The Experts below are selected from a list of 11586 Experts worldwide ranked by ideXlab platform
Qiyao Wang - One of the best experts on this subject based on the ideXlab platform.
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Edwardsiella Comparative Phylogenomics Reveal the New Intra/Inter-Species Taxonomic Relationships, Virulence Evolution and Niche Adaptation Mechanisms
PloS one, 2012Co-Authors: Minjun Yang, Jingfan Xiao, Huajun Zheng, Qin Liu, Yuanxing Zhang, Qiyao WangAbstract:Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC). Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII) based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and Adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/Niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and Niche Adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.
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edwardsiella comparative phylogenomics reveal the new intra inter species taxonomic relationships virulence evolution and Niche Adaptation mechanisms
PLOS ONE, 2012Co-Authors: Minjun Yang, Jingfan Xiao, Huajun Zheng, Qin Liu, Yuanxing Zhang, Qiyao WangAbstract:Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC). Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII) based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and Adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/Niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and Niche Adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.
Marco Fondi - One of the best experts on this subject based on the ideXlab platform.
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Metabolic modelling reveals the specialization of secondary replicons for Niche Adaptation in Sinorhizobium meliloti
Nature Communications, 2016Co-Authors: George C. Dicenzo, Turlough M Finan, Alessio Mengoni, Marco Bazzicalupo, Marco Galardini, Alice Checcucci, Carlo Viti, Lukasz Dziewit, Marco FondiAbstract:The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental Adaptations and/or Niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological Niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological Niches and an overall reprogramming following Niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated Niche Adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes. The genome of some bacteria consists of two or more chromosomes or replicons. Here, diCenzo et al . integrate genome-scale metabolic modelling and growth data from a collection of mutants of the plant symbiont Sinorhizobium meliloti to estimate the fitness contribution of each replicon in three environments.
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metabolic modelling reveals the specialization of secondary replicons for Niche Adaptation in sinorhizobium meliloti
Nature Communications, 2016Co-Authors: George C. Dicenzo, Turlough M Finan, Alessio Mengoni, Marco Bazzicalupo, Marco Galardini, Alice Checcucci, Carlo Viti, Lukasz Dziewit, Marco FondiAbstract:The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental Adaptations and/or Niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological Niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological Niches and an overall reprogramming following Niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated Niche Adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes.
Minjun Yang - One of the best experts on this subject based on the ideXlab platform.
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Edwardsiella Comparative Phylogenomics Reveal the New Intra/Inter-Species Taxonomic Relationships, Virulence Evolution and Niche Adaptation Mechanisms
PloS one, 2012Co-Authors: Minjun Yang, Jingfan Xiao, Huajun Zheng, Qin Liu, Yuanxing Zhang, Qiyao WangAbstract:Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC). Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII) based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and Adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/Niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and Niche Adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.
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edwardsiella comparative phylogenomics reveal the new intra inter species taxonomic relationships virulence evolution and Niche Adaptation mechanisms
PLOS ONE, 2012Co-Authors: Minjun Yang, Jingfan Xiao, Huajun Zheng, Qin Liu, Yuanxing Zhang, Qiyao WangAbstract:Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC). Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII) based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and Adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/Niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and Niche Adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.
Todd D Swarthout - One of the best experts on this subject based on the ideXlab platform.
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pan gwas of streptococcus agalactiae highlights lineage specific genes associated with virulence and Niche Adaptation
Mbio, 2020Co-Authors: Andrea Gori, Odile B Harrison, Ethwako Mlia, Yo Nishihara, Macpherson Mallewa, Queen Dube, Todd D Swarthout, Jia Mun Chan, Jacquline MsefulaAbstract:Streptococcus agalactiae (group B streptococcus; GBS) is a colonizer of the gastrointestinal and urogenital tracts, and an opportunistic pathogen of infants and adults. The worldwide population of GBS is characterized by clonal complexes (CCs) with different invasive potentials. CC17, for example, is a hypervirulent lineage commonly associated with neonatal sepsis and meningitis, while CC1 is less invasive in neonates and more commonly causes invasive disease in adults with comorbidities. The genetic basis of GBS virulence and the extent to which different CCs have adapted to different host environments remain uncertain. We have therefore applied a pan-genome-wide association study (GWAS) approach to 1,988 GBS strains isolated from different hosts and countries. Our analysis identified 279 CC-specific genes associated with virulence, disease, metabolism, and regulation of cellular mechanisms that may explain the differential virulence potential of particular CCs. In CC17 and CC23, for example, we have identified genes encoding pilus, quorum-sensing proteins, and proteins for the uptake of ions and micronutrients which are absent in less invasive lineages. Moreover, in CC17, carriage and disease strains were distinguished by the allelic variants of 21 of these CC-specific genes. Together our data highlight the lineage-specific basis of GBS Niche Adaptation and virulence.IMPORTANCE GBS is a leading cause of mortality in newborn babies in high- and low-income countries worldwide. Different strains of GBS are characterized by different degrees of virulence, where some are harmlessly carried by humans or animals and others are much more likely to cause disease.The genome sequences of almost 2,000 GBS samples isolated from both animals and humans in high- and low- income countries were analyzed using a pan-genome-wide association study approach. This allowed us to identify 279 genes which are associated with different lineages of GBS, characterized by a different virulence and preferred host. Additionally, we propose that the GBS now carried in humans may have first evolved in animals before expanding clonally once adapted to the human host.These findings are essential to help understand what is causing GBS disease and how the bacteria have evolved and are transmitted.
