The Severity of Human Peri-Implantitis Lesions Correlates with the Level Of
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High-Quality Draft Genome Sequences of Five Anaerobic Oral Bacteria and Description of Peptoanaerobacter Stomatis Gen
Sizova et al. Standards in Genomic Sciences (2015) 10:37 DOI 10.1186/s40793-015-0027-8 EXTENDED GENOME REPORT Open Access High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae Maria V. Sizova1, Amanda Chilaka1, Ashlee M. Earl2, Sebastian N. Doerfert1, Paul A. Muller1, Manolito Torralba3, Jamison M. McCorrison3, A. Scott Durkin3, Karen E. Nelson3 and Slava S. Epstein1* Abstract Here we report a summary classification and the features of five anaerobic oral bacteria from the family Peptostreptococcaceae. Bacterial strains were isolated from human subgingival plaque. Strains ACC19a, CM2, CM5, and OBRC8 represent the first known cultivable members of “yet uncultured” human oral taxon 081; strain AS15 belongs to “cultivable” human oral taxon 377. Based on 16S rRNA gene sequence comparisons, strains ACC19a, CM2, CM5, and OBRC8 are distantly related to Eubacterium yurii subs. yurii and Filifactor alocis, with 93.2 – 94.4 % and 85.5 % of sequence identity, respectively. The genomes of strains ACC19a, CM2, CM5, OBRC8 and AS15 are 2,541,543; 2,312,592; 2,594,242; 2,553,276; and 2,654,638 bp long. The genomes are comprised of 2277, 1973, 2325, 2277, and 2308 protein-coding genes and 54, 57, 54, 36, and 28 RNA genes, respectively. Based on the distinct characteristics presented here, we suggest that strains ACC19a, CM2, CM5, and OBRC8 represent a novel genus and species within the family Peptostreptococcaceae, for which we propose the name Peptoanaerobacter stomatis gen. nov., sp. nov. The type strain is strain ACC19aT (=HM-483T; =DSM 28705T;=ATCC BAA-2665T). -
High Quality Permanent Draft Genome Sequence of Chryseobacterium Bovis DSM 19482T, Isolated from Raw Cow Milk
Lawrence Berkeley National Laboratory Recent Work Title High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. Permalink https://escholarship.org/uc/item/4b48v7v8 Journal Standards in genomic sciences, 12(1) ISSN 1944-3277 Authors Laviad-Shitrit, Sivan Göker, Markus Huntemann, Marcel et al. Publication Date 2017 DOI 10.1186/s40793-017-0242-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Laviad-Shitrit et al. Standards in Genomic Sciences (2017) 12:31 DOI 10.1186/s40793-017-0242-6 SHORT GENOME REPORT Open Access High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk Sivan Laviad-Shitrit1, Markus Göker2, Marcel Huntemann3, Alicia Clum3, Manoj Pillay3, Krishnaveni Palaniappan3, Neha Varghese3, Natalia Mikhailova3, Dimitrios Stamatis3, T. B. K. Reddy3, Chris Daum3, Nicole Shapiro3, Victor Markowitz3, Natalia Ivanova3, Tanja Woyke3, Hans-Peter Klenk4, Nikos C. Kyrpides3 and Malka Halpern1,5* Abstract Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study. -
Sporulation Evolution and Specialization in Bacillus
bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Research article From root to tips: sporulation evolution and specialization in Bacillus subtilis and the intestinal pathogen Clostridioides difficile Paula Ramos-Silva1*, Mónica Serrano2, Adriano O. Henriques2 1Instituto Gulbenkian de Ciência, Oeiras, Portugal 2Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal *Corresponding author: Present address: Naturalis Biodiversity Center, Marine Biodiversity, Leiden, The Netherlands Phone: 0031 717519283 Email: [email protected] (Paula Ramos-Silva) Running title: Sporulation from root to tips Keywords: sporulation, bacterial genome evolution, horizontal gene transfer, taxon- specific genes, Bacillus subtilis, Clostridioides difficile 1 bioRxiv preprint doi: https://doi.org/10.1101/473793; this version posted March 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. Abstract Bacteria of the Firmicutes phylum are able to enter a developmental pathway that culminates with the formation of a highly resistant, dormant spore. Spores allow environmental persistence, dissemination and for pathogens, are infection vehicles. In both the model Bacillus subtilis, an aerobic species, and in the intestinal pathogen Clostridioides difficile, an obligate anaerobe, sporulation mobilizes hundreds of genes. -
Parents with Periodontitis Impact the Subgingival Colonization of Their Ofspring Mabelle Freitas Monteiro1, Khaled Altabtbaei2, Purnima S
