Cetobacterium somerae sp. nov. from human feces and emended description of the genus Cetobacterium

Phenorypic and phylogenetic studies were performed on four isolates of an unidentified gram-negative, microaerotolerant, non-spore-forming, rod-shaped bacterium isolated from the feces of children. The unknown organism was bile resistant and produced acetic acid as the major end product of metabolism of peptides and carbohydrates. It possessed a low DNA G + C content of 31 mol %. Comparative 16S rRNA gene sequencing demonstrated that the four isolates were phylogenetically identical (100% 16S rRNA sequence similarity) and represent a hitherto unknown sub-line within the genus Cetobacterium. The novel bacterium displayed approximately 5% sequence divergence with Cetobacterium ceti, and can be readily distinguished from the latter by physiological and biochemical criteria. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown fecal bacterium be classified in the genus Cetobacterium, as Cetobacterium somerae sp. nov. The proposed type strain of Cetobacterium somerae is WAL 14325(T) (ATCC BAA-474(T) = CCUG 46254T).     

Phenylobacterium falsum sp. nov., an Alphaproteobacterium isolated from a nonsaline alkaline groundwater, and emended description of the genus Phenylobacterium

A Gram-negative bacterium designated AC-49T was isolated from an alkaline groundwater with a pH 11.4. This organism formed rod-shaped cells, was strictly aerobic, catalase and oxidase positive, with an optimum growth temperature of 35 degrees C and an optimum pH value of 8.0. Strain AC-49T assimilated primarily amino acids and some Krebs cycle metabolites, did not use sugars for growth. The organism did not grow on L-phenylalanine or antipyrin. The G+ C content of DNA was 66.9 mol%. The phylogenetic analyses based on the 16S rRNA sequencing showed that the closest relatives of strain AC-49T were Phenylobacterium lituiforme and Phenylobacterium immobile, indicating that the organism is a member of the order Caulobacterales of the Alphaproteobacteria. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strain AC-49T, represents a novel species of the genus Phenylobacterium for which we propose the name Phenylobacterium falsum sp. nov.     

Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources

During studies on the bacteriology of appendicitis in children, we often isolated from inflamed and non-inflamed tissue samples, an unusual bile-resistant pigment-producing strictly anaerobic gram-negative rod. Phenotypically this organism resembles members of Bacteroides fragilis group of species, as it is resistant to bile and exhibits a special-potency-disk pattern (resistance to vancomycin, kanamycin and colistin) typical for the B. fragilis group. However, the production of brown pigment on media containing haemolysed blood and a cellular fatty acid composition dominated by iso-C15:0, suggests that the organism most closely resembles species of the genus Porphyromonas. However, the unidentified organism differs from porphyromonads by being bile-resistant and by not producing butyrate as a metabolic end-product. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism represents a distinct sub-line, associated with but distinct from, the miss-classified species Bacteroides putredinis. The clustering of the unidentified bacterium with Bacteroides putredinis was statistically significant, but they displayed > 4% sequence divergence with each other. Chromosomal DNA-DNA pairing studies further confirmed the separateness of the unidentified bacterium and Bacteroides putredinis. Based on phenotypic and phylogenetic considerations, it is proposed that Bacteroides putredinis and the unidentified bacterium from human sources be classified in a new genus Alistipes, as Alistipes putredinis comb. nov. and Alistipes finegoldii sp. nov., respectively. The type strain of Alistipes finegoldii is CCUG 46020(T) (= AHN243(T)).     

伦茨菌属放线菌的研究进展

伦茨菌属(Lentzea)由Yassin等于1995年建立,是一个经典的丝状稀有放线菌类群,目前共包含23个有效描述种。伦茨菌的细胞壁含有meso-二氨基庚二酸,优势甲基萘醌成分为MK-9(H_4),磷酸类脂主要包括磷脂酰乙醇胺、双磷脂酸甘油、磷脂酰甘油和磷脂酰肌醇,基因组DNA的(G+C)含量为68.6mol%–79.6mol%。伦茨菌代谢产物具有显著的生物活性多样性,包括I型人体免疫缺损病毒整合酶的抑制活性、抗肿瘤活性、抗结核活性等,在生物医药研究领域逐步显示出潜在的应用价值。本课题组在研究贵州石灰岩风化壳放线菌多样性时分离获得若干株伦茨菌,采用多相分类方法研究Lentzea xinjiangensis DHS C013~T和Lentzea pudingi DHS C021~T两株菌的分类学地位,证实均为伦茨菌属的新物种。在此研究基础上,引用有关文献和最新研究成果,对伦茨菌属的建立、分类学特征、生态位和物种分布、功能基因组、天然活性产物应用开发等方面的研究进展进行了综述。     

