DOCSLIB.ORG

Thesis Final 4

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Thesis Final 4 Academic supervisors Senior researcher, Nuria Canibe, PhD Department of Animal Science, Faculty of Science and Technology, Aarhus University, 8830, Tjele, Denmark. Senior researcher Emeritus, Bent Borg Jensen, PhD Department of Animal Science, Faculty of Science and Technology, Aarhus University, 8830, Tjele, Denmark. Assessment committee Associated Professor Jan Værum Nørregaard, PhD (Chair) Department of Animal Science, Faculty of Science and Technology, Aarhus University, Tjele, Denmark. Professor Jan Erik Lindberg, PhD Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden. Professor Ulrike Weiler, PhD Institute of Animal Husbandry and Animal Breeding, Behavioral Physiology of Farm Animals, University of Hohenheim, Stuttgart, Germany I Preface This PhD thesis is submitted to the Faculty of Science and Technology, Aarhus University, Denmark, to fulfil the requirements of the PhD degree. It represents my work conducted at Department of Animal Science, in the research group of Immunology and Microbiology, from June 2013 to November 2016, interrupted by a maternity leave, giving in a total period of 3.5 years. This study has been supervised by the main supervisor, senior researcher Nuria Canibe, and the co-supervisor, senior researcher emeritus Bent Borg Jensen. The work was carried under the project ‘Organic pig production without castration’ that is part of the Organic RDD program, which is coordinated by International Centre for Research in Organic Food Systems, ICROFS. It was founded by Danish AgriFish Agency, Ministry of Food, Agriculture and Fisheries (Project 3405-10-OP-00134). The PhD student was supported by a scholarship from the China Scholarship Council (CSC). II Acknowledgments Foremost, I would like to express my sincere appreciation and thanks to both of my supervisors Nuria Canibe and Bent Borg Jensen for their continuous support of my study and research, for their patience, motivation, enthusiasm, and unparalleled knowledge. Without their consistent guidance, it would not be possible to complete this project. I would also like to thank my master supervisor Jiufeng Wang who recommended me to join this group. Besides my supervisors, I would like to thank all my co-authors for their insightful comments and contributions to my papers. I must say a special thank you to Dr Ole Højberg and Dr Samantha Joan Noel, for their guidance, support and encouragment. My sincere thanks also goes to all technicians: Mona Dinsen, Karin Durup, Trine Poulsen, Thomas Rebsdorf, Helle Handll, Kasper Poulsen, Britta Poulsen for skillful technical assistance in carrying out my experiments. I also appreciate help from Henry Johannes Høgh Jørgensen for assisting to perform the catheter surgery. I appreciate my previous and present officemates: Morten Poulsen, Grethe Venås Jakobsen, Zhigang Zhu, joyfully accompany and support. A warm thanks to all my colleagues in the group of Immunology and Microbiology for creating a harmonious environment. In particular, I would like to thank Ann-Sofie Riis Poulsen and Marlene Fredborg, for their willingness to share and help. And a big thanks to our secretory Mette Graves Madsen for all the assistance. Many thanks go to Nørresø kollegiet residents, the Chinese community in Foulum and the International club. Without them, my life in Denmark would not be that colorful. I would also like to thank all of my friends for supporting and understanding. Last but not the least, I am thankful to my family: my selfless parents for being babysitting in Denmark, my talented sister for backing, and my dear husband Jin for supporting me spiritually throughout my PhD and my life in general. In particular, I am grateful to my little daughter Shirley for reminding me that I am a mother besides a PhD. Xiaoqiong Li/ Foulum, December 2016 III List of scientific publications and manuscripts Paper I: Li X, Jensen RL, Højberg O, Canibe N, Jensen BB. 2015. Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and 4-methylphenol- (p-cresol) producing bacterium isolated from pig faeces. International Journal of Systematic and Evolutionary Microbiology 65:1227–33. Paper II: Li X, Højberg O, Noel SJ, Canibe N, Jensen BB. 2016. Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces. Genome Announcements 4:e00042-16. Paper III: Li X, Marshall IPG, Schreiber L, Højberg O, Canibe N, Jensen BB. 2016. Draft Genome Sequence of Megasphaera sp. Strain DJF_B143, an Isolate from Pig Hindgut Unable to Produce Skatole. Genome Announcements 4:e00007-16. Paper IV: Li X, Jensen BB, Højberg O, Noel SJ, Canibe N. Development of a species-specific Taqman-MGB real-time PCR assay to quantify Olsenella scatoligenes in pigs offered a chicory root-based diet (planned to be submitted to Applied Microbiology Biotechnology) Paper V: Li X, Højberg O, Canibe N, Jensen BB. 2016. Phylogenetic diversity of cultivable butyrate-producing bacteria from pig gut content and feces. Journal of Animal Science 94:377–381. Paper VI: Li X, Jensen BB, Canibe N. Effect of chicory roots and exogenous butyrate on skatole production and gut microbiota of entire male pigs (planned to be submitted to Applied and Environmental Microbiology). IV List of abbreviations CYP Cytochromes P450 DF Dietary fiber DGGE Denaturing gradient gel electrophoresis DP Degree of polymerization FISH Fluorescence in situ hybridization FOS Fructo-oligosaccharides GI Gastrointestinal GnRH Hypothalamic gonadotropin-releasing hormone HTS High-throughput sequencing IAA Indole acetic acid IPA Indole propionic acid ITF Inulin-type fructans MGB Minor groove binder NGS Next-generation sequencing NSP Non-starch polysaccharides OTU Operational taxonomic unit QIIME Quantitative Insights Into Microbial Ecology qPCR Quantitative real-time PCR RPS Raw potato starch RS Resistant starch SCFA Short-chain fatty acid TRP L-tryptophan T-RFLP Terminal restriction fragment length polymorphism WGS Whole-genome shotgun V Summary Skatole, a cytotoxic and malodorous compound, is the main causer of boar taint, which is an offensive odor and flavor released upon heating meat from some pubertal or sexually mature male pigs. Due to animal welfare concerns, there is an increasing desire to stop surgical castration within the European Union by 2018, turning boar taint into a challenge in pig production. Skatole is produced by microbial fermentation of L-tryptophan (TRP) in the hindgut. The production involves a two-step process, in which the precursor TRP is first deaminated to indole acetic acid (IAA), which is then further decarboxylated to skatole. Difficulties arise in controlling boar taint, due to the lack of knowledge on the specialized gastrointestinal skatole-producing bacteria. Skatole levels can be reduced by feeding certain dietary fibers (DF), making this strategy an alternative to surgical castration. Dietary fiber sources rich in inulin-type fructans (e.g. chicory roots and Jerusalem artichoke) are the most effective in reducing skatole formation as seen so far. However, the exact mechanism underlying the skatole reducing effect of DF remains unclear. Hence, the objective of this PhD thesis was to screen and characterize the skatole-producing bacteria inhabiting the hindgut of pigs, their metabolism, genome, quantification, and to elucidate the mode of action behind the reducing effect of DF on skatole production in the hindgut of pigs. We screened 122 OTUs, which represent 2678 isolates from the GI-tract of pigs for their ability to produce skatole. Results showed that only one strain, O. scatoligenes SK9K4, had the capacity to produce skatole from IAA, but not from TRP. The 2.47 Mbp draft genome sequence of O. scatoligenes SK9K4T confirmed that it possesses the tyrosine degradation IV (to p-cresol) pathway, and offered the possibility to identify candidate genes for skatole production by comparative genomic analysis. Use of Taqman-MGB qPCR, enabled specific enumeration of O. scatoligenes, and showed that this bacterium only accounted for less than 0.01% of the total bacterial population in the pig hindgut. High levels of dietary chicory roots promoted O. scatoligenes proliferation, and selectively promoted the growth of specific butyrate-producing bacteria such as Megasphaera elsdenii, but not a general increase in the population of butyrogenic bacteria in pig gut. This indicated that the known effect of chicory roots for reducing skatole production is not by inhibiting the growth of the skatole-producing bacteria or by a general increasing of the butyrate-producing bacteria. Intracecal infusion of butyrate alone did failed to reduce skatole formation in the pig hindgut. In conclusion, cultivable skatole-producing bacteria in the pig GI-tract seem to be limited to one VI species, i.e., O. scatoligenes. The known effect of chicory roots for reducing skatole production is neither by inhibiting the growth of this skatole-producing bacteria in the hindgut, nor by inhibition of cell apoptosis by butyrate, but is more likely due to more TRP incorporated into microbial biomass. VII Resumé (Danish summary) Skatol, en cytotoksisk og ildelugtende forbindelse, er den vigtigste komponent af ornelugt, en ubehagelig lugt og smag der frigives ved opvarmning af kød fra specielt seksuelt modne hangrise. Kirurgisk kastration af hangrise er en almindelig
