DOCSLIB.ORG

Université De Lille1-Sciences Et Technologies

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Université De Lille1-Sciences Et Technologies UNIVERSITÉ DE LILLE1-SCIENCES ET TECHNOLOGIES École doctorale de Science de la Matière, de Rayonnement et de l’Environnement THÈSE DE DOCTORAT Spécialité : Ingénierie des Fonctions Biologiques Présentée par ALAA ABDULHUSSAIN AL-SERAIH Pour l’obtention du grade de DOCTEUR DE L’UNIVERSITÉ DE LILLE 1 Propriétés Antagonistes et Probiotiques de Nouvelles Bactéries Lactiques et Levures Isolées des Matières Fécales Humaine et Animale No Ordre 42128 Préparée à l’institut Charles Viollette (ICV)- EA7394 Présentée, le 10 Novembre 2016 devant le jury composé de : Véronique Delcenserie Professeur Université de Liège, Belgique Nathalie Connil Maître de conférence-HDR. Université de Rouen-Haute Normandie Djamel Drider Professeur Université de Lille 1 John Baah Directeur de Recherche et développement Best Environmental Technologies,Canada Benoit Cudennec Maître de conférence. Université de Lille 1 François Krier Maître de conférence. Université de Lille1 Acknowledgements I would like to convey my heartfelt gratitude and sincere appreciation to all the people who have helped and inspired me during my doctoral study. This thesis would not have been possible without the support of many people. First of all, I would like to express my deep appreciation and gratitude to my honorable advisor, Professor Dr. Djamel Drider, for the patient guidance and mentorship he provided to me throughout my PhD study. Professor Drider’s intellectual heft is matched only by his genuine good nature and humility, and I am truly fortunate to have had the opportunity to work with him. Also, with a deep sense of honor, I would like to express my sincere gratitude to Professor Dr. Pascal Dhulster, the director of Charles Viollette Institute, for his unceasing and encouraging support. I would like to thank all of the thesis committee, Professor Dr. Véronique Delcenserie, Dr. Nathalie Connil, Dr. John Baah, Dr. Benoit Cudennec, and Dr François Krier, for accepting the evaluation of my PhD work, and for their insightful comments and encouragement. My sincere thanks also go to Dr. Rabah Boukherroub (IEMN, CNRS) and Professor Dr. Sabine Szunerits (IMEN, Lille 1) for their collaboration and SEM assistance. I would like to extend thanks to Dr. Annee Vachee (Roubaix hospital, France) for her cooperation in the antibiotic resistance analysis. I would also like to express my heartfelt gratitude to Dr. Yanath Belguesmia, Dr. Max Béchet, and Dr. Gabrielle Chataigné for their help, support, and encouragement throughout my PhD work. Similar profound gratitude goes to my friends Ahmed, Ameen, Yazen, Hamza, Mahammed, Qassim, Michael, Debarun, Alexandre, Delphine, Juliette and all other members of the QSA and ProBioGEM teams who provided me a family environment for more than four years. II I would like to extend thanks to the Iraqi Ministry of Higher Education and Scientific Research for giving me the opportunity to do my PhD by awarding the doctoral scholarship. Similar deep gratitude goes to Campus France Organization, especially to Mr. Adrien Chalancon, who successfully managed the dossiers of Iraqi students. Also with deep sense of honor, I wish to express my heartily gratitude to the Best Environmental Technologies Company (Alberta, Canada), especially to Mr. Jim G. Watson and Dr. John Baah for all their support of my PhD project. Finally, I have no words to express my profound gratitude and appreciation to my family. My loving mother, father and brothers Bahaa, Osama, Ahmed, and Amir always gave me unconditional love, support, and encouragement during all the stages of my life. To each of them, I would like to say thank you from the bottom of my heart. No words can either express the deepest gratitude and appreciation I have for my loving wife Hiba, who has always supported me and helped me overcome all difficulties during my studies. She has been there for me every minute of every year of my studies and supported me and my work without complaint. I would like to extend my warmest thanks to my dear son, Murtadha. If this work has sometimes prevented us from sharing important moments of life, know that I never stopped thinking about you. You are the most important people in my life, and I dedicate this work to all of you. III Scientific valorization Publications in peer reviewed journals 1- Al-Seraih A, Flahaut C, Krier F, Cudennec B, Drider D., 2015. Characterization of Candida famata Isolated from Poultry Feces for Possible Probiotic Applications. Probiotics and antimicrobial proteins. 