Lactic Acid Bacteria As Probiotics for the Nose?
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
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. -
Dolosigranulum Pigrum Modulates Immunity Against SARS-Cov-2 in Respiratory Epithelial Cells
pathogens Communication Dolosigranulum pigrum Modulates Immunity against SARS-CoV-2 in Respiratory Epithelial Cells Md. Aminul Islam 1,2 , Leonardo Albarracin 1,3 , Vyacheslav Melnikov 4 , Bruno G. N. Andrade 5 , Rafael R. C. Cuadrat 6,7 , Haruki Kitazawa 1,8,* and Julio Villena 1,3,* 1 Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan; [email protected] (M.A.I.); [email protected] (L.A.) 2 Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh 3 Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET), Tucumán 4000, Argentina 4 Gabrichevsky Research Institute for Epidemiology and Microbiology, 125212 Moscow, Russia; [email protected] 5 AdaptCentre, Munster Technological University (MTU), T12 P928 Cork, Ireland; [email protected] 6 Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), 13125 Berlin, Germany; [email protected] 7 Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke, 14558 Nuthetal, Germany 8 Livestock Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai 981-8555, Japan * Correspondence: [email protected] (H.K.); [email protected] (J.V.) Citation: Islam, M..A.; Albarracin, L.; Melnikov, V.; Andrade, B.G.N.; Abstract: In a previous work, we demonstrated that nasally administered Dolosigranulum pigrum Cuadrat, R.R.C.; Kitazawa, H.; 040417 beneficially modulated the respiratory innate immune response triggered by the activation Villena, J. -
Downloaded from NCBI (NZ AGXA00000000.1) And
bioRxiv preprint doi: https://doi.org/10.1101/678698; this version posted March 4, 2020. 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 Dolosigranulum pigrum cooperation and competition in human nasal microbiota 2 Silvio D. Brugger1, 2, 3, 10*, Sara M. Eslami2,10, Melinda M. Pettigrew4,10, Isabel F. 3 Escapa2,3,5, Matthew T. Henke6, Yong Kong7 and Katherine P. Lemon2,5,8,9* 4 1Department of Infectious Diseases and Hospital Epidemiology, University Hospital 5 Zurich, University of Zurich, Zurich, Switzerland, CH-8006 6 2The Forsyth Institute (Microbiology), Cambridge, MA, USA, 02142 7 3Department of Oral Medicine, Infection and Immunity, Harvard School of Dental 8 Medicine, Boston, MA, USA, 02115 9 4Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New 10 Haven, 11 CT, USA, 06510 12 5Alkek Center for Metagenomics & Microbiome Research, Department of Molecular 13 Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA 77030 14 6Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical 15 School, Boston, MA, USA, 02115 16 7Department of Molecular Biophysics and Biochemistry and W.M. Keck Foundation 17 Biotechnology Resource Laboratory, Yale University, New Haven, CT, USA, 06519 18 8Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, 19 Boston, MA, USA, 02115 1 bioRxiv preprint doi: https://doi.org/10.1101/678698; this version posted March 4, 2020. 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. -
Susan Gottesman, Phd National Institutes of Health
Boston Bacterial Meeting 2017 Crystal structure of Hfq in a complex with sRNA, Keynote speaker: RNA binding interfaces highlighted. Modeled using PDB: 4V2S Susan Gottesman, PhD National Institutes of Health Generously sponsored by: 2017 Boston Bacterial Meeting - Schedule and Introduction Thursday June 15 12:00 pm Registration 12:45 pm Opening Remarks I: Bacterial communities Chair: Matthew Ramsey Stephanie High-throughput analysis of targeted mutant libraries reveals new 1:00 pm Shames Legionella pneumophila effector virulence phenotypes Microbial hitchhiking promotes dispersal and colonization of new niches 1:20 pm Tahoura Samad by staphylococci Interactions between species introduce spurious associations in 1:40 pm Rajita Menon microbiome studies: evidence from inflammatory bowel disease The upper respiratory tract commensal Dolosigranulum pigrum inhibits 2:00 pm Silvio Brugger Staphylococcus aureus 2:20 pm Coffee Break II: Morphogenesis Chair: Eddie Geisinger Determining how bacteria regulate their rate of growth at the single- 2:50 pm Yingjie Sun molecule and single-cell levels by super-resolution microscopy Metabolic control of cell morphogenesis: perturbed TCA cycle halts 3:10 pm Irnov Irnov peptidoglycan biosynthesis Membrane remodeling at the division septum by the bacterial actin 3:30 pm Joseph Conti homolog FtsA 3:50 pm Kristin Little A cell envelope stress response system keeps cells in shape 4:10 pm Poster Session I - Science Center (#1-32, 60-66) III: Treatment strategies Chair: Alex Kostic Sebastien 5:30 pm BRACE for resistance: -
Microbial and Clinical Factors Are Related to Recurrence of Symptoms After Childhood Lower Respiratory Tract Infection
