scholarly journals Tepidanaerobacter syntrophicus gen. nov., sp. nov., an anaerobic, moderately thermophilic, syntrophic alcohol- and lactate-degrading bacterium isolated from thermophilic digested sludges

2006 ◽  
Vol 56 (7) ◽  
pp. 1621-1629 ◽  
Author(s):  
Yuji Sekiguchi ◽  
Hiroyuki Imachi ◽  
Ambar Susilorukmi ◽  
Mizuho Muramatsu ◽  
Akiyoshi Ohashi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic ◽  
Degrading Bacterium

Three anaerobic, moderately thermophilic, syntrophic primary alcohol- and lactate-degrading microbes, designated strains JLT, JE and OL, were isolated from sludges of thermophilic (55 °C) digesters that decomposed either municipal solid wastes or sewage sludge. The strains were strictly anaerobic organisms. All three strains grew at 25–60 °C and pH 5.5–8.5 and optimum growth was observed at 45–50 °C and pH 6.0–7.0. The three organisms grew chemo-organotrophically on a number of carbohydrates in the presence of yeast extract. In co-culture with the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus, all strains could utilize ethanol, glycerol and lactate syntrophically for growth, although these compounds were not metabolized in pure culture without additional external electron acceptors. All strains could reduce thiosulphate. Quinones were not detected. The DNA G+C contents of strains JLT, JE and OL were 38.0, 37.3 and 37.7 mol%, respectively. Major cellular fatty acids of the strains were iso-C15 : 0, C16 : 0 and unsaturated species of C15 : 1. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strains belong to a deeply branched lineage of the phylum Firmicutes; the most closely related species was Thermovenabulum ferriorganovorum (16S rRNA gene sequence similarity of 88 %). The three strains were phylogenetically very closely related to each other (99–100 % 16S rRNA gene sequence similarity) and were physiologically and chemotaxonomically similar. These genetic and phenotypic properties suggest that the strains should be classified as representatives of a novel species and genus; the name Tepidanaerobacter syntrophicus gen. nov., sp. nov. is proposed. The type strain of Tepidanaerobacter syntrophicus is strain JLT (=JCM 12098T=NBRC 100060T=DSM 15584T).

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 Lysobacter ruishenii sp. nov., a chlorothalonil-degrading bacterium isolated from a long-term chlorothalonil-contaminated soil

2011 ◽  
Vol 61 (3) ◽  
pp. 674-679 ◽  
Author(s):  
Guang-Li Wang ◽  
Li Wang ◽  
Hong-Hong Chen ◽  
Bin Shen ◽  
Shun-Peng Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Contaminated Soil ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium

An aerobic, Gram-negative bacterial strain, designated CTN-1T, capable of degrading chlorothalonil was isolated from a long-term chlorothalonil-contaminated soil in China, and was subjected to a polyphasic taxonomic investigation. Strain CTN-1T grew at 15–37 °C (optimum 28–30 °C) and at pH 6.0–9.0 (optimum pH 7.0–7.5). The G+C content of the total DNA was 67.1 mol%. Based on 16S rRNA gene sequence analysis, strain CTN-1T was related most closely to Lysobacter daejeonensis DSM 17634T (97.1 % similarity), L. soli DCY21T (95.7 %), L. concretionis Ko07T (95.5 %), L. gummosus LMG 8763T (95.3 %) and L. niastensis DSM 18481T (95.2 %). The novel strain showed less than 95.0 % 16S rRNA gene sequence similarity to the type strains of other Lysobacter species. The major cellular fatty acids of strain CNT-1T were iso-C16 : 0 (23.0 %), iso-C15 : 0 (21.4 %) and iso-C17 : 1 ω9c (15.3 %). The major isoprenoid quinone was Q-8 (99 %), and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. These chemotaxonomic data supported the affiliation of strain CTN-1T to the genus Lysobacter. Levels of DNA–DNA relatedness between strain CTN-1T and L. daejeonensis DSM 17634T were 34.6–36.1 %. Phylogenetic analysis based on 16S rRNA gene sequences, DNA–DNA hybridization data and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain CTN-1T from recognized species of the genus Lysobacter. Strain CTN-1T is therefore considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter ruishenii sp. nov. is proposed. The type strain is CTN-1T (=DSM 22393T =CGMCC 1.10136T).

scholarly journals Methylothermus subterraneus sp. nov., a moderately thermophilic methanotroph isolated from a terrestrial subsurface hot aquifer

2011 ◽  
Vol 61 (11) ◽  
pp. 2646-2653 ◽  
Author(s):  
Hisako Hirayama ◽  
Yohey Suzuki ◽  
Mariko Abe ◽  
Masayuki Miyazaki ◽  
Hiroko Makita ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Type I ◽  
Rrna Gene Sequence ◽  
Intracytoplasmic Membrane ◽  
Moderately Thermophilic

A novel methane-oxidizing bacterium, strain HTM55T, was isolated from subsurface hot aquifer water from a Japanese gold mine. Strain HTM55T was a Gram-negative, aerobic, motile, coccoid bacterium with a single polar flagellum and the distinctive intracytoplasmic membrane arrangement of a type I methanotroph. Strain HTM55T was a moderately thermophilic, obligate methanotroph that grew on methane and methanol at 37–65 °C (optimum 55–60 °C). The isolate grew at pH 5.2–7.5 (optimum 5.8–6.3) and with 0–1 % NaCl (optimum 0–0.3 %). The ribulose monophosphate pathway was operative for carbon assimilation. The DNA G+C content was 54.4 mol% and the major fatty acids were C16 : 0 (52.0 %) and C18 : 1ω7c (34.8 %). Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HTM55T was closely related to Methylothermus thermalis MYHTT (99.2 % 16S rRNA gene sequence similarity), which is within the class Gammaproteobacteria. However, DNA–DNA relatedness between strain HTM55T and Methylothermus thermalis MYHTT was ≤39 %. On the basis of distinct phylogenetic, chemotaxonomic and physiological characteristics, strain HTM55T represents a novel species of the genus Methylothermus, for which the name Methylothermus subterraneus sp. nov. is proposed. The type strain is HTM55T ( = JCM 13664T = DSM 19750T).

scholarly journals Thermobacillus composti sp. nov., a moderately thermophilic bacterium isolated from a composting reactor

2007 ◽  
Vol 57 (7) ◽  
pp. 1473-1477 ◽  
Author(s):  
Keiko Watanabe ◽  
Norio Nagao ◽  
Shuich Yamamoto ◽  
Tatsuki Toda ◽  
Norio Kurosawa
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Thermophilic Bacterium ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic

A Gram-negative, rod-shaped, spore-forming and moderately thermophilic bacterium, strain KWC4T, was isolated from a composting reactor. Cells of strain KWC4T were 2.0–5.0 μm long and 0.5–0.7 μm in diameter. Strain KWC4T grew aerobically at 32–61 °C, with optimal growth occurring at 50 °C. It grew at pH 5.6–10.1, with optimal growth at around pH 9.0. The optimum NaCl concentration for growth was almost 0 % (w/v), but strain KWC4T was moderately halotolerant and was able to grow at NaCl concentrations up to 4.4 % (w/v). The DNA G+C content of strain KWC4T was 60.0 mol%. The major fatty acids were iso-16 : 0 (39.0 %) and anteiso-15 : 0 (33.3 %). Based on 16S rRNA gene sequence similarity data, strain KWC4T belonged to the genus Thermobacillus and was related to Thermobacillus xylanilyticus. However, strain KWC4T had a 38 bp insertion sequence located near the 3′ end of its 16S rRNA gene that was not present in T. xylanilyticus. The 16S rRNA gene sequence similarity value between strain KWC4T and T. xylanilyticus was 95.7 %. The DNA–DNA hybridization value between strain KWC4T and T. xylanilyticus strain XET was 66 %. On the basis of phenotypic and genotypic evidence, strain KWC4T (=DSM 18247T=JCM 13945T) is the type strain of a novel species, for which the name Thermobacillus composti sp. nov. is proposed.

