MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data

An orange-pigmented, Gram-staining-negative, non-motile, filament-forming, rod-shaped bacterium (BUZ 3T) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach. According to 16S rRNA gene sequence data, it belonged to the family Cytophagaceae, exhibiting low 16S rRNA gene sequence similarity (<90 %) with members of the genera Spirosoma, Rudanella and Fibrella. The DNA G+C content was 52.0 mol%. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 1ω5c and iso-C17 : 0 3-OH. The major polar lipids consisted of phosphatidylethanolamine and several aminolipids. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that strain BUZ 3T represents a novel genus and species, for which the name Fibrisoma limi gen. nov., sp. nov. is proposed. The type strain is BUZ 3T ( = DSM 22564T = CCUG 58137T).

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Alkalimicrobium pacificum gen. nov., sp. nov., a marine bacterium in the family Rhodobacteraceae

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000282 ◽

2015 ◽

Vol 65 (Pt_8) ◽

pp. 2453-2458 ◽

Cited By ~ 17

Author(s):

Gaiyun Zhang ◽

Yanliu Yang ◽

Shuang Wang ◽

Zhilei Sun ◽

Kailin Jiao

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Sequence Data ◽

Sequence Similarity ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Unidentified Phospholipid ◽

The Family

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterium, designated strain F15T, was isolated from a deep-sea sediment of the western Pacific Ocean. The temperature, pH and NaCl ranges for growth were 4–50 °C, pH 6–11 and 0–10 % (w/v), respectively. Strain F15T showed the highest 16S rRNA gene sequence similarity to Sagittula stellata E-37T (96.4 %), followed by Ponticoccus litoralis CL-GR66T (96.4 %), Antarctobacter heliothermus EL-219T (96.3 %) and Thalassococcus lentus YCS-24T (96.0 %). Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain F15T formed a lineage within the family Rhodobacteraceae of the class Alphaproteobacteria. The polar lipid profile of strain F15T comprised significant amounts of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified phospholipid. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 40.2 %), anteiso-C15 : 0 (30.4 %) and anteiso-C17 : 0 (9.7 %). The genomic DNA G+C content of strain F15T was 60.2 mol% and the major respiratory quinone was Q-10. On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain F15T is considered to represent a novel species of a new genus within the family Rhodobacteraceae, for which the name Alkalimicrobium pacificum gen. nov., sp. nov. is proposed. The type strain is F15T ( = LMG 28107T = JCM 19851T = CGMCC 1.12763T = MCCC 1A09948T).

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Planosporangium mesophilum sp. nov., isolated from rhizosphere soil of Bletilla striata

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.026096-0 ◽

2011 ◽

Vol 61 (6) ◽

pp. 1330-1333 ◽

Cited By ~ 9

Author(s):

Yan-Ru Cao ◽

Qian Wang ◽

Rong-Xian Jin ◽

Yi Jiang ◽

Hang-Xian Lai ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Rhizosphere Soil ◽

Sequence Data ◽

Sequence Similarity ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Bletilla Striata

A Gram-stain-positive, non-motile actinomycete, designated strain YIM 48875T, was isolated from rhizosphere soil of Bletilla striata and its taxonomic position was established by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 48875T belonged to the genus Planosporangium, supported by a bootstrap value of 100 %. Cells of strain YIM 48875T showed two kinds of sporangia, which also supported its classification in the genus Planosporangium. Strain YIM 48875T grew optimally at 28 °C, at pH 6.0–8.0 and in the presence of 2 % (w/v) NaCl. The level of 16S rRNA gene sequence similarity between strain YIM 48875T and Planosporangium flavigriseum YIM 46034T was 98.6 %. Strain YIM 48875T exhibited a quinone system with menaquinones MK-9(H4), MK-9(H6) and MK-9(H8) as the predominant compounds, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol mannoside and the major fatty acids iso-C15 : 0 and iso-C16 : 0; these data were markedly different from those for P. flavigriseum YIM 46034T. The level of DNA–DNA relatedness between strain YIM 48875T and P. flavigriseum YIM 46034T was 45.5 %. It is apparent from the genotypic and phenotypic data that strain YIM 48875T represents a novel species of the genus Planosporangium, for which the name Planosporangium mesophilum sp. nov. is proposed. The type strain is YIM 48875T ( = CCTCC AA 209049T = KCTC 19779T).

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Reclassification of Lactobacillus ferintoshensis as a later heterotypic synonym of Lactobacillus parabuchneri

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63779-0 ◽

2005 ◽

Vol 55 (5) ◽

pp. 2195-2198 ◽

Cited By ~ 15

Author(s):

Marc Vancanneyt ◽

Katrien Engelbeen ◽

Marjan De Wachter ◽

Katrien Vandemeulebroecke ◽

Ilse Cleenwerck ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Sequence Data ◽

Sequence Similarity ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Phenotypic Data ◽

Lactobacillus Kefiri

Lactobacillus ferintoshensis has recently been described as a novel species, distinct from its close phylogenetic neighbours Lactobacillus buchneri, Lactobacillus kefiri and Lactobacillus hilgardii. Two highly related species with validly published names, Lactobacillus parakefiri and Lactobacillus parabuchneri, were not considered in the study due to the lack of 16S rRNA gene sequence data at that time. Since the publication of the study, the sequences have become available and have revealed that L. ferintoshensis and L. parabuchneri share 99·7 % 16S rRNA gene sequence similarity. Further genomic and phenotypic data, derived from fluorescent amplified fragment length polymorphism, DNA–DNA hybridization and API 50 CHL analyses, have demonstrated that the species are synonymous.

