Is It Essential to Sequence the Entire 16S Rrna Gene for Bacterial
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Hyphal Proteobacteria, Hirschia Baltica Gen. Nov. , Sp. Nov
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1990, p. 443451 Vol. 40. No. 4 0020-7713/9O/040443-O9$02.00/0 Copyright 0 1990, International Union of Microbiological Societies Taxonomic and Phylogenetic Studies on a New Taxon of Budding, Hyphal Proteobacteria, Hirschia baltica gen. nov. , sp. nov. HEINZ SCHLESNER," CHRISTINA BARTELS, MANUEL SITTIG, MATTHIAS DORSCH, AND ERKO STACKEBRANDTT Institut fur Allgemeine Mikrobiologie, Christian-Albrecht-Universitat, 2300 Kiel, Federal Republic of Germany Four strains of budding, hyphal bacteria, which had very similar chemotaxonomic properties, were isolated from the Baltic Sea. The results of DNA-DNA hybridization experiments, indicated that three of the new isolates were closely related, while the fourth was only moderately related to the other three. Sequence signature and higher-order structural detail analyses of the 16s rRNA of strain IFAM 141gT (T = type strain) indicated that this isolate is related to the alpha subclass of the class Proteobacteriu. Although our isolates resemble members of the genera Hyphomicrobium and Hyphomonas in morphology, assignment to either of these genera was excluded on the basis of their markedly lower DNA guanine-plus-cytosine contents. We propose that these organisms should be placed in a new genus, Hirschiu baltica is the type species of this genus, and the type strain of H. bdtica is strain IFAM 1418 (= DSM 5838). Since the first description of a hyphal, budding bacterium, no1 and formamide were tested at concentrations of 0.02 and Hyphomicrobium vulgare (53), only the following additional 0.1% (vol/vol). Utilization of nitrogen sources was tested in genera having this morphological type have been formally M9 medium containing glucose as the carbon source. -
Prevalence, Distribution, and Phylogeny of Type Two Toxin-Antitoxin Genes Possessed by Cronobacter Species Where C. Sakazakii Homologs Follow Sequence Type Lineages
microorganisms Article Prevalence, Distribution, and Phylogeny of Type Two Toxin-Antitoxin Genes Possessed by Cronobacter Species where C. sakazakii Homologs Follow Sequence Type Lineages Samantha Finkelstein, Flavia Negrete, Hyein Jang, Jayanthi Gangiredla, Mark Mammel, Isha R. Patel, Hannah R. Chase, JungHa Woo, YouYoung Lee, Caroline Z. Wang, Leah Weinstein, Ben D. Tall * and Gopal R. Gopinath Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 MuirKirk Rd, Laurel, MD 20708, USA; sfi[email protected] (S.F.); [email protected] (F.N.); [email protected] (H.J.); [email protected] (J.G.); [email protected] (M.M.); [email protected] (I.R.P.); [email protected] (H.R.C.); [email protected] (J.W.); [email protected] (Y.L.); [email protected] (C.Z.W.); [email protected] (L.W.); [email protected] (G.R.G.) * Correspondence: [email protected] Received: 4 October 2019; Accepted: 9 November 2019; Published: 12 November 2019 Abstract: Cronobacter species are a group of foodborne pathogenic bacteria that cause both intestinal and systemic human disease in individuals of all age groups. Little is known about the mechanisms that Cronobacter employ to survive and persist in foods and other environments. Toxin–antitoxin (TA) genes are thought to play a role in bacterial stress physiology, as well as in the stabilization of horizontally-acquired re-combinatorial elements such as plasmids, phage, and transposons. TA systems have been implicated in the formation of a persistence phenotype in some bacterial species including Escherichia coli and Salmonella. -
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’. -
Mitigating Biofouling on Reverse Osmosis Membranes Via Greener Preservatives
