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

As part of our continuing commitment to Open Access, from January 2023 the Society's founding journal Microbiology will be moving to a fully open access publication model. Read more about it, and our wider OA journey, in this news story.

Browse these key collections:

Methods and Software
Bacteriophage
Microreact

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Articles from the latest issue Latest Articles Rss Feed

- Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance
  
  Tristan P. W. Dennis , Barbara K. Mable , Brian Brunelle, Alison Devault, Ryan W. Carter, Clare L. Ling , Blandina T. Mmbaga , Jo E. B. Halliday , Katarina Oravcova and Taya L. Forde
- RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12
  
  Víctor H. Tierrafría , Claire Rioualen , Heladia Salgado , Paloma Lara, Socorro Gama-Castro , Patrick Lally , Laura Gómez-Romero, Pablo Peña-Loredo, Andrés G. López-Almazo, Gabriel Alarcón-Carranza, Felipe Betancourt-Figueroa, Shirley Alquicira-Hernández, J. Enrique Polanco-Morelos, Jair García-Sotelo , Estefani Gaytan-Nuñez , Carlos-Francisco Méndez-Cruz , Luis J. Muñiz, César Bonavides-Martínez , Gabriel Moreno-Hagelsieb , James E. Galagan, Joseph T. Wade and Julio Collado-Vides
- Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/‘magdeburgensis’ complex
  
  Yasuhiro Gotoh, Yuya Atsuta, Takako Taniguchi, Ruriko Nishida, Keiji Nakamura, Yoshitoshi Ogura, Naoaki Misawa and Tetsuya Hayashi
- Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity
  
  Emilie Dordet-Frisoni , Céline Vandecasteele , Rachel Contarin, Eveline Sagné, Eric Baranowski , Christophe Klopp , Laurent-Xavier Nouvel and Christine Citti
- Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan
  
  Mi Nguyen-Tra Le, Shizuo Kayama, Kelly L. Wyres, Liansheng Yu, Junzo Hisatsune, Masato Suzuki, Koji Yahara, Tsuneko Terachi, Kana Sawa, Shin Takahashi, Toshihiko Okuhara, Kunihiko Kohama, Kathryn E. Holt, Tetsu Mizutani, Hiroki Ohge and Motoyuki Sugai
- Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults, respectively, with both subclades exhibiting extensive genetic diversity
  
  Hannah C. Howson-Wells , Theocharis Tsoleridis , Izzah Zainuddin, Alexander W. Tarr , William L. Irving, Jonathan K. Ball, Louise Berry, Gemma Clark and C. Patrick McClure
- Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure
  
  Lotte J.U. Pronk and Marnix H. Medema
- Investigating plant disease outbreaks with long-read metagenomics: sensitive detection and highly resolved phylogenetic reconstruction applied to Xylella fastidiosa
  
  Marcela A. Johnson, Haijie Liu, Elizabeth Bush, Parul Sharma, Shu Yang, Reza Mazloom, Lenwood S. Heath, Mizuho Nita, Song Li and Boris A. Vinatzer
- Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics
  
  Yiran Li , Rodrigo P. Baptista , Xiaohan Mei and Jessica C. Kissinger
- Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks
  
  Claire Bertelli , Kristen L. Gray , Nolan Woods, Adrian C. Lim, Keith E. Tilley, Geoffrey L. Winsor , Gemma R. Hoad, Ata Roudgar, Adam Spencer, James Peltier, Derek Warren, Amogelang R. Raphenya , Andrew G. McArthur and Fiona S. L. Brinkman
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Most cited this month Most Cited RSS feed

- Completing bacterial genome assemblies with multiplex MinION sequencing
  
  Ryan R. Wick, Louise M. Judd, Claire L. Gorrie and Kathryn E. Holt
- 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
- 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
- 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
- MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  
  James Robertson and John H. E. Nash
- 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
- Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations
  
  Margaret M. C. Lam, Ryan R. Wick, Kelly L. Wyres, Claire L. Gorrie, Louise M. Judd, Adam W. J. Jenney, Sylvain Brisse and Kathryn E. Holt
- NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats
  
  Jason W. Sahl, Darrin Lemmer, Jason Travis, James M. Schupp, John D. Gillece, Maliha Aziz, Elizabeth M. Driebe, Kevin P. Drees, Nathan D. Hicks, Charles Hall Davis Williamson, Crystal M. Hepp, David Earl Smith, Chandler Roe, David M. Engelthaler, David M. Wagner and Paul Keim
- The diversity of Klebsiella pneumoniae surface polysaccharides
  
  Rainer Follador, Eva Heinz, Kelly L. Wyres, Matthew J. Ellington, Michael Kowarik, Kathryn E. Holt and Nicholas R. Thomson
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Articles from the latest issue Latest Articles Rss Feed

Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12

Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/‘magdeburgensis’ complex

Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity

Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan

Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults, respectively, with both subclades exhibiting extensive genetic diversity

Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure

Investigating plant disease outbreaks with long-read metagenomics: sensitive detection and highly resolved phylogenetic reconstruction applied to Xylella fastidiosa

Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics

Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks

Most read this month

Most cited this month Most Cited RSS feed

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

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

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

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats

The diversity of Klebsiella pneumoniae surface polysaccharides