scholarly journals Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake

2010 ◽  
Vol 60 (6) ◽  
pp. 1358-1365 ◽  
Author(s):  
Martin W. Hahn ◽  
Vojtěch Kasalický ◽  
Jan Jezbera ◽  
Ulrike Brandt ◽  
Jitka Jezberová ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Uncultured Bacteria ◽  
The Family ◽  
Gene Similarity ◽  
Type Strains

A chemo-organotrophic, aerobic, facultatively anaerobic, non-motile strain, MWH-C5T, isolated from the water column of the oligomesotrophic Lake Mondsee (Austria), was characterized phenotypically, phylogenetically and chemotaxonomically. The predominant fatty acids of the strain were C16 : 1 ω7c/ω6c, C16 : 0, C12 : 1 and C8 : 0-3OH, the major quinone was ubiquinone Q-8 and the G+C content of the DNA of the strain was 55.5 mol%. 16S rRNA gene similarity to the closest related type strains was 96.6 % (Curvibacter delicatus LMG 4328T) and 95.7 % (Rhodoferax fermentans FR3T). Phylogenetic analysis of 16S rRNA gene sequences revealed the affiliation of the strain with the family Comamonadaceae (Betaproteobacteria); however, the phylogenetic position of the strain did not support an affiliation to any previously described genus within this family. A family-wide comparison of traits revealed that the strain possesses a unique combination of DNA G+C content, major fatty acids and major 3-hydroxy fatty acid. Furthermore, the strain differs in several traits from the closest related genera. Based on the phylogeny of the strain and differences from closely related genera, we propose to establish the new genus and species Limnohabitans curvus gen. nov., sp. nov. to accommodate this strain. The type strain of Limnohabitans curvus is MWH-C5T (=DSM 21645T =CCUG 56720T). The type strain is closely related to a large number of uncultured bacteria detected by cultivation-independent methods in various freshwater systems.

scholarly journals Sediminibacter furfurosus gen. nov., sp. nov. and Gilvibacter sediminis gen. nov., sp. nov., novel members of the family Flavobacteriaceae

2007 ◽  
Vol 57 (2) ◽  
pp. 265-269 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Okinawa Island ◽  
Phenotypic Differences ◽  
Phylogenetic Studies ◽  
The Family ◽  
The City ◽  
Type Strains

Two Gram-negative, chemoheterotrophic, non-motile strains, Mok-1-36T and MAOS-86T, were isolated from marine-sediment samples collected from the coasts of Okinawa island and the city of Odawara in Japan, respectively. Phylogenetic studies based on 16S rRNA gene sequences indicated that Mok-1-36T and MAOS-86T were members of the family Flavobacteriaceae, clustering with members of the genera Ulvibacter and Vitellibacter, respectively. Strains Mok-1-36T and MAOS-86T shared pairwise 16S rRNA gene sequence similarities of 93.5 and 89.1 % with the type strains of Ulvibacter litoralis and Vitellibacter vladivostokensis, respectively. Phylogenetic distinctiveness and phenotypic differences from their phylogenetic neighbours indicated that these strains represent two novel species and genera within the family Flavobacteriaceae, for which the names Sediminibacter furfurosus gen. nov., sp. nov. (MAOS-86T) and Gilvibacter sediminis gen. nov., sp. nov. (Mok-1-36T) are proposed. The type strain of Sediminibacter furfurosus is MAOS-86T (=NBRC 101622T=CIP 109285T) and the type strain of Gilvibacter sediminis is Mok-1-36T (=NBRC 101626T=CIP 109286T).

scholarly journals Alistipes indistinctus sp. nov. and Odoribacter laneus sp. nov., common members of the human intestinal microbiota isolated from faeces

2010 ◽  
Vol 60 (6) ◽  
pp. 1296-1302 ◽  
Author(s):  
Fumiko Nagai ◽  
Masami Morotomi ◽  
Yohei Watanabe ◽  
Hiroshi Sakon ◽  
Ryuichiro Tanaka
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family ◽  
End Products ◽  
Type Strains

