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Microbial Comparative Genomics and Evolutionary Biology 2.0
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Microbial Comparative Genomics and Evolutionary Biology 2.0

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: closed (15 October 2023) | Viewed by 13042

Special Issue Editors

Dr. Vicky Merhej

E-Mail Website
Guest Editor
IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
Interests: comparative genomics; evolutionary biology; antimicrobials; bacteriocins; nonribosomal peptides and polyketides; bacterial resistance; in vitro microbiological assays
Special Issues, Collections and Topics in MDPI journals
Dr. Pierre Pontarotti

E-Mail Website1 Website2
Guest Editor
1. Microbes Evolution Phylogénie et Infection, Institut Recherche et Développement, Aix-Marseille University, 13005 Marseille, France
2. SNC5039 CNRS, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
Interests: evolutionary biology; molecular immunology; comparative genomic; bioinformatic; molecular microbiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent advances in the development of genome sequencing technologies have generated and rendered the genomes of multiple strains of many individual microbial species more accessible than ever before. Comparing genome sequences allows for an in-depth analysis of intra-species diversity and provides a deep understanding of organismal relationships. A particularly attractive application of microbial genomic comparisons is the potential to provide insight into the mechanisms of evolutionary biology. Comparative microbial genomics has already helped to describe genomic features in relation to microbial lifestyles and has provided insight into the functioning mode of the microbial community. This Special Issue, “Microbial Comparative Genomics and Evolutionary Biology”, will focus on the recent progress in microbial evolution using a comparative genomics approach. We are interested in the patterns that characterize the evolution and function of microbes with pathogenic and symbiotic lifestyles and the effects of the microbial lifestyle on genome changes, including genome reduction, the abundance of mobile elements, and host–interaction genes in particular. We invite researchers in the field to submit original research and review articles on the advancement of comparative methods and their applications in evolutionary biology as well as articles showing large-scale genetic intra- and inter-species differences in relation to lifestyle or phenotypes. 

Dr. Vicky Merhej
Dr. Pierre Pontarotti
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 genomics
  • evolutionary genomics
  • computational genomics
  • genome dynamics and microbial lifestyle
  • pangenome and microbial diversity
  • microbial community
  • mechanisms of pathogenicity
  • symbiotic relationships
  • mobile elements
  • lateral transfer of DNA

Related Special Issue

Published Papers (6 papers)

