Microbial Genomics

Microbial Genomics

E-ISSN: 2057-5858

Microbial Genomics is the open access journal of choice for pioneering research in genomics in microbial life. We welcome articles showing novel insights, exciting new applications, or innovative approaches to analysis using genomic data, as well as articles developing our understanding of microbial genomics, from large, long-term studies on microbial evolution and epidemiology to studies with immediate clinical or environmental relevance. More

Editorial Board
Editor-in-Chief: Professor Kathryn Holt, Monash University, Australia and London School of Hygiene and Tropical Medicine, UK
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Journal status	Active

Articles from the latest issue Latest Articles Rss Feed

- Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12
  
  Lin Zhao, Hongyou Chen , Xavier Didelot , Zhenpeng Li, Yinghui Li, Meiling Chen, Yu Du, Hongqun Zhao, Jie Li, Qinghua Hu, Biao Kan, Min Chen and Bo Pang
- Read trimming has minimal effect on bacterial SNP-calling accuracy
  
  Stephen J. Bush
- Comparative genomics of wild-type and laboratory-evolved biofilm-overproducing Deinococcus metallilatus strains
  
  Chulwoo Park, Bora Shin, Wonjae Kim, Hoon Cheong, Soyoon Park and Woojun Park
- Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019
  
  Lingzi Xiaoli, Eileen Benoliel, Yanhui Peng, Janessa Aneke , Pamela K. Cassiday , Meagan Kay, Shelly McKeirnan, Jeffery S. Duchin, Vance Kawakami , Scott Lindquist, Anna M. Acosta , Chas DeBolt , Maria Lucia Tondella and Michael R. Weigand
- Long inverted repeats around the chromosome replication terminus in the model strain Bacillus thuringiensis serovar israelensis BGSC 4Q7
  
  Alexander Bolotin, Benoit Quinquis, Hugo Roume, Michel Gohar, Didier Lereclus and Alexei Sorokin
- Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli
  
  Anish Pandey, Maria Victoria Humbert , Alexandra Jackson, Jade L. Passey , David J. Hampson , David W. Cleary , Roberto M. La Ragione and Myron Christodoulides
- Complete microbial genomes for public health in Australia and the Southwest Pacific
  
  Sarah L. Baines , Anders Gonçalves da Silva , Glen P. Carter , Amy Jennison , Irani Rathnayake , Rikki M. Graham , Vitali Sintchenko , Qinning Wang , Rebecca J. Rockett , Verlaine J. Timms , Elena Martinez, Susan Ballard , Takehiro Tomita , Nicole Isles , Kristy A. Horan, William Pitchers , Timothy P. Stinear , Deborah A. Williamson , Benjamin P. Howden , Torsten Seemann and Communicable Diseases Genomics Network (CDGN)
- Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients
  
  M. Hong Nguyen, Drishti Kaul, Carlene Muto, Shaoji J. Cheng, R. Alex Richter, Vincent M. Bruno, Guojun Liu, Sinem Beyhan , Alexander J. Sundermann , Stephanie Mounaud , A. William Pasculle, William C. Nierman, Eileen Driscoll, Richard Cumbie, Cornelius J. Clancy and Christopher L. Dupont
- Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains
  
  Katlego Kopotsa , Nontombi M. Mbelle and John Osei Sekyere
- Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections
  
  Dmitriy Li , Cameron J. Reid , Timothy Kudinha, Veronica M. Jarocki and Steven P. Djordjevic
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- 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
- 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
- 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
- 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
- CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community
  
  Thomas R. Connor, Nicholas J. Loman, Simon Thompson, Andy Smith, Joel Southgate, Radoslaw Poplawski, Matthew J. Bull, Emily Richardson, Matthew Ismail, Simon Elwood- Thompson, Christine Kitchen, Martyn Guest, Marius Bakke, Samuel K. Sheppard and Mark J. Pallen
- 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
- mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species
  
  Sergio Arredondo-Alonso, Malbert R. C. Rogers, Johanna C. Braat, Tess D. Verschuuren, Janetta Top, Jukka Corander, Rob J. L. Willems and Anita C. Schürch
- 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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Microbial Genomics

Articles from the latest issue Latest Articles Rss Feed

Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

Read trimming has minimal effect on bacterial SNP-calling accuracy

Comparative genomics of wild-type and laboratory-evolved biofilm-overproducing Deinococcus metallilatus strains

Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019

Long inverted repeats around the chromosome replication terminus in the model strain Bacillus thuringiensis serovar israelensis BGSC 4Q7

Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli

Complete microbial genomes for public health in Australia and the Southwest Pacific

Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients

Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections

Most read this month

Most cited this month Most Cited RSS feed

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Completing bacterial genome assemblies with multiplex MinION sequencing

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

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

Identification of Klebsiella capsule synthesis loci from whole genome data

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community

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

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

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