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Advances in Microbial Genomics: Insights from Whole Genomes and Metagenomes
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Advances in Microbial Genomics: Insights from Whole Genomes and Metagenomes

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

Deadline for manuscript submissions: 30 September 2025 | Viewed by 1035

Special Issue Editor

Dr. Marcos Quintela Baluja

E-Mail Website
Guest Editor
Department of Biosciences, Durham University, Durham, DH1 3LE, UK
Interests: microbial; genomics

Special Issue Information

Dear Colleagues,

We invite submissions for the Special Issue "Advances in Microbial Genomics: Insights from Whole Genomes and Metagenomes," which will highlight pioneering research on microbial evolution, genome adaptation, and gene acquisition across varied environmental contexts. Recent advancements in next-generation sequencing and computational methodologies have greatly enhanced our capacity to unravel genetic and epigenetic variations, structural variations, and horizontal gene transfer events—even within complex microbial communities. These insights are vital for comprehending the mechanisms that shape microbial diversity and adaptation.

This Special Issue welcomes original research articles and reviews that explore computational and experimental approaches to studying microbial adaptation and evolutionary processes. Topics of interest include, but are not limited to: 

- High-resolution variant calling in microbial genomes and metagenomes; 

- Gene acquisition and horizontal gene transfer in microbial evolution; 

- Comparative genomics for tracking evolutionary trajectories; 

- Effects of genetic variation on microbial adaptation and antibiotic resistance; 

- Development of novel bioinformatics tools for evolutionary genomics analysis. 

 

We eagerly anticipate contributions to enhance our understanding of microbial genomics and evolution.

Dr. Marcos Quintela Baluja
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 evolution
  • whole-genome sequencing
  • metagenomics
  • horizontal gene transfer
  • antimicrobial resistance
  • computational genomics

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Published Papers (2 papers)

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Research

16 pages, 2891 KB  
Article
Discovery of Novel Genes Encoding Antimicrobial Peptides from the Pedobacter silvilitoris Genome with Broad-Spectrum Antimicrobial Activity
by Woo Young Bang, Jin Hur and Sam Woong Kim
Int. J. Mol. Sci. 2025, 26(13), 6176; https://doi.org/10.3390/ijms26136176 - 26 Jun 2025
Viewed by 352
Abstract
The rising prevalence of antibiotic-resistant bacteria demands exploration of alternative antimicrobials. Antimicrobial peptides (AMPs) are a promising group of compounds naturally produced by microorganisms and could serve as potent agents against resistant pathogens. In this study, we evaluated the antimicrobial potential of the [...] Read more.
The rising prevalence of antibiotic-resistant bacteria demands exploration of alternative antimicrobials. Antimicrobial peptides (AMPs) are a promising group of compounds naturally produced by microorganisms and could serve as potent agents against resistant pathogens. In this study, we evaluated the antimicrobial potential of the cell-free supernatant obtained from Pedobacter silvilitoris—a bacterium originally isolated from decomposing wood—and performed comprehensive genomic screening to uncover novel AMP-encoding genes. The supernatant showed strong inhibitory effects against a diverse selection of pathogens. Scanning electron microscopy (SEM) revealed extensive membrane damage, including pore formation in target bacterial cells, suggesting AMP-mediated activity. A genomic analysis identified 11 candidate AMP genes, named PS_AMP1 to PS_AMP11, based on the significant sequence similarity with known AMPs. Transcriptomic profiling further indicated that several candidates are expressed differentially between the logarithmic and stationary growth phases. Functional assays via gene cloning and peptide synthesis confirmed antimicrobial activity against both Gram-stain-negative and Gram-stain-positive bacteria, with PS_AMP11 emerging as the most effective candidate. Our findings demonstrate that AMPs derived from P. silvilitoris hold substantial promise as alternative antimicrobial agents. Nonetheless, additional structural optimizations may be necessary to fine-tune specificity and to reduce potential host toxicity before clinical deployment. Full article
(This article belongs to the Special Issue Advances in Microbial Genomics: Insights from Whole Genomes and Metagenomes)
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14 pages, 1152 KB  
Article
Study of lug Operon, SCCmec Elements, Antimicrobial Resistance, MGEs, and STs of Staphylococcus lugdunensis Clinical Isolates Through Whole-Genome Sequencing
by Tein-Yao Chang, Lee-Chung Lin, Cheng-Yen Kao and Jang-Jih Lu
Int. J. Mol. Sci. 2025, 26(13), 6106; https://doi.org/10.3390/ijms26136106 - 25 Jun 2025
Viewed by 493
Abstract
Staphylococcus lugdunensis is a coagulase-negative staphylococcus known for its significant pathogenic potential, often causing severe infections such as endocarditis and bacteremia, with virulence comparable to S. aureus. Despite general susceptibility to most antibiotics, the emergence of oxacillin-resistant strains is increasingly concerning. This [...] Read more.
Staphylococcus lugdunensis is a coagulase-negative staphylococcus known for its significant pathogenic potential, often causing severe infections such as endocarditis and bacteremia, with virulence comparable to S. aureus. Despite general susceptibility to most antibiotics, the emergence of oxacillin-resistant strains is increasingly concerning. This study conducted whole-genome sequencing on 20 S. lugdunensis isolates from Chang Gung Memorial Hospital to explore their genetic diversity, antimicrobial resistance mechanisms, and mobile genetic elements. The lugdunin biosynthetic operon, essential for antimicrobial peptide production, was present in multilocus sequence typing (MLST) types 1, 3, and 6 but absent in STs 4, 27, and 29. Additionally, IS256 insertion elements, ranging from 7 to 17 copies, were identified in four strains and linked to multidrug resistance. CRISPR-Cas systems varied across STs, with type III-A predominant in ST1 and ST6 and type IIC in ST4, ST27, and ST29; notably, ST3 lacked CRISPR systems, correlating with a higher diversity of SCCmec elements and an increased potential for horizontal gene transfer. Phage analysis revealed stable phage–host associations in ST1, ST6, and ST29, whereas ST4 displayed a varied prophage profile. Phenotypic resistance profiles generally aligned with genomic predictions, although discrepancies were observed for aminoglycosides and clindamycin. These findings highlight the complex genetic landscape and evolutionary dynamics of S. lugdunensis, emphasizing the need for genomic surveillance to inform clinical management and prevent the spread of resistant strains. Full article
(This article belongs to the Special Issue Advances in Microbial Genomics: Insights from Whole Genomes and Metagenomes)
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