Submit to the Microbial Genomics Methods and Software Collection

06 June 2019

The Microbiology Society is pleased to announce the launch of the new Methods and Software collection in Microbial Genomics.

Guest-edited by Dr Zamin Iqbal (European Bioinformatics Institute) and Dr Caroline Colijn (Simon Fraser University), the collection aims to provide the microbial genomics community with new and systematically validated tools to advance their research. This collection will bring together articles describing novel experimental, bioinformatics, modelling and statistical approaches to the analysis of microbial genomics data, including databases or the integration of genomics with other data streams; as well as systematic comparisons or benchmarking of existing methodologies used in the field of microbial genomics.

Microbial Genomics has published dozens of papers describing methods for microbial genomics analysis. Some of our most highly cited methods papers are those describing novel software packages that have rapidly achieved widespread use in the microbial genomics community (e.g. ARIBA for detecting antimicrobial resistance genes, and Microreact for visualising and sharing genomic epidemiology and phylogeography data). Microbial Genomics articles describing software for organism-specific genome-based typing have also been popular, including serotyping tools for Klebsiella, Escherichia coli, Streptococcus pneumoniae and Neisseria gonorrhoeae.

In addition to methods for applied genomic epidemiology, we have published articles analysing microbial evolution using genomic data, including a modelling study exploring how recombination produces coherent bacterial species clusters, the SimBac tool for simulating bacterial evolution with recombination, and a comparison of evolutionary rates across bacterial species. Strategies for overcoming the challenges of genome assembly from short reads have been widely cited both for bacteria and parasites.

Microbial Genomics has hosted strong methods articles exploring the benefits of new long-read sequencing technologies for assembling bacterial genomes, both in general and specifically applied to plasmid assembly and medical microbiology. Plasmids, mobile genetic elements and horizontal gene transfer are arguably the most intriguing and dynamic phenomena shaping microbial genomes, but are the most challenging to study. Microbial Genomics is home to articles describing some promising new methods to tackle the complexities of plasmid analysis, including MOB-suite, mlplasmids, PlasmidTron and PlaScope; and others introducing new approaches to identifying insertion sequences and transposons.

While individual microbial genomes are tiny, the enormous scale of microbial genomic data necessitates smarter and more computationally efficient methods for data analysis, and Microbial Genomics has published some exciting methodological papers in this area. These include SuperDCA for genome-wide epistasis analysis, PANINI for pan-genome clustering of bacterial populations, and SynerClust for efficient synteny-aware ortholog clustering. Two recent papers explore interesting new applications of machine learning to problems in microbial genomics – plasmid identification, and host specificity prediction.

The Methods and Software collection has been launched alongside the Applied Bioinformatics and Public Health Microbiology meeting. The provisional deadline for the submissions is 31 October 2019 and authors wishing to be considered for collection should submit their manuscript to the online submission system, indicating in their cover letter that the manuscript it is intended for the Methods and Software collection.

You can find the methods and software articles already published in Microbial Genomics online now. The cover image for this collection brings together figures from two of retrospective articles in the collection: a phylogeny richly annotated with insertion sequence sites from the article on ISseeker by Adams et al. 2016 (bottom left); and a genome assembly graph from the article on completing bacterial genomes by Wick et al. 2017 (top right).

Methods and Software collection cover image

Microbial Genomics is a fully Open Access, Open Data, peer-reviewed journal that publishes high-quality, pioneering research into genomic approaches to microbiology. Find out more at