scholarly journals Anaerobic Degradation of Flavonoids by Clostridium orbiscindens

2003 ◽  
Vol 69 (10) ◽  
pp. 5849-5854 ◽  
Author(s):  
Lilian Schoefer ◽  
Ruchika Mohan ◽  
Andreas Schwiertz ◽  
Annett Braune ◽  
Michael Blaut
Keyword(s):  
Propionic Acid ◽  
Human Subjects ◽  
Dry Mass ◽  
Rrna Gene ◽  
Glycosidic Bonds ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Specific Oligonucleotide Probe ◽  
Species Specific ◽  
Human Intestinal Tract

ABSTRACT An anaerobic, quercetin-degrading bacterium was isolated from human feces and identified as Clostridium orbiscindens by comparative 16S rRNA gene sequence analysis. The organism was tested for its ability to transform several flavonoids. The isolated C. orbiscindens strain converted quercetin and taxifolin to 3,4-dihydroxyphenylacetic acid; luteolin and eriodictyol to 3-(3,4-dihydroxyphenyl)propionic acid; and apigenin, naringenin, and phloretin to 3-(4-hydroxyphenyl)propionic acid, respectively. Genistein and daidzein were not utilized. The glycosidic bonds of luteolin-3-glucoside, luteolin-5-glucoside, naringenin-7-neohesperidoside (naringin), quercetin-3-glucoside, quercetin-3-rutinoside (rutin), and phloretin-2′-glucoside were not cleaved. Based on the intermediates and products detected, pathways for the degradation of the flavonol quercetin and the flavones apigenin and luteolin are proposed. To investigate the numerical importance of C. orbiscindens in the human intestinal tract, a species-specific oligonucleotide probe was designed and tested for its specificity. Application of the probe to fecal samples from 10 human subjects proved the presence of C. orbiscindens in 8 out of the 10 samples tested. The numbers ranged from 1.87 × 108 to 2.50 × 109 cells g of fecal dry mass−1, corresponding to a mean count of 4.40 × 108 cells g of dry feces−1.

scholarly journals Quantification of the Flavonoid-Degrading BacteriumEubacterium ramulus in Human Fecal Samples with a Species-Specific Oligonucleotide Hybridization Probe

1999 ◽  
Vol 65 (8) ◽  
pp. 3705-3709 ◽  
Author(s):  
Rainer Simmering ◽  
Brigitta Kleessen ◽  
Michael Blaut
Keyword(s):  
Intestinal Tract ◽  
Oligonucleotide Probe ◽  
Dry Mass ◽  
Bacterial Strains ◽  
Hybridization Probe ◽  
Fecal Samples ◽  
Degrading Bacterium ◽  
Oligonucleotide Hybridization ◽  
Species Specific ◽  
Human Intestinal Tract

ABSTRACT To investigate the occurrence of the flavonoid-degrading bacteriumEubacterium ramulus in the human intestinal tract, an oligonucleotide probe designated S-S-E.ram-0997-a-A-18 was designed and validated, with over 90 bacterial strains representing the dominant described human fecal flora. Application of S-S-E.ram-0997-a-A-18 to fecal samples from 20 subjects indicated the presence of E. ramulus in each individual tested in numbers from 4.4 × 107 to 2.0 × 109 cells/g of fecal dry mass. Six fecal E. ramulus isolates were recognized by S-S-E.ram-0997-a-A-18 but exhibited different band patterns when analyzed by randomly amplified polymorphic DNA.

Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2577-2582 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Joonhong Park ◽  
Soon-Ae Yoo
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-motile, aerobic bacterial strain, designated MJ20T, was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20T belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053T (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200T (98.0 %) and Dyadobacter ginsengisoli KCTC 12589T (96.4 %). The G+C content of the genomic DNA of strain MJ20T was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0 and C16 : 1 ω5c as major components supported the affiliation of strain MJ20T to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. fermentans DSM 18053T (mean±sd of three determinations, 47±7 %) and D. beijingensis JCM 14200T (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20T (=KCTC 22481T =JCM 16232T) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.

scholarly journals Dyadobacter jiangsuensis sp. nov., a methyl red degrading bacterium isolated from a dye-manufacturing factory

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1138-1143 ◽  
Author(s):  
Li Wang ◽  
Liang Chen ◽  
Qi Ling ◽  
Chen-chen Li ◽  
Yong Tao ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Methyl Red ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Low Levels

