DOCSLIB.ORG

WO 2018/165764 Al 20 September 2018 (20.09.2018) W ! P O PCT

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
WO 2018/165764 Al 20 September 2018 (20.09.2018) W ! P O PCT (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/165764 Al 20 September 2018 (20.09.2018) W ! P O PCT (51) International Patent Classification Patrick; 245 Queen Street, Apt. 3 , Charlottetown, Prince C07K 7/06 (2006.01) A61L 29/16 (2006.01) Edward Island CIA 4B9 (CA). A23L 33/135 (2016.01) A61L 31/16 (2006.01) (74) Agent: LOWTHERS, Erica E. et al; Aird & McBurney A23L 33/195 (2016.01) A61P 31/04 (2006.01) LP, Brookfield Place, 181 Bay Street, Suite 1800, Toronto, A61K 35/741 (2015.01) C07K 14/00 (2006.01) Ontario M5J 2T9 (CA). A61K 38/08 (2006.01) C07K 14/195 (2006.01) A61K38/1 (2006.01) C07K 14/315 (2006.01) (81) Designated States (unless otherwise indicated, for every A61K38/1 6 (2006.01) C07K 14/335 (2006.01) kind of national protection available): AE, AG, AL, AM, A61L 15/44 (2006.01) C07K 7/08 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, A61L 27/54 (2006.01) CI2N 1/20 (2006.01) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (21) International Application Number: HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, PCT/CA20 18/0503 19 KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (22) International Filing Date: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, 16 March 2018 (16.03.2018) OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY,TH, TJ, TM, TN, (25) Filing Language: English TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (26) Publication Language: English (84) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 62/472,047 16 March 2017 (16.03.2017) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, (71) Applicant: MICROSINTESIS INC. [CA/CA]; 329 Sum TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, mer Avenue, Oakville, Ontario L6 1S7 (CA). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, (72) Inventors: CELLA, Monica Angela; 39 Ducks Landing, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, Apt. 302, Stratford, Prince Edward Island C1B 2X8 (CA). TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, CURTIS, Sarah M.; 130 Balsam Road, P.O. Box 1065, KM, ML, MR, NE, SN, TD, TG). Atikokan, Ontario POT ICO (CA). ROEPKE, Jonathon (54) Title: COMPOSITIONS AND METHODS INVOLVING PROBIOTIC MOLECULES Biological Rep 1 ^Biological Rep 1 0 5 10 15 Concentration of Cell free supernatant (mg/i Figure 1 (57) Abstract: Provided are peptides that are derived from probiotic bacteria that may be useful for preventing and/or treating enteric infections or non-enteric infections in a subject. The peptides may also find use for reducing the virulence of enteric infections or non- enteric infections in a subject. Also provided are compositions of the peptides and compositions comprising culture fractions of the probiotic bacteria. [Continued on nextpage] WO 2018/165764 Al llll II II 11III II I I III I I llll Hill II I II Published: — with international search report (Art. 21(3)) — in black and white; the international application as filed contained color or greyscale and is availablefor download from PATENTSCOPE Compositions and Methods Involving Probiotic Molecules Field The present invention relates to probiotic molecules. More specifically, the present invention is, in aspects, concerned with probiotic molecules, compositions comprising the probiotic molecules, and various methods and uses of the probiotic molecules. Background A small biopeptide produced by Lactobacillus species has been shown to be effective against enterohemorrhagic Escherichia coli infection [Medellin-Pefia et al. , 2009]. It was shown to influence and down-regulate the transcription of E. coli genes involved in colonization and quorum sensing and was able to prevent the adherence of the E. coli to host epithelial cells [Medellin-Pefia et al. , 2009]. It was demonstrated that the biopeptide influenced the E. coli type III secretion system (T3SS) and was able to interfere with quorum sensing (QS) signalling system and thus resulted in a down-regulation of virulence genes [Medellin-Pefia et al., 2007, Medellin-Pefia and Griffiths, 2009]. International Patent Application Publication No. WO 2009/1 5571 1 describes isolated and characterized molecules derived from probiotic bacteria from the genera Lactobacillus, Lactococcus, Streptococcus or Bifidobacterium for use in compositions and methods for the treatment and/or prevention of infection by harmful pathogenic bacteria such as Salmonella or E. coli. The isolated molecules can also be used in nutritional or medical food products which provide probiotics to the gastrointestinal tract of a mammal. International Patent