DOCSLIB.ORG

Supplemental Materials

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplemental Materials Supplemental Materials Fecal microbiota transfers in ulcerative colitis, a retrospective microbiome analysis Marcel A. de Leeuw & Manuel X. Duval, GeneCreek Contents SUPPLEMENTAL MATERIALS 1 SUPPLEMENTAL DATASET ................................................... 1 FMT DRIVEN CHANGE IN MICROBIOTA ............................................ 1 DONOR MICROBIOME PHENOTYPES ............................................. 1 RESPONDER AND NON-RESPONDER ASSOCIATED TAXA .................................... 2 RESPONDER ASSOCIATED SPECIES .............................................. 3 BIBLIOGRAPHY 6 List of Figures S1 Chao species richness change through FMT ......................................... 1 S2 Strict anaerobe proportion change through FMT ...................................... 1 S3 Donor microbiome assessment, data set ERP013257 ................................... 2 S4 Post-FMT class composition, non-responders ........................................ 2 S5 Post-FMT class composition, responders ........................................... 3 List of Tables S1 Profiling data sets used in the study ............................................. 1 S2 Class level taxa associated with responder and non-responder status, post FMT .................... 3 S3 Interconnected species associated with responder status, post FMT ........................... 4 S4 Additional species associated with responder status, post FMT .............................. 5 S5 Species associated with non-responder status, post FMT ................................. 6 Manuscript under review Manuscript under review Supplemental materials supplemental dataset Table S1: Profiling data sets used in the study. N: number of patients, n: number of samples, 16S: variable regions covered. BioProject SRA N n type 16S publication PRJNA450340 SRP183770 79 201 stool V4 [1] FMT driven change in microbiota Several publications have reported dysbiosis in UC is reduced through FMT. This principle is illustrated using data set SRP108284 and Chao species richness in figure 1. The improvement reaches statistical significance in the samples collected in the second week after a single FMT, but washes out subsequently in the fourth week. 0.029 200 0.0044 150 100 Chao species richness 50 Baseline Donor Week 2 Week 4 Figure S1: Chao species richness change through FMT. Data set SRP108284, 20 patients with single FMT Just like species diversity, the strict anaerobe proportion can be modified through FMT, figure 2. The two donors used in study SRP198502 were selected based on fecal butyrate concentration [2] and had a high propor- tion of strict anaerobes. 0.0032 0.013 1.6e−08 1.0 0.5 Strict anaerobe proportion Strict anaerobe 0.0 Baseline Donor FMT Placebo Figure S2: Strict anaerobe proportion change through FMT. Data set SRP198502, longitudinal randomized study with 6 FMT and 6 placebo. donor microbiome phenotypes Plotting the relation between phylogenetic diversity and oxygen tolerance for donor samples, we found these are related and separate responder and non-responder associated donors, Fig. S3. Phylogenetic diversity shows 1/6 Manuscript under review important variance around the donor means. response NR PR RE 12.5 10.0 7.5 phylogenetic diversity 5.0 −0.4 −0.3 −0.2 −0.1 oxygen tolerance Figure S3: Donor microbiome assessment, data set ERP013257. Lines connect samples from the same donor. NR: nonresponders, PR: partial responders, RE: responders. responder and non-responder associated taxa The following treemaps document the relative abundance post-FMT of classes in non-responders and responders, respectively Fig. S4 and S5. Verrucomicrobia Fusobacteria Firmicutes β-proteo bacteria Bacilli Negativicutes Erysipe Proteo lotrichia bacteria Actino γ-proteo bacteria bacteria Firmicutes Clostridia Bacteroidetes Figure S4: Post-FMT class composition, non-responders. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. 2/6 Manuscript under review Fusobacteria Erysipelo Firmicutes α-pb Verruco Bacilli β-proteo trichia Negativicutes microbia bacteria Proteo bacteria Actino γ-proteo bacteria bacteria Firmicutes Clostridia Bacteroidetes Figure S5: Post-FMT class composition, responders. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. At the class level, DESeq2 analysis detects the following post-FMT taxa as differentially abundant between non-responders and responders, Table S2 Table S2: Class level taxa associated with responder and non-responder status, post FMT. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. log2FC: og2 fold change. All taxa are pAdj<0.05. taxon log2FC association p__Spirochaetes -7.0 NR c__Lentisphaeria -6.9 NR c__Methanobacteria -2.2 NR p__Actinobacteria -2.0 NR c__Negativicutes -1.5 NR unknown 2.6 RE c__Verrucomicrobiae 2.8 RE c__Flavobacteriia 4.8 RE c__Alphaproteobacteria 5.7 RE c__Sphingobacteriia 5.7 RE responder associated species The following, esssentially gram negative, aerobic and facultative species are associated with responder status and are tightly interconnected, 3. 3/6 Manuscript under review Table S3: Interconnected species associated with responder status, post FMT. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. log2FC: og2 fold change. All taxa are pAdj<0.001. taxon class log2FC gram oxygen Corynebacterium kroppenstedtii Actinobacteria 8.5 positive anaerobe Micrococcus luteus Actinobacteria 7.3 positive aerobe Altererythrobacter dongtanensis Alphaproteobacteria 3.1 negative aerobe Brevundimonas terrae Alphaproteobacteria 9.2 negative aerobe Brevundimonas vesicularis Alphaproteobacteria 5.2 negative aerobe Hyphomicrobium zavarzinii Alphaproteobacteria 7.1 negative aerobe Mesorhizobium thiogangeticum Alphaproteobacteria 10.5 negative aerobe Methylobacterium adhaesivum Alphaproteobacteria 7.1 negative aerobe Methylobacterium populi Alphaproteobacteria 10.8 negative aerobe Rubellimicrobium thermophilum Alphaproteobacteria 10.4 negative aerobe Sphingobium subterraneum Alphaproteobacteria 10.6 negative aerobe Sphingomonas kwangyangensis Alphaproteobacteria 9.6 negative aerobe Sphingomonas melonis Alphaproteobacteria 7.1 negative aerobe Sphingopyxis ginsengisoli Alphaproteobacteria 11.9 negative aerobe Xanthobacter autotrophicus Alphaproteobacteria 8.1 negative facultative Staphylococcus epidermidis Bacilli 5.2 positive facultative Delftia tsuruhatensis Betaproteobacteria 3.2 negative aerobe Limnobacter thiooxidans Betaproteobacteria 6.6 negative obligate aerobe Massilia timonae Betaproteobacteria 7.1 negative aerobe Methyloversatilis universalis Betaproteobacteria 3.9 negative facultative Piscinibacter aquaticus Betaproteobacteria 5.5 negative facultative Ralstonia pickettii Betaproteobacteria 10.5 negative aerobe Sphaerotilus natans Betaproteobacteria 8.4 negative facultative Acinetobacter calcoaceticus Gammaproteobacteria 5.2 negative aerobe Acinetobacter johnsonii Gammaproteobacteria 9.6 negative aerobe Acinetobacter junii Gammaproteobacteria 6.8 negative microaerophile Acinetobacter lwoffii Gammaproteobacteria 8.9 negative facultative Methylomonas methanica Gammaproteobacteria 8.7 negative aerobe Pseudomonas aeruginosa Gammaproteobacteria 11.1 negative facultative Pseudomonas fluorescens Gammaproteobacteria 7.6 negative aerobe Pseudomonas putida Gammaproteobacteria 5.7 negative aerobe Stenotrophomonas maltophilia Gammaproteobacteria 13.1 negative aerobe Sediminibacterium goheungense Sphingobacteriia 9.1 negative aerobe Additional species, more loosely interconnected are associated with responder status, table 4. 4/6 Manuscript under review Table S4: Additional species associated with responder status, post FMT. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. log2FC: og2 fold change. All taxa are pAdj<0.001. taxon class log2FC gram oxygen Gordonibacter urolithinfaciens Actinobacteria 6.3 positive anaerobe Abiotrophia defectiva Bacilli 9.6 positive facultative Lactobacillus algidus Bacilli 7.3 positive microaerophile Lactobacillus mucosae Bacilli 3.5 positive anaerobe Staphylococcus simulans Bacilli 7.2 positive facultative Bacteroides rodentium Bacteroidia 14.2 negative anaerobe Parabacteroides goldsteinii Bacteroidia 11.7 negative obligate anaerobe Porphyromonas catoniae Bacteroidia 5.2 negative anaerobe Porphyromonas uenonis Bacteroidia 7.5 negative obligate anaerobe Prevotella