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Comparative Genomics of the Aeromonadaceae Core Oligosaccharide Biosynthetic Regions
CORE Metadata, citation and similar papers at core.ac.uk Provided by Diposit Digital de la Universitat de Barcelona International Journal of Molecular Sciences Article Comparative Genomics of the Aeromonadaceae Core Oligosaccharide Biosynthetic Regions Gabriel Forn-Cuní, Susana Merino and Juan M. Tomás * Department of Genética, Microbiología y Estadística, Universidad de Barcelona, Diagonal 643, 08071 Barcelona, Spain; [email protected] (G.-F.C.); [email protected] (S.M.) * Correspondence: [email protected]; Tel.: +34-93-4021486 Academic Editor: William Chi-shing Cho Received: 7 February 2017; Accepted: 26 February 2017; Published: 28 February 2017 Abstract: Lipopolysaccharides (LPSs) are an integral part of the Gram-negative outer membrane, playing important organizational and structural roles and taking part in the bacterial infection process. In Aeromonas hydrophila, piscicola, and salmonicida, three different genomic regions taking part in the LPS core oligosaccharide (Core-OS) assembly have been identified, although the characterization of these clusters in most aeromonad species is still lacking. Here, we analyse the conservation of these LPS biosynthesis gene clusters in the all the 170 currently public Aeromonas genomes, including 30 different species, and characterise the structure of a putative common inner Core-OS in the Aeromonadaceae family. We describe three new genomic organizations for the inner Core-OS genomic regions, which were more evolutionary conserved than the outer Core-OS regions, which presented remarkable variability. We report how the degree of conservation of the genes from the inner and outer Core-OS may be indicative of the taxonomic relationship between Aeromonas species. Keywords: Aeromonas; genomics; inner core oligosaccharide; outer core oligosaccharide; lipopolysaccharide 1. -
CHAPTER 1: General Introduction and Aims 1.1 the Genus Cronobacter: an Introduction
Diversity and virulence of the genus Cronobacter revealed by multilocus sequence typing (MLST) and comparative genomic analysis Susan Manju Joseph A thesis submitted in partial fulfilment of the requirements of Nottingham Trent University for the degree of Doctor of Philosophy July 2013 Experimental work contained in this thesis is original research carried out by the author, unless otherwise stated, in the School of Science and Technology at the Nottingham Trent University. No material contained herein has been submitted for any other degree, or at any other institution. This work is the intellectual property of the author. You may copy up to 5% of this work for private study, or personal, non-commercial research. Any re-use of the information contained within this document should be fully referenced, quoting the author, title, university, degree level and pagination. Queries or requests for any other use, or if a more substantial copy is required, should be directed in the owner(s) of the Intellectual Property Rights. Susan Manju Joseph ACKNOWLEDGEMENTS I would like to express my immense gratitude to my supervisor Prof. Stephen Forsythe for having offered me the opportunity to work on this very exciting project and for having been a motivating and inspiring mentor as well as friend through every stage of this PhD. His constant encouragement and availability for frequent meetings have played a very key role in the progress of this research project. I would also like to thank my co-supervisors, Dr. Alan McNally and Prof. Graham Ball for all the useful advice, guidance and participation they provided during the course of this PhD study. -
Redalyc.Aeromonas Spp.: La Infección En La Trucha Arcoíris
