scholarly journals Treponema peruense sp. nov., a commensal spirochaete isolated from human faeces

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Claire Belkhou ◽  
Raul Tito Tadeo ◽  
Rodrigo Bacigalupe ◽  
Mireia Valles-Colomer ◽  
Samuel Chaffron ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Species Delineation ◽  
Faecal Microbiota ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812T) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete Treponema succinifaciens (89.48 %). Average nucleotide identity values between strain RCC2812T and all available Treponema genomes from validated type strains were all <73 %, thus clearly lower than the species delineation threshold. The DNA G+C content of RCC2812T was 41.24 mol%. Phenotypic characterization using the API-ZYM and API 20A systems confirmed the divergent position of this bacterium within the genus Treponema . Strain RCC2812T could be differentiated from the phylogenetically most closely related T. succinifaciens by the presence of alkaline phosphatase and α -glucosidase activities. Unlike T. succinifaciens , strain RCC2812T grew equally well with or without serum. Strain RCC2812T is the first commensal Treponema isolated from the human faecal microbiota of remote populations, and based on the collected data represents a novel Treponema species for which the name Treponema peruense sp. nov. is proposed. The type strain is RCC2812T (=LMG 31794T=CIP 111910T).

scholarly journals Streptomyces catbensis sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2146-2151 ◽  
Author(s):  
Yayoi Sakiyama ◽  
Nguyen M. Giang ◽  
Shinji Miyadoh ◽  
Dao Thi Luong ◽  
Duong Van Hop ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Biochemical Traits ◽  
Content Type ◽  
Link Type ◽  
Type Strains ◽  
Physiological And Biochemical

Strain VN07A0015T was isolated from soil collected on Cat Ba Island, Vietnam. The taxonomic position of strain VN07A0015T was near Streptomyces aomiensis M24DS4T (98.5 % 16S rRNA gene sequence similarity) and Streptomyces scabrisporus NBRC 100760T (95.6 %), and it clustered within them; however, this cluster was distant from the type strains of other species of the genus Streptomyces . The aerial mycelia of strain VN07A0015T were greyish and formed imperfect spiral spore chains (retinaculiaperti type) with smooth-surfaced spores. The morphological features of strain VN07A0015T were different from those of the type strains of S. aomiensis and S. scabrisporus . The chemotaxonomic characteristics of strain VN07A0015T were typical for all members of the genus Streptomyces , which possessed ll-type diaminopimelic acid, menaquinone MK-9(H6, H8) and the major fatty acids iso-C16 : 0 and iso-C15 : 0. DNA–DNA relatedness between strain VN07A0015T and S. aomiensis NBRC 106164T was less than 30 %. In addition, some physiological and biochemical traits differed from those of S. aomiensis . Therefore, we propose that strain VN07A0015T be classified in the genus Streptomyces as a representative of Streptomyces catbensis sp. nov. (type strain VN07A0015T = VTCC-A-1889T = NBRC 107860T).

Lysinibacillus manganicus sp. nov., isolated from manganese mining soil

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3568-3573 ◽  
Author(s):  
Hongliang Liu ◽  
Yumei Song ◽  
Fang Chen ◽  
Shixue Zheng ◽  
Gejiao Wang
Keyword(s):  
Cell Wall ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Mining Soil ◽  
Link Type ◽  
Type Strains

A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain Mn1-7T, was isolated from manganese mining soil in Tianjin, China. The closest phylogenetic relatives were Lysinibacillus massiliensis CCUG 49529T (97.2 % 16S rRNA gene sequence similarity), L. xylanilyticus XDB9T (96.7 %), L. sinduriensis JCM 15800T (96.2 %), L. odysseyi NBRC 100172T (95.9 %) and L. boronitolerans NBRC 103108T (95.4 %) (the type species of the genus). DNA–DNA hybridization values for strain Mn1-7T with the type strains of L. massiliensis and L. sinduriensis were 24.9 and 27.7 %, respectively. The genomic DNA G+C content was 38.4 mol%. The major menaquinone was MK-7 and the major fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall peptidoglycan was type A4α (l-Lys–d-Asp), and the predominant cell-wall sugar was xylose. DNA–DNA hybridization results and comparison of phenotypic and chemotaxonomic characters between strain Mn1-7T and the phylogenetically most closely related strains revealed that the isolate represents a novel species of the genus Lysinibacillus , for which the name Lysinibacillus manganicus sp. nov. is proposed. The type strain is Mn1-7T ( = DSM 26584T = CCTCC AB 2012916T).

