scholarly journals Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest

2007 ◽  
Vol 57 (6) ◽  
pp. 1177-1182 ◽  
Author(s):  
Li Zhang ◽  
Zhihong Xu ◽  
Bharat K. C. Patel
Keyword(s):  
Cell Wall ◽  
Fatty Acid ◽  
Leaf Litter ◽  
Cellular Fatty Acid ◽  
Pine Forest ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
A Cell

An aerobic bacterium, designated strain E1HC-02T, was isolated from the decaying leaf litter of a slash pine forest located in southeast Queensland, Australia. Cells of strain E1HC-02T were short irregular rods (0.5–1.0×0.2–0.4 μm) which stained Gram-positive and possessed a cell-wall ultrastructure which appeared to be made of protein subunits. The novel strain grew optimally in 1 % trypticase soy broth (TSB) at 25 °C and at a pH of 9.1. Strain E1HC-02T metabolized a range of carbohydrates, organic acids and amino acids. The G+C content of the DNA was 71±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis of strain E1HC-02T showed that it was a member of the family Microbacteriaceae, phylum Actinobacteria. The cell wall contained a type B2β peptidoglycan, the dominant cellular fatty acid was 18 : 1ω7c and the major hydroxy fatty acid was 2-OH 14 : 0. The major menaquinones were MK-8 (76 %) and MK-7 (24 %) and the glycolipids present were disphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. The chemotaxonomic properties of strain E1HC-02T were distinctly different to all of the 17 genera of the family Microbacteriaceae and hence strain E1HC-02T is designated as representing a novel species of a new genus, Frondicola australicus gen. nov., sp. nov. The type strain of the type species is E1HC-02T (=JCM 13598T=DSM 17894T).

scholarly journals Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (5) ◽  
pp. 941-946 ◽  
Author(s):  
Hidenori Hayashi ◽  
Kensaku Shibata ◽  
Mitsuo Sakamoto ◽  
Shinichi Tomita ◽  
Yoshimi Benno
Keyword(s):  
Fatty Acid ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Phenotypic Characteristics ◽  
Human Faeces ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Fatty Acid Compositions

Six strains (CB7T, CB18, CB23, CB26, CB28 and CB35T) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genus Prevotella and made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related to Prevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related to Prevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of other Prevotella species. Five strains (CB7T, CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35T were MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species, Prevotella copri sp. nov. and Prevotella stercorea sp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7T and CB35T were 45.3 and 48.2 mol%, respectively. The type strains of P. copri and P. stercorea are CB7T (=JCM 13464T=DSM 18205T) and CB35T (=JCM 13469T=DSM 18206T), respectively.

scholarly journals Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque

2005 ◽  
Vol 55 (5) ◽  
pp. 1839-1843 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Makoto Umeda ◽  
Isao Ishikawa ◽  
Yoshimi Benno
Keyword(s):  
Fatty Acid ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Cellular Fatty Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Six bacterial strains isolated from the human oral cavity, PPPA16, PPPA20T, PPPA24, PPPA31, EPPA6 and EPPA7, were characterized by determining phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the isolates represented the same species of the genus Prevotella. The strains were related to Prevotella dentalis with about 89 % similarity. In addition, the isolates were related to Prevotella sp. oral clone IDR-CEC-0032, which is a representative of the numerically dominant cluster VI in carious dentine lesions [Nadkarni et al. (2004). J Clin Microbiol 42, 5238–5244], with about 99 % similarity. The strains were obligately anaerobic, non-pigmenting, non-spore-forming, non-motile, Gram-negative rods. The isolates could be differentiated from other Prevotella species by d-mannitol, d-melezitose, d-sorbitol and d-trehalose fermentation in API 20A tests. The cellular fatty acid composition of strains PPPA16, PPPA20T, PPPA24, PPPA31, EPPA6 and EPPA7 was significantly different from that of other Prevotella species. Compared with other Prevotella species, only these six strains contained dimethyl acetals. The major menaquinones of the clinical isolates were MK-12 and MK-13, whereas the major menaquinones of other Prevotella species were MK-10 and MK-11. On the basis of these data, a novel Prevotella species, Prevotella multisaccharivorax sp. nov., is proposed, with PPPA20T (=JCM 12954T=DSM 17128T) as the type strain.

scholarly journals Methylotenera mobilis gen. nov., sp. nov., an obligately methylamine-utilizing bacterium within the family Methylophilaceae

