The Microscopic Examination of Milk Characterization of Milk Bacteria and Cells
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Exploring Small-Scale Chemostats to Scale up Microbial Processes: 3-Hydroxypropionic Acid Production in S
Lawrence Berkeley National Laboratory Recent Work Title Exploring small-scale chemostats to scale up microbial processes: 3-hydroxypropionic acid production in S. cerevisiae. Permalink https://escholarship.org/uc/item/43h8866j Journal Microbial cell factories, 18(1) ISSN 1475-2859 Authors Lis, Alicia V Schneider, Konstantin Weber, Jost et al. Publication Date 2019-03-11 DOI 10.1186/s12934-019-1101-5 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Lis et al. Microb Cell Fact (2019) 18:50 https://doi.org/10.1186/s12934-019-1101-5 Microbial Cell Factories RESEARCH Open Access Exploring small-scale chemostats to scale up microbial processes: 3-hydroxypropionic acid production in S. cerevisiae Alicia V. Lis1, Konstantin Schneider1,2, Jost Weber1,3, Jay D. Keasling1,4,5,6,7, Michael Krogh Jensen1 and Tobias Klein1,2* Abstract Background: The physiological characterization of microorganisms provides valuable information for bioprocess development. Chemostat cultivations are a powerful tool for this purpose, as they allow defned changes to one single parameter at a time, which is most commonly the growth rate. The subsequent establishment of a steady state then permits constant variables enabling the acquisition of reproducible data sets for comparing microbial perfor- mance under diferent conditions. We performed physiological characterizations of a 3-hydroxypropionic acid (3-HP) producing Saccharomyces cerevisiae strain in a miniaturized and parallelized chemostat cultivation system. The physi- ological conditions under investigation were various growth rates controlled by diferent nutrient limitations (C, N, P). Based on the cultivation parameters obtained subsequent fed-batch cultivations were designed. Results: We report technical advancements of a small-scale chemostat cultivation system and its applicability for reliable strain screening under diferent physiological conditions, i.e. -
Detection of Acid-Producing Bacteria Nachweis Von Säureproduzierenden Bakterien Détection De Bactéries Produisant Des Acides
(19) TZZ ¥ _T (11) EP 2 443 249 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12Q 1/04 (2006.01) G01N 33/84 (2006.01) 19.11.2014 Bulletin 2014/47 (86) International application number: (21) Application number: 10790013.6 PCT/US2010/038569 (22) Date of filing: 15.06.2010 (87) International publication number: WO 2010/147918 (23.12.2010 Gazette 2010/51) (54) DETECTION OF ACID-PRODUCING BACTERIA NACHWEIS VON SÄUREPRODUZIERENDEN BAKTERIEN DÉTECTION DE BACTÉRIES PRODUISANT DES ACIDES (84) Designated Contracting States: (74) Representative: Isarpatent AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Patent- und Rechtsanwälte GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO Friedrichstrasse 31 PL PT RO SE SI SK SM TR 80801 München (DE) (30) Priority: 15.06.2009 US 187107 P (56) References cited: 15.03.2010 US 314140 P US-A- 4 528 269 US-A- 5 098 832 US-A- 5 164 301 US-A- 5 601 998 (43) Date of publication of application: US-A- 5 601 998 US-A- 5 786 167 25.04.2012 Bulletin 2012/17 US-B2- 6 756 225 US-B2- 7 150 977 (73) Proprietor: 3M Innovative Properties Company • DARUKARADHYA J ET AL: "Selective Saint Paul, MN 55133-3427 (US) enumeration of Lactobacillus acidophilus, Bifidobacterium spp., starter lactic acid bacteria (72) Inventors: and non-starter lactic acid bacteria from Cheddar • YOUNG, Robert, F. cheese", INTERNATIONAL DAIRY JOURNAL, Saint Paul, Minnesota 55133-3427 (US) ELSEVIER APPLIED SCIENCE, BARKING, GB, • MACH, Patrick, A. -
Gst Gram Staining Learning Objectives the Student Will Use Aseptic Techniques in the Safe Inoculation of Various Forms of Media