Devosia equisanguinis sp. nov., isolated from horse blood

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
Dominique Clermont ◽  
Alexis Criscuolo ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Horse Blood ◽  
Type Strains

A Gram-stain-negative, aerobic, non-endospore-forming organism isolated from horse blood was studied for its taxonomic allocation. On the basis of 16S rRNA gene sequence similarity comparisons, strain M6-77T grouped within the genus Devosia and was most closely related to Devosia elaeis (97.6 %) and Devosia indica (97.55 %). The 16S rRNA gene sequence similarity to type strains of other Devosia species was below 97.5 %. The average nucleotide identity and digital DNA–DNA hybridization values between the M6-77T genome assembly and those of the closest relative Devosia type strains were <85 and <25 %, respectively. Strain M6-77T grew optimally at 25–37 °C (range: 10–36 °C), at a pH range of pH 6.5–10.5 and in the presence of up to 3 % (w/v) NaCl. The fatty acid profile from whole-cell hydrolysates supported the allocation of the strain to the genus Devosia . Major fatty acids were C18 : 1  ω7c, 11-methyl C18 : 1  ω7c and C16 : 0. The quinone system consisted exclusively of ubiquinone Q-10. The polar lipid profile was composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. In the polyamine pattern, putrescine was predominant and spermidine was detected in moderate amounts. The diamino acid of the peptidoglycan was meso-diaminopimelic acid. In addition, the results of physiological and biochemical tests also allowed phenotypic differentiation of strain M6-77T from the closely related species. Hence, M6-77T represents a new species of the genus Devosia , for which we propose the name Devosia equisanguinis sp. nov., with M6-77T (=CIP 111628T=LMG 30659T=CCM 8868T) as the type strain.

Jannaschia faecimaris sp. nov., isolated from a tidal flat sediment

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 945-951 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, non-motile, rod- or coccoid-shaped bacterial strain, designated HD-22T, belonging to the class Alphaproteobacteria , was isolated from a tidal flat sediment of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HD-22T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HD-22T fell within the clade comprising species of the genus Jannaschia , clustering with the type strains of Jannaschia helgolandensis , Jannaschia donghaensis and Jannaschia rubra , with which it exhibited highest 16S rRNA gene sequence similarity (97.6–98.2 %). Levels of 16S rRNA gene sequence similarity between strain HD-22T and the type strains of the other species of the genus Jannaschia were in the range 94.4–97.5 %. The DNA G+C content was 64.6 mol% and mean DNA–DNA relatedness values between strain HD-22T and the type strains of J. helgolandensis , J. donghaensis and J. rubra were 42.1, 40.1 and 27.0 %, respectively. Strain HD-22T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, demonstrated that strain HD-22T is distinguishable from recognized species of the genus Jannaschia . On the basis of the data presented, strain HD-22T is considered to represent a novel species of the genus Jannaschia , for which the name Jannaschia faecimaris sp. nov. is proposed. The type strain is HD-22T ( = KCTC 32179T = CCUG 63415T).

Loktanella sediminilitoris sp. nov., isolated from tidal flat sediment

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4118-4123 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, designated D1-W3T, was isolated from tidal flat sediment of the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain D1-W3T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Neighbour-joining phylogenetic analyses based on 16S rRNA gene sequences revealed that strain D1-W3T fell within the clade comprising species of the genus Loktanella , clustering with the type strains of Loktanella tamlensis , Loktanella rosea and Loktanella maricola , with which it exhibited the highest 16S rRNA gene sequence similarity values (98.1–98.2 %). The 16S rRNA gene sequence similarity values between strain D1-W3T and the type strains of other species of the genus Loktanella were in the range 93.5–96.5 %. The DNA G+C content of strain D1-W3T was 58.1 mol% and the mean DNA–DNA hybridization values with L. tamlensis KCTC 12722T, L. rosea LMG 22534T and L. maricola DSW-18T were 13–25 %. Strain D1-W3T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and one unidentified aminolipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, showed that strain D1-W3T could be differentiated from other species of the genus Loktanella . On the basis of the data presented, strain D1-W3T represents a novel species of the genus Loktanella , for which the name Loktanella sediminilitoris sp. nov. is proposed. The type strain is D1-W3T ( = KCTC 32383T = CECT 8284T).

