DOCSLIB.ORG

Organic Acid Production from Starchy Waste by Gut Derived Microorganisms”

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Organic Acid Production from Starchy Waste by Gut Derived Microorganisms” Propositions 1. Actinomyces succiniciruminis has potential for industrial succinate production from starchy waste (this thesis) 2. Knowing the relative abundance of each microbial species in a mixed rumen inoculum does not help to predict the fermentation products (this thesis) 3. Phytoplanktons are the real-world savers for the global warming crisis as they are world’s biggest oxygen producers and carbon sequesters (Witman, S. (2017) World’s biggest oxygen producers living in swirling ocean waters. Eos, 98) 4. The best way to protect endangered floras is to bring them into a commercial breeding system 5. Studying abroad elevates cooking skills to the master level 6. There is no real waste in our world Propositions belonging to this thesis entitled: “Organic acid production from starchy waste by gut derived microorganisms” Susakul Palakawong Na Ayudthaya Wageningen, 7 September 2018 Organic acid production from starchy waste by gut derived microorganisms Susakul Palakawong Na Ayudthaya Thesis committee Promotors Prof. Dr Alfons J.M. Stams Personal chair at the Laboratory of Microbiology Wageningen University & Research Prof. Dr Willem M. de Vos Professor of Microbiology Wageningen University & Research Co-promotor Dr Caroline M. Plugge Associate professor, Laboratory of Microbiology Wageningen University & Research Other members Prof. Dr Grietje Zeeman, Wageningen University & Research Dr Bundit Fungsin, Thailand Institute of Scientific and Technological Research, Pathum Thani, Thailand Prof. Dr Gert-Jan W. Euverink, University of Groningen, The Netherlands Dr Marieke E. Bruins, Wageningen University & Research This research was conducted under the auspices of the Graduate School for Socio-Economic and Natural Sciences of the Environment (SENSE). Organic acid production from starchy waste by gut derived microorganisms Susakul Palakawong Na Ayudthaya Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus, Prof. Dr A.P.J. Mol, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Friday 7 September 2018 at 11 a.m. in the Aula. Susakul Palakawong Na Ayudthaya Organic acid production from starchy waste by gut derived microorganisms, 220 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2018) With references, with summary in English ISBN: 978-94-6343-788-2 DOI: https://doi.org/10.18174/451805 Table of Contents Chapter 1 General introduction and thesis outline 7 Chapter 2 Organic acid production from potato starch waste fermentation 27 by rumen microbial communities from Dutch and Thai dairy cows Chapter 3 Actinomyces succiniciruminis sp. nov. and Actinomyces 69 glycerinitolerans sp. nov., two novel organic acid-producing bacteria isolated from rumen Chapter 4 Optimization of succinate production from potato starch waste 97 by Actinomyces succiniciruminis strain Am4T Chapter 5 Microbial diversity and organic acid production of guinea pig 123 fecal samples Chapter 6 Streptococcus caviae sp. nov., isolated from guinea pig fecal 153 samples Chapter 7 General discussion 173 Summary 187 References 191 List of publications 211 Co-author affiliations 212 About the author 213 Acknowledgements 215 SENSE Diploma 218 CHAPTER 1 General introduction and thesis outline Chapter 1 Global energy consumption and waste streams Global energy consumption is steadily increasing. The transportation, chemical and many other industry sectors are largely relying on petroleum and fossil fuels as a primary source of energy. In 2015, fossil fuels comprised of oil (31.7%), coal (28.1%) and natural gas (21.6%) contributed for more than 80% of the total energy supply (13,647 Mt) (IEA, 2017). The rate at which worldwide fossil fuels are consumed is increasing due to world's population increase and the rise in living standards in parts of the world that had consumed very little energy in the past. Fossil fuel reserves are limited, and exploitation will become expensive. Besides, consumption of fossil fuels results in pollution and carbon dioxide formation, which contributes to global warming. Therefore, the search for other energy sources such as natural gas, wind, nuclear and renewable organics is essential to guarantee energy supply. Current bio-based economy prospective Fossil reserves are also important as chemicals precursors, including building blocks for the chemical industry. Hence, chemical technologies based on fossil (petroleum) resources are currently being replaced by green technologies that make use of alternative biobased resources, in the so called biorefinery concept. This is often relying on microbial fermentation and when compared to chemical refinery processes, it is more environmental friendly and more sustainable (less pollution and no net CO2 emission to the atmosphere). In Table 1 the chemical and the bio-fermentation routes are compared. One of the guideline principles of green chemistry defined by the US Environmental Protection Agency (EPA) is promoting the use of renewable feedstocks (http://www.epa.gov/) (Fiorentino and Ripa, 2017). 