The Genera of Lactic Acid Bacteria the Lactic Acid Bacteria Volume 2
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Genomic Stability and Genetic Defense Systems in Dolosigranulum Pigrum A
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.16.440249; this version posted April 18, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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-ND 4.0 International license. 1 Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum a 2 Candidate Beneficial Bacterium from the Human Microbiome 3 4 Stephany Flores Ramosa, Silvio D. Bruggera,b,c, Isabel Fernandez Escapaa,c,d, Chelsey A. 5 Skeetea, Sean L. Cottona, Sara M. Eslamia, Wei Gaoa,c, Lindsey Bomara,c, Tommy H. 6 Trand, Dakota S. Jonese, Samuel Minote, Richard J. Robertsf, Christopher D. 7 Johnstona,c,e#, Katherine P. Lemona,d,g,h# 8 9 aThe Forsyth Institute (Microbiology), Cambridge, MA, USA 10 bDepartment of Infectious Diseases and Hospital Epidemiology, University Hospital 11 Zurich, University of Zurich, Zurich, Switzerland 12 cDepartment of Oral Medicine, Infection and Immunity, Harvard School of Dental 13 Medicine, Boston, MA, USA 14 dAlkek Center for Metagenomics & Microbiome Research, Department of Molecular 15 Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA 16 eVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, 17 Seattle, WA, USA 18 fNew England Biolabs, Ipswich, MA, USA 19 gDivision of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, 20 Boston, MA, USA 21 hSection of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, 22 Baylor College of Medicine, Houston, Texas, USA 23 bioRxiv preprint doi: https://doi.org/10.1101/2021.04.16.440249; this version posted April 18, 2021. -
The Microbiome of Otitis Media with Effusion and the Influence of Alloiococcus Otitidis on Haemophilus Influenzae in Polymicrobial Biofilm
The microbiome of otitis media with effusion and the influence of Alloiococcus otitidis on Haemophilus influenzae in polymicrobial biofilm Chun L Chan Bachelor of Radiography and Medical Imaging (Honours) Bachelor of Medicine, Bachelor of Surgery Department of Otolaryngology, Head and Neck Surgery University of Adelaide, Adelaide, Australia Submitted for the title of Doctor of Philosophy November 2016 C L Chan i This thesis is dedicated to those who have sacrificed the most during my scientific endeavours My amazing family Flora, Aidan and Benjamin C L Chan ii Table of Contents TABLE OF CONTENTS .............................................................................................................................. III THESIS DECLARATION ............................................................................................................................. VII ACKNOWLEDGEMENTS ........................................................................................................................... VIII THESIS SUMMARY ................................................................................................................................... X PUBLICATIONS ARISING FROM THIS THESIS .................................................................................................. XII PRESENTATIONS ARISING FROM THIS THESIS ............................................................................................... XIII ABBREVIATIONS ................................................................................................................................... -
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 -
Wo 2010/025267 A2
(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 4 March 2010 (04.03.2010) WO 2010/025267 A2 (51) International Patent Classification: 02459 (US). MALO, Madhu S. [US/US]; 14 Hudson A61K 33/42 (2006.01) A61P 19/02 (2006.01) Street, Watertown, Massachusetts 02474 (US). A61P 1/12 (2006.01) A61P 37/08 (2006.01) (74) Agent: FASSE, J. Peter; Fish & Richardson P.C., P.O. A61P 31/04 (2006.01) Box 1022, Minneapolis, Minnesota 55440-1022 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2009/055216 kind of national protection available): AE, AG, AL, AM, (22) International Filing Date: AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, 27 August 2009 (27.08.2009) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (25) Filing Language: English HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (26) Publication Language: English KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (30) Priority Data: NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, 61/093,129 29 August 2008 (29.08.2008) US SE, SG, SK, SL, SM, ST, SV, SY, TJ, TM, TN, TR, TT, (71) Applicant (for all designated States except US): THE TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases. -
