Feature Papers in Microbial Genetics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (20 August 2022) | Viewed by 25365

Special Issue Editor

Special Issue Information

Dear Colleagues,

This Special Issue, “Feature Papers in Microbial Genetics”, aims to collect high-quality research articles, review articles, and communications on all aspects of microbial genetics, at the level of individual microorganisms and microbial communities, from different environments/hosts, including ancient ones. We welcome the submission of manuscripts from editorial board members and outstanding scholars invited by the editorial board and editorial office. We aim to represent our Section as an attractive open-access publishing platform for microbial genetics research.

Prof. Dr. Silvia Turroni
Guest Editor

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Published Papers (10 papers)

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Research

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19 pages, 2884 KiB  
Article
Genome Mining Reveals High Biosynthetic Potential of Biocontrol Agent Bacillus velezensis B.BV10
by Rosiana Bertê, Gustavo Manoel Teixeira, João Paulo de Oliveira, Maria Luiza Abreu Nicoletto, Daniel Vieira da Silva, Guilherme Gonçalves de Godoy, Danilo Sipoli Sanches, Juliano Tadeu Vilela de Resende, Ulisses de Padua Pereira, Ulisses Nunes da Rocha and Admilton Gonçalves de Oliveira
Genes 2022, 13(11), 1984; https://doi.org/10.3390/genes13111984 - 30 Oct 2022
Cited by 4 | Viewed by 1952
Abstract
The present study demonstrates the biocontrol potential of a plant growth-promoting bacterial strain using three different approaches: (i) an in vitro evaluation of antagonistic activity against important phytopathogenic fungi; (ii) an evaluation under greenhouse conditions with strawberry plants to assess the control of [...] Read more.
The present study demonstrates the biocontrol potential of a plant growth-promoting bacterial strain using three different approaches: (i) an in vitro evaluation of antagonistic activity against important phytopathogenic fungi; (ii) an evaluation under greenhouse conditions with strawberry plants to assess the control of gray mold; and (iii) an in silico whole genome sequence mining to assign genetic features such as gene clusters or isolated genes to the strain activity. The in vitro assay showed that the B.BV10 strain presented antagonistic activity, inhibiting the mycelial growth in all the phytopathogenic fungi evaluated. The application of the Bacillus velezensis strain B.BV10 under greenhouse conditions reduced the presence of Botrytis cinerea and increased the mean fruit biomass. The genome of B.BV10 was estimated at 3,917,533 bp, with a GC content of 46.6% and 4088 coding DNA sequences, and was identified as B. velezensis. Biosynthetic gene clusters related to the synthesis of the molecules with antifungal activity were found in its genome. Genes related to the regulation/formation of biofilms, motility, and the important properties for the rhizospheric colonization were also found in the genome. The current study offers a comprehensive understanding of the genomic architecture and control activity of phytopathogenic fungi by the B. velezensis strain B.BV10 that may substantiate the industrialization of this strain in the future. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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13 pages, 1646 KiB  
Article
A DNA-Damage Inducible Gene Promotes the Formation of Antibiotic Persisters in Response to the Quorum Sensing Signaling Peptide in Streptococcus mutans
by Delphine Dufour, Haowei Zhao, Siew-Ging Gong and Céline M. Lévesque
Genes 2022, 13(8), 1434; https://doi.org/10.3390/genes13081434 - 12 Aug 2022
Cited by 6 | Viewed by 1715
Abstract
Bacteria use quorum sensing (QS) to communicate with each other via secreted small autoinducers produced by individuals. QS allows bacteria to display a unified response that benefits the species during adaptation to environment, colonization, and defense against competitors. In oral streptococci, the CSP-ComDE [...] Read more.