8 General introduction and thesis outline Table 1. A general comparison between chemical and bio-fermentative routes. (modified from Cukalovic and Stevens, 2008; Law and Mohammad, 2017) Parameter Chemical routes Fermentative routes Non-renewable feedstocks – Biobased feedstock – carbohydrates petrochemicals Price considerations Still cheaper than the renewable Feedstock themselves do not contribute to sources. the price as much as downstream processing Availability Availability expected to Abundant and renewable decrease in time Routes Developed routes, established Routes under constant improvement, young technologies technologies Yields and Generally high Sometimes a large number of side products, productivities diluted media, long reaction times Major disadvantages High energy demands (pressure Sensitivity of microorganisms, nutrient and temperature). Catalysts requirements, complicated product disposal issues recovery, large amounts of waste Environment effect Release CO2 that contributes to Consume CO2 via TCA cycle global warming Public awareness Decreasing popularity Increased interest in improving currently applied routes and innovations Current high costs of production prevent bio-based chemicals to be widely used. Thus, production processes from bio-based resources need to be developed and optimized. It is estimated that in 2050 approximately 30% (by weight) of chemicals will be obtained from renewable biomass (http://www.suschem.org) (Fiorentino and Ripa, 2017). Biomass is an abundant carbon-neutral renewable resource that can be used as a carbon source instead of fossil feedstocks (Fiorentino and Ripa, 2017). Production chains resulting from biomass are considered as “short-cycle carbon systems”, which are more sustainable and preferable than those resulting from fossil resources, which are considered as “long-cycle carbon systems” (Kajaste et al., 2014; Fiorentino and Ripa, 2017). The transition from fossil based to bio-based economy needs the development of innovative processes to exploit the potential of biomass (Pleissner et al., 2017). Thus, utilization of food wastes or biomass and their conversion into valuable products require more attention as the implementation of such system is not yet successfully guaranteed. However, many criteria need to be considered for 9 Chapter 1 biomass utilization in the context of efficient strategies, such as the amount of biomass available for energy and material uses and the positive environment from renewable organic materials and economic feasibility (Venus et al., 2018), as well as the factors presented in Table 1. At present, three biorefinery platforms are known; i) the sugar platform: using purified enzymes to convert biomass into five- and six-carbon sugars and then further convert these into fuels and chemicals by fermentation; ii) the syngas platform: using thermochemical systems to convert biomass into synthesis gas (a mixture of CO, H2 and CO2) and then further convert to fuels and chemicals by chemical or biological catalysts, and iii) the carboxylate platform: using hydrolysis and fermentation with often undefined mixed microorganisms to convert organic feedstocks into short chain carboxylates (Agler et al., 2011; Bosma et al., 2013). The differences between these platforms are largely based on the method of biomass conversion and the chemicals resulting from that. Methane is usually the expected product from anaerobic digestion process, however, not only methane is valuable, but the intermediate compounds as organic acids are also important. Abundance of organic waste streams On one hand, the increase of human population and the associated consumption of food and energy results in a steady increase of organic waste. Approximately one third of the global food production is discarded as waste per year according to the Food and Agriculture Organization of the United Nations (FAO). (http://www.unric.org/en/food-waste). Organic waste, such as food and fiber processing of fruit, vegetable waste, garbage, sewage sludge, cattle manure and/or industrial waste are abundant worldwide (Murto et al., 2004). The European Community Landfill Directive (EPA) has led to an increase in the costs of landfill and a reduction of places for landfill in many countries (EPA; http://ec.europa.eu/environment/waste/target_review.htm). Approximately 87.6 million tonnes per year of food waste are produced in Europe
Load more

Recommended publications
  • Differential Preservation of Endogenous Human and Microbial
    www.nature.com/scientificreports OPEN Diferential preservation of endogenous human and microbial DNA in dental calculus and dentin Received: 20 March 2018 Allison E. Mann1,2,3, Susanna Sabin 1, Kirsten Ziesemer4, Åshild J. Vågene 1, Hannes Accepted: 14 June 2018 Schroeder4,5, Andrew T. Ozga 2,3,6, Krithivasan Sankaranarayanan 3,7, Courtney A. Published: xx xx xxxx Hofman 2,3, James A. Fellows Yates 1, Domingo C. Salazar-García1,8, Bruno Frohlich9,10, Mark Aldenderfer 11, Menno Hoogland4, Christopher Read12, George R. Milner13, Anne C. Stone6,14,15, Cecil M. Lewis Jr.2,3, Johannes Krause1, Corinne Hofman4, Kirsten I. Bos1 & Christina Warinner 1,2,3 Dental calculus (calcifed dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we fnd DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA.
