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

- Ancestral state reconstruction of metabolic pathways across pangenome ensembles
  
  Fotis E. Psomopoulos , Jacques van Helden , Claudine Médigue, Anastasia Chasapi and Christos A. Ouzounis
- Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim
  
  Miquel Sánchez-Osuna , Pilar Cortés , Montserrat Llagostera , Jordi Barbé and Ivan Erill
- Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy
  
  Anna Janowicz , Fabrizio De Massis , Katiuscia Zilli, Massimo Ancora , Manuela Tittarelli , Flavio Sacchini , Elisabetta Di Giannatale , Jason W. Sahl , Jeffrey T. Foster and Giuliano Garofolo
- Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data
  
  Yuanwei Xu, Jessica E. Stockdale , Vijay Naidu , Hollie Hatherell, James Stimson , Helen R. Stagg , Ibrahim Abubakar and Caroline Colijn
- Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales
  
  Henry Secaira-Morocho , José A. Castillo and Adam Driks
- The glycan alphabet is not universal: a hypothesis
  
  Jaya Srivastava , P. Sunthar and Petety V. Balaji
- Optimized use of Oxford Nanopore flowcells for hybrid assemblies
  
  Samuel Lipworth , Hayleah Pickford , Nicholas Sanderson , Kevin K. Chau , James Kavanagh , Leanne Barker , Alison Vaughan , Jeremy Swann , Monique Andersson , Katie Jeffery , Marcus Morgan , Timothy E. A. Peto, Derrick W. Crook , Nicole Stoesser and A. Sarah Walker
- Azithromycin resistance mutations in Streptococcus pneumoniae as revealed by a chemogenomic screen
  
  Hélène Gingras, Kévin Patron, Philippe Leprohon and Marc Ouellette
- Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes
  
  Fanny Berglund , Maria-Elisabeth Böhm, Anton Martinsson, Stefan Ebmeyer, Tobias Österlund, Anna Johnning , D. G. Joakim Larsson and Erik Kristiansson
- Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone
  
  Eleonora Tassinari, Matt Bawn , Gaetan Thilliez , Oliver Charity , Luke Acton, Mark Kirkwood , Liljana Petrovska, Timothy Dallman, Catherine M. Burgess , Neil Hall, Geraldine Duffy and Robert A. Kingsley
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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
- 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
- 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
- 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
- Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients
  
  Anuradha Ravi, Fenella D Halstead, Amy Bamford, Anna Casey, Nicholas M. Thomson, Willem van Schaik, Catherine Snelson, Robert Goulden, Ebenezer Foster-Nyarko, George M. Savva, Tony Whitehouse, Mark J. Pallen and Beryl A. Oppenheim
- 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
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Microbial Genomics

Articles from the latest issue Latest Articles Rss Feed

Ancestral state reconstruction of metabolic pathways across pangenome ensembles

Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim

Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy

Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data

Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales

The glycan alphabet is not universal: a hypothesis

Optimized use of Oxford Nanopore flowcells for hybrid assemblies

Azithromycin resistance mutations in Streptococcus pneumoniae as revealed by a chemogenomic screen

Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes

Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone

Most read this month

Most cited this month Most Cited RSS feed

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

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

Completing bacterial genome assemblies with multiplex MinION sequencing

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

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

Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

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