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Research

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19 pages, 16463 KiB  
Article
Adaptation of the Endolithic Biome in Antarctic Volcanic Rocks
by Andrea Hidalgo-Arias, Víctor Muñoz-Hisado, Pilar Valles, Adelina Geyer, Eva Garcia-Lopez and Cristina Cid
Int. J. Mol. Sci. 2023, 24(18), 13824; https://doi.org/10.3390/ijms241813824 - 7 Sep 2023
Viewed by 1321
Abstract
Endolithic microorganisms, ranging from microeukaryotes to bacteria and archaea, live within the cracks and crevices of rocks. Deception Island in Antarctica constitutes an extreme environment in which endoliths face environmental threats such as intense cold, lack of light in winter, high solar radiation [...] Read more.
Endolithic microorganisms, ranging from microeukaryotes to bacteria and archaea, live within the cracks and crevices of rocks. Deception Island in Antarctica constitutes an extreme environment in which endoliths face environmental threats such as intense cold, lack of light in winter, high solar radiation in summer, and heat emitted as the result of volcanic eruptions. In addition, the endolithic biome is considered the harshest one on Earth, since it suffers added threats such as dryness or lack of nutrients. Even so, samples from this hostile environment, collected at various points throughout the island, hosted diverse and numerous microorganisms such as bacteria, fungi, diatoms, ciliates, flagellates and unicellular algae. These endoliths were first identified by Scanning Electron Microscopy (SEM). To understand the molecular mechanisms of adaptation of these endoliths to their environment, genomics techniques were used, and prokaryotic and eukaryotic microorganisms were identified by metabarcoding, sequencing the V3–V4 and V4–V5 regions of the 16S and 18S rRNA genes, respectively. Subsequently, the sequences were analyzed by bioinformatic methods that allow their metabolism to be deduced from the taxonomy. The results obtained concluded that some of these microorganisms have activated the biosynthesis routes of pigments such as prodigiosin or flavonoids. These adaptation studies also revealed that microorganisms defend themselves against environmental toxins by activating metabolic pathways for the degradation of compounds such as ethylbenzene, xylene and dioxins and for the biosynthesis of antioxidant molecules such as glutathione. Finally, these Antarctic endolithic microorganisms are of great interest in astrobiology since endolithic settings are environmentally analogous to the primitive Earth or the surfaces of extraterrestrial bodies. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology 2.0)
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15 pages, 6674 KiB  
Article
Complete De Novo Assembly of Wolbachia Endosymbiont of Frankliniella intonsa
by Zhijun Zhang, Jiahui Zhang, Qizhang Chen, Jianyun He, Xiaowei Li, Yunsheng Wang and Yaobin Lu
Int. J. Mol. Sci. 2023, 24(17), 13245; https://doi.org/10.3390/ijms241713245 - 26 Aug 2023
Viewed by 1237
Abstract
As an endosymbiont, Wolbachia exerts significant effects on the host, including on reproduction, immunity, and metabolism. However, the study of Wolbachia in Thysanopteran insects, such as flower thrips Frankliniella intonsa, remains limited. Here, we assembled a gap-free looped genome assembly of Wolbachia [...] Read more.
As an endosymbiont, Wolbachia exerts significant effects on the host, including on reproduction, immunity, and metabolism. However, the study of Wolbachia in Thysanopteran insects, such as flower thrips Frankliniella intonsa, remains limited. Here, we assembled a gap-free looped genome assembly of Wolbachia strain wFI in a length of 1,463,884 bp (GC content 33.80%), using Nanopore long reads and Illumina short reads. The annotation of wFI identified a total of 1838 protein-coding genes (including 85 pseudogenes), 3 ribosomal RNAs (rRNAs), 35 transfer RNAs (tRNAs), and 1 transfer-messenger RNA (tmRNA). Beyond this basic description, we identified mobile genetic elements, such as prophage and insertion sequences (ISs), which make up 17% of the entire wFI genome, as well as genes involved in riboflavin and biotin synthesis and metabolism. This research lays the foundation for understanding the nutritional mutualism between Wolbachia and flower thrips. It also serves as a valuable resource for future studies delving into the intricate interactions between Wolbachia and its host. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology 2.0)
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14 pages, 2995 KiB  
Article
The Genome of Fusarium oxysporum f. sp. phaseoli Provides Insight into the Evolution of Genomes and Effectors of Fusarium oxysporum Species
by Yali Hao, Yan Li, Xingxing Ping, Qihong Yang, Zhenchuan Mao, Jianlong Zhao, Xiaofei Lu, Bingyan Xie, Yuhong Yang and Jian Ling
Int. J. Mol. Sci. 2023, 24(2), 963; https://doi.org/10.3390/ijms24020963 - 4 Jan 2023
Cited by 1 | Viewed by 2150
Abstract
Fusarium oxysporum f. sp. phaseoli, the causal agent of cowpea fusarium wilt, is a serious threat to cowpea production in China. In this study, a sample of cowpea fusarium wilt was identified as Fusarium oxysporum f. sp. phaseoli using the methods of [...] Read more.
Fusarium oxysporum f. sp. phaseoli, the causal agent of cowpea fusarium wilt, is a serious threat to cowpea production in China. In this study, a sample of cowpea fusarium wilt was identified as Fusarium oxysporum f. sp. phaseoli using the methods of morphological characters and molecular detection. We further reported the first genome assembly for Fusarium oxysporum f. sp. phaseoli, with 53.7 Mb genome sequence comprising 14,694 genes. Comparative genomic analysis among five Fusarium oxysporum genomes showed that four accessory chromosomes in the five Fusarium oxysporum display similar characteristics, with low sequence similarity (55.35%, vs. overall average of 81.76%), low gene density (2.18 genes/10 kb vs. 3.02 genes/Mb) and highly transposable element density (TEs) (15.01/100 kb vs. 4.89/100 kb), indicating that variable accessory chromosomes are the main source of Fusarium oxysporum evolution. We identified a total of 100 Fusarium oxysporum f. sp. phaseoli-specific effectors in the genome and found 13 specific effector genes located in large insertion or deletion regions, suggesting that insertion or deletion events can cause the emergence of species-specific effectors in Fusarium oxysporum. Our genome assembly of Fusarium oxysporum f. sp. phaseoli provides a valuable resource for the study of cowpea fusarium wilt, and the comparative genomic study of Fusarium oxysporum could contribute to the knowledge of genome and effector-associated pathogenicity evolution in Fusarium oxysporum study. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology 2.0)
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14 pages, 2916 KiB  
Article
Correlation between CRISPR Loci Diversity in Three Enterobacterial Taxa
by Dumitrana Iordache, Gabriela-Maria Baci, Oana Căpriță, Anca Farkas, Andreea Lup and Anca Butiuc-Keul
Int. J. Mol. Sci. 2022, 23(21), 12766; https://doi.org/10.3390/ijms232112766 - 23 Oct 2022
Viewed by 1681
Abstract
CRISPR-Cas is an adaptive immunity system of prokaryotes, composed of CRISPR arrays and the associated proteins. The successive addition of spacer sequences in the CRISPR array has made the system a valuable molecular marker, with multiple applications. Due to the high degree of [...] Read more.
CRISPR-Cas is an adaptive immunity system of prokaryotes, composed of CRISPR arrays and the associated proteins. The successive addition of spacer sequences in the CRISPR array has made the system a valuable molecular marker, with multiple applications. Due to the high degree of polymorphism of the CRISPR loci, their comparison in bacteria from various sources may provide insights into the evolution and spread of the CRISPR-Cas systems. The aim of this study was to establish a correlation between the enterobacterial CRISPR loci, the sequence of direct repeats (DR), and the number of spacer units, along with the geographical origin and collection source. For this purpose, 3474 genomes containing CRISPR loci from the CRISPRCasdb of Salmonella enterica, Escherichia coli, and Klebsiella pneumoniae were analyzed, and the information regarding the isolates was recorded from the NCBI database. The most prevalent was the I-E CRISPR-Cas system in all three studied taxa. E. coli also presents the I-F type, but in a much lesser percentage. The systems found in K. pneumoniae can be classified into I-E and I-E*. The I-E and I-F systems have two CRISPR loci, while I-E* has only one locus upstream of the Cas cluster. PCR primers have been developed in this study for each CRISPR locus. Distinct clustering was not evident, but statistically significant relationships occurred between the different CRISPR loci and the number of spacer units. For each of the queried taxa, the number of spacers was significantly different (p < 0.01) by origin (Africa, Asia, Australia and Oceania, Europe, North America, and South America) but was not linked to the isolation source type (human, animal, plant, food, or laboratory strains). Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology 2.0)
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Review

