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Senegalemassilia Anaerobia Gen. Nov., Sp. Nov
Standards in Genomic Sciences (2013) 7:343-356 DOI:10.4056/sigs.3246665 Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov. Jean-Christophe Lagier1, Khalid Elkarkouri1, Romain Rivet1, Carine Couderc1, Didier Raoult1 and Pierre-Edouard Fournier1* 1 Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France *Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Senegalemassilia anaerobia, genome Senegalemassilia anaerobia strain JC110T sp.nov. is the type strain of Senegalemassilia anaer- obia gen. nov., sp. nov., the type species of a new genus within the Coriobacteriaceae family, Senegalemassilia gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. S. anaerobia is a Gram-positive anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,383,131 bp long genome contains 1,932 protein- coding and 58 RNA genes. Introduction Classification and features Senegalemassilia anaerobia strain JC110T (= CSUR A stool sample was collected from a healthy 16- P147 = DSMZ 25959) is the type strain of S. anaer- year-old male Senegalese volunteer patient living obia gen. nov., sp. nov. This bacterium was isolat- in Dielmo (rural village in the Guinean-Sudanian ed from the feces of a healthy Senegalese patient. zone in Senegal), who was included in a research It is a Gram-positive, anaerobic, indole-negative protocol. Written assent was obtained from this coccobacillus. Classically, the polyphasic taxono- individual. No written consent was needed from his my is used to classify the prokaryotes by associat- guardians for this study because he was older than ing phenotypic and genotypic characteristics [1]. -
Corynebacterium Sp.|NML98-0116
1 Limnochorda_pilosa~GCF_001544015.1@NZ_AP014924=Bacteria-Firmicutes-Limnochordia-Limnochordales-Limnochordaceae-Limnochorda-Limnochorda_pilosa 0,9635 Ammonifex_degensii|KC4~GCF_000024605.1@NC_013385=Bacteria-Firmicutes-Clostridia-Thermoanaerobacterales-Thermoanaerobacteraceae-Ammonifex-Ammonifex_degensii 0,985 Symbiobacterium_thermophilum|IAM14863~GCF_000009905.1@NC_006177=Bacteria-Firmicutes-Clostridia-Clostridiales-Symbiobacteriaceae-Symbiobacterium-Symbiobacterium_thermophilum Varibaculum_timonense~GCF_900169515.1@NZ_LT827020=Bacteria-Actinobacteria-Actinobacteria-Actinomycetales-Actinomycetaceae-Varibaculum-Varibaculum_timonense 1 Rubrobacter_aplysinae~GCF_001029505.1@NZ_LEKH01000003=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_aplysinae 0,975 Rubrobacter_xylanophilus|DSM9941~GCF_000014185.1@NC_008148=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_xylanophilus 1 Rubrobacter_radiotolerans~GCF_000661895.1@NZ_CP007514=Bacteria-Actinobacteria-Rubrobacteria-Rubrobacterales-Rubrobacteraceae-Rubrobacter-Rubrobacter_radiotolerans Actinobacteria_bacterium_rbg_16_64_13~GCA_001768675.1@MELN01000053=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_rbg_16_64_13 1 Actinobacteria_bacterium_13_2_20cm_68_14~GCA_001914705.1@MNDB01000040=Bacteria-Actinobacteria-unknown_class-unknown_order-unknown_family-unknown_genus-Actinobacteria_bacterium_13_2_20cm_68_14 1 0,9803 Thermoleophilum_album~GCF_900108055.1@NZ_FNWJ01000001=Bacteria-Actinobacteria-Thermoleophilia-Thermoleophilales-Thermoleophilaceae-Thermoleophilum-Thermoleophilum_album -
WO 2018/064165 A2 (.Pdf)
(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 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, 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, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage
University of South Carolina Scholar Commons Faculty Publications Biological Sciences, Department of 3-10-2011 Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage John Lightfield Noah R. Fram Bert Ely University of South Carolina - Columbia, [email protected] Follow this and additional works at: https://scholarcommons.sc.edu/biol_facpub Part of the Biology Commons Publication Info Published in PLoS ONE, Volume 6, Issue 3, 2011, pages e17677-. © 2011 Lightfield et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This Article is brought to you by the Biological Sciences, Department of at Scholar Commons. It has been accepted for inclusion in Faculty Publications by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage John Lightfield¤a, Noah R. Fram¤b, Bert Ely* Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America Abstract The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. -
Various Complexes of the Oral Microbial Flora in Periodontal Disease
ISSN: 2394-8418 DOI: https://doi.org/10.17352/jdps CLINICAL GROUP Received: 01 April, 2021 Short Communication Accepted: 08 April, 2021 Published: 10 April, 2021 *Corresponding author: Dr. Sukhvinder Singh Oberoi, Various complexes of the oral BDS, MDS, Associate Professor, Public Health Den- tistry, ESIC Dental College and Hospital, Rohini, Guru microbial fl ora in periodontal Gobind Singh Indraprastha University, India, E-mail: disease Keywords: Periodontal diseases; Red complex; Orange complex Sukhvinder Singh Oberoi1*, Shabina Sachdeva2 and https://www.peertechzpublications.com Shibani Grover3 1Associate Professor, Public Health Dentistry, ESIC Dental College and Hospital, Rohini, Guru Gobind Singh Indraprastha University, India 2Professor, Prosthodontics, Faculty of Dentistry, Jamia Milia Islamia, India 3Dean and Director Professor, Conservative Dentistry and Endodontics, ESIC Dental College and Hospital, Rohini, Guru Gobind Singh Indraprastha University, India Abstract Periodontal diseases, is the infection of the periodontal tissues which eventually can lead to loss of teeth, is a form of aberrant infl ammation resulting from a complex biofi lm of friendly commensal and periodontopathic bacteria and their products, triggering the human infl ammatory response. The cluster analysis has shown that 6 closely associated bacterial complexes are associated with it which are designated with different color codes. The early colonizers are “Blue complex” consisting of Actinomyces species, “Yellow complex” comprising of various Streptococci, “Green complex” comprising Eiknella corrodens and Capnocytophaga species, and “Purple complex” comprising Veillonella parvula and Actinomyces odontolyticus. The late colonizers are “Orange complex” comprising Prevotella, Fusobacterium, Campylobacter and other bacteria and the “Red complex” chiefl y consisting of Porphyromonas gingivalis, Tannerella forsythia, and Treponema Denticola. Periodontal disease is the commonest oral disease affecting are facultative, spirochetes and motile rods. -
Isolation of Lactic-Acid Related Bacteria from the Pig Mucosal P
Aus dem Institut für Tierernährung des Fachbereichs Veterinärmedizin der Freien Universität Berlin Isolation of lactic acid-related bacteria from the pig mucosal proximal gastrointestinal tract, including Olsenella umbonata sp. nov. and Veillonella magna sp. nov. Inaugural-Dissertation zur Erlangung des Grades eines Doktors der Veterinärmedizin an der Freien Universität Berlin vorgelegt von Mareike Kraatz Tierärztin aus Berlin Berlin 2011 Journal-Nr.: 3431 Gedruckt mit Genehmigung des Fachbereichs Veterinärmedizin der Freien Universität Berlin Dekan: Univ.-Prof. Dr. Leo Brunnberg Erster Gutachter: Univ.-Prof. a. D. Dr. Ortwin Simon Zweiter Gutachter: Univ.-Prof. Dr. Lothar H. Wieler Dritter Gutachter: Univ.-Prof. em. Dr. Dr. h. c. Gerhard Reuter Deskriptoren (nach CAB-Thesaurus): anaerobes; Bacteria; catalase; culture media; digestive tract; digestive tract mucosa; food chains; hydrogen peroxide; intestinal microorganisms; isolation; isolation techniques; jejunum; lactic acid; lactic acid bacteria; Lactobacillus; Lactobacillus plantarum subsp. plantarum; microbial ecology; microbial flora; mucins; mucosa; mucus; new species; Olsenella; Olsenella profusa; Olsenella uli; oxygen; pigs; propionic acid; propionic acid bacteria; species composition; stomach; symbiosis; taxonomy; Veillonella; Veillonella ratti Tag der Promotion: 21. Januar 2011 Diese Dissertation ist als Buch (ISBN 978-3-8325-2789-1) über den Buchhandel oder online beim Logos Verlag Berlin (http://www.logos-verlag.de) erhältlich. This thesis is available as a book (ISBN 978-3-8325-2789-1) -
