Comparative Fecal Metagenomics Unveils Unique Functional Capacity
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Paenibacillaceae Cover
The Family Paenibacillaceae Strain Catalog and Reference • BGSC • Daniel R. Zeigler, Director The Family Paenibacillaceae Bacillus Genetic Stock Center Catalog of Strains Part 5 Daniel R. Zeigler, Ph.D. BGSC Director © 2013 Daniel R. Zeigler Bacillus Genetic Stock Center 484 West Twelfth Avenue Biological Sciences 556 Columbus OH 43210 USA www.bgsc.org The Bacillus Genetic Stock Center is supported in part by a grant from the National Sciences Foundation, Award Number: DBI-1349029 The author disclaims any conflict of interest. Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or by the Ohio State University. Cover: Paenibacillus dendritiformus colony pattern formation. Color added for effect. Image courtesy of Eshel Ben Jacob. TABLE OF CONTENTS Table of Contents .......................................................................................................................................................... 1 Welcome to the Bacillus Genetic Stock Center ............................................................................................................. 2 What is the Bacillus Genetic Stock Center? ............................................................................................................... 2 What kinds of cultures are available from the BGSC? ............................................................................................... 2 What you can do to help the BGSC ........................................................................................................................... -
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. -
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. -
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. -
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). -
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. -
Mutually Facilitated Dispersal Between the Nonmotile Fungus Aspergillus Fumigatus and the Swarming Bacterium Paenibacillus Vortex
Mutually facilitated dispersal between the nonmotile fungus Aspergillus fumigatus and the swarming bacterium Paenibacillus vortex Colin J. Inghama,b,c,1, Oren Kalismand, Alin Finkelshteind,e, and Eshel Ben-Jacobd,1 aLaboratory of Microbiology, Wageningen University, 6703 HB, Wageningen, The Netherlands; bJBZ Hospital, Department of Infection Control and Microbiology, 5223 GZ, Den Bosch, The Netherlands; cMicroDish BV, 3584 CH, Utrecht, The Netherlands; dThe Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel; and eThe Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel Edited* by Nigel D. Goldenfeld, University of Illinois at Urbana–Champaign, Urbana, IL, and approved October 19, 2011 (received for review February 25, 2011) In the heterogeneous environment surrounding plant roots (the bials, including putative antifungals. P. vortex is known to limit the rhizosphere), microorganisms both compete and cooperate. Here, growth of Verticillium dahliae, a fungal pathogen of plants (8). we show that two very different inhabitants of the rhizosphere, Members of the genus Paenibacillus have a variety of interactions the nonmotile fungus Aspergillus fumigatus and the swarming with fungi, both antagonistic (9, 10) and cooperative; an example bacterium Paenibacillus vortex, can facilitate each other’s dis- of the latter is stimulation of the growth of the fungus Glomus persal. A. fumigatus conidia (nonmotile asexual fungal spores) intraradices by P. validus (11). can be transported by P. vortex swarms over distances of at least Aspergillus fumigatus is another versatile inhabitant of the −1 30 cm and at rates of up to 10.8 mm h . Moreover, conidia can be rhizosphere and many other environments; its 29.4-Mb genome rescued and transported by P. -
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 -
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. -
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. -
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 ....................................................................................................... -
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.