Mitigating biofouling on reverse osmosis membranes via greener preservatives by Anna Curtin Biology (BSc), Le Moyne College, 2017 A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of MASTER OF APPLIED SCIENCE in the Department of Civil Engineering, University of Victoria © Anna Curtin, 2020 University of Victoria All rights reserved. This Thesis may not be reproduced in whole or in part, by photocopy or other means, without the permission of the author. Supervisory Committee Mitigating biofouling on reverse osmosis membranes via greener preservatives by Anna Curtin Biology (BSc), Le Moyne College, 2017 Supervisory Committee Heather Buckley, Department of Civil Engineering Supervisor Caetano Dorea, Department of Civil Engineering, Civil Engineering Departmental Member ii Abstract Water scarcity is an issue faced across the globe that is only expected to worsen in the coming years. We are therefore in need of methods for treating non-traditional sources of water. One promising method is desalination of brackish and seawater via reverse osmosis (RO). RO, however, is limited by biofouling, which is the buildup of organisms at the water-membrane interface. Biofouling causes the RO membrane to clog over time, which increases the energy requirement of the system. Eventually, the RO membrane must be treated, which tends to damage the membrane, reducing its lifespan. Additionally, antifoulant chemicals have the potential to create antimicrobial resistance, especially if they remain undegraded in the concentrate water. Finally, the hazard of chemicals used to treat biofouling must be acknowledged because although unlikely, smaller molecules run the risk of passing through the membrane and negatively impacting humans and the environment. -
Phage S144, a New Polyvalent Phage Infecting Salmonella Spp. and Cronobacter Sakazakii
International Journal of Molecular Sciences Article Phage S144, a New Polyvalent Phage Infecting Salmonella spp. and Cronobacter sakazakii Michela Gambino 1 , Anders Nørgaard Sørensen 1 , Stephen Ahern 1 , Georgios Smyrlis 1, Yilmaz Emre Gencay 1 , Hanne Hendrix 2, Horst Neve 3 , Jean-Paul Noben 4 , Rob Lavigne 2 and Lone Brøndsted 1,* 1 Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; [email protected] (M.G.); [email protected] (A.N.S.); [email protected] (S.A.); [email protected] (G.S.); [email protected] (Y.E.G.) 2 Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; [email protected] (H.H.); [email protected] (R.L.) 3 Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; [email protected] 4 Biomedical Research Institute and Transnational University Limburg, Hasselt University, BE3590 Diepenbeek, Belgium; [email protected] * Correspondence: [email protected] Received: 25 June 2020; Accepted: 21 July 2020; Published: 22 July 2020 Abstract: Phages are generally considered species- or even strain-specific, yet polyvalent phages are able to infect bacteria from different genera. Here, we characterize the novel polyvalent phage S144, a member of the Loughboroughvirus genus. By screening 211 Enterobacteriaceae strains, we found that phage S144 forms plaques on specific serovars of Salmonella enterica subsp. enterica and on Cronobacter sakazakii. Analysis of phage resistant mutants suggests that the O-antigen of lipopolysaccharide is the phage receptor in both bacterial genera. The S144 genome consists of 53,628 bp and encodes 80 open reading frames (ORFs), but no tRNA genes. -
Enterobacter Sakazakii)
J. Microbiol. Biotechnol. (2011), 21(5), 509–514 doi: 10.4014/jmb.1007.07059 First published online 3 March 2011 The Phenotypic and Genotypic Characterization of Korean Isolates of Cronobacter spp. (Enterobacter sakazakii) Kim, Jung-Beom1, Suk-Ho Kang1, Yong-Bae Park1, Jae-Ho Choi2, Sung-Jin Park2,3, Seung-Hak Cho4, Mi-Sun Park4, Hae Kyung Lee5, Na-Jung Choi2, Ha-Na Kim2, and Deog-Hwan Oh2* 1Division of Health Research and Planning, Gyeonggi-do Research Institute of Health and Environment, Suwon 440-290, Korea 2School of Bioscience and Biotechnology, Kangwon National University, Chuncheon 200-701, Korea 3Center of Senior Industry, Youngdong University, Youngdong-gun, Chungbuk 370-701, Korea 4Division of Enteric Bacterial Infections, Center for Infectious Diseases, National Institute of Health, Seoul 122-701, Korea 5Department of Laboratory Medicine, Catholic University College of Medicine, Uijongbu 480-130, Korea Received: July 30, 2010 / Revised: February 8, 2011 / Accepted: February 11, 2011 This study was conducted to