DOCSLIB.ORG

Das Menschliche Mikrobiom Mehr, Als Wir Erwartet Haben

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Das Menschliche Mikrobiom Mehr, Als Wir Erwartet Haben Das menschliche Mikrobiom Mehr, als wir erwartet haben Tom Fox 16.04.2021 1 © Copyright 2021 Energetica Natura 2 © Copyright 2021 Energetica Natura 3 © Copyright 2021 Energetica Natura Appanna 2018 4 © Copyright 2021 Energetica Natura Pasolli 2019 5 © Copyright 2021 Energetica Natura Man kann schnell die Übersicht verlieren … Gupta 2017 6 © Copyright 2021 Energetica Natura Dennoch: das Mikrobiom ist sehr individuell Gilbert 2018 7 © Copyright 2021 Energetica Natura Besiedelung: die klassische Erklärung … Beckmann / Rüffler 2007 8 © Copyright 2021 Energetica Natura … reicht nicht mehr Stinson 2019 9 © Copyright 2021 Energetica Natura IgG / IgA Bakterienmetaboliten Potentielle aus Muttermilch Plazentabakterien > Darm - Muttermilch Mechanismen stimulieren epigenetische Mechanismen Bakterien > Darm - Muttermilch Mutter-IgG fördert transplazentare Übertragung von Bakterien Pränatale Kolonisation programmiert die spätere Flora Bakterientranslokation Nyangahu 2019 Darm-Plazenta 10 © Copyright 2021 Energetica Natura Weitere Einflussfaktoren Heijtz 2016 11 © Copyright 2021 Energetica Natura Das Mikrobiom ist mehr … Marks 2018 12 © Copyright 2021 Energetica Natura Bakterien: Hauptgruppen (99%) Actinobakterien Bacteroidetes Firmicuten Proteobakterien 13 © Copyright 2021 Energetica Natura Bevor wir total verrückt werden - ein Beispiel: • Stamm (Phyla) • Bacteroidetes • Klasse • Bacteroidia • Ordnung • Bacteroidales • Familie • Bacteroidaceae • Gattung • Bacteroides • Art • Bacteroides faeces 14 © Copyright 2021 Energetica Natura Beispiel: Stamm Actinobakterien • Klasse Acidimicrobiia • Familie Cellulomonadaceae • Familie Patulibacteraceae • Ordnung Acidimicrobiales • Familie Demequinaceae • Familie Solirubrobacteraceae • Unterordnung „Acidimicrobineae“ • Familie Dermabacteraceae • Klasse Thermoleophilia • Familie Acidimicrobiaceae • Familie Dermacoccaceae • Ordnung Thermoleophilales • Familie Iamiaceae • Familie Dermatophilaceae • Familie Thermoleophilaceae • Klasse Actinobacteria • Familie Intrasporangiaceae • Ordnung Acidothermales • Familie Jonesiaceae (inklusive ehemaliger Sanguibacteraceae) • Familie Acidothermaceae • Familie Kytococcaceae • Ordnung Actinomycetales • Familie Microbacteriaceae • Unterordnung Actinomycineae • Familie Micrococcaceae • Familie Actinomycetaceae • Familie Ornithinimicrobiaceae • Unterordnung Actinopolysporineae • Familie Promicromonosporaceae • Familie Actinopolysporaceae • Familie Rarobacteraceae • Unterordnung Catenulisporineae • Familie Ruaniaceae • Familie Actinospicaceae • Familie Tropherymataceae • Familie Catenulisporaceae • Familie Yaniellaceae • Unterordnung Corynebacterineae • Ordnung Micromonosporales • Familie Corynebacteriaceae • Familie Micromonosporaceae • Familie Dietziaceae • Ordnung Mycobacteriales (alternativ: Corynebacteriales) • Familie Mycobacteriaceae • Familie Corynebacteriacea • Familie Nocardiaceae • Familie Dietziaceae • Familie Segniliparaceae • Familie Gordoniaceae • Familie Tsukamurellaceae • Familie Lawsonellaceae • Unterordnung Glycomycineae • Familie Mycobacteriaceae • Familie Glycomycetaceae • Familie Nocardiaceae • Unterordnung Jiangellineae • Familie Segniliparaceae • Familie Jiangellaceae • Familie Tsukamurellaceae • Unterordnung Micromonosporineae • Ordnung Nakamurellales • Familie Micromonosporaceae • Familie Nakamurellaceae • Unterordnung Propionibacterineae • Ordnung Propionibacteriales • Familie Nocardioidaceae • Familie Actinopolymorphaceae • Familie Propionibacteriaceae • Familie Kribbellaceae • Unterordnung Pseudonocardineae • Familie Nocardioidaceae • Familie Pseudonocardiaceae • Familie Propionibacteriaceae • Unterordnung Streptomycineae • Ordnung Pseudonocardiales • Familie Streptomycetaceae • Familie Pseudonocardiaceae • Unterordnung Streptosporangineae • Ordnung Sporichthyales • Familie Nocardiopsaceae • Familie Sporichthyaceae • Familie Streptosporangiaceae • Ordnung Streptosporangiales • Familie Thermomonosporaceae • Familie Streptomycetaceae • Ordnung Actinopolysporales • Klasse Coriobacteriia • Familie Actinopolysporaceae • Ordnung Coriobacteriales • Ordnung Bifidobacteriales • Unterordnung „Coriobacterineae“ • Familie Bifidobacteriaceae • Familie Atopobiaceae • Ordnung Catenulisporales • Familie Coriobacteriaceae • Familie Actinospicaceae • Ordnung Eggerthellales • Familie Catenulisporaceae • Familie Eggerthellaceae • Ordnung Cryptosporangiales • Klasse Nitriliruptoria • Familie Cryptosporangiaceae • Ordnung Egibacterales • Ordnung Frankiales (alternativ: Motilibacterales) • Familie Egibacteraceae • Familie Frankiaceae • Ordnung Egicoccales • Familie Motilibacteraceae • Familie Egicoccaceae • Ordnung Geodermatophilales • Ordnung Euzebyales • Familie Antricoccaceae • Familie Euzebyaceae • Familie Geodermatophilaceae • Ordnung Nitriliruptorales • Ordnung Glycomycetales • Familie Nitriliruptoraceae • Familie Glycomycetaceae • Klasse Rubrobacteria • Ordnung Jatrophihabitantales • Ordnung Gaiellales • Familie Jatrophihabitantaceae • Familie Gaiellaceae • Ordnung Jiangellales • Ordnung Rubrobacterales • Familie Jiangellaceae • Unterordnung „Rubrobacterineae“ • Ordnung Kineosporiales • Familie Rubrobacteraceae • Familie Kineosporiaceae • Ordnung Solirubrobacterales • Ordnung Micrococcales • Familie Baekduiaceae 15 • Familie Beutenbergiaceae • Familie Conexibacteraceae • Familie Bogoriellaceae • Familie Paraconexibacteraceae • Familie Brevibacteriaceae • Familie Parviterribacteraceae © Copyright 2021 Energetica Natura Allein die Mundflora beherbergt 12 verschiedene „phylae (= Stämme)“ Firmicutes Fusobacteriae Proteobacteriae Actinobacteriae Bacteroidetes Chlamydiae Chloroflexi Spirochaetes SR1 Synergistetes Saccharibacteria Gracilibacteria 16 © Copyright 2021 Energetica Natura Bakterien: wer ist wo? Jandhyala 2015 17 © Copyright 2021 Energetica Natura Pilze … Witherden 2017 18 © Copyright 2021 Energetica Natura Viren … Liang 2021 19 © Copyright 2021 Energetica Natura Die grösste Gruppe Viren: Bakteriophagen Shkoporov 2019 20 © Copyright 2021 Energetica Natura Parasiten … 21 © Copyright 2021 Energetica Natura Das menschliche Parasitom A Blastocystis hominis B Enteromonas hominis C Retortamonas intestinalis D Pentratrichomonas hominis E Dientamoeba fragilis F Chilomastix mesnili G Entamoeba hartmani H Endolimax nana I Entamoeba coli J Entamoeba dispar K Isospora belli L Iodamoeba buetschli M Encephalitozoon cuniculi N Candida albicans Lukeš 2015 22 © Copyright 2021 Energetica Natura Parasiten … Definition: „Lebewesen, das aus dem Zusammenleben mit anderen Lebewesen einseitig Nutzen zieht, die es oft auch schädigt und bei denen es Krankheiten hervorrufen kann.