scholarly journals Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces

2006 ◽  
Vol 56 (10) ◽  
pp. 2437-2441 ◽  
Author(s):  
Sylvia H. Duncan ◽  
Rustam I. Aminov ◽  
Karen P. Scott ◽  
Petra Louis ◽  
Thaddeus B. Stanton ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Good Growth ◽  
Strictly Anaerobic ◽  
16S Rrna Gene Sequences ◽  
Weak Growth ◽  
Curved Rods

Seven recently cultured bacterial isolates, although similar in their 16S rRNA gene sequences to Roseburia intestinalis L1-82T (DSM 14610T), were not sufficiently related for inclusion within existing species, forming three separate clusters in a 16S rRNA gene phylogenetic tree. The isolates, which were obtained from human stools, were Gram-variable or Gram-negative, strictly anaerobic, slightly curved rods; cells from all strains measured approximately 0.5×1.5–5.0 μm and were motile. Two strains belonging to one cluster (A2-181 and A2-183T) were the only strains that were able to grow on glycerol and that failed to grow on any of the complex substrates tested (inulin, xylan and amylopectin). Strains belonging to a second cluster (represented by M6/1 and M72/1T) differed from the other isolates in their ability to grow on sorbitol. Isolates belonging to a third cluster (L1-83 and A2-194T) were the only strains that failed to grow on xylose and that gave good growth on inulin (strains M6/1 and M72/1T gave weak growth). All strains were net acetate utilizers. The DNA G+C contents of representative Roseburia strains A2-183T, A2-194T, M72/1T and R. intestinalis L1-82T were 47.4, 41.4, 42.0 and 42.6 mol%, respectively. Based on 16S rRNA gene sequence similarity, three novel Roseburia species are proposed, with the names Roseburia hominis sp. nov. (type strain A2-183T=DSM 16839T=NCIMB 14029T), Roseburia inulinivorans sp. nov. (type strain A2-194T=DSM 16841T=NCIMB 14030T) and Roseburia faecis sp. nov. (type strain M72/1T=DSM 16840T=NCIMB 14031T).

scholarly journals Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

scholarly journals Pontibacter chinhatensis sp. nov., isolated from pond sediment containing discarded hexachlorocyclohexane isomer waste

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2248-2254 ◽  
Author(s):  
Amit Kumar Singh ◽  
Nidhi Garg ◽  
Rup Lal
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Pond Sediment ◽  
The 16S Rrna Gene

A halotolerant, Gram-negative, rod-shaped and light-red-pigmented bacterium, designated LP51T, was isolated from pond sediment near a hexachlorocyclohexane dumpsite located at Chinhat, Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LP51T formed a distinct phyletic clade along with the members of the genus Pontibacter. The 16S rRNA gene sequence similarity to members of the genus Pontibacter ranged from 94.2 to 99.4  %. The cells were motile, aerobic and catalase- and oxidase-positive. The major fatty acids were iso-C15  :  0 (17.8  %), iso-C15  :  0 3-OH (8.8  %), iso-C17  :  0 3-OH (5.7  %), summed feature 3 (C16  :  1ω7c and/or C16  :  1ω6c; 6.5  %) and summed feature 4 (iso-C17  :  1 I and/or anteiso-C17  :  1 B; 30.7  %). The polar lipid profile of strain LP51T showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, unknown aminolipids, unknown polar lipids and unknown glycolipids. DNA–DNA relatedness of strain LP51T with respect to the most closely related type strain, Pontibacter korlensis X14-1T, was 47.2  %. On the basis of this information, it is proposed that the isolate be assigned to a novel species of the genus Pontibacter, for which the name Pontibacter chinhatensis sp. nov. is proposed. The type strain is LP51T ( = CCM 8436T = MCC 2070T).