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pan gwas of streptococcus agalactiae highlights lineage specific genes associated with virulence and Niche Adaptation
bioRxiv, 2019Co-Authors: Andrea Gori, Odile B Harrison, Ethwako Mlia, Yo Nishihara, Jacquline Chinkwitaphiri, Macpherson Mallewa, Queen Dube, Todd D Swarthout, Angela H NobbsAbstract:ABSTRACT Streptococcus agalactiae (Group B streptococcus, GBS) is a coloniser of the gastrointestinal and urogenital tracts, and an opportunistic pathogen of infants and adults. The worldwide population of GBS is characterised by Clonal Complexes (CCs) with different invasive potentials. CC17 for example, is a hypervirulent lineage commonly associated with neonatal sepsis and meningitis, while CC1 is less invasive in neonates and more commonly causes invasive disease in adults with co-morbidities. The genetic basis of GBS virulence and to what extent different CCs have adapted to different host environments remain uncertain. We have therefore applied a pan-genome wide association study approach to 1988 GBS strains isolated from different hosts and countries. Our analysis identified 279 CC-specific genes associated with virulence, disease, metabolism and regulation of cellular mechanisms that may explain the differential virulence potential of particular CCs. In CC17 and CC23 for example, we have identified genes encoding for pilus, quorum sensing proteins, and proteins for the uptake of ions and micronutrients which are absent in less invasive lineages. Moreover, in CC17, carriage and disease strains were distinguished by the allelic variants of 21 of these CC-specific genes. Together our data highlight the lineage-specific basis of GBS Niche Adaptation and virulence, and suggest that human-associated GBS CCs have largely evolved in animal hosts before crossing to the humans and then spreading clonally.
George C. Dicenzo - One of the best experts on this subject based on the ideXlab platform.
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Metabolic modelling reveals the specialization of secondary replicons for Niche Adaptation in Sinorhizobium meliloti
Nature Communications, 2016Co-Authors: George C. Dicenzo, Turlough M Finan, Alessio Mengoni, Marco Bazzicalupo, Marco Galardini, Alice Checcucci, Carlo Viti, Lukasz Dziewit, Marco FondiAbstract:The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental Adaptations and/or Niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological Niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological Niches and an overall reprogramming following Niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated Niche Adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes. The genome of some bacteria consists of two or more chromosomes or replicons. Here, diCenzo et al . integrate genome-scale metabolic modelling and growth data from a collection of mutants of the plant symbiont Sinorhizobium meliloti to estimate the fitness contribution of each replicon in three environments.
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metabolic modelling reveals the specialization of secondary replicons for Niche Adaptation in sinorhizobium meliloti
Nature Communications, 2016Co-Authors: George C. Dicenzo, Turlough M Finan, Alessio Mengoni, Marco Bazzicalupo, Marco Galardini, Alice Checcucci, Carlo Viti, Lukasz Dziewit, Marco FondiAbstract:The genome of about 10% of bacterial species is divided among two or more large chromosome-sized replicons. The contribution of each replicon to the microbial life cycle (for example, environmental Adaptations and/or Niche switching) remains unclear. Here we report a genome-scale metabolic model of the legume symbiont Sinorhizobium meliloti that is integrated with carbon utilization data for 1,500 genes with 192 carbon substrates. Growth of S. meliloti is modelled in three ecological Niches (bulk soil, rhizosphere and nodule) with a focus on the role of each of its three replicons. We observe clear metabolic differences during growth in the tested ecological Niches and an overall reprogramming following Niche switching. In silico examination of the inferred fitness of gene deletion mutants suggests that secondary replicons evolved to fulfil a specialized function, particularly host-associated Niche Adaptation. Thus, genes on secondary replicons might potentially be manipulated to promote or suppress host interactions for biotechnological purposes.