“ 23 © Copyright 2021 Energetica Natura 24 © Copyright 2021 Energetica Natura Im Prinzip ist es dann doch einfach: Bakterien (Parasiten) (Archaea) Viren Kontrolle Pilze 25 © Copyright 2021 Energetica Natura Phagen kontrollieren Bakterien Keen 2018 26 © Copyright 2021 Energetica Natura Die Diversität ändert sich im Laufe des Lebens Kapitan 2019 27 © Copyright 2021 Energetica Natura Beispiel: Kontrolle des Candida albicans Kapitan 2019 28 © Copyright 2021 Energetica Natura Pilze kontrollieren Viren Linnakoski 2018 29 © Copyright 2021 Energetica Natura Und wir wissen auch wie … Linnakoski 2018 30 © Copyright 2021 Energetica Natura Störung im Gleichgewicht Balfour 2016 31 © Copyright 2021 Energetica Natura Parasiten: Die gute Seite Maizels 2019 32 © Copyright 2021 Energetica Natura Unser Mikrobiom ist sehr, sehr alt … 33 © Copyright 2021 Energetica Natura COMMUNICATIONS BIOLOGY | (2021)4:169 | https://doi.org/10.1038/s42003-021-01689-y | www.nature.com/commsbio 34 © Copyright 2021 Energetica Natura Aber: der Mensch hat leider ‚wenig‘ Diversität … entwickelt Gupta 2017 35 © Copyright 2021 Energetica Natura Und das fängt schon bei Primaten an … Clayton 2016 36 © Copyright 2021 Energetica Natura plant-based diet animal-based diet Nahrung ändert das Mikrobiom innerhalb von Tagen David 2014 37 © Copyright 2021 Energetica Natura Dies hat Einfluss auf die kurzkettigen Fettsäuren plant-based diet animal-based diet A: KKFS aus Polysaccharid-Fermentation David 2014 B: KKFS aus Aminosäuren-Fermentation 38 © Copyright 2021 Energetica Natura Faserstoffe: der Treibstoff für Bakterien Myhrstad 2020 39 © Copyright 2021 Energetica Natura Das Ergebnis der Fermentation: Kurzkettige Fettsäuren Butyrat Hauptsächlich durch Firmicuten Acetat Hauptsächlich durch Bakteroidetes Propionat 40 © Copyright 2021 Energetica Natura Hauptaufgaben dieser Fettsäuren • Energieversorgung • Signalgebung 41 © Copyright 2021 Energetica Natura Wie werden diese Fettsäuren aufgenommen? • passiver Membrantransport • MCT-1 • SMCT-1 42 © Copyright 2021 Energetica Natura MCT-1 und SMCT-1 Goncalves 2016 43 © Copyright 2021 Energetica Natura Anzahl MCT-1 bei Entzündung … Thibault 2007 44 © Copyright 2021 Energetica Natura … führt zu weniger KKFS Aufnahme 45 © Copyright 2021 Energetica Natura Anzahl SMCT-1 bei Entzündung … Borthakur 2010 46 © Copyright 2021 Energetica Natura … und in Anwesenheit von Laktobazillen Borthakur 2010 47 © Copyright 2021 Energetica Natura KKFS als Botenstoffe G protein-coupled receptors (GPR): • GPR41 • GPR43 • GPR109a 48 © Copyright 2021 Energetica Natura GPR41 Nakajima 2018 49 © Copyright 2021 Energetica Natura GPR43 Kimura 2014 50 © Copyright 2021 Energetica Natura GPR109a Jobin 2014 51 © Copyright 2021 Energetica Natura Zusammengefasst: Venegas 2019 52 © Copyright 2021 Energetica Natura Das Mikrobiom optimiert das Immunsystem …? 53 © Copyright 2021 Energetica Natura 54 © Copyright 2021 Energetica Natura Effekte ausgewählter
Load more

Recommended publications
  • Halophilic Microorganisms Are Responsible for the Rosy Discolouration of Saline Environments in Three Historical Buildings with Mural Paintings
    Halophilic Microorganisms Are Responsible for the Rosy Discolouration of Saline Environments in Three Historical Buildings with Mural Paintings Jo¨ rg D. Ettenauer1*, Valme Jurado2, Guadalupe Pin˜ ar1, Ana Z. Miller2,3, Markus Santner4, Cesareo Saiz-Jimenez2, Katja Sterflinger1 1 VIBT-BOKU, University of Natural Resources and Life Sciences, Department of Biotechnology, Vienna, Austria, 2 Instituto de Recursos Naturales y Agrobiologia, IRNAS- CSIC, Sevilla, Spain, 3 CEPGIST/CERENA, Instituto Superior Te´cnico, Universidade de Lisboa, Lisboa, Portugal, 4 Bundesdenkmalamt, Abteilung fu¨r Konservierung und