DOCSLIB.ORG

Microbiome Influences on Asthma: from the Environment to Clinical Phenotype

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Microbiome Influences on Asthma: from the Environment to Clinical Phenotype 3/3/2020 Microbiome Influences on Asthma: From the Environment to Clinical Phenotype Yvonne Huang MD Division of Pulmonary and Critical Care Medicine Department of Medicine University of Michigan, Ann Arbor Masoli et al. Allergy 2004; Science 2011 “Wherefore is this disease different from all other diseases?” M. Pappworth, A primer of medicine, 1984 Pavord et al. Lancet 2018 ... 1 3/3/2020 Objectives 1. Explain how microbiome research methods have been applied to understand microbial influences on asthma 2. Articulate key findings from studies of the airway and gut microbiome and their associations with asthma risk or clinical phenotype Multiple Factors Shape Asthma Risk and Phenotype Huang and Boushey. J Allergy Clin Immunol. 2015 Jan;135(1):25-30. Kozik and Huang, Annals Allerg Asth Immunol 2019 2 3/3/2020 Asthma Susceptibility Genes Epithelial cells: Chemokines, Microbial recognition, antimicrobial Immunoregulation peptides Type 2 effector functions Vercelli D. Nature Rev Immunol 2008 Human Microbiological History adapted from Rook, Dig. Dis. 2011 Human Microbiological History Dramatic changes in: Home environments Living standards Dietary consumption “Hygiene hypothesis” (Strachan,1989) Exposures “Old friends hypothesis” (Rook, 2010) “Biodiversity hypothesis” (von Hertzen, 2011) “Biome depletion” (Parker, 2014) • Decrease infectious diseases • Rise in allergic and autoimmune diseases adapted from Rook, Dig. Dis. 2011 3 3/3/2020 Single microbial species Microbial “communities” (Microbiota) “Microbiome” vs. “Microbiota” “Microbiome” vs. “Microbiota” “the entire habitat, including the microorganisms, their genes and Bacteria surrounding environmental Fungi Archaea conditions and interactions”. Viruses Helminths • Marchesi and Ravel, Microbiome 2015 • Environmental Chemicals, the Human Microbiome, and Health Risk: A Research Strategy. National Academies of Sciences, Engineering, and Medicine. 2017. (Committee Report) 4 3/3/2020 Childhood Asthma Risk Microbes and Asthma Risk: Childhood – Environment Microbes and Asthma Risk: Childhood – Environment ① Perinatal, early life exposure to a diverse repertoire of microbes is associated with decreased risk of allergic disease, including asthma. Examples: Growing up in small farm environment, Early life pet exposure 5 3/3/2020 Richness of bacteria or fungi found in mattress dust negatively associated with asthma Ege MJ et al. NEJM 2011 Similar relationships between microbial exposures and asthma risk in studies of Amish vs. Hutterite children Peripheral blood gene expression Increased in Amish Increased in Hutterite Stein et al. NEJM 2016 Microbes and Asthma Risk: Childhood – Gut Microbiome 6 3/3/2020 Microbes and Asthma Risk: Childhood – Gut Microbiome ② Differences in gut microbiome composition and functions in early life are linked to risk for childhood- onset allergy or asthma • Clinical studies • Mechanistic studies Penders, Gut 2007.; Vael BMC Microb 2011 Abrahamsson, Clin Exp Allergy 2014 Arrieta, Science Transl Med 2015 Van Nimwegen, J Allerg Clin Immunol 2011 Trompette, Nature Med 2014 Specific intestinal bacteria and risk of allergic asthma Culture or Molecular high-throughput species-specific PCR vs. approaches examples: • Clostridia (C. difficile) • Bacteroides fragilis • E. coli • Bifidobacteria • Lactobacillus Arrieta et al. Science