Peptoniphilus methioninivorax sp. nov., a Gram-positive anaerobic coccus isolated from retail ground beef

2011 ◽  
Vol 61 (8) ◽  
pp. 1962-1967 ◽  
Author(s):  
Alejandro P. Rooney ◽  
James L. Swezey ◽  
Rüdiger Pukall ◽  
Peter Schumann ◽  
Stefan Spring
Keyword(s):  
Carbon Source ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sole Carbon Source ◽  
Sequence Similarity ◽  
Ground Beef ◽  
Source Analysis ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Gram Positive

Strain NRRL B-23883T was isolated from retail ground beef as part of a study on the genetic diversity of Clostridium perfringens. The strain was found to be a strictly anaerobic, Gram-positive coccus that was able to utilize peptone as a sole carbon source. Analysis of the 16S rRNA gene sequence revealed that the strain was closely related to species within the genera Peptoniphilus and Anaerosphaera, but it was substantially different from the closest recognized species by nearly 10 % sequence divergence. The strain was also found to be closely related (>99 % sequence similarity) to an uncultured bacterial strain that was sequenced from a 16S rRNA gene clone library constructed to characterize the bacterial community of faeces from a captive spotted hyena. Strain NRRL B-23883T shared the peptidoglycan type A4β, l-Orn–d-Glu with members of the genus Peptoniphilus. Further phenotypic analysis revealed that strain NRRL B-23883T was able to utilize glycyl l-methionine as a sole carbon source, in contrast to other species of the genus Peptoniphilus. Therefore, it is proposed that the isolate represents a novel species, Peptoniphilus methioninivorax sp. nov.; the type strain is NRRL B-23883T ( = DSM 22461T).

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 Clostridium lundense sp. nov., a novel anaerobic lipolytic bacterium isolated from bovine rumen

2006 ◽  
Vol 56 (3) ◽  
pp. 625-628 ◽  
Author(s):  
Dores G. Cirne ◽  
Osvaldo D. Delgado ◽  
Sankar Marichamy ◽  
Bo Mattiasson
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rumen Fluid ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Bovine Rumen ◽  
Hybridization Data ◽  
Clostridium Tetanomorphum

A strictly anaerobic, mesophilic, endospore-forming, lipolytic bacterium, designated strain R1T, was isolated from bovine rumen fluid and characterized. Cells of this isolate were Gram-positive, non-motile rods that formed spherical terminal spores. The overall biochemical and physiological characteristics indicated that this strain should be placed in the genus Clostridium. The strain grew at temperatures between 25 and 47 °C (optimum, 37 °C), at pH between 5·0 and 8·5 (optimum pH 5·5–7·0) and in NaCl concentrations of 0–3 % (w/v). The isolate was not able to utilize glucose or other carbohydrates as carbon sources. The DNA G+C content was 31·2 mol%. Sequence analysis of the 16S rRNA gene of R1T revealed that it has the closest match (98 % similarity) with Clostridium tetanomorphum DSM 4474T. The highest levels of DNA–DNA relatedness of the isolate were 61·9 and 54·3 % with Clostridium pascui DSM 10365T and C. tetanomorphum DSM 4474T, respectively. Based on 16S rRNA gene sequence similarity, phylogenetic analysis, DNA G+C content, DNA–DNA hybridization data and distinct phenotypic characteristics, strain R1T (=DSM 17049T=CCUG 50446T) was classified in the genus Clostridium, as a member of a novel species, for which the name Clostridium lundense sp. nov. is proposed.

scholarly journals Isolation and characterization of a novel bacterial strain from a Tris-Acetate-Phosphate agar medium plate of the green micro-alga Chlamydomonas reinhardtii that can utilize common environmental pollutants as a carbon source

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 656 ◽  
Author(s):  
Mautusi Mitra ◽  
Kevin Manoap-Anh-Khoa Nguyen ◽  
Taylor Wayland Box ◽  
Jesse Scott Gilpin ◽  
Seth Ryan Hamby ◽  
...  
Keyword(s):  
Carbon Source ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Chlamydomonas Reinhardtii ◽  
Bacterial Strain ◽  
Sole Carbon Source ◽  
Agar Medium ◽  
Environmental Pollutants ◽  
Rrna Gene ◽  
Motor Oil