Restaurierung, Vienna, Austria Abstract A number of mural paintings and building materials from monuments located in central and south Europe are characterized by the presence of an intriguing rosy discolouration phenomenon. Although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture- dependent and -independent techniques as well as microscopic techniques. The bacterial communities were dominated by halophilic members of Actinobacteria, mainly of the genus Rubrobacter. Representatives of the Archaea were also detected with the predominating genera Halobacterium, Halococcus and Halalkalicoccus. Furthermore, halophilic bacterial strains, mainly of the phylum Firmicutes, could be retrieved from two monuments using special culture media. Inoculation of building materials (limestone and gypsum plaster) with selected isolates reproduced the unaesthetic rosy effect and biodeterioration in the laboratory. Citation: Ettenauer JD, Jurado V, Pin˜ar G, Miller AZ, Santner M, et al.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Marine Rare Actinomycetes: a Promising Source of Structurally Diverse and Unique Novel Natural Products
    Review Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products Ramesh Subramani 1 and Detmer Sipkema 2,* 1 School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji; [email protected] 2 Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands * Correspondence: [email protected]; Tel.: +31-317-483113 Received: 7 March 2019; Accepted: 23 April 2019; Published: 26 April 2019 Abstract: Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
    [Show full text]
  • Caracterización Metagenómica De Genes Asociados a La Síntesis Y Resistencia De Compuestos Antimicrobianos En Suelos De Manglar
    Caracterización metagenómica de genes asociados a la síntesis y resistencia de compuestos antimicrobianos en suelos de manglar Alejandro Sepúlveda Correa Universidad Nacional de Colombia Facultad de Ciencias Agrarias, Departamento de Ciencias Forestales Medellín, Colombia 2021 Caracterización metagenómica de genes asociados a la síntesis y resistencia de compuestos antimicrobianos en suelos de manglar Alejandro Sepúlveda Correa Tesis presentada como requisito parcial para optar al título de: Magister en Bosques y Conservación Directores: Profesor titular Jaime Polanía, Dr.rer.nat. Profesor Javier Vanegas Guerrero, Ph.D. Línea de Investigación: Componente físico, biológico, químico y geológico del medio marino e hídrico continental Facultad de Ciencias Agrarias, Departamento de Ciencias Forestales Medellín, Colombia 2021 A mi familia, especialmente a mi papá, Julio Sepúlveda Arango, y mi mamá, Luz Mary Correa Patiño. Agradecimientos Agradezco al profesor Jaime Polanía, de la Universidad Nacional de Colombia, quien no solo es mi director en la presente tesis, también es mi modelo a seguir en mi formación como científico e investigador; y a mi codirector, el profesor Javier Vanegas, de la Universidad Antonio Nariño, quien me abrió las puertas de su investigación. También agradezco a mi familia y a Yennifer por compartir conmigo en medio de la experiencia de escribir esta tesis y hacer más amenos los tiempos de la pandemia. Este trabajo estuvo enmarcado dentro del proyecto “Diversidad funcional de microorganismos asociados al ciclaje de C, N y P en el manglar la Ranchería (La Guajira) mediante un acercamiento de metatranscriptómica”, contrato 529/14, cofinanciado por Colciencias y las universidades Antonio Nariño y Nacional de Colombia Sede Medellín.