Transl Med 2015 Canadian Longitudinal Birth Cohort study (CHILD) Atopic + wheezy children: Had at age 3 months, decreased Faecalibacterium, Lachnospira, Veillonella, Rothia (FLVR) AW children: Lower fecal short- chain fatty acids Arrieta et al. Science Transl Med 2015 7 3/3/2020 Germ-free mice inoculated with stool from an atopic wheezy 3-mo infant, +/– FLVR bacteria Altered gut microbiota composition in pups of mothers who received AW infant stool + FLVR Decrease in allergic airway inflammation Arrieta et al. Science Transl Med 2015 Bacteria and Asthma Risk: Childhood – Respiratory Bacteria and Asthma Risk: Childhood – Respiratory ③ Differences in upper respiratory (nasopharyngeal) microbiota also linked to risk for childhood asthma * Copenhagen birth cohort * Child Asthma Study (Australia) Bisgaard et al. NEJM 2007; Gollweitzer et al. Nature Med 2014; Teo et al. Cell Host Microb 2015, 2018 8 3/3/2020 Copenhagen Birth Cohort study Pharyngeal colonization at age 1 month with S. pneumoniae, M. catarrhalis, or H. influenzae, associated with increased risk of persistent wheeze or asthma by age 5 Bisgaard H et al. NEJM 2007 Childhood Asthma Study (Australia) The risk for asthma linked to nasal presence of potentially pathogenic bacteria may depend on underlying atopy Teo SM et al. Cell Host Microb 2015 & 2018 Nasal microbiota and loss of asthma control in U.S. school-age children (STICS trial; NHLBI AsthmaNet) Zhou et al. Nat Comm 2019, (STICS trial, Jackson et al. NEJM 2018) 9 3/3/2020 Nasal microbiota and loss of asthma control in U.S. school-age children (STICS trial; NHLBI AsthmaNet) Samples collected at: RD= randomization YZ= yellow zone Zhou et al. Nat Comm 2019, (STICS trial, Jackson et al. NEJM 2018) Asthma Phenotype Susceptibility Pathogenesis Treatment Asthma, Type 2 -“high” (established) Phenotype Treatment: Endotype - responsive Phenotype Type 2-”low” - unresponsive Endotype The Host 10 3/3/2020 Clinical and biological features of adult asthma are associated with altered airway microbiome patterns • Airway hyper-response • Asthma control • Airway immune profiles • Type 2-low • Obese asthma • Treatment response Huang & Boushey, J Allerg Clin Immunol 2015 J Allergy Clin Immunol: Huang 2011 & 2015; Denner 2016, Durack 2017, Taylor 2018, Sharma 2019 Am J Respir Crit Care Med: Goleva 2013 Nat Comm: Michalovich 2019 Severe asthma and the bronchial microbiome • Observational study (n=30) • Clinical stability during 2-3 month study period • poorly controlled despite high dose ICS • Analysis of bronchial epithelial brushings, clinical and immunologic features Huang et al. J Allergy Clin Immunol. 2015 Severe asthma: Airway gene expression patterns associated with airway enrichment in different bacteria Proteobacteria NeuSput “steroid-resistant” signature N NN F NNNNNN N NNNNNNTNNN F F NN TNTNNNNTNNTNTNTTNNTNNF N F FFF F F N NNTNNNNTNNNTTNTNTTNT F FF F FFFF TT TNTTNTTNTNNTNTTTTTT FF F F F T TTTNTTNTTNNNNTTNTTTTTT F F FF FF N TTTNTTTTTN TTNTTF F F F F FF F F TTNTT F F F (IL17-related: CXCL1, -2, -3, IL8, CSF3) T T N T F F F F TT F F F FF F FF “Th17” FF FFFFFFF F F F F FF F F F F T FKBP5 F vs. NMDS2 ActinobacteriaF “steroid-responsive” (FKBP5) F -0.25 -0.20 -0.15 -0.10 -0.05 0.00 0.05 0.10 -0.1 0.0 0.1 0.2 NMDS1 Similar bacterial enrichment Proteobacteria Worsening of asthma patterns correlated with stability of asthma control Actinobacteria Better/stable asthma Huang et al. J Allergy Clin Immunol. 