buccae Bacteroidia 5.0 negative anaerobe Neisseria flavescens Betaproteobacteria 3.7 negative aerobe Oxalobacter formigenes Betaproteobacteria 10.2 negative anaerobe Eubacterium infirmum Clostridia 7.0 positive anaerobe Oribacterium asaccharolyticum Clostridia 6.7 positive anaerobe Oscillibacter ruminantium Clostridia 10.4 negative anaerobe Peptoniphilus lacrimalis Clostridia 5.7 positive anaerobe Ruminococcus champanellensis Clostridia 4.2 positive anaerobe Leptotrichia trevisanii Fusobacteriia 8.3 negative aerobe Haemophilus influenzae Gammaproteobacteria 9.9 negative microaerophile Dialister invisus Negativicutes 3.2 positive anaerobe Dialister propionicifaciens Negativicutes 5.3 negative anaerobe Negativicoccus succinicivorans Negativicutes 8.5 negative microaerophile A large number of mostly non-connected species are associated with non-responder status, table 5. 5/6 Manuscript under review Table S5: Species associated with non-responder status, post FMT. Combined data set ERP013257, SRP135559, ERP116682 and SRP102742. log2FC: og2 fold change. All taxa are pAdj<0.001. taxon log2FC | taxon log2FC Acidaminococcus fermentans -3.51 Hungatella hathewayi -3.59 Actinomyces lingnae -6.05 Lactobacillus fermentum
Load more

Recommended publications
  • Helicobacter Pylori Infection and Its Potential Association with Idiopathic
    Journal of Immunology and Infectious Diseases Volume 2 | Issue 2 ISSN: 2394-6512 Research Article Open Access Helicobacter pylori Infection and its Potential Association with Idiopathic Hypercalciuric Urolithiasis in Pediatric Patients Ali AM*1, Abdelaziz SS2 and Elkhatib WF3,4 1Department of Pediatrics, International Islamic Center for Population Studies and Research, Faculty of Medicine, Al-Azhar University, Cairo, Egypt 2Department of Urology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt 3Department of Microbiology & Immunology, Faculty of Pharmacy, Ain Shams University, African Union Organization St. Abbassia, Cairo, Egypt 4Department of Pharmacy Practice, School of Pharmacy, Hampton University, Kittrell Hall Hampton, Virginia, USA *Corresponding author: Ali AM, Department of Pediatrics, Faculty of Medicine, Al-Azhar University, Cairo, Egypt, Postal Code: 31991, Dr. Noor Mohammad Khan General Hospital, Fax: +966713221417, Tel: +966556847829, E-mail: [email protected] Citation: Ali AM, Abdelaziz SS, Elkhatib WF (2014) Helicobacter pylori Infection and its Potential Association with Idiopathic Hypercalciuric Urolithiasis in Pediatric Patients. J Immunol Infect Dis 2(2): 202. doi: 10.15744/2394-6512.1.203 Received Date: September 24, 2014 Accepted Date: January 05, 2015 Published Date: January 09, 2015 Abstract Objectives: To evaluate the role of Helicobacter pylori infection in the pathogenesis of idiopathic hypercalciuric urolithiasis. Design & Setting: Randomized longitudinal controlled study was carried out at Al-Azhar University Hospitals in Cairo and Dommiat, Egypt as well as at Noor Khan General Hospital in Hafer Al-Baten, Saudi Arabia. Participants: A total of 150 patients categorized into 100 cases (urolithiasis-positive) with urinary stone disease, aged from 5 to 18 years, and met the characteristics of idiopathic urolithiasis in children as well as 50 controls (urolithiasis-negative) that had relatively similar demographic criteria except for idiopathic urolithiasis.
    [Show full text]
  • WO 2015/066625 Al 7 May 2015 (07.05.2015) 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 2015/066625 Al 7 May 2015 (07.05.2015) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/04 (2006.01) G01N 33/15 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/US2014/06371 1 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, 3 November 20 14 (03 .11.20 14) KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (25) Filing Language: English PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, (26) Publication Language: English 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. (30) Priority Data: 61/898,938 1 November 2013 (01. 11.2013) (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicant: WASHINGTON UNIVERSITY [US/US] GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, One Brookings Drive, St.