Bacteria use quorum sensing (QS) to communicate with each other via secreted small autoinducers produced by individuals. QS allows bacteria to display a unified response that benefits the species during adaptation to environment, colonization, and defense against competitors. In oral streptococci, the CSP-ComDE QS is an inducible DNA damage repair system that is pivotal for bacterial survival. In the oral pathogen Streptococcus mutans, the QS system positively influences the formation of antibiotic persisters, cells that can survive antibiotic attack by entering a non-proliferative state. We recently identified a novel gene, pep299, that is activated in the persister cell fraction induced by QS. In this study, we focused our investigation on the role of pep299, a gene encoding a bacteriocin-like peptide, in the formation of antibiotic persisters. Mutant Δ299, unable to produce Pep299, showed a dramatic reduction in the number of stress-induced persisters. Using a co-culture assay, we showed that cells overproducing pep299 induced the formation of persisters in the mutant, suggesting that Pep299 was actively secreted and detected by neighboring cells. Cells exposed to DNA damage conditions activated the gene expression of pep299. Interestingly, our results suggested that the pep299 gene was also involved in the regulation of a QS-inducible toxin–antitoxin system. Our study suggests that the pep299 gene is at the core of the triggered persistence phenotype in S. mutans, allowing cells to transition into a state of reduced metabolic activity and antibiotic tolerance. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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14 pages, 2626 KiB  
Article
Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing
by Jose Carlos Solana, Carmen Chicharro, Emilia García, Begoña Aguado, Javier Moreno and Jose M. Requena
Genes 2022, 13(6), 1070; https://doi.org/10.3390/genes13061070 - 15 Jun 2022
Cited by 5 | Viewed by 2630
Abstract
Parasites of medical importance, such as Leishmania and Trypanosoma, are characterized by the presence of thousands of circular DNA molecules forming a structure known as kinetoplast, within the mitochondria. The maxicircles, which are equivalent to the mitochondrial genome in other eukaryotes, have been [...] Read more.
Parasites of medical importance, such as Leishmania and Trypanosoma, are characterized by the presence of thousands of circular DNA molecules forming a structure known as kinetoplast, within the mitochondria. The maxicircles, which are equivalent to the mitochondrial genome in other eukaryotes, have been proposed as a promising phylogenetic marker. Using whole-DNA sequencing data, it is also possible to assemble maxicircle sequences as shown here and in previous works. In this study, based on data available in public databases and using a bioinformatics workflow previously reported by our group, we assembled the complete coding region of the maxicircles for 26 prototypical strains of trypanosomatid species. Phylogenetic analysis based on this dataset resulted in a robust tree showing an accurate taxonomy of kinetoplastids, which was also able to discern between closely related Leishmania species that are usually difficult to discriminate by classical methodologies. In addition, we provide a dataset of the maxicircle sequences of 60 Leishmania infantum field isolates from America, Western Europe, North Africa, and Eastern Europe. In agreement with previous studies, our data indicate that L. infantum parasites from Brazil are highly homogeneous and closely related to European strains, which were transferred there during the discovery of America. However, this study showed the existence of different L. infantum populations/clades within the Mediterranean region. A maxicircle signature for each clade has been established. Interestingly, two L. infantum clades were found coexisting in the same region of Spain, one similar to the American strains, represented by the Spanish JPCM5 reference strain, and the other, named “non-JPC like”, may be related to an important leishmaniasis outbreak that occurred in Madrid a few years ago. In conclusion, the maxicircle sequence emerges as a robust molecular marker for phylogenetic analysis and species typing within the kinetoplastids, which also has the potential to discriminate intraspecific variability. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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18 pages, 5272 KiB  
Article
Decoding the Gene Variants of Two Native Probiotic Lactiplantibacillus plantarum Strains through Whole-Genome Resequencing: Insights into Bacterial Adaptability to Stressors and Antimicrobial Strength
by Gabriela N. Tenea
Genes 2022, 13(3), 443; https://doi.org/10.3390/genes13030443 - 28 Feb 2022
Cited by 8 | Viewed by 2324
Abstract
