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

- AB_SA: Accessory genes-Based Source Attribution – tracing the source of Salmonella enterica Typhimurium environmental strains
  
  Laurent Guillier , Michèle Gourmelon , Solen Lozach , Sabrina Cadel-Six , Marie-Léone Vignaud, Nanna Munck , Tine Hald and Federica Palma
- Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis
  
  Rebecca J. Hall , Stephen Thorpe , Gavin H. Thomas and A. Jamie Wood
- Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS
  
  Sergio Mascarenhas Morgado and Ana Carolina Paulo Vicente
- The past, present and future of ancient bacterial DNA
  
  Nicolas Arning and Daniel J. Wilson
- Genomic sequence analysis of Dissulfurirhabdus thermomarina SH388 and proposed reassignment to Dissulfurirhabdaceae fam. nov.
  
  Lewis M. Ward , Emma Bertran and David T. Johnston
- Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients
  
  Bede Constantinides , Kevin K. Chau , T. Phuong Quan , Gillian Rodger , Monique I. Andersson , Katie Jeffery , Sam Lipworth , Hyun S. Gweon , Andy Peniket , Graham Pike, Julian Millo , Mary Byukusenge, Matt Holdaway , Cat Gibbons , Amy J. Mathers , Derrick W. Crook , Timothy E.A. Peto, A. Sarah Walker and Nicole Stoesser
- Evaluation of methods for detecting human reads in microbial sequencing datasets
  
  Stephen J. Bush , Thomas R. Connor , Tim E.A. Peto, Derrick W. Crook and A. Sarah Walker
- socru: typing of genome-level order and orientation around ribosomal operons in bacteria
  
  Andrew J. Page, Emma V. Ainsworth and Gemma C. Langridge
- Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank
  
  Jacob Armstrong , Justine K. Rudkin , Naomi Allen , Derrick W. Crook , Daniel J. Wilson , David H. Wyllie and Anne Marie O’Connell
- Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species
  
  Ethan T. Hillman , Ariangela J. Kozik , Casey A. Hooker, John L. Burnett, Yoojung Heo, Violet A. Kiesel, Clayton J. Nevins , Jordan M.K.I. Oshiro , Melissa M. Robins, Riya D. Thakkar, Sophie Tongyu Wu and Stephen R. Lindemann
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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
- 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
- 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
- Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence
  
  Roman Thibeaux, Gregorio Iraola, Ignacio Ferrés, Emilie Bierque, Dominique Girault, Marie-Estelle Soupé-Gilbert, Mathieu Picardeau and Cyrille Goarant
- Correlation between bacterial G+C content, genome size and the G+C content of associated plasmids and bacteriophages
  
  Apostolos Almpanis, Martin Swain, Derek Gatherer and Neil McEwan
- 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
- 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
- Completing bacterial genome assemblies with multiplex MinION sequencing
  
  Ryan R. Wick, Louise M. Judd, Claire L. Gorrie and Kathryn E. Holt
- Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone
  
  Laura Villa, Claudia Feudi, Daniela Fortini, Sylvain Brisse, Virginie Passet, Celestino Bonura, Andrea Endimiani, Caterina Mammina, Ana Maria Ocampo, Judy Natalia Jimenez, Michel Doumith, Neil Woodford, Katie Hopkins and Alessandra Carattoli
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Microbial Genomics

Articles from the latest issue Latest Articles Rss Feed

AB_SA: Accessory genes-Based Source Attribution – tracing the source of Salmonella enterica Typhimurium environmental strains

Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis

Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS

The past, present and future of ancient bacterial DNA

Genomic sequence analysis of Dissulfurirhabdus thermomarina SH388 and proposed reassignment to Dissulfurirhabdaceae fam. nov.

Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

Evaluation of methods for detecting human reads in microbial sequencing datasets

socru: typing of genome-level order and orientation around ribosomal operons in bacteria

Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank

Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species

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

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

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

Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence

Correlation between bacterial G+C content, genome size and the G+C content of associated plasmids and bacteriophages

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

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

Completing bacterial genome assemblies with multiplex MinION sequencing

Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone