BBL™ Trypticase™ Soy Agar B L007516 • Rev
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Identification of Strains Isolated in Thailand and Assigned to the Genera Kozakia and Swaminathania
JOURNAL OF CULTURE COLLECTIONS Volume 6, 2008-2009, pp. 61-68 IDENTIFICATION OF STRAINS ISOLATED IN THAILAND AND ASSIGNED TO THE GENERA KOZAKIA AND SWAMINATHANIA Jintana Kommanee1, Somboon Tanasupawat1,*, Ancharida Akaracharanya2, Taweesak Malimas3, Pattaraporn Yukphan3, Yuki Muramatsu4, Yasuyoshi Nakagawa4 and Yuzo Yamada3,† 1Department of Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand; 2Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; 3BIOTEC Culture Collection, National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand; 4Biological Resource Center, Department of Biotechnology, National Institute of Technology and Evaluation, Kisarazu 292-0818, Japan; †JICA Senior Overseas Volunteer, Japan International Cooperation Agency, Shibuya-ku, Tokyo 151-8558, Japan; Professor Emeritus, Shizuoka University, Suruga-ku, Shizuoka 422-8529, Japan *Corresponding author, e-mail: [email protected] Summary Four isolates, isolated from fruit of sapodilla collected at Chantaburi and designated as CT8-1 and CT8-2, and isolated from seeds of ixora („khem” in Thai, Ixora species) collected at Rayong and designated as SI15-1 and SI15-2, were examined taxonomically. The four isolates were selected from a total of 181 isolated acetic acid bacteria. Isolates CT8-1 and CT8-2 were non motile and produced a levan-like mucous polysaccharide from sucrose or D-fructose, but did not produce a water-soluble brown pigment from D-glucose on CaCO3-containing agar slants. The isolates produced acetic acid from ethanol and oxidized acetate and lactate to carbon dioxide and water, but the intensity of the acetate and lactate oxidation was weak. Their growth was not inhibited by 0.35 % acetic acid (v/v) at pH 3.5. -
Ancient Metaproteomics: a Novel Approach for Understanding Disease And
Ancient metaproteomics: a novel approach for understanding disease and diet in the archaeological record Jessica Hendy PhD University of York Archaeology August, 2015 ii Abstract Proteomics is increasingly being applied to archaeological samples following technological developments in mass spectrometry. This thesis explores how these developments may contribute to the characterisation of disease and diet in the archaeological record. This thesis has a three-fold aim; a) to evaluate the potential of shotgun proteomics as a method for characterising ancient disease, b) to develop the metaproteomic analysis of dental calculus as a tool for understanding both ancient oral health and patterns of individual food consumption and c) to apply these methodological developments to understanding individual lifeways of people enslaved during the 19th century transatlantic slave trade. This thesis demonstrates that ancient metaproteomics can be a powerful tool for identifying microorganisms in the archaeological record, characterising the functional profile of ancient proteomes and accessing individual patterns of food consumption with high taxonomic specificity. In particular, analysis of dental calculus may be an extremely valuable tool for understanding the aetiology of past oral diseases. Results of this study highlight the value of revisiting previous studies with more recent methodological approaches and demonstrate that biomolecular preservation can have a significant impact on the effectiveness of ancient proteins as an archaeological tool for this characterisation. Using the approaches developed in this study we have the opportunity to increase the visibility of past diseases and their aetiology, as well as develop a richer understanding of individual lifeways through the production of molecular life histories. iii iv List of Contents Abstract ............................................................................................................................... -
Differentiating Two Closely Related Alexandrium Species Using Comparative Quantitative Proteomics