AquaTIC ISSN: 1578-4541 [email protected] Universidad de Zaragoza España Zepeda-Velázquez, Andrea Paloma Aeromonas spp.: la infección en la trucha arcoíris (Oncorhynchus mykiss) y su aislamiento en México. AquaTIC, núm. 42, enero-junio, 2015, pp. 1-16 Universidad de Zaragoza Zaragoza, España Disponible en: http://www.redalyc.org/articulo.oa?id=49444322001 Cómo citar el artículo Número completo Sistema de Información Científica Más información del artículo Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto Revista AquaTIC, nº 42 – 2015 1 Revista científica de la Sociedad Española de Acuicultura Revista AquaTIC, nº 42, pp. 01-16. Año 2015 ISSN 1578-4541 http://www.revistaaquatic.com/ Aeromonas spp.: la infección en la trucha arcoíris (Oncorhynchus mykiss) y su aislamiento en México. Andrea Paloma1o Zepeda-Velázquez Centro de Investigación y Estudios Avanzados en Salud Animal. Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma del Estado de México. Carretera Toluca-Atlacomulco km 15.5. Toluca 50200, México, México. e-mail: [email protected] Resumen El género Aeromonas incluye bacterias Gram negativas que se encuentran ampliamente distribuidas en ambientes acuáticos. Estos microorganismos afectan a una amplia variedad de especies animales, incluido el hombre. En acuicultura, diversas especies de Aeromonas infectan especies de cultivo y producen pérdidas económicas significativas. De manera particular, la producción de trucha arcoíris (Oncorhynchus mykiss) contribuye significativamente en la acuicultura de México. En este trabajo se revisa la patogenia de las especies de Aeromonas que infectan a la trucha arcoíris, así como los diversos factores que modifican esta interacción. -
An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity
microorganisms Review An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity Ana Fernández-Bravo and Maria José Figueras * Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, 43201 Reus, Spain; [email protected] * Correspondence: mariajose.fi[email protected]; Tel.: +34-97-775-9321; Fax: +34-97-775-9322 Received: 31 October 2019; Accepted: 14 January 2020; Published: 17 January 2020 Abstract: The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). -
Masarykova Univerzita V Brně Lékařská Fakulta VÝSKYT AEROMONÁD V KLINICKÉM MATERIÁLU a PROSTŘEDÍ Bakalářská Práce
Masarykova univerzita v Brně Lékařská fakulta VÝSKYT AEROMONÁD V KLINICKÉM MATERIÁLU A PROSTŘEDÍ Bakalářská práce v oboru zdravotní laborant Vedoucí bakalářské práce: Autor: Doc. RNDr. Ivo Sedláček, CSc. Eva Kroupová Brno, duben 2012 Jméno a příjmení autora: Eva Kroupová Název bakalářské práce: Výskyt aeromonád v klinickém materiálu a prostředí Pracoviště: MU, Ústav experimentální biologie, Česká sbírka mikroorganismů Vedoucí bakalářské práce: Doc. RNDr. Ivo Sedláček, CSc. Rok obhajoby bakalářské práce: 2012 Souhrn: Ve své práci se věnuji popisu rodu Aeromonas, jejich možnostem izolace a identifikace, která je důležitá zejména v klinické humánní medicíně. Klíčová slova: rod Aeromonas, identifikace, aeromonádové infekce Souhlasím, aby práce byla půjčována ke studijním účelům a byla citována dle platných norem. Prohlašuji, že jsem bakalářskou práci vypracovala samostatně pod vedením Doc. RNDr. Ivo Sedláčka, CSc. a uvedla jsem v seznamu literatury všechny odborné a literární zdroje. V Brně dne…………. ………………………………… (vlastnoruční podpis autora) Ráda bych poděkovala Doc. RNDr. Ivo Sedláčkovi, CSc. za cenné odborné rady a pomoc, kterou mi věnoval při psaní této práce. Seznam zkratek a symbolů bv. biovar DNA deoxyribonukleová kyselina PCR polymerázová řetězová reakce RNA ribonukleová kyselina spp více druhů téhož rodu (bez bližší specifikace) subsp subspecies (poddruh) TCŽS thiosulfát-citrát-žluč-sacharóza agar + pozitivní reakce - negativní reakce v variabilní realce Obsah 1. Úvod ................................................................................................................. -
Identification and Characterization of Aeromonas Species Isolated from Ready- To-Eat Lettuce Products
