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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 September 2025 | Viewed by 6446

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Special Issue Editors

Dr. Marcello Tagliavia

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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

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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

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Keywords

microbial genetics
genomics and metagenomics
gene regulation
microbe–host interactions
adaption and resistance mechanisms
microbial metabolism

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Published Papers (5 papers)

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Research

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11 pages, 5510 KiB

Open AccessCommunication

Genome Announcement of Four Parechovirus A3 Isolates from the United States of America

by Debarpan Dhar, Terry Fei Fan Ng, Christopher J. Harrison, Eric Rhoden, Bernardo A. Mainou, Anjana Sasidharan, Katelyn E. VanDonge, Varun Chandra Boinpelly and Rangaraj Selvarangan

Int. J. Mol. Sci. 2025, 26(9), 4378; https://doi.org/10.3390/ijms26094378 - 5 May 2025

Viewed by 162

Abstract

We report the complete genome sequences of four parechovirus-A3 (PeV-A3) isolates from Children’s Mercy Kansas City (CMKC), United States of America (USA): PeV-A3-MO-12-CMKC/CSF/MO/USA/2012 (isolated in 2012 from cerebrospinal fluid), PeV-A3-8C-CMKC/CSF/MO/USA/2022/ (isolated in 2022 from cerebrospinal fluid), PeV-A3-9C-CMKC/CSF/MO/USA/2022 (isolated in 2022 from cerebrospinal fluid), and PeV-A3-11B-CMKC/Blood/MO/USA/2022 (isolated in 2022 from blood). Sequence analysis revealed multiple mutations throughout the genome of the PeV-A3 isolates in comparison to the prototypic PeV-A3 A308/99 reference sequence (AB084913). Several unique amino acid changes were observed in the PeV-A3 isolates from 2022 that were absent in the PeV-A3 isolate from 2012. Phylogenetic analysis comparison determined that the sequenced PeV-A3 isolates from 2022 cluster together as a separate clade. Full article

(This article belongs to the Special Issue Current Advances and Perspectives in Microbial Genetics and Genomics)

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22 pages, 8650 KiB

Open AccessArticle

Genetic and Genomic Analysis Identifies bcltf1 as the Transcription Factor Coding Gene Mutated in Field Isolate Bc116, Deficient in Light Responses, Differentiation and Pathogenicity in Botrytis cinerea

by Virginia Casado-del Castillo, Vlad Paul Mihaila Novac, Alessandro Gabrielli García, José María García Fernández, Paula Iriondo-Ocampo, José María Díaz-Mínguez and Ernesto Pérez Benito

Int. J. Mol. Sci. 2025, 26(8), 3481; https://doi.org/10.3390/ijms26083481 - 8 Apr 2025

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Abstract

Natural populations provide valuable information and resources for addressing the genetic characterization of biological systems. Botrytis cinerea is a necrotrophic fungus that exhibits complex responses to light. Physiological analysis of B. cinerea populations from vineyards in Castilla y León (Spain) allowed for the identification of isolate Bc116. This field isolate shows a reduced pathogenicity that is conditioned by the light regime. Light also delays germination and accentuates the negative effect it exerts on the vegetative growth of B. cinerea. Bc116 also displays a marked hyperconidiation phenotype and a characteristic sclerotia production pattern. Genetic analysis demonstrates that the alternative phenotypes regarding pathogenicity, conidiation, and pattern of sclerotia production co-segregate in the progeny of crosses between isolate Bc116 and a wild-type field isolate, Bc448, showing that they are under the control of a single locus. By applying a strategy based on bulked segregant analysis, the mutation in Bc116 has been mapped to a 200 kb region on Chr14 and the analysis of this region identifies a 2 kb deletion affecting the bcltf1 gene, encoding the B. cinerea Light Responsive Transcription Factor 1 described in the reference isolate B05.10. Transformation of Bc116 with the B05.10 bcltf1 allele restored the wild-type phenotypes, providing functional evidence that the natural mutant Bc116 is altered in gene bcltf1. This study offers additional information, derived from the analysis of the genetic background of a natural mutant, on the physiological processes regulated by BcLTF1 and supports the key role of this TF in the pathogenicity and photobiology of B. cinerea. Full article

(This article belongs to the Special Issue Current Advances and Perspectives in Microbial Genetics and Genomics)

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10 pages, 258 KiB

Open AccessArticle

The Prevalence and the Underlying Mechanisms of Fosfomycin Resistance of Escherichia coli and Salmonella spp. Among Cattle in Japan

by Yuta Hosoi, Michiko Kawanishi, Saki Harada, Mio Kumakawa, Mari Matsuda and Hideto Sekiguchi

Int. J. Mol. Sci. 2024, 25(24), 13723; https://doi.org/10.3390/ijms252413723 - 23 Dec 2024

Viewed by 758

Abstract

To investigate fosfomycin resistance rates in cattle across Japan, we carried out susceptibility tests. To identify the genes contributing to fosfomycin resistance, we performed whole-genome sequencing on the fosfomycin-resistant strains. Escherichia coli were sampled from healthy cattle (n = 292, combined total from 2017, 2020, 2021, and 2022) and diseased cattle (n = 73, from 2021 to 2022). Salmonella spp. were obtained from diseased cattle (n = 74 from 2021 to 2022). These samples originated from different and non-duplicated farms. The MICs to fosfomycin were measured using an agar dilution method with a breakpoint of 256 μg/mL. We conducted whole-genome sequencing with a MiSeq, followed by in silico analysis of the acquired draft genomes. The resistance rates were 0.3% (95% CI [0–1.9%]), 6.8% (95% CI [2.3–15.3%]), and 1.4% (95% CI [0–7.3%]). The FosA3 gene was detected in five out of six fosfomycin-resistant E. coli strains and one Salmonella spp. strain. The fosfomycin-resistant Salmonella spp. strain also has a fosA7 gene. One E. coli strain showed resistance to fosfomycin without having the fosA3 gene, and with the mutations of glpT, uhpT, uhpT and ptsI, and with the existence of efflux pumps. The nationwide scale of resistance rates to fosfomycin in E. coli isolated from healthy and diseased cattle and that of Salmonella spp. from diseased cattle were revealed for the first time, and the resistance rates were low. In addition, genes linked to the mechanism of fosfomycin resistance were identified. Full article

(This article belongs to the Special Issue Current Advances and Perspectives in Microbial Genetics and Genomics)

15 pages, 3046 KiB

Open AccessArticle

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

Cited by 3 | Viewed by 1973

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 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

Open AccessReview

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 2453

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 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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