scholarly journals Genetic diversity of Leptotrichia and description of Leptotrichia goodfellowii sp. nov., Leptotrichia hofstadii sp. nov., Leptotrichia shahii sp. nov. and Leptotrichia wadei sp. nov.

2004 ◽  
Vol 54 (2) ◽  
pp. 583-592 ◽  
Author(s):  
Emenike R. K. Eribe ◽  
Bruce J. Paster ◽  
Dominique A. Caugant ◽  
Floyd E. Dewhirst ◽  
Verlyn K. Stromberg ◽  
...  
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Light And Electron Microscopy ◽  
Cellular Fatty Acid ◽  
Fatty Acid Analysis ◽  
16S Rdna Sequencing ◽  
Biochemical Tests ◽  
Gram Negative ◽  
Rdna Sequencing ◽  
Sds Page

Sixty strains of Gram-negative, anaerobic, rod-shaped bacteria from human sources initially assigned to Leptotrichia buccalis (n=58) and ‘Leptotrichia pseudobuccalis’ (n=2) have been subjected to polyphasic taxonomy. Full-length 16S rDNA sequencing, DNA–DNA hybridization, RAPD, SDS-PAGE of whole-cell proteins, cellular fatty acid analysis and enzymic/biochemical tests supported the establishment of four novel Leptotrichia species from this collection, Leptotrichia goodfellowii sp. nov. (type strain LB 57T=CCUG 32286T=CIP 107915T), Leptotrichia hofstadii sp. nov. (type strain LB 23T=CCUG 47504T=CIP 107917T), Leptotrichia shahii sp. nov. (type strain LB 37T=CCUG 47503T=CIP 107916T) and Leptotrichia wadei sp. nov. (type strain LB 16T=CCUG 47505T=CIP 107918T). Light and electron microscopy showed that the four novel species were Gram-negative, non-spore-forming and non-motile rods. L. goodfellowii produced arginine dihydrolase, β-galactosidase, N-acetyl-β-glucosaminidase, arginine arylamidase, leucine arylamidase and histidine arylamidase. L. shahii produced α-arabinosidase. L. buccalis and L. goodfellowii fermented mannose and were β-galactosidase-6-phosphate positive. L. goodfellowii, L. hofstadii and L. wadei were β-haemolytic. L. buccalis fermented raffinose. With L. buccalis, L. goodfellowii showed 3·8–5·5 % DNA–DNA relatedness, L. shahii showed 24·5–34·1 % relatedness, L. hofstadii showed 27·3–36·3 % relatedness and L. wadei showed 24·1–35·9 % relatedness. 16S rDNA sequencing demonstrated that L. hofstadii, L. shahii, L. wadei and L. goodfellowii each formed individual clusters with 97, 96, 94 and 92 % similarity, respectively, to L. buccalis.

scholarly journals Olsenella umbonata sp. nov., a microaerotolerant anaerobic lactic acid bacterium from the sheep rumen and pig jejunum, and emended descriptions of Olsenella, Olsenella uli and Olsenella profusa

2011 ◽  
Vol 61 (4) ◽  
pp. 795-803 ◽  
Author(s):  
Mareike Kraatz ◽  
R. John Wallace ◽  
Liselott Svensson
Keyword(s):  
Lactic Acid ◽  
Type Strain ◽  
Culture Media ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Fatty Acid Analysis ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Biochemical Tests ◽  
Sheep Rumen

Strain A2 is an anaerobic, variably Gram-stain-positive, non-spore-forming, small and irregularly rod-shaped bacterium from the ruminal fluid of a sheep that has been described informally as a representative of ‘Olsenella (basonym Atopobium) oviles’. Three phenotypically similar bacterial strains (lac15, lac16 and lac31T) were isolated in concert with Veillonella magna lac18T from the mucosal jejunum of a pig. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strains A2, lac15, lac16 and lac31T formed a genetically coherent group (100 % interstrain sequence similarity) within the bigeneric Olsenella–Atopobium branch of the family Coriobacteriaceae, class Actinobacteria. This group was most closely related to the type strains of the two recognized Olsenella species, namely Olsenella uli (sequence similarity of 96.85 %) and Olsenella profusa (sequence similarity of 97.20 %). The sequence similarity to the type strain of Atopobium minutum, the type species of the genus Atopobium, was 92.33 %. Unlike those of O. uli and O. profusa, outgrown colonies of strains A2, lac15, lac16 and lac31T were opaque and greyish-white with an umbonate elevation on solid culture media. The four novel strains were characterized as being well-adapted and presumably indigenous to the gastrointestinal tract of homoeothermic vertebrates: they were mesophilic, microaerotolerant, neutrophilic and acidotolerant, bile-resistant, mucin-utilizing and markedly peptidolytic lactic acid bacteria. The results of DNA–DNA hybridizations, cellular fatty acid analysis and other differential phenotypic (physiological and biochemical) tests confirmed that strains A2, lac15, lac16 and lac31T represent a novel species of the genus Olsenella. On the basis of the genotypic and phenotypic results, we therefore describe Olsenella umbonata sp. nov., with lac31T ( = CCUG 58604T  = DSM 22620T  = JCM 16156T) as the type strain and A2 ( = CCUG 58212  = DSM 22619  = JCM 16157) as an additionally available reference strain. Also, based on our data, we propose emended descriptions of the genus Olsenella and the species Olsenella uli and Olsenella profusa.

