DOCSLIB.ORG

Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Loyola University Chicago Loyola eCommons Dissertations Theses and Dissertations 2019 Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle Travis Kyle Price Follow this and additional works at: https://ecommons.luc.edu/luc_diss Part of the Microbiology Commons Recommended Citation Price, Travis Kyle, "Assessing the Temporal Dynamics of the Lower Urinary Tract Microbiota and the Effects of Lifestyle" (2019). Dissertations. 3367. https://ecommons.luc.edu/luc_diss/3367 This Dissertation is brought to you for free and open access by the Theses and Dissertations at Loyola eCommons. It has been accepted for inclusion in Dissertations by an authorized administrator of Loyola eCommons. For more information, please contact [email protected]. This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License. Copyright © 2019 Travis Kyle Price LOYOLA UNIVERSITY CHICAGO ASSESSING THE TEMPORAL DYNAMICS OF THE LOWER URINARY TRACT MICROBIOTA AND THE EFFECTS OF LIFESTYLE A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY PROGRAM IN MICROBIOLOGY AND IMMUNOLOGY BY TRAVIS KYLE PRICE CHICAGO, IL MAY 2019 i Copyright by Travis Kyle Price, 2019 All Rights Reserved ii ACKNOWLEDGMENTS I would like to thank everyone that made this thesis possible. First and foremost, I want to thank Dr. Alan Wolfe. I could not have asked for a better mentor. I don’t think there will ever be another period of my life where I grow as a scientist, as a professional, or as a person more than I did under your mentorship. I am forever grateful for that. I want to thank my committee members. My committee chair, Dr. Katherine Knight, for always pushing me to achieve my best and helping shape me into the professional scientist that I am now. Dr. Karen Visick, for always providing insightful comments and thinking and caring about my research as if it was your own. Dr. Qunfeng Dong, for your vast knowledge of bioinformatics and your wonderful input on the research. Dr. Amanda Harrington, for providing the vital perspective of a clinical microbiologist on my work and going out of your way to help me with career aspirations. And to Dr. Elizabeth Mueller, for your amazing leadership of your clinical team, without which, none of this would be possible, and for somehow always finding the time to help me in any way that you could. I want to thank all of my fellow lab members throughout my time in the lab, particularly Evann Hilt and Dr. Krystal Thomas-White; what we accomplished together was incredible. I will always compare my co-workers to your level of excellence. And I am incredibly excited to continue my career journey with Evann at UCLA. None of this work would be possible without Dr. Meghan Pearce, who laid the foundation for the microbiome projects, Roberto Limeira, who’s skills and overall commitment to the lab were vital, and Thomas Halverson, whose hard-work iii and dedication has helped more than you can realize. I want to thank all of the other lab members that I had the pleasure of working with: Dr. Bob Davis, Dr. Dave Christiansen, Bozena Zemaitaitis, Giuseppe Pistone, Danielle Johansen, Katie Diebel, Cesar Montelongo-Hernandez, Dr. Michelle Van Kuiken-Johnson, Dr. Petar Bajic, Dr. Ryan Dornbier, Baylie Hochstedler, Sarah Fied, Nancy Sloan, Omar Abdel-Rahim, Brian Choi, Michael Bochert, Tom Bank, and Dr. Vibha Ahuja. You all helped make a stressful time in my life easier and more enjoyable. I also want to thank the entire Loyola Education and Research Collaborative (LUEREC). In the future, I will undoubtably compare every team that I work with to LUEREC, and I doubt that I will ever find a more talented, dedicated, and all-around enjoyable team of team of people to work with. From our amazingly productive meetings, to our amazingly entertaining karaoke at AUGS each year, it has truly been a memorable experience. Specifically, I want to thank the wonderful urogynecology fellows that I had the pleasure of working with including Dr. Susanne Taege, Dr. Megan Shannon, Dr. Brandon Chen, and in particular Dr. Tanaka Dune for your hard- work and great collaboration. I also want to individually thank Dr. Birte Wolff. We put in so much time and effort into the studies detailed in this thesis. You made what should have been a very stressful process into a fun and productive one. I want to thank the current and former urogynecology and urology professors for their leadership, knowledge, and commitment: Dr. Cynthia Brincat, Dr. Larissa Bresler, Dr. Colleen Fitzgerald, and Dr. Thythy Pham. In particular, Dr. Linda Brubaker for your clinical knowledge and passion for the research. Lastly, I want to thank Mary Tulke, who easily does the work of three people and still finds time to help me whenever I need