Thèse Morgane Wartel
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CUED Phd and Mphil Thesis Classes
High-throughput Experimental and Computational Studies of Bacterial Evolution Lars Barquist Queens' College University of Cambridge A thesis submitted for the degree of Doctor of Philosophy 23 August 2013 Arrakis teaches the attitude of the knife { chopping off what's incomplete and saying: \Now it's complete because it's ended here." Collected Sayings of Muad'dib Declaration High-throughput Experimental and Computational Studies of Bacterial Evolution The work presented in this dissertation was carried out at the Wellcome Trust Sanger Institute between October 2009 and August 2013. This dissertation is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation does not exceed the limit of 60,000 words as specified by the Faculty of Biology Degree Committee. This dissertation has been typeset in 12pt Computer Modern font using LATEX according to the specifications set by the Board of Graduate Studies and the Faculty of Biology Degree Committee. No part of this dissertation or anything substantially similar has been or is being submitted for any other qualification at any other university. Acknowledgements I have been tremendously fortunate to spend the past four years on the Wellcome Trust Genome Campus at the Sanger Institute and the European Bioinformatics Institute. I would like to thank foremost my main collaborators on the studies described in this thesis: Paul Gardner and Gemma Langridge. Their contributions and support have been invaluable. I would also like to thank my supervisor, Alex Bateman, for giving me the freedom to pursue a wide range of projects during my time in his group and for advice. -
J. Gen. Appl. Microbiol., 48, 109–115 (2002)
J. Gen. Appl. Microbiol., 48, 109–115 (2002) Full Paper Haliangium ochraceum gen. nov., sp. nov. and Haliangium tepidum sp. nov.: Novel moderately halophilic myxobacteria isolated from coastal saline environments Ryosuke Fudou,* Yasuko Jojima, Takashi Iizuka, and Shigeru Yamanaka† Central Research Laboratories, Ajinomoto Co., Inc., Kawasaki 210–8681, Japan (Received November 21, 2001; Accepted January 31, 2002) Phenotypic and phylogenetic studies were performed on two myxobacterial strains, SMP-2 and SMP-10, isolated from coastal regions. The two strains are morphologically similar, in that both produce yellow fruiting bodies, comprising several sessile sporangioles in dense packs. They are differentiated from known terrestrial myxobacteria on the basis of salt requirements (2–3% NaCl) and the presence of anteiso-branched fatty acids. Comparative 16S rRNA gene sequencing studies revealed that SMP-2 and SMP-10 are genetically related, and constitute a new cluster within the myxobacteria group, together with the Polyangium vitellinum Pl vt1 strain as the clos- est neighbor. The sequence similarity between the two strains is 95.6%. Based on phenotypic and phylogenetic evidence, it is proposed that these two strains be assigned to a new genus, JCM؍) .Haliangium gen. nov., with SMP-2 designated as Haliangium ochraceum sp. nov .(DSM 14436T؍JCM 11304T؍) .DSM 14365T), and SMP-10 as Haliangium tepidum sp. nov؍11303T Key Words——Haliangium gen. nov.; Haliangium ochraceum sp. nov.; Haliangium tepidum sp. nov.; marine myxobacteria Introduction terized as Gram-negative, rod-shaped gliding bacteria with high GϩC content. Analyses of 16S rRNA gene Myxobacteria are unique in their complex life cycle. sequences reveal that they form a relatively homoge- Under starvation conditions, bacterial cells gather to- neous cluster within the d-subclass of Proteobacteria gether to form aggregates that subsequently differenti- (Shimkets and Woese, 1992). -
Genomic Signatures of Sex, Selection and Speciation in the Microbial World
Genomic signatures of sex, selection and speciation in the microbial world by B. Jesse Shapiro B.Sc. Biology McGill University, 2003 M.Sc. Integrative Bioscience Oxford University, 2004 SUBMITTED TO THE PROGRAM IN COMPUTATIONAL AND SYSTEMS BIOLOGY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN COMPUTATIONAL AND SYSTEMS BIOLOGY AT THE MASSACHUSETTS INSTITUTE OF TECHNOLOGY SEPTEMBER 2010 © 2010 Massachusetts Institute of Technology All rights reserved Signature of Author:...……………………………………………………………………………………….. Program in Computational and Systems Biology August 6, 2010 Certified by:…………………………………………………………………………………………………. Eric J. Alm Assistant Professor of Civil and Environmental Engineering and Biological Engineering Thesis Supervisor Accepted by:………………………………………………………………………………………………… Christopher B. Burge Professor of Biology and Biological Engineering Chair, Computational and Systems Biology Ph.D. Graduate Committee 1 Genomic signatures of sex, selection and speciation in the microbial world by B. Jesse Shapiro Submitted to the Program in Computational and Systems Biology on August 6, 2010 in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Computational and Systems Biology ABSTRACT Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared using the tools of population genetics to infer important genetic changes allowing them to diversify ecologically and adapt to distinct ecological niches. Yet the toolkit of population genetics was developed largely with sexual eukaryotes in mind. In this work, I assess and develop tools for inferring natural selection in microbial genomes. -
Marine Myxobacteria As a Source of Antibiotics—Comparison of Physiology, Polyketide-Type Genes and Antibiotic Production of Three New Isolates of Enhygromyxa Salina