scholarly journals Bacterial load and multi‐drug resistance patterns of some ready‐to‐eat street foods of Dhaka city

2018 ◽  
Vol 27 (1) ◽  
pp. 27-36
Author(s):  
Mihir Lal Saha ◽  
Mist Dilara Akter ◽  
Tahsin Khan ◽  
Aneesa Ansari ◽  
Mohammad Nurul Islam
Keyword(s):  
Drug Resistance ◽  
Klebsiella Pneumoniae ◽  
16S Rdna ◽  
Bacterial Load ◽  
Enterobacter Aerogenes ◽  
Multi Drug Resistance ◽  
16S Rdna Sequencing ◽  
Gram Negative ◽  
Plesiomonas Shigelloides ◽  
Rdna Sequencing

Bacterial load and drug resistance pattern associated with some ready-to-eat (RTE) street foods such as Chatpoti, Fuchka, Singara, Panipuri, Ghugni-muri, Chola and water of Dhaka South City Corporation were investigated. Most of the samples were found to be contaminated and the bacterial load ranged from 2.4 × 104 - 9.2 × 106, 1.2 × 103 - 7.3 × 105 and 1.1 × 103 - 1.6 × 106 cfu/g of aerobic heterotrophic, coliform bacteria and Staphylococcus, respectively. The highest coliform load (7.3 × 105 cfu/ml) was found in the water of Gulistan. The highest aerobic heterotrophic bacteria (9.2 × 106 cfu/g) and Staphylococcus (1.6 × 106 cfu/g) were observed in the Chatpoti of Nilkhet. Among the isolated 100 different bacterial colonies, 20 Gram-positive and 8 Gram-negative isolates were studied in details. Based on the morphological and biochemical analysis, the Grampositive isolates were identified as Staphylococcus (9), Bacillus (4), Kurthia (3), Planococcus (1), Micrococcus (1), Listeria (1) and Renibacterium (1). Gram-negative isolates were identified as Klebsiella pneumoniae (3), Yersinia pestis (1), Y. pseudotuberculosis (1), Escherichia coli (1), Enterobacter aerogenes (1) and Plesiomonas shigelloides (1). The multi-drug resistance (MDR) pattern was found to be diverse. Among the MDR bacteria, Enterobacter aerogenes was found to be resistant against six common antibiotics. Plesiomonas shigelloides and Yersinia pestis were found to be resistant against five antibiotics. The multiple antibiotic resistant (MAR) indices of Gram-negative isolates ranged in between 22.22 and 66.67%. Conventionally identified five bacterial isolates with significant MAR indices were further identified with 16S rDNA sequencing and found to be as Enterobacter cloaceae Ecl1, Plesiomonas shigelloides CIFRI, Aeromonas sp. TIL_WAK_4, Aeromonas sp. 280 and Klebsiella pneumoniae KPS77. Conventional identification was found to be accurate for three isolates but the two Yersinia sp. were identified to be as Aeromonas sp. in 16S rDNA sequencing. Dhaka Univ. J. Biol. Sci. 27(1): 27-36, 2018 (January)

scholarly journals Preliminary Characterization of a Pleomorphic Gram-Negative Rod Associated with Avian Respiratory Disease

1993 ◽  
Vol 5 (1) ◽  
pp. 47-51 ◽  
Author(s):  
Bruce R. Charlton ◽  
Sally E. Channing-Santiago ◽  
Arthur A. Bickford ◽  
Carol J. Cardona ◽  
Richard P. Chin ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Respiratory Disease ◽  
Domestic Fowl ◽  
Cellular Fatty Acid ◽  
Fatty Acid Analysis ◽  
Biochemical Tests ◽  
Gram Negative ◽  
Preliminary Characterization ◽  
Cellular Fatty Acids

An unidentified, pleomorphic, gram-negative rod (PGNR) bacterium has been isolated from domestic fowl with respiratory disease. The PGNR was isolated in 5% of turkey accessions and 3% of chicken accessions, primarily from the respiratory tract. Preliminary characterization of this organism included reviewing accession records, conducting cultural and biochemical tests, and analyzing cellular fatty acids. The PGNR was also compared with other bacteria capable of inhabiting the avian respiratory system. Biochemical and cellular fatty acid analysis failed to identify the organism, however all 14 isolates were similar.