toxins Article Differentiating Two Closely Related Alexandrium Species Using Comparative Quantitative Proteomics Bryan John J. Subong 1,2,* , Arturo O. Lluisma 1, Rhodora V. Azanza 1 and Lilibeth A. Salvador-Reyes 1,* 1 Marine Science Institute, University of the Philippines- Diliman, Velasquez Street, Quezon City 1101, Philippines; [email protected] (A.O.L.); [email protected] (R.V.A.) 2 Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo City, Tokyo 113-8654, Japan * Correspondence: [email protected] (B.J.J.S.); [email protected] (L.A.S.-R.) Abstract: Alexandrium minutum and Alexandrium tamutum are two closely related harmful algal bloom (HAB)-causing species with different toxicity. Using isobaric tags for relative and absolute quantita- tion (iTRAQ)-based quantitative proteomics and two-dimensional differential gel electrophoresis (2D-DIGE), a comprehensive characterization of the proteomes of A. minutum and A. tamutum was performed to identify the cellular and molecular underpinnings for the dissimilarity between these two species. A total of 1436 proteins and 420 protein spots were identified using iTRAQ-based proteomics and 2D-DIGE, respectively. Both methods revealed little difference (10–12%) between the proteomes of A. minutum and A. tamutum, highlighting that these organisms follow similar cellular and biological processes at the exponential stage. Toxin biosynthetic enzymes were present in both organisms. However, the gonyautoxin-producing A. minutum showed higher levels of osmotic growth proteins, Zn-dependent alcohol dehydrogenase and type-I polyketide synthase compared to the non-toxic A. tamutum. Further, A. tamutum had increased S-adenosylmethionine transferase that may potentially have a negative feedback mechanism to toxin biosynthesis. -
Article (Refereed) - Postprint
Article (refereed) - postprint Rogers, Geraint B.; Cuthbertson, Leah; Hoffman, Lucas R.; Wing, Peter A.C.; Pope, Christopher; Hooftman, Danny A.P.; Lilley, Andrew K.; Oliver, Anna; Carroll, Mary P.; Bruce , Kenneth D.; van der Gast, Christopher J.. 2013 Reducing bias in bacterial community analysis of lower respiratory infections. ISME Journal, 7 (4). 10.1038/ismej.2012.145 Copyright © 2013 International Society for Microbial Ecology This version available http://nora.nerc.ac.uk/20879/ NERC has developed NORA to enable users to access research outputs wholly or partially funded by NERC. Copyright and other rights for material on this site are retained by the rights owners. Users should read the terms and conditions of use of this material at http://nora.nerc.ac.uk/policies.html#access This document is the author’s final manuscript version of the journal article following the peer review process. Some differences between this and the publisher’s version may remain. You are advised to consult the publisher’s version if you wish to cite from this article. www.nature.com/ Contact CEH NORA team at [email protected] The NERC and CEH trademarks and logos (‘the Trademarks’) are registered trademarks of NERC in the UK and other countries, and may not be used without the prior written consent of the Trademark owner. 1 Towards unbiased bacterial community analysis in lower respiratory infections 2 3 Geraint B. Rogers1, Leah Cuthbertson2, Lucas R. Hoffman3, Peter A. C. Wing4, Christopher Pope3, Danny A. 4 P. Hooftman2, Andrew K. Lilley1, Anna Oliver2, Mary P. Carroll4, Kenneth D. Bruce1, Christopher J. -
Bacterial Diversity and Functional Analysis of Severe Early Childhood
www.nature.com/scientificreports OPEN Bacterial diversity and functional analysis of severe early childhood caries and recurrence in India Balakrishnan Kalpana1,3, Puniethaa Prabhu3, Ashaq Hussain Bhat3, Arunsaikiran Senthilkumar3, Raj Pranap Arun1, Sharath Asokan4, Sachin S. Gunthe2 & Rama S. Verma1,5* Dental caries is the most prevalent oral disease afecting nearly 70% of children in India and elsewhere. Micro-ecological niche based acidifcation due to dysbiosis in oral microbiome are crucial for caries onset and progression. Here we report the tooth bacteriome diversity compared in Indian children with caries free (CF), severe early childhood caries (SC) and recurrent caries (RC). High quality V3–V4 amplicon sequencing revealed that SC exhibited high bacterial diversity with unique combination and interrelationship. Gracillibacteria_GN02 and TM7 were unique in CF and SC respectively, while Bacteroidetes, Fusobacteria were signifcantly high in RC. Interestingly, we found Streptococcus oralis subsp. tigurinus clade 071 in all groups with