Ldentif Ication of Clinically Relevant Viridans Streptococci by Analysis of Transfer DNA Intergenic Spacer Length Polymorphism
international Journal of Systematic Bacteriology (1 999), 49, 1 59 1-1 598 Printed in Great Britain ldentif ication of clinically relevant viridans streptococci by analysis of transfer DNA intergenic spacer length polymorphism Y. De Gheldre,' P. Vandamme,213H. Goossens3and M. J. Struelens' Author for correspondence: Yves De Gheldre. Tel: + 32 2 555 4517. Fax: + 32 2 555 6459. e-mail : [email protected] 1 Department of The utility of PCR analysis of transfer DNA intergenic spacer length Microbiology, HBpital polymorphism @DNA-ILP)for the identification to the species level of clinically Erasme, Universite Libre de Bruxelles, 808 Route de relevant viridans streptococci was evaluated with a collection of reference Lennik, 1070 Brussels, strains of 15 species of the salivarius, anginosus, mitis and mutans rRNA Belgium homology groups. PCR products generated by using fluorescent, outwardly 2 Laboratory of directed, consensus tDNA primers were analysed by electrophoresis on Microbiology and denaturating polyacrylamide gels and by laser fluorescence scanning. Eleven BCCM/LMG Culture Collection, University of species showed specific and distinct tDNA patterns : Streptococcus cristatus, Ghent, Belgium Streptococcus gordonii, Streptococcus oralis, Streptococcus mitis, 3 Laboratory of Medical Streptococcus pneumoniae, Streptococcus sanguinis, Streptococcus Microbiology, University parasanguinis, Streptococcus anginosus, Streptococcus mutans, Streptococcus Hospital Antwerp, criceti and Streptococcus ratti. Indistinguishable patterns were obtained Antwerp, Belgium among two groups of species : Streptococcus vestibularis and Streptococcus salivarius on the one hand and Streptococcus constellatus and Streptococcus intermedius on the other. 5. mitis strains produced heterogeneous patterns that could be separated into three groups: a group containing S. mitis biovar 1 and two S, mitis biovar 2 groups, one of which clustered with S. -
Type of the Paper (Article
Supplementary Materials S1 Clinical details recorded, Sampling, DNA Extraction of Microbial DNA, 16S rRNA gene sequencing, Bioinformatic pipeline, Quantitative Polymerase Chain Reaction Clinical details recorded In addition to the microbial specimen, the following clinical features were also recorded for each patient: age, gender, infection type (primary or secondary, meaning initial or revision treatment), pain, tenderness to percussion, sinus tract and size of the periapical radiolucency, to determine the correlation between these features and microbial findings (Table 1). Prevalence of all clinical signs and symptoms (except periapical lesion size) were recorded on a binary scale [0 = absent, 1 = present], while the size of the radiolucency was measured in millimetres by two endodontic specialists on two- dimensional periapical radiographs (Planmeca Romexis, Coventry, UK). Sampling After anaesthesia, the tooth to be treated was isolated with a rubber dam (UnoDent, Essex, UK), and field decontamination was carried out before and after access opening, according to an established protocol, and shown to eliminate contaminating DNA (Data not shown). An access cavity was cut with a sterile bur under sterile saline irrigation (0.9% NaCl, Mölnlycke Health Care, Göteborg, Sweden), with contamination control samples taken. Root canal patency was assessed with a sterile K-file (Dentsply-Sirona, Ballaigues, Switzerland). For non-culture-based analysis, clinical samples were collected by inserting two paper points size 15 (Dentsply Sirona, USA) into the root canal. Each paper point was retained in the canal for 1 min with careful agitation, then was transferred to −80ºC storage immediately before further analysis. Cases of secondary endodontic treatment were sampled using the same protocol, with the exception that specimens were collected after removal of the coronal gutta-percha with Gates Glidden drills (Dentsply-Sirona, Switzerland). -
Patterns of Horizontal Gene Transfer Into the Geobacillus Clade