GSt Gram Staining Learning Objectives The student will Use aseptic techniques in the safe inoculation of various forms of media. Follow oral and written instructions and manage time in the lab efficiently. Use the bright field light microscope to view microbes under oil immersion, make accurate observations and appropriate interpretations and store the microscope according to lab procedures. Properly prepare a bacterial smear for accurate staining and describe the chemical basis for simple staining and negative staining. Background/Theory Differential staining distinguishes organisms based on their interactions with multiple stains. In other words, two organisms may appear to be different colors. Differential staining techniques commonly used in clinical settings include Gram staining, acid-fast staining, endospore staining, flagella staining, and capsule staining. This link to the OpenStax Microbiology text provides more detail on these differential staining techniques. (OpenStax CNX, 2018) The Gram stain is a differential staining procedure that involves multiple steps. It was developed by Danish microbiologist Hans Christian Gram in 1884 as an effective method to distinguish between bacteria containing the two most common types of cell walls. (OpenStax CNX, 2018) One type consists of an inner plasma membrane and a thick outer layer of peptidoglycan. The other type consists of a double phospholipid Figure 1 Simplified structures of Gram negative cells (left) and Gram positive bilayer with a thin layer of cells (right) peptidoglycan between the two. The Gram Staining technique remains one of the most frequently used staining techniques. The steps of the Gram stain procedure are listed below and illustrated in Figure. (OpenStax CNX, 2018) 1. -
Chemostat Culture for Yeast Experimental Evolution
Downloaded from http://cshprotocols.cshlp.org/ at Cold Spring Harbor Laboratory Library on August 9, 2017 - Published by Cold Spring Harbor Laboratory Press Protocol Chemostat Culture for Yeast Experimental Evolution Celia Payen and Maitreya J. Dunham1 Department of Genome Sciences, University of Washington, Seattle, Washington 98195 Experimental evolution is one approach used to address a broad range of questions related to evolution and adaptation to strong selection pressures. Experimental evolution of diverse microbial and viral systems has routinely been used to study new traits and behaviors and also to dissect mechanisms of rapid evolution. This protocol describes the practical aspects of experimental evolution with yeast grown in chemostats, including the setup of the experiment and sampling methods as well as best laboratory and record-keeping practices. MATERIALS It is essential that you consult the appropriate Material Safety Data Sheets and your institution’s Environmental Health and Safety Office for proper handling of equipment and hazardous material used in this protocol. Reagents Defined minimal medium appropriate for the experiment For examples, see Protocol: Assembly of a Mini-Chemostat Array (Miller et al. 2015). Ethanol (95%) Glycerol (20% and 50%; sterile) Yeast strain of interest Equipment Agar plates (appropriate for chosen strain) Chemostat array Assemble the apparatus as described in Miller et al. (2013) and Protocol: Assembly of a Mini-Chemostat Array (Miller et al. 2015). Cryo deep-freeze labels Cryogenic vials Culture tubes Cytometer (BD Accuri C6) Glass beads, 4 mm (sterile; for plating yeast cells) Glass cylinder Kimwipes 1Correspondence: [email protected] © 2017 Cold Spring Harbor Laboratory Press Cite this protocol as Cold Spring Harb Protoc; doi:10.1101/pdb.prot089011 559 Downloaded from http://cshprotocols.cshlp.org/ at Cold Spring Harbor Laboratory Library on August 9, 2017 - Published by Cold Spring Harbor Laboratory Press C. -
Microbiology Laboratory Exercises Third Edition 2020