2015 11 3/3/2020 Severe asthma: Less type 2 inflammation, more airway bacterial ‘burden’ Microbiome Type 2-“low” Immune Phenotype Type 2-”high” *similar relationship with % sputum eosinophils Huang et al. J Allergy Clin Immunol. 2015 Obesity in Severe Asthma 5 Bacteroidetes / Phylum (Family) 4 Bacteroidetes (Flavobacteriaceae) * • Prevotella Bacteroidetes (Prevotellaceae) * Bacteroidetes (Rikenellaceae II) Chlorobi (OPB56) 3 Firmicutes (Clostridiales Family XI. Incertae Sedis) * Firmicutes (Clostridiales Family XIII. Incertae Sedis) Firmicutes (Lachnospiraceae) * Firmicutes Fusobacteria (Fusobacteriaceae) -log10 p-value-log10 Proteobacteria (Desulfobacteraceae) 2 Proteobacteria (Helicobacteraceae) * • Clostridiales Spirochaetes (Spirochaetaceae) Tenericutes (Erysipelotrichaceae) Tenericutes (Mycoplasmataceae) • Lachnospiraceae 1 • Fusobacteria 0 -4 -2 0 2 4 Difference in taxon relative abundance (log2) obese vs. nonobese Huang et al. J Allergy Clin Immunol. 2015 Altered respiratory microbiota composition in pediatric and adult asthma studies Pediatric cohorts Adult cohorts • Nasopharyngeal • PSBs, BAL aspirate, swabs, • Induced sputum wash/lavage Haemophilus Haemophilus Streptococcus Moraxella Moraxella Streptococcus Corynebacterium Others… Staphylococcus Alloiococcus Dolosigranulum Marri 2013 Green 2014 Bisgaard, 2010 Huang 2015 severe Kloepfer, 2014 Zhang 2016 Teo et al 2015 asthma Taylor 2018 Depner, 2017 12 3/3/2020 NHLBI AsthmaNet Microbiome study: Mild Asthma and Allergic Individuals without Asthma nasal oral sputum, PSBs BAL T2- sig mean 3-gene (TGM: Expression signature of three, IL-13-inducible genes) Durack et al. J Allergy Clin Immunol. 2017 Atopic subjects without asthma displayed an altered bronchial microbiota pattern that was distinct from the asthma group. ? Microbial-immune interactions related to atopy vs. asthma Controlling for atopic status likely important Durack et al. J Allergy Clin Immunol. 2017 Looking within: nasal microbiota and lung inflammation Nasal Corynebacterium: biomarker of respiratory health in adults? Nasal oral Sputum, Brushes BAL Durack et al. Microbiome 2018 13 3/3/2020 Looking within: nasal microbiota and lung inflammation Nasal Moraxella and asthma-related lung immune responses Durack et al. Microbiome 2018 Univ. of Michigan: • CAARS (Characterization of Adults for Asthma Research Studies) • MICROMAAP (Microbiome Markers of Adult Asthma Phenotype) • Seasonal visits • Clinical events “colds” Exacerbations Med changes • Obesity, metabolic syndrome Gut • Allergies (food) Microbiome • Systemic inflammation • Susceptibility to viral infections 14 3/3/2020 • Obesity, metabolic syndrome Gut • Allergies (food) Microbiome • Systemic inflammation • Susceptibility to viral infections Begley et al. BMJ Resp Res
Load more

Recommended publications
  • Bacterial Communities of the Upper Respiratory Tract of Turkeys
    www.nature.com/scientificreports OPEN Bacterial communities of the upper respiratory tract of turkeys Olimpia Kursa1*, Grzegorz Tomczyk1, Anna Sawicka‑Durkalec1, Aleksandra Giza2 & Magdalena Słomiany‑Szwarc2 The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplifcation of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identifed in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Diferences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identifed, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey focks. Next-generation sequencing has resulted in a marked increase in culture-independent studies characterizing the microbiome of humans and animals1–6. Much of these works have been focused on the gut microbiome of humans and other production animals 7–11.