    [Show full text]
  • ( 12 ) United States Patent
    US009956282B2 (12 ) United States Patent ( 10 ) Patent No. : US 9 ,956 , 282 B2 Cook et al. (45 ) Date of Patent: May 1 , 2018 ( 54 ) BACTERIAL COMPOSITIONS AND (58 ) Field of Classification Search METHODS OF USE THEREOF FOR None TREATMENT OF IMMUNE SYSTEM See application file for complete search history . DISORDERS ( 56 ) References Cited (71 ) Applicant : Seres Therapeutics , Inc. , Cambridge , U . S . PATENT DOCUMENTS MA (US ) 3 ,009 , 864 A 11 / 1961 Gordon - Aldterton et al . 3 , 228 , 838 A 1 / 1966 Rinfret (72 ) Inventors : David N . Cook , Brooklyn , NY (US ) ; 3 ,608 ,030 A 11/ 1971 Grant David Arthur Berry , Brookline, MA 4 ,077 , 227 A 3 / 1978 Larson 4 ,205 , 132 A 5 / 1980 Sandine (US ) ; Geoffrey von Maltzahn , Boston , 4 ,655 , 047 A 4 / 1987 Temple MA (US ) ; Matthew R . Henn , 4 ,689 ,226 A 8 / 1987 Nurmi Somerville , MA (US ) ; Han Zhang , 4 ,839 , 281 A 6 / 1989 Gorbach et al. Oakton , VA (US ); Brian Goodman , 5 , 196 , 205 A 3 / 1993 Borody 5 , 425 , 951 A 6 / 1995 Goodrich Boston , MA (US ) 5 ,436 , 002 A 7 / 1995 Payne 5 ,443 , 826 A 8 / 1995 Borody ( 73 ) Assignee : Seres Therapeutics , Inc. , Cambridge , 5 ,599 ,795 A 2 / 1997 McCann 5 . 648 , 206 A 7 / 1997 Goodrich MA (US ) 5 , 951 , 977 A 9 / 1999 Nisbet et al. 5 , 965 , 128 A 10 / 1999 Doyle et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 ,589 , 771 B1 7 /2003 Marshall patent is extended or adjusted under 35 6 , 645 , 530 B1 . 11 /2003 Borody U .
    [Show full text]
  • From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
    From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases.