investigate the phenotypic and was initially known as yellow-pigmented Enterobacter genotypic characteristics of Korean isolates of Cronobacter cloacae and reclassified based on biochemical characteristics, spp. (Enterobacter sakazakii). A total of 43 Cronobacter DNA-DNA hybridization, and antibiotic susceptibility spp., including 5 clinical isolates, 34 food isolates, 2 patterns in 1980 [5, 18]. Cronobacter spp. infection, which environmental isolates, and 2 reference strains (C. sakazakii causes life-threatening meningitis, septicemia, and necrotizing ATCC 29004 and C. muytjensii ATCC51329) were used in enterocolitis in infants, has been implicated in foodborne this study. Korean isolates of Cronobacter spp. were outbreaks worldwide [17, 22]. The pathogen has been divided into 11 biogroups according to their biochemical isolated from a variety of food, clinical, and environmental profiles and 3 genomic groups based on the analysis of sources including cheese, vegetables, grains, soil, and powdered their 16S rRNA gene sequences. -
Phylogeny and Polyphasic Taxonomy of Caulobacter Species. Proposal of Maricaulis Gen
International Journal of Systematic Bacteriology (1 999), 49, 1053-1 073 Printed in Great Britain Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundirnonas and Caulobacter Wolf-Rainer Abraham,' Carsten StrOmpl,l Holger Meyer, Sabine Lindholst,l Edward R. B. Moore,' Ruprecht Christ,' Marc Vancanneyt,' B. J. Tindali,3 Antonio Bennasar,' John Smit4 and Michael Tesar' Author for correspondence: Wolf-Rainer Abraham. Tel: +49 531 6181 419. Fax: +49 531 6181 41 1. e-mail : [email protected] Gesellschaft fur The genus Caulobacter is composed of prosthecate bacteria often specialized Biotechnologische for oligotrophic environments. The taxonomy of Caulobacter has relied Forschung mbH, primarily upon morphological criteria: a strain that visually appeared to be a Mascheroder Weg 1, D- 38124 Braunschweig, member of the Caulobacter has generally been called one without Germany challenge. A polyphasic approach, comprising 165 rDNA sequencing, profiling Laboratorium voor restriction fragments of 165-235 rDNA interspacer regions, lipid analysis, Microbiologie, Universiteit immunological profiling and salt tolerance characterizations, was used Gent, Gent, Belgium to clarify the taxonomy of 76 strains of the genera Caulobacter, Deutsche Sammlung von Brevundimonas, Hyphomonas and Mycoplana. The described species of the Mikroorganismen und genus Caulobacter formed a paraphyletic group with Caulobacter henricii, Zellkulturen, Caulobacter fusiformis, Caulobacter vibrioides and Mycoplana segnis Braunschweig, Germany (Caulobacter segnis comb. nov.) belonging to Caulobacter sensu stricto. Dept of Microbiology and Caulobacter bacteroides (Brevundimonas bacteroides comb. nov.), C. henricii Immunology, University of subsp. aurantiacus (Brevundimonas aurantiaca comb. nov.), Caulobacter British Columbia, intermedius (Brevundimonas intermedia comb. -
Étude Du Potentiel Biotechnologique De Halomonas Sp. SF2003 : Application À La Production De Polyhydroxyalcanoates (PHA)
THESE DE DOCTORAT DE L’UNIVERSITE BRETAGNE SUD COMUE UNIVERSITE BRETAGNE LOIRE ECOLE DOCTORALE N° 602 Sciences pour l'Ingénieur Spécialité : Génie des procédés et Bioprocédés Par Tatiana THOMAS Étude du potentiel biotechnologique de Halomonas sp. SF2003 : Application à la production de PolyHydroxyAlcanoates (PHA). Thèse présentée et soutenue à Lorient, le 17 Décembre 2019 Unité de recherche : Institut de Recherche Dupuy de Lôme Thèse N° : 542 Rapporteurs avant soutenance : Sandra DOMENEK Maître de Conférences HDR, AgroParisTech Etienne PAUL Professeur des Universités, Institut National des Sciences Appliquées de Toulouse Composition du Jury : Président : Mohamed JEBBAR Professeur des Universités, Université de Bretagne Occidentale Examinateur : Jean-François GHIGLIONE Directeur de Recherche, CNRS Dir. de thèse : Stéphane BRUZAUD Professeur des Universités, Université de Bretagne Sud Co-dir. de thèse : Alexis BAZIRE Maître de Conférences HDR, Université de Bretagne Sud Co-dir. de thèse : Anne ELAIN Maître de Conférences, Université de Bretagne