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Identification of Contaminating Bacteria When Attempting to Isolate Mycobacterium Avium Subsp
Arch Med Vet 47, 97-100 (2015) COMMUNICATION Identification of contaminating bacteria when attempting to isolate Mycobacterium avium subsp. paratuberculosis (MAP) from bovine faecal and tissue samples using the BACTEC MGIT 960 system# Identificación de bacterias contaminantes al aislar Mycobacterium avium subsp. paratuberculosis (MAP) desde muestras de material fecal y tejido de bovinos, utilizando el sistema de cultivo BACTEC-MGIT 960 P Steuera, b, J de Waardc, MT Collinsd, EP Troncosoa, OA Martíneza, C Tejedaa, MA Salgadoa* aBiochemistry and Microbiology Department, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile. bGraduate School, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile. cLaboratorio de Tuberculosis, Instituto de Biomedicina, Caracas, Venezuela. dDeptartment of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, USA. RESUMEN El diagnóstico de la infección por Mycobacterium avium subsp. paratuberculosis (MAP) al utilizar un sistema de cultivo líquido resulta en una mayor sensibilidad, rapidez y automatización. Sin embargo, tiene como desventajas una mayor tasa de contaminación en relación con los sistemas convencionales y también es menos específico. El presente estudio identificó algunas bacterias contaminantes del sistema de cultivo BACTEC-MGIT 960 al procesar muestras clínicas de ganado bovino del sur de Chile. No se detectaron micobacterias en las muestras falsas positivas a MAP mediante la técnica Reacción en Cadena de la Polimerasa-Análisis con Enzimas de Restricción (PRA)-hsp65. Por otra parte, el Análisis de los Espaciadores Intergénicos Ribosomales (RISA) seguido de un análisis de secuenciación, reveló la presencia de Paenibacillus sp., Enterobacterias y Pseudomonas aeruginosa como contaminantes comunes. Los protocolos de eliminación de contaminantes deberían considerar esta información para mejorar los resultados diagnósticos de los sistemas de cultivo líquido. -
Biochemical Characterization and 16S Rdna Sequencing of Lipolytic Thermophiles from Selayang Hot Spring, Malaysia
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Available online at www.sciencedirect.com ScienceDirect IERI Procedia 5 ( 2013 ) 258 – 264 2013 International Conference on Agricultural and Natural Resources Engineering Biochemical Characterization and 16S rDNA Sequencing of Lipolytic Thermophiles from Selayang Hot Spring, Malaysia a a a a M.J., Norashirene , H., Umi Sarah , M.H, Siti Khairiyah and S., Nurdiana aFaculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia. Abstract Thermophiles are well known as organisms that can withstand extreme temperature. Thermoenzymes from thermophiles have numerous potential for biotechnological applications due to their integral stability to tolerate extreme pH and elevated temperature. Because of the industrial importance of lipases, there is ongoing interest in the isolation of new bacterial strain producing lipases. Six isolates of lipases producing thermophiles namely K7S1T53D5, K7S1T53D6, K7S1T53D11, K7S1T53D12, K7S2T51D14 and K7S2T51D19 were isolated from the Selayang Hot Spring, Malaysia. The sampling site is neutral in pH with a highest recorded temperature of 53°C. For the screening and isolation of lipolytic thermopiles, selective medium containing Tween 80 was used. Thermostability and the ability to degrade the substrate even at higher temperature was proved and determined by incubation of the positive isolates at temperature 53°C. Colonies with circular borders, convex in elevation with an entire margin and opaque were obtained. 16S rDNA gene amplification and sequence analysis were done for bacterial identification. The isolate of K7S1T53D6 was derived of genus Bacillus that is the spore forming type, rod shaped, aerobic, with the ability to degrade lipid. -