Changes in the Oral Microflora of Occlusal Surfaces of Teeth with the Onset of Dental Caries
CHANGES IN THE ORAL MICROFLORA OF OCCLUSAL SURFACES OF TEETH WITH THE ONSET OF DENTAL CARIES Árni Rafn Rúnarsson Supervisors and Research Committee Dr. W. Peter Holbrook Dr. Viggó Þór Marteinsson Dr. Jakob K. Kristjánsson Faculty of Odontology University of Iceland November 2009 Ágrip Tannáta er mjög algengur sjúkdómur sem tengist samspili baktería í örveruþekkju “tannsýklu”. Þrjár kenningar hafa verið notað til að lýsa þessum tengslunum á milli baktería og tannátu: (I) Sérhæfða kenningin ,,specific plaque hypothesis“, þar sem segir að fáar ákveðnar tegundir eru taldar valda tannátu; (II) Ósérhæfða kenningin ,,non-specific plaque hypothesis”, þar sem segir að heildarvirkni allra baktería í örveruþekkjunni valdi tannátu; (III) Vistfræðilega kenningin ,,ecological plaque hypothesis”, þar sem segir að breytingar á ríkjandi flóru séu vegna breytinga í vistkerfi, t.d. aukinni sýkursneyslu, sem svo leiði til aukins vaxtar á sýrumyndandi bakteríutegundum. Ræktun með sértæku (e. selective) æti er ágæt leið til að rannsaka sérhæfðu kenninguna. Aftur á móti er mjög erfitt að rannsaka breytingar í tannsýklu og heildar örveruflóru með hefðbundnum ræktunaraðferðum, þegar reynt er að kanna betur vitsfræðilegu kenninguna. Með tilkomu nákvæmra mælitækja sem geta metið heilbrigðar tennur og tannátu á byrjunarstigi á einfaldari hátt (DIAGNOdent®) ásamt því að nýta sameindlíffræðilegar aðferðir, gera okkur kleift að tengja betur staðbundnar breytingar á tannskemmdum við ákveðna bakteríuflóru. Helstu markmið verkefnisins var að skoða bakteríuflóru í tannsýklu á nokkrum mismunandi stigum tannátu; (i) í tannsýklu ofan á glerung heilbrigðra tanna, (ii) tannsýklu úr glerungs-úrkölkun og (iii) úr byrjandi tannskemmdum. Áætlað var að bera að hluta niðurstöður klassískra aðferða með ræktunum saman við greiningu á örveruflóru með sameindalífræðilegum aðferðum, 16S rRNA gena greiningu og T-RFLP greiningu (e. -
Clinical and Microbiological Aspects of Periodontal Disease in Horses in South-East Queensland, Australia
Clinical and microbiological aspects of periodontal disease in horses in South-East Queensland, Australia Teerapol Tum Chinkangsadarn Doctor of Veterinary Medicine A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2015 School of Veterinary Science II Abstract The study of periodontal disease as part of equine dentistry is one of the overlooked fields of study, which truly needs more study and research to clearly understand the nature of the disease, the most appropriate diagnostic technique and prevention or treatment to provide for a good quality of life for horses. The abattoir survey of the oral cavity and dentition of 400 horses from South- East Queensland, Australia, showed that the most common dental abnormality was sharp enamel points (55.3% prevalence). Several types of dental abnormalities were strongly associated with age. The highest frequency of dental abnormalities (97.5%) were observed in senior horses (11-15 years old) and this included periodontal disease that increased to almost fifty percent in senior horses. The findings also confirmed that all horses, not just young horses, should have regular complete dental examinations as early as possible which should limit the development of more severe dental pathologies later in life. The equine oral microbiome found in dental plaque can cause oral disease which involves the some of the endogenous oral microbiota becoming opportunistic pathogens. The conventional method of oral microbiology based on culture dependent techniques usually overestimates the significance of species that are easily grown and overlooks microbial community diversity. Recently, the culture independent techniques using the next generation sequencing (NGS) method can determine the whole bacterial microbiota. -