Background: Chlamydomonas reinhardtii, a green micro-alga can be grown at the lab heterotrophically or photo-heterotrophically in Tris-Phosphate-Acetate (TAP) medium which contains acetate as the sole carbon source. When grown in TAP medium, Chlamydomonas can utilize the exogenous acetate in the medium for gluconeogenesis using the glyoxylate cycle, which is also present in many bacteria and higher plants. A novel bacterial strain, LMJ, was isolated from a contaminated TAP medium plate of Chlamydomonas. We present our work on the isolation and physiological and biochemical characterizations of LMJ. Methods: Several microbiological tests were conducted to characterize LMJ, including its sensitivity to four antibiotics. We amplified and sequenced partially the 16S rRNA gene of LMJ. We tested if LMJ can utilize cyclic alkanes, aromatic hydrocarbons, poly-hydroxyalkanoates, and fresh and combusted car motor oil as the sole carbon source on Tris-Phosphate (TP) agar medium plates for growth. Results: LMJ is a gram-negative rod, oxidase-positive, mesophilic, non-enteric, pigmented, salt-sensitive bacterium. LMJ can ferment glucose, is starch hydrolysis-negative, and is very sensitive to penicillin and chloramphenicol. Preliminary spectrophotometric analyses indicate LMJ produces pyomelanin. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of LMJ showed that it matched to that of an uncultured bacterium clone LIB091_C05_1243. The nearest genus relative of LMJ is an Acidovorax sp. strain. LMJ was able to use alkane hydrocarbons, fresh and combusted car motor oil, poly-hydroxybutyrate, phenanthrene, naphthalene, benzoic acid and phenyl acetate as the sole carbon source for growth on TP-agar medium plates. Conclusions: LMJ has 99.14% sequence identity with the Acidovorax sp. strain A16OP12 whose genome has not been sequenced yet. LMJ’s ability to use chemicals that are common environmental pollutants makes it a promising candidate for further investigation for its use in bioremediation and, provides us with an incentive to sequence its genome.

Mariniplasma anaerobium gen. nov., sp. nov., a novel anaerobic marine mollicute, and proposal of three novel genera to reclassify members of Acholeplasma clusters II–IV

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Kunihiro Okano ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genome Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Optimum Growth ◽  
Circular Chromosome ◽  
Content Type ◽  
Link Type

A novel strictly anaerobic chemoorganotrophic bacterium, designated Mahy22T, was isolated from sulfidic bottom water of a shallow brackish meromictic lake in Japan. Cells of the strain were Gram-stain-negative, non-motile and coccoid in shape with diameters of about 600–800 nm. The temperature range for growth was 15–37 °C, with optimum growth at 30–32 °C. The pH range for growth was pH 6.2–8.9, with optimum growth at pH 7.2–7.4. The strain grew with NaCl concentrations of 5% or below (optimum, 2–3%). Growth of the strain was enhanced by the addition of thiosulfate. The major cellular fatty acids were C16:0 and anteiso-C15:0. Respiratory quinones were not detected. The complete genome sequence of strain Mahy22T possessed a 1 885 846 bp circular chromosome and a 12 782 bp circular genetic element. The G+C content of the genome sequence was 30.1 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Acholeplasmataceae , class Mollicutes . The closest relative of strain Mahy22T with a validly published name was Acholeplasma palmae J233T with a 16S rRNA gene sequence similarity of 90.5%. Based on the results of polyphasic analysis, the name Mariniplasma anaerobium gen. nov., sp. nov. is proposed to accommodate strain Mahy22T, along with reclassification of some Acholeplasma species into Alteracholeplasma gen. nov., Haploplasma gen. nov. and Paracholeplasma gen. nov.