    [Show full text]
  • Oral Actinomyces Species in Health and Disease: Identification, Occurrence and Importance of Early Colonization
    Nanna Sarkonen Oral Actinomyces Species in Health and Disease: Identification, Occurrence and Importance of Early Colonization Publications of the National Public Health Institute A 8/2007 Department of Bacterial and Inflammatory Diseases National Public Health Institute, Helsinki, Finland and Institute of Dentistry, Faculty of Medicine, University of Helsinki, Finland Helsinki 2007 ORAL ACTINOMYCES SPECIES IN HEALTH AND DISEASE: IDENTIFICATION, OCCURRENCE AND IMPORTANCE OF EARLY COLONIZATION Nanna Sarkonen ACADEMIC DISSERTATION To be presented with the permission of the Faculty of Medicine, University of Helsinki, for public examination in the Small Hall, University Main Building, Fabianinkatu 33, on June 15 th, at 12 noon. Department of Bacterial and Inflammatory Diseases National Public Health Institute, Helsinki, Finland and Institute of Dentistry, Faculty of Medicine, University of Helsinki, Finland Helsinki 2007 Publications of the National Public Health Institute KTL A8 / 2007 Copyright National Public Health Institute Julkaisija-Utgivare-Publisher Kansanterveyslaitos (KTL) Mannerheimintie 166 00300 Helsinki Puh. vaihde (09) 474 41, telefax (09) 4744 8408 Folkhälsoinstitutet Mannerheimvägen 166 00300 Helsingfors Tel. växel (09) 474 41, telefax (09) 4744 8408 National Public Health Institute Mannerheimintie 166 FIN-00300 Helsinki, Finland Telephone +358 9 474 41, telefax +358 9 4744 8408 ISBN 951-740-704-5 ISSN 0359-3584 ISBN 951-740-705-2 (pdf) ISSN 1458-6290 (pdf) Edita Prima Oy Helsinki 2007 Supervised by Professor Eija Könönen
    [Show full text]
  • Life As an Endodontic Pathogen Ecological Differences Between the Untreated and Root-filled Root Canals
    Endodontic Topics 2003, 6, 3–28 Copyright r Blackwell Munksgaard Printed in Denmark. All rights reserved ENDODONTIC TOPICS 2003 Life as an endodontic pathogen Ecological differences between the untreated and root-filled root canals GO¨ RAN SUNDQVIST & DAVID FIGDOR This review describes the type of microbial flora in the untreated root canal and the root-filled canal with persistent infection. Recent contributions of molecular methods of microbial identification are outlined along with a discussion of advantages and limitations of these methods. Ecological and environmental factors are the prime reasons for differences in the microbial flora in these distinct habitats. Shared phenotypic traits and an ability to respond to the modified environment select for the species that establish a persistent root canal infection. Introduction enamel and cementum layers are intact, the pulp and root canal are protected from invasion, but loss of these Life is not easy for an endodontic pathogen. Microbes structures by caries, cracks or trauma opens an avenue seeking to establish in the root canal must leave the for penetration of bacteria through the dentinal nutritionally rich and diverse environment of the oral tubules. All bacteria within the oral cavity share the cavity, breach enamel, invade dentine, overwhelm the same opportunities for invading the root canal space; immune response of the pulp and settle in the however only a restricted group of species have been remaining necrotic tissue within the root canal. During identified in infected root canals (4–7). The reason for that time they have to compete in a limited space with the disproportionate ratio between potential and actual other microbes for the available nutrition.
    [Show full text]
  • Characterization of the Vaginal Microbiome in Pregnancy
    CHARACTERIZATION OF THE VAGINAL MICROBIOME IN PREGNANCY A Thesis Submitted to the College of Graduate and Postdoctoral Studies In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Veterinary Microbiology University of Saskatchewan Saskatoon By ALINE COSTA DE FREITAS © Copyright Aline C. Freitas, February, 2018. All rights reserved. PERMISSION TO USE In presenting this thesis in partial fulfillment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis/dissertation in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis/dissertation. Requests for permission to copy or to make other uses of materials in this thesis in whole or part should be addressed to: Head of Department of Veterinary Microbiology University of Saskatchewan Saskatoon, Saskatchewan S7N 5B4 Canada OR Dean College of Graduate and Postdoctoral Studies University of Saskatchewan 116 Thorvaldson Building, 110 Science Place Saskatoon, Saskatchewan S7N 5C9 Canada i ABSTRACT The vaginal microbiome plays an important role in women’s reproductive health.
    [Show full text]
  • The Microbial Ecology and Horticultural Sustainability of Organically and Conventionally Managed Apples
    ABSTRACT Title of Document: THE MICROBIAL ECOLOGY AND HORTICULTURAL SUSTAINABILITY OF ORGANICALLY AND CONVENTIONALLY MANAGED APPLES. Andrea R. Ottesen, PhD, 2008 Directed By: Professor, Dr. Christopher S. Walsh, Plant Sciences and Landscape Architecture Objectives Organically and conventionally managed apple trees (Malus domestica Borkh) were evaluated for three growing seasons (2005-2007) to examine the impact of organic and conventional pesticide applications on the microbial ecology of phyllosphere and soil microflora. An important objective was to establish if organic or conventional selection pressures contribute to an increased presence of enteric pathogens in phyllosphere microflora. The horticultural and economic sustainability of the organic crop was also compared to the conventional crop with regard to fruit yield and input costs. Methods Microbial populations from phyllosphere and soil environments of apple trees were evaluated using clone libraries of 16S rRNA gene fragments. Clones were sequenced and software was used to assess diversity indices, identify shared similarities and compute statistical differences between communities. These measurements were subsequently used to examine treatment effects on the microbial libraries. Phyllosphere Results Eight bacterial phyla and 14 classes were found in this environment. A statistically significant difference between organically and conventionally managed phyllosphere bacterial microbial communities was observed at four of six sampling time points. Unique phylotypes were found associated with each management treatment but no increased human health risk could be associated with either treatment with regard to enteric pathogens. Soil Results Seventeen bacterial phyla spanning twenty-two classes, and two archaeal phyla spanning eight classes, were seen in the 16S rRNA gene libraries of organic and conventional soil samples.
    [Show full text]
  • Genome-Based Taxonomic Classification of the Phylum
    ORIGINAL RESEARCH published: 22 August 2018 doi: 10.3389/fmicb.2018.02007 Genome-Based Taxonomic Classification of the Phylum Actinobacteria Imen Nouioui 1†, Lorena Carro 1†, Marina García-López 2†, Jan P. Meier-Kolthoff 2, Tanja Woyke 3, Nikos C. Kyrpides 3, Rüdiger Pukall 2, Hans-Peter Klenk 1, Michael Goodfellow 1 and Markus Göker 2* 1 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom, 2 Department Edited by: of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Martin G. Klotz, Germany, 3 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Washington State University Tri-Cities, United States The application of phylogenetic taxonomic procedures led to improvements in the Reviewed by: Nicola Segata, classification of bacteria assigned to the phylum Actinobacteria but even so there remains University of Trento, Italy a need to further clarify relationships within a taxon that encompasses organisms of Antonio Ventosa, agricultural, biotechnological, clinical, and ecological importance. Classification of the Universidad de Sevilla, Spain David Moreira, morphologically diverse bacteria belonging to this large phylum based on a limited Centre National de la Recherche number of features has proved to be difficult, not least when taxonomic decisions Scientifique (CNRS), France rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft *Correspondence: Markus Göker genome sequences
    [Show full text]
  • Community and Genomic Analysis of the Human Small Intestine Microbiota
    Community and genomic analysis of the human small intestine microbiota Bartholomeus van den Bogert Thesis committee Promotor Prof. Dr M. Kleerebezem Personal chair in the Host Microbe Interactomics Group Wageningen University Co-promotor Dr E.G. Zoetendal Assistant professor, Laboratory of Microbiology Wageningen University Other members Prof. Dr T. Abee, Wageningen University Dr J. Doré, National Institute for Agricultural Research, INRA, Jouy en Josas, France Prof. Dr P. Hols, Catholic University of Leuven, Belgium Dr A. Nauta, FrieslandCampina Research, Deventer, The Netherlands This research was conducted under the auspices of the Graduate School VLAG (Advanced studies in Food Technology, Agrobiotechnology, Nutrition and Health Sciences). Community and genomic analysis of the human small intestine microbiota Bartholomeus van den Bogert Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Wednesday 9 October 2013 at 4 p.m. in the Aula. Bartholomeus van den Bogert Community and genomic analysis of the human small intestine microbiota, 224 pages PhD thesis, Wageningen University, Wageningen, NL (2013) With references, with summaries in Dutch and English ISBN 978-94-6173-662-8 Summary Our intestinal tract is densely populated by different microbes, collectively called microbiota, of which the majority are bacteria. Research focusing on the intestinal microbiota often use fecal samples as a representative of the bacteria that inhabit the end of the large intestine. These studies revealed that the intestinal bacteria contribute to our health, which has stimulated the interest in understanding their dynamics and activities.
