[Show abstract][Hide abstract] ABSTRACT: The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19-20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments.
[Show abstract][Hide abstract] ABSTRACT: Loktanella hongkongensis UST950701-009P T is a Gram-negative, non-motile and rod-shaped bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the bacterial cells. In the present study we describe the features of L. hongkongensis strain DSM 17492 T together with its genome sequence and annotation and novel aspects of its phenotype. The 3,198,444 bp long genome sequence encodes 3104 protein-coding genes and 57 RNA genes. The two unambiguously identified extrachromosomal replicons contain replication modules of the RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.
[Show abstract][Hide abstract] ABSTRACT: Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2T and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2T to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.
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The online version of this article (doi:10.1186/s40793-015-0032-y) contains supplementary material, which is available to authorized users.
[Show abstract][Hide abstract] ABSTRACT: The marine bacterium Marinovum algicola DG898 is a representative of the Roseobacter group (Rhodobacteraceae, Alphaproteobacteria) and harbors a for Proteobacteria unprecedented wealth of eleven extrachromosomal replicons (ECRs). The relevance of ECRs has previously been exemplified by photosynthesis and biofilm plasmids, but the evolutionary forces for the emergence of multipartite genomes are largely unknown. The newly established genome revealed the exceptional metabolic potential of Marinovum and its adaptation to the phycosphere. Comparative codon usage analyses allowed the identification of eight chromids and three plasmids. Functional gene clustering is documented by the 52-kb biofilm chromid that is required for surface attachment. The most conspicuous finding is the presence of a highly expressed chromid-encoded flagellum gene cluster (FGC, fla2) that is indispensable for swimming motility. M. algicola DG898 harbors an additional chromosome-encoded flagellum (fla1) with unknown function. Comprehensive phylogenetic analyses revealed the presence of a third FGC type (fla3) in Rhodobacteraceae and indicated the transmission of complete FGCs via conjugation. The current Marinovum study indicates a functional correlation of the intracellular fla2-chromid localization and the subcellular positioning of the flagellum. The proposed mechanism might represent - apart from horizontal transfer - a novel driving force for the emergence of multipartite genomes.
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[Show abstract][Hide abstract] ABSTRACT: Background:
Modern biotechnologies often result in high-dimensional data sets with many more variables than observations (n≪p). These data sets pose new challenges to statistical analysis: Variable selection becomes one of the most important tasks in this setting. Similar challenges arise if in modern data sets from observational studies, e.g., in ecology, where flexible, non-linear models are fitted to high-dimensional data. We assess the recently proposed flexible framework for variable selection called stability selection. By the use of resampling procedures, stability selection adds a finite sample error control to high-dimensional variable selection procedures such as Lasso or boosting. We consider the combination of boosting and stability selection and present results from a detailed simulation study that provide insights into the usefulness of this combination. The interpretation of the used error bounds is elaborated and insights for practical data analysis are given.
Stability selection with boosting was able to detect influential predictors in high-dimensional settings while controlling the given error bound in various simulation scenarios. The dependence on various parameters such as the sample size, the number of truly influential variables or tuning parameters of the algorithm was investigated. The results were applied to investigate phenotype measurements in patients with autism spectrum disorders using a log-linear interaction model which was fitted by boosting. Stability selection identified five differentially expressed amino acid pathways.
Stability selection is implemented in the freely available R package stabs (http://CRAN.R-project.org/package=stabs). It proved to work well in high-dimensional settings with more predictors than observations for both, linear and additive models. The original version of stability selection, which controls the per-family error rate, is quite conservative, though, this is much less the case for its improvement, complementary pairs stability selection. Nevertheless, care should be taken to appropriately specify the error bound.