    [Show full text]
  • Information to Users
    INFORMATION TO USERS This manuscript bas been reproJuced from the microfilm master. UMI films the text directly ftom the original or copy submitted. Thus, sorne thesis and dissertation copies are in typewriter face, while others may be itom any type ofcomputer printer. The quality oftbis reproduction is depeDdeDt apoD the quality of the copy sablDitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthlough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will he noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand corner and continuing trom left to right in equal sections with sma1l overlaps. Each original is a1so photographed in one exposure and is included in reduced fonn at the back orthe book. Photographs ineluded in the original manuscript have been reproduced xerographically in this copy. Higher quality 6" x 9" black and white photographie prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. UMI A Bell & Howell Information Company 300 North Zeeb Raad, ADn AJbor MI 48106-1346 USA 313n61-4700 8OO1S21~ NOTE TO USERS The original manuscript received by UMI contains pages with slanted print. Pages were microfilmed as received. This reproduction is the best copy available UMI Oral spirochetes: contribution to oral malodor and formation ofspherical bodies by Angela De Ciccio A thesis submitted to the Faculty ofGraduate Studies and Research, McGill University, in partial fulfillment ofthe requirements for the degree ofMaster ofScience.
    [Show full text]
  • Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
    ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
    [Show full text]
  • MIB–MIP Is a Mycoplasma System That Captures and Cleaves Immunoglobulin G
    MIB–MIP is a mycoplasma system that captures and cleaves immunoglobulin G Yonathan Arfia,b,1, Laetitia Minderc,d, Carmelo Di Primoe,f,g, Aline Le Royh,i,j, Christine Ebelh,i,j, Laurent Coquetk, Stephane Claveroll, Sanjay Vasheem, Joerg Joresn,o, Alain Blancharda,b, and Pascal Sirand-Pugneta,b aINRA (Institut National de la Recherche Agronomique), UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; bUniversity of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France; cInstitut Européen de Chimie et Biologie, UMS 3033, University of Bordeaux, 33607 Pessac, France; dInstitut Bergonié, SIRIC BRIO, 33076 Bordeaux, France; eINSERM U1212, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; fCNRS UMR 5320, ARN Regulation Naturelle et Artificielle, 33607 Pessac, France; gInstitut Européen de Chimie et Biologie, University of Bordeaux, 33607 Pessac, France; hInstitut de Biologie Structurale, University of Grenoble Alpes, F-38044 Grenoble, France; iCNRS, Institut de Biologie Structurale, F-38044 Grenoble, France; jCEA, Institut de Biologie Structurale, F-38044 Grenoble, France; kCNRS UMR 6270, Plateforme PISSARO, Institute for Research and Innovation in Biomedicine - Normandie Rouen, Normandie Université, F-76821 Mont-Saint-Aignan, France; lProteome Platform, Functional Genomic Center of Bordeaux, University of Bordeaux, F-33076 Bordeaux Cedex, France; mJ. Craig Venter Institute, Rockville, MD 20850; nInternational Livestock Research Institute, 00100 Nairobi, Kenya; and oInstitute of Veterinary Bacteriology, University of Bern, CH-3001 Bern, Switzerland Edited by Roy Curtiss III, University of Florida, Gainesville, FL, and approved March 30, 2016 (received for review January 12, 2016) Mycoplasmas are “minimal” bacteria able to infect humans, wildlife, introduced into naive herds (8).
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • Treponema Borrelia Family: Leptospiraceae Genus: Leptospira Gr
    Bacteriology lecture no.12 Spirochetes 3rd class -The spirochetes: are a large ,heterogeneous group of spiral ,motile bacteria. Although, • there are at least eight genera in this family ,only the genera Treponema,Borrelia,and Leptospira which contain organism pathogenic for humans . -There are some reports of intestinal spirochetes ,that have been isolated from biopsy material ,these are Brachyspira pilosicoli,and Brachyspira aalborgi. *Objectives* Taxonomy Order: Spirochaetales Family: Spirochaetaceae Genus: Treponema Borrelia Family: Leptospiraceae Genus: Leptospira -Gram-negative spirochetes -Spirochete from Greek for “coiled hair "they are : *1*Extremely thin and can be very long *2* Motile by periplasmic flagella (axial fibrils or endoflagella) *3*Outer sheath encloses axial fibrils *4*Axial fibrils originate from insertion pores at both poles of cell 1 Bacteriology lecture no.12 Spirochetes 3rd class Spirochaetales Associated Human Diseases Treponema Main Treponema are: - T. pallidum subspecies pallidum - Syphilis: Venereal (sexual) disease 2 Bacteriology lecture no.12 Spirochetes 3rd class - T. pertenue - Yaws Non venereal - T. carateum - Pinta skin disease All three species are morphologically identical Characteristics of T.pallidum 1-They are long ,slender ,helically coiled ,spiral or cork –screw shaped bacilli. 2-T.pallidum has an outer sheath or glycosaminoglycan contain peptidoglycan and maintain the structural integrity of the organisms. 3-Endoflagella (axial filament ) are the flagella-like organelles in the periplasmic space encased by the outer membranes . 4-The endoflagella begin at each end of the organism and wind around it ,extending to and overlapping at the midpoint. 5- Inside the endoflagella is the inner membrane (cytoplasmic membrane)that provide osmotic stability and cover the protoplasmic cylinders .