A Gram-stain-negative, non-motile, rod-shaped bacterial strain, L-1T, which was capable of degrading methyl red was isolated from a dye-manufacturing factory in China. Phenotypic, chemotaxonomic and phylogenetic analyses established affiliation of the isolate to the genus Dyadobacter . Cells occurred in pairs in young cultures but became chains of coccoid cells in old cultures, and produced a flexirubin-like yellow pigment. Strain L-1T could not hydrolyse cellulose, and had a DNA G+C content of 51.3 mol%. The major cellular fatty acids were iso-C15 : 0, C16 : 1ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). C16 : 0, iso-C15 : 0 3-OH and C16 : 0 3-OH were the other major fatty acid components. Comparative 16S rRNA gene sequence analysis showed that strainL-1T was most closely related to Dyadobacter fermentans DSM 18053T (99.2 %), Dyadobacter soli JCM 16232T (98.9 %) and Dyadobacter beijingensis CGMCC 1.6375T (98.7 %). However, the new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to JCM 16232T (41.2±1.8 %), DSM 18053T (38.6±2.6 %) and CGMCC 1.6375T (35.0±2.1 %). Strain L-1T could also be differentiated from its closest phylogenetic relatives based on differences in several phenotypic characteristics. These data suggest that strain L-1T represents a novel species of the genus Dyadobacter , for which the name Dyadobacter jiangsuensis sp. is proposed. The type strain is L-1T (DSM 29057T = CGMCC 1.12969T).

Echinococcus multilocularis in a Eurasian lynx (Lynx lynx) in Turkey

Parasitology ◽  
2018 ◽  
Vol 145 (9) ◽  
pp. 1147-1150 ◽  
Author(s):  
Hamza Avcioglu ◽  
Esin Guven ◽  
Ibrahim Balkaya ◽  
Ridvan Kirman
Keyword(s):  
Echinococcus Multilocularis ◽  
Pcr Analysis ◽  
12S Rrna ◽  
Rrna Gene ◽  
Lynx Lynx ◽  
Eurasian Lynx ◽  
The North ◽  
Specific Pcr ◽  
Gene Sequence Analysis ◽  
Species Specific

AbstractEchinococcus multilocularis is the causative agent of alveolar echinococcosis (AE), one of the most threatening zoonoses in Eurasia. Human AE is widespread in the Erzurum region of Turkey, but the situation of the disease in intermediate and definitive hosts is unknown. A Eurasian lynx (Lynx lynx) was killed in a traffic accident in the north of Erzurum, and was taken to our laboratory. Sedimentation and counting technique (SCT), DNA isolation and polymerase chain reaction (PCR) analysis were performed. The SCT results showed that the lynx was infected with E. multilocularis with a medium (745 worms) worm burden. The DNA of adult worms obtained from the lynx was analyzed with a species-specific PCR, and the worms were confirmed to be E. multilocularis by 12S rRNA gene sequence analysis. This is the first report of E. multilocularis from Eurasian lynx in Turkey.

scholarly journals Distribution of Bifidobacterial Species in Human Intestinal Microflora Examined with 16S rRNA-Gene-Targeted Species-Specific Primers

1999 ◽  
Vol 65 (10) ◽  
pp. 4506-4512 ◽  
Author(s):  
Takahiro Matsuki ◽  
Koichi Watanabe ◽  
Ryuichiro Tanaka ◽  
Masafumi Fukuda ◽  
Hiroshi Oyaizu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Tract ◽  
Bifidobacterium Longum ◽  
Rrna Gene ◽  
Human Feces ◽  
Specific Primers ◽  
Specific Pcr ◽  
Species Specific ◽  
Human Intestinal Tract