Bacterial Succession Within an Ephemeral Hypereutrophic Mojave Desert Playa Lake
Microb Ecol (2009) 57:307–320 DOI 10.1007/s00248-008-9426-3 MICROBIOLOGY OF AQUATIC SYSTEMS Bacterial Succession within an Ephemeral Hypereutrophic Mojave Desert Playa Lake Jason B. Navarro & Duane P. Moser & Andrea Flores & Christian Ross & Michael R. Rosen & Hailiang Dong & Gengxin Zhang & Brian P. Hedlund Received: 4 February 2008 /Accepted: 3 July 2008 /Published online: 30 August 2008 # Springer Science + Business Media, LLC 2008 Abstract Ephemerally wet playas are conspicuous features RNA gene sequencing of bacterial isolates and uncultivated of arid landscapes worldwide; however, they have not been clones. Isolates from the early-phase flooded playa were well studied as habitats for microorganisms. We tracked the primarily Actinobacteria, Firmicutes, and Bacteroidetes, yet geochemistry and microbial community in Silver Lake clone libraries were dominated by Betaproteobacteria and yet playa, California, over one flooding/desiccation cycle uncultivated Actinobacteria. Isolates from the late-flooded following the unusually wet winter of 2004–2005. Over phase ecosystem were predominantly Proteobacteria, partic- the course of the study, total dissolved solids increased by ularly alkalitolerant isolates of Rhodobaca, Porphyrobacter, ∽10-fold and pH increased by nearly one unit. As the lake Hydrogenophaga, Alishwenella, and relatives of Thauera; contracted and temperatures increased over the summer, a however, clone libraries were composed almost entirely of moderately dense planktonic population of ∽1×106 cells ml−1 Synechococcus (Cyanobacteria). A sample taken after the of culturable heterotrophs was replaced by a dense popula- playa surface was completely desiccated contained diverse tion of more than 1×109 cells ml−1, which appears to be the culturable Actinobacteria typically isolated from soils. -
Discovery of a Paenibacillus Isolate for Biocontrol of Black Rot in Brassicas
Lincoln University Digital Thesis Copyright Statement The digital copy of this thesis is protected by the Copyright Act 1994 (New Zealand). This thesis may be consulted by you, provided you comply with the provisions of the Act and the following conditions of use: you will use the copy only for the purposes of research or private study you will recognise the author's right to be identified as the author of the thesis and due acknowledgement will be made to the author where appropriate you will obtain the author's permission before publishing any material from the thesis. Discovery of a Paenibacillus isolate for biocontrol of black rot in brassicas A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy at Lincoln University by Hoda Ghazalibiglar Lincoln University 2014 DECLARATION This dissertation/thesis (please circle one) is submitted in partial fulfilment of the requirements for the Lincoln University Degree of ________________________________________ The regulations for the degree are set out in the Lincoln University Calendar and are elaborated in a practice manual known as House Rules for the Study of Doctor of Philosophy or Masters Degrees at Lincoln University. Supervisor’s Declaration I confirm that, to the best of my knowledge: • the research was carried out and the dissertation was prepared under my direct supervision; • except where otherwise approved by the Academic Administration Committee of Lincoln University, the research was conducted in accordance with the degree regulations and house rules; • the dissertation/thesis (please circle one)represents the original research work of the candidate; • the contribution made to the research by me, by other members of the supervisory team, by other members of staff of the University and by others was consistent with normal supervisory practice. -
Paenibacillaceae Cover
The Family Paenibacillaceae Strain Catalog and Reference • BGSC • Daniel R. Zeigler, Director The Family Paenibacillaceae Bacillus Genetic Stock Center Catalog of Strains Part 5 Daniel R. Zeigler, Ph.D. BGSC Director © 2013 Daniel R. Zeigler Bacillus Genetic Stock Center 484 West Twelfth Avenue Biological Sciences 556 Columbus OH 43210 USA www.bgsc.org The Bacillus Genetic Stock Center is supported in part by a grant from the National Sciences Foundation, Award Number: DBI-1349029 The author disclaims any conflict of interest. Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or by the Ohio State University. Cover: Paenibacillus dendritiformus colony pattern formation. Color added for effect. Image courtesy of Eshel Ben Jacob. TABLE OF CONTENTS Table of Contents .......................................................................................................................................................... 1 Welcome to the Bacillus Genetic Stock Center ............................................................................................................. 2 What is the Bacillus Genetic Stock Center? ............................................................................................................... 2 What kinds of cultures are available from the BGSC? ............................................................................................... 2 What you can do to help the BGSC ........................................................................................................................... -
Complete Genome Sequence of Cohnella Sp. HS21 Isolated from Korean Fir (Abies Koreana) Rhizospheric Soil 구상나무 근권 토
Korean Journal of Microbiology (2019) Vol. 55, No. 2, pp. 171-173 pISSN 0440-2413 DOI https://doi.org/10.7845/kjm.2019.9028 eISSN 2383-9902 Copyright ⓒ 2019, The Microbiological Society of Korea Complete genome sequence of Cohnella sp. HS21 isolated from Korean fir (Abies koreana) rhizospheric soil 1,2 1 1 1 1 2 1 Lingmin Jiang , Se Won Kang , Song-Gun Kim , Jae Cheol Jeong , Cha Young Kim , Dae-Hyuk Kim , Suk Weon Kim * , 1 and Jiyoung Lee * 1 Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Republic of Korea 2 Department of Bioactive Materials, Chonbuk National University, Jeonju 54896, Republic of Korea 구상나무 근권 토양으로부터 분리된 Cohnella sp. HS21의 전체 게놈 서열 지앙 링민1,2 ・ 강세원1 ・ 김성건1 ・ 정재철1 ・ 김차영1 ・ 김대혁2 ・ 김석원1* ・ 이지영1* 1 2 한국생명공학연구원 생물자원센터, 전북대학교 생리활성소재과학과 (Received March 19, 2019; Revised May 7, 2019; Accepted May 7, 2019) The genus Cohnella, which belongs to the family Paenibacillaceae, environmental niches, including mammals (Khianngam et al., inhabits a wide range of environmental niches. Here, we report 2012), the starch production industry (Kämpfer et al., 2006), the complete genome sequence of Cohnella sp. HS21, which fresh water (Shiratori et al., 2010), plant root nodules (Flores- was isolated from the rhizospheric soil of Korean fir (Abies Félix et al., 2014), and soils (Huang et al., 2014; Lee et al., koreana) on the top of Halla Mountain in the Republic of 2015). We have recently isolated the bacterium strain HS21 Korea. Strain HS21 features a 7,059,027 bp circular chromo- some with 44.8% GC-content. -
| Hao Wakati Mwith Oululah M
|HAO WAKATIMWITH US009856500B2 OULULAH M (12 ) United States Patent ( 10 ) Patent No. : US 9 , 856 ,500 B2 Adhikari et al. (45 ) Date of Patent: Jan . 2 , 2018 ( 54 ) METHOD OF CONSOLIDATED ( 56 ) References Cited BIOPROCESSING OF LIGNOCELLULOSIC BIOMASS FOR PRODUCTION OF L - LACTIC U . S . PATENT DOCUMENTS ACID 2005 /0106694 A1 * 5 /2005 Green .. .. .. C12R 1 /07 435 / 146 ( 71) Applicant : Council of Scientific and Industrial Research , New Delhi ( IN ) FOREIGN PATENT DOCUMENTS (72 ) Inventors : Dilip Kumar Adhikari, Mohkampur AU WO 2007140521 A1 * 12/ 2007 .. A61K 8 /97 ( IN ) ; Jayati Trivedi, Mohkampur ( IN ) ; WO WO 2012 / 071392 A2 * 5 / 2012 C12N 1 /21 Deepti Agrawal, Mohkampur ( IN ) WO WO - 2014 /013509 1 / 2014 (73 ) Assignee : Council of Scientific and Industrial OTHER PUBLICATIONS Research , New Delhi ( IN ) Taxonomy Paenibacillus macerans (Bacillus macerans ) (Species Paema Taxon Identifier http : / /www .uniprot .org / taxonomy/ 44252 ( * ) Notice : Subject to any disclaimer, the term of this printed Sep . 