Sud Étude du potentiel biotechnologique de Halomonas sp. SF2003 : application à la production de polyhydroxyalcanoates (PHA) Tatiana Thomas 2019 « Failure is only the opportunity to begin again more intelligently. » Henry Ford « I dettagli fanno la perfezione e la perfezione non è un dettaglio. » Leonardo Da Vinci Étude du potentiel biotechnologique de Halomonas sp. SF2003 : application à la production de polyhydroxyalcanoates (PHA) Tatiana Thomas 2019 Étude du potentiel biotechnologique de Halomonas sp. SF2003 : application à la production de polyhydroxyalcanoates (PHA) Tatiana Thomas 2019 Remerciements Pour commencer, mes remerciements s’adressent à l’Université de Bretagne Sud et Pontivy Communauté qui ont permi le financement et la réalisation de cette thèse entre l’Institut de Recherche Dupuy de Lôme et le Laboratoire de Biotechnologies et Chimie Marines. -
Cronobacter: an Emerging Opportunistic Pathogen Associated with Neonatal Meningitis, Sepsis and Necrotizing Enterocolitis
Journal of Perinatology (2013) 33, 581–585 & 2013 Nature America, Inc. All rights reserved 0743-8346/13 www.nature.com/jp STATE-OF-THE-ART Cronobacter: an emerging opportunistic pathogen associated with neonatal meningitis, sepsis and necrotizing enterocolitis CJ Hunter1,2 and JF Bean1 Members of the genus Cronobacter are an emerging group of opportunist Gram-negative pathogens. This genus was previously thought to be a single species, called Enterobacter sakazakii. Cronobacter spp. typically affect low-birth-weight neonates, causing life-threatening meningitis, sepsis and necrotizing enterocolitis. Outbreaks of disease have been associated with contaminated infant formula, although the primary environmental source remains elusive. Advanced understanding of these bacteria and better classification has been obtained by improved detection techniques and genomic analysis. Research has begun to characterize the virulence factors and pathogenic potential of Cronobacter. Investigations into sterilization techniques and protocols for minimizing the risk of contamination have been reviewed at national and international forums. In this review, we explore the clinical impact of Cronobacter neonatal and pediatric infections, discuss virulence and pathogenesis, and review prevention and treatment strategies. Journal of Perinatology (2013) 33, 581–585; doi:10.1038/jp.2013.26; published online 28 March 2013 Keywords: Cronobacter sakazakii; meningitis; necrotizing enterocolitis; neonatal infections; infant formula INTRODUCTION single clinical setting.10 Cronobacter neonatal infection rates Cronobacter is an emerging genus of opportunistic Gram-negative remain low and are reported in the USA as one Cronobacter pathogens associated with potentially fatal neonatal infections, infection per 100 000 infants, 8.7 per 100 000 low-birth-weight including meningitis, sepsis and necrotizing enterocolitis (NEC).1 neonates, and one Cronobacter infection per 10 660 very low- 13 These infections typically affect our smallest and most vulnerable birth-weight neonates. -
Isolation of Cronobacter Spp.(Formerly Enterobacter Sakazakii) from Infant
BMC Microbiology BioMed Central Research article Open Access Isolation of Cronobacter spp. (formerly Enterobacter sakazakii) from infant food, herbs and environmental samples and the subsequent identification and confirmation of the isolates using biochemical, chromogenic assays, PCR and 16S rRNA sequencing Ziad W Jaradat*†, Qotaiba O Ababneh†, Ismail M Saadoun, Nawal A Samara and Abrar M Rashdan Address: Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, P. O. Box 3030, Irbid-22110, Jordan Email: Ziad W Jaradat* - [email protected]; Qotaiba O Ababneh - [email protected]; Ismail M Saadoun - [email protected]; Nawal A Samara - [email protected]; Abrar M Rashdan - [email protected] * Corresponding author †Equal contributors Published: 27 October 2009 Received: 10 March 2009 Accepted: 27 October 2009 BMC Microbiology 2009, 9:225 doi:10.1186/1471-2180-9-225 This article is available from: http://www.biomedcentral.com/1471-2180/9/225 © 2009 Jaradat et al; 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: Cronobacter spp. (formerly Enterobacter sakazakii), are a group of Gram-negative pathogens that have been implicated as causative agents of meningitis and necrotizing enterocolitis in infants. The pathogens are linked to infant formula; however, they have also been isolated from a wide range of foods and environmental samples. Results: In this study, 233 samples of food, infant formula and environment were screened for the presence of Cronobacter spp. -