MICROBIOLOGY Laboratory Exercises Third Edition Keddis & Rauschenbach 2020 Photo Credits (in order of contribution): Diane Davis, Ines Rauschenbach & Ramaydalis Keddis Acknowledgements: Many thanks to those in the Department of Biochemistry and Microbiology, Rutgers University, who have through the years inspired our enthusiasm for the science and teaching of microbiology, with special thanks to Diane Davis, Douglas Eveleigh and Max Häggblom. Safety: The experiments included in this manual have been deemed safe by the authors when all necessary safety precautions are met. The authors recommend maintaining biosafety level 2 in the laboratory setting and using risk level 1 organisms for all exercises. License: This work is licensed under a Creative Commons Attribution- NonCommercial-NoDerivatives 4.0 International License Microbiology Laboratory Exercises Third Edition 2020 Ramaydalis Keddis, Ph.D. Ines Rauschenbach, Ph.D. Department of Biochemistry and Microbiology Rutgers, The State University of New Jersey CONTENTS PAGE Introduction Schedule ii Best Laboratory Practices Iii Working in a Microbiology Laboratory iv Exercises Preparation of a Culture Medium 1 Culturing and Handling Microorganisms 3 Isolation of a Pure Culture 5 Counting Bacterial Populations 8 Controlling Microorganisms 10 Disinfectants 10 Antimicrobial Agents: Susceptibility Testing 12 Hand Washing 14 The Lethal Effects of Ultraviolet Light 15 Selection of Fungi from Air 17 Microscopy 21 Morphology and Staining of Bacteria 26 Microbial Metabolism 30 Enzyme Assay 32 Metabolic -
Technical Report the Vitek Analyser for Routine Bacterial Identification And
316 J Clin Pathol 1998;51:316–323 Technical report J Clin Pathol: first published as 10.1136/jcp.51.4.316 on 1 April 1998. Downloaded from The Vitek analyser for routine bacterial identification and susceptibility testing: protocols, problems, and pitfalls N Shetty, G Hill, G L Ridgway Abstract covered, maintenance and quality control Automated and semiautomated technol- costs, and the presence of a versatile software ogy in microbiology has seen great ad- package. This report describes our experiences vances in recent years. The choice of with the Vitek system (bioMerieux, UK) in the automated equipment for the identifica- one year since its inception into a busy micro- tion and susceptibility testing of bacteria biology diagnostic laboratory in the United in a routine diagnostic laboratory depends Kingdom. It is worth noting that the choice on speed, accuracy, ease of use, and cost and range of antibiotics on susceptibility factors. The Vitek analyser (bioMerieux, testing cards were custom made for the UK) was installed in a busy diagnostic University College London Hospitals teaching hospital laboratory in London. (UCLH). This report describes one year’s experience. Changes to work practice as a result of incorporating the equipment into Identification and susceptibility testing the laboratory, and the advantages and on the Vitek system disadvantages of automation in key areas Identification of microorganisms is accom- are described in detail, together with pos- plished by biochemical methods. A turbido- sible solutions to problems. The Vitek metrically controlled suspension of pure colo- analyser was found to be valuable for the nies in saline is inoculated into identification http://jcp.bmj.com/ speed and accuracy with which results cards. -
Maintenance of Bacterial Strains
Maintenance of Bacterial Strains Short-term growth and maintenance The simplest method for obtaining strains is to order them from a microbiological supply company. Presque Isle, Ward, and Carolina Biological (see “Resources” page of the Microbes Web site: www.umsl.edu/~microbes) are economical sources of strains that are commonly used in the classroom. Another possible source is a local college or university that teaches a microbiology lab course. If they have strains already prepared for their class, they will probably be willing to provide you with a culture. This is probably not a reasonable ongoing source of strains, but can be useful in an emergency. For short-term maintenance and use, it is best to streak bacteria on some type of rich agar petri plate, such as nutrient agar. Label and date the plate on the bottom of the plate. Streak from the source culture using good sterile technique. The quadrant streak method (see the article on quadrant streaking) is