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Microbial Genomics and Evolution
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Microbial Genomics and Evolution

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

Deadline for manuscript submissions: closed (31 May 2021) | Viewed by 24031

Special Issue Editor

Dr. Louis-Marie Bobay

E-Mail Website
Guest Editor
Department of Biology, University of North Carolina, Greensboro, NC 27411, USA
Interests: evolution of bacterial genome architecture

Special Issue Information

Dear Colleagues,

Microbes have a considerable impact on human health, the environment, and the economy. In the past few decades, great progress has been made in our understanding of microbial genomes and their evolution. The advent of high-throughput technologies has led to the accumulation of a massive amount of genomic data and started to reveal the immense diversity of microbes and their genomes. In addition, metagenomic and single-cell sequencing are now providing us with new insights into the structure and evolution of microbial communities in their natural environments. Although these data are improving our understanding of microbial genomes’ evolution, many fundamental questions have yet to be answered.

Among those unanswered questions, the microevolution and the forces driving the structure and dynamics of microbial populations remain poorly described. Although we have now established that microbes are extremely diverse, the mechanisms underlying microbial diversification and speciation remain to be uncovered and the impact of selection, ecology, and neutral processes on these mechanisms are not yet fully understood. Sequencing technologies have revealed that microbes have an unprecedented degree of genomic diversity, where strains not only differ in allelic profiles, but typically display highly variable gene contents. The diversity of the gene repertoires of a given species, the pan-genome, is an intriguing feature of prokaryotes and the function and evolutionary dynamics of the variable fraction of the pan-genome remain largely unknown. Finally, understanding the precise interaction between microbes and their environment is another complex endeavor that researchers using novel -omics approaches are starting to unveil in more detail.

This Special Issue will focus on microbial genomics and evolution and welcomes genomic and metagenomic studies that aim to understand the evolution of microbes and their genomes.

Dr. Louis-Marie Bobay
Guest Editor

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. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • microbes
  • genomics
  • metagenomics
  • evolution
  • population genetics
  • speciation
  • adaptation
  • genome architecture
  • pan-genome
  • microbial ecology
  • bacteriophages

Published Papers (7 papers)

