Microbial Genomics

E-ISSN: 2057-5858

The Microbiology Society's founding journal, Microbiology, is now fully Open Access (OA). Find out more about the transformation here.

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:

Methods and Software
Bacteriophage
Microreact
Implementation of Genomics in Clinical and Public Health Microbiology
Microbial Genomics of Sexually Transmitted Infections (Open for submissions)

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Phylogenomic investigation of an outbreak of fluoroquinolone-resistant Salmonella enterica subsp. enterica serovar Paratyphi A in Phnom Penh, Cambodia

Travel-associated lineages and unique endemic antimicrobial-susceptible lineages of Neisseria gonorrhoeae predominate in Western Australia

An OmpW-dependent T4-like phage infects Serratia sp. ATCC 39006

An updated catalogue of diverse type II polyketide synthase biosynthetic gene clusters captured from large-scale nucleotide databases

RND pumps across the genus Acinetobacter: AdeIJK is the universal efflux pump

Highly contiguous genomes of human clinical isolates of Giardia duodenalis reveal assemblage- and sub-assemblage-specific presence–absence variation in protein-coding genes

ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies

Global population structure, genomic diversity and carbohydrate fermentation characteristics of clonal complex 119 (CC119), an understudied Shiga toxin-producing E. coli (STEC) lineage including O165:H25 and O172:H25

Rapid adaptations of Legionella pneumophila to the human host

Advantages of analysing both pairwise SNV-distance and differing SNVs between Mycobacterium tuberculosis isolates for recurrent tuberculosis cause determination

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Completing bacterial genome assemblies with multiplex MinION sequencing

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

Identification of Klebsiella capsule synthesis loci from whole genome data

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

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Genome-guided identification of novel head-to-tail cyclized antimicrobial peptides, exemplified by the discovery of pumilarin

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