DOCSLIB.ORG

(12) Patent Application Publication (10) Pub. No.: US 2016/0024489 A1 SERWER (43) Pub

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) Patent Application Publication (10) Pub. No.: US 2016/0024489 A1 SERWER (43) Pub US 2016.0024489A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2016/0024489 A1 SERWER (43) Pub. Date: Jan. 28, 2016 (54) METHODS OF ISOLATING BACTERIAL Related U.S. Application Data STRANS (60) Provisional application No. 61/785,392, filed on Mar. (71) Applicant: THE BROAD OF REGENTS OF THE 14, 2013. UNIVERSITY OF TEXAS SYSTEM, Austin, TX (US) Publication Classification (72) Inventor: Philip SERWER, San Antonio, TX (US) (51) Int. Cl. (73) Assignee: THE BROAD OF REGENTS OF THE CI2PCI2N 7/04I5/0 30:2006.O1 8: UNIVERSITY OF TEXAS SYSTEM, (52) U.S. Cl Austin, TX (US) CPC. CI2N 15/01 (2013.01): CI2P 7/04 (2013.01) (21) Appl. No.: 14/776,028 (57) ABSTRACT (22) PCT Filed: Mar. 14, 2014 Certain embodiments are directed to methods of developing (86). PCT No.: PCT/US1.4/27001 bacterial strains having a selected metabolism for producing S371 (c)(1), a target molecule(s) O bacterial strains or bacteriophage (2) Date: Sep. 14, 2015 strains comprising a modified gene encoding a selected agent. US 2016/0024489 A1 Jan. 28, 2016 METHODS OF SOLATING BACTERIAL evolution of one biological entity is associated with and STRANS depends on a change in a second biological entity. Each biological entity in a co-evolutionary relationship exerts 0001. This application claims priority to U.S. Provisional selective pressures on the other, thereby affecting each oth Application Ser. No. 61/785,392 filed Mar. 14, 2013, which is er's evolution. In certain aspects co-evolution occurs when incorporated herein by reference in its entirety. certain viruses and their hosts are exposed to selective pres sure. Viruses typically replicate more rapidly than their hosts STATEMENT REGARDING FEDERALLY and, therefore, evolve more rapidly. If virus-host gene FUNDED RESEARCH exchange occurs, then the virus can accelerate the evolution 0002 This invention was made with government support of the host. under GM24365 awarded by the National Institutes of 0009. Applicant notes that selection can be used to pro Health. The government has certain rights in the invention. duce essentially any molecule capable of being produced by a bacterium. In certain aspects the target molecule is metha BACKGROUND nol. In certain aspects the methods are initiated by selecting a 0003 1. Field of the Invention methanol-dependent strain. A methanol dependent strain is a 0004 Embodiments of this invention are directed gener bacterium that can use only methanol as a source of carbon. ally to biology and microbiology. Certain aspects are directed Methanol dependent strains have been isolated and are known to co-evolution and production of microbes with a selected to exist, e.g., Methanomonas methylovora (Kouno et al., J. metabolism. Gen. Appl. Microbiol. 19:11-21, 1973). 0010 Certain aspects use at least two co-dependent bac 0005 2. Background terial strains. The term “co-dependent refers to bacterial 0006. The use of microbes in producing a number of use strains that rely on a metabolite or nutrient produced by the ful molecules on a commercial scale has been a long-sought other bacterial strain for growth and reproduction. The term after goal. Bioconversion of various molecules to particular “rely, as used in the context of co-dependency, means that in products can use a variety of bacteria that have evolved the the absence of such metabolite or nutrient the dependent capacity to metabolize a Substrate(s) to a target product. For bacterial Strains grows or replicates at a significantly lower example, methanotrophs can metabolize methane to metha level or not at all. In certain aspects at 3, 4, 5 or more bacteria nol. Some bacterial genes can be evolved to have useful can be used in the co-evolution compositions. In a further properties (conferring of resistance to herbicides, for aspect additional bacteriophage can be included in the co example) that can be transferred to other organisms (food evolution compositions. The additional bacteriophage can be plants, for example). There remains a need to develop bacteria specific for other bacterium in the mixture, such as the having improved characteristics for Scaling and commercial metabolite-dependent bacterium. In other aspects more than production of Such bacterial products. on one bacteriophage can be present for a single bacterium. In still a further aspect more than one bacterial strain can be SUMMARY Susceptible to a single bacteriophage. 