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 Ruminococcus champanellensis sp. nov., a cellulose-degrading bacterium from human gut microbiota

2012 ◽  
Vol 62 (1) ◽  
pp. 138-143 ◽  
Author(s):  
Christophe Chassard, ◽  
Eve Delmas, ◽  
Céline Robert, ◽  
Paul A. Lawson ◽  
Annick Bernalier-Donadille
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Physiological Data ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Cellulolytic Strain

A strictly anaerobic, cellulolytic strain, designated 18P13T, was isolated from a human faecal sample. Cells were Gram-positive non-motile cocci. Strain 18P13T was able to degrade microcrystalline cellulose but the utilization of soluble sugars was restricted to cellobiose. Acetate and succinate were the major end products of cellulose and cellobiose fermentation. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Ruminococcus of the family Ruminococcaceae. The closest phylogenetic relative was the ruminal cellulolytic strain Ruminococcus flavefaciens ATCC 19208T (<95 % 16S rRNA gene sequence similarity). The DNA G+C content of strain 18P13T was 53.05±0.7 mol%. On the basis of phylogenetic analysis, and morphological and physiological data, strain 18P13T can be differentiated from other members of the genus Ruminococcus with validly published names. The name Ruminococcus champanellensis sp. nov. is proposed, with 18P13T ( = DSM 18848T = JCM 17042T) as the type strain.

scholarly journals Clostridium aestuarii sp. nov., from tidal flat sediment

2007 ◽  
Vol 57 (6) ◽  
pp. 1315-1317 ◽  
Author(s):  
Seil Kim ◽  
Hyunyoung Jeong ◽  
Jongsik Chun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

A strictly anaerobic, halophilic, motile, endospore-forming, rod-shaped bacterium, designated strain HY-45-18T, was isolated from a sediment sample of a tidal flat in Korea. The isolate produced butyric acid, propionic acid, glycerol and H2 as fermentation end products from glucose. Strain HY-45-18T is halophilic as it was unable to grow in the absence of sea salts. A 16S rRNA gene sequence analysis clearly indicated that the tidal flat isolate is a member of cluster I of the order Clostridiales, which contains the type species of Clostridium, Clostridium butyricum. The closest phylogenetic neighbour of strain HY-45-18T was Clostridium ganghwense KCTC 5146T (96.5 % 16S rRNA gene sequence similarity). Several phenotypic characteristics can be readily used to differentiate the isolate from phylogenetically related clostridia. Therefore, strain HY-45-18T represents a novel species of the genus Clostridium, for which the name Clostridium aestuarii sp. nov. is proposed. The type strain is HY-45-18T (=IMSNU 40129T=KCTC 5147T=JCM 13194T).

scholarly journals Meiothermus hypogaeus sp. nov., a moderately thermophilic bacterium isolated from a hot spring

2012 ◽  
Vol 62 (1) ◽  
pp. 112-117 ◽  
Author(s):  
Koji Mori ◽  
Takao Iino ◽  
Jun-ichiro Ishibashi ◽  
Hiroyuki Kimura ◽  
Moriyuki Hamada ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Moderately Thermophilic