ABSTRACT In order to clarify the distribution of bifidobacterial species in the human intestinal tract, a 16S rRNA-gene-targeted species-specific PCR technique was developed and used with DNAs extracted from fecal samples obtained from 48 healthy adults and 27 breast-fed infants. To cover all of the bifidobacterial species that have been isolated from and identified in the human intestinal tract, species-specific primers for Bifidobacterium longum, B. infantis,B. dentium, and B. gallicum were developed and used with primers for B. adolescentis, B. angulatum, B. bifidum, B. breve, and the B. catenulatum group (B. catenulatum andB. pseudocatenulatum) that were developed in a previous study (T. Matsuki, K. Watanabe, R. Tanaka, and H. Oyaizu, FEMS Microbiol. Lett. 167:113–121, 1998). The specificity of the nine primers was confirmed by PCR, and the species-specific PCR method was found to be a useful means for identifying Bifidobacteriumstrains isolated from human feces. The results of an examination of bifidobacterial species distribution showed that the B. catenulatum group was the most commonly found taxon (detected in 44 of 48 samples [92%]), followed by B. longum andB. adolescentis, in the adult intestinal bifidobacterial flora and that B. breve, B. infantis, andB. longum were frequently found in the intestinal tracts of infants. The present study demonstrated that qualitative detection of the bifidobacterial species present in human feces can be accomplished rapidly and accurately.

scholarly journals Lysinibacillus cresolivorans sp. nov., an m-cresol-degrading bacterium isolated from coking wastewater treatment aerobic sludge

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4250-4255 ◽  
Author(s):  
Yuan Ren ◽  
Shao-yi Chen ◽  
Hai-yan Yao ◽  
Liu-jie Deng
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Aerobic Treatment ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Aerobic Sludge

A Gram-stain-positive, rod-shaped, facultatively anaerobic, endospore-forming bacterium (designated strain SC03T) was isolated from the aerobic treatment sludge of a coking plant (Shaoguan City, China). The optimal pH and temperature for growth were pH 7.0 and 35 °C. On the basis of 16S rRNA gene sequence analysis, strain SC03T was related to the genus Lysinibacillus and the similarity between strain SC03T and the most closely related type strain, Lysinibacillus macroides LMG 18474T, was 94.4 %. The genomic G+C content of the DNA of strain SC03T was 41.2 mol%. Chemotaxonomic data supported the affiliation of strain SC03T to the genus Lysinibacillus. These properties include MK-7 as the predominant menaquinone; iso-C15 : 0 and iso-C16 : 0 as major fatty acids; A4α (l-Lys–d-Asp) as the cell-wall peptidoglycan type; and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine plus three unknown phospholipids as polar lipids. The phenotypic, phylogenetic and chemotaxonomic characters enable the differentiation of strain SC03T from recognized Lysinibacillus species. Thus, strain SC03T represents a novel species of the genus Lysinibacillus, for which the name Lysinibacillus cresolivorans sp. nov. is proposed. The type strain is SC03T ( = NRRL B-59352T = CCTCC M 208210T).

scholarly journals Rhodococcus qingshengii sp. nov., a carbendazim-degrading bacterium

2007 ◽  
Vol 57 (12) ◽  
pp. 2754-2757 ◽  
Author(s):  
Jing-Liang Xu ◽  
Jian He ◽  
Zhi-Chun Wang ◽  
Kun Wang ◽  
Wen-Jun Li ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Rhodococcus Erythropolis ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Mycolic Acids ◽  
Hybridization Data ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Good Agreement

A Gram-positive, aerobic, non-motile, mesophilic strain, djl-6T, able to degrade carbendazim, was isolated from a carbendazim-contaminated soil sample from Jiangsu province, China. The taxonomic position of this isolate was analysed by using a polyphasic approach. Chemotaxonomic analysis including peptidoglycan type, diagnostic sugar composition, fatty acid profile, menaquinones, polar lipids and mycolic acids showed that the characteristics of strain djl-6T were in good agreement with those of the genus Rhodococcus. DNA–DNA hybridization showed that it had low genomic relatedness with Rhodococcus baikonurensis DSM 44587T (31.8 %), Rhodococcus erythropolis DSM 43066T (23.8 %) and Rhodococcus globerulus DSM 43954T (17.7 %), the three type strains to which strain djl-6T was most closely related based on 16S rRNA gene sequence analysis (99.78, 99.25 and 98.91 % similarity, respectively). Based on the phenotypic properties and DNA–DNA hybridization data, strain djl-6T (=CGMCC 1.6580T =KCTC 19205T) is proposed as the type strain of a novel Rhodococcus species, Rhodococcus qingshengii sp. nov.

scholarly journals Sphingobium aromaticiconvertens sp. nov., a xenobiotic-compound-degrading bacterium from polluted river sediment