Application Publication No. WO 201 5/021 530 describes molecules derived from probiotic bacteria that are provided for use in compositions and methods for the treatment and/or prevention of infection by pathogenic viruses. The isolated molecules can also be used in nutritional or medical food products which provide probiotics to the gastrointestinal tract of a mammal. There is a need for alternative therapies to overcome or mitigate at least some of the deficiencies of the prior art, and/or to provide a useful alternative. Description of the Drawings The present invention will be further understood from the following description with reference to the Figures, in which: Figure 1 shows a lactate dehydrogenase cell toxicity assay. Dose response curve of cell toxicity inhibition with cell free supernatant. Error bars represent standard deviation. Figure 2 shows a lactate dehydrogenase cell toxicity assay. Dose response curve of cell toxicity inhibition with cell free supernatant. Error bars represent standard deviation. Summary In accordance with an aspect, there is provided a peptide comprising the amino acid sequence MALPPK, wherein the peptide has fewer than 19 amino acid residues. In accordance with an aspect, there is provided a peptide consisting of the amino acid sequence MALPPK. In accordance with an aspect, there is provided a peptide comprising the amino acid sequence CVLPPK, wherein the peptide comprises fewer than 68 amino acid residues. In accordance with an aspect, there is provided a peptide consisting of the amino acid sequence CVLPPK. In accordance with an aspect, there is provided a peptide comprising the amino acid sequence HLLPLP, wherein the peptide comprises fewer than 9 amino acid residues. In accordance with an aspect, there is provided a peptide consisting of the amino acid sequence HLLPLP. In accordance with an aspect, there is provided a peptide comprising the sequence XX[L or l]PPK, wherein each X independently designates a hydrophobic amino acid, wherein the peptide has fewer than 19 amino acid residues. In accordance with an aspect, there is provided a peptide consisting of the sequence XX[L or l]PPK, wherein each X independently designates a hydrophobic amino acid. In accordance with an aspect, there is provided a peptide consisting of the sequence XiX 2[L or l]PPK, wherein X is selected from N , C, Q , M , S, and T and wherein X2 is selected from A , I, L , and V. In accordance with an aspect, there is provided a peptide comprising or consisting of a sequence selected from the group consisting of LPVPK, ALPK, EVLNCLALPK, LPLP, HLLPLPL, YVPEPF, KYVPEPF, and EMPFKPYPVEPF, wherein the peptide comprises 4 , 5 , 6 , 7 , 8 , 9 , 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid residues In an aspect, the peptide is derived from a probiotic bacteria selected from Lactobacillus, Lactococcus, Streptococcus, Bifidobacterium, Pediococcus and combinations thereof. In an aspect, the Lactobacillus is selected from Lactobacillus acidophilus (La-5), Lactobacillus fermentum, Lactobacillus rhamnosus, Lactobacillus reuteri, Lactobacillus helveticus, and Lactobacillus plantarum. In an aspect, the Lactococcus is Lactococcus lactis. In an aspect, the Bifidobacterium is selected from Bifidobacterium longum, Bifidobacterium bifidum, Bifidobacterium infantis and Bifidobacterium crudilactis and mixtures thereof. In an aspect, the Streptococcus is Streptococcus thermophilus. In an aspect, the peptide is combined with one or more of an antiviral, a sugar source, an edible food product, a nutritional supplement and ingestible liquid. In an aspect, the peptide is concentrated from a cell-free supernatant or fraction thereof. In an aspect, the peptide is provided as a dried culture fraction, such as lyophilized or spray-dried. In an aspect, the dried culture fraction is a cell-free supernatant. In accordance with an aspect, there is provided a composition comprising the peptide described herein. In an aspect, the composition is a food product, beverage product, health product, medicament, or nutritional supplement. In an aspect, the composition comprises live probiotic bacteria from which the peptides are derived. In an aspect, the composition comprises live probiotic bacteria other than the bacteria from which the peptides are derived. In an aspect, the peptides in the composition are purified. In accordance with an aspect, there is provided a method of treating and/or preventing an infection in a subject and/or for reducing the virulence of an infection in a subject, the method comprising administering the peptide or the composition described herein to a subject in need thereof. In an aspect, the infection is an enteric infection. In an aspect, the infection is a non-enteric infection.