    [Show full text]
  • BD-CS-057, REV 0 | AUGUST 2017 | Page 1
    EXPLIFY RESPIRATORY PATHOGENS BY NEXT GENERATION SEQUENCING Limitations Negative results do not rule out viral, bacterial, or fungal infections. Targeted, PCR-based tests are generally more sensitive and are preferred when specific pathogens are suspected, especially for DNA viruses (Adenovirus, CMV, HHV6, HSV, and VZV), mycobacteria, and fungi. The analytical sensitivity of this test depends on the cellularity of the sample and the concentration of all microbes present. Analytical sensitivity is assessed using Internal Controls that are added to each sample. Sequencing data for Internal Controls is quantified. Samples with Internal Control values below the validated minimum may have reduced analytical sensitivity or contain inhibitors and are reported as ‘Reduced Analytical Sensitivity’. Additional respiratory pathogens to those reported cannot be excluded in samples with ‘Reduced Analytical Sensitivity’. Due to the complexity of next generation sequencing methodologies, there may be a risk of false-positive results. Contamination with organisms from the upper respiratory tract during specimen collection can also occur. The detection of viral, bacterial, and fungal nucleic acid does not imply organisms causing invasive infection. Results from this test need to be interpreted in conjunction with the clinical history, results of other laboratory tests, epidemiologic information, and other available data. Confirmation of positive results by an alternate method may be indicated in select cases. Validated Organisms BACTERIA Achromobacter
    [Show full text]
  • Title: Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients Wellinton M. Do Nasci
    medRxiv preprint doi: https://doi.org/10.1101/2020.12.07.20245530; this version posted December 8, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Title: Gut microbiome profiles and associated metabolic pathways in HIV-infected treatment-naïve patients Wellinton M. do Nascimento1,2, Aline Machiavelli2, Luiz G. E. Ferreira3, Luisa Cruz Silveira1, Suwellen S. D. de Azevedo4, Gonzalo Bello4, Daniel P. Smith5, Melissa P. Mezzari5, Joseph Petrosino5, Rubens Tadeu Delgado Duarte6, Carlos R. Zaráte- Bládes2§*, and Aguinaldo R. Pinto1* 1 Laboratório de Imunologia Aplicada, LIA, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, Florianópolis, SC, 88034-040, Brazil. 2 Laboratório de Imunoregulação, iREG, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, Florianópolis, SC, 88034-040, Brazil. 3 Hospital Regional Homero de Miranda Gomes, Rua Adolfo Donato da Silva, s/n, São José, SC, 88103-901, Brazil. 4 Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro, RJ, 21045-900, Brazil. 5 Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, United States. 6 Laboratório de Ecologia Molecular e Extremófilos, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Campus Universitário da Trindade, Florianópolis, SC, 88034-040, Brazil. *contributed equally to this work NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
    [Show full text]
  • Studies on Oral Colonization of Periodontopathogenic Bacterium
    Studies on oral colonization of periodontopathogenic bacterium Eikenella corrodens 㸦ṑ࿘⑓ཎᛶ⣽⳦ (LNHQHOODFRUURGHQV ࡢཱྀ⭍ෆᐃ╔࡟㛵ࡍࡿ◊✲㸧 㻌 㻌 FARIHA JASIN MANSUR 2017 㻌 㻌 DEDICATED TO MY BELOVED PARENTS CONTENTS CONTENTS…………………………………………………………. 1 LIST OF ABBREVIATIONS ……………………………………. 2 CHAPTER 1: GENERAL INTRODUCTION …………………………………... 4 CHAPTER 2 .………………………………………………………. 11 2.1 ABSTRACT ……………………………………………………. 12 2.2 INTRODUCTION ……………………………………………... 13 2.3 MATERIALS AND METHODS ……………………………… 16 2.4 RESULTS AND DISCUSSION ……………………………….. 21 CHAPTER 3 ………………………………………………………... 31 3.1 ABSTRACT …………………………………………………….. 32 3.2 INTRODUCTION ……………………………………………… 33 3.3 MATERIALS AND METHODS ………………………………. 35 3.4 RESULTS AND DISCUSSION ………………………………... 38 CHAPTER 4: GENERAL CONCLUSION ………………………………………... 44 SUMMARY ………………………………………………………….. 50 JAPANESE SUMMARY ……………………………………………. 52 ACKNOWLEDGEMENTS …………………………………………. 54 REFERENCES ……………………………………………………….. 56 LIST OF PUBLICATIONS ………………………………………….. 65 㻝㻌 㻌 LIST OF ABBREVIATIONS CE Cell envelope GalNAc㻌㻌㻌㻌㻌㻌 N-acetyl-D-galactosamine g Gram g/L Gram/litre HA㻌㻌㻌㻌㻌㻌㻌㻌 Hemagglutination ∆hlyA hlyA-deficient strain H hour IL Interleukin IPTG Isopropyl β-D-1-thiogalactopyranoside LB㻌 㻌 㻌 㻌 Luria broth M Molar mM Milimolar min Minute mL Mililitre mg/mL Milligram/mililitre NaCl Sodium chloride ORF Open reading frame PBS Phosphate-buffered saline㻌 PCR Polymerase chain reaction pH㻌㻌 㻌 㻌㻌㻌㻌㻌㻌㻌Potential of hydrogen SDS–PAGE Sodium dodecyl sulfate polyacrylamide gel electrophoresis TSB Tryptic soy broth 㻞㻌 㻌 μL Microlitre μM Micromolar
