scholarly journals Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Adrian Wallner ◽  
Eoghan King ◽  
Eddy L. M. Ngonkeu ◽  
Lionel Moulin ◽  
Gilles Béna
Keyword(s):  
Virulence Factors ◽  
Phylogenetic Analyses ◽  
Opportunistic Pathogen ◽  
Distinct Species ◽  
Burkholderia Cenocepacia ◽  
Ecological Niches ◽  
Comparative Genomic ◽  
Genetic Traits ◽  
Genomic Analyses ◽  
Different Strains

Abstract Background Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genomes, the large majority were isolated from a clinical context. However, several isolates originate from other environmental sources ranging from aerosols to plant endosphere. Plants can represent reservoirs for human infections as some pathogens can survive and sometimes proliferate in the rhizosphere. We therefore investigated if B. cenocepacia had the same potential. Results We selected genome sequences from 31 different strains, representative of the diversity of ecological niches of B. cenocepacia, and conducted comparative genomic analyses in the aim of finding specific niche or host-related genetic determinants. Phylogenetic analyses and whole genome average nucleotide identity suggest that strains, registered as B. cenocepacia, belong to at least two different species. Core-genome analyses show that the clade enriched in environmental isolates lacks multiple key virulence factors, which are conserved in the sister clade where most clinical isolates fall, including the highly virulent ET12 lineage. Similarly, several plant associated genes display an opposite distribution between the two clades. Finally, we suggest that B. cenocepacia underwent a host jump from plants/environment to animals, as supported by the phylogenetic analysis. We eventually propose a name for the new species that lacks several genetic traits involved in human virulence. Conclusion Regardless of the method used, our studies resulted in a disunited perspective of the B. cenocepacia species. Strains currently affiliated to this taxon belong to at least two distinct species, one having lost several determining animal virulence factors.

scholarly journals Comparative genomic analysis of gene clusters of Pseudomonas aeruginosa that define specific biofilm formation in deciphering target regions for novel treatment options

2020 ◽  
Author(s):  
Michael Ambutsi ◽  
Oleg Reva ◽  
Patrick Okoth
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Biofilm Formation ◽  
Phylogenetic Analyses ◽  
Treatment Options ◽  
Gene Clusters ◽  
Opportunistic Pathogen ◽  
Natural Resistance ◽  
Future Research ◽  
Ecological Niches ◽  
Comparative Genomic

Abstract Background Pseudomonas aeruginosa is an opportunistic pathogen associated with numerous nosocomial infections that are difficult to treat as a result of natural resistance to various antibiotics, particularly because of biofilm formation. The purpose of this study was to determine the distribution of biofilm formation genes in sequences of this opportunistic pathogen and their association with different ecological niches. In total, 13 genes responsible for biofilm formation by P. aeruginosa were identified and used in the study. They were clustered into seven categories based on the role they play in the biofilm formation process. The study also analyzed 185 complete genome sequences of P. aeruginosa strains retrieved from the NCBI and IPCD databases. These were classified into 14 categories based on the ecological niches they occupy. Results Phylogenetic analyses of the biofilm formation genes indicated a strong co-evolution of a majority of these genes, n=10 . Exceptions were the genes fliC, algD, and algU which may have been exchanged by horizontal gene transfer or evolved faster than the other genes of this functional group as they are more important in terms of a proper response of the biofilm formation to specific environmental stimuli in different habitats. The BLAST Ring Image Generator (BRIG) analysis was used to visualize the distribution of biofilm formation genes between different strains of P. aeruginosa . Conclusions fliC, algD, and algU genes were identified as potential targets for antibiofilm therapies. These findings could inform the development of antibiofilm therapies that target processes mediated by these genes. Also, this study provides useful information that can guide the direction of future research.

scholarly journals Assessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Chiara Tarracchini ◽  
Gabriele Andrea Lugli ◽  
Leonardo Mancabelli ◽  
Christian Milani ◽  
Francesca Turroni ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Human Population ◽  
Gardnerella Vaginalis ◽  
Comparative Genomic ◽  
Genetic Traits ◽  
Content Type ◽  
Microbial Taxon ◽  
Virulence Potential ◽  
Genomic Analyses ◽  
Phylogenomic Analyses