signifcant abundance in SC and RC. Positive correlation between low and high abundant bacteria as well as with TCS, PTS and ABC transporters were seen from co-occurrence network analysis. This could lead to persistence of SC niche resulting in RC. Comparative in vitro assessment of bioflm formation showed that the standard culture of S. oralis and its phylogenetically similar clinical isolates showed profound bioflm formation and augmented the growth and enhanced bioflm formation in S. mutans in both dual and multispecies cultures. Interaction among more than 700 species of microbiota under diferent micro-ecological niches of the human oral cavity1,2 acts as a primary defense against various pathogens. Tis has been observed to play a signifcant role in child’s oral and general health. -
Tryptic Soy Agar • Trypticase™ Soy Agar (Soybean-Casein Digest Agar)
Tryptic Soy Agar • Trypticase™ Soy Agar (Soybean-Casein Digest Agar) Intended Use plate counting, isolation of microorganisms from a variety Tryptic (Trypticase) Soy Agar (TSA) is used for the isolation and of specimen types and as a base for media containing blood.4-7 cultivation of nonfastidious and fastidious microorganisms. It It is also recommended for use in industrial applications when is not the medium of choice for anaerobes. testing water and wastewater,8 food,9-14 dairy products,15 and cosmetics.10,16 The 150 × 15 mm-style plates of Trypticase Soy Agar are convenient for use with Taxo™ factor strips in the isolation and Since TSA does not contain the X and V growth factors, it can differentiation of Haemophilus species. conveniently be used in determining the requirements for these growth factors by isolates of Haemophilus by the addition of X, Sterile Pack and Isolator Pack plates are useful for monitoring V and XV Factor Strips to inoculated TSA plates.5 The 150 mm surfaces and air in clean rooms, Isolator Systems and other plate provides a larger surface area for inoculation, making the environmentally-controlled areas when sterility of the medium “satellite” growth around the strips easier to read. is of importance. With the Sterile Pack and Isolator Pack plates, the entire double- Hycheck™ hygiene contact slides are used for assessing the wrapped (Sterile Pack) or triple-wrapped (Isolator Pack) product microbiological contamination of surfaces and fluids. is subjected to a sterilizing dose of gamma radiation, so that the Tryptic (Trypticase) Soy Agar meets United States Pharmacopeia contents inside the outer package(s) are sterile.17 This allows the (USP), European Pharmacopoeia (EP) and Japanese Pharmaco- inner package to be aseptically removed without introducing poeia (JP)1-3 performance specifications, where applicable. -
Interdental and Subgingival Microbiota May Affect the Tongue Microbial Ecology and Oral Malodour in Health, Gingivitis and Periodontitis
medRxiv preprint doi: https://doi.org/10.1101/2021.04.29.21256204; this version posted April 30, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Interdental and subgingival microbiota may affect the tongue microbial ecology and oral malodour in health, gingivitis and periodontitis Abish S. Stephen1, Narinder Dhadwal2, Vamshidhar Nagala2, Cecilia Gonzales-Marin2, David G. Gillam2, David J. Bradshaw3, Gary R. Burnett3, Robert P. Allaker1 1Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Queen Mary University of London, London, UK 2Adult Oral Health Centre, Institute of Dentistry, Queen Mary's School of Medicine & Dentistry, London, UK. 3GlaxoSmithKline Consumer Healthcare, Weybridge, UK. *Correspondence: Abish Stephen, Centre for Oral Immunobiology and Regenerative Medicine, Blizard Building, 4 Newark Street, London, E1 2AT, United Kingdom Tel: +44 (0)20 7882 7157; Fax: +44 (0)20 7882 2191; Email: [email protected] NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. 1 medRxiv preprint doi: https://doi.org/10.1101/2021.04.29.21256204; this version posted April 30, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. ABSTRACT Background and Objective: Oral malodour is often observed in gingivitis and chronic periodontitis patients, and the tongue microbiota is thought to play a major role in malodorous gas production, including Volatile Sulfur Compounds (VSCs) such as hydrogen sulfide (H2S) and methanethiol. -
BD Industry Catalog
