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 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 Deciphering the Origins and Tracking the Evolution of Cholera Epidemics with Whole-Genome-Based Molecular Epidemiology

mBio ◽  
2013 ◽  
Vol 4 (5) ◽  
Author(s):  
Yonatan H. Grad ◽  
Matthew K. Waldor
Keyword(s):  
Point Mutations ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Cholera Outbreak ◽  
Outbreak Strain ◽  
Security Forces ◽  
Content Type ◽  
Cholera Epidemic ◽  
Genomic Analyses ◽  
The World

ABSTRACT The devastating Haitian cholera outbreak that began in October 2010 is the first known cholera epidemic in this island nation. Epidemiological and genomic data have provided strong evidence that United Nations security forces from Nepal introduced toxigenic Vibrio cholerae O1, the cause of epidemic cholera, to Haiti shortly before the outbreak arose. However, some have contended that indigenous V. cholerae contributed to the outbreak. In a recent paper (mBio 4:e00398-13, 2013), L. S. Katz et al. explored the nature and rate of changes in this ancient pathogen’s genome during an outbreak, based on whole-genome sequencing of 23 Haitian V. cholerae clinical isolates obtained over a 20-month period. Notably, they detected point mutations, deletions, and inversions but found no insertion of horizontally transmitted DNA, arguing strongly against the idea that autochthonous V. cholerae donated DNA to the outbreak strain. Furthermore, they found that Haitian epidemic V. cholerae isolates were virtually untransformable. Comparative genomic analyses revealed that the Haitian isolates were nearly identical to isolates from Nepal and that the Nepalese-Haitian isolates were distinguishable from isolates circulating elsewhere in the world. Reconstruction of the phylogeny of the Haitian isolates was consistent with a single introduction of V. cholerae to Haiti sometime between late July and late October 2010, dates remarkably concordant with epidemiological observations. In aggregate, this paper provides additional compelling evidence that the V. cholerae strain responsible for the Haitian cholera epidemic came from Nepal and illustrates the power of whole-genome-based analyses for epidemiology, pathogen evolution, and forensics.

scholarly journals Comparative genomic insights into Yersinia hibernica – a commonly misidentified Yersinia enterocolitica-like organism

2020 ◽  
Vol 6 (9) ◽  
Author(s):  
Scott Van Nguyen ◽  
Dechamma Mundanda Muthappa ◽  
Athmanya K. Eshwar ◽  
James F. Buckley ◽  
Brenda P. Murphy ◽  
...  
Keyword(s):  
Public Health ◽  
Yersinia Enterocolitica ◽  
Type Species ◽  
Zebrafish Embryo ◽  
Comparative Genomic ◽  
Infection Model ◽  
Content Type ◽  
Link Type ◽  
Integrative Conjugative Element ◽  
Virulence Potential

Food-associated outbreaks linked to enteropathogenic Yersinia enterocolitica are of concern to public health. Pigs and their meat are recognized risk factors for transmission of Y. enterocolitica . This study aimed to describe the comparative genomics of Y. enterocolitica along with a number of misclassified Yersinia isolates, now constituting the recently described Yersinia hibernica . The latter was originally cultured from an environmental sample taken at a pig slaughterhouse. Unique features were identified in the genome of Y. hibernica, including a novel integrative conjugative element (ICE), denoted as ICE Yh-1 contained within a 255 kbp region of plasticity. In addition, a zebrafish embryo infection model was adapted and applied to assess the virulence potential among Yersinia isolates including Y. hibernica .

scholarly journals Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Eva Wagner ◽  
Andreas Zaiser ◽  
Rebekka Leitner ◽  
Narciso M. Quijada ◽  
Nadja Pracser ◽  
...  
Keyword(s):  
Food Processing ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Specific Sequence ◽  
Equal Distribution ◽  
Genetic Traits ◽  
Virulence Potential ◽  
Genetic Features ◽  
Source Category