ABSTRACT Gardnerella vaginalis is described as a common anaerobic vaginal bacterium whose presence may correlate with vaginal dysbiotic conditions. In the current study, we performed phylogenomic analyses of 72 G. vaginalis genome sequences, revealing noteworthy genome differences underlying a polyphyletic organization of this taxon. Particularly, the genomic survey revealed that this species may actually include nine distinct genotypes (GGtype1 to GGtype9). Furthermore, the observed link between sialidase and phylogenomic grouping provided clues of a connection between virulence potential and the evolutionary history of this microbial taxon. Specifically, based on the outcomes of these in silico analyses, GGtype3, GGtype7, GGtype8, and GGtype9 appear to have virulence potential since they exhibited the sialidase gene in their genomes. Notably, the analysis of 34 publicly available vaginal metagenomic samples allowed us to trace the distribution of the nine G. vaginalis genotypes identified in this study among the human population, highlighting how differences in genetic makeup could be related to specific ecological properties. Furthermore, comparative genomic analyses provided details about the G. vaginalis pan- and core genome contents, including putative genetic elements involved in the adaptation to the ecological niche as well as many putative virulence factors. Among these putative virulence factors, particularly noteworthy genes identified were the gene encoding cholesterol-dependent cytolysin (CDC) toxin vaginolysin and genes related to microbial biofilm formation, iron uptake, adhesion to the vaginal epithelium, as well as macrolide antibiotic resistance. IMPORTANCE The identification of nine different genotypes among members of G. vaginalis allowed us to distinguish an uneven distribution of virulence-associated genetic traits within this taxon and thus suggest the potential occurrence of putative pathogen and commensal G. vaginalis strains. These findings, coupled with metagenomics microbial profiling of human vaginal microbiota, permitted us to get insights into the distribution of the genotypes among the human population, highlighting the presence of different structural communities in terms of G. vaginalis genotypes.

scholarly journals Cutibacterium acnes as an Opportunistic Pathogen: An Update of Its Virulence-Associated Factors

2021 ◽  
Vol 9 (2) ◽  
pp. 303 ◽  
Author(s):  
Constance Mayslich ◽  
Philippe Alain Grange ◽  
Nicolas Dupin
Keyword(s):  
Virulence Factors ◽  
Current Knowledge ◽  
Opportunistic Pathogen ◽  
Bacterial Attachment ◽  
Molecular Structures ◽  
Ecological Niches ◽  
Target Cells ◽  
Skin Microbiota ◽  
Host Immune Responses ◽  
Cutibacterium Acnes

Cutibacterium acnes is a member of the skin microbiota found predominantly in regions rich in sebaceous glands. It is involved in maintaining healthy skin and has long been considered a commensal bacterium. Its involvement in various infections has led to its emergence as an opportunist pathogen. Interactions between C. acnes and the human host, including the human skin microbiota, promote the selection of C. acnes strains capable of producing several virulence factors that increase inflammatory capability. This pathogenic property may be related to many infectious mechanisms, such as an ability to form biofilms and the expression of putative virulence factors capable of triggering host immune responses or enabling C. acnes to adapt to its environment. During the past decade, many studies have identified and characterized several putative virulence factors potentially involved in the pathogenicity of this bacterium. These virulence factors are involved in bacterial attachment to target cells, polysaccharide-based biofilm synthesis, molecular structures mediating inflammation, and the enzymatic degradation of host tissues. C. acnes, like other skin-associated bacteria, can colonize various ecological niches other than skin. It produces several proteins or glycoproteins that could be considered to be active virulence factors, enabling the bacterium to adapt to the lipophilic environment of the pilosebaceous unit of the skin, but also to the various organs it colonizes. In this review, we summarize current knowledge concerning characterized C. acnes virulence factors and their possible implication in the pathogenicity of C. acnes.

scholarly journals Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants

2020 ◽  
Vol 8 (11) ◽  
pp. 1679
Author(s):  
Valentina Méndez ◽  
Miryam Valenzuela ◽  
Francisco Salvà-Serra ◽  
Daniel Jaén-Luchoro ◽  
Ximena Besoain ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Phylogenetic Analyses ◽  
Plant Diseases ◽  
Genomic Diversity ◽  
Clavibacter Michiganensis ◽  
Tomato Plants ◽  
Clavibacter Michiganensis Subsp ◽  
Genomic Analyses ◽  
Encoding Genes ◽  
Genomic Similarity

