Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T))

Saccharomonospora marina Liu et al. 2010 is a member of the genus Saccharomonospora, in the family Pseudonocardiaceae that is poorly characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Here we describe the features of this organism, together with the complete genome sequence (permanent draft status), and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).     

Complete genome sequence of Saccharomonospora viridis type strain (P101)

Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified among the usually Gram-positive actinomycetes. Members of the species are frequently found in hot compost and hay, and its spores can cause farmer's lung disease, bagassosis, and humidifier fever. Strains of the species S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP). The strain described in this study has been isolated from peat-bog in Ireland. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Rhodospirillum rubrum type strain (S1)

Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.     

Complete genome sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b

Here we present the genome of strain Exiguobacterium sp. AT1b, a thermophilic member of the genus Exiguobacterium whose representatives were isolated from various environments along a thermal and physicochemical gradient. This genome was sequenced to be a comparative resource for the study of thermal adaptation with a psychroactive representative of the genus, Exiguobacterium sibiricum strain 255-15, that was previously sequenced by the U.S. Department of Energy's (DOE's) Joint Genome Institute (JGI) (http://genome.ornl.gov/microbial/exig/).     

Transfer of 'Thermoactinomyces glaucus' IFO 12530 and 'Thermoactinomyces monosporus' IFO 14050 to the genus Saccharomonospora as members of Saccharomonospora glauca

Two available strains of 'Thermoactinomyces glaucus' and 'Thermoactinomyces monosporus', 'T. glaucus' IFO 12530 and 'T. monosporus' IFO 14050, were considered not to be members of the genus Thermoactinomyces and that they belonged to the genus Saccharomonospora on the basis of the colors of colonies and 16S rDNA sequences. Some chemotaxonomic characteristics also showed that the two strains belong to the genus Saccharomonospora. The two strains contained meso-diaminopimelic acid, galactose, and arabinose in the cell wall and MK-9(H(4)) as the predominant menaquinone. The genomic DNAs of the two strains had a G+C content of 69 mol%. The 16S rDNAs of 'T. glaucus' IFO 12530 and 'T. monosporus' IFO 14050 showed only 1 and 2 bp sequence differences, respectively, from that of the type strain of Saccharomonospora glauca. Furthermore, the two strains of 'T. glaucus' and 'T. monosporus' and the type strain of S. glauca shared identical 16S-23S rDNA ITS sequences. The levels of DNA-DNA relatedness confirm that the two strains of 'T. glaucus' and 'T. monosporus' are members of Saccharomonospora glauca. Therefore it is proposed that 'T. glaucus' IFO 12530 and 'T. monosporus' IFO 14050 should be considered as strains belonging to Saccharomonospora glauca.     

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T))

Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes. The genome of H. aurantiacus strain 114-95(T) is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005.     

四株糖单孢菌分离株的分类学研究

从广西地区的土样中,分离到4株细胞壁Ⅳ型,糖型A, 无枝菌酸的假诺卡氏菌科的放线菌菌株,编号分别为191、221、202、和212。根据4株 菌的形态学特征和细胞化学特征,将其归入糖单孢菌属。与该属5个已知种的7个代表株进行 的rDNA的BamHI酶切片段长度类型分析(Ribotyping)的结果表明：191为青绿色糖单孢菌(S.viridis),202为青灰色糖单孢菌(S.caesia),221和212为相同的与青绿色糖单孢菌(S .viridis)的亲缘关系最近的种,但不同于已知的任何一个种。     

Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139)

Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5(th) sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Draft genome sequence of an efficient antibiotic-producing industrial strain of Saccharomonospora azurea, SZMC 14600

Although certain rare actinomycetes have been recognized as prolific sources of bioactive natural products, their potential for producing biologically active metabolites still remains unexplored. With the aim of gaining global insights into the genetic background and the metabolic capability of Saccharomonospora azurea SZMC 14600, whole-genome sequencing was performed.     

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR)

Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus Syntrophobotulus within the family Peptococcaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of tree of life. When grown in pure culture with glyoxylate as carbon source the organism utilizes glyoxylate through fermentative oxidation, whereas, when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria, it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic or inorganic carbon source is utilized by S. glycolicus. The subdivision of the family Peptococcaceae into genera does not reflect the natural relationships, particularly regarding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in significant conflict with the 16S rRNA data. S. glycolicus is already the ninth member of the family Peptococcaceae with a completely sequenced and publicly available genome. The 3,406,739 bp long genome with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Meiothermus silvanus type strain (VI-R2)