Transfer of the members of the genus Brachiola (microsporidia) to the genus Anncaliia based on ultrastructural and molecular data

Two microsporidian genera, AnncaliiaIssi, Krylova, & Nicolaeva 1993 and BrachiolaCali et al. 1998, possess a Nosema-type life cycle and unique cell surface ornamentations, which include precocious electron-dense coating of the plasmalemma and a variety of secretory structures deposited on the parasite surface and scattered in the host cell cytoplasm. Comparative analysis of ultrastructure of Anncaliia meligethi (the type species of the genus Anncaliia) and of B. vesicularum and B. algerae (the best-studied members of the genus Brachiola) clearly demonstrated that these microsporidia share many distinctive morphological features. The comparison of small subunit ribosomal DNA sequences showed high sequence identity of A. meligethi and B. algerae. Phylogenetic analyses indicated that the rDNA sequences of A. meligethi clustered with those of B. algerae suggesting a close relatedness of these microsporidia. The combination of molecular and morphological data provided clear evidence that these microsporidia belong to the same genus and therefore, warranted emendation of the genus Anncaliia and establishments of the following new combinations: Anncaliia vesicularum nov. comb., Anncaliia algerae nov. comb., Anncaliia connori nov. comb., and Anncaliia gambiae nov. comb. The generic name Brachiola is submerged according to the rule of priority.     

Tepidimonas thermarum sp. nov., a new slightly thermophilic betaproteobacterium isolated from the Elisenquelle in Aachen and emended description of the genus Tepidimonas

Several non-pigmented bacterial isolates, with an optimum growth temperature of about 50-55 degrees C, were recovered from the Elisenquelle at Aachen, Germany. Phylogenetic analysis of the 16S rRNA gene sequence of strains AA-1(T) and AA-2 indicated that these organisms represent a new species of the genus Tepidimonas. The major fatty acids of strains AA-1(T) and AA-2 are 16:0 and 16:1 omega7c. Ubiquinone 8 is the major respiratory quinone, the major polar lipids are phosphotidylethanolamine and phosphotidylglycerol. The new isolates are aerobic; thiosulfate is oxidized to sulfate in the presence of a metabolizable carbon source. The organism assimilated organic acids and amino acids, but did not assimilate carbohydrates or polyols. On the basis of the phylogenetic analyses, physiological and biochemical characteristics, we propose that strains AA-1(T) (=LMG 23094(T); =CIP 108777(T)) and AA-2 (=LMG 23095; =CIP 108778) represents a new species for which we recommend the name Tepidimonas thermarum.     

Thermus kawarayensis sp. nov., a new member of the genus Thermus, isolated from Japanese hot springs

A long-rod-shaped thermophilic microorganism, strain KW11, was isolated from a hot springs located in the Kawarayu, Gunma, Japan. Cloning and preliminary sequence analysis of 16S rDNA showed that this isolate belongs to the genus Thermus. The cells were 10–20 m long, about 0.8 m in diameter, and produced no pigment in contrast with most of the Thermus species previously reported. KW11 was an aerobic heterotroph and grew at temperatures ranging from 40–73°C, with optimal growth occurring at 68°C. The pH range for growth was from 5.8–8.9, with optimal growth around pH 7. KW11 was sensitive to ampicillin, penicillin G, kanamycin, and streptomycin. The G+C content of DNA was 69 mol%. The main fatty acids were 16:0 (52.9%), iso-15:0 (22.1%), and iso-17:0 (15.6%). The 16S rDNA sequence of KW11 showed 96.0, 95.8, and 95.4% similarity with the sequences of T. aquaticus, T. igniterrae, and T. thermophilus, respectively, and less than 95% with other Thermus species. The physiological differences and phylogenetic evidence indicated that strain KW11 represents T. kawarayensis, a novel species of the genus Thermus. The type strain is isolate KW11^T (JCM12314, DSM16200).     