Abstract Background Listeria (L.) monocytogenes strains show a high diversity regarding stress tolerance and virulence potential. Genome studies have mainly focused on specific sequence types (STs) predominantly associated with either food or human listeriosis. This study focused on the prevalent ST155, showing equal distribution among clinical and food isolates. We evaluated the virulence potential of 20 ST155 strains and performed comparative genomic analysis of 130 ST155 strains isolated from food, food processing environments and human listeriosis cases in different countries and years. Results The in vitro virulence assays using human intestinal epithelial Caco2 and hepatocytic HEPG2 cells showed an impaired virulence phenotype for six of the 20 selected ST155 strains. Genome analysis revealed no distinct clustering of strains from the same source category (food, food processing environment, and clinical isolates). All strains harbored an intact inlA and inlB locus, except four strains, which had an internal deletion in the inlA gene. All strains harbored LIPI-1, but prfA was present in a longer variant in six strains, all showing impaired virulence. The longer PrfA variant resulted in lower expression of inlA, inlB, and prfA, and no expression of hly and actA. Regarding stress-related gene content, SSI-1 was present, whereas qacH was absent in all strains. 34.6% of the strains harbored a plasmid. All but one ST155 plasmids showed high conservation and harbored cadA2, bcrABC, and a triphenylmethane reductase. Conclusions This study contributes to an enhanced understanding of L. monocytogenes ST155 strains, being equally distributed among isolates from humans, food, and food processing environments. The conservation of the present genetic traits and the absence of unique inherent genetic features makes these types of STs especially interesting since they are apparently equally adapted to the conditions in food processing environments, as well as in food as to the human host environment. However, a ST155-specific mutation resulting in a longer PrfA variant impaired the virulence potential of several ST155 strains.

scholarly journals Genetic Determinants of Hydroxycinnamic Acid Metabolism in Heterofermentative Lactobacilli

2019 ◽  
Vol 86 (5) ◽  
Author(s):  
Gautam Gaur ◽  
Jee-Hwan Oh ◽  
Pasquale Filannino ◽  
Marco Gobbetti ◽  
Jan-Peter van Pijkeren ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
Phenolic Acids ◽  
Phenolic Acid ◽  
Acid Metabolism ◽  
Hydroxycinnamic Acid ◽  
Hydroxycinnamic Acids ◽  
Comparative Genomic ◽  
Plant Metabolites ◽  
Content Type ◽  
Genomic Analyses

ABSTRACT Phenolic acids are among the most abundant phenolic compounds in edible parts of plants. Lactic acid bacteria (LAB) metabolize phenolic acids, but the enzyme responsible for reducing hydroxycinnamic acids to phenylpropionic acids (HcrB) was only recently characterized in Lactobacillus plantarum. In this study, heterofermentative LAB species were screened for their hydroxycinnamic acid metabolism. Data on strain-specific metabolism in combination with comparative genomic analyses identified homologs of HcrB as putative phenolic acid reductases. Par1 and HcrF both encode putative multidomain proteins with 25% and 63% amino acid identity to HcrB, respectively. Of these genes, par1 in L. rossiae and hcrF in L. fermentum were overexpressed in response to hydroxycinnamic acids. The deletion of par1 in L. rossiae led to the loss of phenolic acid metabolism. The strain-specific metabolism of phenolic acids was congruent with the genotype of lactobacilli; however, phenolic acid reductases were not identified in strains of Weissella cibaria that reduced hydroxycinnamic acids to phenylpropionic acids. Phylogenetic analysis of major genes involved in hydroxycinnamic acid metabolism in strains of the genus Lactobacillus revealed that Par1 was found to be the most widely distributed phenolic acid reductase, while HcrB was the least abundant, present in less than 9% of Lactobacillus spp. In conclusion, this study increased the knowledge on the genetic determinants of hydroxycinnamic acid metabolism, explaining the species- and strain-specific metabolic variations in lactobacilli and providing evidence of additional enzymes involved in hydroxycinnamic acid metabolism of lactobacilli. IMPORTANCE The metabolism of secondary plant metabolites, including phenolic compounds, by food-fermenting lactobacilli is a significant contributor to the safety, quality, and nutritional quality of fermented foods. The enzymes mediating hydrolysis, reduction, and decarboxylation of phenolic acid esters and phenolic acids in lactobacilli, however, are not fully characterized. The genomic analyses presented here provide evidence for three novel putative phenolic acid reductases. Matching comparative genomic analyses with phenotypic analysis and quantification of gene expression indicates that two of the three putative phenolic acid reductases, Par1 and HcrF, are involved in reduction of hydroxycinnamic acids to phenylpropionic acids; however, the activity of Par2 may be unrelated to phenolic acids and recognizes other secondary plant metabolites. These findings expand our knowledge on the metabolic potential of lactobacilli and facilitate future studies on activity and substrate specificity of enzymes involved in metabolism of phenolic compounds.