Master's thesis Noelle Umutoni Identification and Characterization of Aeromonas species isolated 2019 from ready-to-eat lettuce Master's thesis products. Noelle Umutoni NTNU May 2019 Norwegian University of Science and Technology Faculty of Natural Sciences Department of Biotechnology and Food Science Identification and Characterization of Aeromonas species isolated from ready- to-eat lettuce products. Noelle Umutoni Food science and Technology Submission date: May 2019 Supervisor: Lisbeth Mehli Norwegian University of Science and Technology Department of Biotechnology and Food Science Preface This thesis covers 45 ECTS-credits and was carried out as part of the M. Sc. programme for Food and Technology at the institute of Biotechnology and Food Science, faculty of natural sciences at the Norwegian University of Science and Technology in Trondheim in spring 2019. First, I would like to express my gratitude to my main supervisor Associate professor Lisbeth Mehli. Thank you for the laughs, advice, and continuous encouragement throughout the project. Furthermore, appreciations to PhD Assistant professor Gunn Merethe Bjørge Thomassen for valuable help in the lab. Great thanks to my family and friends for their patience and encouragement these past years. Thank you for listening, despite not always understanding the context of my studies. A huge self-five to myself, for putting in the work. Finally, a tremendous thank you to Johan – my partner in crime and in life. I could not have done this without you. You kept me fed, you kept sane. I appreciate you from here to eternity. Mama, we made it! 15th of May 2019 Author Noelle Umutoni I Abstract Aeromonas spp. -
Comparative Genomics of the Aeromonadaceae Core Oligosaccharide Biosynthetic Regions
International Journal of Molecular Sciences Article Comparative Genomics of the Aeromonadaceae Core Oligosaccharide Biosynthetic Regions Gabriel Forn-Cuní, Susana Merino and Juan M. Tomás * Department of Genética, Microbiología y Estadística, Universidad de Barcelona, Diagonal 643, 08071 Barcelona, Spain; [email protected] (G.-F.C.); [email protected] (S.M.) * Correspondence: [email protected]; Tel.: +34-93-4021486 Academic Editor: William Chi-shing Cho Received: 7 February 2017; Accepted: 26 February 2017; Published: 28 February 2017 Abstract: Lipopolysaccharides (LPSs) are an integral part of the Gram-negative outer membrane, playing important organizational and structural roles and taking part in the bacterial infection process. In Aeromonas hydrophila, piscicola, and salmonicida, three different genomic regions taking part in the LPS core oligosaccharide (Core-OS) assembly have been identified, although the characterization of these clusters in most aeromonad species is still lacking. Here, we analyse the conservation of these LPS biosynthesis gene clusters in the all the 170 currently public Aeromonas genomes, including 30 different species, and characterise the structure of a putative common inner Core-OS in the Aeromonadaceae family. We describe three new genomic organizations for the inner Core-OS genomic regions, which were more evolutionary conserved than the outer Core-OS regions, which presented remarkable variability. We report how the degree of conservation of the genes from the inner and outer Core-OS may be indicative of the taxonomic relationship between Aeromonas species. Keywords: Aeromonas; genomics; inner core oligosaccharide; outer core oligosaccharide; lipopolysaccharide 1. Introduction Aeromonads are an heterogeneous group of Gram-negative bacteria emerging as important pathogens of both gastrointestinal and extraintestinal diseases in a great evolutionary range of animals: from fish to mammals, including humans [1]. -
Aeromonas Strains
A Rapid MALDI-TOF MS Identification Database at Genospecies Level for Clinical and Environmental Aeromonas Strains Cinzia Benagli1*, Antonella Demarta1, AnnaPaola Caminada1, Dominik Ziegler2, Orlando Petrini1, Mauro Tonolla1,3 1 Institute of Microbiology, Bellinzona, Switzerland, 2 Mabritec AG, Riehen, Switzerland, 3 Microbial Ecology, Microbiology Unit, Plant Biology Department University of Geneva, Gene`ve, Switzerland Abstract The genus Aeromonas has undergone a number of taxonomic and nomenclature revisions over the past 20 years, and new (sub)species and biogroups are continuously described. Standard identification methods such as biochemical characterization have deficiencies and do not allow clarification of the taxonomic position. This report describes the development of a matrix-assisted laser desorption/ionisation–time of flight mass spectrometry (MALDI-TOF MS) identification database for a rapid identification of clinical and environmental Aeromonas isolates. Citation: Benagli C, Demarta A, Caminada A, Ziegler D, Petrini O, et al. (2012) A Rapid MALDI-TOF MS Identification Database at Genospecies Level for Clinical and Environmental Aeromonas Strains. PLoS ONE 7(10): e48441. doi:10.1371/journal.pone.0048441 Editor: Mikael Skurnik, University of Helsinki, Finland Received May 10, 2012; Accepted September 25, 2012; Published October 31, 2012 Copyright: ß 2012 Benagli et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: No current external funding sources for this study. Competing Interests: The authors have read the journal’s policy and have the following conflicts: Dominik Ziegler is employed by Mabritec AG. -