Olegusella Massiliensis Gen. Nov., Sp. Nov., Strain KHD7T, a New Bacterial Genus Isolated from the Female Genital Tract of a Patient with Bacterial Vaginosis
Anaerobe 44 (2017) 87e95 Contents lists available at ScienceDirect Anaerobe journal homepage: www.elsevier.com/locate/anaerobe Research Paper Anaerobes in the microbiome Olegusella massiliensis gen. nov., sp. nov., strain KHD7T, a new bacterial genus isolated from the female genital tract of a patient with bacterial vaginosis Khoudia Diop a, Awa Diop a, Florence Bretelle a, b,Fred eric Cadoret a, Caroline Michelle a, Magali Richez a, Jean-François Cocallemen b, Didier Raoult a, c, Pierre-Edouard Fournier a, * Florence Fenollar a, a Aix Marseille Univ, Institut Hospitalo-Universitaire Mediterranee-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Facultedemedecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France b Department of Gynecology and Obstetrics, Gynepole, Marseille, Pr Boubli et D'Ercole, Hopital^ Nord, Assistance Publique-Hopitaux^ de Marseille, AMU, Aix- Marseille Universite, France c Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia article info abstract Article history: Strain KHD7T, a Gram-stain-positive rod-shaped, non-sporulating, strictly anaerobic bacterium, was Received 18 August 2016 isolated from the vaginal swab of a woman with bacterial vaginosis. We studied its phenotypic char- Received in revised form acteristics and sequenced its complete genome. The major fatty acids were C16:0 (44%), C18:2n6 (22%), 2 February 2017 and C18:1n9 (14%). The 1,806,744 bp long genome exhibited 49.24% GþC content; 1549 protein-coding Accepted 15 February 2017 and 51 RNA genes. Strain KHD7T exhibited a 93.5% 16S rRNA similarity with Olsenella uli, the phyloge- netically closest species in the family Coriobacteriaceae. -
Report of Isolation of Cryptobacterium Curtum from a Pelvic Abscess Siddharth Sridhar,1 Samson S.Y
JMM Case Reports (2015) DOI 10.1099/jmmcr.0.000067 Report of isolation of Cryptobacterium curtum from a pelvic abscess Siddharth Sridhar,1 Samson S.Y. Wong,1,2,3 Emily W.T. Tam,1 Susanna K.P. Lau1,2,3 and Patrick C.Y. Woo1,2,3 Correspondence 1Department of Microbiology, University of Hong Kong, University Pathology Building, Queen Mary Patrick C.Y. Woo Hospital, Hong Kong SAR, PR China [email protected] 2State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong SAR, PR China 3Research Centre of Infection and Immunology, University of Hong Kong, University Pathology Building, Queen Mary Hospital, Hong Kong SAR, PR China Introduction: To the best of our knowledge, this is the first reported case of isolation of Cryptobacterium curtum from an infected site outside the oral cavity. Case presentation: We report a patient who presented with fever and abdominal pain following an endoscopic procedure. Imaging confirmed a retroperitoneal abscess secondary to duodenal perforation complicating the endoscopic procedure. Surgical drainage of the abscess was carried out. Microbiological analysis of the pus revealed, among other bacteria, an anaerobic Gram-positive rod-shaped bacterium that was definitively identified as Cryptobacterium curtum by 16S rRNA gene sequencing. The patient improved after multiple episodes of retroperitoneal lavage and a prolonged course of antibiotics. Conclusion: This case demonstrates that C. curtum can be isolated outside the oral cavity in polymicrobial infected sites. The pathogenic significance of this organism in contributing to pyogenic infection requires further study. Received 2 December 2014 Accepted 2 June 2015 Keywords: Cryptobacterium curtum; pelvic abscess; opportunistic infection. -
