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

- Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes
  
  Ana R. Freitas , Ana P. Tedim , Carla Novais , Val F. Lanza and Luísa Peixe
- Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software
  
  Charlotte Couchoud , Xavier Bertrand , Benoit Valot and Didier Hocquet
- Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada
  
  Lu Ya Ruth Wang , Cassandra C. Jokinen, Chad R. Laing , Roger P. Johnson, Kim Ziebell and Victor P. J. Gannon
- Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors
  
  Yuhao Chen, Thomas C. Brook, Cho Zin Soe , Ian O'Neill, Cristina Alcon-Giner, Onnicha Leelastwattanagul , Sarah Phillips , Shabhonam Caim , Paul Clarke , Lindsay J. Hall and Lesley Hoyles
- Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species
  
  Zhixiao Xu, Na Li, Yaqiong Guo, Yaoyu Feng and Lihua Xiao
- Microevolution in the major outer membrane protein OmpA of Acinetobacter baumannii
  
  Alejandro M. Viale and Benjamin A. Evans
- Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands
  
  Ethan R. Wyrsch , Piklu Roy Chowdhury , Louise Wallis , Max L. Cummins , Tiziana Zingali , Kate J. Brandis and Steven P. Djordjevic
- Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in Escherichia coli ST58
  
  Ethan R. Wyrsch , Piklu Roy Chowdhury , Veronica M. Jarocki , Kate J. Brandis and Steven P. Djordjevic
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Most cited this month Most Cited RSS feed

- 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
- On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data
  
  Sergio Arredondo-Alonso, Rob J. Willems, Willem van Schaik and Anita C. Schürch
- 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
- 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
- Completing bacterial genome assemblies with multiplex MinION sequencing
  
  Ryan R. Wick, Louise M. Judd, Claire L. Gorrie and Kathryn E. Holt
- Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene
  
  Max L. Cummins, Cameron J. Reid, Piklu Roy Chowdhury, Rhys N. Bushell, Nicolas Esbert, Kelly A. Tivendale, Amir H. Noormohammadi, Shaiful Islam, Marc S. Marenda, Glenn F. Browning, Philip F. Markham and Steven P. Djordjevic
- Genome-scale rates of evolutionary change in bacteria
  
  Sebastian Duchêne, Kathryn E. Holt, François-Xavier Weill, Simon Le Hello, Jane Hawkey, David J. Edwards, Mathieu Fourment and Edward C. Holmes
- Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes
  
  Paul O. Sheridan, Jennifer C. Martin, Trevor D. Lawley, Hilary P. Browne, Hugh M. B. Harris, Annick Bernalier-Donadille, Sylvia H. Duncan, Paul W. O'Toole, Karen P. Scott and Harry J. Flint
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Microbial Genomics

Articles from the latest issue Latest Articles Rss Feed

Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada

Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors

Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species

Microevolution in the major outer membrane protein OmpA of Acinetobacter baumannii

Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands

Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in Escherichia coli ST58

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

On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data

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

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

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

Completing bacterial genome assemblies with multiplex MinION sequencing

Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene

Genome-scale rates of evolutionary change in bacteria

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes