Microbiological Study in Petrol-Spiked Soil
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The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. -
Mycoplana Ramosa and Mycoplana Segnis
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1990, p. 43U2 Vol. 40, No. 4 0020-7713/90/040434-09$02.00/0 Copyright 0 1990, International Union of Microbiological Societies Recharacterization and Emended Description of the Genus Mycoplana and Description of Two New Species, Mycoplana ramosa and Mycoplana segnis TEIZI URAKAMI,l* HIROMI OYANAG1,l HISAYA ARAK1,l KEN-ICHIRO SUZUKI,’ AND KAZUO KOMAGATA3 Niigata Research Laboratory, Mitsubishi Gas Chemical Co., Tayuhama, Niigata 950-31I; Japan Collection of Microorganisms, The Institute of Physical and Chemical Research, Wako-shi, Saitama 351 -012; and Institute of Applied Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113,3 Japan The phenotypic and chemotaxonomic characteristics of Mycuplana strains were examined. These strains were gram-negative, peritrichously flagellated, branching, filament-forming bacteria. The cellular fatty acids consisted of large amounts of straight-chain unsaturated ClSz1acid, as well as straight-chain saturated C16:o acid and unsaturated ClGZ1acid. The major ubiquinone was ubiquinone Q-lo. The Mycoplana strains were divided into four groups, including one group containing Mycuplana dimurpha ATCC 4279T (= IF0 13291T = NCIB 9439T) (T = type strain) and another group containing Mycuplana bullata ATCC 427tlT (= IF0 13290T = NCIB 9440T), on the basis of DNA base composition, major hydroxy fatty acid composition, mucosity of colonies, acid production from sugars, and utilization of carbon compounds. This division into groups was supported by the results of DNA-DNA homology experiments. Two new species, Mycoplana rumusa and Mycoplana segnis, are proposed. The type strain of M. ramusa is strain TKO053 (= NCIB 9440), and the type strain of M. segnis is strain TKO059 (= IF0 13240 = ATCC 21756). -
Supplementary Information the Biodiversity and Geochemistry Of
Supplementary Information The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica Figure S1. Principal component analysis of the bacterial OTUs. Samples cluster according to habitats. Figure S2. Principal component analysis of the eukaryotic OTUs. Samples cluster according to habitats. Figure S3. Principal component analysis of selected trace elements that cause the separation (primarily Zr, Ba and Sr). Figure S4. Partial canonical correspondence analysis of the bacterial abundances and all non-collinear environmental variables (i.e., after identification and exclusion of redundant predictor variables) and without spatial effects. Samples from Lake 3 in Utsteinen clustered with higher nitrate concentration and samples from Dubois with a higher TC abundance. Otherwise no clear trends could be observed. Table S1. Number of sequences before and after quality control for bacterial and eukaryotic sequences, respectively. 16S 18S Sample ID Before quality After quality Before quality After quality filtering filtering filtering filtering PES17_36 79285 71418 112519 112201 PES17_38 115832 111434 44238 44166 PES17_39 128336 123761 31865 31789 PES17_40 107580 104609 27128 27074 PES17_42 225182 218495 103515 103323 PES17_43 219156 213095 67378 67199 PES17_47 82531 79949 60130 59998 PES17_48 123666 120275 64459 64306 PES17_49 163446 158674 126366 126115 PES17_50 107304 104667 158362 158063 PES17_51 95033 93296 - - PES17_52 113682 110463 119486 119205 PES17_53 126238 122760 72656 72461 PES17_54 120805 117807 181725 181281 PES17_55 112134 108809 146821 146408 PES17_56 193142 187986 154063 153724 PES17_59 226518 220298 32560 32444 PES17_60 186567 182136 213031 212325 PES17_61 143702 140104 155784 155222 PES17_62 104661 102291 - - PES17_63 114068 111261 101205 100998 PES17_64 101054 98423 70930 70674 PES17_65 117504 113810 192746 192282 Total 3107426 3015821 2236967 2231258 Table S2. -
Chemical Analysis of the Alphaproteobacterium Strain MOLA1416 Associated with the Marine Lichen Lichina Pygmaea D
Chemical analysis of the Alphaproteobacterium strain MOLA1416 associated with the marine lichen Lichina pygmaea D. Parrot, L. Intertaglia, P. Jéhan, M. Grube, M.T. Suzuki, S. Tomasi To cite this version: D. Parrot, L. Intertaglia, P. Jéhan, M. Grube, M.T. Suzuki, et al.. Chemical analysis of the Alphapro- teobacterium strain MOLA1416 associated with the marine lichen Lichina pygmaea. Phytochemistry, Elsevier, 2018, 145, pp.57-67. 10.1016/j.phytochem.2017.10.005. hal-01639693 HAL Id: hal-01639693 https://hal-univ-rennes1.archives-ouvertes.fr/hal-01639693 Submitted on 18 May 2020 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. Chemical analysis of the Alphaproteobacterium strain MOLA1416 associated with the marine lichen Lichina pygmaea Delphine Parrota, 1 Laurent Intertagliab Philippe Jehanc Martin Grubed Marcelino T. Suzukie Sophie Tomasia, ∗ [email protected] aUMR CNRS 6226, Institut des Sciences Chimiques de Rennes, Equipe CORINT “Chimie Organique et Interfaces”, UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne Loire, 2 Avenue du Pr. Léon Bernard, F-35043, Rennes, France bSorbonne Universités, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), F-66650, Banyuls/Mer, France cCRMPO, Université de Rennes 1, 35042, Rennes Cedex, France dInstitut für Pflanzenwissenschaften Karl-Franzens-Universität Graz, Austria eSorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650, Banyuls/Mer, France ∗Corresponding author. -
Role of Gut Microbiome in Multiple Sclerosis Jasminka Hasic Telalovic* and Azra Music
Hasic Telalovic and Music BMC Medical Informatics and Decision Making (2020) 20:262 https://doi.org/10.1186/s12911-020-01263-2 RESEARCH ARTICLE Open Access Using data science for medical decision making case: role of gut microbiome in multiple sclerosis Jasminka Hasic Telalovic* and Azra Music Abstract Background: A decade ago, the advancements in the microbiome data sequencing techniques initiated the development of research of the microbiome and its relationship with the host organism. The development of sophisticated bioinformatics and data science tools for the analysis of large amounts of data followed. Since then, the analyzed gut microbiome data, where microbiome is defined as a network of microorganisms inhabiting the human intestinal system, has been associated with several conditions such as irritable bowel syndrome - IBS, colorectal cancer, diabetes, obesity, and metabolic syndrome, and lately in the study of Parkinson’s and Alzheimer’s diseases as well. This paper aims to provide an understanding of differences between microbial data of individuals who have been diagnosed with multiple sclerosis and those who were not by exploiting data science techniques on publicly available data. Methods: This study examines the relationship between multiple sclerosis (MS), an autoimmune central nervous system disease, and gut microbial community composition, using the samples acquired by 16s rRNA sequencing technique. We have used three different sets of MS samples sequenced during three independent studies (Jangi et al, Nat Commun 7:1–11, 2016), (Miyake et al, PLoS ONE 10:0137429, 2015), (McDonald et al, Msystems 3:00031–18, 2018) and this approach strengthens our results. Analyzed sequences were from healthy control and MS groups of sequences. -
Phylogeny and Polyphasic Taxonomy of Caulobacter Species. Proposal of Maricaulis Gen
International Journal of Systematic Bacteriology (1 999), 49, 1053-1 073 Printed in Great Britain Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundirnonas and Caulobacter Wolf-Rainer Abraham,' Carsten StrOmpl,l Holger Meyer, Sabine Lindholst,l Edward R. B. Moore,' Ruprecht Christ,' Marc Vancanneyt,' B. J. Tindali,3 Antonio Bennasar,' John Smit4 and Michael Tesar' Author for correspondence: Wolf-Rainer Abraham. Tel: +49 531 6181 419. Fax: +49 531 6181 41 1. e-mail : [email protected] Gesellschaft fur The genus Caulobacter is composed of prosthecate bacteria often specialized Biotechnologische for oligotrophic environments. The taxonomy of Caulobacter has relied Forschung mbH, primarily upon morphological criteria: a strain that visually appeared to be a Mascheroder Weg 1, D- 38124 Braunschweig, member of the Caulobacter has generally been called one without Germany challenge. A polyphasic approach, comprising 165 rDNA sequencing, profiling Laboratorium voor restriction fragments of 165-235 rDNA interspacer regions, lipid analysis, Microbiologie, Universiteit immunological profiling and salt tolerance characterizations, was used Gent, Gent, Belgium to clarify the taxonomy of 76 strains of the genera Caulobacter, Deutsche Sammlung von Brevundimonas, Hyphomonas and Mycoplana. The described species of the Mikroorganismen und genus Caulobacter formed a paraphyletic group with Caulobacter henricii, Zellkulturen, Caulobacter fusiformis, Caulobacter vibrioides and Mycoplana segnis Braunschweig, Germany (Caulobacter segnis comb. nov.) belonging to Caulobacter sensu stricto. Dept of Microbiology and Caulobacter bacteroides (Brevundimonas bacteroides comb. nov.), C. henricii Immunology, University of subsp. aurantiacus (Brevundimonas aurantiaca comb. nov.), Caulobacter British Columbia, intermedius (Brevundimonas intermedia comb. -
Host–Microbe Interactions As a Driver of Acclimation to Salinity Gradients in Brown Algal Cultures
The ISME Journal (2016) 10, 51–63 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Host–microbe interactions as a driver of acclimation to salinity gradients in brown algal cultures Simon M Dittami1, Laëtitia Duboscq-Bidot2, Morgan Perennou3, Angélique Gobet1, Erwan Corre4, Catherine Boyen1 and Thierry Tonon1 1Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; 2Institut de Recherche Thérapeutique de l’Université de Nantes, UMR 1087, Plateforme Génomique, Nantes, France; 3Plateforme de Séquençage-Génotypage, FR 2424 CNRS UPMC, Station Biologique, CS 90074, Roscoff, France and 4ABiMS platform, FR 2424 CNRS UPMC, Station Biologique, Roscoff, France Like most eukaryotes, brown algae live in association with bacterial communities that frequently have beneficial effects on their development. Ectocarpus is a genus of small filamentous brown algae, which comprises a strain that has recently colonized freshwater, a rare transition in this lineage. We generated an inventory of bacteria in Ectocarpus cultures and examined the effect they have on acclimation to an environmental change, that is, the transition from seawater to freshwater medium. Our results demonstrate that Ectocarpus depends on bacteria for this transition: cultures that have been deprived of their associated microbiome do not survive a transfer to freshwater, but restoring their microflora also restores the capacity to acclimate to this change. Furthermore, the transition between the two culture media strongly affects the bacterial community composition. Examining a range of other closely related algal strains, we observed that the presence of two bacterial operational taxonomic units correlated significantly with an increase in low salinity tolerance of the algal culture. -
Variation and Diversification of the Microbiome of Schlechtendalia
bioRxiv preprint doi: https://doi.org/10.1101/351882; this version posted June 20, 2018. 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 Variation and diversification of the microbiome of Schlechtendalia 2 chinensis on two alternate host plants 3 Haixia Wu1,2, Xiaoming Chen1,2*, Hang Chen1,2, Qin Lu1,2, Zixiang Yang1,2, Weibin 4 Ren1,2, Juan Liu1,2, Shuxia Shao2,3 ,Chao Wang1,2, Kirst King-Jones4, Ming-Shun 5 Chen5 6 7 1 Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, 8 China. 9 2 The Key Laboratory of Cultivating and Utilization of Resources Insects, State 10 Forestry Administration, Kunming, China. 11 3 Southwest Forestry University, Bailongsi, Kunming City, Yunnan 650224, PR. 12 China 13 4 Department of Biological Sciences, University of Alberta, G-504 Biological 14 Sciences Bldg., Edmonton, Alberta T6G 2E9, Canada. 15 5 Department of Entomology, Kansas State University, Manhattan, KS 66506, USA 16 17 *Correspondence author: 18 E-mail: [email protected] 19 20 1 bioRxiv preprint doi: https://doi.org/10.1101/351882; this version posted June 20, 2018. 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. 21 Abstract 22 Schlechtendalia chinensis, a gall-inducing aphid, has two host plants in its life 23 cycle. -
Taxonomy of Rhizobia Frédéric Zakhia, Philippe De Lajudie
Taxonomy of rhizobia Frédéric Zakhia, Philippe de Lajudie To cite this version: Frédéric Zakhia, Philippe de Lajudie. Taxonomy of rhizobia. Agronomie, EDP Sciences, 2001, 21 (6-7), pp.569-576. 10.1051/agro:2001146. hal-00886134 HAL Id: hal-00886134 https://hal.archives-ouvertes.fr/hal-00886134 Submitted on 1 Jan 2001 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. Agronomie 21 (2001) 569–576 569 © INRA, EDP Sciences, 2001 Review article Taxonomy of rhizobia Frédéric ZAKHIA, Philippe de LAJUDIE* Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR 113 INRA/AGRO-M/CIRAD/IRD, TA 10 / J, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France (Received 15 January 2001; revised 8 March 2001; accepted 13 March 2001) Abstract – Rhizobia are the bacteria that form nitrogen-fixing symbioses with legumes. Based on their characterisation by polypha- sic taxonomy, their classification has undergone great changes in recent years. The current six rhizobium genera and 28 recognised species are reviewed here. Rhizobium / taxonomy Résumé – Taxonomie des rhizobia. Les rhizobia sont les bactéries qui forment des symbioses fixatrices d’azote avec des plantes de la famille des légumineuses. Suite à l’adoption de la taxonomie polyphasique comme critère de caractérisation, leur classification a subi de nombreux remaniements ces dernières années. -
DETERMIN I\ TIVE BACTERIO:LOGY
BERGEY'S MA~JUAL OF DETERMIN i\ TIVE BACTERIO:LOGY BY ROBERT S. BREED Late Professor Emeritus, GorneU University, Genevo•, New York E. G. D. MURRAY Research Professor, University of Western Ontario, London, Ontario, Canada NATHAN R. SMITH Senior Bacteriologist, Retired, Plant lndustry Station, U. S. Department of Agriculture, Beltaville, Maryland and Ninety.jour Gontributars Whose Names Appear on the Immediately FoUowing Pages BALTIMORE THlf WILLIAMS & WILKINS COMPANY 1957 CONTENTS .................................· ...................... ··············· 1 Influencing the Classification Used in This Edition of the Manual. .. 4 KQ."T."•'""'· are Named and Identified ........................................... 15 I. Protophyta Sachs, 1874, emend. Krassilnikov, 1949 ..................... 29 I. Schizophyceae Cohn, 1879 ..................... , ........................ 30 Class II. Schizomycetes von N aegeli, 1857 ....................................... 33 · Order I. Pseudomonadales Orla-Jensen, 1921 ......... : ........................ 35 Suborder I. Rhodobacteriineae Breed, Murray and Hitchens, 1944 ......... , .. 35 Family I. Thiorhodaceae Molisch, 1907 ..................................... 38 Genus I. Thiosarcina Winogradsky, 1888 ........................... 39 Genus II. Thiopedia Winogradsky, 1888 ............................. 40 Genus III. Thiocapsa Winogradsky, 1888 ............................ 41 Genus IV. Thiodictyon Winogradsky, 1888 .......... .' ................ 41 Genus V. 'l'hiothece Winogradsky, 1888 ............................ -
Genome Sequence and Phenotypic Characterization of Caulobacter Segnis Sagar Patel University of South Carolina-Columbia
University of South Carolina Scholar Commons Senior Theses Honors College Spring 5-10-2014 Genome Sequence and Phenotypic Characterization of Caulobacter Segnis Sagar Patel University of South Carolina-Columbia Follow this and additional works at: https://scholarcommons.sc.edu/senior_theses Part of the Biology Commons, Genetics Commons, and the Genomics Commons Recommended Citation Patel, Sagar, "Genome Sequence and Phenotypic Characterization of Caulobacter Segnis" (2014). Senior Theses. 8. https://scholarcommons.sc.edu/senior_theses/8 This Thesis is brought to you by the Honors College at Scholar Commons. It has been accepted for inclusion in Senior Theses by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. GENOME SEQUENCE AND PHENOTYPIC CHARACTERIZATION OF CAULOBACTER SEGNIS By Sagar Patel Submitted in Partial Fulfillment of the Requirements for Graduation with Honors from the South Carolina Honors College May 2014 Approved: Dr. Bert Ely Director of Thesis Dr. Latia Scott Second Reader Steve Lynn, Dean For South Carolina Honors College Genomic Sequence and Phenotypic Characterization of Caulobacter segnis Patel TABLE OF CONTENTS Thesis Summary...................................................................................................................3 Abstract ................................................................................................................................6 Introduction ..........................................................................................................................7 -
Federal Register / Voi. 45, No. 251 / Tuesday, December 30, 1980 / Notices 85861
Federal Register / Voi. 45, No. 251 / Tuesday, December 30, 1980 / Notices 85861 Atmosphere (NACOA) will meet Date & Time: January 23-24,1981, 8:30 computers for university-based Theoretical Thursday and Friday, January 15-16, a.m.-5:00 p.m. each day. Physics research and recommend an 1981. The Subgroup will meet in the B- Place: Hilton Inn, Room 339, Salt Lake appropriate strategy for meeting the 100 conference room of Page Building City, Utah. / computational needs of this area of No. 1, 2001 Wisconsin Avenue, NW., Type of Meeting: Closed. research. Washington, D.C. Contact Person: Dr. Fred Stollnitz Agenda: The session, which will be open to the Program Director, Psychobiology Ja nu ary 15, 1981, 9 a.m. to 5 p.m.: Review of public, will convene at 9:00 a.m. and Program, Room 320, National Science available studies on the usage of computers adjourn at 4:00 p.m. each day. The Foundation, Washington, D.C. (202) for theoretical research by university agenda for the meeting of the Marine 357-7949. scientists. Preliminary discussion of Transportation Subgroup is as follows: Purpose of Subcommittee: To provide Subcommittee recommendations. advice and recommendations Ocean Problems and Transoceanic Shipping Ja nu ary 16, 1981, 9 a.m. to 5 p.m.: concerning support for research in Continuation of previous day’s discussion. A. If.S. merchant marine capabilities to psychobiology. Ja nu ary 17, 1981, 9 a.m. to 5 p.m.: meet national trade and defense needs. Agenda: To review and evaluate Continuation of previous day's discussion.