Quantification of Slackia and Eggerthella Spp. in Human Feces
fmicb-07-00658 May 5, 2016 Time: 16:44 # 1 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 09 May 2016 doi: 10.3389/fmicb.2016.00658 Quantification of Slackia and Eggerthella spp. in Human Feces and Adhesion of Representatives Strains to Caco-2 Cells Gyu-Sung Cho1, Felix Ritzmann2, Marie Eckstein2, Melanie Huch2, Karlis Briviba3, Diana Behsnilian4, Horst Neve1 and Charles M. A. P. Franz1* 1 Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany, 2 Department of Safety and Quality of Fruit and Vegetables, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany, 3 Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, Edited by: Federal Research Institute of Nutrition and Food, Karlsruhe, Germany, 4 Department of Food Technology and Bioprocess Andrea Gomez-Zavaglia, Engineering, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Karlsruhe, Germany Center for Research and Development in Food Cryotechnology – Consejo Nacional Eggerthella and Slackia spp. are gut associated bacteria that have been suggested to De Investigaciones Científicas Y play roles in host lipid and xenobiotic metabolism. A quantitative PCR method for the Técnicas, Argentina selective enumeration of bacteria belonging to either the genus Eggerthella or Slackia Reviewed by: was developed in order to establish the numbers of these bacteria occurring in human Paula Carasi, Universidad Nacional de La Plata, feces. The primers developed for selective amplification of these genera were tested first Argentina in conventional PCR to test for their specificity. -
Comparison of Proteogenomic Approaches Across Kingdoms: A
Comparison of Proteogenomic Approaches Across Kingdoms: A Joint Effort in Gene Modeling Samuel Purvine1, Kim Hixson1, Carrie Nicora1, Muktak Aklujkar3, Ellen Panisko1, Lee Ann McCue1, Matthew Monroe1, Athanasios Lykidis2, Nikos Kyrpides2, Deanna Auberry1, Derek Lovely3, Igor Grigoriev2, Scott Baker1, Mary Lipton1, Gordon Anderson1, Richard Smith1 1Pacific Northwest National Laboratory, Richland, WA; 2Lawrence Berkeley National Laboratory, Berkeley, CA; 3University of Massachusetts, Boston, MA Accumulated data for microbial proteogenomics observed total observed % coverage N-terminus Organism ORFs annotated Challenges – Bacterial & Archaeal peptides (≥ 2 peptides) correction Goals (≥ 2 peptides) ORFs Conclusions • Combine direct observation of gene products The Genomic Encyclopedia of Bacteria and Archaea (GEBA) Escherichia coli K-12 24054 1809 4331 42% 236 • GeneMark gene predictions for bacteria and with genome sequence information to: project at the Joint Genome Institute (JGI) is systematically Geobacter sulfurreducens PCA 29123 2005 3446 58% 138 archaea show excellent fidelity, with the vast Halorhabdus utahensis AX-2, DSM 12940 12595 1308 3037 43% 222 filling in gaps in the bacterial and archaeal branches of the tree majority of observed gene products falling within – Examine the accuracy of gene models for Brachybacterium faecium DSM 4810 18828 1442 3129 46% 311 of life, which have been largely ignored by genome sequencing predicted genes diverse bacteria and archaea Cryptobacterium curtum DSM 15641 11793 900 1368 66% 168 projects. However, gene finding algorithms were developed Sanguibacter keddieii DSM 10542 13086 1384 3746 37% 265 • Proteomics data identify numerous alternate – Provide modifications to gene models, based on observations and knowledge from a narrow range of Slackia heliotrinireducens DSM 20476 14048 1080 2819 38% 198 protein start sites, as well as alternate ORFs thereby improving genome annotation well-studied organisms.