Microbial Genomics

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

Browse these key collections:

Methods and Software
Bacteriophage
Microreact

Journal status	Active

Articles from the latest issue Latest Articles Rss Feed

- ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data
  
  Kyrylo Bessonov , Chad Laing , James Robertson , Irene Yong, Kim Ziebell , Victor P. J. Gannon , Anil Nichani , Gitanjali Arya , John H. E. Nash and Sara Christianson
- Single-cell genomics-based analysis reveals a vital ecological role of Thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia
  
  Yu-Ting Wu , Pei-Wen Chiang, Kshitij Tandon, Denis Yu Rogozin, Andrey G. Degermendzhy and Sen-Lin Tang
- Using whole-genome sequencing to assess the diversity of Paenibacillus larvae within an outbreak and a beekeeping operation
  
  Bojan Papić , Majda Golob , Irena Zdovc , Jana Avberšek , Metka Pislak Ocepek and Darja Kušar
- Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom
  
  Yu Wan , Ewurabena Mills, Rhoda C.Y. Leung , Ana Vieira , Xiangyun Zhi , Nicholas J. Croucher , Neil Woodford, Elita Jauneikaite , Matthew J. Ellington and Shiranee Sriskandan

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
- 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
- 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
- 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
- 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
- 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
- EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens
  
  Duo Peng and Rick Tarleton
- Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii
  
  Mohammad Hamidian and Steven J. Nigro
- In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages
  
  Danielle J. Ingle, Mary Valcanis, Alex Kuzevski, Marija Tauschek, Michael Inouye, Tim Stinear, Myron M. Levine, Roy M. Robins-Browne and Kathryn E. Holt
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Microbial Genomics

Articles from the latest issue Latest Articles Rss Feed

ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data

Single-cell genomics-based analysis reveals a vital ecological role of Thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia

Using whole-genome sequencing to assess the diversity of Paenibacillus larvae within an outbreak and a beekeeping operation

Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom

Most read this month

Most cited this month Most Cited RSS feed

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

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

Identification of Klebsiella capsule synthesis loci from whole genome data

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

Completing bacterial genome assemblies with multiplex MinION sequencing

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

EuPaGDT: a web tool tailored to design CRISPR guide RNAs for eukaryotic pathogens

Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii

In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages