Microbial Genomics

E-ISSN: 2057-5858

Microbial Genomics pioneers all areas of genome research spanning the breadth of microbial life including viruses, bacteria, archaea and microbial eukaryotes. We welcome articles showing novel insights, new applications, or innovative approaches using genomic data. Content ranges from comparative and functional genomics of model organisms to population-scale evolution, epidemiology and microbiome studies, and real-world genomics applications with clinical, veterinary or environmental relevance. See full journal scope

As part of our continuing commitment to Open Access, from January 2023 the Society's founding journal Microbiology will be moving to a fully open access publication model. Read more about it, and our wider OA journey, in this news story.

Browse these key collections:

Methods and Software
Bacteriophage
Microreact

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Articles from the latest issue Latest Articles Rss Feed

- Identification and characterization of virus-encoded circular RNAs in host cells
  
  Shuting Chen, Jie Zheng , Bingyue Zhang , Xinyue Tang , Yewei Cun , Tao Wu, Yue Xu, Ting Ma, Jingxin Cheng, Zuoren Yu and Haiyun Wang
- Virulence plasmid pINV as a genetic signature for Shigella flexneri phylogeny
  
  Giulia Pilla , Gabriele Arcari, Christoph M. Tang and Alessandra Carattoli
- Genome plasticity driven by aneuploidy and loss of heterozygosity in Trypanosoma cruzi
  
  Lissa Cruz-Saavedra , Philipp Schwabl, Gustavo A. Vallejo, Julio C. Carranza, Marina Muñoz, Luz Helena Patino , Alberto Paniz-Mondolfi, Martin S. Llewellyn and Juan David Ramírez
- Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials
  
  Jiarui Sun , Apoorva Prabhu , Samuel T. N. Aroney and Christian Rinke
- Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit
  
  Vivien Price, Steven J. Dunn, Robert A. Moran, Jonathan Swindells and Alan McNally
- GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes
  
  Robert A. Moran, Haiyang Liu, Emma L. Doughty, Xiaoting Hua, Elizabeth A. Cummins, Tomas Liveikis, Alan McNally, Zhihui Zhou, Willem van Schaik and Yunsong Yu
- A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation
  
  Kristina M. Ceres , Michael J Stanhope and Yrjö T. Gröhn
- Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13
  
  Sophie Belman , Sona Soeng, Chansovannara Soputhy, Rebecca Gladstone, Paulina A. Hawkins, Robert F. Breiman, Lesley McGee, Stephen D. Bentley, Stephanie W. Lo and Paul Turner
- Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance
  
  Shaimaa F. Mouftah , Ben Pascoe , Jessica K. Calland , Evangelos Mourkas , Naomi Tonkin, Charlotte Lefevre , Danielle Deuker, Sunny Smith, Harry Wickenden, Matthew D. Hitchings , Samuel K. Sheppard and Mohamed Elhadidy
- Curation of the AMRFinderPlus databases: applications, functionality and impact
  
  Michael Feldgarden , Vyacheslav Brover, Boris Fedorov, Daniel H. Haft, Arjun B. Prasad and William Klimke
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- Completing bacterial genome assemblies with multiplex MinION sequencing
  
  Ryan R. Wick, Louise M. Judd, Claire L. Gorrie and Kathryn E. Holt
- 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
- 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
- MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies
  
  James Robertson and John H. E. Nash
- 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
- Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations
  
  Margaret M. C. Lam, Ryan R. Wick, Kelly L. Wyres, Claire L. Gorrie, Louise M. Judd, Adam W. J. Jenney, Sylvain Brisse and Kathryn E. Holt
- 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
- 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
- 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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Articles from the latest issue Latest Articles Rss Feed

Identification and characterization of virus-encoded circular RNAs in host cells

Virulence plasmid pINV as a genetic signature for Shigella flexneri phylogeny

Genome plasticity driven by aneuploidy and loss of heterozygosity in Trypanosoma cruzi

Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials

Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit

GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes

A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation

Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13

Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance

Curation of the AMRFinderPlus databases: applications, functionality and impact

Most read this month

Most cited this month Most Cited RSS feed

Completing bacterial genome assemblies with multiplex MinION sequencing

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

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

MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

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

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

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