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 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 Paucisalibacillus globulus gen. nov., sp. nov., a Gram-positive bacterium isolated from potting soil

2006 ◽  
Vol 56 (8) ◽  
pp. 1841-1845 ◽  
Author(s):  
Inês Nunes ◽  
Igor Tiago ◽  
Ana Luísa Pires ◽  
Milton S. da Costa ◽  
António Veríssimo
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Positive Bacterium ◽  
Gram Positive ◽  
Respiratory Quinone ◽  
Bootstrap Analysis

A Gram-positive bacterium, designated B22T, was isolated from potting soil produced in Portugal. This organism is a catalase-positive, oxidase-negative, motile, spore-forming, aerobic rod that grows optimally at 37 °C and pH 8.0–8.5. Optimal growth occurs in media containing 1 % (w/v) NaCl, although the organism can grow in 0–8 % NaCl. The cell wall peptidoglycan is of the A4α type with a cross-linkage containing d-Asp. The major respiratory quinone is menaquinone 7 and the major fatty acids are anteiso-15 : 0, anteiso-17 : 0 and iso-15 : 0. The DNA G+C content is 37.9 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain B22T formed a new branch within the family Bacillaceae. The novel isolate is phylogenetically closely related to members of genera of moderately halophilic bacilli and formed a coherent cluster with species of the genera Salinibacillus, Virgibacillus, Oceanobacillus and Lentibacillus, supported by bootstrap analysis at a confidence level of 71 %. Strain B22T exhibited 16S rRNA gene pairwise sequence similarity values of 94.7–94.3 % with members of the genus Salinibacillus, 95.1–92.8 % with members of the genus Virgibacillus, 94.7–93.2 % with members of the genus Oceanobacillus and 93.1–92.3 % with members of the genus Lentibacillus. On the basis of phylogenetic analysis and physiological and biochemical characteristics, it is proposed that strain B22T represents a novel species in a new genus, Paucisalibacillus globulus gen. nov., sp. nov. Strain B22T (=LMG 23148T=CIP 108857T) is the type strain of Paucisalibacillus globulus.

scholarly journals Terrisporobacter petrolearius sp. nov., isolated from an oilfield petroleum reservoir

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3522-3526 ◽  
Author(s):  
Yu Deng ◽  
Xiang Guo ◽  
Yanwei Wang ◽  
Mingxiong He ◽  
Kedong Ma ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Petroleum Reservoir ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile

A Gram-staining-positive, spore-forming, strictly anaerobic bacterium, designated strain LAM0A37T, was isolated from enrichment samples collected from a petroleum reservoir in Shengli oilfield. Cells of strain LAM0A37T were rod-shaped and motile by peritrichous flagella. The optimal temperature and pH for growth were 40 °C and 7.0–7.5, respectively. The strain did not require NaCl for growth but tolerated up to 3 % (w/v) NaCl. Strain LAM0A37T was able to utilize glucose, fructose, maltose, xylose, sorbitol, cellobiose, melibiose and melezitose as sole carbon sources. Sulfite was used as an electron acceptor. The main products of glucose fermentation were acetate and CO2. The predominant fatty acid was C16 : 0 (23.6 %). The main polar lipid profile comprised of five glycolipids, six phospholipids and two lipids. No menaquinone was detected. The genomic DNA G+C content was 27.1 ± 0.2 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate was a member of the genus Terrisporobacter, and was most closely related to Terrisporobacter glycolicus JCM 1401T and Terrisporobacter mayombei DSM 6539T with 98.3 % 16S rRNA gene sequence similarity to both. DNA–DNA hybridization values between strain LAM0A37T and type strains of Terrisporobacter glycolicus and Terrisporobacter mayombei were 45.6 ± 0.3 % and 38.3 ± 0.4 %, respectively. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0A37T is suggested to represent a novel species of the genus Terrisporobacter, for which the name Terrisporobacter petrolearius sp. nov. is proposed. The type strain is LAM0A37T ( = ACCC 00740T = JCM 19845T).

scholarly journals Sporosalibacterium faouarense gen. nov., sp. nov., a moderately halophilic bacterium isolated from oil-contaminated soil