Caracterización De Bacterias Aeromonadales Móviles Aisladas De Peces Cultivados En Uruguay
UNIVERSIDAD DE LA REPÚBLICA FACULTAD DE VETERINARIA Programa de Posgrados CARACTERIZACIÓN DE BACTERIAS AEROMONADALES MÓVILES AISLADAS DE PECES CULTIVADOS EN URUGUAY Alejandro Perretta TESIS DE MAESTRÍA EN SALUD ANIMAL URUGUAY 2016 i ii iii UNIVERSIDAD DE LA REPÚBLICA FACULTAD DE VETERINARIA Programa de Posgrados CARACTERIZACIÓN DE BACTERIAS AEROMONADALES MÓVILES AISLADAS DE PECES CULTIVADOS EN URUGUAY Alejandro Perretta _________________________ _________________________ Dr. Pablo Zunino Dra. Karina Antúnez Director de Tesis Codirectora de Tesis 2016 iv INTEGRACIÓN DEL TRIBUNAL DE DEFENSA DE TESIS Claudia Piccini; MS, PhD Departamento de Microbiología Instituto de Investigaciones Biológicas "Clemente Estable"- Ministerio de Educación y Cultura - Uruguay Laura Bentancor; MS, PhD Departamento de Bacteriología y Virología Instituto de Higiene - Facultad de Medicina Universidad de la República - Uruguay Martín Fraga; MS, PhD Plataforma de Salud Animal Instituto de Investigaciones Agropecuarias - Uruguay 2016 v vi vii DEDICATORIA …para Federíco, Anaclara y Valeria viii AGRADECIMIENTOS - A Pablo Zunino y Karina Antúnez, gracias por compartir el conocimiento conmigo, abrirme las puertas del IIBCE para poder llevar a cabo este trabajando y por la paciencia y el apoyo en todo momento. - A Daniel Carnevia por el apoyo contínuo y la colaboración brindada en cada uno de mis emprendimientos. - A todo el personal docente y no docente del Instituto de Investigaciones Pesqueras de la Facultad de Veterinaria por tantos años de apoyo y colaboración. - A Belén Branchiccela y todo el personal del Departamento de Microbiología del IIBCE por el apoyo y la colaboración en todas las tareas llevadas a cabo allí. - A Rodrigo Puentes, Uruguaysito Benavides y todo el personal del Área Inmunología de la Facultad de Veterinaria por la colaboración con las taréas de biología molecular llevadas a cabo. -
Aerobic Midgut Microbiota of Sand Fly Vectors of Zoonotic Visceral
Karimian et al. Parasites & Vectors (2019) 12:10 https://doi.org/10.1186/s13071-018-3273-y RESEARCH Open Access Aerobic midgut microbiota of sand fly vectors of zoonotic visceral leishmaniasis from northern Iran, a step toward finding potential paratransgenic candidates Fateh Karimian1, Hassan Vatandoost1, Yavar Rassi1, Naseh Maleki-Ravasan2, Mehdi Mohebali3, Mohammad Hasan Shirazi4, Mona Koosha1, Nayyereh Choubdar1 and Mohammad Ali Oshaghi1* Abstract Background: Leishmaniasis is caused by Leishmania parasites and is transmitted to humansthroughthebiteofinfected sand flies. Development of Leishmania to infective metacyclic promastigotes occurs within the sand fly gut where the gut microbiota influences development of the parasite. Paratransgenesis is a new control method in which symbiotic bacteria are isolated, transformed and reintroduced into the gut through their diet to express anti-parasitic molecules. In the present study, the midgut microbiota of three sand fly species from a steppe and a mountainous region of northern Iran, where zoonotic visceral leishmaniasis (ZVL) is endemic, was investigated. Methods: Briefly, adult female sand flies was collected during summer 2015 and, after dissection, the bacterial composition of the guts were analyzed using a culture-dependent method. Bacterial DNA from purified colonies was extracted to amplify the 16S rRNA gene which was then sequenced. Results: Three ZVL sand fly vectors including Phlebotomus major, P. kandelakii and P. halepensis were found in the highlighted regions. In total, 39 distinct aerobic bacterial species were found in the sand fly midguts. The sand fly microbiota was dominated by Proteobacteria (56.4%) and Firmicutes (43.6%). Bacterial richness was significantly higher in the steppe region than in the mountainous region (32 vs 7species).Phlebotomus kandelakii,the most important ZVL vector in the study area, had the highest bacterial richness among the three species. -