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16 pages, 2625 KiB  
Review
The Role of the Oral Microbiome in the Development of Diseases
by Małgorzata Kozak and Andrzej Pawlik
Int. J. Mol. Sci. 2023, 24(6), 5231; https://doi.org/10.3390/ijms24065231 - 9 Mar 2023
Cited by 15 | Viewed by 3689
Abstract
Periodontal disease (PD) is a complex and infectious illness that begins with a disruption of bacterial homeostasis. This disease induces a host inflammatory response, leading to damage of the soft and connective tooth-supporting tissues. Moreover, in advanced cases, it can contribute to tooth [...] Read more.
Periodontal disease (PD) is a complex and infectious illness that begins with a disruption of bacterial homeostasis. This disease induces a host inflammatory response, leading to damage of the soft and connective tooth-supporting tissues. Moreover, in advanced cases, it can contribute to tooth loss. The aetiological factors of PDs have been widely researched, but the pathogenesis of PD has still not been totally clarified. There are a number of factors that have an effect on the aetiology and pathogenesis of PD. It is purported that microbiological, genetic susceptibility and lifestyle can determine the development and severity of the disease. The human body’s defence response to the accumulation of plaque and its enzymes is known to be a major factor for PD. The oral cavity is colonised by a characteristic and complex microbiota that grows as diverse biofilms on all mucosal and dental surfaces. The aim of this review was to provide the latest updates in the literature regarding still-existing problems with PD and to highlight the role of the oral microbiome in periodontal health and disease. Better awareness and knowledge of the causes of dysbiosis, environmental risk factors and periodontal therapy can reduce the growing worldwide prevalence of PDs. The promotion of good oral hygiene, limiting smoking, alcohol consumption and exposure to stress and comprehensive treatment to decrease the pathogenicity of oral biofilm can help reduce PD as well as other diseases. Evidence linking disorders of the oral microbiome to various systemic diseases has increased the understanding of the importance of the oral microbiome in regulating many processes in the human body and, thus, its impact on the development of many diseases. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology 2.0)
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11 pages, 2128 KiB  
Review
History of the Study of the Genus Thiothrix: From the First Enrichment Cultures to Pangenomic Analysis
by Nikolai V. Ravin, Tatyana S. Rudenko, Dmitry D. Smolyakov, Alexey V. Beletsky, Maria V. Gureeva, Olga S. Samylina and Margarita Yu. Grabovich
Int. J. Mol. Sci. 2022, 23(17), 9531; https://doi.org/10.3390/ijms23179531 - 23 Aug 2022
Cited by 7 | Viewed by 2138
Abstract
Representatives of the genus Thiothrix are filamentous, sulfur-oxidizing bacteria found in flowing waters with counter-oriented sulfide and oxygen gradients. They were first described at the end of the 19th century, but the first pure cultures of this species only became available 100 years [...] Read more.
Representatives of the genus Thiothrix are filamentous, sulfur-oxidizing bacteria found in flowing waters with counter-oriented sulfide and oxygen gradients. They were first described at the end of the 19th century, but the first pure cultures of this species only became available 100 years later. An increase in the number of described Thiothrix species at the beginning of the 21st century shows that the classical phylogenetic marker, 16S rRNA gene, is not informative for species differentiation, which is possible based on genome analysis. Pangenome analysis of the genus Thiothrix showed that the core genome includes genes for dissimilatory sulfur metabolism and central metabolic pathways, namely the Krebs cycle, Embden–Meyerhof–Parnas pathway, glyoxylate cycle, Calvin–Benson–Bassham cycle, and genes for phosphorus metabolism and amination. The shell part of the pangenome includes genes for dissimilatory nitrogen metabolism and nitrogen fixation, for respiration with thiosulfate. The dispensable genome comprises genes predicted to encode mainly hypothetical proteins, transporters, transcription regulators, methyltransferases, transposases, and toxin–antitoxin systems. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology 2.0)
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