2006 ◽  
Vol 56 (12) ◽  
pp. 2819-2823 ◽  
Author(s):  
Marina G. Kalyuzhnaya ◽  
Sarah Bowerman ◽  
Jimmie C. Lara ◽  
Mary E. Lidstrom ◽  
Ludmila Chistoserdova
Keyword(s):  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Methylamine Dehydrogenase ◽  
Carbon And Nitrogen ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Lake Washington ◽  
Ribulose Monophosphate Cycle ◽  
Ph Range ◽  
Single Flagellum

A novel obligate methylamine utilizer (strain JLW8T), isolated from Lake Washington sediment, was characterized taxonomically. The isolate was an aerobic, Gram-negative bacterium. Cells were rod-shaped and motile by means of a single flagellum. Reproduction was by binary fission and no resting bodies were formed. Growth was observed within a pH range of 5–8.5, with optimum growth at pH 7.5. It utilized methylamine as a single source of energy, carbon and nitrogen. Methylamine was oxidized via methylamine dehydrogenase and formaldehyde was assimilated via the ribulose monophosphate cycle. The cellular fatty acid profile was dominated by C16 : 0 ω7c and C16 : 0 and the major phospholipid was phosphatidylethanolamine. The DNA G+C content was 54 mol%. 16S rRNA gene sequence analysis indicated that the new isolate was closely related (97–98 % similarity) to a broad group of sequences from uncultured or uncharacterized Betaproteobacteria, but only distantly related (93–96 % similarity) to known methylotrophs of the family Methylophilaceae. Strain JLW8T (=ATCC BAA-1282T=DSM 17540T) is proposed as the type strain of a novel species in a new genus within the family Methylophilaceae, Methylotenera mobilis gen. nov., sp. nov.

Prevotella pleuritidis sp. nov., isolated from pleural fluid

2007 ◽  
Vol 57 (8) ◽  
pp. 1725-1728 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Kiyofumi Ohkusu ◽  
Takayuki Masaki ◽  
Hirofumi Kako ◽  
Takayuki Ezaki ◽  
...  
Keyword(s):  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Cellular Fatty Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A strain isolated from pleural fluid of a patient with suppurative pleuritis (strain GTC 3021T) was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Prevotella. The isolate was related to Prevotella enoeca ATCC 51261T with about 92 % 16S rRNA gene sequence similarity. The strain was an obligately anaerobic, non-pigmenting, non-spore-forming, non-motile, Gram-negative rod. Although the phenotypic and biochemical characteristics of the strain were similar to those of P. enoeca JCM 12259T, the cellular fatty acid composition of the isolate was significantly different from that of P. enoeca JCM 12259T (C18 : 1 ω9c and anteiso-C15 : 0 fatty acid content). Based on these data, we propose a novel Prevotella species, Prevotella pleuritidis sp. nov., with the type strain GTC 3021T (=JCM 14110T =CCUG 54350T). The G+C content of the type strain is 45.4 mol%.

scholarly journals Pseudonocardia Pini Sp. Nov., An Endophytic Actinobacterium Isolated From Roots of the Pine Tree Callitris Preissii

2021 ◽  
Author(s):  
Onuma Kaewkla ◽  
Christopher Milton Mathew Franco
Keyword(s):  
Genome Mining ◽  
South Australia ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Pine Tree ◽  
Gene Sequence Analysis ◽  
Endophytic Actinobacterium ◽  
The Family ◽  
Genes Encoding ◽  
Diamino Acid

Abstract A Gram positive, aerobic, actinobacterial strain with rod-shaped spores, CAP47RT, which was isolated from the surface-sterilized root of a native pine tree (Callitris preissii), South Australia is described. The major cellular fatty acid of this strain was iso-H-C16:1 and major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was identified as meso-diaminopimelic acid. These chemotaxonomic data confirmed the affiliation of strain CAP47RT to the genus Pseudonocardia. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the familyPseudonocardiaceae, being most closely related to Pseudonocardia xishanensis JCM 17906T (98.8%), Pseudonocardia oroxyli DSM 44984T (98.7%),Pseudonocardia thailandensis CMU-NKS-70T (98.7%), and Pseudonocardia ailaonensis DSM 44979T (97.9%). The results of the polyphasic study which contain genome comparisons of ANIb, ANIm and digital DNA-DNA hybridization revealed the differentiation of strain CAP47RT from the closest species with validated names. This strain represents a novel species and the name proposed for this microorganism is Pseudonocardia pini sp. nov., indicating the source of actinobacteria from a pine tree. The type strain is CAP47RT (= DSM 108967T = NRRL B-65534T). Genome mining revealed that this strain contained a variety of genes encoding enzymes to degrade hazard chemicals.