Tsukamurella spumae sp. nov., a novel actinomycete associated with foaming in activated sludge plants

A polyphasic taxonomic study was undertaken to establish the taxonomic position of six representative strains isolated from activated sewage sludge foam. The organisms were found to have chemical and morphological properties consistent with their assignment to the genus Tsukamurella. DNA:DNA relatedness studies showed that five out of the six isolates formed a distinct genomic species, the remaining strain was most closely associated with this taxon. The five isolates had a unique phenotypic profile that served to distinguish them from representatives of the validly described species of Tsukamurella. The combination of the genotypic and phenotypic data indicated that the five strains should be classified as a new species in the genus Tsukamurella. The name proposed for this taxon is Tsukamurella spumae, the type strain is N1171T (= DSM 44.113T = NCIMB 13947T). It was also shown that some of the reference strains were misclassified as Tsukamurella paurometabola.     

Unification of the genera Nonlabens, Persicivirga, Sandarakinotalea and Stenothermobacter into a single emended genus, Nonlabens, and description of Nonlabens agnitus sp. nov

Phylogenetic analyses based on 16S rRNA gene sequences showed that a bacterial isolate, designated JC2678(T), represents a distinct phyletic line within the suprageneric monophyletic clade containing the genera Nonlabens, Persicivirga, Stenothermobacter and Sandarakinotalea. The polyphasic data presented in this study demonstrated that the members belonging to the Nonlabens-like clade overall constitute a single genus. Therefore, it is proposed to transfer the members of genera Persicivirga O'Sullivan et al. 2006, Stenothermobacter Lau et al. 2006 and Sandarakinotalea Khan et al. 2006 to the genus Nonlabens Lau et al. 2005. Thus, P. dokdonensis (Yoon et al. 2006) Nedashkovskaya et al. 2009, P. ulvanivorans Barbeyron et al. 2010, P. xylanidelens O'Sullivan et al. 2006, Sandarakinotalea sediminis Khan et al. 2006 and Stenothermobacter spongiae Lau et al. 2006 should be transferred to Nonlabens dokdonensis comb. nov., Nonlabens ulvanivorans comb. nov., Nonlabens xylanidelens comb. nov., Nonlabens sediminis comb. nov. and Nonlabens spongiae comb. nov., respectively. In addition, strain JC2678(T) (=KACC 14155(T)=JCM 17109(T)) is proposed to constitute a novel species belonging to the genus Nonlabens with the name of Nonlabens agnitus sp. nov.     

Gordonia namibiensis sp. nov., a novel nitrile metabolising actinomycete recovered from an African sand

A polyphasic approach was used to establish the taxonomic position of two actinomycetes isolated from a Namibian soil and shown to utilise nitrile compounds as growth substrates. The organisms, strains NAM-BN063AT and NAM-BN063B, had chemical and morphological properties consistent with their assignment to the genus Gordonia. Direct 165 rRNA sequencing studies confirmed the taxonomic position of the strains following the generation of phylogenetic trees using four different algorithms. The strains consistently formed a distinct phylogenetic line within the evolutionary radiation occupied by gordoniae and were most closely related to Gordonia rubropertincta DSM 43197T. DNA:DNA relatedness studies indicated that the two organisms belonged to a genomic species that was readily distinguished from G. rubropertincta. The unique phenotypic profile of the strains sharply separated them from representatives of all of the validly described species of Gordonia. The combination of genotypic and phenotypic data indicates that the two strains should be classified in the genus Gordonia as a new species. The name proposed for this taxon is Gordonia namibiensis, the type strain is NAM-BN063AT (= DSM 44568T = NCIMB 13780T).     

Genetic interrelationships of proteolyticClostridium botulinum types A,B, and F and other members of theClostridium botulinum complex as revealed by small-subunit rRNA gene sequences

The phylogenetic interrelationships of members of theClostridium botulinum complex of species was investigated by direct sequencing of their 16S rRNA genes. Comparative analysis of the 16S rRNA sequences demonstrated the presence of four phylogenetically distinct lineages corresponding to: i) proteolyticC. botulinum types A, B, and F, andC. sporogenes, ii) saccharolytic types B, E and F, iii) types C and D andC. novyi type A, and iv) type G andC. subterminale. The phylogenetic groupings obtained from the 16S rRNA were in complete agreement with the four divisions recognised within the species complex on the basis of phenotypic criteria.     