good for obtaining well-isolated colonies. Incubate the plate only until good colonies have formed. Do not leave the culture in the incubator beyond that time, or the cells will die on the plate. Store the plate in the refrigerator. It will keep for about a month. For class use, it is best to streak a fresh plate 2-3 days before the strain will be needed for class. Use the fresh plate as the source of cultures for the class. For broth cultures for a class, it is best to grow a larger volume culture in a flask (if possible, with shaking) overnight and then dispense aliquots of the master culture into sterile test tubes using a sterile pipette. -
The Genus Staphylococcus 19 171
43038_CH19_0171.qxd 1/3/07 3:53 PM Page 171 THE GENUS STAPHYLOCOCCUS 19 171 The Genus 19 Staphylococcus embers of the genus Staphylococcus are gram-positive spherical organisms about 1 micrometer in diameter. They M occur singly, in pairs, and in irregular clusters, and form yel- low, orange, or white colonies on agar media. They are salt tolerant and grow on ordinary bacteriological media as well as on the selective media used in this exercise. Up to three species of Staphylococcus are studied in this exercise. Cer- tain strains of Staphylococcus aureus are the cause of food poisoning and toxic shock syndrome. They also are the cause of boils and carbuncles. A second species, S. epidermidis, usually is a saprobe of the skin that is rarely involved in human infection. The third species, S. saprophyticus, is an opportunistic species that may cause urinary tract infections in women of childbearing years. In this exercise, staphylococcal species will be isolated from the body’s environment and their properties examined. A. Isolation of Staphylococci Species of Staphylococcus are tolerant to salt and, therefore, they can be PURPOSE: to isolate and selected out from a mixture of bacteria in a high-salt medium. In addition, identify staphylococcal species from the nasal cavity S. aureus ferments mannitol, an alcoholic derivative of the hexose mannose, and other environments. while S. epidermidis and S. saprophyticus do not. Therefore, if the differential medium contains mannitol, the two species may be differentiated from one another. In this section, we will use mannitol salt agar, a medium that is both selective and differential. -
Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I. -
Francisella Tularensis 6/06 Tularemia Is a Commonly Acquired Laboratory Colony Morphology Infection; All Work on Suspect F
Francisella tularensis 6/06 Tularemia is a commonly acquired laboratory Colony Morphology infection; all work on suspect F. tularensis cultures .Aerobic, fastidious, requires cysteine for growth should be performed at minimum under BSL2 .Grows poorly on Blood Agar (BA) conditions with BSL3 practices. .Chocolate Agar (CA): tiny, grey-white, opaque A colonies, 1-2 mm ≥48hr B .Cysteine Heart Agar (CHA): greenish-blue colonies, 2-4 mm ≥48h .Colonies are butyrous and smooth Gram Stain .Tiny, 0.2–0.7 μm pleomorphic, poorly stained gram-negative coccobacilli .Mostly single cells Growth on BA (A) 48 h, (B) 72 h Biochemical/Test Reactions .Oxidase: Negative A B .Catalase: Weak positive .Urease: Negative Additional Information .Can be misidentified as: Haemophilus influenzae, Actinobacillus spp. by automated ID systems .Infective Dose: 10 colony forming units Biosafety Level 3 agent (once Francisella tularensis is . Growth on CA (A) 48 h, (B) 72 h suspected, work should only be done in a certified Class II Biosafety Cabinet) .Transmission: Inhalation, insect bite, contact with tissues or bodily fluids of infected animals .Contagious: No Acceptable Specimen Types .Tissue biopsy .Whole blood: 5-10 ml blood in EDTA, and/or Inoculated blood culture bottle Swab of lesion in transport media . Gram stain Sentinel Laboratory Rule-Out of Francisella tularensis Oxidase Little to no growth on BA >48 h Small, grey-white opaque colonies on CA after ≥48 h at 35/37ºC Positive Weak Negative Positive Catalase Tiny, pleomorphic, faintly stained, gram-negative coccobacilli (red, round, and random) Perform all additional work in a certified Class II Positive Biosafety Cabinet Weak Negative Positive *Oxidase: Negative Urease *Catalase: Weak positive *Urease: Negative *Oxidase, Catalase, and Urease: Appearances of test results are not agent-specific. -
