Microbial Genomics

E-ISSN: 2057-5858

Microbial Genomics pioneers all areas of genome research spanning the breadth of microbial life including viruses, bacteria, archaea and microbial eukaryotes. We welcome articles showing novel insights, new applications, or innovative approaches using genomic data. Content ranges from comparative and functional genomics of model organisms to population-scale evolution, epidemiology and microbiome studies, and real-world genomics applications with clinical, veterinary or environmental relevance. See full journal scope

Browse these key collections:

Genomics, Epidemiology and Evolution of Campylobacter, Helicobacter and Related Organisms (Open for submissions)
Establishing whole genome sequencing at the core of epidemiological surveillance (Open for submissions)
Microbial Genomics of Sexually Transmitted Infections (Open for submissions)

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One size does not fit all – Trehalose metabolism by Clostridioides difficile is variable across the five phylogenetic lineages

Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh

Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii

Complex evolutionary history of photosynthesis in Bradyrhizobium

Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK

Evaluation of sequence hybridization for respiratory viruses using the Twist Bioscience Respiratory Virus Research panel and the OneCodex Respiratory Virus sequence analysis workflow

IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli

A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia’s Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris)

Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia

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MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification

ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Identification of Klebsiella capsule synthesis loci from whole genome data

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive

mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes