• Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis sp. nov., two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil.

      Huber, Katharina J; Wüst, Pia K; Rohde, Manfred; Overmann, Jörg; Foesel, Bärbel U; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2014-06)
      Acidobacteria constitute an abundant fraction of the soil microbial community and are currently divided into 26 subdivisions. Most cultivated members of the Acidobacteria are affiliated with subdivision 1, while only a few representatives of subdivisions 3, 4, 8, 10 and 23 have been isolated and described so far. Two novel isolates of subdivision 4 of the Acidobacteria were isolated from subtropical savannah soils and are characterized in the present work. Cells of strains A22_HD_4H(T) and Ac_23_E3(T) were immotile rods that divided by binary fission. Colonies were pink and white, respectively. The novel strains A22_HD_4H(T) and Ac_23_E3(T) were aerobic mesophiles with a broad range of tolerance towards pH (4.0-9.5 and 3.5-10.0, respectively) and temperature (15-44 and 12-47 °C, respectively). Both showed chemo-organoheterotrophic growth on some sugars, the amino sugar N-acetylgalactosamine, a few amino acids, organic acids and various complex protein substrates. Major fatty acids of A22_HD_4H(T) and Ac_23_E3(T) were iso-C(15 : 0), summed feature 1 (C(13 : 0) 3-OH/iso-C(15 : 1) H), summed feature 3 (C(16 : 1)ω7c/C(16 : 1)ω6c) and anteiso-C(17 : 0). The major quinone was MK-8; in addition, MK-7 occurred in small amounts. The DNA G+C contents of A22_HD_4H(T) and Ac_23_E3(T) were 53.2 and 52.6 mol%, respectively. The closest described relative was Blastocatella fastidiosa A2-16(T), with 16S rRNA gene sequence identity of 93.2 and 93.3%, respectively. Strains A22_HD_4H(T) and Ac_23_E3(T) displayed 16S rRNA gene sequence similarity of 97.4% to each other. On the basis of the low DNA-DNA hybridization value, the two isolates represent different species. Based on morphological, physiological and molecular characteristics, the new genus Aridibacter gen. nov. is proposed, with two novel species, the type species Aridibacter famidurans sp. nov. (type strain A22_HD_4H(T) = DSM 26555(T) = LMG 27985(T)) and a second species, Aridibacter kavangonensis sp. nov. (type strain Ac_23_E3(T) = DSM 26558(T) = LMG 27597(T)).
    • Azithromycin Synergizes with Cationic Antimicrobial Peptides to Exert Bactericidal and Therapeutic Activity Against Highly Multidrug-Resistant Gram-Negative Bacterial Pathogens

      Lin, Leo; Nonejuie, Poochit; Munguia, Jason; Hollands, Andrew; Olson, Joshua; Dam, Quang; Kumaraswamy, Monika; Rivera, Heriberto; Corriden, Ross; Rohde, Manfred; Hensler, Mary E.; Burkart, Michael D.; Pogliano, Joe; Sakoulas, George; Nizet, Victor (2015-06)
    • Belliella kenyensis sp. nov., isolated from an alkaline lake.

      Akhwale, Juliah Khayeli; Göker, Markus; Rohde, Manfred; Schumann, Peter; Klenk, Hans-Peter; Boga, Hamadi Iddi; Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 7 38124 Braunschweig, Germany. (2015-02)
      A red-pigmented, Gram-reaction-negative, aerobic bacterial strain, designated No.164(T), was isolated from sediment sample from the alkaline Lake Elmenteita located in the Kenyan Rift Valley. Results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Belliella, with the highest sequence similarity (97 %) to Belliella pelovolcani DSM 46698(T). Optimal growth temperature was 30-35 °C, at pH 7.0-12.0 in the presence of 0-4 % (w/v) NaCl. Flexirubins were absent. The respiratory menaquinone (MK-7), predominant cellular fatty acids (iso-C15 : 0, anteiso-C15 : 0 and a mixture of C16 : 1ω7c and/or iso-C15 : 0 2-OH) and DNA G+C content (38.1 mol%) of strain No.164(T) were consistent with those of other members of the genus Belliella. The polar lipids consisted of phosphatidylethanolamine, eight unspecified lipids and one unspecified phospholipid. Several phenotypic characteristics can be used to differentiate this isolate from those of other species of the genus Belliella. The results of polyphasic analyses presented in this study indicated that this isolate should be classified as representing a novel species of the genus Belliella. The name Belliella kenyensis sp. nov. is therefore proposed; the type strain is strain No.164(T) ( = DSM 46651(T) = CECT 8551(T)).
    • Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments.

      Golyshina, Olga V; Kublanov, Ilya V; Tran, Hai; Korzhenkov, Alexei A; Lünsdorf, Heinrich; Nechitaylo, Taras Y; Gavrilov, Sergey N; Toshchakov, Stepan V; Golyshin, Peter N; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2016-12-14)
      The order Thermoplasmatales (Euryarchaeota) is represented by the most acidophilic organisms known so far that are poorly amenable to cultivation. Earlier culture-independent studies in Iron Mountain (California) pointed at an abundant archaeal group, dubbed 'G-plasma'. We examined the genomes and physiology of two cultured representatives of a Family Cuniculiplasmataceae, recently isolated from acidic (pH 1-1.5) sites in Spain and UK that are 16S rRNA gene sequence-identical with 'G-plasma'. Organisms had largest genomes among Thermoplasmatales (1.87-1.94 Mbp), that shared 98.7-98.8% average nucleotide identities between themselves and 'G-plasma' and exhibited a high genome conservation even within their genomic islands, despite their remote geographical localisations. Facultatively anaerobic heterotrophs, they possess an ancestral form of A-type terminal oxygen reductase from a distinct parental clade. The lack of complete pathways for biosynthesis of histidine, valine, leucine, isoleucine, lysine and proline pre-determines the reliance on external sources of amino acids and hence the lifestyle of these organisms as scavengers of proteinaceous compounds from surrounding microbial community members. In contrast to earlier metagenomics-based assumptions, isolates were S-layer-deficient, non-motile, non-methylotrophic and devoid of iron-oxidation despite the abundance of methylotrophy substrates and ferrous iron in situ, which underlines the essentiality of experimental validation of bioinformatic predictions.
    • Characterization of Five Zoonotic Streptococcus suis Strains from Germany, Including One Isolate from a Recent Fatal Case of Streptococcal Toxic Shock-Like Syndrome in a Hunter.

      Eisenberg, Tobias; Hudemann, Christoph; Hossain, Hamid M; Hewer, Angela; Tello, Khodr; Bandorski, Dirk; Rohde, M; Valentin-Weigand, Peter; Baums, Christoph Georg; Infectious Diseases, College of Veterinary Medicine, University Leipzig, Leipzig. (2015-12)
      A Streptococcus suis isolate from a German hunter with streptococcal toxic shock-like syndrome (STSLS) and four additional zoonotic isolates were genotyped as mrp(+) epf* (variant 1890) sly(+) cps2(+). All five zoonotic German strains were characterized by high multiplication in human blood samples ex vivo, but induction of only low levels of proinflammatory cytokines compared to a Chinese STSLS strain.
    • Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum.

      Spring, Stefan; Bunk, Boyke; Spröer, Cathrin; Schumann, Peter; Rohde, Manfred; Tindall, Brian J; Klenk, Hans-Peter; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2016)
      The recently isolated strain L21-Fru-ABTrepresents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABTrepresents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate. On the basis of the analyses of phenotypic, genomic and environmental data, it is proposed that strain L21-Fru-ABTand related bacteria are specifically adapted to the utilization of sulfated glycopolymers produced in microbial mats or biofilms.
    • Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005.

      Panschin, Irina; Huang, Sixing; Meier-Kolthoff, Jan P; Tindall, Brian J; Rohde, Manfred; Verbarg, Susanne; Lapidus, Alla; Han, James; Trong, Stephan; Haynes, Matthew; Reddy, T B K; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia N; Mavromatis, Konstantinos; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Klenk, Hans-Peter; Kyrpides, Nikos C; Hahnke, Richard L; helmholtzzentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig (2016)
      Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose. Conclusively, both Gramella type strains exhibit characteristic physiological, morphological and genomic differences that might be linked to their habitat. Furthermore, the identified enzymes mediating polysaccharide decomposition, are of biotechnological interest.
    • Comparison of mcl-Poly(3-hydroxyalkanoates) synthesis by different Pseudomonas putida strains from crude glycerol: citrate accumulates at high titer under PHA-producing conditions.

      Poblete-Castro, Ignacio; Binger, Danielle; Oehlert, Rene; Rohde, Manfred; Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany. (2014)
      Achieving a sustainable society requires, among other things, the use of renewable feedstocks to replace chemicals obtained from petroleum-derived compounds. Crude glycerol synthesized inexpensively as a byproduct of biodiesel production is currently considered a waste product, which can potentially be converted into value-added compounds by bacterial fermentation. This study aimed at evaluating several characterized P. putida strains to produce medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHA) using raw glycerol as the only carbon/energy source.
    • Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat.

      Ben Hania, Wajdi; Joseph, Manon; Schumann, Peter; Bunk, Boyke; Fiebig, Anne; Spröer, Cathrin; Klenk, Hans-Peter; Fardeau, Marie-Laure; Spring, Stefan; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2015)
      During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central Pacific) strain L21-RPul-D2(T) was isolated. The closest phylogenetic neighbor was Spirochaeta africana Z-7692(T) that shared a 16S rRNA gene sequence identity value of 90% with the novel strain and thus was only distantly related. A comprehensive polyphasic study including determination of the complete genome sequence was initiated to characterize the novel isolate. Cells of strain L21-RPul-D2(T) had a size of 0.2 - 0.25 × 8-9 μm, were helical, motile, stained Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions for growth were 35°C, a salinity of 50 g/l NaCl and a pH around 7.0. Preferred substrates for growth were carbohydrates and a few carboxylic acids. The novel strain had an obligate fermentative metabolism and produced ethanol, acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain L21-RPul-D2(T) was aerotolerant, but oxygen did not stimulate growth. Major cellular fatty acids were C14:0, iso-C15:0, C16:0 and C18:0. The major polar lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. Whole-cell hydrolysates contained L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The complete genome sequence was determined and annotated. The genome comprised one circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C content was determined from the genome sequence as 51.9 mol%. There were no predicted genes encoding cytochromes or enzymes responsible for the biosynthesis of respiratory lipoquinones. Based on significant differences to the uncultured type species of the genus Spirochaeta, S. plicatilis, as well as to any other phylogenetically related cultured species it is suggested to place strain L21-RPul-D2(T) (=DSM 27196(T) = JCM 18663(T)) in a novel species and genus, for which the name Salinispira pacifica gen. nov., sp. nov. is proposed.
    • Complete genome sequence of C130_2, a novel myovirus infecting pathogenic Escherichia coli and Shigella strains.

      Sváb, Domonkos; Falgenhauer, Linda; Rohde, Manfred; Chakraborty, Trinad; Tóth, István; Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2018-09-20)
      The genome sequence of a novel virulent bacteriophage, named " C130_2", that is morphologically a member of the family Myoviridae is reported. The 41,775-base-pair double-stranded DNA genome of C130_2 contains 59 ORFs but exhibits overall low sequence similarity to bacteriophage genomes for which sequences are publicly available. Phylogenetic analysis indicated that C130_2 represents a new phage type. C130_2 could be propagated well on enterohemorrhagic Escherichia coli (EHEC) O157:H7 and other pathogenic E. coli strains, as well as on strains of various Shigella species.
    • Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

      Stackebrandt, Erko; Zeytun, Ahmet; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Chang, Yun-juan; Land, Miriam; Hauser, Loren; Rohde, Manfred; Pukall, Rüdiger; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter (2014-01-09)
    • Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.

      Meier-Kolthoff, Jan P; Hahnke, Richard L; Petersen, Jörn; Scheuner, Carmen; Michael, Victoria; Fiebig, Anne; Rohde, Christine; Rohde, Manfred; Fartmann, Berthold; Goodwin, Lynne A; Chertkov, Olga; Reddy, Tbk; Pati, Amrita; Ivanova, Natalia N; Markowitz, Victor; Kyrpides, Nikos C; Woyke, Tanja; Göker, Markus; Klenk, Hans-Peter; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2014)
      Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083(T) together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.
    • Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy

      Meier-Kolthoff, Jan P; Hahnke, Richard L; Petersen, Jörn; Scheuner, Carmen; Michael, Victoria; Fiebig, Anne; Rohde, Christine; Rohde, Manfred; Fartmann, Berthold; Goodwin, Lynne A; Chertkov, Olga; Reddy, TBK; Pati, Amrita; Ivanova, Natalia N; Markowitz, Victor; Kyrpides, Nikos C; Woyke, Tanja; Göker, Markus; Klenk, Hans-Peter; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2014-12-08)
      Abstract Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083T together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083T in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.
    • Complete genome sequence of Pirellula staleyi type strain (ATCC 27377).

      Clum, Alicia; Tindall, Brian J; Sikorski, Johannes; Ivanova, Natalia; Mavrommatis, Konstantinos; Lucas, Susan; Glavina, Tijana; Del Rio; Nolan, Matt; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Brettin, Thomas; Han, Cliff; Detter, John C; Kuske, Cheryl; Bruce, David; Goodwin, Lynne; Ovchinikova, Galina; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Chain, Patrick; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla; Helmholtz Centre for infection research, Inhoffenstr. 7, D-38124 Braunschweig, Germany. (2009)
      Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the family Planctomycetaceae. Members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other Planctomycetes by a lack of true stalks. Strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. 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 order Planctomyces and only the second sequence from the phylum Planctobacteria/Planctomycetes. The 6,196,199 bp long genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305(T)), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae.

      Scheuner, Carmen; Tindall, Brian J; Lu, Megan; Nolan, Matt; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Mavromatis, Konstantinos; Ivanova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Jeffries, Cynthia D; Hauser, Loren; Land, Miriam; Mwirichia, Romano; Rohde, Manfred; Abt, Birte; Detter, John C; Woyke, Tanja; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Göker, Markus; Kyrpides, Nikos C; Klenk, Hans-Peter; Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany. (2014)
      Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448(T), were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
    • Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

      Scheuner, Carmen; Tindall, Brian J; Lu, Megan; Nolan, Matt; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Pagani, Ioanna; Mavromatis, Konstantinos; Ivanova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Jeffries, Cynthia D; Hauser, Loren; Land, Miriam; Mwirichia, Romano; Rohde, Manfred; Abt, Birte; Detter, John C; Woyke, Tanja; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Göker, Markus; Kyrpides, Nikos C; Klenk, Hans-Peter (2014-12-08)
      Abstract Planctomyces brasiliensis Schlesner 1990 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. The first strains of P. brasiliensis, including the type strain IFAM 1448T, were isolated from a water sample of Lagoa Vermelha, a salt pit near Rio de Janeiro, Brasil. This is the second completed genome sequence of a type strain of the genus Planctomyces to be published and the sixth type strain genome sequence from the family Planctomycetaceae. The 6,006,602 bp long genome with its 4,811 protein-coding and 54 RNA genes is a part of the G enomic E ncyclopedia of Bacteria and Archaea project. Phylogenomic analyses indicate that the classification within the Planctomycetaceae is partially in conflict with its evolutionary history, as the positioning of Schlesneria renders the genus Planctomyces paraphyletic. A re-analysis of published fatty-acid measurements also does not support the current arrangement of the two genera. A quantitative comparison of phylogenetic and phenotypic aspects indicates that the three Planctomyces species with type strains available in public culture collections should be placed in separate genera. Thus the genera Gimesia, Planctopirus and Rubinisphaera are proposed to accommodate P. maris, P. limnophilus and P. brasiliensis, respectively. Pronounced differences between the reported G + C content of Gemmata obscuriglobus, Singulisphaera acidiphila and Zavarzinella formosa and G + C content calculated from their genome sequences call for emendation of their species descriptions. In addition to other features, the range of G + C values reported for the genera within the Planctomycetaceae indicates that the descriptions of the family and the order should be emended.
    • Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437T)

