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Microorganisms
Special Issues
Microbial Evolutionary Genomics and Bioinformatics
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Microbial Evolutionary Genomics and Bioinformatics

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".

Deadline for manuscript submissions: 30 September 2025 | Viewed by 1955

Special Issue Editor

Prof. Dr. Agostinho Antunes

E-Mail Website
Guest Editor
1. CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixoes, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal
2. Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
Interests: genomics (from animals to microorganisms); evolution, molecular ecology; conservation; biotechnology; bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a curated collection that brings together the latest research at the intersection of microbial evolution, genomics, and bioinformatics. This issue aims to provide a comprehensive overview of how advanced computational methods and genomic data are revolutionizing our understanding of microbial life and its evolutionary history. The key themes and topics covered in this Special Issue include, but are not limited to:

  1. Microbiomes genomics;
  2. Bacteria genomics diversity and evolution;
  3. Virus genomics and evolution;
  4. Microbial pathogenicity genomics;
  5. Bioinformatics advances in microbial research;
  6. Microbial-genome-encoded bioactive molecules. 

Research articles and comprehensive reviews are also welcome.

You may choose our Joint Special Issue in Applied Microbiology.

Prof. Dr. Agostinho Antunes
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. 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.

Keywords

  • microbiomes genomics
  • bacteria genomics diversity and evolution
  • irus genomics and evolution
  • microbial pathogenicity genomics
  • bioinformatics advances in microbial research
  • microbial-genome-encoded bioactive molecules

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Published Papers (2 papers)

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Research

21 pages, 2707 KiB  
Article
Distribution of Genetic Determinants Associated with CRISPR-Cas Systems and Resistance to Antibiotics in the Genomes of Archaea and Bacteria
by Laura Antequera-Zambrano, Ángel Parra-Sánchez, Lenin González-Paz, Eduardo Fernandez and Gema Martinez-Navarrete
Microorganisms 2025, 13(6), 1321; https://doi.org/10.3390/microorganisms13061321 - 6 Jun 2025
Viewed by 482
Abstract
The CRISPR-Cas system represents an adaptive immune mechanism found across diverse Archaea and Bacteria, allowing them to defend against invading genetic elements such as viruses and plasmids. Despite its broad distribution, the prevalence and complexity of CRISPR-Cas systems differ significantly between these domains. [...] Read more.
The CRISPR-Cas system represents an adaptive immune mechanism found across diverse Archaea and Bacteria, allowing them to defend against invading genetic elements such as viruses and plasmids. Despite its broad distribution, the prevalence and complexity of CRISPR-Cas systems differ significantly between these domains. This study aimed to characterize and compare the genomic distribution, structural features, and functional implications of CRISPR-Cas systems and associated antibiotic resistance genes in 30 archaeal and 30 bacterial genomes. Through bioinformatic analyses of CRISPR arrays, cas gene architectures, direct repeats (DRs), and thermodynamic properties, we observed that Archaea exhibit a higher number and greater complexity of CRISPR loci, with more diverse cas gene subtypes exclusively of Class 1. Bacteria, in contrast, showed fewer CRISPR loci, comprising a mix of Class 1 and Class 2 systems, with Class 1 representing the majority (~75%) of the detected systems. Notably, Bacteria lacking CRISPR-Cas systems displayed a higher prevalence of antibiotic resistance genes, suggesting a possible inverse correlation between the presence of these immune systems and the acquisition of such genes. Phylogenetic and thermodynamic analyses further highlighted domain-specific adaptations and conservation patterns. These findings support the hypothesis that CRISPR-Cas systems play a dual role: first, as a defense mechanism preventing the integration of foreign genetic material—reflected in the higher complexity and diversity of CRISPR loci in Archaea—and second, as a regulator of horizontal gene transfer, evidenced by the lower frequency of antibiotic resistance genes in organisms with active CRISPR-Cas systems. Together, these results underscore the evolutionary and functional diversification of CRISPR-Cas systems in response to environmental and selective pressures. Full article
(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)
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19 pages, 12303 KiB  
Article
Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2
by Fuminori Mizukoshi, Ryusuke Kimura, Tatsuya Shirai, Asumi Hirata-Saito, Eri Hiraishi, Kosuke Murakami, Yen Hai Doan, Hiroyuki Tsukagoshi, Nobuhiro Saruki, Takeshi Tsugawa, Kana Kidera, Yoshiyuki Suzuki, Naomi Sakon, Kazuhiko Katayama, Tsutomu Kageyama, Akihide Ryo and Hirokazu Kimura
Microorganisms 2025, 13(2), 322; https://doi.org/10.3390/microorganisms13020322 - 1 Feb 2025
Viewed by 958
Abstract
Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using [...] Read more.
Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using bioinformatics tools such as the Bayesian phylogenetics software BEAST 2 package (v.2.7.6), we constructed time-scale evolutionary trees based on the gene sequences. Most of the recent common ancestors (MRCAs) of the RdRp region and VP1 gene in the present HuSaV GI.1 diverged around 1930 and 1933, respectively. The trees of the HuSaV GI.1 RdRp region and VP1 gene were divided into two clusters. Further, the MRCAs of the RdRp region and VP1 gene in HuSaV GI.2 diverged in 1960 and 1943, respectively. The evolutionary rates were higher for VP1 gene in HuSaV GI.1 than that in HuSaV GI.2, furthermore, were higher in GI.1 Cluster B than GI.1 Cluster A. In addition, a steep increase was observed in the time-scaled genome population size of the HuSaV GI.1 Cluster B. These results indicate that the HuSaV GI.1 Cluster B may be evolving more actively than other genotypes. The conformational B-cell epitopes were predicted with a higher probability in RdRp for GI.1 and in VP1 for GI.2, respectively. These results suggest that the RdRp region and VP1 gene in HuSaV GI.1 and GI.2 evolved uniquely. These findings suggest unique evolutionary patterns in the RdRp region and VP1 gene of HuSaV GI.1 and GI.2, emphasizing the need for a ‘One Health’ approach to better understand and combat this pathogen. Full article
(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)
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