Microbial Genomics in the Age of Omics and Artificial Intelligence

Dear Colleagues,

Since the advent of next-generation sequencing technologies, the number of genome projects documented in online genomic databases has increased exponentially, particularly for bacterial genomes. This heightened interest in bacterial organisms is primarily attributed to their ubiquitous presence and their diverse applications across industry, agriculture, research, and numerous other fields. Of particular significance are pathogenic bacteria, which warrant close attention due to their medical and veterinary relevance and their prominent role in integrated one health approaches.

The application of omics technologies—including genomics, transcriptomics, proteomics, metabolomics, among others—holds significant potential for advancements in pangenomics, phylogenomics, whole-genome multi-locus sequence typing, reverse vaccinology, subtractive genomics, studies on genome plasticity (focusing on pathogenicity and resistance islands), protein–protein interactions, and metabolic pathway predictions. Furthermore, these approaches are increasingly complemented by artificial intelligence techniques, particularly machine learning.

This Special Issue invites manuscript submissions that enhance our comprehension of host–pathogen interactions. Topics of interest include, but are not limited to, the identification of virulence factors and resistance-associated genes within pathogenicity and resistance islands using pangenomic strategies, the discovery of novel vaccine and drug targets through reverse vaccinology and subtractive genomics to address the escalating issue of multi-drug resistance, and the prediction of protein–protein interactions and metabolic pathways, accompanied by analyses of biofilm formation. Submissions focusing on one health perspectives, genomic islands, and pangenomic approaches with a particular emphasis on antibiotic resistance are highly encouraged.

Prof. Dr. Sandeep Tiwari
Dr. Arun Kumar Jaiswal
Prof. Dr. Siomar De Castro Soares
Dr. Flávia Figueira Aburjaile
Prof. Dr. Vasco Ariston De Carvalho Azevedo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

• artificial intelligence
• microbial genomes
• genome plasticity
• next-generation sequencing
• one health approach
• pangenomics
• reverse vaccinology