    [Show full text]
  • Complete Genome Sequence of Jiangella Gansuensis Strain YIM 002T (DSM 44835T), the Type Species of the Genus Jiangella and Source of New Antibiotic Compounds
    UC Davis UC Davis Previously Published Works Title Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds. Permalink https://escholarship.org/uc/item/34s6p01n Journal Standards in genomic sciences, 12(1) ISSN 1944-3277 Authors Jiao, Jian-Yu Carro, Lorena Liu, Lan et al. Publication Date 2017 DOI 10.1186/s40793-017-0226-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Jiao et al. Standards in Genomic Sciences (2017) 12:21 DOI 10.1186/s40793-017-0226-6 SHORTGENOMEREPORT Open Access Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds Jian-Yu Jiao1, Lorena Carro2, Lan Liu1, Xiao-Yang Gao3, Xiao-Tong Zhang1, Wael N. Hozzein4,12, Alla Lapidus5,6, Marcel Huntemann7, T. B. K. Reddy7, Neha Varghese7, Michalis Hadjithomas7, Natalia N. Ivanova7, Markus Göker8, Manoj Pillay9, Jonathan A. Eisen10, Tanja Woyke7, Hans-Peter Klenk2,8*, Nikos C. Kyrpides7,11 and Wen-Jun Li1,13* Abstract Jiangella gansuensis strain YIM 002T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the Genomic Encyclopedia of Bacteria and Archaea project, and here we describe the complete genome sequence and annotation of this taxon.
    [Show full text]
  • Jiangella Anatolica Sp. Nov. Isolated from Coastal Lake Soil
    [This is a post-peer-review, pre-copyedit version of an article published in Antonie van Leeuwenhoek. The final authenticated version is available online at: http://dx.doi.org/10.1007/s10482-018-01222-y] Jiangella anatolica sp. nov. isolated from coastal lake soil Hilal Ay1*, Imen Nouioui2, Lorena Carro2¥, Hans-Peter Klenk2, Demet Cetin3, José M. Igual4, Nevzat Sahin1, Kamil Isik5 1H. Ay, N. Sahin Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey *Corresponding author: [email protected], Tel: +90 362 312 1919, Fax: +90 362 457 6081 2I. Nouioui, L. Carro, H.-P. Klenk School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, Newcastle upon Tyne, NE1 7RU, UK ¥Present address: Dpto. de Microbiología y Genética. Universidad de Salamanca, Salamanca, 37007, Spain. 3D. Cetin Science Teaching Programme, Gazi Faculty of Education, Gazi University, 06500, Ankara, Turkey 4J. M. Igual Instituto de Recursos Naturales y Agrobiologia de Salamanca, Consejo Superior de Investigaciones Cientificas (IRNASA-CSIC), Salamanca, Spain 5K. Isik Department of Biology, Faculty of Science and Arts, Ondokuz Mayis University, Samsun, Turkey Introduction The genus Jiangella was first proposed by Song et al. (2005) within the family Nocardioidaceae. However, Tang et al. (2011) established the family Jiangellaceae to accommodate the genera Jiangella (Song et al. 2005) and Haloactinopolyspora (Tang et al. 2011) mainly based on phylogenetic analysis of phylum Actinobacteria. Currently, the family Jiangellaceae includes the genera Jiangella, Haloactinopolyspora and the recently described Phytoactinopolyspora (Li et al. 2015). The type genus Jiangella encompasses aerobic, Gram-positive, filamentous actinomycetes with substrate mycelium fragmented into short and elongated rods.