A novel moderately thermophilic, red-pigmented bacterium, designated strain AZM34c11T, was isolated from the bottom of a 1000 m-deep drilled well located in a Japanese hot spring. Cells were Gram-negative and grew optimally at 50 °C, at pH 7.6 and with 0–0.3 % (w/v) NaCl. Analysis of the 16S rRNA gene sequence revealed that the isolate belonged to the genus Meiothermus. Levels of 16S rRNA gene sequence similarity between strain AZM34c11T and the type strains of recognized Meiothermus species were 88.2–94.8 %. Strain AZM34c11T was distinguished from recognized Meiothermus species by its cellular fatty acid profile: iso-C16 : 0 was one of the predominant components and hydroxy fatty acids were present only in trace amounts. The strain could also be differentiated based on its growth substrate preferences and characteristic enzyme reactions. On the basis of these results, strain AZM34c11T is considered to represent a novel species of the genus Meiothermus, for which the name Meiothermus hypogaeus sp. nov. is proposed. The type strain is AZM34c11T ( = NBRC 106114T  = DSM 23238T).

scholarly journals Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium

2004 ◽  
Vol 54 (5) ◽  
pp. 1469-1476 ◽  
Author(s):  
Muriel Derrien ◽  
Elaine E. Vaughan ◽  
Caroline M. Plugge ◽  
Willem M. de Vos
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Akkermansia Muciniphila ◽  
Degrading Bacterium ◽  
Degrading Bacteria

The diversity of mucin-degrading bacteria in the human intestine was investigated by combining culture and 16S rRNA-dependent approaches. A dominant bacterium, strain MucT, was isolated by dilution to extinction of faeces in anaerobic medium containing gastric mucin as the sole carbon and nitrogen source. A pure culture was obtained using the anaerobic soft agar technique. Strain MucT was a Gram-negative, strictly anaerobic, non-motile, non-spore-forming, oval-shaped bacterium that could grow singly and in pairs. When grown on mucin medium, cells produced a capsule and were found to aggregate. Strain MucT could grow on a limited number of sugars, including N-acetylglucosamine, N-acetylgalactosamine and glucose, but only when a protein source was provided and with a lower growth rate and final density than on mucin. The G+C content of DNA from strain MucT was 47·6 mol%. 16S rRNA gene sequence analysis revealed that the isolate was part of the division Verrucomicrobia. The closest described relative of strain MucT was Verrucomicrobium spinosum (92 % sequence similarity). Remarkably, the 16S rRNA gene sequence of strain MucT showed 99 % similarity to three uncultured colonic bacteria. According to the data obtained in this work, strain MucT represents a novel bacterium belonging to a new genus in subdivision 1 of the Verrucomicrobia; the name Akkermansia muciniphila gen. nov., sp. nov. is proposed; the type strain is MucT (=ATCC BAA-835T=CIP 107961T).

scholarly journals Diaphorobacter polyhydroxybutyrativorans sp. nov., a novel poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-degrading bacterium isolated from biofilms

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2913-2918 ◽  
Author(s):  
Tianlei Qiu ◽  
Zhengyan Zuo ◽  
Junlian Gao ◽  
Min Gao ◽  
Meilin Han ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Degrading Bacterium

A novel Gram-stain-negative, facultatively aerobic and rod-shaped strain, designated SL-205T, was isolated from the biofilms of a denitrifying reactor using poly(3-hydoxybutyrate-co-3-hydroxyvalerate) as the sole carbon source in Beijing, PR China. A polyphasic taxonomic characterization was performed on the novel isolate. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain SL-205T is a member of the genus Diaphorobacter. High levels of 16S rRNA gene sequence similarity were found between strain SL-205T and Diaphorobacter nitroreducens NA10BT (99.4 %) and Diaphorobacter oryzae RF3T (98.5 %), respectively. However, the DNA–DNA relatedness values between strain SL-205T and D. nitroreducens NA10BT and D. oryzae RF3T were 57 ± 1 % and 45 ± 1.5 %, respectively. The G+C content of the genomic DNA of strain SL-205T was 66.8 mol%. The major fatty acids consisted of summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. Ubiquinone Q-8 was the only respiratory quinone; the polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one uncharacterized phospholipid. We conclude that strain SL-205T represents a novel species of the genus Diaphorobacter for which the name Diaphorobacter polyhydroxybutyrativorans is proposed; the type strain is SL-205T ( = ACCC 19739T = DSM 29460T).

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