Algoriphagus pacificus sp. nov. and Algoriphagus oliviformis sp. nov., isolated from a mariculture fishpond

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Huibin Lu ◽  
Zhipeng Cai ◽  
Tongchu Deng ◽  
Youfeng Qian ◽  
Meiying Xu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, non-flagellated, non-spore-forming and non-motile strains (YJ13CT and H41T) were isolated from a mariculture fishpond in PR China. Comparisons based on 16S rRNA gene sequences indicated that YJ13CT and H41T shared 16S rRNA gene sequences similarities between 92.6 and 99.2 % with species of the genus Algoriphagus . YJ13CT only shared 93.8 % 16S rRNA gene sequence similarity with H41T. The reconstructed phylogenetic and phylogenomic trees indicated that YJ13CT and H41T clustered closely with species of the genus Algoriphagus . The calculated pairwise orthologous average nucleotide identity with usearch (OrthoANIu) values between strains YJ13CT and H41T and other related strains were all less than 79.5 %. The OrthoANIu value between YJ13CT and H41T was only 69.9 %. MK-7 was the predominant respiratory quinone of YJ13CT and H41T and their major cellular fatty acids contained iso-C15 : 0, C16 : 1 ω7c and C17 : 1 ω9c. The polar lipids profiles of YJ13CT and H41T consisted of phosphatidylethanolamine and several kinds of unidentified lipids. Combining the above descriptions, strains YJ13CT and H41T represent two distinct novel species of the genus Algoriphagus , for which the names Algoriphagus pacificus sp. nov. (type strain YJ13CT=GDMCC 1.2178T=KCTC 82450T) and Algoriphagus oliviformis sp. nov. (type strain H41T=GDMCC 1.2179T=KCTC 82451T) are proposed.

scholarly journals Clostridium jejuense sp. nov., isolated from soil

2004 ◽  
Vol 54 (5) ◽  
pp. 1465-1468 ◽  
Author(s):  
Hyunyoung Jeong ◽  
Hana Yi ◽  
Yuji Sekiguchi ◽  
Mizuho Muramatsu ◽  
Yoichi Kamagata ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Monophyletic Clade

A strictly anaerobic, mesophilic, endospore-forming bacterium, designated strain HY-35-12T, was isolated from a soil sample in Jeju, Korea. Cells of this isolate were Gram-positive, motile rods that formed oval to spherical terminal spores. Strain HY-35-12T grew optimally at 30 °C, pH 7·0 and 0–0·5 % (w/v) NaCl. The isolate produced pyruvate, lactate, acetate, formate and hydrogen as fermentation end products from glucose. The G+C content of DNA of the isolate was 41 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism formed a monophyletic clade with Clostridium xylanovorans and Clostridium aminovalericum in cluster XIVa of the genus Clostridium. The closest phylogenetic neighbour was C. xylanovorans, with 96·65 % 16S rRNA gene sequence similarity. Several physiological and chemotaxonomic properties were identified that enable strain HY-35-12T to be distinguished from phylogenetically related clostridia. On the basis of polyphasic characteristics, it is proposed that strain HY-35-12T (=IMSNU 40003T=KCTC 5026T=DSM 15929T) represents a novel species, Clostridium jejuense sp. nov.

scholarly journals Demequina activiva sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2042-2047 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Sung-Min Won ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
South Sea ◽  
Type Strains

A Gram-stain-positive, facultatively anaerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated BS-12MT, was isolated from a tidal flat sediment on the South Sea, South Korea. Strain BS-12MT grew optimally at 35 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain BS-12MT fell within the cluster comprising the type strains of species of the genus Demequina, joining the type strain of Demequina aestuarii with which it shared the highest sequence similarity (98.6 %). It exhibited 16S rRNA gene sequence similarity of 96.1–97.9 % to the type strains of other species of the genus Demequina. The peptidoglycan type of strain BS-12MT was A4β based on l-Orn − l-Ser − d-Glu. Strain BS-12MT contained demethylmenaquinone-9(H4) as the major menaquinone and anteiso-C15:0 and C16:0 as the major fatty acids. The major polar lipids of strain BS-12MT were phosphatidylinositol and phosphatidylinositolmannoside. The DNA G+C content of strain BS-12MT was 70.7 mol% and its DNA–DNA relatedness values with the type strains of five phylogenetically related species of the genus Demequina were 15–34 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain BS-12MT is separate from other species of the genus Demequina. On the basis of the data presented, strain BS-12MT is considered to represent a novel species of the genus Demequina, for which the name Demequina activiva sp. nov. is proposed. The type strain is BS-12MT ( = KCTC 29674T = NBRC 110675T).

scholarly journals Thalassobius maritimus sp. nov., isolated from seawater

2012 ◽  
Vol 62 (1) ◽  
pp. 8-12 ◽  
Author(s):  
Sooyeon Park ◽  
Mi-Hwa Lee ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The Mean ◽  
Type Strains