scholarly journals Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment

2006 ◽  
Vol 56 (4) ◽  
pp. 771-776 ◽  
Author(s):  
Dong H. Choi ◽  
Byung C. Cho
Keyword(s):  
Fatty Acid ◽  
Tidal Flat ◽  
Marine Bacterium ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Solid Media ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Type Strains

A rod-shaped marine bacterium, designated strain CL-TF09T, isolated from a tidal flat in Ganghwa, Korea, was characterized based on its physiological and biochemical features, fatty acid profile and phylogenetic position. 16S rRNA gene sequence analysis revealed a clear affiliation with the family Flavobacteriaceae. Strain CL-TF09T showed the closest phylogenetic relationship with the genera Tenacibaculum and Polaribacter; sequence similarities between CL-TF09T and the type strains of Tenacibaculum and Polaribacter species ranged from 90·7 to 91·8 %. Cells of strain CL-TF09T were non-motile and grew on solid media as yellow colonies. The strain grew in the presence of 1–5 % sea salts, within a temperature range of 5–30 °C and at pH 7–8. The strain had iso-C15 : 0 3-OH (17·4 %), iso-C15 : 0 (16·7 %), anteiso-C15 : 0 (15·1 %) and iso-C16 : 0 3-OH (13·4 %) as predominant fatty acids. The DNA G+C content was 33·9 mol%. Based on the physiological, fatty acid composition and phylogenetic data presented, strain CL-TF09T is considered to represent a novel genus and species of the family Flavobacteriaceae, for which the name Lutibacter litoralis gen. nov., sp. nov. is proposed. The type strain is CL-TF09T (=KCCM 42118T=JCM 13034T).

scholarly journals Microbispora clausenae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f.

2020 ◽  
Vol 70 (12) ◽  
pp. 6213-6219
Author(s):  
Onuma Kaewkla ◽  
Wilaiwan Koomsiri ◽  
Arinthip Thamchaipenet ◽  
Christopher Milton Mathew Franco
Keyword(s):  
Medicinal Plant ◽  
Type Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Endophytic Actinobacterium ◽  
The Family

An endophytic actinobacterium, strain CLES2T, was discovered from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f., collected from the Phujong-Nayoa National Park, Ubon Ratchathani Province, Thailand. The results of a polyphasic taxonomic study identified this strain as a member of the genus Microbispora and a Gram-stain-positive, aerobic actinobacterium. It had well-developed substrate mycelia, which were non-motile and possessed paired spores. A phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Streptosporangiaceae , being most closely related to Microbispora bryophytorum NEAU-TX2-2T (99.4 %), Microbispora camponoti 2C-HV3T (99.2 %), Microbispora catharanthi CR1-09T (99.2 %) and Microbispora amethystogenes JCM 3021T and Microbispora fusca NEAU-HEGS1-5T (both at 99.1 %). The major cellular fatty acid of this strain was iso-C16 : 0 and major menaquinone was MK-9(H4). The polar lipid profile of strain CLES2T contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylinositol dimannosides. These chemotaxonomic data confirmed the affiliation of strain CLES2T to the genus Microbispora . The DNA G+C content of this strain was 70 mol%. Digital DNA–DNA hybridization and average nucleotide identity blast values between strain CLES2T and M. catharanthi CR1-09T were 62.4 and 94.0 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain CLES2T from its closest species with valid names. The name proposed for the new species is Microbispora clausenae sp. nov. The type strain is CLES2T (=DSM 101759T=NRRL B-65340T).

scholarly journals Prevotella shahii sp. nov. and Prevotella salivae sp. nov., isolated from the human oral cavity