www.nature.com/scientificreports OPEN Parents with periodontitis impact the subgingival colonization of their ofspring Mabelle Freitas Monteiro1, Khaled Altabtbaei2, Purnima S. Kumar3,4*, Márcio Zafalon Casati1, Karina Gonzales Silverio Ruiz1, Enilson Antonio Sallum1, Francisco Humberto Nociti‑Junior1 & Renato Corrêa Viana Casarin1,4 Early acquisition of a pathogenic microbiota and the presence of dysbiosis in childhood is associated with susceptibility to and the familial aggregation of periodontitis. This longitudinal interventional case–control study aimed to evaluate the impact of parental periodontal disease on the acquisition of oral pathogens in their ofspring. Subgingival plaque and clinical periodontal metrics were collected from 18 parents with a history of generalized aggressive periodontitis and their children (6–12 years of age), and 18 periodontally healthy parents and their parents at baseline and following professional oral prophylaxis. 16S rRNA amplicon sequencing revealed that parents were the primary source of the child’s microbiome, afecting their microbial acquisition and diversity. Children of periodontitis parents were preferentially colonized by Filifactor alocis, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Streptococcus parasanguinis, Fusobacterium nucleatum and several species belonging to the genus Selenomonas even in the absence of periodontitis, and these species controlled inter‑bacterial interactions. These pathogens also emerged as robust discriminators of the microbial signatures of children of parents with periodontitis. Plaque control did not modulate this pathogenic pattern, attesting to the microbiome’s resistance to change once it has been established. This study highlights the critical role played by parental disease in microbial colonization patterns in their ofspring and the early acquisition of periodontitis‑related species and underscores the need for greater surveillance and preventive measures in families of periodontitis patients. -
A Case Study of Salivary Microbiome in Smokers and Non-Smokers in Hungary: Analysis by Shotgun Metagenome Sequencing
Journal of Oral Microbiology ISSN: (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/zjom20 A case study of salivary microbiome in smokers and non-smokers in Hungary: analysis by shotgun metagenome sequencing Roland Wirth , Gergely Maróti , Róbert Mihók , Donát Simon-Fiala , Márk Antal , Bernadett Pap , Anett Demcsák , Janos Minarovits & Kornél L. Kovács To cite this article: Roland Wirth , Gergely Maróti , Róbert Mihók , Donát Simon-Fiala , Márk Antal , Bernadett Pap , Anett Demcsák , Janos Minarovits & Kornél L. Kovács (2020) A case study of salivary microbiome in smokers and non-smokers in Hungary: analysis by shotgun metagenome sequencing, Journal of Oral Microbiology, 12:1, 1773067, DOI: 10.1080/20002297.2020.1773067 To link to this article: https://doi.org/10.1080/20002297.2020.1773067 © 2020 The Author(s). Published by Informa View supplementary material UK Limited, trading as Taylor & Francis Group. Published online: 07 Jun 2020. Submit your article to this journal Article views: 84 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=zjom20 JOURNAL OF ORAL MICROBIOLOGY 2020, VOL. 12, 1773067 https://doi.org/10.1080/20002297.2020.1773067 A case study of salivary microbiome in smokers and non-smokers in Hungary: analysis by shotgun metagenome sequencing Roland Wirtha, Gergely Marótib, Róbert Mihókc, Donát Simon-Fialac, Márk Antalc, Bernadett Papb, Anett Demcsákd, Janos Minarovitsd and Kornél L. Kovács -
Product Sheet Info
Product Information Sheet for HM-13 Oribacterium sinus, Strain F0268 2% yeast extract (ATCC medium 1834) or equivalent Wilkins-Chalgren anaerobe agar with 5% defibrinated sheep blood or equivalent Catalog No. HM-13 Incubation: Temperature: 37°C For research use only. Not for human use. Atmosphere: Anaerobic (80% N2:10% CO2:10% H2) Propagation: Contributor: 1. Keep vial frozen until ready for use, then thaw. Jacques Izard, Assistant Member of the Staff, Department of 2. Transfer the entire thawed aliquot into a single tube of Molecular Genetics, The Forsyth Institute, Boston, broth. Massachusetts 3. Use several drops of the suspension to inoculate an agar slant and/or plate. Manufacturer: 4. Incubate the tube, slant and/or plate at 37°C for 48 to BEI Resources 72 hours. Product Description: Citation: Bacteria Classification: Lachnospiraceae, Oribacterium Acknowledgment for publications should read “The following Species: Oribacterium sinus reagent was obtained through BEI Resources, NIAID, NIH as Strain: F0268 part of the Human Microbiome Project: Oribacterium sinus, Original Source: Oribacterium sinus (O. sinus), strain F0268 Strain F0268, HM-13.” was isolated in June 1980 from the subgingival plaque of a 27-year-old white female patient with severe periodontitis in Biosafety Level: 1 the United States.1,2 Appropriate safety procedures should always be used with Comments: O. sinus, strain F0268 (HMP ID 6123) is a this material. Laboratory safety is discussed in the following reference genome for The Human Microbiome Project publication: U.S. Department of Health and Human Services, (HMP). HMP is an initiative to identify and characterize Public Health Service, Centers for Disease Control and human microbial flora. -
