Bacterial Genomics

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...

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

Global pneumococcal sequence cluster lineage for invasive pneumococcal isolates in Denmark from summer 2019 to 2023 www.nature.com/articles/s41...

Halomonas sp. MC140, a polyhydroxyalkanoate (PHA) producer isolated from the Arctic environment - Scientific Reports Scientific Reports - Halomonas sp. MC140, a polyhydroxyalkanoate (PHA) producer isolated from the Arctic environment

Halomonas sp. MC140, a polyhydroxyalkanoate (PHA) producer isolated from the Arctic environment www.nature.com/articles/s41...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

Universal rules govern plasmid copy number www.nature.com/articles/s41...

Scaling laws of bacterial and archaeal plasmids - Nature Communications The capacity of a plasmid to express genes is constrained by parameters such as its length and copy number. Here, Maddamsetti et al. present a computational method that enables rapid and accurate dete...

Scaling laws of bacterial and archaeal plasmids www.nature.com/articles/s41...

Complete genome analysis of the cellulose producing strain Komagataeibacter sucrofermentans SMEG01 - Scientific Reports Scientific Reports - Complete genome analysis of the cellulose producing strain Komagataeibacter sucrofermentans SMEG01

Complete genome analysis of the cellulose producing strain Komagataeibacter sucrofermentans SMEG01 www.nature.com/articles/s41...

The identification Mycobacterium tuberculosis genes that modulate long term survival in the presence of rifampicin and streptomycin - Scientific Reports Scientific Reports - The identification Mycobacterium tuberculosis genes that modulate long term survival in the presence of rifampicin and streptomycin

The identification Mycobacterium tuberculosis genes that modulate long term survival in the presence of rifampicin and streptomycin www.nature.com/articles/s41...

Multidrug-resistant Klebsiella pneumoniae ST70 harboring blaNDM in a migratory Penguin - Scientific Reports Scientific Reports - Multidrug-resistant Klebsiella pneumoniae ST70 harboring blaNDM in a migratory Penguin

Multidrug-resistant Klebsiella pneumoniae ST70 harboring blaNDM in a migratory Penguin www.nature.com/articles/s41...

Tracking international and regional dissemination of the KPC/NDM co-producing Klebsiella pneumoniae - Nature Communications This study is an analysis of carbapenem-resistant Klebsiella pneumoniae from 2005 to 2024, which showed significant differences across countries, and Clone Group 1 emerged as the principal disseminati...

Tracking international and regional dissemination of the KPC/NDM co-producing Klebsiella pneumoniae www.nature.com/articles/s41...

A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections - Nature Communications Bacteria can undergo adaptive evolution during severe infections, leading to treatment failure. The authors use within-host evolution genomic analysis to investigate persistent Staphylococcus aureus i...

A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections www.nature.com/articles/s41...

TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity - npj Vaccines npj Vaccines - TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity

TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity www.nature.com/articles/s41...

Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA - Nature Communications A large outbreak of shigellosis occurred in Albuquerque, New Mexico in 2021–2023 and affected non-human primates at a local zoo as well as humans. Here, the authors describe the outbreak investigation...

Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA www.nature.com/articles/s41...

Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut - Scientific Reports Scientific Reports - Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut

Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut www.nature.com/articles/s41...

Cas3 of type I-Fa CRISPR-Cas system upregulates bacterial biofilm formation and virulence in Acinetobacter baumannii - Communications Biology Deletion of cas3(type I-Fa) significantly reduced the biofilm formation, virulence and pathogenicity to mice. Mechanism analysis proved that this maybe because cas3 can lead to the down-regulation of ...

Cas3 of type I-Fa CRISPR-Cas system upregulates bacterial biofilm formation and virulence in Acinetobacter baumannii www.nature.com/articles/s42...

HiBC: a publicly available collection of bacterial strains isolated from the human gut - Nature Communications Here, the authors present and characterise a collection of human gut bacteria including novel taxa associated with health conditions and a large diversity of plasmids. All isolates, their genomes and ...

HiBC: a publicly available collection of bacterial strains isolated from the human gut www.nature.com/articles/s41...