    [Show full text]
  • Robust Taxonomic Classification of Uncharted Microbial Sequences and Bins with CAT and BAT
    bioRxiv preprint doi: https://doi.org/10.1101/530188; this version posted January 24, 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. Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT F.A. Bastiaan von Meijenfeldt1,†, Ksenia Arkhipova1,†, Diego D. Cambuy1, Felipe H. Coutinho2,3, Bas E. Dutilh1,2,* 1 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, The Netherlands. 2 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands. 3 Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. * To whom correspondence should be addressed. Tel: +31 30 253 4212; Email: [email protected]. † These authors contributed equally to this work. Present Address: [Felipe H. Couthinho], Evolutionary Genomics Group, Departamento de Produccíon y Microbiología, Universidad Miguel Hernández, Campus San Juan, San Juan, Alicante 03550, Spain. ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) of unknown microorganisms. We show that the standard best-hit approach often leads to classifications that are too specific. We present tools to classify high- quality metagenomic contigs (Contig Annotation Tool, CAT) and MAGs (Bin Annotation Tool, BAT) and thoroughly benchmark them with simulated metagenomic sequences that are classified against a reference database where related sequences are increasingly removed, thereby simulating increasingly unknown queries. We find that the query sequences are correctly classified at low taxonomic ranks if closely related organisms are present in the reference database, while classifications are made higher in the taxonomy when closely related organisms are absent, thus avoiding spurious classification specificity.
    [Show full text]
  • Uncommon Pathogens Causing Hospital-Acquired Infections in Postoperative Cardiac Surgical Patients
    Published online: 2020-03-06 THIEME Review Article 89 Uncommon Pathogens Causing Hospital-Acquired Infections in Postoperative Cardiac Surgical Patients Manoj Kumar Sahu1 Netto George2 Neha Rastogi2 Chalatti Bipin1 Sarvesh Pal Singh1 1Department of Cardiothoracic and Vascular Surgery, CN Centre, All Address for correspondence Manoj K Sahu, MD, DNB, Department India Institute of Medical Sciences, Ansari Nagar, New Delhi, India of Cardiothoracic and Vascular Surgery, CTVS office, 7th floor, CN 2Infectious Disease, Department of Medicine, All India Institute of Centre, All India Institute of Medical Sciences, New Delhi-110029, Medical Sciences, Ansari Nagar, New Delhi, India India (e-mail: [email protected]). J Card Crit Care 2020;3:89–96 Abstract Bacterial infections are common causes of sepsis in the intensive care units. However, usually a finite number of Gram-negative bacteria cause sepsis (mostly according to the hospital flora). Some organisms such as Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus are relatively common. Others such as Stenotrophomonas maltophilia, Chryseobacterium indologenes, Shewanella putrefaciens, Ralstonia pickettii, Providencia, Morganella species, Nocardia, Elizabethkingia, Proteus, and Burkholderia are rare but of immense importance to public health, in view of the high mortality rates these are associated with. Being aware of these organisms, as the cause of hospital-acquired infections, helps in the prevention, Keywords treatment, and control of sepsis in the high-risk cardiac surgical patients including in ► uncommon pathogens heart transplants. Therefore, a basic understanding of when to suspect these organ- ► hospital-acquired isms is important for clinical diagnosis and initiating therapeutic options. This review infection discusses some rarely appearing pathogens in our intensive care unit with respect to ► cardiac surgical the spectrum of infections, and various antibiotics that were effective in managing intensive care unit these bacteria.
