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A Special Issue of Microorganisms (ISSN 2076-2607) belonging to the section "Microbiomes".

Deadline for manuscript submissions: closed (31 May 2026) | Viewed by 11232

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Prof. Dr. Agostinho Antunes

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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; antimicrobial peptides
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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:

Microbiomes genomics;
Bacteria genomics diversity and evolution;
Virus genomics and evolution;
Microbial pathogenicity genomics;
Bioinformatics advances in microbial research;
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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized 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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Related Special Issue

Microbial Evolutionary Genomics and Bioinformatics—2nd Edition in Microorganisms

Published Papers (7 papers)

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Research

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14 pages, 1778 KB

Open AccessArticle

Molecular Epidemiology of the bla_CTX-M Gene in Escherichia coli from a Pig Farm: Antimicrobial Resistance Profiles, Genetic Background, and Its Horizontal Transfer and Environmental Dissemination

by Ri-Han Jiang, Zi-Kui Liu, Bing Han, Dan-Ni Liao, Ji-Yun Li and Yong Wu

Microorganisms 2026, 14(5), 1007; https://doi.org/10.3390/microorganisms14051007 - 29 Apr 2026

Viewed by 950

Abstract

This study investigated the epidemiology, antimicrobial resistance, and transmission risks of β-lactamase, cefotaxime-hydrolyzing, Munich (bla_CTX-M)-positive Escherichia coli (CTX-M-EC) in large-scale pig farms in Jiangxi Province (China). In total, 278 samples (manure, wastewater, drinking water, and flies) were collected. CTX-M-EC strains were isolated and analyzed using antimicrobial susceptibility testing, resistance gene profiling, multilocus sequence typing, and genetic environment analysis with gene transfer assessed by transduction experiments. Twenty-seven CTX-M-EC strains (9.71%) were isolated, all exhibiting multi-drug resistance with 100% resistance to cefotaxime, ciprofloxacin, and tetracycline, and >90% resistance to ceftazidime, florfenicol, and trimethoprim-sulfamethoxazole. Four bla_CTX-M subtypes were identified. bla_CTX-M-55 was the predominant subtype (70.37%) and was distributed across diverse sequence types and serotypes. Each strain harbored multiple antibiotic resistance genes, plasmids, and virulence genes. Mobile elements such as ISEcp1 and IS26 were detected surrounding the bla_CTX-M gene, and 96.29% of strains successfully transferred the bla_CTX-M gene via transduction. Clones highly homologous to pig manure strains were detected in flies and sewage, suggesting that this resistance gene can spread between animals, the environment, and vectors. These findings highlight the high transmission risk of bla_CTX-M and underscore the need for rational antibiotic use, waste management, and vector control within a One Health framework. Full article

(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)

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15 pages, 3042 KB

Open AccessCommunication

Cross-Species Amyloid-like Features Shared by Mammalian and Clostridioides difficile Proteins

by Weichen Gong

Microorganisms 2026, 14(4), 821; https://doi.org/10.3390/microorganisms14040821 - 2 Apr 2026

Cited by 1 | Viewed by 660

Abstract

Functional amyloids are widely distributed in bacteria and play important roles in biofilm formation and microbial physiology. However, most currently known bacterial amyloids have been identified through sequence homology to a limited number of prototype proteins, such as the curli subunit CsgA of Escherichia coli. This approach may overlook amyloidogenic sequences that lack recognizable similarity to these canonical systems. In this study, a cross-species, motif-based computational strategy was used to explore whether conserved sequence features derived from mammalian serum amyloid A (SAA) proteins could provide clues for identifying potential amyloidogenic motifs in bacterial proteomes. Comparative analysis of mammalian SAA isoforms identified a conserved sequence segment with predicted aggregation propensity, within which the hydrophobic motif SIAIILCILIL was observed in murine SAA3. Database searches revealed that similar sequence motifs occur in several proteins encoded by Gram-positive bacteria, including multiple proteins in Clostridioides difficile. To further explore whether C. difficile produces extracellular structures capable of interacting with amyloid-binding dyes, Congo Red-supplemented agar assays were performed. After 48 h of growth, both clinical isolates and a laboratory reference strain exhibited Congo Red-binding colony phenotypes. Because Congo Red binding can arise from several extracellular components and cannot be attributed to a specific protein or sequence motif, these observations should be interpreted cautiously. Taken together, this study presents a motif-based computational framework for identifying candidate amyloidogenic motifs across species and highlights sequence features in bacterial proteomes that may warrant further biochemical and structural investigation. The results should be regarded as hypothesis-generating and provide a basis for future experimental validation of potential amyloid-forming proteins in bacteria. Full article

(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)

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20 pages, 2884 KB

Open AccessArticle

Comparative Analysis of Lineage Structure, Cellulose Locus Context, and Mobilome Diversity Across Complete Komagataeibacter Genomes

by Mustafa Guzel

Microorganisms 2026, 14(3), 653; https://doi.org/10.3390/microorganisms14030653 - 13 Mar 2026