29 , 2016 . * patent is extended or adjusted under 35 Nakamura et al . 1988 . Taxonomic Study of Bacillus coagulans Hammer 1915 with a Proposal for Bacillus smithii sp . nov . Inter U . S . C . 154 ( b ) by 201 days . national Journal of Systematic Bacteriology , vol . 38 , pp . 63 - 73. * Ryckeboer et al . 2003 . Microbiological aspects of biowaste during (21 ) Appl . No. : 14 /415 , 652 composting in a monitored compost bin . Journal of Applied Micro biology , vol. 94 , 127 - 137 . * (22 ) PCT Filed : Jul . 17, 2013 Partanan et al 2010 . Bacterial diversity at different stages of the composting process . BMC Microbiology vol. 10 , pp . 94 - 104 ( 1 - 11) . * ( 86 ) PCT No. -
Genome Snapshot of Paenibacillus Polymyxa ATCC 842T
J. Microbiol. Biotechnol. (2006), 16(10), 1650–1655 Genome Snapshot of Paenibacillus polymyxa ATCC 842T JEONG, HAEYOUNG, JIHYUN F. KIM, YON-KYOUNG PARK, SEONG-BIN KIM, CHANGHOON KIM†, AND SEUNG-HWAN PARK* Laboratory of Microbial Genomics, Systems Microbiology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), P.O. Box 115, Yuseong, Daejeon 305-600, Korea Received: May 11, 2006 Accepted: June 22, 2006 Abstract Bacteria belonging to the genus Paenibacillus are rhizosphere and soil, and their useful traits have been facultatively anaerobic endospore formers and are attracting analyzed [3, 6-8, 10, 15, 22, 26]. At present, the genus growing ecological and agricultural interest, yet their genome Paenibacillus consists of 84 species (NCBI Taxonomy information is very limited. The present study surveyed the Homepage at http://www.ncbi.nlm.nih.gov/Taxonomy/ genomic features of P. polymyxa ATCC 842 T using pulse-field taxonomyhome.html, February 2006). gel electrophoresis of restriction fragments and sample genome Nonetheless, despite the growing interest in Paenibacillus, sequencing of 1,747 reads (approximately 17.5% coverage of its genomic information is very scarce. Most of the completely the genome). Putative functions were assigned to more than sequenced organisms currently belong to the Bacillaceae 60% of the sequences. Functional classification of the sequences family, in particular to the Bacillus genus, whereas data on showed a similar pattern to that of B. subtilis. Sequence Paenibacillaceae sequences is limited even at the draft analysis suggests nitrogen fixation and antibiotic production level. P. polymyxa, the type species of the genus Paenibacillus, by P. polymyxa ATCC 842 T, which may explain its plant is also of great ecological and agricultural importance, owing growth-promoting effects. -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Cohnella Algarum Sp. Nov., Isolated from a Freshwater Green Alga Paulinella Chromatophora
TAXONOMIC DESCRIPTION Lee and Jeon, Int J Syst Evol Microbiol 2017;67:4767–4772 DOI 10.1099/ijsem.0.002377 Cohnella algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora Yunho Lee and Che Ok Jeon* Abstract A Gram-stain-positive, facultatively aerobic and endospore-forming bacterium, designated strain Pch-40T, was isolated from a freshwater green alga, Paulinella chromatophora. Cells were motile rods with a monotrichous polar flagellum showing catalase- and oxidase-positive reactions. Strain Pch-40T grew at 20–50 C (optimum, 37–40 C), at pH 5.0–11.0 (optimum, pH 7.0) and in the presence of 0–4.0 % (w/v) NaCl (optimum, 0 %). Menaquinone-7 was detected as the sole isoprenoid quinone. T T The genomic DNA G+C content of strain Pch-40 was 55.6 mol%. The major cellular fatty acids of strain Pch-40 were C16 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pch-40T