Two anaerobic, non-spore-forming, non-motile, Gram-negative-staining bacteria, strains YIT 12060T and YIT 12061T, were isolated from human faeces. Cells of strain YIT 12060T were coccoid to rod-shaped with round ends, positive for catalase, negative for indole and oxidase production, produced succinic and acetic acids as end products of glucose metabolism in peptone/yeast extract/glucose medium and had a DNA G+C content of 55.2 mol%. The main respiratory quinones were MK-10 (40 %) and MK-11 (57 %). Fatty acid analysis demonstrated the presence of a high concentration of iso-C15 : 0 (56 %). Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to species of the genus Alistipes, with 90.9–92.6 % gene sequence similarities to type strains of this species. Phylogenetic analysis and biochemical data supported the affiliation of strain YIT 12060T to the genus Alistipes of the family ‘Rikenellaceae’. Strain YIT 12060T therefore represents a novel species of the genus Alistipes for which the name Alistipes indistinctus sp. nov. is proposed; the type strain is YIT 12060T (=DSM 22520T=JCM 16068T). Cells of the other isolate, strain YIT 12061T, were pleomorphic rods that were asaccharolytic, catalase- and oxidase-negative, positive for gelatin hydrolysis and indole production, produced small amounts of succinic, acetic and iso-valeric acids as end products of metabolism in peptone/yeast extract medium and had a DNA G+C content of approximately 42.4 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family ‘Porphyromonadaceae’ and related to the type strains of Odoribacter splanchnicus (89.6 %) and Odoribacter denticanis (86.2 %); similarity values with strains of recognized species within the family ‘Porphyromonadaceae’ were less than 84 %. Biochemical data supported the affiliation of strain YIT 12061T to the genus Odoribacter. Strain YIT 12061T therefore represents a novel species for which the name Odoribacter laneus sp. nov. is proposed; the type strain is YIT 12061T (=DSM 22474T=JCM 16069T).

scholarly journals Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.

2004 ◽  
Vol 54 (6) ◽  
pp. 2163-2167 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Dna Relatedness ◽  
Gene Similarity ◽  
Type Strains

A Gram-variable, endospore-forming moderately halophilic rod, strain SF-121, was isolated from a marine solar saltern of the Yellow Sea in Korea. The result of 16S rRNA gene sequence analysis showed that strain SF-121 has highest sequence similarity (99·7 %) with the type strain of Bacillus halodenitrificans. Phylogenetic analyses based on 16S rRNA gene sequences revealed that B. halodenitrificans DSM 10037T and strain SF-121 are more closely related to the genus Virgibacillus than to the genus Bacillus. Strain SF-121 and B. halodenitrificans DSM 10037T exhibited 16S rRNA gene similarity levels of 95·3–97·5 % with the type strains of Virgibacillus species and 94·0 % with the type strain of Bacillus subtilis. DNA–DNA relatedness and phenotypic data indicated that B. halodenitrificans DSM 10037T and strain SF-121 are members of the same species. B. halodenitrificans DSM 10037T and strain SF-121 exhibited DNA–DNA relatedness values of 9–11 % with the type strains of Virgibacillus carmonensis and Virgibacillus marismortui. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genetic data, B. halodenitrificans should be reclassified in the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.

scholarly journals Hymenobacter yonginensis sp. nov., isolated from a mesotrophic artificial lake

2011 ◽  
Vol 61 (7) ◽  
pp. 1511-1514 ◽  
Author(s):  
Yochan Joung ◽  
Sung-Heun Cho ◽  
Haneul Kim ◽  
Seung Bum Kim ◽  
Kiseong Joh
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Artificial Lake ◽  
Type Strains

A non-motile, red-pigmented bacterium, designated strain HMD1010T, was isolated from an artificial lake located within the campus of Hankuk University of Foreign Studies, Yongin, Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1010T formed a lineage within the genus Hymenobacter and was closely related to the type strains of Hymenobacter rigui (96.7 % sequence similarity) and H. gelipurpurascens (95.6 %). The major fatty acids were C16 : 1ω5c (21.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %), iso-C15 : 0 (14.5 %) and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I; 11.9 %). The DNA G+C content was 60.4 mol%. On the basis of the evidence presented in this study, strain HMD1010T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter yonginensis sp. nov. was proposed. The type strain is HMD1010T ( = KCTC 22745T  = CECT 7546T).