0007 Certain embodiments are directed to methods of 0011 Certain embodiments are directed to co-evolving accelerating development of bacterial strains having a fermentation compositions comprising (a) a metabolite-de selected metabolism for producing a target molecule(s), or pendent bacterium whose propagation is dependent on a first bacterial strains or bacteriophage strains comprising a modi metabolite, (b) a metabolite-producing bacterium that pro fied gene encoding a selected agent. duces the first metabolite and requires an essential nutrient for 0008 Certain embodiments are directed to accelerating propagation, and (c) a co-evolving bacteriophage that propa the development of bacteria that produce a target molecule, gates in and co-evolves with the metabolite-producing bacte e.g., produce methanol in commercial amounts. Target mol rium. In certain aspects a metabolite can be methanol or ecule-producing bacteria are bacteria that produce a target another carbon source. In a further aspect the metabolite molecule in quantities that can be used in down stream pro producing bacteria is an auxotroph, e.g., an amino acid or cesses. Down stream process can include, but are not limited fatty acid auxotroph. In certain aspects the bacteriophage is a to isolation of the target molecule or use of a medium con member of the Myoviridae. In a further aspect the bacterioph taining the target molecule in a down stream process. Quan age is a long-genome bacteriophage. A long-genome bacte tities of target molecules produced in the context of the riophage has a genome of at least 150, 200, 250, 300 or more described methods are increased over the amount produced kilobases (Kb). In certain aspects the bacteriophage can be by a non-modified or non-selected bacterial strain. In certain engineered to encode 1,2,3,4, 5, or more proteins or enzymes aspects the target molecule is produced at a level that is 10, (endogenous or heterologous proteins or enzymes) that can 100, 1000, 10,000, or more times the starting bacterium. In be utilized or evolved to produce a metabolite. certain aspects the amount is a commercially significant 0012 Certain embodiments are directed to methods of amount in that the cost of producing the target molecule is less developing a bacterial strain that produces a target metabolite, that the value of the amount of target molecule produced. In comprising the steps of: (a) Exposing at least two co-depen certain aspects an inefficient target molecule-producing bac dent bacterial strains and a co-evolving bacteriophage to a terial Strain is exposed to co-evolution mixture under selec selection medium having an initial concentration of exog tive pressures. An inefficient target molecule-producing bac enous target metabolite, wherein a first bacterium is a target terial strain can be a strain of cells that produce low levels of metabolite-dependent bacterium and a second bacterium is a the target molecule or harbor a metabolic pathway that can be target metabolite-producing bacterium. The co-evolving bac altered to produce the target molecule when exposed to the teriophage is selective for the target metabolite-producing appropriate selective pressures or methodology. Co-evolu bacterium; (b) incubating the selection medium comprising tion or co-evolving refers to a process where the change or the co-dependent bacteria and co-evolving bacteriophage; (c) US 2016/0024489 A1 Jan. 28, 2016 reducing the concentration of exogenous target metabolite; 0020. Throughout this application, the term “about is and (d) isolating a second target metabolite-producing bacte used to indicate that a value includes the standard deviation of rium (evolved bacterium) that has evolved from the first target error for the device or method being employed to determine metabolite-producing bacterium, the evolved bacterium pro the value. duces the target metabolite at levels greater than the first 0021. The use of the term “or” in the claims is used to target metabolite-producing bacterium. The methods can fur mean “and/or unless explicitly indicated to refer to alterna ther comprise exposing the selection medium containing the tives only or the alternatives are mutually exclusive, although bacteria and bacteriophage to a mutagenic agent. The the disclosure supports a definition that refers to only alter mutagenic agent can be a chemical mutagen or electromag natives and “and/or. It is also contemplated that anything netic radiation. In certain aspects the target metabolite is listed using the term “or may also be specifically excluded. methanol. 0022. As used in this specification and claim(s), the words 0013. Other embodiments are directed to methods of pro “comprising (and any form of comprising, such as "com ducing methanol comprising (a) incubating or fermenting a prise' and "comprises”), “having (and any form of having, production medium containing an evolved methanol-produc such as “have and “has'), “including' (and any form of ing bacteria; and (b) isolating methanol from the production including, such as “includes and “include’) or “containing medium. (and any form of containing, such as “contains and “con 0014 Certain embodiments are directed to producing a tain’) are inclusive or open-ended and do not exclude addi variant of a target gene, which can encode an enzyme that tional, unrecited elements or method steps. modifies or metabolizes a selective agent, e.g., herbicide 0023. Other objects, features and advantages of the resistance gene and its encoded protein.
