Microbial Genomics logo Microbial Genomics

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

For everything you need to know when preparing a submission check out our new submission checklist . 

Browse these key collections:

• Genomics, Epidemiology and Evolution of Campylobacter, Helicobacter and Related Organisms  
• Establishing whole genome sequencing at the core of epidemiological surveillance 
• Microbial Genomics of Sexually Transmitted Infections 

   

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

    Oliver Schwengers , Lukas Jelonek , Marius Alfred Dieckmann , Sebastian Beyvers , Jochen Blom and Alexander Goesmann

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

    James Robertson and John H. E. Nash

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

    Alfred Ferrer Florensa , Rolf Sommer Kaas , Philip Thomas Lanken Conradsen Clausen , Derya Aytan-Aktug and Frank M. Aarestrup

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

    Andrew J. Page , Ben Taylor , Aidan J. Delaney , Jorge Soares , Torsten Seemann , Jacqueline A. Keane and Simon R. Harris

• • Completing bacterial genome assemblies with multiplex MinION sequencing

    Ryan R. Wick , Louise M. Judd , Claire L. Gorrie and Kathryn E. Holt

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

    Johann Beghain , Antoine Bridier-Nahmias , Hervé Le Nagard , Erick Denamur and Olivier Clermont

• • Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies

    George Bouras , Ghais Houtak , Ryan R. Wick , Vijini Mallawaarachchi , Michael J. Roach , Bhavya Papudeshi , Lousie M. Judd , Anna E. Sheppard , Robert A. Edwards and Sarah Vreugde

• • How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

    George Bouras , Louise M. Judd , Robert A. Edwards , Sarah Vreugde , Timothy P. Stinear and Ryan R. Wick

• • Identification of Klebsiella capsule synthesis loci from whole genome data

    Kelly L. Wyres , Ryan R. Wick , Claire Gorrie , Adam Jenney , Rainer Follador , Nicholas R. Thomson and Kathryn E. Holt

• • Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

    Silvia Argimón , Khalil Abudahab , Richard J. E. Goater , Artemij Fedosejev , Jyothish Bhai , Corinna Glasner , Edward J. Feil , Matthew T. G. Holden , Corin A. Yeats , Hajo Grundmann , Brian G. Spratt and David M. Aanensen
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