Morphological,biochemical, and molecular characterization of Oscillatoria kawamurae (Oscillatoriales,Cyanobacteria) isolated from different geographical regions

Oscillatoria kawamurae is an unusual freshwater cyanobacterium because of its large trichome and ambiguous gas vacuole. Because little is known about its phenotypic or genotypic characteristics, this study conducted morphological, biochemical, and genetic characterization of O. kawamurae strains isolated from Japan, Laos, and Myanmar. All strains displayed similar morphological characteristics; however some differences were observed in vegetative cell widths, trichome colors, and the distribution patterns of their gas vacuole‐like structures. The in vivo and phycobiliprotein absorption spectra revealed the two different trichome colors found in the four representative strains of O. kawamurae (Inle1, Lao7, Biwa6, and Inba3). These different trichome colors corresponded to the different ratios of phycoerythrin and phycocyanin, the two types of phycobilin pigments: 0.25 for olive‐green strain (Inle1) and 0.65–0.73 for brown‐green strains (Biwa6, Inba3, and Lao7). Cellular fatty acid compositions of the four strains were C14:0, C15:0, C16:0, C16:1c, C17:0, C18:0, C18:1c, C18:3α and C18:4, whereas two strains (Biwa6 and Inba3) lacked C17:0. Of the fatty acids, palmitic acid (C16:0) was predominant. PCR experiments using primers targeting a gas vesicle gene (gvpA) recovered gvpA fragments from all O. kawamurae strains, suggesting that this species has true gas vacuoles. The 16S rDNA sequences of all of the strains were identical regardless of their different trichome colors and/or geographic origins. Phylogenetic analyses based on the 16S rDNA sequences indicated that O. kawamurae forms a monophyletic clade with O. princeps CCALA 1115 clB1 and O. duplisecta ETS‐06. We discuss the taxonomy of O. kawamurae based on the data obtained in this study.     

Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria

Large numbers of putatively novel streptomycetes were isolated from environmental samples collected from in and around the root system of the tropical angiosperm, Paraserianthes falcataria. Representative isolates were assigned to 37 multi-membered and 107 single membered colour groups based on their ability to form pigments on oatmeal and peptone yeast extract iron agars. The largest taxon, colour group 3, encompassed 94 isolates which had morphological properties typical of members of the Streptomyces violaceusniger clade. Twelve representatives of this taxon chosen on the basis of Curie-point pyrolysis mass spectrometric data were compared with representatives of the validly described species which constitute the Streptomyces violaceusniger clade. Six out of the twelve representative strains were readily distinguished from one another and from the marker strains using a combination of genotypic and phenotypic properties. These organisms were consequently considered to merit species status as Streptomyces asiaticus sp. nov., Streptomyces cangkringensis sp. nov., Streptomyces indonesiensis sp. nov., Streptomyces javensis sp. nov., Streptomyces rhizosphaerius sp. nov. and Streptomyces yogyakartensis sp. nov.     

The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis

Strains of Nitrobacter mediate the second step in the nitrification process by oxidizing nitrite to nitrate. The phylogenetic diversity of the genus is currently not well investigated. In this study, a rep-PCR profile and the nearly complete 16S rRNA gene sequence of 30 strains, comprising a wide physiological as well as ecological diversity and encompassing representatives of the four species, were determined. The sequence diversity of the 16S rRNA gene between different species was low, indicating the need for additional phylogenetic markers. Therefore, primers were developed for amplifying the complete nxrX gene and a 380bp fragment of the nxrB1 gene, which are both genes involved in the nitrite oxidation process. These genes confirmed the division into phylogenetic groups revealed by the 16S rRNA gene but showed a better discriminatory power. They can be a valuable additional tool for phylogenetic analysis within the genus Nitrobacter and can assist in the identification of new Nitrobacter isolates.     

Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant

A Gram-negative, motile, rod-shaped, non-spore-forming bacterial strain, designated as Ko03(T), was isolated from microbial granules, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The isolate was positive for catalase and oxidase, but negative for gelatinase and beta-galactosidase. Phylogenetic analyses using the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Comamonas, its closest neighbors being Comamonas koreensis KCTC 12005(T) (95.9% sequence similarity), Comamonas nitrativorans DSM 13191(T) (95.7%), and Comamonas odontotermitis LMG 23579(T) (95.7%). Strain Ko03(T) had a genomic DNA G+C content of 68.4 mol% and the predominant respiratory quinone was Q-8. The major fatty acids were C(16:1) omega7c (44.7%), C(16:0) (28.1%), C(18:1) (16.1%), and C(10:0) 3-OH (3.5%). These chemo-taxonomic results supported the affiliation of strain Ko03(T) to the genus Comamonas. However, low 16S rRNA gene sequence similarity values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Ko03(T) from recognized Comamonas species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Ko03(T) represents a novel species of the genus Comamonas, for which the name Comamonas granuli sp. nov. is proposed. The type strain is Ko03(T) (= KCTC 12199(T) = NBRC 101663(T)).     