Load more

Recommended publications
  • Bioprospecting from Marine Sediments of New Brunswick, Canada: Exploring the Relationship Between Total Bacterial Diversity and Actinobacteria Diversity
    Mar. Drugs 2014, 12, 899-925; doi:10.3390/md12020899 OPEN ACCESS marine drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Bioprospecting from Marine Sediments of New Brunswick, Canada: Exploring the Relationship between Total Bacterial Diversity and Actinobacteria Diversity Katherine Duncan 1, Bradley Haltli 2, Krista A. Gill 2 and Russell G. Kerr 1,2,* 1 Department of Biomedical Sciences, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada; E-Mail: [email protected] 2 Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada; E-Mails: [email protected] (B.H.); [email protected] (K.A.G.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-902-566-0565; Fax: +1-902-566-7445. Received: 13 November 2013; in revised form: 7 January 2014 / Accepted: 21 January 2014 / Published: 13 February 2014 Abstract: Actinomycetes are an important resource for the discovery of natural products with therapeutic properties. Bioprospecting for actinomycetes typically proceeds without a priori knowledge of the bacterial diversity present in sampled habitats. In this study, we endeavored to determine if overall bacterial diversity in marine sediments, as determined by 16S rDNA amplicon pyrosequencing, could be correlated with culturable actinomycete diversity, and thus serve as a powerful tool in guiding future bioprospecting efforts. Overall bacterial diversity was investigated in eight marine sediments from four sites in New Brunswick, Canada, resulting in over 44,000 high quality sequences (x̄ = 5610 per sample). Analysis revealed all sites exhibited significant diversity (H’ = 5.4 to 6.7).
    [Show full text]
  • The Common Ancestor of Archaea and Eukarya Was Not an Archaeon
    Hindawi Publishing Corporation Archaea Volume 2013, Article ID 372396, 18 pages http://dx.doi.org/10.1155/2013/372396 Review Article The Common Ancestor of Archaea and Eukarya Was Not an Archaeon Patrick Forterre1,2 1 Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France 2 Universite´ Paris-Sud, Institut de Gen´ etique´ et Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France Correspondence should be addressed to Patrick Forterre; [email protected] Received 22 July 2013; Accepted 24 September 2013 Academic Editor: Gustavo Caetano-Anolles´ Copyright © 2013 Patrick Forterre. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one.
    [Show full text]
  • WO 2018/107129 Al O
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/107129 Al 14 June 2018 (14.06.2018) W !P O PCT (51) International Patent Classification: VARD COLLEGE [US/US]; 17 Quincy Street, Cam- C12N 15/09 (2006.01) C12N 15/11 (2006.01) bridge, MA 02138 (US). C12N 15/10 (2006.01) C12Q 1/68 (2006 .01) (72) Inventors: ABUDAYYEH, Omar; 77 Massachusetts Av (21) International Application Number: enue, Cambridge, MA 02139 (US). COLLINS, James PCT/US20 17/065477 Joseph; 77 Massachusetts Avenue, Cambridge, MA 02 139 (US). GOOTENBERG, Jonathan; 17 Quincy Street, (22) International Filing Date: Cambridge, MA 02138 (US). ZHANG, Feng; 415 Main 08 December 2017 (08.12.2017) Street, Cambridge, MA 02142 (US). LANDER, Eric, S.; (25) Filing Language: English 415 Main Street, Cambridge, MA 02142 (US). (26) Publication Language: English (74) Agent: NLX, F., Brent; Johnson, Marcou & Isaacs, LLC, 27 City Square, Suite 1, Hoschton, GA 30548 (US). (30) Priority Data: 62/432,553 09 December 20 16 (09. 12.20 16) US (81) Designated States (unless otherwise indicated, for every 62/456,645 08 February 2017 (08.02.2017) US kind of national protection available): AE, AG, AL, AM, 62/471,930 15 March 2017 (15.03.2017) US AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, 62/484,869 12 April 2017 (12.04.2017) US CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, 62/568,268 04 October 2017 (04.10.2017) US DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (71) Applicants: THE BROAD INSTITUTE, INC.