Viewed by 1008

Abstract

Komagataeibacter strains are important bacterial cellulose producers, yet closely related isolates can differ in cellulose yield, pellicle properties, and genetic stability during propagation. Such variability suggests that lineage structure and mobile genetic elements both contribute to strain-level genomic divergence. Here, complete genome comparisons were used to integrate vertical relatedness, gene-content structure, cellulose-associated signatures, and mobilome heterogeneity across 22 closed Komagataeibacter assemblies. A maximum likelihood phylogeny inferred from 642 single copy core genes provided the lineage scaffold. An anvi’o pangenome analysis defined a constant core gene cluster component across genomes and a noncore fraction that accounted for most of the genome differences in gene content. Targeted features linked to cellulose biosynthesis and local c-di-GMP-associated context were extracted from each genome. These features captured differences in bcs neighborhood composition and the presence of nearby GGDEF and EAL domain signals. The resulting feature matrix was projected by principal component analysis to summarize between-genome variation. Mobilome profiles were strongly strain dependent. Plasmid homology clustering identified 12 clusters comprising 36 plasmids from 13 genomes, including two dominant clusters of seven and six plasmids. Mash-based distance summaries further distinguished clusters consistent with conserved backbones from clusters consistent with heterogeneous, module-driven relationships. Prophage sequences, assessed as VIBRANT-predicted regions, were widespread but sparse per genome and dominated by medium length fragments. Insertion sequence burden ranged from 50 to 181 elements per genome, indicating substantial differences in transposition-associated sequence content. Pairwise association tests did not support robust cross module covariation beyond expected relationships among pangenome composition metrics at the current sampling depth. Overall, these results provide a complete genome reference framework linking lineage structure and mobilome heterogeneity, and they define reusable resources for comparative studies in bacterial cellulose biotechnology. Full article

(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)

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16 pages, 921 KB

Open AccessArticle

Evolution of Translational Machinery in Fast- and Slow-Growing Bacteria

by Xuhua Xia

Microorganisms 2026, 14(2), 377; https://doi.org/10.3390/microorganisms14020377 - 5 Feb 2026

Cited by 1 | Viewed by 1140

Abstract

Bacterial species differ dramatically in their growth rates, reflecting distinct ecological strategies and physiological constraints. Because protein synthesis is a major determinant of cellular replication, I examined how genomic investment in the translation machinery varies across bacteria with widely different doubling times. Using 20 bacterial species spanning two major bacterial kingdoms (Bacillati and Pseudomonadati), I quantified ribosomal RNA (rrn) operon number, total tRNA gene number, and the allocation of tRNA genes among amino acids. Rapidly replicating Vibrio natriegens has 11 rrn operons and 129 tRNA genes in its genome, whereas slowly replicating Borrelia burgdorferi has only one rrn operon and 32 tRNA genes. I show that both the rrn operon number and the tRNA gene number decline sharply with increasing generation time, a pattern observed independently within each bacterial kingdom. Moreover, tRNA gene allocation is highly non-uniform: amino acids that are frequently used in proteins and encoded by large synonymous codon families are supported by disproportionately more tRNA genes. This relationship is well described by a simple model incorporating amino acid usage and codon family size, as illustrated in rapidly growing species such as Vibrio natriegens and Clostridium perfringens. In contrast, slow-growing bacteria maintain relatively minimalist translation systems. Together, these results demonstrate that bacterial genomes are systematically optimized for translation in a manner tightly coupled to growth strategy, revealing how natural selection tunes both the capacity and structure of the translation machinery. Full article

(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)

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21 pages, 2707 KB

Open AccessArticle

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

Cited by 5 | Viewed by 3518

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. 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 KB

Open AccessArticle

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

Cited by 2 | Viewed by 2203

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 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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27 pages, 2397 KB

Open AccessReview

Advances in Decoding Bacterial N-Terminal Proteoforms: Technologies, Challenges, and Functional Insights

by Valdes Snauwaert and Petra Van Damme

Microorganisms 2026, 14(8), 1671; https://doi.org/10.3390/microorganisms14081671 - 30 Jul 2026

Viewed by 582

Abstract

The bacterial proteome is a highly dynamic landscape rather than simply a static reflection of the genome. Recent research has revealed that proteome complexity extends far beyond canonical gene annotation, with N-terminal (Nt-)proteoforms emerging as an important underexplored additional regulatory layer. These molecular variants originate from a single genetic locus through alternative translation initiation at internal or external in-frame start sites, thereby generating N-terminal heterogeneity that can influence protein stability, subcellular localization, interaction networks, and the stoichiometric assembly of multiprotein complexes. While recent advances in riboproteogenomics, N-terminomics, and computational annotation strategies have enabled proteoform mapping at single-amino-acid resolution, rapid high-throughput discovery currently outpaces downstream functional characterization. This review discusses the technological advances driving Nt-proteoform discovery, including emerging ribosome profiling and proteogenomic approaches, and further evaluates strategies for the functional characterization of Nt-proteoforms. Particular emphasis is placed on the transition from conventional plasmid-based heterologous expression systems towards precise genome-engineering approaches that enable selective manipulation of alternative translation initiation events within their native genomic context. Such targeted strategies are essential to bridge the gap between Nt-proteoform identification and functional understanding, ultimately uncovering how individual bacterial genomic loci can encode proteoforms with distinct and potentially divergent functional roles in bacterial physiology and pathogenesis. Ultimately, we hypothesize that alternative translation initiation represents a biologically meaningful post-transcriptional regulatory mechanism that contributes to maximizing prokaryotic coding capacity without expanding genome size, rather than merely constituting stochastic translational noise. Full article

(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)

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