Reticulibacter mediterranei gen. nov., sp. nov., within the new family Reticulibacteraceae fam. nov., and Ktedonospora formicarum gen. nov., sp. nov., Ktedonobacter robiniae sp. nov., Dictyobacter formicarum sp. nov. and Dictyobacter arantiisoli sp. nov., belonging to the class Ktedonobacteria

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Shuhei Yabe ◽  
Yu Zheng ◽  
Chiung-mei Wang ◽  
Yasuteru Sakai ◽  
Keietsu Abe ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
New Family ◽  
The Family ◽  
Gene Similarity

The aerobic, Gram-positive, mesophilic Ktedonobacteria strains, Uno17T, SOSP1-1T, 1-9T, 1-30T and 150040T, formed mycelia of irregularly branched filaments, produced spores or sporangia, and numerous secondary metabolite biosynthetic gene clusters. The five strains grew at 15–40 °C (optimally at 30 °C) and pH 4.0–8.0 (optimally at pH 6.0–7.0), and had 7.21–12.67 Mb genomes with 49.7–53.7 mol% G+C content. They shared MK9(H2) as the major menaquinone and C16 : 1-2OH and iso-C17 : 0 as the major cellular fatty acids. Phylogenetic and phylogenomic analyses showed that Uno17T and SOSP1-9T were most closely related to members of the genus Dictyobacter , with 94.43–96.21 % 16S rRNA gene similarities and 72.16–81.56% genomic average nucleotide identity. The strain most closely related to SOSP1-1T and SOSP1-30T was Ktedonobacter racemifer SOSP1-21T, with 91.33 and 98.84 % 16S rRNA similarities, and 75.13 and 92.35% average nucleotide identities, respectively. Strain 150040T formed a distinct clade within the order Ktedonobacterales , showing <90.47 % 16S rRNA gene similarity to known species in this order. Based on these results, we propose: strain 150040T as Reticulibacter mediterranei gen. nov., sp. nov. (type strain 150 040T=CGMCC 1.17052T=BCRC 81202T) within the family Reticulibacteraceae fam. nov. in the order Ktedonobacterales ; strain SOSP1-1T as Ktedonospora formicarum gen. nov., sp. nov. (type strain SOSP1-1T=CGMCC 1.17205T=BCRC 81203T) and strain SOSP1-30T as Ktedonobacter robiniae sp. nov. (type strain SOSP1-30T=CGMCC 1.17733T=BCRC 81205T) within the family Ktedonobacteraceae ; strain Uno17T as Dictyobacter arantiisoli sp. nov. (type strain Uno17T=NBRC 113155T=BCRC 81116T); and strain SOSP1-9T as Dictyobacter formicarum sp. nov. (type strain SOSP1-9T=CGMCC 1.17206T=BCRC 81204T) within the family Dictyobacteraceae .

scholarly journals Lutibacter holmesii sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Lutibacter

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3991-3996 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Stefanie Van Trappen ◽  
Natalia V. Zhukova ◽  
Paul De Vos
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Urchin ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Strongylocentrotus Intermedius ◽  
The Family ◽  
Type Strains

