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

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 (31 March 2022) | Viewed by 19607

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 accessible the genomes of multiple strains of many individual microbial species. The comparison of genome sequences allows an in depth analysis of intra-species diversity and provides a deep understanding of organismal relationships. A particularly attractive application of microbial genomic comparison is the potential to give insights 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 evolutionary using a comparative genomics approach. We are interested in the patterns that characterize the evolution and function of microbes with pathogenic and symbiotic lifestyles, in particular, the effects of the microbial lifestyle on genome change including genome reduction, the abundance of mobile elements, and host-interaction genes. 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 phenotype. 

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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8 pages, 1517 KiB  
Communication
RadA, a Key Gene of the Circadian Rhythm of Escherichia coli
by Aissatou Bailo Diallo, Soraya Mezouar, Asma Boumaza, Oksana Fiammingo, Benjamin Coiffard, Pierre Pontarotti, Benoit Desnues and Jean-Louis Mege
Int. J. Mol. Sci. 2022, 23(11), 6136; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23116136 - 30 May 2022
Cited by 5 | Viewed by 2117
Abstract
Circadian rhythms are present in almost all living organisms, and their activity relies on molecular clocks. In prokaryotes, a functional molecular clock has been defined only in cyanobacteria. Here, we investigated the presence of circadian rhythms in non-cyanobacterial prokaryotes. The bioinformatic approach was [...] Read more.
Circadian rhythms are present in almost all living organisms, and their activity relies on molecular clocks. In prokaryotes, a functional molecular clock has been defined only in cyanobacteria. Here, we investigated the presence of circadian rhythms in non-cyanobacterial prokaryotes. The bioinformatic approach was used to identify a homologue of KaiC (circadian gene in cyanobacteria) in Escherichia coli. Then, strains of E. coli (wild type and mutants) were grown on blood agar, and sampling was made every 3 h for 24 h at constant conditions. Gene expression was determined by qRT-PCR, and the rhythmicity was analyzed using the Cosinor model. We identified RadA as a KaiC homologue in E. coli. Expression of radA showed a circadian rhythm persisting at least 3 days, with a peak in the morning. The circadian expression of other E. coli genes was also observed. Gene circadian oscillations were lost in radA mutants of E. coli. This study provides evidence of molecular clock gene expression in E. coli with a circadian rhythm. Such a finding paves the way for new perspectives in antibacterial treatment. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology)
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20 pages, 3511 KiB  
Article
A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application
by Maria K. Syrokou, Spiros Paramithiotis, Eleftherios H. Drosinos, Loulouda Bosnea and Marios Mataragas
Int. J. Mol. Sci. 2022, 23(5), 2487; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23052487 - 24 Feb 2022
Cited by 14 | Viewed by 3053
Abstract
The comparative genome analysis of six Lactiplantibacillus plantarum subsp. argentoratensis strains previously isolated from spontaneously fermented Greek wheat sourdoughs is presented. Genomic attributes related to food safety have been studied according to the European Food Safety Authority (EFSA) suggestions for the use of [...] Read more.
The comparative genome analysis of six Lactiplantibacillus plantarum subsp. argentoratensis strains previously isolated from spontaneously fermented Greek wheat sourdoughs is presented. Genomic attributes related to food safety have been studied according to the European Food Safety Authority (EFSA) suggestions for the use of lactic acid bacteria (LAB) in the production of foods. Bioinformatic analysis revealed a complete set of genes for maltose, sucrose, glucose, and fructose fermentation; conversion of fructose to mannitol; folate and riboflavin biosynthesis; acetoin production; conversion of citrate to oxaloacetate; and the ability to produce antimicrobial compounds (plantaricins). Pathogenic factors were absent but some antibiotic resistance genes were detected. CRISPR and cas genes were present as well as various mobile genetic elements (MGEs) such as plasmids, prophages, and insertion sequences. The production of biogenic amines by these strains was not possible due to the absence of key genes in their genome except lysine decarboxylase associated with cadaverine; however, potential degradation of these substances was identified due to the presence of a blue copper oxidase precursor and a multicopper oxidase protein family. Finally, comparative genomics and pan-genome analysis showed genetic differences between the strains (e.g., variable pln locus), and it facilitated the identification of various phenotypic and probiotic-related properties. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology)
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23 pages, 3729 KiB  
Article
Plasmidome of Listeria spp.—The repA-Family Business
by Cora Chmielowska, Dorota Korsak, Elvira Chapkauskaitse, Przemysław Decewicz, Robert Lasek, Magdalena Szuplewska and Dariusz Bartosik
Int. J. Mol. Sci. 2021, 22(19), 10320; https://doi.org/10.3390/ijms221910320 - 25 Sep 2021
Cited by 5 | Viewed by 3056
Abstract
Bacteria of the genus Listeria (phylum Firmicutes) include both human and animal pathogens, as well as saprophytic strains. A common component of Listeria spp. genomes are plasmids, i.e., extrachromosomal replicons that contribute to gene flux in bacteria. This study provides an in-depth [...] Read more.