Load more

Recommended publications
  • Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles Received: 10 January 2017 Angela B
    www.nature.com/scientificreports OPEN Gut Dysbiosis and Neurobehavioral Alterations in Rats Exposed to Silver Nanoparticles Received: 10 January 2017 Angela B. Javurek1, Dhananjay Suresh 2, William G. Spollen3,4, Marcia L. Hart5, Sarah Accepted: 19 April 2017 A. Hansen6, Mark R. Ellersieck7, Nathan J. Bivens 8, Scott A. Givan 3,4,9, Anandhi Published: xx xx xxxx Upendran10,11, Raghuraman Kannan11,12 & Cheryl S. Rosenfeld 4,13,14,15 Due to their antimicrobial properties, silver nanoparticles (AgNPs) are being used in non-edible and edible consumer products. It is not clear though if exposure to these chemicals can exert toxic effects on the host and gut microbiome. Conflicting studies have been reported on whether AgNPs result in gut dysbiosis and other changes within the host. We sought to examine whether exposure of Sprague- Dawley male rats for two weeks to different shapes of AgNPs, cube (AgNC) and sphere (AgNS) affects gut microbiota, select behaviors, and induces histopathological changes in the gastrointestinal system and brain. In the elevated plus maze (EPM), AgNS-exposed rats showed greater number of entries into closed arms and center compared to controls and those exposed to AgNC. AgNS and AgNC treated groups had select reductions in gut microbiota relative to controls. Clostridium spp., Bacteroides uniformis, Christensenellaceae, and Coprococcus eutactus were decreased in AgNC exposed group, whereas, Oscillospira spp., Dehalobacterium spp., Peptococcaeceae, Corynebacterium spp., Aggregatibacter pneumotropica were reduced in AgNS exposed group. Bacterial reductions correlated with select behavioral changes measured in the EPM. No significant histopathological changes were evident in the gastrointestinal system or brain. Findings suggest short-term exposure to AgNS or AgNC can lead to behavioral and gut microbiome changes.
    [Show full text]
  • Antibitoic Treatment for Tuberculosis Induces a Profound Dysbiosis of the Gut Microbiome That Persists Long After Therapy Is Completed
    ANTIBITOIC TREATMENT FOR TUBERCULOSIS INDUCES A PROFOUND DYSBIOSIS OF THE GUT MICROBIOME THAT PERSISTS LONG AFTER THERAPY IS COMPLETED A Thesis Presented to the Faculty of the Weill Cornell Graduate School of Medical Sciences in Partial Fulfillment of the Requirements for the Degree of Masters of Science by Matthew F. Wipperman May 2017 © 2017 Matthew F. Wipperman ABSTRACT Mycobacterium tuberculosis, the cause of Tuberculosis (TB), infects one third of the world’s population and causes substantial mortality worldwide. In its shortest format, treatment of drug sensitive TB requires six months of multidrug therapy with a mixture of broad spectrum and mycobacterial specific antibiotics, and treatment of multidrug resistant TB is much longer. The widespread use of this regimen worldwide makes this one the largest exposures of humans to antimicrobials, yet the effects of antimycobacterial agents on intestinal microbiome composition and long term stability are unknown. We compared the microbiome composition, assessed by both 16S rDNA and metagenomic DNA sequencing, of Haitian TB cases during antimycobacterial treatment and following cure by 6 months of TB therapy. TB treatment does not perturb overall diversity, but nonetheless dramatically depletes multiple immunologically significant commensal bacteria. The perturbation by TB therapy lasts at least 1.5 years after completion of treatment, indicating that the effects of TB treatment are long lasting and perhaps permanent. These results demonstrate that TB treatment has dramatic and durable effects on the intestinal microbiome and highlight unexpected extreme consequences of treatment for the world’s most common infection on human ecology. BIOGRAPHICAL SKETCH NAME POSITION TITLE Wipperman, Matthew Frederick Postdoctoral Researcher at eRA COMMONS USER NAME Memorial Sloan Kettering Cancer Center MFWIPPERMAN DEGREE INSTITUTION AND (if MM/YY FIELD OF STUDY LOCATION applicable) Franklin & Marshall College B.A.