    [Show full text]
  • The LUCA and Its Complex Virome in Another Recent Synthesis, We Examined the Origins of the Replication and Structural Mart Krupovic , Valerian V
    PERSPECTIVES archaea that form several distinct, seemingly unrelated groups16–18. The LUCA and its complex virome In another recent synthesis, we examined the origins of the replication and structural Mart Krupovic , Valerian V. Dolja and Eugene V. Koonin modules of viruses and posited a ‘chimeric’ scenario of virus evolution19. Under this Abstract | The last universal cellular ancestor (LUCA) is the most recent population model, the replication machineries of each of of organisms from which all cellular life on Earth descends. The reconstruction of the four realms derive from the primordial the genome and phenotype of the LUCA is a major challenge in evolutionary pool of genetic elements, whereas the major biology. Given that all life forms are associated with viruses and/or other mobile virion structural proteins were acquired genetic elements, there is no doubt that the LUCA was a host to viruses. Here, by from cellular hosts at different stages of evolution giving rise to bona fide viruses. projecting back in time using the extant distribution of viruses across the two In this Perspective article, we combine primary domains of life, bacteria and archaea, and tracing the evolutionary this recent work with observations on the histories of some key virus genes, we attempt a reconstruction of the LUCA virome. host ranges of viruses in each of the four Even a conservative version of this reconstruction suggests a remarkably complex realms, along with deeper reconstructions virome that already included the main groups of extant viruses of bacteria and of virus evolution, to tentatively infer archaea. We further present evidence of extensive virus evolution antedating the the composition of the virome of the last universal cellular ancestor (LUCA; also LUCA.
    [Show full text]
  • Phenotypic and Microbial Influences on Dairy Heifer Fertility and Calf Gut Microbial Development
    Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Animal Science, Dairy Rebecca R. Cockrum Kristy M. Daniels Alan Ealy Katharine F. Knowlton September 17, 2020 Blacksburg, VA Keywords: microbiome, fertility, inoculation Phenotypic and microbial influences on dairy heifer fertility and calf gut microbial development Connor E. Owens ABSTRACT (Academic) Pregnancy loss and calf death can cost dairy producers more than $230 million annually. While methods involving nutrition, climate, and health management to mitigate pregnancy loss and calf death have been developed, one potential influence that has not been well examined is the reproductive microbiome. I hypothesized that the microbiome of the reproductive tract would influence heifer fertility and calf gut microbial development. The objectives of this dissertation were: 1) to examine differences in phenotypes related to reproductive physiology in virgin Holstein heifers based on outcome of first insemination, 2) to characterize the uterine microbiome of virgin Holstein heifers before insemination and examine associations between uterine microbial composition and fertility related phenotypes, insemination outcome, and season of breeding, and 3) to characterize the various maternal and calf fecal microbiomes and predicted metagenomes during peri-partum and post-partum periods and examine the influence of the maternal microbiome on calf gut development during the pre-weaning phase. In the first experiment, virgin Holstein heifers (n = 52) were enrolled over 12 periods, on period per month. On -3 d before insemination, heifers were weighed and the uterus was flushed.
    [Show full text]
  • Evolution of Bacterial Communities in the Wheat Crop Rhizosphere
    bs_bs_banner Environmental Microbiology (2014) doi:10.1111/1462-2920.12452 Evolution of bacterial communities in the wheat crop rhizosphere Suzanne Donn, John A. Kirkegaard, Geetha Perera, per year, yet need to lift to at least 1.5% per year by 2050 Alan E. Richardson and Michelle Watt* to avoid food price increases (Fischer and Edmeades, CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2010). Intensive cereal systems, including wheat following 2601, Australia. wheat rotations, dominate many global food production systems and yields have been declining in these systems, often due to undiagnosed soil biological causes (Lobell Summary et al., 2009). Developing a predictive understanding of the The gap between current average global wheat yields links between soil biology, agronomy and crop perfor- and that achievable through best agronomic manage- mance would be a first step towards improving productivity ment and crop genetics is large. This is notable in of intensive cereals, and would have a major impact on intensive wheat rotations which are widely used. global food production (Cassman, 1999). Expectations are that this gap can be reduced by Globally, expectations are high that soil biology can be manipulating soil processes, especially those that manipulated through crop management and genetics involve microbial ecology. Cross-year analysis of the to increase yields in agricultural production systems soil microbiome in an intensive wheat cropping (Morrissey et al., 2004; Welbaum et al., 2004). Rhizobial system revealed that rhizosphere bacteria changed associations with legumes for N2-fixation, crop species much more than the bulk soil community. Dominant rotation for pathogen control and mycorrhizal associations factors influencing populations included binding to are obvious examples that have had clear productivity roots, plant age, site and planting sequence.