Igniting taxonomic curiosity: The amazing story of Amazonocrinis with the description of a new genus Ahomia gen. nov. and novel species of Ahomia,Amazonocrinis, and Dendronalium from the biodiversity-rich northeast region of India

Five cyanobacterial strains exhibiting Nostoc-like morphology were sampled from the biodiversity hotspots of the northeast region of India and characterized using a polyphasic approach. Molecular and phylogenetic analysis using the 16S rRNA gene indicated that the strains belonged to the genera Amazonocrinis and Dendronalium. In the present investigation, the 16S rRNA gene phylogeny clearly demarcated two separate clades of Amazonocrinis. The strain MEG8-PS clustered along with Amazonocrinis nigriterrae CENA67, which is the type strain of the genus. The other three strains ASM11-PS, RAN-4C-PS, and NP-KLS-5A-PS clustered in a different clade that was phylogenetically distinct from the Amazonocrinis sensu stricto clade. Interestingly, while the 16S rRNA gene phylogeny exhibited two separate clusters, the 16S–23S ITS region analysis did not provide strong support for the phylogenetic observation. Subsequent analyses raised questions regarding the resolving power of the 16S–23S ITS region at the genera level and the associated complexities in cyanobacterial taxonomy. Through this study, we describe a novel genus Ahomia to accommodate the members clustering outside the Amazonocrinis sensu stricto clade. In addition, we describe five novel species, Ahomia kamrupensis, Ahomia purpurea, Ahomia soli, Amazonocrinis meghalayensis, and Dendronalium spirale, in accordance with the International Code of Nomenclature for algae, fungi, and plants (ICN). Apart from further enriching the genera Amazonocrinis and Dendronalium, the current study helps to resolve the taxonomic complexities revolving around the genus Amazonocrinis and aims to attract researchers to the continued exploration of the tropical and subtropical cyanobacteria for interesting taxa and lineages.     

Taxonomic relationships ofThiobacillus halophilus,T. aquaesulis,and other species ofThiobacillus,as determined using 16S rDNA sequencing

Total base sequences of the 16S rRNA genes ofThiobacillus halophilus andThiobacillus aquaesulis show that these bacteria fall into the gamma- and beta-subdivisions, respectively of the Proteobacteria. The closest relative ofT. halophilus isThiobacillus hydrothermalis (with 98.7% similarity), and the closest relative ofT. aquaesulis isThiobacillus thioparus (93.2% similarity). Physiological properties and mol% G+C content of their DNA serve to confirm that these four organisms are all distinct species. It is reiterated that the species currently assigned to the genusThiobacillus are clearly so diverse that they need reclassification into several genera. The type species,T. thioparus, is unequivocally placed in the beta-subdivision of the Proteobacteria, thus requiring that the use of the genus nameThiobacillus be restricted to the chemolithoautotrophic species falling into that group.T. aquaesulis andT. thioparus may thus be regarded as true species ofThiobacillus. The relatively large number of obligately chemolithoautotrophicThiobacillus species falling in the gamma-subdivision of the Proteobacteria need further study in order to assess the case for reclassification into one or more new or different genera.     

The phylogenetic diversity of thermophilic members of the genus Bacillus as revealed by 16S rDNA analysis

Abstract Sixteen thermophilic strains of the genus Bacillus , representing eight validly described and six invalidly described species, as well as one unassigned strain, were investigated by comparative 16S rDNA analyses and the sequences compared to the existing database for the genera Bacillus and Alicyclobacillus . The majority of strains were found to cluster in two groups represented by B. stearothermophilus and B. pallidus. Bacillus smithii, B. thermocloacae , and B. thermoruber are phylogenetically well separated and cluster within the radiation of mesophilic bacilli. The as yet undescribed taxon 'B. flavothermus' warrants species status. B. schlegelii and B. tusciae group peripherally with members of Alicyclobacillus and may be reclassified when more phenotypic data support their phylogenetic position.