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Molecular Microbiology in the Omics Era: Genomics, Metagenomics and Computational Insights

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 597

Special Issue Editor

Institute of Microbiology Chinese Academy of Sciences, Beijing, China
Interests: microbial genomics; metagenomics; multi-omics integration; evolution; bioinformatics

Special Issue Information

Dear Colleagues,

This Special Issue highlights transformative advances in molecular microbiology driven by omics technologies and computational biology. We welcome studies leveraging genomics, metagenomics, transcriptomics, and bioinformatics to unravel microbial diversity, evolution, host–microbe interactions, and functional mechanisms at the molecular level. Topics include, but are not limited to, the following:

  • High-throughput sequencing approaches for pathogen surveillance or microbiome analysis;
  • Computational tools for genome annotation, comparative genomics, or metagenomic assembly;
  • Molecular mechanisms of antimicrobial resistance (AMR) and virulence;
  • Integrative multi-omics strategies to study microbial communities;
  • AI and machine learning applications in microbial data analysis.

Both original research and reviews addressing methodological innovations or translational insights are encouraged. By bridging wet-lab experiments with in silico analyses, this Special Issue aims to showcase how omics-driven approaches are redefining microbiology research in the post-genomic era.

Dr. Fei Liu
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Keywords

  • microbial genomics
  • metagenomics
  • computational biology
  • antimicrobial resistance
  • host–microbe interactions
  • multi-omics integration
  • bioinformatics tools
  • machine learning in microbiology

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Published Papers (1 paper)

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Research

27 pages, 20860 KiB  
Article
Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities
by Ilia V. Popov, Andrey D. Manakhov, Vladislav E. Gorobets, Kristina B. Diakova, Ekaterina A. Lukbanova, Aleksey V. Malinovkin, Koen Venema, Alexey M. Ermakov and Igor V. Popov
Int. J. Mol. Sci. 2025, 26(13), 5941; https://doi.org/10.3390/ijms26135941 - 20 Jun 2025
Viewed by 447
Abstract
Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia [...] Read more.
Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings. Full article
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