Characterization of Streptomyces sp. UK-201 from Lachhiwala Reserve forest, a biodiversity hot spot of the Himalayas

Background: Multi-drug resistance among pathogens is emerging due to slow pace of development of new antimicrobials by combinatorial chemistry. Natural products from microorganisms from under-explored habitats can be lead molecules for such discoveries. Objective: The major objectives were to characterize isolate UK-201, taxonomically identify UK-201 based on 16S rDNA sequencing and execute metabolite fingerprinting of ethyl acetate extract of UK-201 by GC-MS. Method: In search of new antimicrobial compounds, Streptomyces isolate UK-201 exhibiting broad spectrum antimicrobial and antifungal activity, obtained from under-explored Lachhiwala Reserve forest, of the Himalayas was selected in this study. Isolate UK-201 was identified by 16S rDNA sequencing. Ethyl acetate extract of this isolate exhibited antimicrobial activity against all selected panel of Gram positive, Gram negative bacteria and fungi among other organic solvent extracts. Hence, EA extract was partially purified by column chromatography. Active fractions were pooled and analysed by GC-MS. Obtained compounds were tentatively identified by collated data analysis based on Similarity Index, observed Retention Index from Databases and calculated Retention Index. Results: Isolate UK-201 showed 97.46% similarity to Streptomyces niveiscabiei, 96.88% to S. sasae and S. puniciscabiei, 96.72% to S. capoamus and S. yaanensis. Low similarity percentage indicated the taxonomic novelty of the isolate and was confirmed by comparing with phenotypic characteristics with nearest matches. Metabolite fingerprinting showed the presence of twenty-four compounds and could be novel. Conclusion: This study showed that bioprospection from under-explored habitats conferred novel bio and chemodiversity.

Download Full-text

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

Current Pharmaceutical Analysis ◽

10.2174/1573412916666200206160836 ◽

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.

Download Full-text

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

Dhaka University Journal of Biological Sciences ◽

10.3329/dujbs.v27i1.46408 ◽

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)

Download Full-text

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

Journal of Healthcare Engineering ◽

10.1155/2017/5284145 ◽

2017 ◽

Vol 2017 ◽

pp. 1-7 ◽

Cited By ~ 1

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.

Download Full-text

Evaluation of MALDI-TOF mass spectrometry and MALDI BioTyper in comparison to 16S rDNA sequencing for the identification of bacteria isolated from Arctic sea water

PLoS ONE ◽

10.1371/journal.pone.0181860 ◽

2017 ◽

Vol 12 (7) ◽

pp. e0181860 ◽

Cited By ~ 19

Author(s):

Anna Maria Timperio ◽

Susanna Gorrasi ◽

Lello Zolla ◽

Massimiliano Fenice

Keyword(s):

Mass Spectrometry ◽

16S Rdna ◽

Sea Water ◽

16S Rdna Sequencing ◽

Maldi Tof Mass Spectrometry ◽

Maldi Tof ◽

Rdna Sequencing ◽

Arctic Sea ◽

Maldi Biotyper ◽

Identification Of Bacteria

Download Full-text

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

Journal of Food Safety ◽

10.1111/jfs.12800 ◽

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

Download Full-text

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

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2018.v11i6.24955 ◽

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.

Download Full-text