    [Show full text]
  • Phylogenetic Foundation of Spirochetes
    J. Mol. Microbiol. Biotechnol. (2000) 2(4): 341-344. JMMBSpirochete Symposium Phylogeny on341 Spirochete Physiology Phylogenetic Foundation of Spirochetes Bruce J. Paster* and Floyd E. Dewhirst Spirochaetales that is divided into three families; namely the Spirochaetaceae, the Brachyspiraceae, and the Department of Molecular Genetics, The Forsyth Institute, Leptospiraceae. The phylogenetic relationships of 140 Fenway, Boston, Massachusetts 02115, USA representatives of each genus are shown in Figure 1. The Spirochaetaceae are separated into 6 genera— Borrelia, Brevinema, Cristispira, Spirochaeta, “Spironema”, Abstract and Treponema. New genera of termite spirochetes, such as Clevelandina, Diplocalyx, and Hollandina, have been The spirochetes are free-living or host-associated, described on the basis of differences in ultrastructural traits helical bacteria, some of which are pathogenic to man (Breznak, 1984). It has been suggested that they also and animal. Comparisons of 16S rRNA sequences belong in the family Spirochaetaceae, but no sequence demonstrate that the spirochetes represent a information is presently available to determine their monophyletic phylum within the bacteria. The phylogenetic position within the spirochetes. spirochetes are presently classified in the Class The Brachyspiraceae contain the genus Brachyspira Spirochaetes in the order Spirochetales and are (Serpulina). Due to the close phylogenetic relationship of divided into three major phylogenetic groupings, or B. aarlborgi to species characterized as Serpulina, it has families. The first family Spirochaetaceae contains been recommended that a single genus be justified. Thus, species of the genera Borrelia, Brevinema, Cristispira, Brachyspira takes precedence over Serpulina since the Spirochaeta, Spironema, and Treponema. The second former genus was listed first as a valid name (Hovind- family Brachyspiraceae contains the genus Hougen et al., 1983).
    [Show full text]
  • Characterization of the First Cultured Representative of Verrucomicrobia Subdivision 5 Indicates the Proposal of a Novel Phylum
    The ISME Journal (2016) 10, 2801–2816 OPEN © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum Stefan Spring1, Boyke Bunk2, Cathrin Spröer3, Peter Schumann3, Manfred Rohde4, Brian J Tindall1 and Hans-Peter Klenk1,5 1Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 2Department Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; 3Department Central Services, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany and 4Central Facility for Microscopy, Helmholtz-Centre of Infection Research, Braunschweig, Germany The recently isolated strain L21-Fru-ABT represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. Phylogenetic analyses based on 16S rRNA genes, RpoB proteins and gene content indicated that strain L21-Fru-ABT represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated Verrucomicrobia subdivision 5. A survey of environmental 16S rRNA gene sequences revealed that members of this newly recognized phylum are wide-spread and ecologically important in various anoxic environments ranging from hypersaline sediments to wastewater and the intestine of animals. Characteristic phenotypic traits of the novel strain included the formation of extracellular polymeric substances, a Gram-negative cell wall containing peptidoglycan and the absence of odd-numbered cellular fatty acids. Unusual metabolic features deduced from analysis of the genome sequence were the production of sucrose as osmoprotectant, an atypical glycolytic pathway lacking pyruvate kinase and the synthesis of isoprenoids via mevalonate.