Early View Original article Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection Emma M. de Koff, Wing Ho Man, Marlies A. van Houten, Arine M. Vlieger, Mei Ling J.N. Chu, Elisabeth A.M. Sanders, Debby Bogaert Please cite this article as: de Koff EM, Man WH, van Houten MA, et al. Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection. ERJ Open Res 2021; in press (https://doi.org/10.1183/23120541.00939-2020). This manuscript has recently been accepted for publication in the ERJ Open Research. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJOR online. Copyright ©The authors 2021. This version is distributed under the terms of the Creative Commons Attribution Non-Commercial Licence 4.0. For commercial reproduction rights and permissions contact [email protected] Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection Emma M. de Koff1,2, Wing Ho Man1,3, Marlies A. van Houten1,4, Arine M. Vlieger5, Mei Ling J.N. Chu2, Elisabeth A.M. Sanders2,6, Debby Bogaert2,7 1. Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, Netherlands 2. Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital and University Medical Centre Utrecht, Utrecht, Netherlands 3. Department of Paediatrics, Willem-Alexander Children’s Hospital and Leiden University Medical Centre, Leiden, Netherlands 4. -
Optimizing Identification of Clinically Relevant Gram-Positive Organisms by Use of the Bruker Biotyper Matrix-Assisted Laser
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital Commons@Becker Washington University School of Medicine Digital Commons@Becker Open Access Publications 2013 Optimizing identification of clinically relevant gram-positive organisms by use of the bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system Erin McElvania TeKippe Washington University School of Medicine in St. Louis Sunni Shuey St. Louis Children's Hospital David W. Winkler St. Louis Children's Hospital Meghan A. Butler St. Louis Children's Hospital Carey-Ann Burnham Washington University School of Medicine in St. Louis Follow this and additional works at: http://digitalcommons.wustl.edu/open_access_pubs Recommended Citation McElvania TeKippe, Erin; Shuey, Sunni; Winkler, David W.; Butler, Meghan A.; and Burnham, Carey-Ann, ,"Optimizing identification of clinically relevant gram-positive organisms by use of the bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system." Journal of Clinical Microbiology.51,5. 1421-1427. (2013). http://digitalcommons.wustl.edu/open_access_pubs/2333 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Optimizing Identification of Clinically Relevant Gram-Positive Organisms by Use of the Bruker Biotyper Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry System Downloaded from Erin McElvania TeKippe, Sunni Shuey, David W. Winkler, Meghan A. Butler and Carey-Ann D. Burnham J. Clin. Microbiol. 2013, 51(5):1421. -
Bacterial Microbiota Analysis Present in the Nose and Pharynx of a Mexican Young Population
Int.J.Curr.Microbiol.App.Sci (2016) 5(6): 223-235 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 5 Number 6 (2016) pp. 223-235 Journal homepage: http://www.ijcmas.com Original Research Article http://dx.doi.org/10.20546/ijcmas.2016.506.026 Bacterial Microbiota Analysis Present in the Nose and Pharynx of a Mexican Young Population Ana Karina Rodríguez-Vicente1, Jaime Bustos-Martínez2, Dolores Reyes-Duarte3 and Teresita Sainz-Espuñes4* 1Doctorado en Ciencias Biológicas y de la Salud. Universidad Autónoma Metropolitana-Xochimilco. Mexico City, Mexico 2Departamento de Atención a la Salud. Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico 3Departamento de Procesos y Tecnología. Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico 4Departamento de Sistemas Biológicos. Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico *Corresponding author email id: ABSTRACT Culture-independent microbiota is relatively unexplored in Mexican population. The aim of this study was to characterize the microbiota of Mexican young healthy adults by means of K eywo rd s traditional culture and metagenomic analysis in order to provide novel insights and have a better understanding about the healthy baselines from which to detect differences associated Bacterial with diseases. The bacterial microbiota of the nose and pharynx from 75 healthy Microbiota, nonsmoking Mexican young adults was examined by conventional cultures and culture- Nose and independent methods. The hypervariable region (V6-V8) of the16S rRNA gene was PCR Pharynx , amplified from isolated DNA and DGGE analyzed, bands excised were sequenced and metagenomic phylogenetic analys is was done. The study showed that the bacterial microbiota of analysis . the pharynx was richer than that of the nose. -
WO 2015/071474 A2 21 May 2015 (21.05.2015) P O P C T
(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 2015/071474 A2 21 May 2015 (21.05.2015) P O P C T (51) International Patent Classification: Krzysztof; Simmeringer Hauptstrasse 45/8, A-1 110 Vi C12N 15/11 (2006.01) enna (AT). FONFARA, Ines; Helmstedter Strasse 144, 38102 Braunschweig (DE). (21) International Application Number: PCT/EP2014/074813 (74) Agent: PILKINGTON, Stephanie Joan; Potter Clarkson LLP, The Belgrave Centre, Talbot Street, Nottingham NG1 (22) International Filing Date: 5GG (GB). 17 November 2014 (17.1 1.2014) (81) Designated States (unless otherwise indicated, for every (25) Filing Language: English kind of national protection available): AE, AG, AL, AM, (26) Publication Language: English AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (30) Priority Data: DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, 61/905,835 18 November 2013 (18. 11.2013) US HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (71) Applicant: CRISPR THERAPEUTICS AG [CH/CH]; KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, Aeschenvorstadt 36, CH-4051 Basel (CH). 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, (72) Inventors: CHARPENTIER, Emmanuelle; Boeckler- SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, strasse 18, 38102 Braunschweig (DE). -