Imperial College London London Institute of Medical Sciences Patterns of Horizontal Gene Transfer into the Geobacillus Clade Alexander Dmitriyevich Esin September 2018 Submitted in part fulfilment of the requirements for the degree of Doctor of Philosophy of Imperial College London For my grandmother, Marina. Without you I would have never been on this path. Your unwavering strength, love, and fierce intellect inspired me from childhood and your memory will always be with me. 2 Declaration I declare that the work presented in this submission has been undertaken by me, including all analyses performed. To the best of my knowledge it contains no material previously published or presented by others, nor material which has been accepted for any other degree of any university or other institute of higher learning, except where due acknowledgement is made in the text. 3 The copyright of this thesis rests with the author and is made available under a Creative Commons Attribution Non-Commercial No Derivatives licence. Researchers are free to copy, distribute or transmit the thesis on the condition that they attribute it, that they do not use it for commercial purposes and that they do not alter, transform or build upon it. For any reuse or redistribution, researchers must make clear to others the licence terms of this work. 4 Abstract Horizontal gene transfer (HGT) is the major driver behind rapid bacterial adaptation to a host of diverse environments and conditions. Successful HGT is dependent on overcoming a number of barriers on transfer to a new host, one of which is adhering to the adaptive architecture of the recipient genome. -
an Emerging Pathogen for Salmonid Culture Jesús L
, an emerging pathogen for salmonid culture Jesús L. Romalde, Carmen Ravelo, Iván Valdés, Beatriz Magariños, Eduardo de la Fuente, Carolina San Martín, Rubén Avendaño-Herrera, Alicia E. Toranzo To cite this version: Jesús L. Romalde, Carmen Ravelo, Iván Valdés, Beatriz Magariños, Eduardo de la Fuente, et al.. , an emerging pathogen for salmonid culture. Veterinary Microbiology, Elsevier, 2008, 130 (1-2), pp.198. 10.1016/j.vetmic.2007.12.021. hal-00532381 HAL Id: hal-00532381 https://hal.archives-ouvertes.fr/hal-00532381 Submitted on 4 Nov 2010 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. Accepted Manuscript Title: Streptococcus phocae, an emerging pathogen for salmonid culture Authors: Jesus´ L. Romalde, Carmen Ravelo, Ivan´ Valdes,´ Beatriz Magarinos,˜ Eduardo de la Fuente, Carolina San Mart´ın, Ruben´ Avendano-Herrera,˜ Alicia E. Toranzo PII: S0378-1135(07)00644-X DOI: doi:10.1016/j.vetmic.2007.12.021 Reference: VETMIC 3926 To appear in: VETMIC Received date: 25-6-2007 Revised date: 12-12-2007 Accepted date: 13-12-2007 Please cite this article as: Romalde, J.L., Ravelo, C., Valdes,´ I., Magarinos,˜ B., de la Fuente, E., Mart´ın, C.S., Avendano-Herrera,˜ R., Toranzo, A.E., Streptococcus phocae, an emerging pathogen for salmonid culture, Veterinary Microbiology (2007), doi:10.1016/j.vetmic.2007.12.021 This is a PDF file of an unedited manuscript that has been accepted for publication. -
Reviewing the Pathogenic Potential of the Otitis-Associated Bacteria Alloiococcus Otitidis and Turicella Otitidis
REVIEW published: 14 February 2020 doi: 10.3389/fcimb.2020.00051 Reviewing the Pathogenic Potential of the Otitis-Associated Bacteria Alloiococcus otitidis and Turicella otitidis Rachael Lappan 1,2, Sarra E. Jamieson 3 and Christopher S. Peacock 1,3* 1 The Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia, 2 Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia, 3 Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia Alloiococcus otitidis and Turicella otitidis are common bacteria of the human ear. They have frequently been isolated from the middle ear of children with otitis media (OM), though their potential role in this disease remains unclear and confounded due to their presence as commensal inhabitants of the external auditory canal. In this review, we summarize the current literature on these organisms with an emphasis on their role in Edited by: OM. Much of the literature focuses on the presence and abundance of these organisms, Regie Santos-Cortez, and little work has been done to explore their activity in the middle ear. We find there University of Colorado, United States is currently insufficient evidence available to determine whether these organisms are Reviewed by: Kevin Mason, pathogens, commensals or contribute indirectly to the pathogenesis of OM. However, The Ohio State University, building on the knowledge currently available, we suggest future approaches aimed at United States providing stronger evidence to determine whether A. otitidis and T. otitidis are involved in Joshua Chang Mell, Drexel University, United States the pathogenesis of OM. -
Are You Suprised ?
