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).

Nesterenkonia suensis sp. nov., a haloalkaliphilic actinobacterium isolated from a salt pan

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 41-46 ◽  
Author(s):  
Lucretia Govender ◽  
Lureshini Naidoo ◽  
Mathabatha Evodia Setati
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Salt Pan ◽  
Type Strains

A Gram-positive, non-motile, non-spore-forming actinobacterium designated strain Sua-BAC020T was isolated from brine from Sua salt pan in Botswana. The strain was alkaliphilic and moderately halophilic, displaying optimal growth at 35–37 °C, pH 9 and 2.5 % (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain Sua-BAC020T belonged to the genus Nesterenkonia , sharing 96.2–99.0 % sequence similarity with the type strains of recognized species within this genus. DNA–DNA hybridization with the type strains of species that showed the closest phylogenetic affiliation, Nesterenkonia xinjiangensis (16S rRNA gene sequence similarity, 98.9 %), Nesterenkonia aethiopica (99.0 %), Nesterenkonia halophila (97.5 %), Nesterenkonia flava (97.4 %) and Nesterenkonia halobia (97.2 %), gave relatedness values of 10–45 %. The peptidoglycan type of strain Sua-BAC020T was A4α, l-Lys–Gly–d-Asp. Cells of the isolate contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and unidentified glycolipids as major polar lipids, MK-8, MK-9 and MK-7 were the predominant menaquinones, and the major fatty acids (>10 %) were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C content of strain Sua-BAC020T was 64.8 mol%. Based on DNA–DNA hybridization, and physiological and biochemical tests, strain Sua-BAC020T is distinct from all recognized Nesterenkonia species, suggesting that this strain represents a novel species, for which the name Nesterenkonia suensis sp. nov. is proposed. The type strain is Sua-BAC020T ( = DSM 22748T = NCCB 100309T).

Halobacillus fulvus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi) in Thailand

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Auttaporn Booncharoen ◽  
Wonnop Visessanguan ◽  
Nattakorn Kuncharoen ◽  
Supalurk Yiamsombut ◽  
Pannita Santiyanont ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
Rrna Gene ◽  
Content Type ◽  
Moderately Halophilic ◽  
Link Type ◽  
Moderately Halophilic Bacterium

An aerobic, Gram-stain-positive, endospore-forming, rod-shaped and moderately halophilic strain SKP4-6T, was isolated from shrimp paste (Ka-pi) collected from Samut Sakhon Province, Thailand. Phylogenetic analysis revealed that strain SKP4-6T belonged to the genus Halobacillus and was most closely related to Halobacillus salinus JCM 11546T (98.6 %), Halobacillus locisalis KCTC 3788T (98.6 %) and Halobacillus yeomjeoni KCTC 3957T (98.6 %) based on 16S rRNA gene sequence similarity. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strain SKP4-6T and its related species were 18.2–19.3 % and 69.84–84.51 %, respectively, which were lower than the threshold recommended for species delineation. The strain grew optimally at 30–40 °C, at pH 7.0 and with 10–15 % (w/v) NaCl. It contained l-Orn–d-Asp in the cell wall peptidoglycan. The DNA G+C content was 44.8 mol%. The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The predominant isoprenoid quinone was MK-7. Phosphatidylglycerol and diphosphatidylglycerol were present as major polar lipids. Based on this polyphasic approach, digital DNA–DNA relatedness and ANI values, strain SKP4-6T represents a novel species of the genus Halobacillus , for which the name Halobacillus fulvus sp. nov. is proposed. The type strain is SKP4-6T (=JCM 32624T=TISTR 2595T).

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).

Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2684-2689 ◽  
Author(s):  
V. Venkata Ramana ◽  
P. Shalem Raj ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two strains (JA643T and JA755) of Gram-stain-negative, facultatively anaerobic phototrophic, bacteria capable of growth at low temperatures (10–15 °C) were isolated from freshwater streams from different geographical regions of India. Both strains contain bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid (PL), unidentified amino lipids (AL1–AL6, AL9) and an unidentified lipid (L1) were the polar lipids present in both strains. The major cellular fatty acid was C18 : 1ω7c (76–79 % of the total). Bacteriohopane derivatives (BHD1,2), unidentified hopanoids (UH1–5), diplopterol (DPL) and diploptene (DPE) were the major hopanoids of both strains. The DNA G+C content was 64.2–64.5 mol%. 16S rRNA gene sequence-based phylogenetic analysis showed that both strains are closely related to the genus Rhodomicrobium and clustered with Rhodomicrobium vannielii DSM 162T (99 % sequence similarity). However, both strains exhibited only 46.1 % DNA–DNA hybridization with R. vannielii DSM 162T. Strains JA643T and JA755 shared >99 % 16S rRNA gene sequence similarity and were >85 % related on the basis of DNA–DNA hybridization; they are therefore considered to represent a novel species in the genus Rhodomicrobium , for which the name Rhodomicrobium udaipurense sp. nov. is proposed. The type strain is JA643T ( = KCTC 15219T = NBRC 109057T).

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).

Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae , and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 735-743 ◽  
Author(s):  
Hong Chen ◽  
Mareike Jogler ◽  
Manfred Rohde ◽  
Hans-Peter Klenk ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Dna Hybridization ◽  
Hydroxy Fatty Acid ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Two novel chemo-organoheterotrophic members of the Sphingomonadaceae were isolated from alpine and pre-alpine lakes. Cells stained Gram-negative, were motile and rod-shaped, and formed yellow, circular, convex colonies on different agar media. Strains 301T and 469T were strictly aerobic, catalase- and oxidase-positive, and grew at temperatures between 10 and 40 °C (optimum, 28 °C), and at pH values between 5 and 10 (optimum, pH 7). Both strains contained Q-10 as the dominant quinone, sphingoglycolipids and 2-hydroxymyristic acid, whereas 3-hydroxy fatty acids were absent. Major fatty acids of strain 301T were C18 : 1ω7c (53.3 %) and C16 : 1ω7c (22.9 %), with C14 : 0 2-OH (10.8 %) as the major 2-hydroxy fatty acid. Fatty acids of strain 469T were dominated by C18 : 1ω7c (34.4 %), C16 : 1ω7c (32.0 %) and C14 : 0 2-OH (15.2 %) as the major 2-hydroxy fatty acid. The genomic DNA G+C contents of strains 301T and 469T were 63.4 and 64.6 mol%, respectively. 16S rRNA gene sequence comparison indicated that both strains belonged to the genus Sphingobium . This classification was supported by the presence of spermidine as the major polyamine. The phylogenetically closest relatives of strain 301T were Sphingobium amiense DSM 16289T, Sphingobium vermicomposti DSM 21299T, Sphingobium yanoikuyae DSM 7462T and Sphingobium scionense DSM 19371T (98.8, 98.0, 97.9 and 97.4 % sequence similarity, respectively). DNA–DNA hybridization of genomic DNA yielded similarities in the range 43.2–12.1 % between strain 301T and the type strains of these four Sphingobium species. Closest relatives of strain 469T were Sphingomonas suberifaciens DSM 7465T and Sphingobium scionense DSM 19371T (97.1 and 96.5 % 16S rRNA gene sequence similarity, respectively). The degree of DNA–DNA hybridization between strain 469T and Sphingomonas suberifaciens DSM 7465T was 17.9 %. Based on the results of the molecular analyses and their phenotypic characteristics, strains 301T and 469T represent two novel species of the genus Sphingobium . The name Sphingobium limneticum sp. nov. is proposed for strain 301T( = DSM25076T = LMG 26659T). The name Sphingobium boeckii sp. nov. is proposed for strain 469T ( = DSM 25079T = LMG 26901T). The polyphasic analysis also suggests that Sphingomonas suberifaciens should be reclassified as Sphingobium suberifaciens comb. nov. with Ca1T ( = EY 2404T = ATCC 49355T = CIP 105429T = DSM 7465T = ICMP 12535T = NBRC 15211T = JCM 8521T = LMG 17323T = NCPPB 3629T) as the type strain.

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.

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