Load more

Recommended publications
  • Supplementary Information
    doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig.
    [Show full text]
  • Review Article Yersinia Enterocolitica: Mode of Transmission, Molecular Insights of Virulence, and Pathogenesis of Infection
    SAGE-Hindawi Access to Research Journal of Pathogens Volume 2011, Article ID 429069, 10 pages doi:10.4061/2011/429069 Review Article Yersinia enterocolitica: Mode of Transmission, Molecular Insights of Virulence, and Pathogenesis of Infection Yeasmin Sabina,1 Atiqur Rahman,2 Ramesh Chandra Ray,3 and Didier Montet4 1 Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh 2 Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh 3 Central Tuber Crops Research Institute, Bhubaneswar, India 4 Centre International de Recherche en Agronomie pour le Developpement (CIRAD), Montpellier, France Correspondence should be addressed to Yeasmin Sabina, y [email protected] Received 19 April 2011; Revised 28 May 2011; Accepted 5 June 2011 Academic Editor: Latiful Bari Copyright © 2011 Yeasmin Sabina et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Although Yersinia enterocolitica is usually transmitted through contaminated food and untreated water, occasional transmission such as human-to-human, animal-to-human and blood transfusion associated transmission have also identified in human disease. Of the six Y. enterocolitica biotypes, the virulence of the pathogenic biotypes, namely, 1B and 2–5 is attributed to the presence of a highly conserved 70-kb virulence plasmid, termed pYV/pCD and certain chromosomal genes. Some biotype 1A strains, despite lacking virulence plasmid (pYV) and traditional chromosomal virulence genes, are isolated frequently from humans with gastrointestinal diseases similar to that produced by isolates belonging known pathogenic biotypes. Y. enterocolitica pathogenic biotypes have evolved two major properties: the ability to penetrate the intestinal wall, which is thought to be controlled by plasmid genes, and the production of heat-stable enterotoxin, which is controlled by chromosomal genes.