A DAMB 711 Microbiology Exam 2A 100 points September 27, 2011 Your name: _____________________________________________ Exam # ___________ Seat # ____________ 1 I. Multiple Choice: Choose the ONE BEST answer. Mark the correct answer in Part 1 of your answer sheet. 1. Which of the following conveys the highest risk of nosocomial infection to a hospitalized patient? A. the hospital environment (rooms, floors, fomites) B. invasive medical devices (catheters, respirators, etc.) C. hospital personnel, including physicians D. mechanical vectors 2. The clonality of pathogenic bacteria refers to: A. the environmental regulation of genes encoding virulence factors B. the acquisition of virulence determinants encoded on extra-chromosomal elements C. the infective dose of a specific species of bacteria D. opportunistic pathogens E. only a few strains in a species will be the etiologic agent of a disease 3. Diseases caused by this genus of bacteria are never transmitted through contaminated food. A. Listeria B. Staphylococcus C. Mycobacteria D. Corynebacteria 4. When Vibrio cholera is moved from a high salt, basic environment to isotonic conditions, with neutral pH a sensor kinase in the bacterium phosphorylates a response regulator that initiates transcription. This is an example of: A. the environmental regulation of genes encoding virulence factors B. the acquisition of virulence determinants encoded on extra-chromosomal elements C. the infective dose of a specific species of bacteria D. opportunistic pathogens E. only a few strains in a species will be the etiologic agent of a disease 5. In which form of tuberculosis is a patient coughing up infectious material? A. miliary B. active C. latent/dormant D. -
Microbiota Network and Mathematic Microbe Mutualism in Colostrum and Mature Milk Collected in Two Different Geographic Areas: Italy Versus Burundi
The ISME Journal (2017) 11, 875–884 OPEN © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Microbiota network and mathematic microbe mutualism in colostrum and mature milk collected in two different geographic areas: Italy versus Burundi Lorenzo Drago1,2, Marco Toscano1, Roberta De Grandi2, Enzo Grossi3, Ezio M Padovani4 and Diego G Peroni5,6 1Clinical Chemistry and Microbiology Laboratory, IRCCS Galeazzi Orthopaedic Institute, Milan, Italy; 2Clinical Microbiology Laboratory, Department of Biomedical Science for Health, University of Milan, Milan, Italy; 3Villa Santa Maria Institute, Via IV Novembre Tavernerio, Como, Italy; 4Pediatric Department, University of Verona & Pro-Africa Foundation, Verona, Italy; 5Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Pisa, Italy and 6International Inflammation (in-FLAME) Network of the World Universities Network, Sydney, NSW, Australia Human milk is essential for the initial development of newborns, as it provides all nutrients and vitamins, such as vitamin D, and represents a great source of commensal bacteria. Here we explore the microbiota network of colostrum and mature milk of Italian and Burundian mothers using the auto contractive map (AutoCM), a new methodology based on artificial neural network (ANN) architecture. We were able to demonstrate the microbiota of human milk to be a dynamic, and complex, ecosystem with different bacterial networks among different populations containing diverse microbial hubs and central nodes, which change during the transition from colostrum to mature milk. Furthermore, a greater abundance of anaerobic intestinal bacteria in mature milk compared with colostrum samples has been observed. The association of complex mathematic systems such as ANN and AutoCM adopted to metagenomics analysis represents an innovative approach to investigate in detail specific bacterial interactions in biological samples.