scholarly journals Terrimicrobium sacchariphilum gen. nov., sp. nov., an anaerobic bacterium of the class ‘Spartobacteria’ in the phylum Verrucomicrobia, isolated from a rice paddy field

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1718-1723 ◽  
Author(s):  
Yan-Ling Qiu ◽  
Xiao-zhu Kuang ◽  
Xiao-shuang Shi ◽  
Xian-zheng Yuan ◽  
Rong-bo Guo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Paddy Field ◽  
Gene Sequence ◽  
Rice Paddy ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Rice Paddy Field

A strictly anaerobic, mesophilic, carbohydrate-fermenting bacterium, designated NM-5T, was isolated from a rice paddy field. Cells of strain NM-5T were Gram-stain-negative, non-motile, non-spore-forming, short rods (0.5–0.7 µm×0.6–1.2 µm). The strain grew optimally at 37 °C (growth range 20–40 °C) and pH 7.0 (pH 5.5–8.0). The strain could grow fermentatively on arabinose, xylose, fructose, galactose, glucose, ribose, mannose, cellobiose, lactose, maltose and sucrose. The main end-products of glucose fermentation were acetate and propionate. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required but stimulated the growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The DNA G+C content was 46.3 mol%. The major cellular fatty acids were iso-C14 : 0, C18 : 0 and C16 : 0. 16S rRNA gene sequence analysis revealed that strain NM-5T belongs to the class ‘S partobacteria’, subdivision 2 of the bacterial phylum Verrucomicrobia . Phylogenetically, the closest species was ‘Chthoniobacter flavus’ (89.6 % similarity in 16S rRNA gene sequence). A novel genus and species, Terrimicrobium sacchariphilum gen. nov., sp. nov., is proposed. The type strain of the type species is NM-5T ( = JCM 17479T = CGMCC 1.5168T).

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 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 Caloranaerobacter ferrireducens sp. nov., an anaerobic, thermophilic, iron (III)-reducing bacterium isolated from deep-sea hydrothermal sulfide deposits

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1714-1718 ◽  
Author(s):  
Xiang Zeng ◽  
Zhao Zhang ◽  
Xi Li ◽  
Mohamed Jebbar ◽  
Karine Alain ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Sea Salts ◽  
Content Type ◽  
Link Type

A thermophilic, anaerobic, iron-reducing bacterium (strain DY22619T) was isolated from a sulfide sample collected from an East Pacific Ocean hydrothermal field at a depth of 2901 m. Cells were Gram-stain-negative, motile rods (2–10 µm in length, 0.5 µm in width) with multiple peritrichous flagella. The strain grew at 40–70 °C inclusive (optimum 60 °C), at pH 4.5–8.5 inclusive (optimum pH 7.0) and with sea salts concentrations of 1–10 % (w/v) (optimum 3 % sea salts) and NaCl concentrations of 1.5–5.0 % (w/v) (optimum 2.5 % NaCl). Under optimal growth conditions, the generation time was around 55 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, amino acids, carbohydrates and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamate, methionine, threonine, fructose, mannose, galactose, glucose, palatinose, rhamnose, turanose, gentiobiose, xylose, sorbose, pyruvate, tartaric acid, α-ketobutyric acid, α-ketovaleric acid, galacturonic acid and glucosaminic acid. Strain DY22619T was strictly anaerobic and facultatively dependent on various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulfate, thiosulfate or nitrate. The genomic DNA G+C content was 29.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that the closest relative of strain DY22619T was Caloranaerobacter azorensis MV1087T, sharing 97.41 % 16S rRNA gene sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus Caloranaerobacter , for which the name Caloranaerobacter http://dx.doi.org/10.1601/nm.4081 ferrireducens sp. nov. is proposed. The type strain is DY22619T ( = JCM 19467T = DSM 27799T = MCCC1A06455T).

scholarly journals Clostridium ganghwense sp. nov., isolated from tidal flat sediment