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Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64284-0 ◽

2007 ◽

Vol 57 (4) ◽

pp. 796-802 ◽

Cited By ~ 47

Author(s):

Iftikhar Ahmed ◽

Akira Yokota ◽

Toru Fujiwara

Keyword(s):

Fatty Acids ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Sequence Data ◽

Diaminopimelic Acid ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

The Novel ◽

Rrna Gene Sequence

A motile, Gram-positive, boron-tolerant and moderately halotolerant rod-shaped bacterium was isolated from a soil naturally high in boron minerals found in the Hisarcik area of Turkey. The novel isolate, designated T-16XT, produced spherical or ellipsoidal endospores in a non-bulging or slightly swollen sporangium in a terminal position and survived in a medium containing up to 450 mM boron. Whereas it tolerated 11 % (w/v) NaCl, it also grew without NaCl or boron. The temperature range for growth was 16–37 °C (optimum 25–28 °C) and the pH range for growth was 6.0–10.0 (optimum pH 7.5–8.5). The DNA G+C content was 35.8 mol% and the major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0 at 18.2 and 45.7 % of the total fatty acids, respectively. MK-7 (90 %) was the predominant respiratory quinone system and meso-diaminopimelic acid was the predominant diamino acid of the cell-wall peptidoglycan. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the novel strain is closely related to the type strains of Gracilibacillus orientalis (96.7 % similarity), G. halotolerans (95.5 %) and G. dipsosauri (95.4 %). However, the maximum DNA hybridization value for this strain with these closely related strains was less than 26.2 %. On the basis of 16S rRNA gene sequence data and chemotaxonomic and physiological features, the organism T-16XT (=DSM 17256T=IAM 15263T=ATCC BAA-1190T) is proposed to be a member of the genus Gracilibacillus as the type strain of the novel species Gracilibacillus boraciitolerans sp. nov.

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Streptomyces synnematoformans sp. nov., a novel actinomycete isolated from a sand dune soil in Egypt

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.65037-0 ◽

2007 ◽

Vol 57 (9) ◽

pp. 2009-2013 ◽

Cited By ~ 17

Author(s):

Wael N. Hozzein ◽

Michael Goodfellow

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sand Dune ◽

Gene Sequence ◽

Sequence Data ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Type Strains ◽

Dune Soil

A polyphasic taxonomic study was undertaken to establish the status of a novel actinomycete, strain S155T, isolated from a sand dune soil in Egypt. The organism formed characteristic synnemata-like structures and exhibited chemical and morphological features consistent with its classification in the genus Streptomyces. An almost-complete 16S rRNA gene sequence of the isolate was compared with corresponding sequences of representative streptomycetes. The 16S rRNA gene sequence data supported the assignment of the strain to the genus Streptomyces and showed that it formed a distinct phyletic line; the organism was most similar to the type strains of Streptomyces ruber (97.0 %), Streptomyces rubiginosus (97.0 %), Streptomyces roseiscleroticus (96.9 %) and Streptomyces thermoalcalitolerans (97.1 %). It was readily distinguished from the type strains of these species using a combination of phenotypic properties. On the basis of these results, strain S155T (=CGMCC 4.2055T =DSM 41902T) is proposed as the type strain of the novel species Streptomyces synnematoformans sp. nov.

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Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63070-0 ◽

2004 ◽

Vol 54 (6) ◽

pp. 2121-2129 ◽

Cited By ~ 73

Author(s):

Ingrid Groth ◽

Carlos Rodríguez ◽

Barbara Schütze ◽

Petra Schmitz ◽

Eckhard Leistner ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Trees ◽

Gene Sequence ◽

Sequence Data ◽

16S Rrna Gene Sequence ◽

Morphological Properties ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Phenotypic Data

A polyphasic study was carried out to establish the taxonomic positions of six strains isolated from diverse soil samples and provisionally assigned to the genus Kitasatospora. The isolates were found to have chemical and morphological properties consistent with their classification as Kitasatospora strains. Direct 16S rRNA gene sequence data confirmed the taxonomic position of the strains following the generation of phylogenetic trees by using three tree-making algorithms. Five of the isolates were considered to merit species status using complementary genotypic and phenotypic data. These organisms were designated Kitasatospora arboriphila sp. nov. (HKI 0189T=2291-120T=DSM 44785T=NCIMB 13973T), Kitasatospora gansuensis sp. nov. (HKI 0314T=2050-015T=DSM 44786T=NCIMB 13974T), Kitasatospora nipponensis sp. nov. (HKI 0315T=2148-013T=DSM 44787T=NCIMB 13975T), Kitasatospora paranensis sp. nov. (HKI 0190T=2292-041T=DSM 44788T=NCIMB 13976T) and Kitasatospora terrestris sp. nov. (HKI 0186T=2293-012T=DSM 44789T=NCIMB 13977T). The remaining organism, isolate HKI 0316 (=2122-022=DSM 44790=NCIMB 13978), was considered to be a strain of Kitasatospora kifunensis on the basis of 16S rRNA gene sequence, DNA–DNA relatedness and phenotypic data.

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