Bacterial Genomics

Rapid dissemination of Staphylococcus aureus in the neonatal intensive care unit is associated with invasive infection www.nature.com/articles/s41...

A novel polyhydroxyalkanoate-storing bacterium Thauera carbonocopians sp. nov. isolated from a sequencing batch reactor fed with volatile fatty acids www.nature.com/articles/s41...

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

Genome contamination may lead to an overestimation of horizontal gene transfer inferences www.nature.com/articles/s41...

Aeromonas in South Asia: genomic insights into an environmental pathogen and reservoir of antimicrobial resistance www.nature.com/articles/s41...

A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems www.nature.com/articles/s41...

Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes www.nature.com/articles/s41...

Genomic dissection of the clonal background and global dissemination of hypervirulent Klebsiella pneumoniae CG23-KL57 lineage www.nature.com/articles/s41...

Bacterial chromatin remodeling associated with transcription-induced domains at pathogenicity Islands www.nature.com/articles/s41...

Persistent virulent phages exist across bacterial isolates - Nature Microbiology 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.

Persistent virulent phages exist across bacterial isolates www.nature.com/articles/s41...

High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications 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...

High frequency body site translocation of nosocomial Pseudomonas aeruginosa www.nature.com/articles/s41...

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy - Nature Communications 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...

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy www.nature.com/articles/s41...

Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi - Nature Communications 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...

Circulation of Salmonella spp. between humans, animals and the environment in animal-owning households in Malawi www.nature.com/articles/s41...

PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks - Nature Communications 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...

PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks www.nature.com/articles/s41...

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

Complete genome sequencing of 18 urea-utilizing Vibrio strains isolated from coral www.nature.com/articles/s41...

Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult - Nature Communications 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.

Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult www.nature.com/articles/s41...

A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses - Communications Biology 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.

A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses www.nature.com/articles/s42...

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

Elucidating the role of group A Streptococcus genomics and pharyngeal microbiota in acute paediatric pharyngitis www.nature.com/articles/s41...

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

Combined genomic and phenomic analyses reveals multifunctionality of Paenibacillus polymyxa K16 for plant’s nutrition, growth and health www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap www.nature.com/articles/s41...

Determination of the prevalence of hypervirulent Klebsiella pneumoniae strains in Northeast Iran, Mashhad www.nature.com/articles/s41...

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

Amycolatopsis cyclosori sp. nov., isolated from the rhizosphere soil of Cyclosorus parasiticus www.nature.com/articles/s41...

Bringing the uncultivated microbial majority of freshwater ecosystems into culture www.nature.com/articles/s41...

Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium - Nature Microbiology 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.

Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium www.nature.com/articles/s41...

Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong - Nature Communications 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...

Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong www.nature.com/articles/s41...

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

Genome-based reclassification of Micromonospora veneta Kaewkla et al. 2022 as a later heterotypic synonym of Micromonospora coerulea Jensen 1932 (Approved lists 1980) www.nature.com/articles/s41...

Pan-genus analysis and typing of antimicrobial resistance plasmids in Acinetobacter www.nature.com/articles/s44...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria - Nature Communications 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 ...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria www.nature.com/articles/s41...

Genomes of 211 Actinomycete Strains from Diverse Environments - Scientific Data Scientific Data - Genomes of 211 Actinomycete Strains from Diverse Environments

Genomes of 211 Actinomycete Strains from Diverse Environments www.nature.com/articles/s41...

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

Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh www.nature.com/articles/s41...

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

Streptomyces maremycinicus sp. nov. and its secondary metabolite-biosynthetic gene clusters www.nature.com/articles/s41...