    [Show full text]
  • New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces LILLIAN V
    INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 24, No. 2 April 1974, p. 260-277 Printed in U.S.A. Copyright 0 1974 International Association of Microbiological Societies New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces LILLIAN V. HOLDEMAN and W. E. C. MOORE Anaerobe Laboratory, Virginia Polytechnic Institute and State University, Blacksburg, Virginia24061 A new genus of anaerobic cocci, Coprococcus, and 12 new species of anaerobes, Coprococcus eutactus, C. catus, C. comes, RuminococCus callidus, R. torques, Streptococcus hansenii, Bacteroides eggerthii, Eubacterium eligens, E. formicigenerans, E. hallii, Lactobacillus rogosae, and Clostridium nexile, are described. Emended descriptions and proposed neotype strains for Strepto- coccus constellatus (Prkvot) comb. nov., S. morbillorum (Prkvot) comb. nov., S. in termedius PrCvot, and Eubacterium biiorme (Eggerth) PrCvot are presented. During quantitative and qualitative studies of The moles percent guanine plus cytosine (G+C) the human fecal flora, a large number of content of the deoxyribonucleic acid (DNA) prepara- previously undescribed bacterial species was tions was determined by the thermal melting point encountered as predominant members of the (T,) method (7) by using an automatic recording flora. Of these species, those for which we have spectrophotometer (Gilford Instrument Laboratories). DNA from Escherichia coli B was included in each set nine or more isolates from six or more persons of analyses as a standard. are described here. In addition, the taxonomic position of some species of cocci is discussed, RESULTS AND DISCUSSION and for Eubacterium biforme (Eggerth) Prbvot, an emended description is presented and a Anaerobic Cocci neotype strain is designated.
    [Show full text]
  • Functional Deficits in Gut Microbiome of Young and Middle-Aged
    nutrients Article Functional Deficits in Gut Microbiome of Young and Middle-Aged Adults with Prediabetes Apparent in Metabolizing Bioactive (Poly)phenols Xuhuiqun Zhang , Anqi Zhao, Amandeep K. Sandhu, Indika Edirisinghe and Britt M. Burton-Freeman * Department of Food Science and Nutrition and Center for Nutrition Research, Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL 60616, USA; [email protected] (X.Z.); [email protected] (A.Z.); [email protected] (A.K.S.); [email protected] (I.E.) * Correspondence: [email protected]; Tel.: +1-708-341-7078 Received: 20 October 2020; Accepted: 20 November 2020; Published: 23 November 2020 Abstract: Background: Gut microbiota metabolize select dietary (poly)phenols to absorbable metabolites that exert biological effects important in metabolic health. Microbiota composition associated with health/disease status may affect its functional capacity to yield bioactive metabolites from dietary sources. Therefore, this study assessed gut microbiome composition and its related functional capacity to metabolize fruit (poly)phenols in individuals with prediabetes and insulin resistance (PreDM-IR, n = 26) compared to a metabolically healthy Reference group (n = 10). Methods: Shotgun sequencing was used to characterize gut microbiome composition. Targeted quantitative metabolomic analyses of plasma and urine collected over 24 h were used to assess microbial-derived metabolites in response to a (poly)phenol-rich raspberry test drink. Results: PreDM-IR compared to the Reference group: (1) enriched Blautia obeum and Blautia wexlerae and depleted Bacteroides dorei and Coprococcus eutactus. Akkermansia muciniphila and Bacteroides spp. were depleted in the lean PreDM-IR subset; and (2) impaired microbial catabolism of select (poly)phenols resulting in lower 3,8-dihydroxy-urolithin (urolithin A), phenyl-γ-valerolactones and various phenolic acids concentrations (p < 0.05).