    [Show full text]
  • Antarctic Rahnella Inusitata: a Producer of Cold-Stable Β-Galactosidase Enzymes
    International Journal of Molecular Sciences Article Antarctic Rahnella inusitata: A Producer of Cold-Stable β-Galactosidase Enzymes Kattia Núñez-Montero 1,2,†, Rodrigo Salazar 1,3,†, Andrés Santos 1,3,†, Olman Gómez-Espinoza 2,4 , Scandar Farah 1 , Claudia Troncoso 1,3 , Catalina Hoffmann 1, Damaris Melivilu 1, Felipe Scott 5 and Leticia Barrientos Díaz 1,* 1 Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, Temuco 4810296, Chile; [email protected] (K.N.-M.); [email protected] (R.S.); [email protected] (A.S.); [email protected] (S.F.); [email protected] (C.T.); [email protected] (C.H.); [email protected] (D.M.) 2 Biotechnology Investigation Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago 159-7050, Costa Rica; [email protected] 3 Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile 4 Laboratory of Plant Physiology and Molecular Biology, Institute of Agroindustry, Department of Agronomic Sciences and Natural Resources, Faculty of Agricultural and Forestry Sciences, Universidad de La Frontera, Temuco 4811230, Chile 5 Green Technology Research Group, Facultad de Ingenieria y Ciencias Aplicadas, Universidad de los Andes, Santiago 7620001, Chile; [email protected] * Correspondence: [email protected]; Tel.: +56-45-259-2802 Citation: Núñez-Montero, K.; † These authors contributed equally to this work. Salazar, R.; Santos, A.; Gómez- Espinoza, O.; Farah, S.; Troncoso, C.; Abstract: There has been a recent increase in the exploration of cold-active β-galactosidases, as it Hoffmann, C.; Melivilu, D.; Scott, F.; offers new alternatives for the dairy industry, mainly in response to the current needs of lactose- Barrientos Díaz, L.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8,835,117 B2 Mitchell Et Al
    US008835117B2 (12) United States Patent (10) Patent No.: US 8,835,117 B2 Mitchell et al. (45) Date of Patent: Sep. 16, 2014 (54) NUCLEICACIDS FOR DETECTION AND OTHER PUBLICATIONS DISCRIMINATION OF GENOTYPES OF CHLAMYDOPHILA PSITTAC Nazarenko, I. Methods in Molecular Biology (2006) 335: 95-114.* Jeffrey et al. Microbiology (2007) 153: 2679-2688.* 75) Inventors: Stephaniep L. Mitchell, Somerville, MA Geens et al. Journal of Clinical Microbiology (2005) 43(5): 2456 (US); Jonas M. Winchell, Lilburn, GA 2461. (US) Geens et al., “Development of a Chlamydophila psittaci species specific and genotype-specific real-time PCR.” Vet. Res., 36: 787 (73) Assignee: The United States of America as 797, 2005. represented by the Secretary of the Geens et al., “Sequencing of the Chlamydophila psittaci OmpA Gene Department of Health and Human Reveals a New Genotype, E/B, and the Need for a Rapid Discrimi Services, Centers for Disease Control natory Genotyping Method.” J. Clin. Microbiol. 43(5): 2456-2461, and Prevention, Washington, DC (US) 2005. Heddema, “Genotyping of Chlamydophila psittaci in Human (*) Notice: Subject to any disclaimer, the term of this Samples.” Emerging Infectious Diseases, 12(12): 1989-1990, 2006. patent is extended or adjusted under 35 Menard, “Development of a real-time PCR for the detection of U.S.C. 154(b) by 82 days. Chlamydia psittaci,” J. Med. Microbiol. 55(Pt. 4): 471-473, 2006. Mitchellet al., “Genotyping of Chlamydophilapsittaci by Real-Time (21) Appl. No.: 13/322,787 PCR and High-Resolution Melt Analysis,” Journal of Clinical Microbiology, 47(1): 175-181, 2009. (22) PCT Filed: May 28, 2010 Sachse et al., “Genotyping of Chlamydophila psittaci using a new DNA microarray assay based on sequence analysis of ompA genes.” (86).
    [Show full text]
  • Yersinia Enterocolitica Infections in People and Other Animals
    Copyright is owned by the Author of the thesis. Permission is given for a copy to be downloaded by an individual for the purpose of research and private study only. The thesis may not be reproduced elsewhere without the permission of the Author. YERSINIA ENTEROCOLITICA INFECTIONS IN PEOPLE AND OTHER ANIMALS )- fl· .L +- � l""'-' A NEW ZEALAND STUDY STANLEY GORDON FENWICK A thesis presented in partial fulfilment of the requirements fo r the degree of Doctor of Philosophy in Veterinary Microbiology Massey University July 1997 MASSEY UNIVERSITY LIBRARY THESIS COPYRIGHT FORM I Title of Thesis: / I ffoflL I I V I PIease delete section not applicable. ( ) (a) I give permission for my thesis to be made available to readers in Massey University Library under conditions determined by the Librarian. (b) I do not wish my thesis t a e available to readers without my written consent for ... ( ) (a) I agree that my thesis, or a copy, may be sent to another institution under conditions determined by the Librarian. (b) I do not wish my thesis, or a "nr,u--f?'I e sent to another institution without my written consent for onths. (a) I agree that my thesis may be copied for Library use. (b) copied for Library use for _ months. Signed: Date: ****************************************************************************** he copyright of this thesis belongs to the author. Readers must sign their name in the space elow to show that they recognise this. They are asked to add their permanent address. AME and ADDRESS DATE ; I .. :1 ABSTRACT During the past three decades, Yersinia enterocolitica has risen to worldwide prominence from an obscure and taxonomically undefmed organism to a common zoonotic pathogen, capable of causing a wide range of clinical syndromes in both animals and people.