Seven Gram-staining-negative, strictly aerobic, pale-yellow-pigmented, rod-shaped and non-motile strains were isolated from the sea urchin Strongylocentrotus intermedius collected from Troitsa Bay, Sea of Japan. Phylogenetic analyses based on 16S rRNA gene sequences showed that these isolates were affiliated with the family Flavobacteriaceae. The novel isolates showed 99.9–100 % 16S rRNA gene sequence similarity to each other and were closely related to the type strains of the recognized members of the genus Lutibacter with sequence similarities of 95.8–98.4 %. The G+C content of the genomic DNA was 35–36 mol%. DNA–DNA relatedness among the sea urchin isolates was 95–99 % and between strain KMM 6277T and its most closely related type strains, Lutibacter agarilyticus KCTC 23842T and Lutibacter litoralis JCM 13034T, was 38 and 27 %, respectively. The prevalent fatty acids were iso-C15 : 0, anteiso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c fatty acids), iso-C15 : 1 and C15 : 0. The polar lipid profile was composed of the phosphatidylethanolamine, one unknown aminolipid and one unknown lipid. The main respiratory isoprenoid quinone was MK-6.The results of phylogenetic, phenotypic and genotypic analyses indicated that the novel strains represent a novel species within the genus Lutibacter, for which the name Lutibacter holmesii sp. nov. is proposed. The type strain is KMM 6277T ( = CCUG 62221T = LMG 26737T).

scholarly journals Terrabacter aeriphilus sp. nov., isolated from an air sample

2010 ◽  
Vol 60 (5) ◽  
pp. 1130-1134 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Jung-A. Son ◽  
Seung-Hee Yoo ◽  
Byung-Yong Kim ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Air Sample ◽  
Type Strains

A novel actinomycete, designated strain 5414T-18T, was isolated from an air sample collected from the Taean region, Korea. The strain contained oxidase and grew in the presence of 7 % NaCl. A neighbour-joining tree constructed on the basis of the 16S rRNA gene sequence showed that strain 5414T-18T is a member of the genus Terrabacter, sharing 97.8–98.3 % 16S rRNA gene sequence similarities to type strains of species of the genus Terrabacter (98.3 % sequence similarity with Terrabacter lapilli LR-26T). It contained peptidoglycan containing ll-diaminopimelic acid of A3γ type, with three glycine residues as the interpeptide bridge. Whole-cell sugars were glucose, mannose and ribose. Mycolic acids were absent. The predominant menaquinone was MK-8(H4). The major fatty acids (>7 % of total fatty acids) were iso-C15 : 0, iso-C16 : 0, C17 : 1 ω8c and iso-C14 : 0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and an unidentified phosphoglycolipid. The DNA G+C content of the type strain was 73 mol%. Strain 5414T-18T exhibited DNA–DNA relatedness levels of 44, 43, 39, 34 and 34 % to the type strains of Terrabacter lapilli, Terrabacter aerolatus, Terrabacter terrae, Terrabacter tumescens and Terracoccus luteus, respectively. These findings suggest that strain 5414T-18T represents a novel species within the genus Terrabacter. The name Terrabacter aeriphilus sp. nov. is proposed for this novel species, with the type strain 5414T-18T (=KACC 20693T=DSM 18563T).

scholarly journals Halobacillus dabanensis sp. nov. and Halobacillus aidingensis sp. nov., isolated from salt lakes in Xinjiang, China

2005 ◽  
Vol 55 (5) ◽  
pp. 1991-1996 ◽  
Author(s):  
W. Y. Liu ◽  
J. Zeng ◽  
L. Wang ◽  
Y. T. Dou ◽  
S. S. Yang
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Salt Lakes ◽  
Rrna Gene ◽  
Dna Relatedness ◽  
Type Strains