2011 ◽  
Vol 61 (1) ◽  
pp. 99-104 ◽  
Author(s):  
Raja Rezgui ◽  
Zouhaier Ben Ali Gam ◽  
Said Ben Hamed ◽  
Marie-Laure Fardeau ◽  
Jean-Luc Cayol ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Yeast Extract ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Gram Positive ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacterium ◽  
The Family

A novel strictly anaerobic, moderately halophilic and mesophilic bacterium, designated strain SOL3f37T, was isolated from a hydrocarbon-polluted soil surrounding a deep petroleum environment located in south Tunisia. Cells of strain SOL3f37T stained Gram-positive and were motile, straight and spore-forming. Strain SOL3f37T had a typical Gram-positive-type cell-wall structure, unlike the thick, multilayered cell wall of its closest relative Clostridiisalibacter paucivorans. The major fatty acids were iso-C15 : 0 (41 %), iso-C14 : 0 3-OH and/or iso-C15 : 0 dimethyl acetal (21.6 %), iso-C13 : 0 (4.4 %), anteiso-C15 : 0 (3.9 %) and iso-C15 : 1 (2.8 %). Strain SOL3f37T grew between 20 and 48 °C (optimum 40 °C) and at pH 6.2–8.1 (optimum pH 6.9). Strain SOL3f37T required at least 0.5 g NaCl l−1 and grew in the presence of NaCl concentrations up to 150 g l−1 (optimum 40 g l−1). Yeast extract (2 g l−1) was required for degradation of pyruvate, fumarate, fructose, glucose and mannitol. Also, strain SOL3f37T grew heterotrophically on yeast extract, peptone and bio-Trypticase, but was unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content was 30.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SOL3f37T was a member of the family Clostridiaceae in the order Clostridiales; strain SOL3f37T was related to members of various genera of the family Clostridiaceae. It exhibited highest 16S rRNA gene sequence similarity (93.4 %) with Clostridiisalibacter paucivorans 37HS60T, 91.8 % with Thermohalobacter berrensis CTT3T and 91.7 % with Caloranaerobacter azorensis MV1087T. On the basis of genotypic, phenotypic and phylogenetic data, it is suggested that strain SOL3f37T represents a novel species in a new genus. The name Sporosalibacterium faouarense gen. nov., sp. nov. is proposed, with SOL3f37T (=DSM 21485T =JCM 15487T) as the type strain of Sporosalibacterium faouarense.

Desulfotomaculum defluvii sp. nov., a sulfate-reducing bacterium isolated from the subsurface environment of a landfill

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2290-2295 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
Stefan Spring ◽  
Pinnaka Anil Kumar ◽  
Shanmugam Mayilraj ◽  
Hans-Peter Klenk ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A novel sulfate-reducing, strictly anaerobic and endospore-forming bacterium, designated strain A5LFS102T, was isolated from a subsurface landfill sample. The strain was characterized using a polyphasic approach. Optimal growth was observed at 37 °C and pH 7.5 with sulfate as an electron acceptor. Sulfite and thiosulfate were utilized as electron acceptors. The respiratory isoprenoid quinone was menaquinone MK-7. 16S rRNA gene sequence analysis assigned strain A5LFS102T to the genus Desulfotomaculum . Both 16S rRNA and dissimilatory sulfate reductase (dsr) genes were compared with those of representative members of the genus Desulfotomaculum . Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A5LFS102T was closely related to Desulfotomaculum aeronauticum DSM 10349T (94.6 % sequence similarity). The G+C content of the DNA was 45.4 mol%. The total cellular fatty acid profile was dominated by C16 fatty acids. These phenotypic and genotypic data showed that strain A5LFS102T should be recognized as representative of a novel species of the genus Desulfotomaculum , for which the name Desulfotomaculum defluvii sp. nov. is proposed. The type strain is A5LFS102T ( = DSM 23699T = JCM 14036T = MTCC 7767T).

Sign in / Sign up

Export Citation Format

Share Document