    [Show full text]
  • Epidemiology and Comparative Analysis of Yersinia in Ireland Author(S) Ringwood, Tamara Publication Date 2013 Original Citation Ringwood, T
    UCC Library and UCC researchers have made this item openly available. Please let us know how this has helped you. Thanks! Title Epidemiology and comparative analysis of Yersinia in Ireland Author(s) Ringwood, Tamara Publication date 2013 Original citation Ringwood, T. 2013. Epidemiology and comparative analysis of Yersinia in Ireland. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2013, Tamara Ringwood http://creativecommons.org/licenses/by-nc-nd/3.0/ Item downloaded http://hdl.handle.net/10468/1294 from Downloaded on 2021-10-07T12:07:10Z Epidemiology and Comparative Analysis of Yersinia in Ireland by Tamara Ringwood A thesis presented for the Degree of Doctor of Philosophy National University of Ireland, Cork University College Cork Coláiste na hOllscoile Corcaigh Department of Microbiology Head of Department: Prof. Gerald F. Fitzgerald Supervisor: Prof. Michael B. Prentice April 2013 Contents List of Tables .............................................................................................................................................. iv List of figures ............................................................................................................................................. vi Declaration ............................................................................................................................................... viii Acknowledgements ................................................................................................................................
    [Show full text]
  • Clinical Isolates of Yersinia Enterocolitica in Finland 117 2013 117
    Leila M. Sihvonen Leila Leila M. Sihvonen Clinical isolates of Yersinia enterocolitica in Finland Leila M. Sihvonen Identification and Epidemiology Clinical isolates of Yersinia enterocolitica in Finland Identification and Epidemiology Clinical isolates of Clinical isolates Yersinia enterocolitica is a foodborne bacterium that causes gastroenteritis and post-infectious complications, such as reactive arthritis, in humans. Y. enterocolitica species is divided into six biotypes, which differ in their ability to cause illness. The Y. enterocolitica incidence in Finland has been among the highest in the EU, but there has been little information on the occurrence of different Y. enterocolitica biotypes. enterocolitica Yersinia In this thesis Y. enterocolitica strains isolated from Finnish patients were characterised and the symptoms and sources of infections were analysed RESEARCH RESEARCH in a case-control study. The majority of clinical isolates of Y. enterocolitica were found to belong to biotype 1A, the status of which as a true pathogen is controversial. Furthermore, the study investigated the microbiological identification and molecular typing methods for Y. enterocolitica. The MLVA method was found to be appropriate for investigating foodborne outbreaks. in Finland This study adds to the understanding of epidemiology of Y. enterocolitica in Finland and emphasises the importance of correct identification of Yersinia strains in order to evaluate the clinical importance of the microbiological findings. National Institute for Health and Welfare P.O. Box 30 (Mannerheimintie 166) FI-00271 Helsinki, Finland 117 Telephone: 358 29 524 6000 117 117 2013 ISBN 978-952-302-064-1 www.thl.fi RESEARCH NRO 117 2014 Leila M. Sihvonen Clinical isolates of Yersinia enterocolitica in Finland Identification and Epidemiology ACADEMIC DISSERTATION To be presented with the permission of the Faculty of Agriculture and Forestry, University of Helsinki, for public examination in Auditorium 1041, Biocenter 2, Viikinkaari 5, on 17.01.2014, at 12 noon.
