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

- Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland
  
  Joseph Crispell , Sophie Cassidy, Kevin Kenny , Guy McGrath , Susan Warde, Henrietta Cameron, Gianluigi Rossi , Teresa MacWhite , Piran C. L. White , Samantha Lycett , Rowland R. Kao , John Moriarty and Stephen V. Gordon
- The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites
  
  Feifei Xu , Alejandro Jiménez-González , Elin Einarsson , Ásgeir Ástvaldsson , Dimitra Peirasmaki , Lars Eckmann, Jan O. Andersson , Staffan G. Svärd and Jon Jerlström-Hultqvist
- Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia
  
  Chandler Roe , Marc Stegger , Berit Lilje, Thor Bech Johannesen, Kim Lee Ng , Raphael N. Sieber , Elizabeth Driebe, David M. Engelthaler and Paal Skytt Andersen
- Whole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes
  
  Rajendra KC , Kelvin W.C. Leong , Nicholas M. Harkness, Julia Lachowicz, Sanjay S. Gautam , Louise A. Cooley , Belinda McEwan, Steve Petrovski , Gunasegaran Karupiah and Ronan F. O'Toole
- Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
  
  Ana Elena Pérez-Cobas , Laura Gomez-Valero and Carmen Buchrieser
- A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics
  
  Martinique Frentrup, Zhemin Zhou , Matthias Steglich , Jan P. Meier-Kolthoff , Markus Göker , Thomas Riedel, Boyke Bunk , Cathrin Spröer, Jörg Overmann , Marion Blaschitz, Alexander Indra, Lutz von Müller, Thomas A. Kohl , Stefan Niemann, Christian Seyboldt, Frank Klawonn , Nitin Kumar, Trevor D. Lawley, Sergio García-Fernández , Rafael Cantón , Rosa del Campo , Ortrud Zimmermann , Uwe Groß, Mark Achtman and Ulrich Nübel
- Comparative genome analysis of Erysipelothrix rhusiopathiae isolated from domestic pigs and wild boars suggests host adaptation and selective pressure from the use of antibiotics
  
  Robert Söderlund , Nicoletta Formenti , Stefania Caló , Mario Chiari , Mate Zoric , Giovanni Loris Alborali , Tina Sørensen Dalgaard , Eva Wattrang and Helena Eriksson
- Defining the transcriptional responses of Aspergillus nidulans to cation/alkaline pH stress and the role of the transcription factor SltA
  
  Irene Picazo, Oier Etxebeste , Elena Requena, Aitor Garzia and Eduardo Antonio Espeso
- Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences
  
  Katharine S. Walter , Caroline Colijn , Ted Cohen , Barun Mathema , Qingyun Liu , Jolene Bowers , David M. Engelthaler , Apurva Narechania, Darrin Lemmer , Julio Croda and Jason R. Andrews
- Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage
  
  Carla Rodrigues , Camille d’Humières, Grégory Papin, Virginie Passet, Etienne Ruppé and Sylvain Brisse
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Most cited this month Most Cited RSS feed

- 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
- 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
- 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
- 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
- Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes
  
  Nicola De Maio, Liam P. Shaw, Alasdair Hubbard, Sophie George, Nicholas D. Sanderson, Jeremy Swann, Ryan Wick, Manal AbuOun, Emma Stubberfield, Sarah J. Hoosdally, Derrick W. Crook, Timothy E. A. Peto, Anna E. Sheppard, Mark J. Bailey, Daniel S. Read, Muna F. Anjum, A. Sarah Walker, Nicole Stoesser and on behalf of the REHAB consortium
- 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
- 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
- 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
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Microbial Genomics

Articles from the latest issue Latest Articles Rss Feed

Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites

Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia

Whole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses

A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

Comparative genome analysis of Erysipelothrix rhusiopathiae isolated from domestic pigs and wild boars suggests host adaptation and selective pressure from the use of antibiotics

Defining the transcriptional responses of Aspergillus nidulans to cation/alkaline pH stress and the role of the transcription factor SltA

Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences

Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage

Most read this month

Most cited this month Most Cited RSS feed

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

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

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

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

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

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

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

Identification of Klebsiella capsule synthesis loci from whole genome data