2004 ◽  
Vol 54 (3) ◽  
pp. 877-883 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Masahito Suzuki ◽  
Yi Huang ◽  
Makoto Umeda ◽  
Isao Ishikawa ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid Composition ◽  
Fatty Acid ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Gene Sequence ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Two bacterial strains, EHS11T and EPSA11T, which were isolated from the human oral cavity, were characterized in terms of phenotypic and biochemical characteristics, cellular fatty acid profiles and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that each of the isolates belonged to a novel species of the genus Prevotella. Strain EHS11T was related to Prevotella loescheii (about 95 % similarity), whereas strain EPSA11T was related to Prevotella oris (about 94 % similarity). Both strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid composition of strain EPSA11T was very similar to that of P. oris JCM 8540T. On the other hand, the cellular fatty acid composition of strain EHS11T was significantly different from those of other Prevotella species. The predominant fatty acids in strain EHS11T are C18 : 1 ω9c, C16 : 0 and C16 : 0 3-OH, whereas other Prevotella species, except for P. loescheii JCM 8530T, possess anteiso-C15 : 0, iso-C17 : 0 3-OH and C18 : 1 ω9c. The predominant fatty acids in P. loescheii JCM 8530T are anteiso-C15 : 0, C16 : 0 and C18 : 1 ω9c. DNA–DNA hybridization experiments revealed a genomic distinction of strains EHS11T and EPSA11T from P. loescheii JCM 8530T and P. oris JCM 8540T. On the basis of these data, two novel Prevotella species are proposed: Prevotella shahii sp. nov. and Prevotella salivae sp. nov. The type strains of P. shahii and P. salivae are EHS11T (=JCM 12083T=DSM 15611T) and EPSA11T (=JCM 12084T=DSM 15606T), respectively.

scholarly journals Auritidibacter ignavus gen. nov., sp. nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of the members of the family Yaniellaceae Li et al. 2008 to the family Micrococcaceae and emended description of the suborder Micrococcineae

2011 ◽  
Vol 61 (2) ◽  
pp. 223-230 ◽  
Author(s):  
A. F. Yassin ◽  
H. Hupfer ◽  
C. Siering ◽  
H.-P. Klenk ◽  
P. Schumann
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Straight Chain ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Emended Description ◽  
A Cell ◽  
Branched Chain

A Gram-reaction-positive, aerobic, catalase-positive, non-spore-forming, rod-shaped bacterium designated IMMIB L-1656T was isolated from an ear swab of a man and characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain IMMIB L-1656T is related to members of the family Micrococcaceae (<95.1 % sequence similarity). Anaylsis using different phylogenetic algorithms consistently grouped strain IMMIB L-1656T with members of the genus Yaniella. The organism posessed a cell-wall murein based on l-lysine (variation A4α, type l-Lys–Gly–l-Glu), MK-10 as the predominant menaquinone and long-chain cellular fatty acids of straight-chain and branched-chain saturated types (with iso-C15 : 0 and anteiso-C17 : 0 predominating). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol in addition to unknown glycolipids. The DNA G+C content was 59.7 mol%. Based on its distinctive genotypic and phenotypic characteristics, strain IMMIB L-1656T represents a novel species in a novel genus, for which the name Auritidibacter ignavus gen. nov., sp. nov. is proposed. We also propose that members of the family Yaniellaceae be transferred to the family Micrococcaceae with amendments to the description of the suborder Micrococcineae. The type strain of Auritidibacter ignavus is IMMIB L-1656T (=DSM 45359T =CCUG 57943T).

scholarly journals Mariniflexile gromovii gen. nov., sp. nov., a gliding bacterium isolated from the sea urchin Strongylocentrotus intermedius

2006 ◽  
Vol 56 (7) ◽  
pp. 1635-1638 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Jangryul Kwak ◽  
Valery V. Mikhailov ◽  
Kyung Sook Bae
Keyword(s):  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Respective Type ◽  
Gliding Bacterium ◽  
Type Strains ◽  
Sequence Similarities

A marine bacterium, designated strain KMM 6038T, was subjected to taxonomic analysis via a polyphasic approach. Cells of the strain were heterotrophic, orange-pigmented, Gram-negative and motile by means of gliding. 16S rRNA gene sequence analysis indicated that strain KMM 6038T was closely related to the type species of the genera Algibacter and Yeosuana, members of the family Flavobacteriaceae, with sequence similarities of 93.8 and 93.6 % to the respective type strains. However, several chemotaxonomic and phenotypic characteristics, such as the cellular fatty acid profile (iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, C15 : 0, C15 : 1 ω6c, iso-C15 : 0 3-OH and iso-C17 : 0 3-OH) and the low G+C content of the DNA (35.7 mol%), indicated that the strain should be separated from these two genera. From the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, the bacterium should be classified as representing a novel genus and species, for which the name Mariniflexile gromovii gen. nov., sp. nov. is proposed. The type strain of Mariniflexile gromovii is KMM 6038T (=KCTC 12570T=LMG 22578T).

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