Bacteria of the genus Listeria (phylum Firmicutes) include both human and animal pathogens, as well as saprophytic strains. A common component of Listeria spp. genomes are plasmids, i.e., extrachromosomal replicons that contribute to gene flux in bacteria. This study provides an in-depth insight into the structure, diversity and evolution of plasmids occurring in Listeria strains inhabiting various environments under different anthropogenic pressures. Apart from the components of the conserved plasmid backbone (providing replication, stable maintenance and conjugational transfer functions), these replicons contain numerous adaptive genes possibly involved in: (i) resistance to antibiotics, heavy metals, metalloids and sanitizers, and (ii) responses to heat, oxidative, acid and high salinity stressors. Their genomes are also enriched by numerous transposable elements, which have influenced the plasmid architecture. The plasmidome of Listeria is dominated by a group of related replicons encoding the RepA replication initiation protein. Detailed comparative analyses provide valuable data on the level of conservation of these replicons and their role in shaping the structure of the Listeria pangenome, as well as their relationship to plasmids of other genera of Firmicutes, which demonstrates the range and direction of flow of genetic information in this important group of bacteria. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology)
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20 pages, 5575 KiB  
Article
Evidence for the Role of CYP51A and Xenobiotic Detoxification in Differential Sensitivity to Azole Fungicides in Boxwood Blight Pathogens
by Stefanos Stravoravdis, Robert E. Marra, Nicholas R. LeBlanc, Jo Anne Crouch and Jonathan P. Hulvey
Int. J. Mol. Sci. 2021, 22(17), 9255; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22179255 - 26 Aug 2021
Cited by 1 | Viewed by 2125
Abstract
Boxwood blight, a fungal disease of ornamental plants (Buxus spp.), is caused by two sister species, Calonectria pseudonaviculata (Cps) and C. henricotiae (Che). Compared to Cps, Che is documented to display reduced sensitivity to fungicides, including the [...] Read more.
Boxwood blight, a fungal disease of ornamental plants (Buxus spp.), is caused by two sister species, Calonectria pseudonaviculata (Cps) and C. henricotiae (Che). Compared to Cps, Che is documented to display reduced sensitivity to fungicides, including the azole class of antifungals, which block synthesis of a key fungal membrane component, ergosterol. A previous study reported an ergosterol biosynthesis gene in Cps, CYP51A, to be a pseudogene, and RNA-Seq data confirm that a functional CYP51A is expressed only in Che. The lack of additional ergosterol biosynthesis genes showing significant differential expression suggests that the functional CYP51A in Che could contribute to reduced azole sensitivity when compared to Cps. RNA-Seq and bioinformatic analyses found that following azole treatment, 55 genes in Cps, belonging to diverse pathways, displayed a significant decrease in expression. Putative xenobiotic detoxification genes overexpressed in tetraconazole-treated Che encoded predicted monooxygenase and oxidoreductase enzymes. In summary, expression of a functional CYP51A gene and overexpression of predicted xenobiotic detoxification genes appear likely to contribute to differential fungicide sensitivity in these two sister taxa. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology)
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27 pages, 13049 KiB  
Article
Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.
by Sarah Vanwijnsberghe, Charlotte Peeters, Emmelie De Ridder, Charles Dumolin, Anneleen D. Wieme, Nico Boon and Peter Vandamme
Int. J. Mol. Sci. 2021, 22(13), 7003; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22137003 - 29 Jun 2021
Cited by 10 | Viewed by 3043
Abstract
We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, [...] Read more.
We performed a taxonomic and comparative genomics analysis of 67 novel Paraburkholderia isolates from forest soil. Phylogenetic analysis of the recA gene revealed that these isolates formed a coherent lineage within the genus Paraburkholderia that also included Paraburkholderiaaspalathi, Paraburkholderiamadseniana, Paraburkholderiasediminicola, Paraburkholderiacaffeinilytica, Paraburkholderiasolitsugae and Paraburkholderiaelongata and four unidentified soil isolates from earlier studies. A phylogenomic analysis, along with orthoANIu and digital DNA–DNA hybridization calculations revealed that they represented four different species including three novel species and P. aspalathi. Functional genome annotation of the strains revealed several pathways for aromatic compound degradation and the presence of mono- and dioxygenases involved in the degradation of the lignin-derived compounds ferulic acid and p-coumaric acid. This co-occurrence of multiple Paraburkholderia strains and species with the capacity to degrade aromatic compounds in pristine forest soil is likely caused by the abundant presence of aromatic compounds in decomposing plant litter and may highlight a diversity in micro-habitats or be indicative of synergistic relationships. We propose to classify the isolates representing novel species as Paraburkholderia domus with LMG 31832T (=CECT 30334) as the type strain, Paraburkholderia nemoris with LMG 31836T (=CECT 30335) as the type strain and Paraburkholderia haematera with LMG 31837T (=CECT 30336) as the type strain and provide an emended description of Paraburkholderia sediminicola Lim et al. 2008. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology)
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Review

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24 pages, 4249 KiB  
Review
Rhizomal Reclassification of Living Organisms
by Ahmad Ibrahim, Philippe Colson, Vicky Merhej, Rita Zgheib, Mohamad Maatouk, Sabrina Naud, Fadi Bittar and Didier Raoult
Int. J. Mol. Sci. 2021, 22(11), 5643; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115643 - 26 May 2021
Cited by 12 | Viewed by 4703
Abstract
Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant [...] Read more.
Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies. Full article
(This article belongs to the Special Issue Microbial Comparative Genomics and Evolutionary Biology)
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