    [Show full text]
  • ( Eikenella Corrodens のクオラムセンシングと バイオフィルム形成の関連性に関する研究）
    Studies on the relationship between quorum sensing and biofilm formation of Eikenella corrodens ( Eikenella corrodens のクオラムセンシングと バイオフィルム形成の関連性に関する研究） by MOHAMMAD MINNATUL KARIM Thesis Submitted to the United Graduate School of Agricultural Sciences Tottori University, Japan In partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY (PhD) The United Graduate School of Agricultural Sciences Tottori University, Japan September, 2013 1 DEDICATED TO MY BELOVED PARENTS 2 CONTENTS CONTENTS...............................................................................................ⅰ LIST OF ABBREVIATIONS...................................................................ⅱ GENERAL INTRODUCTION................................................................. 1 OBJECTIVES........................................................................................... 10 CHAPTER 1 ............................................................................................. 11 The Periodontopathogenic Bacterium Eikenella corrodens Produces an Autoinducer-2-Inactivating Enzyme 1.1 ABSTRACT ………………………………………………………… 12 1.2 INTRODUCTION …………………………………………………....13 1.3 MATERIALS AND METHODS ……………………………………..15 1.4 RESULTS …………………………………………………………… 19 1.5 DISCUSSION ………………………………………………………. 22 1.6 FIGURES …………………………………………………………….25 CHAPTER 2 …………………………………………………………… 32 LuxS affects biofilm maturation and detachment of the periodontopathogenic bacterium Eikenella corrodens 2.1 ABSTRACT …………………………………………………………. 33 2.2 INTRODUCTION …………………………………………………....34
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • Antibiotic Use Guidelines for Companion Animal Practice (2Nd Edition) Iii
    ii Antibiotic Use Guidelines for Companion Animal Practice (2nd edition) iii Antibiotic Use Guidelines for Companion Animal Practice, 2nd edition Publisher: Companion Animal Group, Danish Veterinary Association, Peter Bangs Vej 30, 2000 Frederiksberg Authors of the guidelines: Lisbeth Rem Jessen (University of Copenhagen) Peter Damborg (University of Copenhagen) Anette Spohr (Evidensia Faxe Animal Hospital) Sandra Goericke-Pesch (University of Veterinary Medicine, Hannover) Rebecca Langhorn (University of Copenhagen) Geoffrey Houser (University of Copenhagen) Jakob Willesen (University of Copenhagen) Mette Schjærff (University of Copenhagen) Thomas Eriksen (University of Copenhagen) Tina Møller Sørensen (University of Copenhagen) Vibeke Frøkjær Jensen (DTU-VET) Flemming Obling (Greve) Luca Guardabassi (University of Copenhagen) Reproduction of extracts from these guidelines is only permitted in accordance with the agreement between the Ministry of Education and Copy-Dan. Danish copyright law restricts all other use without written permission of the publisher. Exception is granted for short excerpts for review purposes. iv Foreword The first edition of the Antibiotic Use Guidelines for Companion Animal Practice was published in autumn of 2012. The aim of the guidelines was to prevent increased antibiotic resistance. A questionnaire circulated to Danish veterinarians in 2015 (Jessen et al., DVT 10, 2016) indicated that the guidelines were well received, and particularly that active users had followed the recommendations. Despite a positive reception and the results of this survey, the actual quantity of antibiotics used is probably a better indicator of the effect of the first guidelines. Chapter two of these updated guidelines therefore details the pattern of developments in antibiotic use, as reported in DANMAP 2016 (www.danmap.org).
    [Show full text]
  • 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.
    [Show full text]