    [Show full text]
  • Schnelle Identifizierung Von Oralen Actinomyces-Arten Des Subgingivalen Biofilms Mittels MALDI-TOF-MS
    Schnelle Identifizierung von oralen Actinomyces-Arten des subgingivalen Biofilms mittels MALDI-TOF-MS Publikationspromotion zur Erlangung des akademischen Grades Dr. med. dent. an der Medizinischen Fakultät der Universität Leipzig eingereicht von: Toralf Harald Borgmann geboren am 14.04.1988 in Dresden angefertigt am: Institut für Mikrobiologie und Infektionsepidemiologie der Universität Leipzig Betreuer: Prof. Dr. med. A. C. Rodloff, OÄ Dr. medic. Catalina-Suzana Stingu, Prof. Dr. K. Eschrich Beschluss über die Verleihung des Doktorgrades vom: 17.11.2015. Inhaltsverzeichnis 1. Bibliographische Beschreibung 3 2. Einführung 5 2.1. Einleitung 5 2.2. MALDI-TOF-MS-Analyse von Bakterien 6 2.3. Actinomyces 9 2.4. Grundlagen zur Bearbeitung und Auswertung der Spektren mit Klassifikation und Clusteranalyse 14 2.4.1. Zentroide 14 2.4.2. Ähnlichkeitsanalyse 14 2.4.3. Hierarchisch-agglomeratives Verfahren und Darstellung der Ergebnisse 15 2.4.4. Klassifikation 16 3. Publikation 19 4. Zusammenfassung 26 5. Literaturverzeichnis 30 6. Anlagen 39 Erklärung über die eigenständige Abfassung der Arbeit 39 Lebenslauf 40 Danksagung 42 1. Bibliographische Beschreibung Name: Borgmann, Toralf Harald Titel: Schnelle Identifizierung von oralen Actinomyces-Arten des subgingivalen Biofilms mittels MALDI-TOF-MS Universität Leipzig, Publikationspromotion 42 S1, 116 Lit.2, 5 Abbildungen, 1 Tabelle , 3 Anlagen Referat: Aktinomyzeten sind ein Teil der residenten Flora des menschlichen Verdauungstraktes, des Urogenitalsystems und der Haut. Die zeitraubende Isolation und Identifikation der Aktinomyzeten durch konventionelle Methoden stellt sich häufig als sehr schwierig dar. In den letzten Jahren hat sich jedoch die Matrix-unterstützte Laser-Desorption/Ionisation- Flugzeit-Massenspektrometrie (MALDI-TOF-MS) als Alternative zu etablierten Verfahren entwickelt und stellt heutzutage eine schnelle und simple Methode zur Bakterien- identifikation dar.
    [Show full text]
  • Non-Contiguous Finished Genome Sequence and Description of Streptococcus Varani Sp. Nov
    TAXONOGENOMICS: GENOME OF A NEW ORGANISM Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov. S. Bakour1, J. Rathored1,C.I.Lo1,2, O. Mediannikov1,2, M. Beye1, C. B. Ehounoud1, P. Biagini3, D. Raoult1,2,4, P.-E. Fournier1 and F. Fenollar1,2 1) Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille cedex 05, France, 2) Campus international UCAD-IRD, Dakar, Senegal, 3) Equipe Emergence et Co-évolution Virale, UMR 7268 – Aix-Marseille Université/ EFS / CNRS, IHU Méditerranée Infection, Marseille, France and 4) Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia Abstract Strain FF10T (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10T. Results support strain FF10T being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov. New Microbes and New Infections © 2016 The Authors. Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases. Keywords: Culturomics, genome, Streptococcus varani, taxonogenomics, Varanus niloticus Original Submission: 5 February 2016; Accepted: 14 March 2016 Article published online: 19 March 2016 molars of Sprague-Dawley rats [3], Streptococcus oriloxodontae Corresponding author: P.-E.
    [Show full text]
  • This Electronic Thesis Or Dissertation Has Been Downloaded from the King’S Research Portal At
    This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ The Microbial Community Ecology of the Cystic Fibrosis Lung Cuthbertson, Leah Forbes Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 06. Oct. 2021 The Microbial Community Ecology of the Cystic Fibrosis Lung A thesis submitted for the degree of Doctor of Philosophy in the Institute of Pharmaceutical Science, Molecular Microbiology Research Laboratory, King's College London By Leah Cuthbertson Pharmaceutical Sciences Research Division Kings College London October 2014 PhD – Kings College London – 2014 Declaration “I declare that I have personally prepared this report and that it has not in whole or in part been submitted for any degree or qualification.
    [Show full text]