    [Show full text]
  • Étude Du Potentiel Biotechnologique De Halomonas Sp. SF2003 : Application À La Production De Polyhydroxyalcanoates (PHA)
    THESE DE DOCTORAT DE L’UNIVERSITE BRETAGNE SUD COMUE UNIVERSITE BRETAGNE LOIRE ECOLE DOCTORALE N° 602 Sciences pour l'Ingénieur Spécialité : Génie des procédés et Bioprocédés Par Tatiana THOMAS Étude du potentiel biotechnologique de Halomonas sp. SF2003 : Application à la production de PolyHydroxyAlcanoates (PHA). Thèse présentée et soutenue à Lorient, le 17 Décembre 2019 Unité de recherche : Institut de Recherche Dupuy de Lôme Thèse N° : 542 Rapporteurs avant soutenance : Sandra DOMENEK Maître de Conférences HDR, AgroParisTech Etienne PAUL Professeur des Universités, Institut National des Sciences Appliquées de Toulouse Composition du Jury : Président : Mohamed JEBBAR Professeur des Universités, Université de Bretagne Occidentale Examinateur : Jean-François GHIGLIONE Directeur de Recherche, CNRS Dir. de thèse : Stéphane BRUZAUD Professeur des Universités, Université de Bretagne Sud Co-dir. de thèse : Alexis BAZIRE Maître de Conférences HDR, Université de Bretagne Sud Co-dir. de thèse : Anne ELAIN Maître de Conférences, Université de Bretagne Sud Étude du potentiel biotechnologique de Halomonas sp. SF2003 : application à la production de polyhydroxyalcanoates (PHA) Tatiana Thomas 2019 « Failure is only the opportunity to begin again more intelligently. » Henry Ford « I dettagli fanno la perfezione e la perfezione non è un dettaglio. » Leonardo Da Vinci Étude du potentiel biotechnologique de Halomonas sp. SF2003 : application à la production de polyhydroxyalcanoates (PHA) Tatiana Thomas 2019 Étude du potentiel biotechnologique de Halomonas sp. SF2003 : application à la production de polyhydroxyalcanoates (PHA) Tatiana Thomas 2019 Remerciements Pour commencer, mes remerciements s’adressent à l’Université de Bretagne Sud et Pontivy Communauté qui ont permi le financement et la réalisation de cette thèse entre l’Institut de Recherche Dupuy de Lôme et le Laboratoire de Biotechnologies et Chimie Marines.
    [Show full text]
  • Abstract Tracing Hydrocarbon
    ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants.
    [Show full text]
  • Biology and Biotechnology of Actinobacteria Biology and Biotechnology of Actinobacteria Joachim Wink Fatemeh Mohammadipanah Javad Hamedi Editors
    Joachim Wink Fatemeh Mohammadipanah Javad Hamedi Editors Biology and Biotechnology of Actinobacteria Biology and Biotechnology of Actinobacteria Joachim Wink Fatemeh Mohammadipanah Javad Hamedi Editors Biology and Biotechnology of Actinobacteria Editors Joachim Wink Fatemeh Mohammadipanah Microbial Strain Collection; College of Science Helmholtz- Centre for Infection Research University of Tehran Braunschweig Tehran Germany Iran Javad Hamedi College of Science University of Tehran Tehran Iran ISBN 978-3-319-60338-4 ISBN 978-3-319-60339-1 (eBook) DOI 10.1007/978-3-319-60339-1 Library of Congress Control Number: 2017955832 © Springer International Publishing AG 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made.