Metabolite fingerprinting of novel Streptomyces UK-238 from the Himalayan forest

2020 ◽  
Vol 16 ◽  
Author(s):  
Nidhi Srivastava ◽  
Indira P. Sarethy
Keyword(s):  
Ethyl Acetate ◽  
16S Rdna ◽  
Retention Index ◽  
Ethyl Acetate Extract ◽  
Similarity Index ◽  
Antimicrobial Drug ◽  
16S Rdna Sequencing ◽  
Metabolite Fingerprinting ◽  
Streptomyces Sp ◽  
Rdna Sequencing

Aims: Characterization of antimicrobial metabolites of novel Streptomyces sp. UK-238. Background: Novel antimicrobial drug discovery is urgently needed due to emerging multi antimicrobial drug resistance among pathogens. Since many years, natural products have provided the basic skeletons for many therapeutic compounds including antibiotics. Bioprospection of un/under explored habitats and focussing on selective isolation of actinobacteria as major reservoir of bio and chemodiversity has yielded good results. Objective: The main objectives of the study were the identification of UK-238 by 16S rDNA sequencing and antimicrobial metabolite fingerprinting of culture extracts. Method: In the present study, a promising isolate, UK-238, has been screened for antimicrobial activity and metabolite fingerprinting from the Himalayan Thano Reserve forest. It was identified by 16S rDNA sequencing. Ethyl acetate extract was partially purified by column chromatography. The pooled active fractions were fingerprinted by GC-MS and compounds were tentatively identified by collated data analysis based on Similarity Index, observed Retention Index from Databases and calculated Retention Index. Results: UK-238 was identified as Streptomyces sp. with 98.4% similarity to S. niveiscabiei. It exhibited broad-spectrum antibacterial and antifungal activity. GC-MS analysis of active fractions of ethyl acetate extract showed the presence of eighteen novel antimicrobial compounds belonging to four major categories- alcohols, alkaloid, esters and peptide. Conclusion: The study confirms that bioprospection of underexplored habitats can elaborate novel bio and chemodiversity.

scholarly journals 2-Way k-Means as a Model for Microbiome Samples

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Weston J. Jackson ◽  
Ipsita Agarwal ◽  
Itsik Pe’er
Keyword(s):  
Unsupervised Learning ◽  
16S Rdna ◽  
Mixture Model ◽  
Vaginal Microbiome ◽  
16S Rdna Sequencing ◽  
Sequencing Data ◽  
Cluster Assignment ◽  
Rdna Sequencing

Motivation. Microbiome sequencing allows defining clusters of samples with shared composition. However, this paradigm poorly accounts for samples whose composition is a mixture of cluster-characterizing ones and which therefore lie in between them in the cluster space. This paper addresses unsupervised learning of 2-way clusters. It defines a mixture model that allows 2-way cluster assignment and describes a variant of generalized k-means for learning such a model. We demonstrate applicability to microbial 16S rDNA sequencing data from the Human Vaginal Microbiome Project.

Analysis of the bacterial floral structure and diversity of Xuanwei ham by 16S rDNA sequencing

2020 ◽  
Vol 40 (4) ◽  
Author(s):  
Luying Shan ◽  
Yinjiao Li ◽  
Shi Zheng ◽  
Yuanmiao Wei ◽  
Ying Shang
Keyword(s):  
16S Rdna ◽  
16S Rdna Sequencing ◽  
Floral Structure ◽  
Rdna Sequencing

scholarly journals ISOLATION, PURIFICATION, AND CHARACTERIZATION OF LIPASE FROM BACILLUS SP. FROM KITCHEN GREASE

2018 ◽  
Vol 11 (6) ◽  
pp. 224
Author(s):  
Jaiganesh R ◽  
Jaganathan Mk
Keyword(s):  
16S Rdna ◽  
Solvent Tolerance ◽  
16S Rdna Sequencing ◽  
Bacillus Sp ◽  
Purification And Characterization ◽  
Lipase Enzyme ◽  
Sequencing Method ◽  
Rdna Sequencing ◽  
Solvent Tolerant

Objective: The objective of this work was to isolation, purification and characterization of solvent tolerant lipase from Bacillus sp. The objective of this work was to isolation, purification and characterization of solvent tolerant lipase from Bacillus sp. from kitchen grease for a variety of applications including organic synthetic reactions and preparation of enantiomerically pure pharmaceuticals.Methods: Lipase producing isolates were screened from kitchen grease on a selective medium rhodamine B olive oil agar, and tributyrin agar was used to screen the lipase and esterase producing an organism, respectively. The isolate identified using 16S rDNA sequencing method and enzyme activity was quantitatively assayed. Lipase production was characterized in different conditions.Results: The isolate showed highest lipase activity was which later was identified as Bacillus sp. using 16S rDNA sequencing method. The lipase was purified using ammonium sulfate precipitation. The isolate showed excellent tolerance to methanol, ethanol, acetonitrile, and moderate tolerance to butanol. The increased biomass concentration, maximum production, and activity were achieved at 37°C in 24 h incubation, then gradual reduction in production was observed. The maximum activity of lipase enzyme was obtained at pH between 6 and 9.Conclusion: The isolate produce solvent tolerance lipase enzyme and it can be a promising candidate of solvent tolerance lipase enzyme for variety of industrial applications.

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