clearly belonged to the genus Cohnella of the family Paenibacillaceae. Strain Pch-40T was most closely related to Cohnella rhizosphaerae CSE-5610T with a 96.1 % 16S rRNA gene sequence similarity. The phenotypic and chemotaxonomic features and the phylogenetic inference clearly suggested that strain Pch-40T represents a novel species of the genus Cohnella, for which the name Cohnella algarum sp. nov. is proposed. The type strain is strain Pch-40T (=KACC 19279T=JCM 32033T). The genus Cohnella, belonging to the family Paenibacilla- useful compounds for industry [14, 15]. -
Beno Cornellgrad 0058F 10677.Pdf
BACILLALES INFLUENCE QUALITY AND SAFETY OF DAIRY PRODUCTS A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Sarah Marie Beno December 2017 © 2017 Sarah Marie Beno BACILLALES INFLUENCE QUALITY AND SAFETY OF DAIRY PRODUCTS Sarah Marie Beno, Ph. D. Cornell University 2017 Bacillales, an order of Gram-positive bacteria, are commonly isolated from dairy foods and at various points along the dairy value chain. Three families of Bacillales are analyzed in this work: (i) Listeriaceae (represented by Listeria monocytogenes), (ii) Paenibacillaceae (represented by Paenibacillus), and (iii) Bacillaceae (represented by the Bacillus cereus group). These families impact both food safety and food quality. Most Listeriaceae are non- pathogenic, but L. monocytogenes has one of the highest mortality rates of foodborne pathogens. Listeria spp. are often reported in food processing environments. Here, 4,430 environmental samples were collected from 9 small cheese-processing facilities and tested for Listeria and L. monocytogenes. Prevalence varied by processing facility, but across all facilities, 6.03 and 1.35% of samples were positive for L. monocytogenes and other Listeria spp., respectively. Each of these families contains strains capable of growth at refrigeration temperatures. To more broadly understand milk spoilage bacteria, genetic analyses were performed on 28 Paenibacillus and 23 B. cereus group isolates. While no specific genes were significantly associated with cold-growing Paenibacillus, the growth variation and vast genetic data introduced in this study provide a strong foundation for the development of detection strategies. Some species within the B. -
Brevibacillus Massiliensis Sp. Nov
Standards in Genomic Sciences (2013) 8:1-14 DOI:10.4056/sigs.3466975 Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Perrine Hugon1†, Ajay Kumar Mishra1†, Jean-Christophe Lagier1, Thi Thien Nguyen1, Carine Couderc1, Didier Raoult1 and Pierre-Edouard Fournier1* 1Aix-Marseille Université, URMITE, Faculté de médecine, France † These two authors have equal contribution * Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Brevibacillus massiliensis, genome, culturomics, taxono-genomics Brevibacillus massiliensis strain phRT sp. nov. is the type strain of B. massiliensis sp. nov., a new species within the genus Brevibacillus. This strain was isolated from the fecal flora of a woman suffering from morbid obesity. B. massiliensis is a Gram-positive aerobic rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,051,018 bp long genome (1 chromosome but no plasmid) contains 5,051 protein-coding and 84 RNA genes, and exhibits a G+C content of 53.1%. Introduction Brevibacillus massiliensis strain phRT (= CSUR brevis and B. centrosporus were isolated from in- P177 = DSM 25447) is the type strain of B. door dust in schools, day care centers for children massiliensis sp. nov. This bacterium is a Gram- and animal sheds [26], and fecal flora of children, positive, spore-forming, indole negative, aerobic respectively [27]. However, several Brevibacillus and motile bacillus that was isolated from the species are also frequently isolated from humans, stool of a 26-year-old woman suffering from mor- notably in nosocomial infections, causing breast bid obesity.