      Mavromatis, Konstantinos; Stackebrandt, Erko; Munk, Christine; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Rohde, Manfred; Gronow, Sabine; Göker, Markus; Detter, John C.; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Woyke, Tanja (2014-01-16)
    • Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)).

      Kappler, Ulrike; Davenport, Karen; Beatson, Scott; Lapidus, Alla; Pan, Chongle; Han, Cliff; Montero-Calasanz, Maria Del Carmen; Land, Miriam; Hauser, Loren; Rohde, Manfred; Göker, Markus; Ivanova, Natalia; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C; Helmholtzzentrum für Infektionsforschung, 38124 Braunschweig (2016)
      Thioalkalimicrobium cyclicum Sorokin et al. 2002 is a member of the family Piscirickettsiaceae in the order Thiotrichales. The γ-proteobacterium belongs to the colourless sulfur-oxidizing bacteria isolated from saline soda lakes with stable alkaline pH, such as Lake Mono (California) and Soap Lake (Washington State). Strain ALM 1(T) is characterized by its adaptation to life in the oxic/anoxic interface towards the less saline aerobic waters (mixolimnion) of the stable stratified alkaline salt lakes. Strain ALM 1(T) is the first representative of the genus Thioalkalimicrobium whose genome sequence has been deciphered and the fourth genome sequence of a type strain of the Piscirickettsiaceae to be published. The 1,932,455 bp long chromosome with its 1,684 protein-coding and 50 RNA genes was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program (CSP) 2008.
    • Complete genome sequence of the halophilic bacterium Spirochaeta africana type strain (Z-7692(T)) from the alkaline Lake Magadi in the East African Rift.

      Liolos, Konstantinos; Abt, Birte; Scheuner, Carmen; Teshima, Hazuki; Held, Brittany; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Rohde, Manfred; Tindall, Brian J; Detter, John C; Göker, Markus; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C (2013)
      Spirochaeta africana Zhilina et al. 1996 is an anaerobic, aerotolerant, spiral-shaped bacterium that is motile via periplasmic flagella. The type strain of the species, Z-7692(T), was isolated in 1993 or earlier from a bacterial bloom in the brine under the trona layer in a shallow lagoon of the alkaline equatorial Lake Magadi in Kenya. Here we describe the features of this organism, together with the complete genome sequence, and annotation. Considering the pending reclassification of S. caldaria to the genus Treponema, S. africana is only the second 'true' member of the genus Spirochaeta with a genome-sequenced type strain to be published. The 3,285,855 bp long genome of strain Z-7692(T) with its 2,817 protein-coding and 57 RNA genes is a part of the G enomic E ncyclopedia of B acteria and A rchaea project.
    • Complete genome sequence of the moderate thermophile Anaerobaculum mobile type strain (NGAT)

      Mavromatis, Konstantinos; Stackebrandt, Erko; Held, Brittany; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Rohde, Manfred; Spring, Stefan; Göker, Markus; Woyke, Tanja; Detter, John C.; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C. (2014-01-16)