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Current Advances and Perspectives in Microbial Genetics and Genomics
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Current Advances and Perspectives in Microbial Genetics and Genomics

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: 20 March 2025 | Viewed by 1940

Special Issue Editors

Dr. Marcello Tagliavia

E-Mail Website
Guest Editor
IRIB-CNR (Institute for Biomedical Research and Innovation, Italian National Research Council), Palermo, Italy
Interests: development of improved molecular tools for genetic engineering of GRAS bacteria and their exploitation for in vivo expression and delivery of therapeutic molecules, including recombinant immunotherapeutics; exploiting microbial enzymes for regenerative medicine and biomedical applications; analysis and targeting of mechanisms involved in the virulence of human pathogenic bacteria; profiling of environmental microbial communities
Dr. Lucila Saavedra

E-Mail Website
Guest Editor
CERELA-CONICET (Reference Center for Lactobacilli-National Scientific and Technical Research Council of Argentina), Chacabuco 145, Tucumán, Argentina
Interests: genomics characterization of lactic acid bacteria (LAB) isolated from artisanal fermented foods; genomic and functional characterization of bioactive compounds produced by LAB; impact of neuroactive compounds produced by LAB on the gut–brain axis and its potential role in neurodegenerative diseases

Special Issue Information

Dear Colleagues,

Progress and innovation in microbial genetics and genomics have been remarkable in recent years, revolutionizing our understanding of microbial life with profound implications for human health, agriculture, environmental conservation, and biotechnology. Continued investment in research and technology development is essential to further unlocking the potential of microbial systems for addressing global challenges.

This Special Issue welcomes submissions dealing with microbial genetics, genomics, and metagenomics, focusing specifically on bacteria, archaea, and bacteriophages. We encourage research articles that explore diverse aspects, including, but not limited to, gene regulation, microbe–host interactions, antibiotic resistance mechanisms aiding the development of new antimicrobial strategies or the discovery of novel antimicrobial compounds or biomolecules of biotechnological interest from diverse microbial sources, metabolic pathways of environmental and commensal bacteria (including xenobiotic degradation), and the fascinating evolutionary trajectories of microbial genomes. Whether investigating genetic diversity within bacterial populations or elucidating the role of phages in shaping microbial communities, we welcome contributions that improve our understanding of the intricate molecular mechanisms that drive microbial life.

Dr. Marcello Tagliavia
Dr. Lucila Saavedra
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. 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 genetics
  • genomics and metagenomics
  • gene regulation
  • microbe–host interactions
  • adaption and resistance mechanisms
  • microbial metabolism

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Published Papers (2 papers)

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Research

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15 pages, 3046 KiB  
Article
Evolution and Competitive Struggles of Lactiplantibacillus plantarum under Different Oxygen Contents
by Sojeong Heo, Eun Jin Jung, Mi-Kyung Park, Moon-Hee Sung and Do-Won Jeong
Int. J. Mol. Sci. 2024, 25(16), 8861; https://doi.org/10.3390/ijms25168861 - 14 Aug 2024
Viewed by 773
Abstract
Lactiplantibacillus (Lb.) plantarum is known as a benign bacterium found in various habitats, including the intestines of animals and fermented foods. Since animal intestines lack oxygen, while fermented foods provide a limited or more oxygen environment, this study aimed to investigate [...] Read more.
Lactiplantibacillus (Lb.) plantarum is known as a benign bacterium found in various habitats, including the intestines of animals and fermented foods. Since animal intestines lack oxygen, while fermented foods provide a limited or more oxygen environment, this study aimed to investigate whether there were genetic differences in the growth of Lb. plantarum under aerobic vs. anaerobic conditions. Genomic analysis of Lb. plantarum obtained from five sources—animals, dairy products, fermented meat, fermented vegetables, and humans—was conducted. The analysis included not only an examination of oxygen-utilizing genes but also a comparative pan-genomic analysis to investigate evolutionary relationships between genomes. The ancestral gene analysis of the evolutionary pathway classified Lb. plantarum into groups A and B, with group A further subdivided into A1 and A2. It was confirmed that group A1 does not possess the narGHIJ operon, which is necessary for energy production under limited oxygen conditions. Additionally, it was found that group A1 has experienced more gene acquisition and loss compared to groups A2 and B. Despite an initial assumption that there would be genetic distinctions based on the origin (aerobic or anaerobic conditions), it was observed that such differentiation could not be attributed to the origin. However, the evolutionary process indicated that the loss of genes related to nitrate metabolism was essential in anaerobic or limited oxygen conditions, contrary to the initial hypothesis. Full article
(This article belongs to the Special Issue Current Advances and Perspectives in Microbial Genetics and Genomics)
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Review

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21 pages, 9593 KiB  
Review
Essential Genes Discovery in Microorganisms by Transposon-Directed Sequencing (Tn-Seq): Experimental Approaches, Major Goals, and Future Perspectives
by Gemma Fernández-García, Paula Valdés-Chiara, Patricia Villazán-Gamonal, Sergio Alonso-Fernández and Angel Manteca
Int. J. Mol. Sci. 2024, 25(20), 11298; https://doi.org/10.3390/ijms252011298 - 21 Oct 2024
Viewed by 780
Abstract
Essential genes are crucial for microbial viability, playing key roles in both the primary and secondary metabolism. Since mutations in these genes can threaten organism viability, identifying them is challenging. Conditionally essential genes are required only under specific conditions and are important for [...] Read more.
Essential genes are crucial for microbial viability, playing key roles in both the primary and secondary metabolism. Since mutations in these genes can threaten organism viability, identifying them is challenging. Conditionally essential genes are required only under specific conditions and are important for functions such as virulence, immunity, stress survival, and antibiotic resistance. Transposon-directed sequencing (Tn-Seq) has emerged as a powerful method for identifying both essential and conditionally essential genes. In this review, we explored Tn-Seq workflows, focusing on eubacterial species and some yeast species. A comparison of 14 eubacteria species revealed 133 conserved essential genes, including those involved in cell division (e.g., ftsA, ftsZ), DNA replication (e.g., dnaA, dnaE), ribosomal function, cell wall synthesis (e.g., murB, murC), and amino acid synthesis (e.g., alaS, argS). Many other essential genes lack clear orthologues across different microorganisms, making them specific to each organism studied. Conditionally essential genes were identified in 18 bacterial species grown under various conditions, but their conservation was low, reflecting dependence on specific environments and microorganisms. Advances in Tn-Seq are expected to reveal more essential genes in the near future, deepening our understanding of microbial biology and enhancing our ability to manipulate microbial growth, as well as both the primary and secondary metabolism. Full article
(This article belongs to the Special Issue Current Advances and Perspectives in Microbial Genetics and Genomics)
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