A Novel Primer Targeted Gyrb Gene for the Identification of Cronobacter Sakazakii in Powdered Infant Formulas (PIF) and Baby Foods in Iran
Received: 21 July 2018 Revised: 18 November 2018 Accepted: 26 November 2018 DOI: 10.1111/jfs.12609 ORIGINAL ARTICLE A novel primer targeted gyrB gene for the identification of Cronobacter sakazakii in powdered infant formulas (PIF) and baby foods in Iran Afsaneh Mashoufi1 |KiarashGhazvini2 | Mohammad Hashemi1 | Majid Ghayour Mobarhan1 | Vida Vakili3 | Asma Afshari1 1Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Abstract Sciences, Mashhad, Iran The aim of this study was to perform a molecular identification and design a polymerase chain 2Department of Microbiology, Faculty of reaction (PCR) method based on a specific gene (gyrase subunit B [gyrB]) for rapid detection of Medicine, Mashhad University of Medical Cronobacter sakazakii. In this study, from February 2017 to January 2018, 100 powdered infant Sciences, Mashhad, Iran formula milks (PIF1-6) and 100 baby food items (BF1-8) (total number = 200 samples) were pur- 3Department of Social Medicine, Faculty of Medicine, Mashhad University of Medical chased from different commercial brands from different pharmacies of the Mashhad city, Iran Sciences, Mashhad, Iran from different pharmacies of the Mashhad city, Iran. Correspondence After isolation of Cronobacter, DNA extraction and PCR assay were performed to detect and Asma Afshari, Department of Nutrition, confirm genus and species of isolated bacteria with 16S ribosomal RNA (16S rRNA) and designed Faculty of Medicine, Mashhad University of gyrB primers, respectively. The abundance of C. sakazakii in PIFs and baby foods by culture Medical Sciences, Mashhad, Iran. Email: [email protected] method were 5/100 (5%) and 8/100 (8%), respectively; also, the final analysis based on gyrB Funding information primer pairs in PIF and baby food showed contamination rates of 0/100 (0%) and 3/100 (3%), Mashhad University of medical science, respectively. -
High-Throughput 16S Rrna Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens
foods Article High-Throughput 16S rRNA Gene Sequencing of Butter Microbiota Reveals a Variety of Opportunistic Pathogens Mikhail Y. Syromyatnikov 1,2,*, Anastasia V. Kokina 1,2, Sergey A. Solodskikh 1,2, Anna V. Panevina 1, Evgeny S. Popov 3 and Vasily N. Popov 1,2 1 Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia; [email protected] (A.V.K.); [email protected] (S.A.S.); [email protected] (A.V.P.); [email protected] (V.N.P.) 2 Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia 3 Department of Service and Restaurant Business, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia; [email protected] * Correspondence: [email protected]; Tel.: +7-(473)-239-92-81 Received: 8 April 2020; Accepted: 8 May 2020; Published: 9 May 2020 Abstract: Microbial contamination of dairy products with a high fat content (e.g., butter) has been studied insufficiently. No studies using modern molecular methods to investigate microbial communities in butter have been conducted so far. In this work, we used high-throughput sequencing and Sanger sequencing of individual bacterial colonies to analyze microbial content of commercially available butter brands. A total of 21 samples of commercially available butter brands were analyzed. We identified a total of 94 amplicon sequence variants corresponding to different microbial taxa. The most abundant lactic acid bacteria in butter were Lactobacillus kefiri, Lactobacillus parakefiri, Lactococcus taiwanensis and Lactococcus raffinolactis. A large amount of Streptococcus spp. bacteria (87.9% of all identified bacteria) was found in one of the butter samples.