[Show abstract][Hide abstract] ABSTRACT: In recent years a large number of isolates were obtained from saline environments that are phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, which were originally identified in seawater samples using cultivation independent methods and are characterized by high seasonal abundances in coastal environments. To date a sound taxonomic framework for the classification of these ecologically important isolates and related species in accordance with their evolutionary relationships is missing. In this study we demonstrate that a reliable allocation of members of the oligotrophic marine gammaproteobacteria (OMG) group and related species to higher taxonomic ranks is possible by phylogenetic analyses of whole proteomes but also of the RNA polymerase beta subunit, whereas phylogenetic reconstructions based on 16S rRNA genes alone resulted in unstable tree topologies with only insignificant bootstrap support. The identified clades could be correlated with distinct phenotypic traits illustrating an adaptation to common environmental factors in their evolutionary history. Genome wide gene-content analyses revealed the existence of two distinct ecological guilds within the analyzed lineage of marine gammaproteobacteria which can be distinguished by their trophic strategies. Based on our results a novel order within the class Gammaproteobacteria is proposed, which is designated Cellvibrionales ord. nov. and comprises the five novel families Cellvibrionaceae fam. nov., Halieaceae fam. nov., Microbulbiferaceae fam. nov., Porticoccaceae fam. nov., and Spongiibacteraceae fam. nov.
Frontiers in Microbiology 04/2015; 6:281. DOI:10.3389/fmicb.2015.00281 · 3.99 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A novel strain, designated No. 7(T), was isolated from a sediment sample collected from the alkaline, saline Lake Elmenteita located in the Kenyan Rift Valley. The optimal growth for the strain was found to be at temperature 30-35 °C, at pH 8.0-12.0 in the presence of 7.0-10.0 % (w/v) NaCl. The strain was observed to form a light green beige abundant aerial mycelium on Horikoshi 1 agar and to have morphological and chemotaxonomic characteristics typical of members of the genus Streptomyces. The peptidoglycan was found to contain LL-diaminopimelic acid as the diamino acid, with no diagnostic sugars identified. The predominant menaquinone was identified as MK-9(H6). The main polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown phospholipid. Cellular fatty acids were found to consist of saturated branched-chain acids with iso-C15:0, anteiso-C15:0, iso-C16:0 and anteiso-C17:0 acids predominating. The type strain had a genomic DNA G+C content of 72.8 mol% and formed a distinct phyletic line within the genus Streptomyces. Based on the chemotaxonomic results, 16S rRNA gene sequence analysis and the low DNA-DNA hybridization value with the type strain of Streptomyces calidiresistens, it is proposed that strain No. 7(T) (= DSM 42118 = CECT 8549) represents a novel species, Streptomyces alkaliphilus. The INSDC accession number for the 16S rRNA gene sequence of strain No. 7(T) is KF976730.
Antonie van Leeuwenhoek 03/2015; 107(5). DOI:10.1007/s10482-015-0418-2 · 1.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24T together with its genome sequence and annotation generated from a culture of DSM 17069T. The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.
[Show abstract][Hide abstract] ABSTRACT: Pontibacter roseus is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1T along with its complete genome sequence and annotation from a culture of DSM 17521T. The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic Encyclopedia of Type Strains: KMG-I project.
[Show abstract][Hide abstract] 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
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.
[Show abstract][Hide abstract] 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
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.
[Show abstract][Hide abstract] ABSTRACT: Pseudohaliea rubra strain DSM 19751T is an aerobic marine gammaproteobacterium that was isolated from surface coastal seawater of the Mediterranean Sea. Here,
we present its genome sequence and annotation. Genome analysis revealed the presence of genes involved in the synthesis of
bacteriochlorophyll-a and the reserve compound glycogen.