In this study, whole-genome resequencing of two native probiotic Lactiplantibacillus plantarum strains—UTNGt21A and UTNGt2—was assessed in order to identify variants and perform annotation of genes involved in bacterial adaptability to different stressors, as well as their antimicrobial strength. A total of 21,906 single-nucleotide [...] Read more.
In this study, whole-genome resequencing of two native probiotic Lactiplantibacillus plantarum strains—UTNGt21A and UTNGt2—was assessed in order to identify variants and perform annotation of genes involved in bacterial adaptability to different stressors, as well as their antimicrobial strength. A total of 21,906 single-nucleotide polymorphisms (SNPs) were detected in UTNGt21A, while 17,610 were disclosed in the UTNGt2 genome. The comparative genomic analysis revealed a greater number of deletions, transversions, and transitions within the UTNGt21A genome, while a small difference in the number of insertions was detected between the strains. A divergent number of types of variant annotations were detected in both strains, and categorized in terms of low, moderate, and high modifier impact on the protein effectiveness. Although both native strains shared common specific genes involved in the stress response to the gastrointestinal environment, which may qualify as a putative probiotic (bile salt, acid, temperature, osmotic stress), they were different in their antimicrobial gene cluster organization, with UTNGt21A displaying a complex bacteriocin gene arrangement and dissimilar gene variants that might alter their defense mechanisms and overall inhibitory capacity. The genome comparison revealed 34 and 9 genomic islands (GIs) in the UTNGt21A and UTNGt2 genomes, respectively, with the overrepresentation of genes involved in defense mechanisms and carbohydrate utilization. In addition, pan-genome analysis disclosed the presence of various strain-specific genes (shell genes), suggesting a high genome variation between strains. This genome analysis illustrates that the bacteriocin signature and gene variants reflect a niche-inherent pattern. These extensive genomic datasets will guide us to understand the potential benefits of the native strains and their utility in the food or pharmaceutical sectors. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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13 pages, 2268 KiB  
Article
The Distribution of Campylobacter jejuni Virulence Genes in Genomes Worldwide Derived from the NCBI Pathogen Detection Database
by Pedro Panzenhagen, Ana Beatriz Portes, Anamaria M. P. dos Santos, Sheila da Silva Duque and Carlos Adam Conte Junior
Genes 2021, 12(10), 1538; https://doi.org/10.3390/genes12101538 - 28 Sep 2021
Cited by 16 | Viewed by 3277
Abstract
Campylobacter jejuni (C. jejuni) is responsible for 80% of human campylobacteriosis and is the leading cause of gastroenteritis globally. The relevant public health risks of C. jejuni are caused by particular virulence genes encompassing its virulome. We analyzed 40,371 publicly available [...] Read more.
Campylobacter jejuni (C. jejuni) is responsible for 80% of human campylobacteriosis and is the leading cause of gastroenteritis globally. The relevant public health risks of C. jejuni are caused by particular virulence genes encompassing its virulome. We analyzed 40,371 publicly available genomes of C. jejuni deposited in the NCBI Pathogen Detection Database, combining their epidemiologic metadata with an in silico bioinformatics analysis to increase our current comprehension of their virulome from a global perspective. The collection presented a virulome composed of 126 identified virulence factors that were grouped in three clusters representing the accessory, the softcore, and the essential core genes according to their prevalence within the genomes. The multilocus sequence type distribution in the genomes was also investigated. An unexpected low prevalence of the full-length flagellin flaA and flaB locus of C. jejuni genomes was revealed, and an essential core virulence gene repertoire prevalent in more than 99.99% of genomes was identified. Altogether, this is a pioneer study regarding Campylobacter jejuni that has compiled a significant amount of data about the Multilocus Sequence Type and virulence factors concerning their global prevalence and distribution over this database. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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Review