Biofire Blood Culture Identification System (BCID) Fact Sheet
BioFire Blood Culture Identification System (BCID) Fact Sheet What is BioFire BioFire BCID is a multiplex polymerase chain reaction (PCR) test designed to BCID? identify 24 different microorganism targets and three antibiotic resistance genes from positive blood culture bottles. What is the purpose The purpose of BCID is to rapidly identify common microorganisms and of BCID? antibiotic resistance genes from positive blood cultures so that antimicrobial therapy can be quickly optimized by the physician and the antibiotic stewardship pharmacist. It is anticipated that this will result in improved patient outcomes, decreased length of stay, improved antibiotic stewardship, and decreased costs. When will BCID be BCID is performed on all initially positive blood cultures after the gram stain is routinely performed and reported. performed? When will BCID not For blood cultures on the same patient that subsequently become positive with be routinely a microorganism showing the same morphology as the initial positive blood performed? culture, BCID will not be performed. BCID will not be performed on positive blood cultures with gram positive bacilli unless Listeria is suspected. BCID will not be performed on blood culture bottles > 8 hours after becoming positive. BCID will not be performed between 10PM-7AM on weekdays and 2PM-7AM on weekends. BCID will not be performed for clinics that have specifically opted out of testing. How soon will BCID After the blood culture becomes positive and the gram stain is performed and results be available? reported, the bottle will be sent to the core Microbiology lab by routine courier. BCID testing will then be performed. It is anticipated that total turnaround time will generally be 2-3 hours after the gram stain is reported. -
Time-To-Positivity, Type of Culture Media and Oxidase Test Performed on Positive Blood Culture Vials to Predict Pseudomonas Aeru
Original Nazaret Cobos-Trigueros1 Time-to-positivity, type of culture media and oxidase Yuliya Zboromyrska2 Laura Morata1 test performed on positive blood culture vials to predict Izaskun Alejo2 Cristina De La Calle1 Pseudomonas aeruginosa in patients with Gram-negative Andrea Vergara2 Celia Cardozo1 bacilli bacteraemia 1 Maria P. Arcas 1 1 Department of Infectious Diseases, Hospital Clínic, IDIBAPS, Barcelona University, Barcelona, Spain. Alex Soriano 2Department of Clinical Microbiology, Hospital Clínic, Barcelona University, Barcelona, Spain. Francesc Marco2 Josep Mensa1 Manel Almela2 Jose A. Martinez1 ABSTRACT Tiempo de positividad, tipo de medio de cultivo y prueba de oxidasa realizada en Introduction. The aim of this study was to determine the viales de hemocultivo positivos para predecir usefulness of oxidase test and time-to-positivity (TTP) in aer- Pseudomonas aeruginosa en pacientes con obic and anaerobic blood culture vials to detect the presence bacteriemia por bacilos gramnegativos of Pseudomonas aeruginosa in patients with Gram-negative bacilli (GNB) bacteraemia. RESUMEN Material and methods. TTP was recorded for each aer- obic and anaerobic blood culture vial of monomicrobial bac- Introducción. El objetivo del estudio fue determinar la utili- teraemia due to GNB. Oxidase test was performed in a pellet dad de la prueba de oxidasa y del tiempo de positividad del hemo- of the centrifuged content of the positive blood culture. An cultivo (TPH) para detectar la presencia de Pseudomonas aerugino- algorithm was developed in order to perform the oxidase test sa en pacientes con bacteriemia por bacilos gramnegativos (BGN). efficiently taking into account TTP and type of vial. Material y métodos. Se registró el TPH de cada vial ae- Results.