    [Show full text]
  • I GENOMIC and TRANSCRIPTOMIC ANALYSES of Jeotgalibacillus
    i GENOMIC AND TRANSCRIPTOMIC ANALYSES OF Jeotgalibacillus malaysiensis TO PROVIDE INSIGHTS INTO ITS OSMOTIC ADAPTATION AMIRA SURIATY BINTI YAAKOP A thesis submitted in fulfilment of the requirements for the award of the degree of Doctor of Philosophy (Bioscience) Faculty of Biosciences and Medical Engineering Universiti Teknologi Malaysia AUGUST 2017 iii iv ACKNOWLEDGEMENT I would like to take this opportunity to dedicate my endless gratitude, sincere appreciation and profound regards to my dearest supervisor, Dr. Goh Kian Mau for his scholastic guidance. He has been instrumental in guiding my research, giving me encouragement, guidance, critics and friendship. Without you this thesis will not be presented as it is today. Furthermore, I would like to convey my appreciation toward my labmates Ms. Chia Sing and Mr. Ummirul, Ms. Suganthi and Ms. Chitra for their guidance and support Not forgetting the helpful lab assistant Mdm. Sue, Mr. Khairul and Mr. Hafizi for all their assistances throughout my research. My sincere appreciation also extends to all my others lab mates in extremophiles laboratory who have provided assistance at various occasions. Last but not least, my special gratitude to my husband, Mohd Hanafi bin Suki who see me up and down throughout this PHD journeys, my lovely parents Noora’ini Mohamad and Yaakop Jaafar, my family members for their support and concern. Not to forget, my friends who had given their helps, motivational and guidance all the time with love. Their mentorship was truly appreciated. v ABSTRACT The genus Jeotgalibacillus under the family of Planococcaceae is one of the understudy genera. In this project, a bacterium strain D5 was isolated from Desaru beach, Johor.
    [Show full text]
  • CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative
    CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative Genomics and Epigenomics of Sporosarcina ureae A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Biology By Andrew Oliver August 2016 The thesis of Andrew Oliver is approved by: _________________________________________ ____________ Sean Murray, Ph.D. Date _________________________________________ ____________ Gilberto Flores, Ph.D. Date _________________________________________ ____________ Kerry Cooper, Ph.D., Chair Date California State University, Northridge ii Acknowledgments First and foremost, a special thanks to my advisor, Dr. Kerry Cooper, for his advice and, above all, his patience. If I can be half the scientist you are someday, I would be thrilled. I would like to also thank everyone in the Cooper lab, especially my colleagues Courtney Sams and Tabitha Bayangnos. It was a privilege to work along side you. More thanks to my committee members, Dr. Gilberto Flores and Dr. Sean Murray. Dr. Flores, you were instrumental in guiding me to ask the right questions regarding bacterial taxonomy. Dr. Murray, your contributions to my graduate studies would make this section run on for pages. I thank you for taking me under your wing from the beginning. Acknowledgement and thanks to the Baresi lab, especially Dr. Larry Baresi and Tania Kurbessoian for their partnership in this research. Also to Bernardine Pregerson for all the work that lays at the foundation of this study. This research would not be what it is without the help of my childhood friend, Matthew Kay. You wrote programs, taught me coding languages, and challenged me to go digging for answers to very difficult questions.