2006 ◽  
Vol 56 (4) ◽  
pp. 691-693 ◽  
Author(s):  
Seil Kim ◽  
Hyunyoung Jeong ◽  
Sanggoo Kim ◽  
Jongsik Chun
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Sea Salts ◽  
Tidal Flat Sediment

A Gram-negative, strictly anaerobic, halophilic, motile, sporulating and rod-shaped bacterium, designated strain HY-42-06T, was isolated from tidal flat sediment from Ganghwa Island in South Korea. The isolate produced glycerol, ethanol and CO2 as fermentation end-products from glucose. Strain HY-42-06T grew optimally at 35 °C, pH 7·5 and 3 % (w/v) artificial sea salts. No growth was observed in the absence of sea salts. In phylogenetic analyses based on 16S rRNA gene sequence, strain HY-42-06T showed a distinct phyletic line within the members of cluster I of the order Clostridiales. The closest phylogenetic neighbour to strain HY-42-06T was Clostridium novyi ATCC 17861T (94·91 % 16S rRNA gene sequence similarity). Several phenotypic characters readily differentiate the tidal flat isolate from phylogenetically related clostridia. On the basis of polyphasic evidence, strain HY-42-06T should be classified as a representative of a novel species, for which the name Clostridium ganghwense sp. nov. is proposed. The type strain is HY-42-06T (=IMSNU 40127T=KCTC 5146T=JCM 13193T).

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 Parasutterella secunda sp. nov., isolated from human faeces and proposal of Sutterellaceae fam. nov. in the order Burkholderiales

2011 ◽  
Vol 61 (3) ◽  
pp. 637-643 ◽  
Author(s):  
Masami Morotomi ◽  
Fumiko Nagai ◽  
Yohei Watanabe
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A novel, strictly anaerobic, non-spore-forming, Gram-reaction-negative coccobacillus bacterium, designated strain YIT 12071T, was isolated from human faeces. Biochemically, this strain was largely unreactive and asaccharolytic. Growth of this strain in peptone-yeast-extract broth was weak, producing no visible turbidity, and no short-chain fatty acids were detected as an end product of metabolism. Following 16S rRNA gene sequence analysis, strain YIT 12071T was found to be most closely related to Parasutterella excrementihominis (90 % sequence similarity) and phylogenetically distinct from other known genera belonging to the order Burkholderiales. Biochemical data supported the affiliation of this strain with the genus Parasutterella. Strain YIT 12071T, therefore, represents a novel species of the genus Parasutterella, for which the name Parasutterella secunda sp. nov. is proposed. The type strain is YIT 12071T (=DSM 22575T =JCM 16078T). On the basis of 16S rRNA gene sequence analysis, species of the genera Sutterella and Parasutterella form a distinct and deep evolutionary lineage of descent in the order Burkholderiales. This lineage could not be associated with any of the four known families of the order Burkholderiales. The distinct phylogenetic position and the unusual combination of chemotaxonomic characteristics shared by these genera, such as the predominant quinones and cellular fatty acid compositions, suggest that they constitute a novel family in the order Burkholderiales, for which the name Sutterellaceae fam. nov. is proposed to accommodate the genera Sutterella and Parasutterella.

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 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 Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters

2010 ◽  
Vol 60 (6) ◽  
pp. 1394-1400 ◽  
Author(s):  
Christopher D. Ogg ◽  
Bharat K. C. Patel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yeast Extract ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Casamino Acids ◽  
Gene Similarity

A strictly anaerobic, thermophilic bacterium, designated strain AeBT, was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeBT were slightly curved rods (2.5–6.0×1.0 μm) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone–yeast extract–Casamino acids medium at 50 °C (range 37–55 °C) and pH 7 (range pH 5–9). Strain AeBT grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeBT increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4±1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeBT is a member of the family Clostridiaceae, class Clostridia, phylum ‘Firmicutes’, and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8–90.9 %). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain AeBT is considered to represent a novel species in a new genus, for which the name Fervidicella metallireducens gen. nov., sp. nov. is proposed; the type strain is AeBT (=JCM 15555T=KCTC 5667T).

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