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Mar. Drugs 2010, 8, 2466-2479; doi:10.3390/md8092466 OPEN ACCESS Marine Drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Marine Myxobacteria as a Source of Antibiotics—Comparison of Physiology, Polyketide-Type Genes and Antibiotic Production of Three New Isolates of Enhygromyxa salina Till F. Schäberle 1, Emilie Goralski 1, Edith Neu 1, Özlem Erol 1, Georg Hölzl 2, Peter Dörmann 2, Gabriele Bierbaum 3 and Gabriele M. König 1,* 1 Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany; E-Mails: [email protected] (T.F.S.); [email protected] (E.G.); [email protected] (E.N.); [email protected] (Ö.E.) 2 Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany; E-Mails: [email protected] (G.H.); [email protected] (P.D.) 3 Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany; E-Mail: [email protected] (G.B.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +49-228-733747; Fax: +49-228-733250. Received: 12 August 2010; in revised form: 25 August 2010 / Accepted: 1 September 2010 / Published: 3 September 2010 Abstract: Three myxobacterial strains, designated SWB004, SWB005 and SWB006, were obtained from beach sand samples from the Pacific Ocean and the North Sea. -
Genes for Degradation and Utilization of Uronic Acid-Containing Polysaccharides of a Marine Bacterium Catenovulum Sp
Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4 Go Furusawa, Nor Azura Azami and Aik-Hong Teh Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia ABSTRACT Background. Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. Methods. To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. Results. The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in Submitted 5 August 2020 the QB4 genome based on the CAZy database. -
A Taxonomic Framework for Emerging Groups of Ecologically
Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology 2015, 6, 281. Copyright: Copyright © 2015 Spring, Scheuner, Göker and Klenk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. DOI link to article: http://dx.doi.org/10.3389/fmicb.2015.00281 Date deposited: 07/03/2016 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk ORIGINAL RESEARCH published: 09 April 2015 doi: 10.3389/fmicb.2015.00281 A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data Stefan Spring 1*, Carmen Scheuner 1, Markus Göker 1 and Hans-Peter Klenk 1, 2 1 Department Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 School of Biology, Newcastle University, Newcastle upon Tyne, UK Edited by: Marcelino T. Suzuki, Sorbonne Universities (UPMC) and In recent years a large number of isolates were obtained from saline environments that are Centre National de la Recherche phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, Scientifique, France which were originally identified in seawater samples using cultivation independent Reviewed by: Fabiano Thompson, methods and are characterized by high seasonal abundances in coastal environments. -
Mining the Yucatan Coastal Microbiome for the Identification of Non
toxins Article Mining the Yucatan Coastal Microbiome for the Identification of Non-Ribosomal Peptides Synthetase (NRPS) Genes Mario Alberto Martínez-Núñez * and Zuemy Rodríguez-Escamilla * UMDI-Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Puerto de Abrigo s/n, Sisal, Yucatán CP 97355, Mexico * Correspondence: [email protected] (M.A.M.-N.); [email protected] (Z.R.-E.); Tel.: +52-999-341-0860 (ext. 7631) (M.A.M.-N.) Received: 21 February 2020; Accepted: 16 April 2020; Published: 26 May 2020 Abstract: Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. -
Marine-Derived Myxobacteria of the Suborder Nannocystineae: an Underexplored Source of Structurally Intriguing and Biologically Active Metabolites
Marine-derived myxobacteria of the suborder Nannocystineae: An underexplored source of structurally intriguing and biologically active metabolites Antonio Dávila-Céspedes‡, Peter Hufendiek‡, Max Crüsemann‡, Till F. Schäberle and Gabriele M. König* Review Open Access Address: Beilstein J. Org. Chem. 2016, 12, 969–984. Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, doi:10.3762/bjoc.12.96 53115 Bonn, Germany Received: 22 February 2016 Email: Accepted: 25 April 2016 Gabriele M. König* - [email protected] Published: 13 May 2016 * Corresponding author ‡ Equal contributors This article is part of the Thematic Series "Natural products in synthesis and biosynthesis II". Keywords: Enhygromyxa; genome mining; myxobacteria; Nannocystineae; Guest Editor: J. S. Dickschat natural products © 2016 Dávila-Céspedes et al; licensee Beilstein-Institut. License and terms: see end of document. Abstract Myxobacteria are famous for their ability to produce most intriguing secondary metabolites. Till recently, only terrestrial myxobac- teria were in the focus of research. In this review, however, we discuss marine-derived myxobacteria, which are particularly inter- esting due to their relatively recent discovery and due to the fact that their very existence was called into question. The to-date- explored members of these halophilic or halotolerant myxobacteria are all grouped into the suborder Nannocystineae. Few of them were chemically investigated revealing around 11 structural types belonging to the polyketide, non-ribosomal peptide, hybrids thereof or terpenoid class of secondary metabolites. A most unusual structural type is represented by salimabromide from Enhygromyxa salina. In silico analyses were carried out on the available genome sequences of four bacterial members of the Nannocystineae, revealing the biosynthetic potential of these bacteria. -
The Soil Microbial Food Web Revisited: Predatory Myxobacteria As Keystone Taxa?