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Research

19 pages, 4275 KiB  
Article
Genome Mining and Comparative Genome Analysis Revealed Niche-Specific Genome Expansion in Antibacterial Bacillus pumilus Strain SF-4
by Sajid Iqbal, John Vollmers and Hussnain Ahmed Janjua
Genes 2021, 12(7), 1060; https://doi.org/10.3390/genes12071060 - 12 Jul 2021
Cited by 13 | Viewed by 3867
Abstract
The present study reports the isolation of antibacterial exhibiting Bacillus pumilus (B. pumilus) SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic [...] Read more.
The present study reports the isolation of antibacterial exhibiting Bacillus pumilus (B. pumilus) SF-4 from soil field. The genome of this strain SF-4 was sequenced and analyzed to acquire in-depth genomic level insight related to functional diversity, evolutionary history, and biosynthetic potential. The genome of the strain SF-4 harbor 12 Biosynthetic Gene Clusters (BGCs) including four Non-ribosomal peptide synthetases (NRPSs), two terpenes, and one each of Type III polyketide synthases (PKSs), hybrid (NRPS/PKS), lipopeptide, β-lactone, and bacteriocin clusters. Plant growth-promoting genes associated with de-nitrification, iron acquisition, phosphate solubilization, and nitrogen metabolism were also observed in the genome. Furthermore, all the available complete genomes of B. pumilus strains were used to highlight species boundaries and diverse niche adaptation strategies. Phylogenetic analyses revealed local diversification and indicate that strain SF-4 is a sister group to SAFR-032 and 150a. Pan-genome analyses of 12 targeted strains showed regions of genome plasticity which regulate function of these strains and proposed direct strain adaptations to specific habitats. The unique genome pool carries genes mostly associated with “biosynthesis of secondary metabolites, transport, and catabolism” (Q), “replication, recombination and repair” (L), and “unknown function” (S) clusters of orthologous groups (COG) categories. Moreover, a total of 952 unique genes and 168 exclusively absent genes were prioritized across the 12 genomes. While newly sequenced B. pumilus SF-4 genome consists of 520 accessory, 59 unique, and seven exclusively absent genes. The current study demonstrates genomic differences among 12 B. pumilus strains and offers comprehensive knowledge of the respective genome architecture which may assist in the agronomic application of this strain in future. Full article
(This article belongs to the Special Issue Microbial Genomics and Evolution)
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22 pages, 2701 KiB  
Article
The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania infantum and Their Analyses in Yeast
by Molka Mokdadi, Yosser Zina Abdelkrim, Josette Banroques, Emmeline Huvelle, Rafeh Oualha, Hilal Yeter-Alat, Ikram Guizani, Mourad Barhoumi and N. Kyle Tanner
Genes 2021, 12(2), 212; https://doi.org/10.3390/genes12020212 - 01 Feb 2021
Cited by 3 | Viewed by 2479
Abstract
DEAD-box RNA helicases are ubiquitous proteins found in all kingdoms of life and that are associated with all processes involving RNA. Their central roles in biology make these proteins potential targets for therapeutic or prophylactic drugs. The Ded1/DDX3 subfamily of DEAD-box proteins is [...] Read more.
DEAD-box RNA helicases are ubiquitous proteins found in all kingdoms of life and that are associated with all processes involving RNA. Their central roles in biology make these proteins potential targets for therapeutic or prophylactic drugs. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest because of their important role(s) in translation. In this paper, we identified and aligned the protein sequences of 28 different DEAD-box proteins from the kinetoplast-protozoan parasite Leishmania infantum, which is the cause of the visceral form of leishmaniasis that is often lethal if left untreated, and compared them with the consensus sequence derived from DEAD-box proteins in general, and from the Ded1/DDX3 subfamily in particular, from a wide variety of other organisms. We identified three potential homologs of the Ded1/DDX3 subfamily and the equivalent proteins from the related protozoan parasite Trypanosoma brucei, which is the causative agent of sleeping sickness. We subsequently tested these proteins for their ability to complement a yeast strain deleted for the essential DED1 gene. We found that the DEAD-box proteins from Trypanosomatids are highly divergent from other eukaryotes, and consequently they are suitable targets for protein-specific drugs. Full article
(This article belongs to the Special Issue Microbial Genomics and Evolution)
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14 pages, 1769 KiB  
Article
Whole Genome Analysis of Environmental Pseudomonas mendocina Strains: Virulence Mechanisms and Phylogeny
by Lidia Ruiz-Roldán, María de Toro and Yolanda Sáenz
Genes 2021, 12(1), 115; https://doi.org/10.3390/genes12010115 - 19 Jan 2021
Cited by 3 | Viewed by 2847
Abstract
Pseudomonas mendocina is an environmental bacterium, rarely isolated in clinical specimens, although it has been described as producing endocarditis and sepsis. Little is known about its genome. Whole genome sequencing can be used to learn about the phylogeny, evolution, or pathogenicity of these [...] Read more.