Two moderately halophilic spore-forming bacteria were isolated from salt lakes in the Xinjiang region of China. The two strains, designated AD-6T and D-8T, were aerobic, Gram-positive, rod-shaped and motile by means of peritrichous flagella. Strains AD-6T and D-8T grew in the presence of 0·5–20 % and 0·5–25 % (w/v) NaCl in complex medium, respectively. Their cell-wall peptidoglycan was of the l-orn–d-Asp type. The major menaquinone found in both strains was menaquinone-7 (MK-7). The fatty acid profile contained a large amount of branched fatty acids; the main fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. The DNA G+C content of strains D-8T and AD-6T was 41·4 and 42·2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains D-8T and AD-6T were located in the genus Halobacillus. Levels of 16S rRNA gene sequence similarity between the isolated strains and the type strains of Halobacillus species were in the range 96·2–99·5 %. DNA–DNA relatedness values of 17·0–52·2 % were found between the two strains and other Halobacillus species. The DNA–DNA relatedness value between D-8T and AD-6T was 50·6 %. On the basis of phenotypic and chemotaxonomic properties, phylogenetic analysis and genomic distinctiveness, strains D-8T and AD-6T should be placed in the genus Halobacillus as two novel species, for which the names Halobacillus dabanensis sp. nov. (type strain=JCM 12772T=CGMCC 1.3704T) and Halobacillus aidingensis sp. nov. (type strain=JCM 12771T=CGMCC 1.3703T) are proposed, respectively.

scholarly journals Nocardioides panacihumi sp. nov., isolated from soil of a ginseng field

2007 ◽  
Vol 57 (9) ◽  
pp. 2143-2146 ◽  
Author(s):  
Dong-Shan An ◽  
Wan-Taek Im ◽  
Sung-Taik Lee ◽  
Min-Ho Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
The Family ◽  
Established Species ◽  
Type Strains

A novel bacterial strain designated Gsoil 616T was isolated from a soil sample of a ginseng field in Pocheon province (South Korea) and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-positive, strictly aerobic, non-motile, non-spore-forming and rod- or coccoid-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Nocardioides in the family Nocardioidaceae but was clearly separated from established species of this genus. The 16S rRNA gene sequence similarities between strain Gsoil 616T and the type strains of Nocardioides species with validly published names ranged from 91.8 to 96.1 %. The G+C content of the genomic DNA was 73 mol%. Phenotypic and chemotaxonomic data [major menaquinone MK-8(H4) and major fatty acid iso-C16 : 0] supported the affiliation of strain Gsoil 616T to the genus Nocardioides. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate from other Nocardioides species. Therefore, strain Gsoil 616T represented a novel species within the genus Nocardioides, for which the name Nocardioides panacihumi sp. nov. is proposed. The type strain is Gsoil 616T (=KCTC 19187T =DSM 18660T).

Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov., isolated from a tidal flat

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Sooyeon Park ◽  
Jung-Sook Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Genomic Sequences ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

Two Gram-stain-negative and non-flagellated bacteria, YSTF-M3T and YSTF-M6T, were isolated from a tidal flat from Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strains YSTF-M3T and YSTF-M6T belong to the genera Kordia and Olleya of the family Flavobacteriaceae , respectively. The 16S rRNA gene sequence similarities between strain YSTF-M3T and the type strains of Kordia species and between strain YSTF-M6T and the type strains of Olleya species were 94.1–98.4 and 97.3–98.3 %, respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M3T and the type strains of five Kordia species and between those of strain YSTF-M6T and the type strains of three Olleya species were in ranges of 77.0–83.2 and 20.7–27.1 % and 79.4–81.5 and 22.3–23.9 %, respectively. The DNA G+C contents of strain YSTF-M3T and YSTF-M6T from genomic sequences were 34.1 and 31.1 %, respectively. Both strains contained MK-6 as predominant menaquinone and phosphatidylethanolamine as only major phospholipid identified. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strains YSTF-M3T and YSTF-M6T are separated from recognized species of the genera Kordia and Olleya , respectively. On the basis of the data presented, strains YSTF-M3T (=KACC 21639T=NBRC 114499T) and YSTF-M6T (=KACC 21640T=NBRC 114500T) are considered to represent novel species of the genera Kordia and Olleya , respectively, for which the names Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov. are proposed.

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