverse promoter...

Nectar bacteria turn floral sugar into a weapon: Acinetobacter converts glucose to gluconic acid, acidifies nectar, and triggers pollen tube burst, revealing a nectar-adapted strategy coupling glucose...

Bacterial genomes often include extrachromosomal replicons, ranging from small plasmids to chromosome-scale replicons. Here, Czarnecki et al. analyse more than 40,000 complete bacterial genomes and sh...

This Review summarizes recent advances in bacterial single-cell transcriptomics approaches, while also discussing technological and computational challenges remaining to be met and the need for standa...

Scientific Reports - Metabolomics-based and functional validation to explore the effect of the gut microbe-associated metabolite guanidinoacetic acid on rectal adenocarcinoma

While cheese is enjoyed globally, most of the known physiochemical and microbial characteristics are from western cheeses. Here, the authors expand the global catalogue of cheeses by investigating 235...

Global genomic analysis of carbapenem-resistant Enterobacter hormaechei reveals blaNDM-1 and mcr-9 on IncHI2/IncX3 plasmids, with high-risk clones ST171/ST190 driving cross-border and cross-habitat tr...

Streptococcus pyogenes is a human pathogen responsible for a range of diseases. Here, the authors reconstruct an ancient S. pyogenes genome from a pre-Columbian Bolivian mummy, supporting that the pat...

The seventh cholera pandemic, driven by El Tor Vibrio cholerae, evolved separately in Bangladesh and India, with the Ganges Basin acting as the global source, and its evolution has been shaped by...

Scientific Data - Complete genome sequence of Sphingomonas sp. gentR, a high-level gentamicin-resistant bacterium

Bacteria of the genus Fusobacterium are associated with diverse diseases, but taxonomic ambiguities complicate species-level identification. Here, the authors describe practical methods for Fusobacter...

Little is known about the ecology and evolution of the nosocomial pathogen Acinetobacter baumannii outside the hospital. Here, Wilharm et al. show that the lifestyle of A. baumannii includes soil-dwel...

In this work, authors use whole genome tracking in a neonatal intensive care unit to reveal a strong link between Staphylococcus aureus colonization and invasive infection, pinpointing critical new ta...

Scientific Reports - A novel polyhydroxyalkanoate-storing bacterium Thauera carbonocopians sp. nov. isolated from a sequencing batch reactor fed with volatile fatty acids

Nature Communications - Genome contamination may lead to an overestimation of horizontal gene transfer inferences

The bacterial genus Aeromonas includes emerging human pathogens, often misidentified as Vibrio cholerae. Here, the authors analyse genomic sequences of over 1,800 Aeromonas isolates, showing that clin...

Extracellular contractile injection systems (eCISs) are bacteriophage tail-derived toxin delivery complexes that are present in many prokaryotes. Here, the authors present an analysis of eCIS tail fib...

The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical phage lifestyles.

Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...

It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core genomes across 50 major bacte...

In this work, Wilson et al., examined sharing of Salmonella between humans, animals and the environment using household samples from Malawi. They revealed an interconnected web of Salmonella circulati...

Prokaryotic pan-genome analysis is crucial for understanding microbial diversity, however current analytical methods often struggle to balance accuracy and computational efficiency. Here the authors p...

Scientific Data - Complete genome sequencing of 18 urea-utilizing Vibrio strains isolated from coral

In this work, authors tracked a pneumococcal serotype 3 strain persisting for a year in a healthy adult, revealing limited genetic change but stable multidrug resistance and features linked to vaccine escape.

This review explores the genomic diversity, ecology, and functional potential of the bacterial family Endozoicomonadaceae in marine symbioses, highlighting their mutualistic to parasitic spectrum and key gaps to be addressed in future research.

Scientific Reports - Elucidating the role of group A Streptococcus genomics and pharyngeal microbiota in acute paediatric pharyngitis

Scientific Reports - Combined genomic and phenomic analyses reveals multifunctionality of Paenibacillus polymyxa K16 for plant’s nutrition, growth and health

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Scientific Reports - Determination of the prevalence of hypervirulent Klebsiella pneumoniae strains in Northeast Iran, Mashhad

The Journal of Antibiotics - Amycolatopsis cyclosori sp. nov., isolated from the rhizosphere soil of Cyclosorus parasiticus

A large fraction of aquatic bacteria remains uncultured. Here, the authors cultivated 627 strains of abundant freshwater bacteria from 14 European lakes, thus generating a collection that includes man...

Isolates and metagenome-assembled genomes from a global survey show quasi-endemic and cosmopolitan lineages of SAR11-IIIb, with patterns driven by temperature and latitude.

E. coli is common in humans, animals and the environment but the extent of circulation between ecological niches is unclear. Here, the authors sample ~1,000 E. coli strains from different urban aquati...

Scientific Reports - Genome-based reclassification of Micromonospora veneta Kaewkla et al. 2022 as a later heterotypic synonym of Micromonospora coerulea Jensen 1932 (Approved lists 1980)

npj Antimicrobials and Resistance - Pan-genus analysis and typing of antimicrobial resistance plasmids in Acinetobacter

The authors investigate the distribution of the aminoglycoside resistance gene npmA in Gram-positive bacteria via a mobile genetic element, highlighting its global presence and cross-species transfer ...

Scientific Data - Genomes of 211 Actinomycete Strains from Diverse Environments

Scientific Reports - Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh

The Journal of Antibiotics - Streptomyces maremycinicus sp. nov. and its secondary metabolite-biosynthetic gene clusters

Scientific Reports - Global pneumococcal sequence cluster lineage for invasive pneumococcal isolates in Denmark from summer 2019 to 2023