    [Show full text]
  • Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces LILLIAN V
    INTERNATIONAL JOURNAL of SYSTEMATIC BACTERIOLOGY Vol. 24, No. 2 April 1974, p. 260-277 Printed in U.S.A. Copyright 0 1974 International Association of Microbiological Societies New Genus, Coprococcus, Twelve New Species, and Emended Descriptions of Four Previously Described Species of Bacteria from Human Feces LILLIAN V. HOLDEMAN and W. E. C. MOORE Anaerobe Laboratory, Virginia Polytechnic Institute and State University, Blacksburg, Virginia24061 A new genus of anaerobic cocci, Coprococcus, and 12 new species of anaerobes, Coprococcus eutactus, C. catus, C. comes, RuminococCus callidus, R. torques, Streptococcus hansenii, Bacteroides eggerthii, Eubacterium eligens, E. formicigenerans, E. hallii, Lactobacillus rogosae, and Clostridium nexile, are described. Emended descriptions and proposed neotype strains for Strepto- coccus constellatus (Prkvot) comb. nov., S. morbillorum (Prkvot) comb. nov., S. in termedius PrCvot, and Eubacterium biiorme (Eggerth) PrCvot are presented. During quantitative and qualitative studies of The moles percent guanine plus cytosine (G+C) the human fecal flora, a large number of content of the deoxyribonucleic acid (DNA) prepara- previously undescribed bacterial species was tions was determined by the thermal melting point encountered as predominant members of the (T,) method (7) by using an automatic recording flora. Of these species, those for which we have spectrophotometer (Gilford Instrument Laboratories). DNA from Escherichia coli B was included in each set nine or more isolates from six or more persons of analyses as a standard. are described here. In addition, the taxonomic position of some species of cocci is discussed, RESULTS AND DISCUSSION and for Eubacterium biforme (Eggerth) Prbvot, an emended description is presented and a Anaerobic Cocci neotype strain is designated.
    [Show full text]
  • Comparative Fecal Metagenomics Unveils Unique Functional Capacity
    Lamendella et al. BMC Microbiology 2011, 11:103 http://www.biomedcentral.com/1471-2180/11/103 RESEARCHARTICLE Open Access Comparative fecal metagenomics unveils unique functional capacity of the swine gut Regina Lamendella1,4, Jorge W Santo Domingo2*, Shreya Ghosh1, John Martinson3 and Daniel B Oerther1,5 Abstract Background: Uncovering the taxonomic composition and functional capacity within the swine gut microbial consortia is of great importance to animal physiology and health as well as to food and water safety due to the presence of human pathogens in pig feces. Nonetheless, limited information on the functional diversity of the swine gut microbiome is available. Results: Analysis of 637, 722 pyrosequencing reads (130 megabases) generated from Yorkshire pig fecal DNA extracts was performed to help better understand the microbial diversity and largely unknown functional capacity of the swine gut microbiome. Swine fecal metagenomic sequences were annotated using both MG-RAST and JGI IMG/M-ER pipelines. Taxonomic analysis of metagenomic reads indicated that swine fecal microbiomes were dominated by Firmicutes and Bacteroidetes phyla. At a finer phylogenetic resolution, Prevotella spp. dominated the swine fecal metagenome, while some genes associated with Treponema and Anareovibrio species were found to be exclusively within the pig fecal metagenomic sequences analyzed. Functional analysis revealed that carbohydrate metabolism was the most abundant SEED subsystem, representing 13% of the swine metagenome. Genes associated with stress, virulence, cell wall and cell capsule were also abundant. Virulence factors associated with antibiotic resistance genes with highest sequence homology to genes in Bacteroidetes, Clostridia, and Methanosarcina were numerous within the gene families unique to the swine fecal metagenomes.