    [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]
  • Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergol
    applied sciences Article Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland Magdalena Dyda 1,2,* , Agnieszka Laudy 3, Przemyslaw Decewicz 4 , Krzysztof Romaniuk 4, Martyna Ciezkowska 4, Anna Szajewska 5 , Danuta Solecka 6, Lukasz Dziewit 4 , Lukasz Drewniak 4 and Aleksandra Skłodowska 1 1 Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] 2 Research and Development for Life Sciences Ltd. (RDLS Ltd.), Miecznikowa 1/5a, 02-096 Warsaw, Poland 3 Laboratory of Environmental Analysis, Museum of King John III’s Palace at Wilanow, Stanislawa Kostki Potockiego 10/16, 02-958 Warsaw, Poland; [email protected] 4 Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] (P.D.); [email protected] (K.R.); [email protected] (M.C.); [email protected] (L.D.); [email protected] (L.D.) 5 The Main School of Fire Service, Slowackiego 52/54, 01-629 Warsaw, Poland; [email protected] 6 Department of Plant Molecular Ecophysiology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +48-786-28-44-96 Citation: Dyda, M.; Laudy, A.; Abstract: The aim of the presented investigation was to describe seasonal changes of microbial com- Decewicz, P.; Romaniuk, K.; munity composition in situ in different biocenoses on historical sandstone of the Northern Pergola in Ciezkowska, M.; Szajewska, A.; the Museum of King John III’s Palace at Wilanow (Poland).
    [Show full text]
  • Viruses of Hyperthermophilic Archaea: Entry and Egress from the Host Cell
    Viruses of hyperthermophilic archaea : entry and egress from the host cell Emmanuelle Quemin To cite this version: Emmanuelle Quemin. Viruses of hyperthermophilic archaea : entry and egress from the host cell. Microbiology and Parasitology. Université Pierre et Marie Curie - Paris VI, 2015. English. NNT : 2015PA066329. tel-01374196 HAL Id: tel-01374196 https://tel.archives-ouvertes.fr/tel-01374196 Submitted on 30 Sep 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Pierre et Marie Curie – Paris VI Unité de Biologie Moléculaire du Gène chez les Extrêmophiles Ecole doctorale Complexité du Vivant ED515 Département de Microbiologie - Institut Pasteur 7, quai Saint-Bernard, case 32 25, rue du Dr. Roux 75252 Paris Cedex 05 75015 Paris THESE DE DOCTORAT DE L’UNIVERSITE PIERRE ET MARIE CURIE Spécialité : Microbiologie Pour obtenir le grade de DOCTEUR DE L’UNIVERSITE PIERRE ET MARIE CURIE VIRUSES OF HYPERTHERMOPHILIC ARCHAEA: ENTRY INTO AND EGRESS FROM THE HOST CELL Présentée par M. Emmanuelle Quemin Soutenue le 28 Septembre 2015 devant le jury composé de : Prof. Guennadi Sezonov Président du jury Prof. Christa Schleper Rapporteur de thèse Dr. Paulo Tavares Rapporteur de thèse Dr.
    [Show full text]
  • Product Sheet Info
    Product Information Sheet for HM-331 Sporosarcina sp., Strain 2681 Incubation: Temperature: 37°C Atmosphere: Aerobic Catalog No. HM-331 Propagation: 1. Keep vial frozen until ready for use, then thaw. For research use only. Not for human use. 2. Transfer the entire thawed aliquot into a single tube of broth. Contributor: 3. Use several drops of the suspension to inoculate an Kimberlee A. Musser, Ph.D., Chief, Bacterial Diseases, agar slant and/or plate. Division of Infectious Diseases, Wadsworth Center, New York 4. Incubate the tubes and plate at 37°C for 48 hours. State Department of Health, Albany, New York Citation: Manufacturer: NIH Biodefense and Emerging Infections Acknowledgment for publications should read “The following reagent was obtained through the NIH Biodefense and Research Resource Repository Emerging Infections Research Resources Repository, NIAID, NIH as part of the Human Microbiome Project: Sporosarcina Product Description: sp., Strain 2681, HM-331.” Bacteria Classification: Planococcaceae, Sporosarcina Species: Sporosarcina sp. Biosafety Level: 2 Strain: 2681 Original Source: Sporosarcina sp., strain 2681 was isolated Appropriate safety procedures should always be used with 1 this material. Laboratory safety is discussed in the following from human blood. Comments: Sporosarcina sp., strain 2681 is a reference publication: U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and genome for The Human Microbiome Project (HMP). HMP Prevention, and National Institutes of Health. Biosafety in is an initiative to identify and characterize human microbial flora. The complete genome of Sporosarcina sp., strain Microbiological and Biomedical Laboratories. 5th ed. Washington, DC: U.S. Government Printing Office, 2007; see 2681 is currently being sequenced at the Human Genome www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm.
    [Show full text]