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
• Microbial Genomics of Eukaryotes

   

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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

• • 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

• • 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

• • 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

• • 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

• • ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

    Martin Hunt , Alison E Mather , Leonor Sánchez-Busó , Andrew J Page , Julian Parkhill , Jacqueline A Keane and Simon R Harris

• • 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

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

    Mickael Silva , Miguel P. Machado , Diogo N. Silva , Mirko Rossi , Jacob Moran-Gilad , Sergio Santos , Mario Ramirez and João André Carriço
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