Reclassification of Lactobacillus kimchii and Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2383-2387 ◽  
Author(s):  
Huili Pang ◽  
Maki Kitahara ◽  
Zhongfang Tan ◽  
Yanping Wang ◽  
Guangyong Qin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Characterization and identification of strain CW 1 ( = JCM 17161) isolated from corn silage were performed. Strain CW 1 was a Gram-positive, catalase-negative and homofermentative rod that produced the dl-form of lactic acid. This strain exhibited more than 99.6 % 16S rRNA gene sequence similarity and greater than 82 % DNA–DNA reassociation with type strains of Lactobacillus kimchii , L. bobalius and L. paralimentarius . To clarify the taxonomic positions of these type strains, phenotypic characterization, 16S rRNA gene sequencing, ribotyping and DNA–DNA relatedness were examined. The three type strains displayed different l-arabinose, lactose, melibiose, melezitose, raffinose and N-acetyl-β-glucosaminidase fermentation patterns. Phylogenetic analysis showed that L. paralimentarius is a closer neighbour of L. kimchii and L. bobalius , sharing 99.5–99.9 % 16S rRNA gene sequence similarity, which was confirmed by the high DNA–DNA relatedness (≥82 %) between L. paralimentarius JCM 10415T, L. bobalius JCM 16180T and L. kimchii JCM 10707T. Therefore, it is proposed that L. kimchii and L. bobalius should be reclassified as later synonyms of L. paralimentarius .

scholarly journals Actinoplanes abujensis sp. nov., isolated from Nigerian arid soil

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 960-965 ◽  
Author(s):  
Anil Sazak ◽  
Nevzat Sahin ◽  
Mustafa Camas
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Arid Soil ◽  
Link Type ◽  
Type Strains

A novel actinobacterial strain, A4029T, isolated from arid soil of Abuja, Nigeria, and provisionally assigned to the genus Actinoplanes , was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence similarity studies showed that strain A4029T belonged to the genus Actinoplanes , being most closely related to Actinoplanes brasiliensis DSM 43805T (98.9 %) and Actinoplanes deccanensis DSM 43806T (98.0 %); similarity to other type strains of the genus Actinoplanes ranged from 96.2 to 97.9 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol; characteristic sugars arabinose and xylose; major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, C17 : 1ω9c and iso-C14 : 0] confirmed the affiliation of strain A4029T to the genus Actinoplanes . The results of DNA–DNA hybridizations and phylogenetic analysis, together with phenotypic and biochemical test data, allowed strain A4029T to be differentiated from strains of other Actinoplanes species. Therefore, strain A4029T represents a novel species, for which the name Actinoplanes abujensis sp. nov. is proposed, with A4029T ( = DSM 45518T = NRRL B-24835T = KCTC 19984T) as the type strain.

scholarly journals Defluviimonas aquaemixtae sp. nov., isolated from the junction between a freshwater spring and the ocean

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4191-4197 ◽  
Author(s):  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Freshwater Spring ◽  
Type Strains

A Gram-stain-negative, coccoid- or short-rod-shaped and non-gliding bacterial strain, designated CDM-7T, was isolated from the zone where the ocean meets a freshwater spring at Jeju island, South Korea, and was subjected to a polyphasic taxonomic study. Strain CDM-7T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain CDM-7T falls within the clade comprising species of the genus Defluviimonas, clustering with the type strain of Defluviimonas aestuarii , with which it exhibited the highest 16S rRNA gene sequence similarity value (98.4 %). The 16S rRNA gene sequence similarity values between strain CDM-7T and the type strains of Defluviimonas denitrificans and Defluviimonas indica were 97.1 and 96.2 %, respectively. The genomic DNA G+C content was 66.8 mol% and the mean DNA–DNA relatedness values between strain CDM-7T and the type strains of D. aestuarii and D. denitrificans were 15.6±2.5 and 6.7±3.2 %, respectively. Strain CDM-7T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain CDM-7T is distinguishable from other species of the genus Defluviimonas . On the basis of the data presented, strain CDM-7T is considered to represent a novel species of the genus Defluviimonas , for which the name Defluviimonas aquaemixtae sp. nov. is proposed. The type strain is CDM-7T ( = KCTC 42108T = CECT 8626T).