    [Show full text]
  • General Intoduction
    UNIVERSITÁ DEGLI STUDI DI CATANIA Dipartimento di Agricoltura, Alimentazione e Ambiente PhD Research in Food Production and Technology- XXVIII cycle Alessandra Pino Lactobacillus rhamnosus: a versatile probiotic species for foods and human applications Doctoral thesis Promoter Prof. C.L. Randazzo Co-promoter Prof. C. Caggia TRIENNIUM 2013-2015 Science knows no country, because knowledge is the light that illuminated the word 2 TABLE OF CONTENTS CHAPTER 1 General introduction and thesis outline 1 CHAPTER 2 Lactobacillus rhamnosus in Pecorino Siciliano 36 production and ripening CHAPTER 3 Lactobacillus rhamnosus in table olives 80 production CHAPTER 4 Lactobacillus rhamnosus GG for Bacterial 115 Vaginosis treatment CHAPTER 5 Lactobacillus rhamnosus GG supplementation 159 in Systemic Nickel allergy Syndrome patients APPENDICES List of figures 212 List of tables 216 List of pubblications 218 Poster presentations 220 Acknowledgements 221 Chapter 1 General introduction and thesis outline 4 Chapter 1 INTRODUCTION The term probiotic is a relatively new word meaning “for life”, used to designate microorganisms that are associated with the beneficial effects for humans and animals. These microorganisms contribute to intestinal microbial balance and play an important role in maintaining health. Several definitions of “probiotic” have been used over the years but the one derived by the Food and Agriculture Organization of the United Nations/World Health Organization (2001) (29), endorsed by the International Scientific Association for Probiotics
    [Show full text]
  • Taxonomic Studies of Two Species of Peptococci and Inhibition of Peptostreptococcus Anaerobius by Sodium Polyanethol Sulfonate;
    ,Taxonomic Studies of Two Species of Peptococci and Inhibition of Peptostreptococcus anaerobius by Sodium Polyanethol Sulfonate; by Susan Emily Holt West1, \\ ! Thesis submitted to the Graduate Faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE in Microbiology (Anaerobe Laboratory) APPROVED: •r• /' ., ~ T. £. Wilkins, Chairman _,.-,--------------- L. V. Holdeman E. R. Stout April, 1977 Blacksburg, Virginia ACKNOWLEDGEMENTS Initial thanks are due Tracy D. Wilkins for serving as chairman of my thesis committee. To Lillian V. Holdeman of my committee I am especially grateful, both for her many specific suggestions concerning this thesis, and also for the general training I have recieved from her, and for the attitude toward research that I believe I have learned from her. Ernest R. Stout, also a member of the committee, has fulfilled his duties conscientiously and has provided much encouragement and support. I owe special thanks to , who initially stimulated my interest in bacteriology many years ago, and who has continued to show interest in the progress of my career. Several other scientists have been helpful: of the Anaerobe Laboratory determined the percent guanine plus cytosine content of the deoxyribonucleic acid of the type strain of Peptococcus niger; of the Becton-Dickinson Company first suggested the direction of our research on sodium polyanethol sulfonate inhibition of anaerobic cocci; and of the Institut fur Klinische Mikrobiologie und Infektionshygiene der Universitat Erlangen-NUrnberg, West Germany, very kindly sent cultures of Escherichia coli C and Serratia marcescens SM 29. of the Department ·of Foreign Languages, VPI & SU, provided translations of the German texts of several papers that were significant in the Peptococcus anaerobius project.
    [Show full text]
  • Effect of Predatory Bacteria on the Gut Bacterial Microbiota in Rats
    www.nature.com/scientificreports OPEN Effect of predatory bacteria on the gut bacterial microbiota in rats Kenneth Shatzkes1, Chi Tang1, Eric Singleton1, Sean Shukla1, Michael Zuena1, Shilpi Gupta2, Sonal Dharani2, Joseph Rinaggio3, Nancy D. Connell1 & Daniel E. Kadouri2 Received: 01 November 2016 Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are Gram-negative proteobacteria that Accepted: 24 January 2017 are obligate predators of other Gram-negative bacteria and are considered potential alternatives Published: 06 March 2017 to antibiotics. Most studies focusing on predatory bacteria have been performed in vitro, thus the effect of predatory bacteria on a live host, including the impact on the ecology of the native microbiota, has yet to be fully examined. In this study, intrarectal inoculations of Sprague-Dawley rats with predatory bacteria were performed. Additionally, feces were collected for seven days post- inoculation to determine the effect on gut bacterial diversity. Rat colonic tissue exhibited no abnormal histopathological effects due to predatory bacteria. A modest increase in pro-inflammatory cytokines was measured in the colons of rats inoculated with predatory bacteria by 24 and 48 hours, with all but IL-13 returning to baseline by seven days. V4 16S rRNA gene sequencing of fecal DNA demonstrated minimal shifts in taxonomic representation over the week due to predatory bacteria. Changes in bacterial populations due to exposure to B. bacteriovorus are predicted to contribute to health, however, an overgrowth of Prevotella was observed due to exposure to M. aeruginosavorus. This study further addresses safety concerns associated with the potential use of predatory bacteria to treat infections. With the rise of multi-drug resistant (MDR) bacterial infections over the last decade1, researchers have begun to develop new ways to treat infections for the future post-antibiotic era2.