it. iv I want to thank Dr. Catherine Putonti and her unbelievably hard-working lab. The collaboration with your lab has been incredibly productive and I personally want to thank you, Carine Mores, and Dr. Jason Shapiro for all your help with the genomic analyses in this thesis. I also want to thank the entire clinical microbiology team past and present. In particular Violet Rekasius, Joyce Tjhio, Kathy McKinley, and Sharon Desjarlais. Working with you all and seeing your passion for the field of clinical microbiology has had such a strong influence on my life and my career choices. Thank you for always being there to help or have a quick chat. I want to specially thank D. Paul Schreckenberger. You had an amazing ability to make anyone feel confident in themselves. Your passion for clinical microbiology will always be an inspiration to me. I wish that the time I knew you could have been much longer. Finally, I would like to thank my friends and family for all of their support. In particular, Jon for sticking by my side during one of the most stressful and demanding periods of my life. v TABLE OF CONTENTS ACKNOWLEDGMENTS iii LIST OF TABLES x LIST OF FIGURES xiii LIST OF ABBREVIATIONS xvi ABSTRACT xix CHAPTER I: INTRODUCTION AND LITERATURE REVIEW 1 The Human Microbiota 1 The Role of the Human Microbiota 2 Measuring the Microbiome 3 Analyzing Microbiome Data 5 “Urine Denial”: The Concept of Bladder Sterility 7 The Discovery of the Female Urinary Microbiota and Microbiome 9 Urine is Not Sterile: Now What? 13 Correlations with Health and Disease 16 Description of Urinary Bacterial Isolates 21 Other Urinary Microorganisms 25 Description of the Male Urinary Microbiota 25 Correlations with Health and Disease 28 Correlations with Lifestyle and Preliminary Measures of Stability 30 Differences between the Male and Female Urinary Microbiota 31 The Microbiome is Shaped by Environment 31 The GI Microbiota and Lifestyle 33 Description of GI Tract Physiology 33 Correlations between the GI Microbiota and Lifestyle 34 Temporal Dynamics of the GI Microbiota 36 The Vaginal Microbiota and Lifestyle 39 Description of Vaginal Tract Physiology 39 Correlations between the Vaginal Microbiota, BV Risk, and Lifestyle 40 Temporal Dynamics of the Vaginal Microbiota 41 UTI Risk and Lifestyle 44 Current Understanding of UTI and an Overview of Risk Factors 44 vi Probiotics and UTI Risk 45 Correlations between UTI Risk and Lifestyle 47 Correlations between UTI Risk and Urine Properties 53 Longitudinal Assessment of the Lower Urinary Tract Microbiota 54 Rational and Problems 55 What Specimen to Collect? 56 Preliminary Findings 63 Summary 64 CHAPTER II: MATERIALS AND METHODS 67 Overview of Clinical Studies 67 MAGnUM Study 68 ProFUM Study 70 PARTNER Study 76 Bacterial Identification Methods 80 Specimen Collection 80 Expanded Culture Protocol 81 16S Sequencing Protocol 82 Dipstick Urinalysis 85 Storage of Bacterial Isolates 85 Statistical Analyses 85 Whole Genome Sequencing 86 DNA Extraction and Library Prep 86 Assembly and Annotation 87 Bacterial Assays: Experimental Procedures 88 Bacterial Strains and Growth Conditions 88 Urothelial Cell Adherence Assays 93 Biofilm Assays 94 Growth Competition Assays 95 CHAPTER III: FEASIBILITY PROJECT: MAGnUM STUDY 96 Overview of MAGnUM Study 96 Longitudinal Assessment of the Microbiota of the Male LUT 96 Longitudinal Assessment of the Microbiota of the Female LUT 100 Summary 106 CHAPTER IV: EFFECT OF INTRINSIC LIFESTYLE FACTORS ON LUT MICROBIOTA 109 Overview of ProFUM Study 109 Screening Eligible Participants 109 vii ProFUM Specimen Integrity 112 Qualitative Description of the Longitudinal LUT Microbiota and Microbiome 115 Measuring the Overall Stability of the LUT Microbiota 122 Menstruation and LUT Microbiota Variability 125 Urine Properties and Constituents and LUT Microbiota Variability 138 Summary 143 CHAPTER V: EFFECT OF EXTRINSIC LIFESTYLE FACTORS ON LUT MICROBIOTA 147 Sexual Activity and LUT Microbiota Variability 147 Hygiene and LUT Microbiota Variability 159 Oral Probiotics and LUT Microbiota Variability 163 Summary 165 CHAPTER VI: MECHANISTIC DETERMINATION AND SIGNIFICANCE OF LUT MICROBIOTA VARIABILITY AND VAGINAL INTERCOURSE 168 Introduction and Rationale 168 Assessing the Clinical Significance of LUT Microbiota Variability Following Vaginal Intercourse 170 Effect of Urinary Isolates on UPEC Adherence to Urothelial Cells 170 Effect of Urinary Isolates on UPEC Biofilm Formation 172 Effect of Urinary Isolates on UPEC Growth 175 Assessing the Ability of Urinary Isolates to Adhere to Urothelial Cells 181 Assessing the Biological Significance of LUT Microbiota Variability Following Vaginal Intercourse 183 Overview of PARTNER
Recommended publications
  • Downloaded Skin Zaka Electronic Gmbh, Cologne, Germany)

    Downloaded Skin Zaka Electronic Gmbh, Cologne, Germany)

    Li et al. Microbiome (2021) 9:47 https://doi.org/10.1186/s40168-020-00995-7 RESEARCH Open Access Characterization of the human skin resistome and identification of two microbiota cutotypes Zhiming Li1,2†, Jingjing Xia3,4,5†, Liuyiqi Jiang3†, Yimei Tan4,6†, Yitai An1,2, Xingyu Zhu4,7, Jie Ruan1,2, Zhihua Chen1,2, Hefu Zhen1,2, Yanyun Ma4,7, Zhuye Jie1,2, Liang Xiao1,2, Huanming Yang1,2, Jian Wang1,2, Karsten Kristiansen1,2,8, Xun Xu1,2,9, Li Jin4,10, Chao Nie1,2*, Jean Krutmann4,5,11*, Xiao Liu1,12,13* and Jiucun Wang3,4,10,14* Abstract Background: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity. Results: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures.
  • Neonatal Septicemia Caused by a Rare Pathogen: Raoultella Planticola

    Neonatal Septicemia Caused by a Rare Pathogen: Raoultella Planticola

    Chen et al. BMC Infectious Diseases (2020) 20:676 https://doi.org/10.1186/s12879-020-05409-5 CASE REPORT Open Access Neonatal septicemia caused by a rare pathogen: Raoultella planticola - a report of four cases Xianrui Chen1,2,3, Shaoqing Guo1,2,3* , Dengli Liu1,2,3 and Meizhen Zhong1,2,3 Abstract Background: Raoultella planticola(R.planticola) is a very rare opportunistic pathogen and sometimes even associated with fatal infection in pediatric cases. Recently,the emergence of carbapenem resistance strains are constantly being reported and a growing source of concern for pediatricians. Case presentation: We reported 4 cases of neonatal septicemia caused by Raoultella planticola. Their gestational age was 211 to 269 days, and their birth weight was 1490 to 3000 g.The R. planticola infections were detected on the 9th to 27th day after hospitalizationandoccuredbetweenMayandJune.They clinically manifested as poor mental response, recurrent cyanosis, apnea, decreased heart rate and blood oxygen, recurrent jaundice, fever or nonelevation of body temperature. The C-reactive protein and procalcitonin were elevated at significantly in the initial phase of the infection,and they had leukocytosis or leukopenia. Prior to R.planticola infection,all of them recevied at least one broad-spectrum antibiotic for 7- 27d.All the R.planticola strains detected were only sensitive to amikacin, but resistant to other groups of drugs: cephalosporins (such as cefazolin, ceftetan,etc) and penicillins (such as ampicillin-sulbactam,piperacillin, etc),and even developed resistance to carbapenem. All the infants were clinically cured and discharged with overall good prognosis. Conclusion: Neonatal septicemia caused by Raoultella planticola mostly occured in hot and humid summer, which lack specific clinical manifestations.
  • 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

    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
  • CTX-M-9 Group ESBL-Producing Raoultella Planticola Nosocomial