PRODUCT CATALOG INDUSTRIAL MICROBIOLOGY BD Diagnostics Diagnostic Systems Table of Contents Table of Contents 1. Dehydrated Culture Media and Ingredients 5. Stains & Reagents 1.1 Dehydrated Culture Media and Ingredients .................................................................3 5.1 Gram Stains (Kits) ......................................................................................................75 1.1.1 Dehydrated Culture Media ......................................................................................... 3 5.2 Stains and Indicators ..................................................................................................75 5 1.1.2 Additives ...................................................................................................................31 5.3. Reagents and Enzymes ..............................................................................................75 1.2 Media and Ingredients ...............................................................................................34 1 6. Identification and Quality Control Products 1.2.1 Enrichments and Enzymes .........................................................................................34 6.1 BBL™ Crystal™ Identification Systems ..........................................................................79 1.2.2 Meat Peptones and Media ........................................................................................35 6.2 BBL™ Dryslide™ ..........................................................................................................80 -
The Role of the Intestinal Microbiota in Inflammatory Bowel Disease Seth Bloom Washington University in St
Washington University in St. Louis Washington University Open Scholarship All Theses and Dissertations (ETDs) 1-1-2012 The Role of the Intestinal Microbiota in Inflammatory Bowel Disease Seth Bloom Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/etd Recommended Citation Bloom, Seth, "The Role of the Intestinal Microbiota in Inflammatory Bowel Disease" (2012). All Theses and Dissertations (ETDs). 555. https://openscholarship.wustl.edu/etd/555 This Dissertation is brought to you for free and open access by Washington University Open Scholarship. It has been accepted for inclusion in All Theses and Dissertations (ETDs) by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Molecular Microbiology and Microbial Pathogenesis Dissertation Examination Committee: Thaddeus S. Stappenbeck, Chair Paul M. Allen Wm. Michael Dunne David B. Haslam David A. Hunstad Phillip I. Tarr Herbert W. “Skip” Virgin, IV The Role of the Intestinal Microbiota in Inflammatory Bowel Disease by Seth Michael Bloom A dissertation presented to the Graduate School of Arts and Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy May 2012 Saint Louis, Missouri Copyright By Seth Michael Bloom 2012 ABSTRACT OF THE DISSERTATION The Role of the Intestinal Microbiota in Inflammatory Bowel Disease by Seth Michael Bloom Doctor of Philosophy in Biology and Biomedical Sciences Molecular Microbiology and Microbial Pathogenesis Washington University in St. Louis, 2012 Professor Thaddeus S. Stappenbeck, Chairperson Inflammatory bowel disease (IBD) arises from complex interactions of genetic, environmental, and microbial factors. -
View Preprint
A peer-reviewed version of this preprint was published in PeerJ on 13 March 2019. View the peer-reviewed version (peerj.com/articles/6594), which is the preferred citable publication unless you specifically need to cite this preprint. Eisenhofer R, Weyrich LS. 2019. Assessing alignment-based taxonomic classification of ancient microbial DNA. PeerJ 7:e6594 https://doi.org/10.7717/peerj.6594 Assessing alignment-based taxonomic classification of ancient microbial DNA Raphael Eisenhofer Corresp., 1, 2 , Laura Susan Weyrich 1, 2 1 Australian Centre for Ancient DNA, University of Adelaide, Adelaide, South Australia, Australia 2 Centre of Excellence for Australia Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia Corresponding Author: Raphael Eisenhofer Email address: [email protected] The field of paleomicrobiology—the study of ancient microorganisms—is rapidly growing due to recent methodological and technological advancements. It is now possible to obtain vast quantities of DNA data