The genus Clavibacter has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean C. michiganensis subsp. michiganensis strains VL527, MSF322 and OP3, and to define their phylogenomic positions within the species, Clavibacter michiganensis. VL527 and MSF322 genomes possess 3,396,632 and 3,399,199 bp, respectively, with a pCM2-like plasmid in strain VL527, with pCM1- and pCM2-like plasmids in strain MSF322. OP3 genome is composed of a chromosome and three plasmids (including pCM1- and pCM2-like plasmids) of 3,466,104 bp. Genomic analyses confirmed the phylogenetic relationships of the Chilean strains among C.michiganensis subsp. michiganensis and showed their low genomic diversity. Different virulence levels in tomato plants were observable. Phylogenetic analyses of the virulence factors revealed that the pelA1 gene (chp/tomA region)—that grouped Chilean strains in three distinct clusters—and proteases and hydrolases encoding genes, exclusive for each of the Chilean strains, may be involved in these observed virulence levels. Based on genomic similarity (ANIm) analyses, a proposal to combine and reclassify C. michiganensis subsp. phaseoli and subsp. chilensis at the species level, as C. phaseoli sp. nov., as well as to reclassify C. michiganensis subsp. californiensis as the species C. californiensis sp. nov. may be justified.

Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae

Holzforschung ◽  
2018 ◽  
Vol 72 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Yu Song ◽  
Xin Yao ◽  
Bing Liu ◽  
Yunhong Tan ◽  
Richard T. Corlett
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Inverted Repeats ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Tropical Asia ◽  
Length Difference ◽  
The Family ◽  
Genomic Analyses

AbstractAlseodaphneis a genus of timber trees (ca. 40 spp.) belonging to thePerseagroup of the Lauraceae. It is widely distributed in tropical Asia, but is often confused withDehaasiaandNothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences ofA. semecarpifoliawill be reported, the type species ofAlseodaphne, and two China-endemic species,A. gracilisandA. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the threeAlseodaphneplastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci includingpsbD-trnM,ndhF-rpl32,rpl32-trnLandycf1among the threeAlseodaphnespecies were identified as useful plastid candidate barcodes forAlseodaphneand Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPerseagroup comprising species ofAlseodaphne,Phoebe,PerseaandMachilus.

scholarly journals Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales

2020 ◽  
Author(s):  
Pieter De Maayer ◽  
Talia Pillay ◽  
Teresa A Coutinho
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Biological Functions ◽  
Flagellar Motility ◽  
Common Features ◽  
Genomic Analyses ◽  
Ecological Success

Abstract Background: Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of flagella is highly energy intensive and therefore flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility. Results: Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4,028 (~20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales. Conclusions: Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.

scholarly journals Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3203-3215 ◽  
Author(s):  
Chantal Campbell ◽  
Mobolaji Adeolu ◽  
Radhey S. Gupta
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Core Protein ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Conserved Signature Indels ◽  
The Family ◽  
Genomic Analyses

The class Negativicutes is currently divided into one order and two families on the basis of 16S rRNA gene sequence phylogenies. We report here comprehensive comparative genomic analyses of the sequenced members of the class Negativicutes to demarcate its different evolutionary groups in molecular terms, independently of phylogenetic trees. Our comparative genomic analyses have identified 14 conserved signature indels (CSIs) and 48 conserved signature proteins (CSPs) that either are specific for the entire class or differentiate four main groups within the class. Two CSIs and nine CSPs are shared uniquely by all or most members of the class Negativicutes, distinguishing this class from all other sequenced members of the phylum Firmicutes. Four other CSIs and six CSPs were specific characteristics of the family Acidaminococcaceae, two CSIs and four CSPs were uniquely present in the family Veillonellaceae, six CSIs and eight CSPs were found only in Selenomonas and related genera, and 17 CSPs were identified uniquely in Sporomusa and related genera. Four additional CSPs support a pairing of the groups containing the genera Selenomonas and Sporomusa. We also report detailed phylogenetic analyses for the Negativicutes based on core protein sequences and 16S rRNA gene sequences, which strongly support the four main groups identified by CSIs and by CSPs. Based on the results from different lines of investigation, we propose a division of the class Negativicutes into an emended order Selenomonadales containing the new families Selenomonadaceae fam. nov. and Sporomusaceae fam. nov. and two new orders, Acidaminococcales ord. nov. and Veillonellales ord. nov., respectively containing the families Acidaminococcaceae and Veillonellaceae.