    CTX-M-9 Group ESBL-Producing Raoultella Planticola Nosocomial

    Tufa et al. Ann Clin Microbiol Antimicrob (2020) 19:36 https://doi.org/10.1186/s12941-020-00380-0 Annals of Clinical Microbiology and Antimicrobials CASE REPORT Open Access CTX-M-9 group ESBL-producing Raoultella planticola nosocomial infection: frst report from sub-Saharan Africa Tafese Beyene Tufa1,2,3*† , Andre Fuchs2,3†, Torsten Feldt2,3, Desalegn Tadesse Galata1, Colin R. Mackenzie4, Klaus Pfefer4 and Dieter Häussinger2,3 Abstract Background: Raoultella are Gram-negative rod-shaped aerobic bacteria which grow in water and soil. They mostly cause nosocomial infections associated with surgical procedures. This case study is the frst report of a Raoultella infec- tion in Africa. Case presentation We report a case of a surgical site infection (SSI) caused by Raoultella planticola which developed after caesarean sec- tion (CS) and surgery for secondary small bowel obstruction. The patient became febrile with neutrophilia (19,157/µL) 4 days after laparotomy and started to develop clinical signs of a SSI on the 8 th day after laparotomy. The patient con- tinued to be febrile and became critically ill despite empirical treatment with ceftriaxone and vancomycin. Raoultella species with extended antimicrobial resistance (AMR) carrying the CTX-M-9 β-lactamase was isolated from the wound discharge. Considering the antimicrobial susceptibility test, ceftriaxone was replaced by ceftazidime. The patient recovered and could be discharged on day 29 after CS. Conclusions: Raoultella planticola was isolated from an infected surgical site after repeated abdominal surgery. Due to the infection the patient’s stay in the hospital was prolonged for a total of 4 weeks. It is noted that patients under- going surgical and prolonged inpatient treatment are at risk for infections caused by Raoultella.
  • Evaluation of MALDI Biotyper for Identification of Taylorella Equigenitalis and Taylorella Asinigenitalis Kristina Lantz Iowa State University

    Evaluation of MALDI Biotyper for Identification of Taylorella Equigenitalis and Taylorella Asinigenitalis Kristina Lantz Iowa State University

    Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis Kristina Lantz Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons, and the Veterinary Medicine Commons Recommended Citation Lantz, Kristina, "Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis" (2017). Graduate Theses and Dissertations. 16520. https://lib.dr.iastate.edu/etd/16520 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Evaluation of MALDI Biotyper for identification of Taylorella equigenitalis and Taylorella asinigenitalis by Kristina Lantz A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Veterinary Microbiology Program of Study Committee: Ronald Griffith, Major Professor Steve Carlson Matthew Erdman Timothy Frana The student author and the program of study committee are solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit
  • Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis

    Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis

    Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method.
  • How Are Gene Sequence Analyses Modifying Bacterial Taxonomy? the Case of Klebsiella

    How Are Gene Sequence Analyses Modifying Bacterial Taxonomy? the Case of Klebsiella

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Hemeroteca Cientifica Catalana REVIEW ARTICLE INTERNATIONAL MICROBIOLOGY (2004) 7:261-268 www.im.microbios.org Julio Martínez1 How are gene sequence Lucía Martínez1,2 Mónica Rosenblueth1 analyses modifying Jesús Silva3 Esperanza Martínez-Romero1* bacterial taxonomy? The case of Klebsiella 1 Genomic Science Center, National University of México (UNAM), Cuernavaca, Mexico 2Research Center of Biological Summary. Bacterial names are continually being changed in order to and Medical Sciences, Faculty of Medicine more adequately describe natural groups (the units of microbial diversity) and Surgery, Autonomous University and their relationships. The problems in Klebsiella taxonomy are illustra- Benito Juárez, Oaxaca, Mexico tive and common to other bacterial genera. Like other bacteria, Klebsiella 3National Institute of Public Health, spp. were isolated long ago, when methods to identify and classify bacte- Cuernavaca, Mexico ria were limited. However, recently developed molecular approaches have led to taxonomical revisions in several cases or to sound proposals of novel species. [Int Microbiol 2004; 7(4):261-268] Received 30 September 2004 Accepted 20 October 2004 Key words: Klebsiella · Enterobacteria · pathogenic bacteria · species *Corresponding author: concept · bacterial taxonomy · phylogeny E. Martínez-Romero Centro de Ciencias Genómicas, UNAM Apdo. Postal 565-A Cuernavaca, Morelos, México Tel. 52-7773131697. Fax 52-7773135581 E-mail: [email protected] which ammonium is produced from gaseous dinitrogen. Introduction Klebsiella variicola may also serve as a model to define a bacterial species (see below). Although Klebsiella species are Historically, the classification of Klebsiella species, like that widely distributed in water, soil, and plants as well as in of many other bacteria, was based on their pathogenic fea- sewage water, it is the human pathogens that have rendered tures or origin.
  • Bioresource Technology 100 (2009) 68–73