Desulfosporosinus burensis sp. nov., a spore-forming, mesophilic, sulfate-reducing bacterium isolated from a deep clay environment

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 593-598 ◽  
Author(s):  
Bruno Mayeux ◽  
Marie-Laure Fardeau ◽  
Manon Bartoli-Joseph ◽  
Laurie Casalot ◽  
Agnès Vinsot ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type ◽  
Physiological Properties ◽  
Curved Rod ◽  
Type Strains

A novel anaerobic, Gram-positive, spore-forming, curved rod-shaped, mesophilic and sulfate-reducing bacterium was isolated from pore water collected in a borehole at −490 m in Bure (France). This strain, designated BSREI1T, grew at temperatures between 5 °C and 30 °C (optimum 25 °C) and at a pH between 6 and 8 (optimum 7). It did not require NaCl for growth, but tolerated it up to 1.5 % NaCl. Sulfate, thiosulfate and elemental sulfur were used as terminal electron acceptors. Strain BSREI1T used crotonate, formate, lactate, pyruvate, fructose, glycerol and yeast extract as electron donors in the presence of sulfate. The sole quinone was MK-7. The G+C content of the genomic DNA was 43.3 mol%. Strain BSREI1T had the type strains of Desulfosporosinus lacus (16S rRNA gene sequence similarity of 96.83 %), Desulfosporosinus meridiei (96.31 %) and Desulfosporosinus hippei (96.16 %) as its closest phylogenetic relatives. On the basis of phylogenetic and physiological properties, strain BSREI1T is proposed as a representative of a novel species of the genus Desulfosporosinus , Desulfosporosinus burensis sp. nov.; the type strain is BSREI1T ( = DSM 24089T = JCM 17380T).

scholarly journals Rhodovulum mangrovi sp. nov., a phototrophic alphaproteobacterium isolated from a mangrove forest sediment sample

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3168-3173 ◽  
Author(s):  
P. Nupur ◽  
T. N. R. Srinivas ◽  
S. Takaichi ◽  
P. Anil Kumar
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Electron Donors ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A novel Gram-staining-negative, purple non-sulfur bacterium, strain AK41T, was isolated from a sediment sample collected from Coringa mangrove forest, Andhra Pradesh, India. A red–brownish-coloured culture was obtained on modified Pfennig medium after enrichment with 2 % NaCl and 0.3 % pyruvate under 2000 lx illumination. Individual cells were ovoid–rod-shaped and non-motile. Bacteriochlorophyll a and carotenoids of the spheroidene series were present as photosynthetic pigments. Strain AK41T was halophilic and grew photoheterotrophically with a number of organic compounds as carbon sources and electron donors. It was unable to grow photoautotrophically. It did not utilize sulfide or thiosulfate as electron donors. The fatty acids were found to be dominated by C16 : 0 and C18 : 1ω7c. Strain AK41T contained phosphatidylglycerol, phosphatidylethanolamine, an unknown aminolipid and four unknown lipids as polar lipids. Q-10 was the predominant respiratory quinone. The DNA G+C content of strain AK41T was 68.9 mol%. 16S rRNA gene sequence analysis indicated that strain AK41T was a member of the genus Rhodovulum and was closely related to Rhodovulum sulfidophilum , with 96.0 % similarity to the type strain; the 16S rRNA gene sequence similarity to the type strains of other species of the genus Rhodovulum was 93.9–95.8 %. Phylogenetic analyses indicated that strain AK41T clustered with the type strains of Rhodovulum marinum , Rdv. kholense , Rdv. sulfidophilum and Rdv. visakhapatnamense with sequence similarity of 95.9–96.2 %. Based on data from the current study, strain AK41T is proposed to represent a novel species of the genus Rhodovulum , for which the name Rhodovulum mangrovi sp. nov. is proposed. The type strain of Rhodovulum mangrovi is AK41T ( = MTCC 11825T = JCM 19220T).

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