A Gram-stain-negative, aerobic, motile, rod-shaped bacterial strain, GSW-M6T, was isolated from seawater of Geoje island, Korea, and was subjected to a polyphasic taxonomic study. Strain GSW-M6T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain GSW-M6T clustered with Thalassobius aestuarii, Thalassobius gelatinovorus and Thalassobius mediterraneus. Strain GSW-M6T exhibited 96.2–96.9 % 16S rRNA gene sequence similarity to the type strains of these three Thalassobius species. Strain GSW-M6T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profiles of strain GSW-M6T and the type strains of the three Thalassobius species were similar, with phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid as common major components. The DNA G+C content of strain GSW-M6T was 57 mol%. The mean level of DNA–DNA relatedness between strain GSW-M6T and the type strain of Thalassobius gelatinovorus was 17 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, enabled strain GSW-M6T to be differentiated from recognized species of the genus Thalassobius. On the basis of the data presented, strain GSW-M6T is considered to represent a novel species of the genus Thalassobius, for which the name Thalassobius maritimus sp. nov. is proposed. The type strain is GSW-M6T ( = KCTC 23347T  = CCUG 60021T).

scholarly journals Megasphaera paucivorans sp. nov., Megasphaera sueciensis sp. nov. and Pectinatus haikarae sp. nov., isolated from brewery samples, and emended description of the genus Pectinatus

2006 ◽  
Vol 56 (4) ◽  
pp. 695-702 ◽  
Author(s):  
Riikka Juvonen ◽  
Maija-Liisa Suihko
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Temperature Tolerance ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gene Similarity

Seven unidentified strictly anaerobic, Gram-negative, non-spore-forming bacteria from spoiled beer or the brewery environment were characterized. Based on 16S rRNA gene sequence analyses, all strains were affiliated to the Sporomusa sub-branch of the class ‘Clostridia’. Three of the strains were non-motile cocci, on average 1·5×1·2 μm or 1·2×1·0 μm, occurring mainly singly or in pairs. They shared nearly identical (>99 %) 16S rRNA gene sequences, being most closely related to the species of the Megasphaera–Anaeroglobus group (⩽93·9 % similarity). According to DNA–DNA hybridization results, the coccoid strains represented two genospecies, neither of which was related to any of the recognized Megasphaera species. Several phenotypic characteristics and/or DNA G+C content also differentiated the strains from each other and from their closest relatives. The other four novel strains were motile, slightly curved to helical rods, 0·6−0·8×3−50 μm or more in size. They shared identical 16S rRNA gene sequences and ribofragment patterns. The highest 16S rRNA gene similarity was found between these isolates and Pectinatus cerevisiiphilus ATCC 29359T (95·6 %) and Pectinatus frisingensis ATCC 33332T (93·6 %). The novel strains also differed from recognized Pectinatus species in their sugar utilization, proteolytic activity, catalase activity, antibiotic resistance and temperature tolerance. The results suggest that the bacteria belong to three novel species, for which the names Megasphaera paucivorans sp. nov. (type strain VTT E-032341T=DSM 16981T), Megasphaera sueciensis sp. nov. (type strain VTT E-97791T=DSM 17042T) and Pectinatus haikarae sp. nov. (type strain VTT E-88329T=DSM 16980T) are proposed.

scholarly journals Jeotgalibacillus salarius sp. nov., isolated from a marine saltern, and reclassification of Marinibacillus marinus and Marinibacillus campisalis as Jeotgalibacillus marinus comb. nov. and Jeotgalibacillus campisalis comb. nov., respectively

2010 ◽  
Vol 60 (1) ◽  
pp. 15-20 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Peter Schumann ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Diamino Acid ◽  
Type Strains

