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William H Gerwick – One of the best experts on this subject based on the ideXlab platform.

Niclas Engene – One of the best experts on this subject based on the ideXlab platform.

  • moorea producens gen nov sp nov and moorea bouillonii comb nov tropical marine cyanobacteria rich in bioactive secondary metabolites
    International Journal of Systematic and Evolutionary Microbiology, 2012
    Co-Authors: Niclas Engene, Erin C Rottacker, Jan Kastovský, Tara Byrum, Hyukjae Choi, Mark H. Ellisman, Jiři Komarek, William H Gerwick
    Abstract:

    The filamentous cyanobacterial Genus Moorea gen. nov., described here under the provisions of the International Code of Botanical Nomenclature, is a cosmopolitan pan-tropical group abundant in the marine benthos. Members of the Genus Moorea are photosynthetic (containing phycocyanin, phycoerythrin, allophycocyanin and chlorophyll a), but non-diazotrophic (lack heterocysts and nitrogenase reductase genes). The cells (discoid and 25–80 µm wide) are arranged in long filaments (<10 cm in length) and often form extensive mats or blooms in shallow water. The cells are surrounded by thick polysaccharide sheaths covered by a rich diversity of heterotrophic micro-organisms. A distinctive character of this Genus is its extraordinarily rich production of bioactive secondary metabolites. This is matched by genomes rich in polyketide synthase and non-ribosomal peptide synthetase biosynthetic genes which are dedicated to secondary metabolism. The encoded natural products are sometimes responsible for harmful algae blooms and, due to morphological resemblance to the Genus Lyngbya , this group has often been incorrectly cited in the literature. We here describe two species of the Genus Moorea: Moorea producens sp. nov. (type species of the Genus) with 3LT as the nomenclature type, and Moorea bouillonii comb. nov. with PNG5-198R as the nomenclature type.

  • Moorea producens gen. nov., sp. nov. and Moorea bouillonii comb. nov., tropical marine cyanobacteria rich in bioactive secondary metabolites.
    International Journal of Systematic and Evolutionary Microbiology, 2012
    Co-Authors: Niclas Engene, Erin C Rottacker, Jan Kastovský, Tara Byrum, Hyukjae Choi, Mark H. Ellisman, Jiři Komarek, William H Gerwick
    Abstract:

    The filamentous cyanobacterial Genus Moorea gen. nov., described here under the provisions of the International Code of Botanical Nomenclature, is a cosmopolitan pan-tropical group abundant in the marine benthos. Members of the Genus Moorea are photosynthetic (containing phycocyanin, phycoerythrin, allophycocyanin and chlorophyll a), but non-diazotrophic (lack heterocysts and nitrogenase reductase genes). The cells (discoid and 25–80 µm wide) are arranged in long filaments (

Xiao-hua Zhang – One of the best experts on this subject based on the ideXlab platform.

  • Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios
    BMC Genomics, 2018
    Co-Authors: Heyu Lin, Min Yu, Xiaolei Wang, Xiao-hua Zhang
    Abstract:

    BackgroundVibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level.ResultsTwo Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal genegene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the Genus. The chitinase A genes were estimated to have evolved along with the Genus, and have undergone significant purifying selective force to conserve the ancestral state.ConclusionsVibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the Genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the Genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches.

  • Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios.
    BMC Genomics, 2018
    Co-Authors: Heyu Lin, Xiaolei Wang, Xiao-hua Zhang
    Abstract:

    Vibrios are among the most diverse and ecologically important marine bacteria, which have evolved many characteristics and lifestyles to occupy various niches. The relationship between genome features and environmental adaptation strategies is an essential part for understanding the ecological functions of vibrios in the marine system. The advent of complete genome sequencing technology has provided an important method of examining the genetic characteristics of vibrios on the genomic level. Two Vibrio genomes were sequenced and found to occupy many unique orthologues families which absent from the previously genes pool of the complete genomes of vibrios. Comparative genomics analysis found vibrios encompass a steady core-genome and tremendous pan-genome with substantial gene gain and horizontal genegene transfer events in the evolutionary history. Evolutionary analysis based on the core-genome tree suggested that V. fischeri emerged ~ 385 million years ago, along with the occurrence of cephalopods and the flourish of fish. The relatively large genomes, the high number of 16S rRNA gene copies, and the presence of R-M systems and CRISPR system help vibrios live in various marine environments. Chitin-degrading related genes are carried in nearly all the Vibrio genomes. The number of chitinase genes in vibrios has been extremely expanded compared to which in the most recent ancestor of the Genus. The chitinase A genes were estimated to have evolved along with the Genus, and have undergone significant purifying selective force to conserve the ancestral state. Vibrios have experienced extremely genome expansion events during their evolutionary history, allowing them to develop various functions to spread globally. Despite their close phylogenetic relationships, vibrios were found to have a tremendous pan-genome with a steady core-genome, which indicates the highly plastic genome of the Genus. Additionally, the existence of various chitin-degrading related genes and the expansion of chitinase A in the Genus demonstrate the importance of the chitin utilization for vibrios. Defensive systems in the Vibrio genomes may protect them from the invasion of external DNA. These genomic features investigated here provide a better knowledge of how the evolutionary process has forged Vibrio genomes to occupy various niches.