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. -
Periodontal, Metabolic, and Cardiovascular Disease
Pteridines 2018; 29: 124–163 Research Article Open Access Hina Makkar, Mark A. Reynolds#, Abhishek Wadhawan, Aline Dagdag, Anwar T. Merchant#, Teodor T. Postolache*# Periodontal, metabolic, and cardiovascular disease: Exploring the role of inflammation and mental health Journal xyz 2017; 1 (2): 122–135 The First Decade (1964-1972) https://doi.org/10.1515/pteridines-2018-0013 receivedResearch September Article 13, 2018; accepted October 10, 2018. List of abbreviations Abstract: Previous evidence connects periodontal AAP: American Academy of Periodontology Max Musterman, Paul Placeholder disease, a modifiable condition affecting a majority of AGEs: Advanced glycation end products Americans,What withIs So metabolic Different and cardiovascular About morbidity AgP: Aggressive periodontitis and mortality. This review focuses on the likely mediation AHA: American Heart Association ofNeuroenhancement? these associations by immune activation and their anti-CL: Anti-cardiolipin potentialWas istinteractions so anders with mental am Neuroenhancement?illness. Future anti-oxLDL: Anti-oxidized low-density lipoprotein longitudinal, and ideally interventional studies, should AP: Acute periodontitis focus on reciprocal interactions and cascading effects, as ASCVD: Atherosclerotic cardiovascular disease wellPharmacological as points for effective and Mentalpreventative Self-transformation and therapeutic C. pneumoniae in Ethic : Chlamydia pneumoniae interventionsComparison across diagnostic domains to reduce CAL: Clinical attachment loss morbidity,Pharmakologische -
Das Mikrobiom Periimplantärer Läsionen Der Nachweis Dysbiotischer Veränderungen in Assoziation Mit Dem Schweregrad Der Erkrankung
Das Mikrobiom periimplantärer Läsionen Der Nachweis dysbiotischer Veränderungen in Assoziation mit dem Schweregrad der Erkrankung Inaugural-Dissertation zur Erlangung des Doktorgrades der Hohen Medizinischen Fakultät der Rheinischen Friedrich-Wilhelms-Universität Bonn Annika Therese Kröger aus Aachen 2020 Angefertigt mit der Genehmigung der Medizinischen Fakultät der Universität Bonn 1. Gutachter: Prof. Dr. med. dent. Moritz Kebschull 2. Gutachter: Prof. Dr. Achim Hörauf Tag der Mündlichen Prüfung: 07.10.2020 Aus der Poliklinik für Parodontologie, Zahnerhaltung und Präventive Zahnheilkunde Direktor: Prof. Dr. med. Dr. med. dent. Søren Jepsen Meinen Eltern 5 Inhaltsverzeichnis Abkürzungsverzeichnis 7 1. Einleitung 8 1.1 Periimplantitis 8 1.1.1 Dentale Implantate und umgebendes Gewebe in periimplantären gesunden Situationen 8 1.1.2 Periimplantitis 10 1.1.3 Periimplantitis versus Parodontitis 14 1.2 Das Mikrobiom bei Periimplantitis und Parodontitis 17 1.3 16s rRNA Sequenzierung 18 1.3.1 Hochdurchsatzsequenziermethodiken 18 1.3.2 Das 16s Gen 18 1.4 Hypothese und Fragestellung dieser Studie 19 2. Material und Methoden 21 2.1 Studienpopulation 21 2.1.1 Allgemeines 21 2.1.2 Ein- und Ausschlusskriterien 21 2.1.3 Dokumentierte Parameter 22 2.2 Probengewinnung und -aufbereitung 23 2.3 16s rRNA Sequenzierung und Datenaufbereitung 24 2.3.1 ‚Paired-End‘-Hochdurchsatz-Sequenzierung der V3-V4 Region des 16s rRNA Genes 25 2.3.2 Post-Sequenzierungs-Prozesse 28 2.4 Statistische Analyse 32 2.4.1 Assoziation mit PD 32 2.4.2 Netzwerkanalyse 33 2.4.3 Mikrobieller Dysbiose Index 34 2.4.4 Signifikante Unterschiede der bakteriellen Charakteristika 34 6 3. Ergebnisse 35 3.1 Studienpopulation (Tab. -
Peri-Implantitis Review a Quarterly Review of the Latest Publications Related to the Study of Peri-Implant Inflammation and Bone Loss