Pseudomonas mendocina is an environmental bacterium, rarely isolated in clinical specimens, although it has been described as producing endocarditis and sepsis. Little is known about its genome. Whole genome sequencing can be used to learn about the phylogeny, evolution, or pathogenicity of these isolates. Thus, the aim of this study was to analyze the resistome, virulome, and phylogenetic relationship of two P. mendocina strains, Ps542 and Ps799, isolated from a healthy Anas platyrhynchos fecal sample and a lettuce, respectively. Among all of the small number of P.mendocina genomes available in the National Center for Biotechnology Information (NCBI) repository, both strains were placed within one of two well-defined phylogenetic clusters. Both P. mendocina strains lacked antimicrobial resistance genes, but the Ps799 genome showed a MOBP3 family relaxase. Nevertheless, this study revealed that P. mendocina possesses an important number of virulence factors, including a leukotoxin, flagella, pili, and the Type 2 and Type 6 Secretion Systems, that could be responsible for their pathogenesis. More phenotypical and in vivo studies are needed to deepen the association with human infections and the potential P. mendocina pathogenicity. Full article
(This article belongs to the Special Issue Microbial Genomics and Evolution)
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17 pages, 1688 KiB  
Article
Metabolic Specialization and Codon Preference of Lignocellulolytic Genes in the White Rot Basidiomycete Ceriporiopsis subvermispora
by Alex Gonzalez, Gino Corsini, Sergio Lobos, Daniela Seelenfreund and Mario Tello
Genes 2020, 11(10), 1227; https://doi.org/10.3390/genes11101227 - 20 Oct 2020
Cited by 3 | Viewed by 2550
Abstract
Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. Its lignocellulose degrading system is formed by cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignocellulose. [...] Read more.
Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. Its lignocellulose degrading system is formed by cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignocellulose. To determine if this metabolic specialization has modified codon usage of the lignocellulolytic system, improving its adaptation to the fungal translational machine, we analyzed the adaptation to host codon usage (CAI), tRNA pool (tAI, and AAtAI), codon pair bias (CPB), and the number of effective codons (Nc). These indexes were correlated with gene expression of C. subvermispora, in the presence of glucose and Aspen wood. General gene expression was not correlated with the index values. However, in media containing Aspen wood, the induction of expression of lignocellulose-degrading genes, showed significantly (p < 0.001) higher values of CAI, AAtAI, CPB, tAI, and lower values of Nc than non-induced genes. Cellulose-binding proteins and manganese peroxidases presented the highest adaptation values. We also identified an expansion of genes encoding glycine and glutamic acid tRNAs. Our results suggest that the metabolic specialization to use wood as the sole carbon source has introduced a bias in the codon usage of genes involved in lignocellulose degradation. This bias reduces codon diversity and increases codon usage adaptation to the tRNA pool available in C. subvermispora. To our knowledge, this is the first study showing that codon usage is modified to improve the translation efficiency of a group of genes involved in a particular metabolic process. Full article
(This article belongs to the Special Issue Microbial Genomics and Evolution)
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9 pages, 668 KiB  
Article
The New Klebsiella pneumoniae ST152 Variants with Hypermucoviscous Phenotype Isolated from Renal Transplant Recipients with Asymptomatic Bacteriuria—Genetic Characteristics by WGS
by Magdalena Wysocka, Roxana Zamudio, Marco R Oggioni, Justyna Gołębiewska, Aleksandra Dudziak and Beata Krawczyk
Genes 2020, 11(10), 1189; https://doi.org/10.3390/genes11101189 - 13 Oct 2020
Cited by 9 | Viewed by 2688
Abstract
Klebsiella pneumoniae (Kp) is one of the most important etiological factors of urinary tract infections in renal transplant (RTx) recipients. We described the antimicrobial susceptibility phenotypes and genomic features of two hypermucoviscous (HM) Kp isolates recovered from RTx recipients with asymptomatic bacteriuria (ABU). [...] Read more.
Klebsiella pneumoniae (Kp) is one of the most important etiological factors of urinary tract infections in renal transplant (RTx) recipients. We described the antimicrobial susceptibility phenotypes and genomic features of two hypermucoviscous (HM) Kp isolates recovered from RTx recipients with asymptomatic bacteriuria (ABU). Using whole genome sequencing (WGS) data, we showed that the strains belong to the ST152 lineage with the KL149 capsular serotype, but without rmpA/magA genes, which is typical for HM+ hypervirulent Kp. These new strains carried virulence-associated genes that predispose for urinary tract infections (UTIs). Likewise, both strains carried the ecp gene encoding pilus common for extended-spectrum β-lactamase (ESBL) Escherichia coli. Although the two ST152 isolates were closely related and differed by only nine single nucleotide polymorphisms (SNPs) in their chromosomes, they had different plasmid compositions and chromosomal elements, with isolate KP28872 carrying an ESBL plasmid and an integrative conjugative element. These two isolates are an example of the high plasticity of the K. pneumoniae accessory genome. The identification of patients with ABU matched with the correct epidemiological profiling of isolates could facilitate interventions to prevent or rapidly treat K. pneumoniae infections. Full article