scholarly journals Aerobiology from an Inactive Pyrite Mine: the Genome Sequence of the Airborne Pseudomonas sp. Strain L5B5

2021 ◽  
Vol 10 (48) ◽  
Author(s):  
Jose L. Gonzalez-Pimentel ◽  
Irene Domínguez-Moñino ◽  
Valme Jurado ◽  
Ana Teresa Caldeira ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
Virulence Factors ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Pseudomonas Sp ◽  
Circular Chromosome ◽  
Content Type ◽  
Genomic Analyses ◽  
Air Sample

Pseudomonas sp. strain L5B5 is an antimicrobial-producing bacterium isolated from an air sample collected in a pyrite mine in Lousal, Portugal. Genomic analyses predicted genes involved in virulence factors. Here, we report the complete genome sequence of this bacterium, which consists of a circular chromosome with a length of 6,811,662 bp.

scholarly journals Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes

2013 ◽  
Vol 13 (1) ◽  
pp. 143-153 ◽  
Author(s):  
Anastasios D. Tsaousis ◽  
Eleni Gentekaki ◽  
Laura Eme ◽  
Daniel Gaston ◽  
Andrew J. Roger
Keyword(s):  
Subcellular Fractionation ◽  
Comparative Genomic ◽  
Cluster Assembly ◽  
Iron Sulfur Cluster ◽  
Content Type ◽  
Sulfur Cluster ◽  
Evolutionary Diversification ◽  
Iron Sulfur ◽  
History Of ◽  
Phylogenomic Analyses

ABSTRACT The cytosolic iron/sulfur cluster assembly (CIA) machinery is responsible for the assembly of cytosolic and nuclear iron/sulfur clusters, cofactors that are vital for all living cells. This machinery is uniquely found in eukaryotes and consists of at least eight proteins in opisthokont lineages, such as animals and fungi. We sought to identify and characterize homologues of the CIA system proteins in the anaerobic stramenopile parasite Blastocystis sp. strain NandII. We identified transcripts encoding six of the components—Cia1, Cia2, MMS19, Nbp35, Nar1, and a putative Tah18—and showed using immunofluorescence microscopy, immunoelectron microscopy, and subcellular fractionation that the last three of them localized to the cytoplasm of the cell. We then used comparative genomic and phylogenetic approaches to investigate the evolutionary history of these proteins. While most Blastocystis homologues branch with their eukaryotic counterparts, the putative Blastocystis Tah18 seems to have a separate evolutionary origin and therefore possibly a different function. Furthermore, our phylogenomic analyses revealed that all eight CIA components described in opisthokonts originated before the diversification of extant eukaryotic lineages and were likely already present in the last eukaryotic common ancestor (LECA). The Nbp35, Nar1 Cia1, and Cia2 proteins have been conserved during the subsequent evolutionary diversification of eukaryotes and are present in virtually all extant lineages, whereas the other CIA proteins have patchy phylogenetic distributions. Cia2 appears to be homologous to SufT, a component of the prokaryotic sulfur utilization factors (SUF) system, making this the first reported evolutionary link between the CIA and any other Fe/S biogenesis pathway. All of our results suggest that the CIA machinery is an ubiquitous biosynthetic pathway in eukaryotes, but its apparent plasticity in composition raises questions regarding how it functions in nonmodel organisms and how it interfaces with various iron/sulfur cluster systems (i.e., the iron/sulfur cluster, nitrogen fixation, and/or SUF system) found in eukaryotic cells.

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