Meiothermus silvanus (Tenreiro et al. 1995) Nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16S rRNA gene sequence similarity. Meiothermus constitutes an evolutionary lineage separate from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. M. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biofouler. This is the second completed genome sequence of a member of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,721,669 bp long genome with its 3,667 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Meiothermus ruber type strain (21)

Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members share relatively low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary lineage from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Aminobacterium colombiense type strain (ALA-1)

Aminobacterium colombiense Baena et al. 1999 is the type species of the genus Aminobacterium. This genus is of large interest because of its isolated phylogenetic location in the family Synergistaceae, its strictly anaerobic lifestyle, and its ability to grow by fermentation of a limited range of amino acids but not carbohydrates. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the family Synergistaceae and the first genome sequence of a member of the genus Aminobacterium. The 1,980,592 bp long genome with its 1,914 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T))

Segniliparus rugosus represents one of two species in the genus Segniliparus, the sole genus in the family Segniliparaceae. A unique and interesting feature of this family is the presence of extremely long carbon-chain length mycolic acids bound in the cell wall. S. rugosus is also a medically important species because it is an opportunistic pathogen associated with mammalian lung disease. This report represents the second species in the genus to have its genome sequenced. The 3,567,567 bp long genome with 3,516 protein-coding and 49 RNA genes is part of the NIH Roadmap for Medical Research, Human Microbiome Project.     

2株WU多瘤病毒全基因组序列测定和分析

WU多瘤病毒(WUPyV)是多瘤病毒科多瘤病毒属的新成员,近来发现与人呼吸道感染等有关。本研究对2株WUPyV进行全基因组序列测定和拼接,获得这2株病毒全基因组序列,并与已上传到GenBank的国内外几株WUPyV的全基因组序列和氨基酸序列进行比对和系统进化分析。这2株WUPyV是环状、双链DNA病毒,基因组全长5 228bp,比GenBank已知WUPyV全序列少1bp。缺失的一对碱基位于位点4 536处,属于大T抗原的非编码区。病毒全基因组编码5个蛋白,分别是3个衣壳蛋白VP2、VP3、VP1与大T抗原和小T抗原。系统进化分析显示相对中国福建福州的FZ18株,另一株FZTF株与参考株-澳大利亚的B0株关系较近。     

Cloning, characterization and taxonomic significance of genes for the 5S ribosomal RNA of Leptonema illini strain 3055.

The genes encoding the 5S ribosomal RNA (rRNA) for Leptonema illini strain 3055 were isolated and sequenced. The 5S RNA molecule encoded was 117 nucleotides long. The genome of strain 3055 contained two genes for 5S rRNA that were located close together. The nucleotide sequences of the Leptonema illini genes exhibited less similarity to the rRNA gene of Leptospira interrogans strain Moulton and also to those of typical eubacterial genes than did the rRNA genes of other leptospires. However, the overall secondary structure of the 5S rRNA encoded exhibited a strong similarity to that of typical eubacterial 5S rRNA. Southern hybridization of the 5S rRNA gene probe with the genomic DNA of strain 965, which is currently classified as Leptospira biflexa, showed the latter to have close similarity to that of strain 3055. The physical map of strain 965 was quite similar to that of strain 3055 and was greatly different from that of any other strains of L. biflexa. In the organization of 5S rRNA genes, strain 965 is sufficiently different from other members of the genus Leptospira to be regarded as a member of the genus Leptonema.     

Complete genome sequence of strain s85, a novel member of the family Flavobacteriaceae

An agar-degrading marine bacterium identified as a novel member of the family Flavobacteriaceae (strain S85) was isolated from seawater in Micronesia. The sequenced strain S85 genome is composed of 3,384,629 bp in a circular chromosome, which includes 2,883 complete open reading frames.     

Complete genome sequence of Tolumonas auensis type strain (TA 4)

Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4(T) is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.     

不同放线菌属的化学与分子分类

随着科学的发展与新技术在分类学中不断地应用,放线菌分类学已从经典的形态分类转向化学分类(细胞壁化学组份,磷酸类脂,枝菌酸及甲基萘醌等).现在有些国家又开展了分子分类.本实验室自80年代始开展了放线菌化学分类,建立了上述化学指征的分析方法.自90年代起,又开展了分子分类,DNA-DNA杂交、23S rRNA寡核甘酸序列分析.近来,许多人用16S rRNA部分序列区分微生物不同的基因种.作者选用了23S rRNA部分序列区分放线菌的不同属种.现将研究结果简报如下:1 材料和方法1.1菌种菌株10,13,23,C_(43),350,41,53,4650及N分离自云南省土壤中.C_(51)及3306来自日本微生物菌种保藏中心.