scholarly journals Comparative Study of the Molecular Basis of Pathogenicity of M. bovis Strains in a Mouse Model

2018 ◽  
Vol 20 (1) ◽  
pp. 5 ◽  
Author(s):  
Guangyu Cheng ◽  
Tariq Hussain ◽  
Naveed Sabir ◽  
Jiamin Ni ◽  
Miaoxuan Li ◽  
...  
Keyword(s):  
Mouse Model ◽  
Immune Responses ◽  
Virulence Factors ◽  
Genomic Analysis ◽  
Interferon Γ ◽  
Comparative Genomic ◽  
Interleukin 17 ◽  
Nucleotide Polymorphisms ◽  
Serum Samples ◽  
Different Strains

It is widely accepted that different strains of Mycobacterium tuberculosis have variable degrees of pathogenicity and induce different immune responses in infected hosts. Similarly, different strains of Mycobacterium bovis have been identified but there is a lack of information regarding the degree of pathogenicity of these strains and their ability to provoke host immune responses. Therefore, in the current study, we used a mouse model to evaluate various factors involved in the severity of disease progression and the induction of immune responses by two strains of M. bovis isolated from cattle. Mice were infected with both strains of M. bovis at different colony-forming unit (CFU) via inhalation. Gross and histological findings revealed more severe lesions in the lung and spleen of mice infected with M. bovis N strain than those infected with M. bovis C68004 strain. In addition, high levels of interferon-γ (IFN-γ), interleukin-17 (IL-17), and IL-22 production were observed in the serum samples of mice infected with M. bovis N strain. Comparative genomic analysis showed the existence of 750 single nucleotide polymorphisms and 145 small insertions/deletions between the two strains. After matching with the Virulence Factors Database, mutations were found in 29 genes, which relate to 17 virulence factors. Moreover, we found an increased number of virulent factors in M. bovis N strain as compared to M. bovis C68004 strain. Taken together, our data reveal that variation in the level of pathogenicity is due to the mutation in the virulence factors of M. bovis N strain. Therefore, a better understanding of the mechanisms of mutation in the virulence factors will ultimately contribute to the development of new strategies for the control of M. bovis infection.

scholarly journals Isolation of Prasinoviruses of the Green Unicellular Algae Ostreococcus spp. on a Worldwide Geographical Scale

2009 ◽  
Vol 76 (1) ◽  
pp. 96-101 ◽  
Author(s):  
Laure Bellec ◽  
Nigel Grimsley ◽  
Yves Desdevises
Keyword(s):  
Phylogenetic Analyses ◽  
Marker Gene ◽  
Distinct Species ◽  
Mantel Test ◽  
Ecological Niches ◽  
Dna Viruses ◽  
Viral Marker ◽  
Geographical Scale ◽  
Clade C ◽  
Seawater Samples

ABSTRACT Ostreococcus spp. are extremely small unicellular eukaryotic green algae found worldwide in marine environments, and they are susceptible to attacks by a diverse group of large DNA viruses. Several biologically distinct species of Ostreococcus are known and differ in the ecological niches that they occupy: while O. tauri (representing clade C strains) is found in marine lagoons and coastal seas, strains belonging to clade A, exemplified by O. lucimarinus, are present in different oceans. We used laboratory cultures of clonal isolates of these two species to assay for the presence of viruses in seawater samples from diverse locations. In keeping with the distributions of their host strains, we found a decline in the abundance of O. tauri viruses from a lagoon in southwest France relative to the Mediterranean Sea, whereas in the ocean, no O. tauri viruses were detected. In contrast, viruses infecting O. lucimarinus were detected from distantly separated oceans. DNA sequencing, phylogenetic analyses using a conserved viral marker gene, and a Mantel test revealed no relationship between geographic and phylogenetic distances in viruses infecting O. lucimarinus.

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