    [Show full text]
  • International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485
    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’.
    [Show full text]
  • Insights Into the Evolution of Sialic Acid Catabolism Among Bacteria Salvador Almagro-Moreno1,2 and E Fidelma Boyd*1
    BMC Evolutionary Biology BioMed Central Research article Open Access Insights into the evolution of sialic acid catabolism among bacteria Salvador Almagro-Moreno1,2 and E Fidelma Boyd*1 Address: 1Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA and 2Department of Microbiology, National University of Ireland, University College Cork, Cork, Ireland Email: Salvador Almagro-Moreno - [email protected]; E Fidelma Boyd* - [email protected] * Corresponding author Published: 26 May 2009 Received: 16 September 2008 Accepted: 26 May 2009 BMC Evolutionary Biology 2009, 9:118 doi:10.1186/1471-2148-9-118 This article is available from: http://www.biomedcentral.com/1471-2148/9/118 © 2009 Almagro-Moreno and Boyd; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Sialic acids comprise a family of nine-carbon amino sugars that are prevalent in mucus rich environments. Sialic acids from the human host are used by a number of pathogens as an energy source. Here we explore the evolution of the genes involved in the catabolism of sialic acid. Results: The cluster of genes encoding the enzymes N-acetylneuraminate lyase (NanA), epimerase (NanE), and kinase (NanK), necessary for the catabolism of sialic acid (the Nan cluster), are confined 46 bacterial species, 42 of which colonize mammals, 33 as pathogens and 9 as gut commensals. We found a putative sialic acid transporter associated with the Nan cluster in most species.
    [Show full text]
  • Mycoplasma Spermatophilum, a New Species Isolated from Human Spermatozoa and Cervix AURIOL C
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1991, p. 229-233 Vol. 41, No. 2 0020-7713/91/020229-05$02.oo/o Copyright 0 1991, International Union of Microbiological Societies Mycoplasma spermatophilum, a New Species Isolated from Human Spermatozoa and Cervix AURIOL C. HILL Medical Research Council Toxicology Unit, Woodmansterne Road, Carshalton, Surrey SM5 4EF, United Kingdom A mycoplasma isolated from human spermatozoa and a human cervix was shown to be serologically distinct from 98 previously recognized MycopEasma and AchoZepZasma spp. Six mycoplasma colonies were cloned and examined in detail for morphology, growth, and biochemical characteristics; five of these were from sperm samples and one was from a cervix. These strains were closely related and had the following properties: guanine-plus-cytosine content of 32 mol%, requirement for sterol, and anaerobic growth. Glucose was not metabolized, and arginine and urea were not hydrolyzed. Strain AH159 (= NCTC 11720) is the type strain of a new species, Mycoplasma spermatophilum. Twelve named Mycoplasma and Acholeplasma species colony isolated from each patient was cloned to produce a have been isolated from the respiratory or genital tracts of pure culture; this was done by initially filtering a broth humans (6). Mycoplasma buccale, Mycoplasma faucium, culture through a 220-nm-pore-size membrane filter, cultur- Mycoplasma lipophilum , Mycoplasma orale, Mycoplasma ing the filtrate on solid medium, transferring a single result- pneumoniae, and Mycoplasma salivarium are found almost ing colony to another agar plate, and inoculating the subse- exclusively in respiratory tracts. Mycoplasma fermentans quent growth into broth. This whole procedure was repeated has been found infrequently in urogenital tracts, while My- an additional four times; thus, the organisms were filter coplasma primatum, a species commonly present in nonhu- cloned five times (29).