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18 pages, 848 KiB  
Review
Make It Less difficile: Understanding Genetic Evolution and Global Spread of Clostridioides difficile
by Mariachiara Mengoli, Monica Barone, Marco Fabbrini, Federica D’Amico, Patrizia Brigidi and Silvia Turroni
Genes 2022, 13(12), 2200; https://doi.org/10.3390/genes13122200 - 24 Nov 2022
Cited by 6 | Viewed by 2543
Abstract
Clostridioides difficile is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection [...] Read more.
Clostridioides difficile is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection can lead to fulminant colitis associated with shock, hypotension, megacolon, and, in severe cases, death. It is therefore of the utmost urgency to fully characterize this pathogen and better understand its spread, in order to reduce infection rates and improve therapy success. This review aims to provide a state-of-the-art overview of the genetic variation of C. difficile, with particular regard to pathogenic genes and the correlation with clinical issues of its infection. We also summarize the current typing techniques and, based on them, the global distribution of the most common ribotypes. Finally, we discuss genomic surveillance actions and new genetic engineering strategies as future perspectives to make it less difficile. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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13 pages, 829 KiB  
Review
Unravelling Metagenomics Approach for Microbial Biofuel Production
by Km Sartaj, Alok Patel, Leonidas Matsakas and Ramasare Prasad
Genes 2022, 13(11), 1942; https://doi.org/10.3390/genes13111942 - 25 Oct 2022
Cited by 2 | Viewed by 2396
Abstract
Renewable biofuels, such as biodiesel, bioethanol, and biobutanol, serve as long-term solutions to fossil fuel depletion. A sustainable approach feedstock for their production is plant biomass, which is degraded to sugars with the aid of microbes-derived enzymes, followed by microbial conversion of those [...] Read more.
Renewable biofuels, such as biodiesel, bioethanol, and biobutanol, serve as long-term solutions to fossil fuel depletion. A sustainable approach feedstock for their production is plant biomass, which is degraded to sugars with the aid of microbes-derived enzymes, followed by microbial conversion of those sugars to biofuels. Considering their global demand, additional efforts have been made for their large-scale production, which is ultimately leading breakthrough research in biomass energy. Metagenomics is a powerful tool allowing for functional gene analysis and new enzyme discovery. Thus, the present article summarizes the revolutionary advances of metagenomics in the biofuel industry and enlightens the importance of unexplored habitats for novel gene or enzyme mining. Moreover, it also accentuates metagenomics potentials to explore uncultivable microbiomes as well as enzymes associated with them. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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25 pages, 1318 KiB  
Review
Large-Scale Sequencing of Borreliaceae for the Construction of Pan-Genomic-Based Diagnostics
by Kayla M. Socarras, Benjamin S. Haslund-Gourley, Nicholas A. Cramer, Mary Ann Comunale, Richard T. Marconi and Garth D. Ehrlich
Genes 2022, 13(9), 1604; https://doi.org/10.3390/genes13091604 - 8 Sep 2022
Cited by 2 | Viewed by 2303
Abstract
The acceleration of climate change has been associated with an alarming increase in the prevalence and geographic range of tick-borne diseases (TBD), many of which have severe and long-lasting effects—particularly when treatment is delayed principally due to inadequate diagnostics and lack of physician [...] Read more.
The acceleration of climate change has been associated with an alarming increase in the prevalence and geographic range of tick-borne diseases (TBD), many of which have severe and long-lasting effects—particularly when treatment is delayed principally due to inadequate diagnostics and lack of physician suspicion. Moreover, there is a paucity of treatment options for many TBDs that are complicated by diagnostic limitations for correctly identifying the offending pathogens. This review will focus on the biology, disease pathology, and detection methodologies used for the Borreliaceae family which includes the Lyme disease agent Borreliella burgdorferi. Previous work revealed that Borreliaceae genomes differ from most bacteria in that they are composed of large numbers of replicons, both linear and circular, with the main chromosome being the linear with telomeric-like termini. While these findings are novel, additional gene-specific analyses of each class of these multiple replicons are needed to better understand their respective roles in metabolism and pathogenesis of these enigmatic spirochetes. Historically, such studies were challenging due to a dearth of both analytic tools and a sufficient number of high-fidelity genomes among the various taxa within this family as a whole to provide for discriminative and functional genomic studies. Recent advances in long-read whole-genome sequencing, comparative genomics, and machine-learning have provided the tools to better understand the fundamental biology and phylogeny of these genomically-complex pathogens while also providing the data for the development of improved diagnostics and therapeutics. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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17 pages, 945 KiB  
