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

Latest articles

- Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198
  
  Jane Hawkey , Simon Le Hello, Benoît Doublet , Sophie A. Granier , Rene S. Hendriksen , W. Florian Fricke , Pieter-Jan Ceyssens , Camille Gomart , Helen Billman-Jacobe , Kathryn E. Holt and François-Xavier Weill
- A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network
  
  Charles H. D. Williamson, Nathan E. Stone, Amalee E. Nunnally, Heidie M. Hornstra , David M. Wagner , Chandler C. Roe , Adam J. Vazquez , Nivedita Nandurkar, Jacob Vinocur , Joel Terriquez, John Gillece , Jason Travis , Darrin Lemmer , Paul Keim and Jason W. Sahl
- Putative novel cps loci in a large global collection of pneumococci
  
  Andries J. van Tonder , Rebecca A. Gladstone , Stephanie W. Lo , Moon H. Nahm, Mignon du Plessis , Jennifer Cornick , Brenda Kwambana-Adams , Shabir A. Madhi , Paulina A. Hawkins , Rachel Benisty, Ron Dagan, Dean Everett, Martin Antonio, Keith P. Klugman , Anne von Gottberg , Robert F. Breiman, Lesley McGee , Stephen D. Bentley and The Global Pneumococcal Sequencing Consortium
- Endemic fluoroquinolone-resistant Salmonella enterica serovar Kentucky ST198 in northern India
  
  Jaspreet Mahindroo , Duy Pham Thanh, To Nguyen Thi Nguyen, Balvinder Mohan , Siddhartha Thakur , Stephen Baker and Neelam Taneja
- Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes
  
  Rebecca Weiser, Angharad E. Green , Matthew J. Bull , Edward Cunningham-Oakes , Keith A. Jolley , Martin C. J. Maiden , Amanda J. Hall, Craig Winstanley , Andrew J. Weightman , Denise Donoghue, Alejandro Amezquita, Thomas R. Connor and Eshwar Mahenthiralingam
- Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization
  
  Jumamurat R. Bayjanov , Jery Baan , Malbert R. C. Rogers, Annet Troelstra, Rob J. L. Willems and Willem van Schaik
- Enterohaemorrhagic Escherichia coli O121:H19 acquired an extended-spectrum β-lactamase gene during the development of an outbreak in two nurseries
  
  Koji Kikuchi, Kenichi Lee , Hiroyuki Ueno, Kentaro Tomari, Sumie Kobori, Akihiko Kaetsu, Mari Matsui, Satowa Suzuki, Tsuyoshi Sekizuka, Makoto Kuroda , Motonobu Miyazaki and Makoto Ohnishi
- Domestication of Campylobacter jejuni NCTC 11168
  
  Ben Pascoe , Lisa K. Williams , Jessica K. Calland, Guillaume Meric , Matthew D. Hitchings , Myles Dyer, Joseph Ryder , Sophie Shaw , Bruno S. Lopes, Cosmin Chintoan-Uta , Elaine Allan, Ana Vidal, Catherine Fearnley, Paul Everest, Justin A. Pachebat , Tristan A. Cogan , Mark P. Stevens , Thomas J. Humphrey , Thomas S. Wilkinson , Alison J. Cody , Frances M. Colles , Keith A. Jolley , Martin C. J. Maiden , Norval Strachan, Bruce M. Pearson , Dennis Linton , Brendan W. Wren , Julian Parkhill , David J. Kelly , Arnoud H. M. van Vliet , Ken J. Forbes and Samuel K. Sheppard
- Genomics of vancomycin-resistant Enterococcus faecium
  
  Claire Gorrie , Charlie Higgs , Glen Carter, Timothy P. Stinear and Benjamin Howden
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Most Cited This Month

- 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
- 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
- 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
- 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
- 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
- Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data
  
  Andrew J. Page, Nishadi De Silva, Martin Hunt, Michael A. Quail, Julian Parkhill, Simon R. Harris, Thomas D. Otto and Jacqueline A. Keane
- 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 electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer
  
  Dawn E. Holmes, Yan Dang, David J. F. Walker and Derek R. Lovley
- 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

Latest articles

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network

Putative novel cps loci in a large global collection of pneumococci

Endemic fluoroquinolone-resistant Salmonella enterica serovar Kentucky ST198 in northern India

Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes

Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization

Enterohaemorrhagic Escherichia coli O121:H19 acquired an extended-spectrum β-lactamase gene during the development of an outbreak in two nurseries

Domestication of Campylobacter jejuni NCTC 11168

Genomics of vancomycin-resistant Enterococcus faecium

Most Read This Month

Most Cited This Month

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

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Identification of Klebsiella capsule synthesis loci from whole genome data

Genome-scale rates of evolutionary change in bacteria

Completing bacterial genome assemblies with multiplex MinION sequencing

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

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

The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer

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