A Gram-variable, motile and rod-shaped bacterial strain, ASL-1T, was isolated from a marine saltern located on the coast of the Yellow Sea, Korea. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain ASL-1T clustered with Jeotgalibacillus alimentarius YKJ-13T and that this cluster joined the clade comprising the type strains of two Marinibacillus species. Strain ASL-1T exhibited 16S rRNA gene sequence similarity values of 97.3 % to J. alimentarius YKJ-13T and 96.5 % to the type strains of Marinibacillus marinus and Marinibacillus campisalis. The chemotaxonomic properties of strain ASL-1T were similar to those of one or two of the genera Jeotgalibacillus and Marinibacillus. The peptidoglycan type was A1α linked directly through l-lysine as the diamino acid. Strain ASL-1T contained MK-7 as the predominant menaquinone with the presence of a significant amount of MK-8. The predominant fatty acid was anteiso-C15 : 0. The DNA G+C content was 42.9 mol%. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain ASL-1T could be differentiated from J. alimentarius and the two Marinibacillus species. On the basis of the data presented, strain ASL-1T represents a novel species within the genus Jeotgalibacillus, for which the name Jeotgalibacillus salarius sp. nov. is proposed. The type strain is ASL-1T (=KCTC 13257T=CCUG 56751T). It is also proposed that Marinibacillus marinus and Marinibacillus campisalis be reclassified as Jeotgalibacillus marinus comb. nov. (type strain 581T=DSM 1297T=ATCC 29841T=CCUG 28884T=CIP 103308T=LMG 6930T) and Jeotgalibacillus campisalis comb. nov. (type strain SF-57T=KCCM 41644T=JCM 11810T), respectively.

scholarly journals Paenibacillus pasadenensis sp. nov. and Paenibacillus barengoltzii sp. nov., isolated from a spacecraft assembly facility

2006 ◽  
Vol 56 (7) ◽  
pp. 1509-1514 ◽  
Author(s):  
Shariff Osman ◽  
Masataka Satomi ◽  
Kasthuri Venkateswaran
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Paenibacillus Barengoltzii

Two novel spore-forming, Gram-positive, mesophilic, heterotrophic bacteria representing two novel species were isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) at Pasadena, CA, USA. The incidence of similar strains was examined by screening the growing collection of isolates (~400 strains) obtained from the JPL-SAF using species-specific PCR primer sets designed from the 16S rRNA gene sequences of strains SAFN-016T and SAFN-007T. Phylogenetic analysis of 16S rRNA gene sequences placed these novel isolates within the genus Paenibacillus. Two strains, SAFN-016T and SAFN-125, shared 98 % 16S rRNA gene sequence similarity with Paenibacillus timonensis and 97 % similarity with Paenibacillus macerans. Strain SAFN-007T showed 95.2 % 16S rRNA gene sequence similarity with Paenibacillus kobensis, its nearest phylogenetic neighbour. The results of DNA–DNA hybridization, physiological tests and biochemical analysis allowed genotypic and phenotypic differentiation of the isolates from currently recognized Paenibacillus species. Strain SAFN-007T and strains SAFN-016T and SAFN-125 are representatives of two separate novel species, for which the names Paenibacillus pasadenensis sp. nov. (type strain SAFN-007T=ATCC BAA-1211T=NBRC 101214T) and Paenibacillus barengoltzii sp. nov. (type strain SAFN-016T=ATCC BAA-1209T=NBRC 101215T) are proposed.

scholarly journals Sphingomicrobium aestuariivivum sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2678-2683 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Eun Sun Joo ◽  
Sung-Min Won ◽  
Myung Kyum Kim ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, designated AH-M8T, was isolated from a tidal flat sediment collected from Aphae Island in the south-western sea, South Korea. Strain AH-M8T grew optimally at 35 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0  % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain AH-M8T belonged to the genus Sphingomicrobium, clustering with the type strain of Sphingomicrobium astaxanthinifaciens, with which it shared 99.0 % 16S rRNA gene sequence similarity. Sequence similarities to the type strains of other species of the genus Sphingomicrobium were 95.4–96.0  %. Strain AH-M8T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major polar lipids of strain AH-M8T were phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and one unidentified glycolipid. The major polyamine is triamine sym-homospermidine. The DNA G+C content of strain AH-M8T was 66.7 mol% and its mean DNA–DNA relatedness value with S. astaxanthinifaciens JCM 18551T was 21  %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain AH-M8T is separated from other species of the genus Sphingomicrobium. On the basis of the data presented, strain AH-M8T is considered to represent a novel species of the genus Sphingomicrobium, for which the name Sphingomicrobium aestuariivivum sp. nov. is proposed. The type strain is AH-M8T ( = KCTC 42286T = NBRC 110678T).

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