    [Show full text]
  • HL7 Implementation Guide for CDA Release 2: NHSN Healthcare Associated Infection (HAI) Reports, Release 2 (U.S
    CDAR2L3_IG_HAIRPT_R2_D2_2009FEB HL7 Implementation Guide for CDA Release 2: NHSN Healthcare Associated Infection (HAI) Reports, Release 2 (U.S. Realm) Draft Standard for Trial Use February 2009 © 2009 Health Level Seven, Inc. Ann Arbor, MI All rights reserved HL7 Implementation Guide for CDA R2 NHSN HAI Reports Page 1 Draft Standard for Trial Use Release 2 February 2009 © 2009 Health Level Seven, Inc. All rights reserved. Co-Editor: Marla Albitz Contractor to CDC, Lockheed Martin [email protected] Co-Editor/Co-Chair: Liora Alschuler Alschuler Associates, LLC [email protected] Co-Chair: Calvin Beebe Mayo Clinic [email protected] Co-Chair: Keith W. Boone GE Healthcare [email protected] Co-Editor/Co-Chair: Robert H. Dolin, M.D. Semantically Yours, LLC [email protected] Co-Editor Jonathan Edwards CDC [email protected] Co-Editor Pavla Frazier RN, MSN, MBA Contractor to CDC, Frazier Consulting [email protected] Co-Editor: Sundak Ganesan, M.D. SAIC Consultant to CDC/NCPHI [email protected] Co-Editor: Rick Geimer Alschuler Associates, LLC [email protected] Co-Editor: Gay Giannone M.S.N., R.N. Alschuler Associates LLC [email protected] Co-Editor Austin Kreisler Consultant to CDC/NCPHI [email protected] Primary Editor: Kate Hamilton Alschuler Associates, LLC [email protected] Primary Editor: Brett Marquard Alschuler Associates, LLC [email protected] Co-Editor: Daniel Pollock, M.D. CDC [email protected] HL7 Implementation Guide for CDA R2 NHSN HAI Reports Page 2 Draft Standard for Trial Use Release 2 February 2009 © 2009 Health Level Seven, Inc. All rights reserved. Acknowledgments This DSTU was produced and developed in conjunction with the Division of Healthcare Quality Promotion, National Center for Preparedness, Detection, and Control of Infectious Diseases (NCPDCID), and Centers for Disease Control and Prevention (CDC).
    [Show full text]
  • Microbial Signatures of Oral Dysbiosis, Periodontitis and Edentulism 2 Revealed by Gene Meter Methodology 3 4 M
    bioRxiv preprint doi: https://doi.org/10.1101/070367; this version posted August 19, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Microbial Signatures of Oral Dysbiosis, Periodontitis and Edentulism 2 Revealed by Gene Meter Methodology 3 4 M. Colby Hunter1, Alex E. Pozhitkov2, and Peter A. Noble#3 5 6 *Corresponding author, Peter A Noble, Email: [email protected] 7 8 Authors’ affiliations: 9 10 1. Program in Microbiology, Alabama State University, Montgomery, AL 36101 11 2. Department of Oral Health, University of Washington, Box 3574444, Seattle, Washington 12 98195-7444 Ph: 206-409-6664 13 3. Department of Periodontics, University of Washington, Box 3574444, Seattle, Washington 14 98195-7444 Ph: 206-409-6664 15 16 Authors’ emails: 17 18 Hunter: [email protected] 19 Pozhitkov: [email protected] 20 Noble: [email protected] 21 22 bioRxiv preprint doi: https://doi.org/10.1101/070367; this version posted August 19, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 ABSTRACT (N=305 WORDS) 24 25 Conceptual models suggest certain microorganisms (e.g., the red complex) are indicative of a specific 26 disease state (e.g., periodontitis); however, recent studies have questioned the validity of these models. 27 Here, the abundances of 500+ microbial species were determined in 16 patients with clinical signs of 28 one of the following oral conditions: periodontitis, established caries, edentulism, and oral health.
    [Show full text]