    Bioresource Technology 100 (2009) 68–73

    Bioresource Technology 100 (2009) 68–73 Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Proteolytic activity in stored aerobic granular sludge and structural integrity Sunil S. Adav a, Duu-Jong Lee a,*, Juin-Yih Lai b a Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan b Department of Chemical Engineering, R&D Center of Membrane Technology, Chung Yuan Christian University, Chungli 32023, Taiwan article info abstract Article history: Aerobic granules lose stability during storage. The goal of this work was to highlight the main cause of Received 13 April 2008 stability loss for stored granules as intracellular protein hydrolysis. The quantity of extracellular proteins Received in revised form 24 May 2008 was noted to be significantly lower during granule storage, and protease enzyme activities were corre- Accepted 27 May 2008 spondingly higher in the cores of stored granules. The proteolytic bacteria, which secrete highly active Available online 9 July 2008 protease enzymes, were for the first time isolated and characterized by analyzing 16S rDNA sequences. The proteolytic bacteria belonged to the genera Pseudomonas, Raoultella, Acinetobacter, Pandoraea, Klebsi- Keywords: ella, Bacillus and uncultured bacterium, and were grouped into Proteobacteria, Enterobacteria and Firmi- Aerobic granules cutes. The PB1 (Pseudomonas aeruginosa) strain, which exhibited very high proteolytic activity during the Protease Proteolytic bacteria skim milk agar test, was located at the core regime with active protease enzymes, and was close to the EPS obligate anaerobic strain Bacteroides sp. Hence, the extracellular proteins in stored granules were pro- posed to be hydrolyzed by enzymes secreted by proteolytic bacteria with the hydrolyzed products ulti- mately being used by nearby anaerobic strains.
  • Identification and Metabolic Activities of Bacterial Species Belonging to the Enterobacteriaceae on Salted Cattle Hides and Sheep Skins by K

    Identification and Metabolic Activities of Bacterial Species Belonging to the Enterobacteriaceae on Salted Cattle Hides and Sheep Skins by K

    186 IDENTIFicATION And METABOLic ACTIVITIES OF BACTERIAL SPEciES BELONGinG TO THE ENTEROBACTERIACEAE ON SALTED CATTLE HidES And SHEEP SKins by K. ULUSOY1 AND M. BIrbIR*2 1Marmara University, Institute of Pure and Applied Science, GOZTEPE, ISTANBUL 34722, TURKEY 2Marmara University, Faculty of Science and Letters, Department of Biology, GOZTEPE, ISTANBUL 34722, TURKEY ABSTRACT and skin samples contain different species of Enterobacteriaceae which may cause deterioration of hides The detailed examination of the Enterobacteriaceae on salted and skins; therefore, effective antibacterial applications should hides and skins offers important information to assess faecal be applied to hides and skins to eradicate these microorganisms contamination of salted hides and skins, its roles in hide and prevent substantial economical losses in leather industry. spoilage, and efficiency of hide preservation. Hence, salted cattle hide and skin samples were obtained from different INTRODUCTION countries and examined. Total counts of Gram-negative bacteria on hide and skin samples, respectively, were 104-106 Cattle hides and sheep skins may be contaminated by and 105-106 CFU/g; of Enterobacteriaceae 104-105 and 105-106 members of the family Enterobacteriaceae. The family is CFU/g; of proteolytic Enterobacteriaceae 103-105 and 105-106 prevalent in nature, normally found in soil, human and animal CFU/g; of lipolytic Enterobacteriaceae 102-105 and 104-105 intestines, water, decaying vegetation, fruits, grains, insects CFU/g; and of each species belonging to
  • Standoff Detection and Classification of Bacteria by Multispectral Laser-Induced Fluorescence

    Standoff Detection and Classification of Bacteria by Multispectral Laser-Induced Fluorescence