The ISME Journal https://doi.org/10.1038/s41396-021-00958-2 ARTICLE The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? 1 1 1,2 1 1 Sebastian Petters ● Verena Groß ● Andrea Söllinger ● Michelle Pichler ● Anne Reinhard ● 1 1 Mia Maria Bengtsson ● Tim Urich Received: 4 October 2018 / Revised: 24 February 2021 / Accepted: 4 March 2021 © The Author(s) 2021. This article is published with open access Abstract Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5–9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized fi 1234567890();,: 1234567890();,: predatory bacteria af liated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. -
A Genomic View of Trophic and Metabolic Diversity in Clade-Specific
A genomic view of trophic and metabolic diversity in clade-specic Lamellodysidea sponge microbiomes Sheila Podell ( [email protected] ) University of California San Diego https://orcid.org/0000-0001-7073-5190 Jessica M. Blanton University of California San Diego Aaron Oliver University of California San Diego Michelle A. Schorn Wageningen Universiteit Vinayak Agarwal Georgia Institute of Technology Jason S. Biggs University of Guam Marine Laboratory Bradley S. Moore University of California San Diego Eric E. Allen University of California San Diego Research Keywords: Lamellodysidea, sponge microbiome, cyanosponge, Hormoscilla, PBDE, Methylospongia, Prochloron Posted Date: February 21st, 2020 DOI: https://doi.org/10.21203/rs.2.17204/v2 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on June 23rd, 2020. See the published version at https://doi.org/10.1186/s40168-020-00877-y. Page 1/31 Abstract Background: Marine sponges and their microbiomes contribute signicantly to carbon and nutrient cycling in global reefs, processing and remineralizing dissolved and particulate organic matter. Lamellodysidea herbacea sponges obtain additional energy from abundant photosynthetic Hormoscilla cyanobacterial symbionts, which also produce polybrominated diphenyl ethers (PBDEs) chemically similar to anthropogenic pollutants of environmental concern. Potential contributions of non-Hormoscilla bacteria to Lamellodysidea microbiome metabolism and the synthesis and degradation of additional secondary metabolites are currently unknown. Results: This study has determined relative abundance, taxonomic novelty, metabolic capacities, and secondary metabolite potential in 21 previously uncharacterized, uncultured Lamellodysidea-associated microbial populations by reconstructing near-complete metagenome-assembled genomes (MAGs) to complement 16S rRNA gene amplicon studies. -
Bacterial Microcompartments
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Rev Manuscript Author Microbiol. Author Manuscript Author manuscript; available in PMC 2018 November 01. Published in final edited form as: Nat Rev Microbiol. 2018 May ; 16(5): 277–290. doi:10.1038/nrmicro.2018.10. Bacterial microcompartments Cheryl A. Kerfeld1,2,3,*, Clement Aussignargues1,3, Jan Zarzycki4, Fei Cai2, and Markus Sutter1,2,3 1MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA 2Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 3Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA 4Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany Abstract Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread, found across the Kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than sixty years ago, it is mainly in the last decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but it is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs. -
Phylogenetic Profile of Copper Homeostasis in Deltaproteobacteria
Phylogenetic Profile of Copper Homeostasis in Deltaproteobacteria A Major Qualifying Report Submitted to the Faculty of Worcester Polytechnic Institute In Partial Fulfillment of the Requirements for the Degree of Bachelor of Science By: __________________________ Courtney McCann Date Approved: _______________________ Professor José M. Argüello Biochemistry WPI Project Advisor 1 Abstract Copper homeostasis is achieved in bacteria through a combination of copper chaperones and transporting and chelating proteins. Bioinformatic analyses were used to identify which of these proteins are present in Deltaproteobacteria. The genetic environment of the bacteria is affected by its lifestyle, as those that live in higher concentrations of copper have more of these proteins. Two major transport proteins, CopA and CusC, were found to cluster together frequently in the genomes and appear integral to copper homeostasis in Deltaproteobacteria. 2 Acknowledgements I would like to thank Professor José Argüello for giving me the opportunity to work in his lab and do some incredible research with some equally incredible scientists. I need to give all of my thanks to my supervisor, Dr. Teresita Padilla-Benavides, for having me as her student and teaching me not only lab techniques, but also how to be scientist. I would also like to thank Dr. Georgina Hernández-Montes and Dr. Brenda Valderrama from the Insituto de Biotecnología at Universidad Nacional Autónoma de México (IBT-UNAM), Campus Morelos for hosting me and giving me the opportunity to work in their lab. I would like to thank Sarju Patel, Evren Kocabas, and Jessica Collins, whom I’ve worked alongside in the lab. I owe so much to these people, and their support and guidance has and will be invaluable to me as I move forward in my education and career.