    [Show full text]
  • LEPTOSPIRA: Morphology, Classification and Pathogenesis
    iolog ter y & c P a a B r f a o s Mohammed i l Journal of Bacteriology and t et al. J Bacteriol Parasitol 2011, 2:6 o a l n o r DOI: 10.4172/2155-9597.1000120 g u y o J Parasitology ISSN: 2155-9597 Research Article Open Access LEPTOSPIRA: Morphology, Classification and Pathogenesis Haraji Mohammed1*, Cohen Nozha2, Karib Hakim3, Fassouane Abdelaziz4 and Belahsen Rekia1 1Laboratoire de Biotechnologie, Biochimie et Nutrition, Faculté des sciences d’El Jadida, Maroc. 2Laboratoire de Microbiologie et d’Hygiène des Aliments et de l’Environnement Institut Pasteur Maroc, Casablanca, Maroc 3Unité HIDAOA, Département de Pathologie et de santé publique vétérinaire, Institut Agronomique et Vétérinaire Hassan II, Rabat; Maroc. 4Ecole Nationale de Commerce et de Gestion d’El Jadida ; Maroc Abstract Leptospirosis, caused by the pathogenic leptospires, is one of the most widespread zoonotic diseases known. Leptospirosis cases can occur either sporadically or in epidemics, Humans are susceptible to infection by a variety of serovars. These bacteria are antigenically diverse. Changes in the antigenic composition of lipopolysaccharide (LPS) are thought to account for this antigenic diversity. The presence of more than 200 recognized antigenic types (termed serovars) of pathogenic leptospires have complicated our understanding of this genus. Definitive diagnosis is suggested by isolation of the organism by culture or a positive result on the microscopic agglutination test (MAT). Only specialized laboratories perform serologic tests; hence, the decision to treat should not be delayed while waiting for the test results. Keywords: Leptospirosis; Leptospira; Serovar; Morphology; Patho- Morphology of Leptospira genesis Leptospires are corkscrew-shaped bacteria, which differ from other Introduction spirochaetes by the presence of end hooks.
    [Show full text]
  • Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets
    fmicb-08-00825 May 5, 2017 Time: 16:5 # 1 ORIGINAL RESEARCH published: 09 May 2017 doi: 10.3389/fmicb.2017.00825 Dietary High Zinc Oxide Modulates the Microbiome of Ileum and Colon in Weaned Piglets Ting Yu1†, Cui Zhu1†, Shicheng Chen2†, Lei Gao3, Hang Lv4, Ruowei Feng1, Qingfeng Zhu1, Jinsong Xu1, Zhuang Chen1* and Zongyong Jiang1,4* 1 Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China, 2 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA, 3 Key Laboratory of Crops Genetics and Improvement of Guangdong Province, Guangzhou, China, 4 Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science (South China), Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China Dietary zinc oxide (ZnO) at pharmacological level has been widely used to prevent and treat diarrhea in weaning piglets. Despite its importance for promoting animal health and performance, the influence of microbiome profiles in intestinal tracts by ZnO needs to be comprehensively investigated. In this study, we conducted a comparative microbial community analysis in the ileum and colon of piglets fed by either control Edited by: diet, high ZnO (3,000 mg/kg) supplement or antibiotics (300 mg/kg chlortetracycline Jana Seifert, and 60 mg/kg colistin sulfate) supplement. Our results showed that both high University of Hohenheim, Germany dietary ZnO and in-feed antibiotics supplementations significantly increased 5 phyla Reviewed by: Metzler-Zebeli Barbara, of Spirochaetes, Tenericutes, Euryarchaeota, Verrucomicrobia, TM7, and reduced 1 University of Veterinary phyla of Chlamydiae in ileal digesta.