    Adv. Opt. Techn. 2017; 6(2): 75–83 Research Article Open Access Frank Duschek*, Lea Fellner, Florian Gebert, Karin Grünewald, Anja Köhntopp, Marian Kraus, Peter Mahnke, Carsten Pargmann, Herbert Tomaso and Arne Walter Standoff detection and classification of bacteria by multispectral laser-induced fluorescence DOI 10.1515/aot-2016-0066 OCIS codes: 160.1435; 280.1415; 300.2530; 280.0280; Received December 2, 2016; accepted February 6, 2017; previously 000.3860. published online March 31, 2017 Abstract: Biological hazardous substances such as cer- tain fungi and bacteria represent a high risk for the broad 1 Introduction public if fallen into wrong hands. Incidents based on Hazardous bacteria represent a major threat to modern bio-agents are commonly considered to have unpredict- societies if released into the environment. Aerosols of bac- able and complex consequences for first responders and teria can occur naturally when infected animals or humans people. The impact of such an event can be minimized spread a pathogen, but they can also be released by acci- by an early and fast detection of hazards. The presented dents and as a terrorist attack. Once people are infected, approach is based on optical standoff detection apply- bacteria may easily spread aided by the fact that their detri- ing laser-induced fluorescence (LIF) on bacteria. The LIF mental effects can occur with a certain time delay. Therefore, bio-detector has been designed for outdoor operation fast and reliable detection and identification of bacteria is at standoff distances from 20 m up to more than 100 m. essential for the containment and the decontamination of The detector acquires LIF spectral data for two different affected areas and people.
  • Architecture of Class 1, 2, and 3 Integrons from Gram Negative Bacteria Recovered Among Fruits and Vegetables

    Architecture of Class 1, 2, and 3 Integrons from Gram Negative Bacteria Recovered Among Fruits and Vegetables

    ORIGINAL RESEARCH published: 13 September 2016 doi: 10.3389/fmicb.2016.01400 Architecture of Class 1, 2, and 3 Integrons from Gram Negative Bacteria Recovered among Fruits and Vegetables Daniela Jones-Dias 1, 2 †, Vera Manageiro 1, 2 †, Eugénia Ferreira 1, Paula Barreiro 3, Luís Vieira 3, Inês B. Moura 1, 2 and Manuela Caniça 1* 1 National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal, 2 Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, Oporto, Portugal, 3 Innovation and Technology Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal The spread of antibiotic resistant bacteria throughout the food chain constitutes a public health concern. To understand the contribution of fresh produce in shaping antibiotic resistance bacteria and integron prevalence in the food chain, 333 antibiotic resistance Edited by: Gram negative isolates were collected from organic and conventionally produced fruits David W. Graham, (pears, apples, and strawberries) and vegetables (lettuces, tomatoes, and carrots). Newcastle University, UK Although low levels of resistance have been detected, the bacterial genera identified Reviewed by: Sylvie Nazaret, in the assessed fresh produce are often described not only as environmental, but Centre National de la Recherche mostly as commensals and opportunistic pathogens. The genomic characterization of Scientifique, France Joakim Larsson, integron-harboring isolates revealed a high number of mobile genetic elements and University of Gothenburg, Sweden clinically relevant antibiotic resistance genes, of which we highlight the presence of *Correspondence: as mcr-1, qnrA1, blaGES−11, mphA, and oqxAB.
  • Enrichment of CO2 -Fixing Bacteria in Cylinder-Type Electrochemical

    Enrichment of CO2 -Fixing Bacteria in Cylinder-Type Electrochemical

    J. Microbiol. Biotechnol. (2011), 21(6), 590–598 doi: 10.4014/jmb.1101.01032 First published online 20 April 2011 Enrichment of CO2-Fixing Bacteria in Cylinder-Type Electrochemical Bioreactor with Built-In Anode Compartment Jeon, Bo Young1, Il Lae Jung2, and Doo Hyun Park1* 1Department of Biological Engineering, Seokyeong University, Seoul 136-704, Korea 2Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon 305-353, Korea Received: January 21, 2011 / Revised: March 26, 2011 / Accepted: March 27, 2011 Bacterial assimilation of CO2 into stable biomolecules or NADH) with reduction energy generated by the + o using electrochemical reducing power may be an effective metabolic oxidation of NH4 , S , or H2, which functions as method to reduce atmospheric CO2 without fossil fuel an electron donor for the respiration and reduction of CO2 combustion. For the enrichment of the CO2-fixing bacteria [10, 22, 26, 28]. In a variety of metabolic carboxylation using electrochemical reducing power as an energy source, reactions, CO2 is assimilated into the biomolecules via the a cylinder-type electrochemical bioreactor with a built-in biochemical reducing power regenerated in tandem with anode compartment was developed. A graphite felt cathode the oxidation of organic compounds [29, 31, 32]. Meanwhile, modified with neutral red (NR-graphite cathode) was the biochemical reducing power can be regenerated in used as a solid electron mediator to induce bacterial cells combination with H2O decomposition by the electromagnetic to fix CO2 using electrochemical reducing power. Bacterial power in the photoautotrophic metabolism, along with O2 CO2 consumption was calculated based on the variation in generation [7].