from ancient specimens in a high-throughput manner and use this information to investigate the dynamics and evolution of past microbial communities. However, we still know very little about how the characteristics of ancient DNA influence our ability to accurately assign microbial taxonomies (i.e. identify species) within ancient metagenomic samples. Here, we use both simulated and published metagenomic data sets to investigate how ancient DNA characteristics affect alignment-based taxonomic classification. We find that nucleotide-to-nucleotide, rather than nucleotide-to-protein, alignments are preferable when assigning taxonomies to DNA fragment lengths routinely identified within ancient specimens (<60 bp). We determine that deamination (a form of ancient DNA damage) and random sequence substitutions corresponding to ~100,000 years of genomic divergence minimally impact alignment-based classification. -
BD™ Tryptic Soy Broth (TSB)
INSTRUCTIONS FOR USE – READY-TO-USE BOTTLED MEDIA BA-257107.06 Rev.: March 2019 BD Tryptic Soy Broth (TSB) INTENDED USE BD Tryptic Soy Broth (Soybean-Casein Digest Medium) is a general purpose liquid enrichment medium used in qualitative procedures for the sterility test and for the enrichment and cultivation of aerobic microorganisms that are not excessively fastidious. In clinical microbiology, it may be used for the suspension, enrichment and cultivation of strains isolated on other media. PRINCIPLES AND EXPLANATION OF THE PROCEDURE Microbiological method. Tryptic Soy Broth (TSB) is a nutritious medium that will support the growth of a wide variety of microorganisms, especially common aerobic and facultatively anaerobic bacteria.1,2 Because of its capacity for growth promotion, this formulation was adopted by The United States Pharmacopeia (USP) and the European Pharmacopeia (EP) as a sterility test medium.3,4 In clinical microbiology, the medium is used in a variety of procedures, e.g., for the preparation of the inoculum and for suspending strains for Kirby-Bauer disc diffusion susceptibility testing, and for the microbiological test procedure of culture media according to the CLSI standards.5,6 However, unsupplemented Tryptic Soy Broth is not recommended as a primary enrichment medium directly inoculated with the clinical specimen but can be used for pure cultures previously isolated from clinical specimens. In BD Tryptic Soy Broth, enzymatic digests of casein and soybean provide amino acids and other complex nitrogenous substances. Glucose (=dextrose) is an energy source. Sodium chloride maintains the osmotic equilibrium. Dibasic potassium phosphate acts as a buffer to control pH. -
BBL™ Chromagar™ Orientation and BBL™ Trypticase™ Soy Agar with 5% Sheep Blood (TSA II)–I Plate™, Ctn
BBL™ CHROMagar™ Orientation and % BBL™ Trypticase™ Soy Agar with 5% Sheep Blood (TSA II)—I Plate™ 8083714 • Rev. 01 • October 2008 QUALITY CONTROL PROCEDURES I INTRODUCTION BBL™ CHROMagar™ Orientation is a nonselective medium for the isolation, differentiation and enumeration of urinary tract pathogens. BBL™ Trypticase™ Soy Agar with 5% Sheep Blood is used for the growth of fastidious organisms and for the visualization of hemolytic reactions. II PERFORMANCE TEST PROCEDURE A. BBL CHROMagar Orientation 1. Inoculate representative samples with dilutions of the cultures listed below. a. Streak inoculate with 103-104 CFUs of all organisms. b. Incubate plates at 35 ± 2°C in an aerobic atmosphere. c. Include Trypticase™ Soy Agar with 5% Sheep Blood (TSA II) plates as nonselective controls for all organisms. 2. Examine plates after 18–24 h for amount of growth and color formation. 3. Expected Results Organisms ATCC™ Recovery Colony Color *Enterobacter cloacae 13047 Fair to heavy growth Dark blue to medium blue with or without violet halos in the surrounding medium *Enterococcus faecalis 29212 Fair to heavy growth Blue-green of small size colonies *Escherichia coli 25922 Fair to heavy growth Transparent, dark rose to pink, with or without of medium to large halos size colonies Klebsiella pneumoniae 33495 Fair to heavy growth Medium blue to dark blue, mucoid *Proteus mirabilis 43071 Fair to heavy growth Transparent, pale beige to brown, surrounded by of medium size colonies. a brown halo. In areas of dense growth, the Swarming is partially medium