2007 ◽  
Vol 57 (2) ◽  
pp. 306-310 ◽  
Author(s):  
Rolf-Michael Wittich ◽  
Hans-Jürgen Busse ◽  
Peter Kämpfer ◽  
Marja Tiirola ◽  
Monika Wieser ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
River Elbe

A bacterial strain capable of degrading some monochlorinated dibenzofurans, designated RW16T, was isolated from aerobic River Elbe sediments. The strain was characterized based on 16S rRNA gene sequence analysis, DNA G+C content, physiological characteristics, polyamines, ubiquinone and polar lipid pattern and fatty acid composition. This analysis revealed that strain RW16T represents a novel species of the genus Sphingobium. The DNA G+C content of strain RW16T, 60.7 mol%, is the lowest yet reported for the genus. 16S rRNA gene sequence analysis placed strain RW16T as an outlier in the genus Sphingobium. The name Sphingobium aromaticiconvertens sp. nov. is proposed for this dibenzofuran-mineralizing organism, with type strain RW16T (=DSM 12677T=CIP 109198T).

scholarly journals Screening And Genome Sequencing of a di-n-butyl Phthalate Degrading Bacterium J2 Isolated From Peanut Field Soil

2021 ◽  
Author(s):  
Mingqing Wang ◽  
Lina Yu ◽  
Jie Sun ◽  
Jie Bi ◽  
Yu Song ◽  
...  
Keyword(s):  
Gene Annotation ◽  
Rrna Genes ◽  
Trna Genes ◽  
Rrna Gene ◽  
Reading Frame ◽  
Plastic Films ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
Protein Encoding ◽  
Butyl Phthalate

Abstract Di-n-butyl phthalate (DBP) is commonly used plasticizers in agricultural plastic films, and is a priority pollutant due to its toxicity to human health. A newly isolated strain J2, which used DBP as its sole carbon source, was screened from peanut filed soil by continuous enrichment cultivation. Based on morphological, physiological characteristics and 16S rRNA gene sequence analysis (GenBank accession No. OK598965), it was identified as Priestia sp. J2. The research results revealed the optimal conditions for DBP degradation as 35 oC and pH 8.0. The strain could effectively degrade 97.6% DBP within 5 days. Substrate tests showed that strain J2 could utilize shorter side-chained PAEs, but could not utilize long-chained PAEs. The whole genome comprises a complete chromosome of 5,067,299 bp and four plasmids of 147,924 bp, 75,940 bp, 11,604 bp, 11,333 bp (GenBank accession No. CP086208-CP086212). This genome harbors 5,585 predicted protein-encoding genes, 130 tRNA genes, and 42 rRNA genes. Gene annotation analyses showed a DBP-degrading gene contained an open reading frame of 930 bp, and the enzyme was named Est-J2-1. The amino acid sequence of the Est-J2-1 exhibited no significant homology with those of reported DBP-degrading enzymes, suggesting the enzyme is a novel enzyme. The gene of Est-J2-1 was found to be located on the chromosome. This study provided strain resource for DBP removal from farmland and other environments.

Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4707-4718 ◽  
Author(s):  
Peter Vandamme ◽  
Evie De Brandt ◽  
Kurt Houf ◽  
Joana Falcão Salles ◽  
Jan Dirk van Elsas ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Rhizosphere Soil ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis

Analysis of partial gyrB gene sequences revealed six taxa in a group of 17 Burkholderia glathei -like isolates which were further examined by (GTG)5-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA–DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and an analysis of cell and colony morphology and more than 180 biochemical characteristics. The results demonstrated that one taxon consisting of three human clinical isolates represented Burkholderia zhejiangensis , a recently described methyl-parathion-degrading bacterium isolated from a wastewater-treatment system in China. The remaining taxa represented five novel species isolated from soil or rhizosphere soil samples, and could be distinguished by both genotypic and phenotypic characteristics. We therefore propose to formally classify these bacteria as Burkholderia humi sp. nov. (type strain, LMG 22934T = CCUG 63059T), Burkholderia choica sp. nov. (type strain, LMG 22940T = CCUG 63063T), Burkholderia telluris sp. nov. (type strain, LMG 22936T = CCUG 63060T), Burkholderia udeis sp. nov. (type strain, LMG 27134T = CCUG 63061T) and Burkholderia terrestris sp. nov. (type strain, LMG 22937T = CCUG 63062T).

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