Review
Vacuolal and Peroxisomal Calcium Ion Transporters in Yeasts and Fungi: Key Role in the Translocation of Intermediates in the Biosynthesis of Fungal Metabolites
by Juan F. Martín
Genes 2022, 13(8), 1450; https://doi.org/10.3390/genes13081450 - 15 Aug 2022
Cited by 7 | Viewed by 1974
Abstract
The intracellular calcium content in fungal cells is influenced by a large number of environmental and nutritional factors. Sharp changes in the cytosolic calcium level act as signals that are decoded by the cell gene expression machinery, resulting in several physiological responses, including [...] Read more.
The intracellular calcium content in fungal cells is influenced by a large number of environmental and nutritional factors. Sharp changes in the cytosolic calcium level act as signals that are decoded by the cell gene expression machinery, resulting in several physiological responses, including differentiation and secondary metabolites biosynthesis. Expression of the three penicillin biosynthetic genes is regulated by calcium ions, but there is still little information on the role of this ion in the translocation of penicillin intermediates between different subcellular compartments. Using advanced information on the transport of calcium in organelles in yeast as a model, this article reviews the recent progress on the transport of calcium in vacuoles and peroxisomes and its relation to the translocation of biosynthetic intermediates in filamentous fungi. The Penicillium chrysogenum PenV vacuole transporter and the Acremonium chrysogenum CefP peroxisomal transporter belong to the transient receptor potential (TRP) class CSC of calcium ion channels. The PenV transporter plays an important role in providing precursors for the biosynthesis of the tripeptide δ-(-α-aminoadipyl-L-cysteinyl-D-valine), the first intermediate of penicillin biosynthesis in P. chrysogenum. Similarly, CefP exerts a key function in the conversion of isopenicillin N to penicillin N in peroxisomes of A. chrysogenum. These TRP transporters are different from other TRP ion channels of Giberella zeae that belong to the Yvc1 class of yeast TRPs. Recent advances in filamentous fungi indicate that the cytosolic calcium concentration signal is connected to the calcitonin/calcineurin signal transduction cascade that controls the expression of genes involved in the subcellular translocation of intermediates during fungal metabolite biosynthesis. These advances open new possibilities to enhance the expression of important biosynthetic genes in fungi. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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13 pages, 302 KiB  
Review
Lessons to Learn from the Gut Microbiota: A Focus on Amyotrophic Lateral Sclerosis
by Ana Cristina Calvo, Inés Valledor-Martín, Laura Moreno-Martínez, Janne Markus Toivonen and Rosario Osta
Genes 2022, 13(5), 865; https://doi.org/10.3390/genes13050865 - 12 May 2022
Cited by 5 | Viewed by 2923
Abstract
The gut microbiota is able to modulate the development and homeostasis of the central nervous system (CNS) through the immune, circulatory, and neuronal systems. In turn, the CNS influences the gut microbiota through stress responses and at the level of the endocrine system. [...] Read more.
The gut microbiota is able to modulate the development and homeostasis of the central nervous system (CNS) through the immune, circulatory, and neuronal systems. In turn, the CNS influences the gut microbiota through stress responses and at the level of the endocrine system. This bidirectional communication forms the “gut microbiota–brain axis” and has been postulated to play a role in the etiopathology of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Numerous studies in animal models of ALS and in patients have highlighted the close communication between the immune system and the gut microbiota and, therefore, it is possible that alterations in the gut microbiota may have a direct impact on neuronal function and survival in ALS patients. Consequently, if the gut dysbiosis does indeed play a role in ALS-related neurodegeneration, nutritional immunomodulatory interventions based on probiotics, prebiotics, and/or postbiotics could emerge as innovative therapeutic strategies. This review aimed to shed light on the impact of the gut microbiota in ALS disease and on the use of potential nutritional interventions based on different types of biotics to ameliorate ALS symptoms. Full article
(This article belongs to the Special Issue Feature Papers in Microbial Genetics)
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