The Microbiome of the Middle Meatus in Healthy Adults
The Microbiome of the Middle Meatus in Healthy Adults Vijay R. Ramakrishnan1*, Leah M. Feazel2, Sarah A. Gitomer1, Diana Ir2, Charles E. Robertson4, Daniel N. Frank2,3 1 Department of Otolaryngology-Head and Neck Surgery, University of Colorado, Aurora, Colorado, United States of America, 2 Division of Infectious Diseases, University of Colorado, Aurora, Colorado, United States of America, 3 Microbiome Research Consortium, University of Colorado, Aurora, Colorado, United States of America, 4 Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America Abstract Rhinitis and rhinosinusitis are multifactorial disease processes in which bacteria may play a role either in infection or stimulation of the inflammatory process. Rhinosinusitis has been historically studied with culture-based techniques, which have implicated several common pathogens in disease states. More recently, the NIH Human Microbiome Project has examined the microbiome at a number of accessible body sites, and demonstrated differences among healthy and diseased patients. Recent DNA-based sinus studies have suggested that healthy sinuses are not sterile, as was previously believed, but the normal sinonasal microbiome has yet to be thoroughly examined. Middle meatus swab specimens were collected from 28 consecutive patients presenting with no signs or symptoms of rhinosinusitis. Bacterial colonization was assessed in these specimens using quantitative PCR and 16S rRNA pyrosequencing. All subjects were positive for bacterial colonization of the middle meatus. Staphylococcus aureus, Staphylococcus epidermidis and Propionibacterium acnes were the most prevalent and abundant microorganisms detected. Rich and diverse bacterial assemblages are present in the sinonasal cavity in the normal state, including opportunistic pathogens typically found in the nasopharynx. -
1 Dolosigranulum Pigrum Cooperation and Competition in Human Nasal Microbiota
bioRxiv preprint doi: https://doi.org/10.1101/678698; this version posted June 21, 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-ND 4.0 International license. 1 Dolosigranulum pigrum cooperation and competition in human nasal microbiota 2 Silvio D. Brugger1, 2, 3, 8*, Sara M. Eslami2,8, Melinda M. Pettigrew4,8, Isabel F. Escapa2,3, Matthew 3 M. Henke5, Yong Kong6 and Katherine P. Lemon2,7,9* 4 1Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 5 University of Zurich, Zurich, Switzerland, CH-8006 6 2The Forsyth Institute (Microbiology), Cambridge, MA, USA, 02142 7 3Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, 8 Boston, MA, USA, 02115 9 4Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, 10 CT, USA, 06510 11 5 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 12 Boston, MA, USA, 02115 13 6Department of Molecular Biophysics and Biochemistry and W.M. Keck Foundation 14 Biotechnology Resource Laboratory, Yale University, New Haven, CT, USA, 06519 15 7Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, 16 MA, USA, 02115 17 8These authors contributed equally 18 9Lead Contact 19 *Correspondence: [email protected] and [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/678698; this version posted June 21, 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. -
The Potential Pathogenicity of Dolosigranulum Pigrum in Multiple Sclerosis, and the Occurrence of the Organism in the Upper Respiratory Tract
The potential pathogenicity of Dolosigranulum pigrum in multiple sclerosis, and the occurrence of the organism in the upper respiratory tract by Francis Mark Jorge MSc CSci FIBMS CBiol MSB A portfolio of research and development in a professional context Submitted in partial fulfilment of the Degree of Professional Doctorate in Biomedical Science School of Pharmacy and Biomedical Sciences Faculty of Science University of Portsmouth May 2014 Abstract The bacterial toxins hypothesis in multiple sclerosis postulates that bacterial toxins from the human nasopharynx access the central nervous system and are implicated in the disease. Dolosigranulum pigrum was originally found in acute multiple sclerosis tissues. This study seeks to determine if the organism is found in human nasal tracts and explores the relationship between Dolosigranulum pigrum infection and multiple sclerosis by measuring antibody to the bacterium in multiple sclerosis patients and matched controls. Eighty eight clinical specimens were cultured onto blood agar and analysed using rabbit anti-Dolosigranulum pigrum sera, and fluorescein isothiocyanate. None tested positive for Dolosigranulum pigrum. Dolosigranulum pigrum was looked for using a novel polymerase chain reaction test. Thirty samples tested positive, 17 male, 13 female, with an age range from 8 days to 74 years. Twelve were sent for sequencing, seven matched Dolosigranulum pigrum, two showed mixed amplicons and three produced signals not matching Dolosigranulum pigrum. Sixty five multiple sclerosis sera and matched controls were tested for anti- Dolosigranulum pigrum using a novel enzyme linked immunosorbant assay. The multiple sclerosis group showed raised antibodies, significantly different to the controls, p ≤ 0.001. Fifteen of the multiple sclerosis sera and controls were Western blotted.