Alla Lapidus – One of the best experts on this subject based on the ideXlab platform.

  • High-quality permanent draft genome sequence of the extremely osmotolerant diphenol degrading bacterium Halotalea alkalilenta AW-7^T, and emended description of the Genus Halotalea
    Standards in Genomic Sciences, 2015
    Co-Authors: Spyridon Ntougias, Alla Lapidus, Alex Copeland, T B K Reddy, Amrita Pati, Natalia N. Ivanova, Victor M. Markowitz, Hans-peter Klenk, Tanja Woyke, Constantinos Fasseas
    Abstract:

    Members of the Genus Halotalea (family Halomonadaceae ) are of high significance since they can tolerate the greatest glucose and maltose concentrations ever reported for known bacteria and are involved in the degradation of industrial effleffluents. Here, the characteristics and the permanent-draft genome sequence and annotation of Halotalea alkalilenta AW-7^T are described. The microorganism was sequenced as a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project at the DOE Joint Genome Institute, and it is the only strain within the Genus Halotalea having its genome sequenced. The genome is 4,467,826 bp long and consists of 40 scaffolds with 64.62 % average GC content. A total of 4,104 genes were predicted, comprising of 4,028 protein-coding and 76 RNA genes. Most protein-coding genes (87.79 %) were assigned to a putative function. Halotalea alkalilenta AW-7^T encodes the catechol and protocatechuate degradation to β-ketoadipate via the β-ketoadipate and protocatechuate ortho-cleavage degradation pathway, and it possesses the genetic ability to detoxify fluoroacetate, cyanate and acrylonitrile. An emended description of the Genus Halotalea Ntougias et al. 2007 is also provided in order to describe the delayed fermentation ability of the type strain.

  • Complete genome sequence of Paludibacter propionicigenes type strain (WB4 T )
    Standards in genomic sciences, 2011
    Co-Authors: Sabine Gronow, Alla Lapidus, Christine Munk, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan Fang Cheng, Roxane Tapia, Cliff Han
    Abstract:

    Paludibacter propionicigenes Ueki et al. 2006 is the type species of the Genus Paludibacter, which belongs to the family Porphyromonadaceae. The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the Genus Dysgonomonas. This is the first completed genome sequence of a member of the Genus Paludibacter and the third sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  • Complete genome sequence of Paludibacter propionicigenes type strain (WB4^T)
    Standards in Genomic Sciences, 2011
    Co-Authors: Sabine Gronow, Alla Lapidus, Christine Munk, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan Fang Cheng, Roxane Tapia, Cliff Han
    Abstract:

    Paludibacter propionicigenes Ueki et al. 2006 is the type species of the Genus Paludibacter , which belongs to the family Porphyromonadaceae . The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the Genus Dysgonomonas . This is the first completed genome sequence of a member of the Genus Paludibacter and the third sequence from the family Porphyromonadaceae . The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the G enomic E ncyclopedia of B acteria and A rchaea project.

Jan Fang Cheng – One of the best experts on this subject based on the ideXlab platform.

  • Complete genome sequence of Paludibacter propionicigenes type strain (WB4 T )
    Standards in genomic sciences, 2011
    Co-Authors: Sabine Gronow, Alla Lapidus, Christine Munk, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan Fang Cheng, Roxane Tapia, Cliff Han
    Abstract:

    Paludibacter propionicigenes Ueki et al. 2006 is the type species of the Genus Paludibacter, which belongs to the family Porphyromonadaceae. The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the Genus Dysgonomonas. This is the first completed genome sequence of a member of the Genus Paludibacter and the third sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  • Complete genome sequence of Paludibacter propionicigenes type strain (WB4^T)
    Standards in Genomic Sciences, 2011
    Co-Authors: Sabine Gronow, Alla Lapidus, Christine Munk, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan Fang Cheng, Roxane Tapia, Cliff Han
    Abstract:

    Paludibacter propionicigenes Ueki et al. 2006 is the type species of the Genus Paludibacter , which belongs to the family Porphyromonadaceae . The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the Genus Dysgonomonas . This is the first completed genome sequence of a member of the Genus Paludibacter and the third sequence from the family Porphyromonadaceae . The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the G enomic E ncyclopedia of B acteria and A rchaea project.

  • Complete genome sequence of Segniliparus rotundus type strain (CDC 1076^T)
    Standards in Genomic Sciences, 2010
    Co-Authors: Johannes Sikorski, Alla Lapidus, Alex Copeland, Matt Nolan, Susan Lucas, Monica Misra, Tijana Glavina Del Rio, Feng Chen, Hope Tice, Jan Fang Cheng
    Abstract:

    Segniliparus rotundus Butler 2005 is the type species of the Genus Segniliparus , which is currently the only Genus in the corynebacterial family Segniliparaceae . This family is of large interest because of a novel late-emerging Genus-specific mycolate pattern. The type strain has been isolated from human sputum and is probably an opportunistic pathogen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Segniliparaceae . The 3,157,527 bp long genome with its 3,081 protein-coding and 52 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project.