(This article belongs to the Special Issue Microbial Genomics and Evolution)
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17 pages, 14156 KiB  
Article
Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina
by Long Song, Jing Qin Wu, Chong Mei Dong and Robert F. Park
Genes 2020, 11(9), 1107; https://doi.org/10.3390/genes11091107 - 21 Sep 2020
Cited by 5 | Viewed by 3106
Abstract
The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in [...] Read more.
The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and identify candidate avirulence genes. Using a long-read based de novo genome assembly of an isolate of Pt (‘Pt104’) as the reference, whole-genome resequencing data of 12 Pt pathotypes derived from three lineages Pt104, Pt53, and Pt76 were analyzed. Candidate avirulence genes were identified by correlating virulence profiles with small variants (SNP and InDel) and CNV, and RNA-seq data of an additional three Pt isolates to validate expression of genes encoding secreted proteins (SPs). Out of the annotated 29,043 genes, 2392 genes were selected as SP genes with detectable expression levels. Small variant comparisons between the isolates identified 27–40 candidates and CNV analysis identified 14–31 candidates for each Avr gene, which when combined, yielded the final 40, 64, and 69 candidates for AvrLr1, AvrLr15, and AvrLr24, respectively. Taken together, our results will facilitate future work on experimental validation and cloning of Avr genes. In addition, the integrated framework of data analysis that we have developed and reported provides a more comprehensive approach for Avr gene mining than is currently available. Full article
(This article belongs to the Special Issue Microbial Genomics and Evolution)
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14 pages, 1300 KiB  
Article
Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events
by Mohammed A. Rohaim, Rania F. El Naggar, Mohammed A. Abdelsabour, Mahmoud H. A. Mohamed, Ibrahim M. El-Sabagh and Muhammad Munir
Genes 2020, 11(6), 605; https://doi.org/10.3390/genes11060605 - 29 May 2020
Cited by 22 | Viewed by 5577
Abstract
In the last 5 years, frequent outbreaks of infectious bronchitis virus (IBV) are observed in both broiler and layer chicken flocks in the Kingdom of Saudi Arabia (KSA) in spite of extensive usage of vaccines. The IBV is a widespread avian coronavirus affecting [...] Read more.
In the last 5 years, frequent outbreaks of infectious bronchitis virus (IBV) are observed in both broiler and layer chicken flocks in the Kingdom of Saudi Arabia (KSA) in spite of extensive usage of vaccines. The IBV is a widespread avian coronavirus affecting both vaccinated and unvaccinated chicken flocks and is attributed to significant economic losses, around the globe. In the present study, 58 (n = 58) samples were collected from four different commercial poultry flocks from 8 KSA districts during 2019. A total of nine positive isolates (9/58; 15.5%), based on real-time reverse transcriptase PCR targeting nucleocapsid (N) gene, were used for further genetic characterization and evolutionary analysis. Genetic characterization of the partial spike (S1) gene revealed the clustering of the reported isolates into three different genotypes, whereas four additional isolates were grouped within 4/91 genotype, two isolates within IS/885 genotype, one isolate was closely related to IS/1494/06, and two isolates were grouped within classic serotype (vaccine-like strains). Phylodynamic revealed clustering of four isolated viruses within GI-13 lineage, three isolates within GI-23 lineage, and two isolates within GI-1 lineage. Results indicate that there are high evolutionary distances between the newly identified IBV strains in this study and the commercially used vaccines (GI-1), suggesting that IBV strains circulating in the KSA are under constant evolutionary pressures. Selective pressure biostatistics analyses consistently demonstrate the presence of a higher positive score which highlights the role of natural selection, a mechanism of virus evolution on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. Recombination analysis revealed emergence of two isolates through recombination events resulting in new recombinant viruses. Taken together, these finding demonstrate the genetic and evolutionary insights into the currently circulating IBV genotypes in KSA, which could help to better understand the origin, spread, and evolution of infectious bronchitis viruses, and to ascertain the importance of disease monitoring as well as re-evaluation for the currently used vaccines and vaccination programs. Full article
(This article belongs to the Special Issue Microbial Genomics and Evolution)
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