[Show abstract][Hide abstract] ABSTRACT: A gamma radiation-resistant, Gram reaction-positive, aerobic and chemoorganotrophic actinobacterium, initially designated Geodermatophilus obscurus subsp. dictyosporus G-5T, was not validly named at the time of initial publication (1968). G-5T formed black-colored colonies on GYM agar. The optimal growth range was 25–35 °C, at pH 6.5–9.5 and in the absence of NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The DNA G + C content of the strain was 75.3 mol %. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The main polar lipids were phosphatidylcholine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine and one unspecified glycolipid; MK-9(H4) was the dominant menaquinone and galactose was detected as a diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids, iso-C16:0 and iso-C15:0. The 16S rRNA gene showed 94.8–98.4 % sequence identity with the members of the genus Geodermatophilus. Based on phenotypic results and 16S rRNA gene sequence analysis, strain G-5T is proposed to represent a novel species, Geodermatophilus dictyosporus and the type strain is G-5T (=DSM 43161T = CCUG 62970T = MTCC 11558T = ATCC 25080T = CBS 234.69T = IFO 13317T = KCC A-0154T = NBRC 13317T). The INSDC accession number is HF970584.
[Show abstract][Hide abstract] ABSTRACT: A red-pigmented, Gram-reaction-negative, aerobic bacterial strain, designated No.164T, 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 belonged to the genus Belliella, with the highest sequence similarity (97%) to Belliella pelovolcani DSM 46698T. 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.164T 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 Belliella species. The polyphasic data presented in this study indicated that this isolate should be classiﬁed to represent a novel species in the genus Belliella. The name Belliella kenyensis sp. nov. is therefore proposed; the type strain is strain No.164T (= DSM 46651 = CECT 8551).
International Journal of Systematic and Evolutionary Microbiology 11/2014; DOI:10.1099/ijs.0.066951-0 · 2.51 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.
Frontiers in Microbiology 08/2014; 5:416. DOI:10.3389/fmicb.2014.00416 · 3.99 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently ∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
[Show abstract][Hide abstract] ABSTRACT: Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well charac-terized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3 T is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly dif-fers from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chro-mosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclo-pedia of Bacteria and Archaea project. Introduction Strain LA3 T (= DSM 5069 = NBRC 107925) is the type strain of the species Thermotoga thermarum , one out of currently nine species in the genus Thermotoga . The genus name was derived from the Greek word thermê, heat, and the Latin word toga, Roman outer garment; Thermotoga,
[Show abstract][Hide abstract] ABSTRACT: A novel Gram-reaction-positive, aerobic actinobacterium, tolerant to mitomycin C, heavy metals, metalloids, hydrogen peroxide, desiccation, and ionizing-and UV-radiation, designated G18 T , was isolated from dolomitic marble collected from outcrops in Samara (Namibia). The growth range was 15–35 ∘ C, at pH 5.5–9.5 and in presence of 1% NaCl, forming greenish-black coloured colonies on GYM Streptomyces agar. Chemotaxonomic and molecular characteristics of the isolate matched those described for other representatives of the genus Geodermatophilus. The peptidoglycan contained meso-diaminopimelic acid as diagnostic diaminoacid. The main phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, and small amount of diphosphatidylglycerol. MK-9(H 4) was the dominant menaquinone and galactose was detected as diagnostic sugar. The major cellular fatty acids were branched-chain saturated acids iso-C 16:0 and iso-C 15:0 and the unsaturated C 17:1 íµí¼8c and C 16:1 íµí¼7c. The 16S rRNA gene showed 97.4–99.1% sequence identity with the other representatives of genus Geodermatophilus. Based on phenotypic results and 16S rRNA gene sequence analysis, strain G18 T is proposed to represent a novel species, Geodermatophilus poikilotrophi. Type strain is G18 T (= DSM 44209 T = CCUG 63018 T). The INSDC accession number is HF970583. The novel R software package lethal was used to compute the lethal doses with confidence intervals resulting from tolerance experiments.
BioMed Research International 07/2014; DOI:10.1155/2014/914767 · 2.71 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter species are effective colonizers of marine surfaces, including frequent associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the scallop Pecten maximus. Here we describe the features of this organism, together with the complete genome sequence, comprising eight circular replicons with a total of 4,448 genes. In addition to a high number of extrachromosomal replicons, the genome contains six genomic island and three putative prophage regions, as well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses confirm previous results, which indicated that the originally reported P. gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP 105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P. gallaeciensis.