    [Show full text]
  • Mapping and Characterization of Bacterial Propanediol Oxidoreductases for Potential Use in Biocatalysis Systems
    Mapping and characterization of bacterial propanediol oxidoreductases for potential use in biocatalysis systems Master's thesis Jakob Lundin 2010-02-09 Supervisor; Mikael Widersten, Department of Biochemistry and Organic chemistry, Uppsala University. Co-supervisor; Cecilia Blikstad, Department of Biochemistry and Organic chemistry, Uppsala University . Uppsala University, 2010-02-09, Master’s thesis Jakob Lundin Table of Contents I. Background................................................................................................................................. 5 I.I. Outlook and potential ................................................................................................................ 5 I.II. Context ..................................................................................................................................... 5 I.III. Propane-1,2-diol oxidoreductase, FucO, introduction and origin........................................... 7 I.III.I. Enzyme classification ...................................................................................................... 7 I.III.II. Biological role of FucO.................................................................................................. 7 I.III.III. Present state of knowledge; catalytic mechanism and structural considerations.......... 8 I.IV. Bacterial sources of FucO, included in the study.................................................................... 9 I.IV.I. Shewanella pealeana .......................................................................................................
    [Show full text]
  • Downloaded from the VFDB Data- Base (Virulence Factors Database) Containing Nucleotide Sample Collection and Metagenomic Sequencing Sequences of 2585 Genes [53]
    Dubinkina et al. Microbiome (2017) 5:141 DOI 10.1186/s40168-017-0359-2 RESEARCH Open Access Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease Veronika B. Dubinkina1,2,3,4, Alexander V. Tyakht2,5*, Vera Y. Odintsova2, Konstantin S. Yarygin1,2, Boris A. Kovarsky2, Alexander V. Pavlenko1,2, Dmitry S. Ischenko1,2, Anna S. Popenko2, Dmitry G. Alexeev1,2, Anastasiya Y. Taraskina6, Regina F. Nasyrova6, Evgeny M. Krupitsky6, Nino V. Shalikiani7, Igor G. Bakulin7, Petr L. Shcherbakov7, Lyubov O. Skorodumova2, Andrei K. Larin2, Elena S. Kostryukova1,2, Rustam A. Abdulkhakov8, Sayar R. Abdulkhakov8,9, Sergey Y. Malanin9, Ruzilya K. Ismagilova9, Tatiana V. Grigoryeva9, Elena N. Ilina2 and Vadim M. Govorun1,2 Abstract Background: Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative “shotgun” metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts—with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group. Results: Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients.
    [Show full text]
  • Influence of a Dietary Supplement on the Gut Microbiome of Overweight Young Women Peter Joller 1, Sophie Cabaset 2, Susanne Maur
    medRxiv preprint doi: https://doi.org/10.1101/2020.02.26.20027805; this version posted February 27, 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. It is made available under a CC-BY-NC-ND 4.0 International license . 1 Influence of a Dietary Supplement on the Gut Microbiome of Overweight Young Women Peter Joller 1, Sophie Cabaset 2, Susanne Maurer 3 1 Dr. Joller BioMedical Consulting, Zurich, Switzerland, [email protected] 2 Bio- Strath® AG, Zurich, Switzerland, [email protected] 3 Adimed-Zentrum für Adipositas- und Stoffwechselmedizin Winterthur, Switzerland, [email protected] Corresponding author: Peter Joller, PhD, Spitzackerstrasse 8, 6057 Zurich, Switzerland, [email protected] PubMed Index: Joller P., Cabaset S., Maurer S. Running Title: Dietary Supplement and Gut Microbiome Financial support: Bio-Strath AG, Mühlebachstrasse 38, 8008 Zürich Conflict of interest: P.J none, S.C employee of Bio-Strath, S.M none Word Count 3156 Number of figures 3 Number of tables 2 Abbreviations: BMI Body Mass Index, CD Crohn’s Disease, F/B Firmicutes to Bacteroidetes ratio, GALT Gut-Associated Lymphoid Tissue, HMP Human Microbiome Project, KEGG Kyoto Encyclopedia of Genes and Genomes Orthology Groups, OTU Operational Taxonomic Unit, SCFA Short-Chain Fatty Acids, SMS Shotgun Metagenomic Sequencing, NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.02.26.20027805; this version posted February 27, 2020.
    [Show full text]