12 Fall 2015 Aron J. Saffer DDS MS Diplomate of the American Board of Periodontology Peri-implantitis Review A quarterly review of the latest publications related to the study of Peri-implant inflammation and bone loss A service of Dr. Aron Saffer and the Jerusalem Perio Center to provide useful, up -to date information concerning one of the most complex and troubling problems facing dental professionals today. Peri-implantitis : Microbiology • Are the Bacteria of Peri-implantitis the same as Periodontal disease? • Are we treating the infection correctly? MICROBIAL METHODS EMPLOYED • Are screw-retained restorations better than cement IN THE DIAGNOSIS OF THE retained restorations at preventing peri-implantitis PERIODONTAL PATHOGEN: Bacterial Cultivation: a method in What Does the latest Literature say? You might be surprised which the bacteria taken from infected site and is allowed to multiply on a predetermined culture media. Using light Peri-implant mucositis and Peri-implantitis is an inflammatory response microscopy the bacteria is generally due to bacteriorly driven infections, affecting the mucosal tissue and identified. eventually the bone surrounding implants. The condition was traditionally regarded to be microbiologically similar to Periodontitis. Earlier research had demonstrated that the pathogens which were found in patients with periodontal disease had similar pathogens in the sulcus around infected implants. In fact, one hypothesis suggested that the infected gingiva was a resevoir for the bacteria that would eventually translocate and infect the mucosal crevice around implants. With newer microbiological identification techniques evidence is emerging . to suggest that the ecosystem around teeth and implants differ in many ways. Have we been taking “the easy way out” by lumping ALL gingival and mucosal infection together regardless whether it surrounds a human tooth or titanium metal. -
University of Oklahoma Graduate College
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MICROBIOLOGY OF WATER AND WASTEWATER: DISCOVERY OF A NEW GENUS NUMERICALLY DOMINANT IN MUNICIPAL WASTEWATER AND ANTIMICROBIAL RESISTANCES IN NUMERICALLY DOMINANT BACTERIA FROM OKLAHOMA LAKES A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY By Toby D. Allen Norman, Oklahoma 2005 UMI Number: 3203299 UMI Microform 3203299 Copyright 2006 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest Information and Learning Company 300 North Zeeb Road P.O. Box 1346 Ann Arbor, MI 48106-1346 MICROBIOLOGY OF WATER AND WASTEWATER: DISCOVERY OF A NEW GENUS NUMERICALLY DOMINANT IN MUNICIPAL WASTEWATER AND ANTIMICROBIAL RESISTANCES IN NUMERICALLY DOMINANT BACTERIA FROM OKLAHOMA LAKES A DISSERTATION APPROVED FOR THE DEPARTMENT OF BOTANY AND MICROBIOLOGY BY ____________________________ Dr. Ralph S. Tanner ____________________________ Dr. Kathleen E. Duncan ____________________________ Dr. David P. Nagle ____________________________ Dr. Mark A. Nanny ____________________________ Dr. Marvin Whiteley Copyright by Toby D. Allen 2005 All Rights Reserved “Science advances through tentative answers to a series of more and more subtle questions which reach deeper and deeper into the essence of natural phenomena” – Louis Pasteur iv ACKNOWLEDGEMENTS I consider myself fortunate to have had the opportunity to work on the projects contained in this work. I am grateful to have had the support and guidance of Dr. Ralph Tanner, who gave me the opportunity conduct research in his laboratory and to the Department of Botany and Microbiology, which has supported me in the form of teaching and research assistantships. -
Influence of the Dental Topical Application of a Nisin-Biogel
Influence of the dental topical application of a nisin-biogel in the oral microbiome of dogs: a pilot study Eva Cunha1, Sara Valente1, Mariana Nascimento2, Marcelo Pereira2, Luís Tavares1, Ricardo Dias2 and Manuela Oliveira1 1 CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal 2 BioISI: Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal ABSTRACT Periodontal disease (PD) is one of the most widespread inflammatory diseases in dogs. This disease is initiated by a polymicrobial biofilm in the teeth surface (dental plaque), leading to a local inflammatory response, with gingivitis and/or several degrees of periodontitis. For instance, the prevention of bacterial dental plaque formation and its removal are essential steps in PD control. Recent research revealed that the antimicrobial peptide nisin incorporated in the delivery system guar gum (biogel) can inhibit and eradicate bacteria from canine dental plaque, being a promising compound for prevention of PD onset in dogs. However, no information is available regarding its effect on the dog’s oral microbiome. In this pilot study, the influence of the nisin-biogel on the diversity of canine oral microbiome was evaluated using next generation sequencing (NGS), aiming to access the viability of nisin-biogel to be used in long-term experiment in dogs. Composite toothbrushing samples of the supragingival plaque from two dogs were collected at three timepoints: T1—before any application of the nisin-biogel to the animals’ teeth surface; T2—one hour after one application of the nisin-biogel; and T3—one hour after a total of three applications of the nisin-biogel, each 48 hours.