    [Show full text]
  • Isolation and Diversity of Sediment Bacteria in The
    bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Isolation and Diversity of Sediment Bacteria in the 2 Hypersaline Aiding Lake, China 3 4 Tong-Wei Guan, Yi-Jin Lin, Meng-Ying Ou, Ke-Bao Chen 5 6 7 Institute of Microbiology, Xihua University, Chengdu 610039, P. R. China. 8 9 Author for correspondence: 10 Tong-Wei Guan 11 Tel/Fax: +86 028 87720552 12 E-mail: [email protected] 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 bioRxiv preprint doi: https://doi.org/10.1101/638304; this version posted May 14, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 29 Abstract A total of 343 bacteria from sediment samples of Aiding Lake, China, were isolated using 30 nine different media with 5% or 15% (w/v) NaCl. The number of species and genera of bacteria recovered 31 from the different media significantly varied, indicating the need to optimize the isolation conditions. 32 The results showed an unexpected level of bacterial diversity, with four phyla (Firmicutes, 33 Actinobacteria, Proteobacteria, and Rhodothermaeota), fourteen orders (Actinopolysporales, 34 Alteromonadales, Bacillales, Balneolales, Chromatiales, Glycomycetales, Jiangellales, Micrococcales, 35 Micromonosporales, Oceanospirillales, Pseudonocardiales, Rhizobiales, Streptomycetales, and 36 Streptosporangiales), including 17 families, 41 genera, and 71 species.
    [Show full text]
  • Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
    Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food.
    [Show full text]
  • Table S8. Detailed Information in the Water Microbial Community at Phylum, Family, and Genus Level
    Table S8. Detailed information in the water microbial community at phylum, family, and genus level (a) The annotation information of water microbial community at phylum level No. Phylum The number of contigs Abundance(%) 1 Proteobacteria 10948 54.43516309 2 Bacteroidetes 3601 17.90473349 3 Actinobacteria 3029 15.0606603 4 Cyanobacteria 1032 5.131264916 5 Firmicutes 535 2.660103421 6 Planctomycetes 306 1.521479714 7 Verrucomicrobia 295 1.466785998 8 Tenericutes 77 0.382856006 9 Deinococcus-Thermus 48 0.238663484 10 Chlorobi 36 0.178997613 11 Spirochaetes 35 0.174025457 12 Fusobacteria 29 0.144192522 13 Chloroflexi 27 0.13424821 14 Acidobacteria 21 0.104415274 15 Gemmatimonadetes 18 0.089498807 16 Chlamydiae 9 0.044749403 17 Nitrospirae 8 0.039777247 18 Armatimonadetes 7 0.034805091 19 Lentisphaerae 7 0.034805091 20 Kiritimatiellaeota 7 0.034805091 21 Aquificae 7 0.034805091 22 Synergistetes 5 0.02486078 23 Ignavibacteriae 4 0.019888624 24 Thermotogae 4 0.019888624 25 Candidatus Saccharibacteria 3 0.014916468 26 Calditrichaeota 3 0.014916468 27 Fibrobacteres 2 0.009944312 28 Candidatus Gracilibacteria 2 0.009944312 29 Deferribacteres 2 0.009944312 30 Chrysiogenetes 2 0.009944312 31 Dictyoglomi 1 0.004972156 32 Elusimicrobia 1 0.004972156 33 Thermodesulfobacteria 1 0.004972156 (b) The annotation information of Proteobacteria at family level No. Family of Proteobacteria The number of contigs Abundance(%) 1 Rhodobacteraceae 4661 42.57398612 2 Comamonadaceae 1616 14.76068688 3 Pseudomonadaceae 413 3.772378517 4 Burkholderiaceae 322 2.941176471
    [Show full text]