Screening Hydrolase-Producing Environmental Bacteria Towards Their Application in Bioremediation Microbiology
Screening hydrolase-producing environmental bacteria towards their application in bioremediation Maria Cristina Lopes Matias Thesis to obtain the Master of Science Degree in Microbiology Supervisor: Professor Rogério Paulo de Andrade Tenreiro Co-supervisor: Professor Nuno Gonçalo Pereira Mira Examination Committee Chairperson: Professor Isabel Maria de Sá Correia Leite de Almeida Supervisor: Professor Rogério Paulo de Andrade Tenreiro Member of the Committee: Professor Ana Cristina Anjinho Madeira Viegas October 2019 Declaration I declare that this document is an original work of my own authorship and that it fulfills all the requirements of the Code of Conduct and Good Practices of the Universidade de Lisboa. i Preface The work presented in this thesis was performed at Lab Bugworkers | M&B-BioISI, Faculty of Sciences of the University of Lisbon (Lisbon, Portugal), during the period from September 2017 to October 2019, under the supervision of Professor Rogério Tenreiro. The thesis was co-supervised at Instituto Superior Técnico (Lisbon, Portugal) by Professor Nuno Mira. ii Acknowledgments This thesis is the end result of the work developed within the Microbiology & Biotechnology Group of Biosystems and Integrative Sciences Institute (M&B-BioISI), at Lab Bugworkers | M&B-BioISI, located in the Innovation Centre from the Faculty of Sciences of the University of Lisbon, Tec Labs. It would not have been successfully achieved without the help and collaboration of several people, to whom I would like to express my sincere gratitude. First, and foremost, I would like to thank my supervisor, Professor Rogério Tenreiro, for challenging me with this project. I have to thank him for the patience for my endless questions, for letting me error along the way (and learn with those errors), and for all the ideas to improve my work. -
Aeromonas Spp
UNIVERSIDAD AUTÓNOMA DEL ESTADO DE MÉXICO MAESTRÍA Y DOCTORADO EN CIENCIAS AGROPECUARIAS Y RECURSOS NATURALES CARACTERIZACIÓN FENOTÍPICA Y GENOTÍPICA DE AISLAMIENTOS DE Aeromonas spp. OBTENIDOS DE TRUCHA ARCOÍRIS ( Oncorhynchus mykiss ) T E S I S QUE PARA OBTENER EL GRADO DE DOCTOR EN CIENCIAS AGROPECUARIAS Y RECURSOS NATURALES PRESENTA: M. en C. VICENTE VEGA SÁNCHEZ El Cerrillo Piedras Blancas, Toluca, Estado de México. Agosto 2014 RESUMEN El desarrollo de cultivos en condiciones intensivas conlleva el riesgo de aparición de enfermedades infecciosas, las cuales pued en generar importantes pérdidas económicas; las infecciones causadas por bacterias del género Aeromonas tienen una distribución mundial, particularmente en patologías de peces en numerosos países. En México se ha reportado una prevalencia del 48.77% para este género bacteriano . El objetivo del presente trabajo fue identificar al nivel de especie, aislamientos de Aeromonas spp. utilizando métodos moleculares, conocer el patrón de sensibilidad antimicrobiana a diversos antimicrobianos e identificar genes que codifican para la resistencia antimicrobiana en los aislamientos. Las especies identificadas fueron A. veronii (29.2%), A. bestiarum (20.8%), A. hydrophila (16.7%), A. sobria (10.4%), A. media (8.3%), A. popoffii (6.2%), A. allosaccharophila (2.1%), A. caviae (2.1%), A. salmonicida (2.1%) y “ Aeromonas lusitana” (2.1%), la cual está pendiente su reporte como especie nueva. Se observó una correcta identificación entre métodos bioquímicos y secuenciación de genes housekeeping del 12% (6/50) y del 70% (35/55) entre la identificación por RFLP del gen 16S DNAr y genes que codifican para proteínas esenciales o housekeeping . Se detectó la presencia de patrones atípicos obtenidos por RFLP del gen 16S DNAr los cuales complican la correcta identificación.