    [Show full text]
  • Attachment of Treponema Denticola Strains to Monolayers of Epithelial Cells of Different Origin 29
    PDF hosted at the Radboud Repository of the Radboud University Nijmegen The following full text is a publisher's version. For additional information about this publication click this link. http://hdl.handle.net/2066/145980 Please be advised that this information was generated on 2021-10-08 and may be subject to change. ATTACHMENT OF TREPONEMA DENTICOLA, IN PARTICULAR STRAIN ATCC 33520, TO EPITHELIAL CELLS AND ERYTHROCYTES. - AN IN VITRO STUDY - L—J Print: Offsetdrukkerij Ridderprint B.V., Ridderkerk ATTACHMENT OF TREPONEMA DENTICOLA, IN PARTICULAR STRAIN ATCC 33520, TO EPITHELIAL CELLS AND ERYTHROCYTES. - AN IN VITRO STUDY - een wetenschappelijke proeve op het gebied van de Medische Wetenschappen Proefschrift ter verkrijging van de graad van doctor aan de Katholieke Universiteit Nijmegen, volgens besluit van het College van Decanen in het openbaar te verdedigen op vrijdag 19 mei 1995 des namiddags te 3.30 uur precies door Robert Antoine Cornelius Keulers geboren op 4 april 1957 te Geertruidenberg Promotor: Prof. Dr. K.G. König. Co-promotores: Dr. J.C. Maltha Dr. F.H.M. Mikx Ouders, Familie, Vrienden Table of contents Page Chapter 1: General introduction 9 Chapter 2: Attachment of Treponema denticola strains to monolayers of epithelial cells of different origin 29 Chapter 3: Attachment of Treponema denticola strains ATCC 33520, ATCC 35405, Bll and Ny541 to a morphologically distinct population of rat palatal epithelial cells 35 Chapter 4: Involvement of treponemal surface-located protein and carbohydrate moieties in the attachment of Treponema denticola ATCC 33520 to cultured rat palatal epithelial cells 43 Chapter 5: Hemagglutination activity of Treponema denticola grown in serum-free medium in continuous culture 51 Chapter 6: Development of an in vitro model to study the invasion of oral spirochetes: A pilot study 59 Chapter 7: General discussion 71 Chapter 8: Summary, Samenvatting, References 85 Appendix: Ultrastructure of Treponema denticola ATCC 33520 113 Dankwoord 121 Curriculum vitae 123 Chapter 1 General introduction Table of contents chapter 1 Page 1.1.
    [Show full text]
  • Data Sheet on Spiroplasma Citri
    Prepared by CABI and EPPO for the EU under Contract 90/399003 Data Sheets on Quarantine Pests Spiroplasma citri The vectors of Spiroplasma citri are individually included in EU Directive 77/93. Since their importance only arises in relation to S. citri, they are covered in this data sheet. IDENTITY • Spiroplasma citri Name: Spiroplasma citri Saglio et al. Taxonomic position: Bacteria: Tenericutes: Mollicutes Common names: Stubborn, little leaf (English) Stubborn (French) Bayer computer code: SPIRCI EU Annex designation: II/A2 • Circulifer tenellus Name: Circulifer tenellus (Baker) Synonyms: Neoaliturus tenellus (Baker) Eutettix tenellus Baker Taxonomic position: Insecta: Hemiptera: Homoptera: Cicadellidae Common names: Beet leafhopper (English) Cicadelle de la betterave (French) Saltahojas de la remolacha (Spanish) Notes on taxonomy and nomenclature: Oman (1970) argues for the retention of Circulifer and Neoaliturus as separate genera; in his concept both tenellus and haematoceps are placed in Circulifer. Nast (1972) treats the two genera as Neoaliturus notwithstanding Oman's (1970) arguments for the retention of the two genera. He includes 17 species in the Palaearctic region of which 14 are recorded from the Mediterranean Basin. The two species, tenellus and haematoceps, are both included in Circulifer by della Giustina (1989), who reports that tenellus is confirmed in Corsica. Bayer computer code: CIRCTE EU Annex designation: II/A2 • Neoaliturus haematoceps Name: Neoaliturus haematoceps (Mulsant & Rey) Synonyms: Circulifer haematoceps (Mulsant & Rey) Jassus haematoceps Mulsant & Rey Taxonomic position: Insecta: Hemiptera: Homoptera: Cicadellidae Bayer computer code: NEOAHA EU Annex designation: II/A2 (under the name Circulifer haematoceps) HOSTS • Spiroplasma citri The principal economic hosts of S. citri are susceptible Citrus spp.
    [Show full text]