7, 233-41. 2- Al-Seraih A, Belguesmiaa Y, Baah J, Szuneritsc S, Boukherroubc R, Drider D., 2016. Enterocin B3A-B3B produced by LAB collected from infant feces: potential utilization in the food industry for Listeria monocytogenes biofilm management. In Antonie van Leeuwenhoek Journal of Microbiology (Under review). 3- Al-Seraih, Kergourlay G, Cudennec B, Baah J, Belguesmia Y, Drider D., 2016. Enterococcus faecalis B3A-B3B: Genome analysis and experimental evidences to claim its beneficial attributes. (Manuscript in preparation). Posters and workshops 1- Al-Seraih A, Flahaut C, Krier F, Cudennec B, Drider D. Characterization of Candida famata Isolated from Poultry Feces for Possible Probiotic Applications. Annual Conference of Microbiology Society. 21-24 March 2016, Liverpool, UK. 2- Al-Seraih A, Belguesmia Y, Desriac F, Drider D. Enterocin B3A-B3B from infant origin helps nisin to control growth of the foodborne pathogen Listeria monocytogenes. AMP. 6-8 June 2016. Montpellier, France. 3- 2nd International workshop on (Bioinformatics Tools for PKS and NRPS Discovery from Genomic Data for the Product), University of Lille1. 28-30 October, 2015. Lille, France. IV ABSTRACT In this study, we isolated probiotic yeasts and lactic acid bacteria (LAB) from different microbial sources. Eighty-one (81) yeasts and seventy (70) LAB isolates were randomly selected and identified from fecal samples of poultry feces and healthy Iraqi infants, respectively. The yeast strains were obtained from a farm of broiler chickens located in the city of Lille. They were clustered into 22 groups by GTG5-rep PCR technique, then identified as Debaryomyces hansenii, (teleomorph of Candida famata) species using the biochemical ID-32C system and molecular sequencing of 26S rDNA and ITS1-5.8-ITS2 rDNA region methods. Only one yeast strain, designated as Candida famata Y.5 (C. famata Y.5), exhibited antimicrobial activity against Listeria innocua. For more accurate discrimination, the antagonistic strain C. famata Y.5 was identified by MALDI-TOF-MS technology. Further characterization of this anti-Listeria strain, permitted to unveil its probiotic potential. Thus, C. famata Y.5 appeared to be a non-hemolytic strain. In vitro tests of cytotoxicity and adhesion on human Caco-2 epithelial cells confirmed the safety traits of this strain. C. famata Y.5 displayed good surface properties, especially auto-aggregation, in addition to high survival ability under harsh conditions mimicking those of the gastrointestinal tract (GIT). The LAB strains were isolated from fecal samples of a group of Iraqi children living in the north of France. LAB strains were obtained from six blind donors and then identified as 41 cocci and 29 bacilli. Two strains displayed antagonistic activities against Gram-positive bacteria (GPB) including: Listeria monocytogenes, Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Clostridium perfringens but not against fungi or Gram-negative bacteria (GNB), except for Salmonella Newport. The biochemical, MALDI-TOF-MS, and molecular (16S rDNA sequencing) methods identified these two strains as Enterococcus faecalis B3A-B3B and B20A-B20B . Bacteriocin produced by strain B3A-B3B, designed as V enterocin B3A-B3B, was purified by a simplified two-step procedure including a liquid-liquid phase extraction and reverse phase high-performance liquid chromatography (RP-HPLC). The predicted molecular mass of this enterocin consists of two peptides of 5,176.31 Da (B3A) and 5,182.21 Da (B3B). Notably, B3A-B3B hampered the biofilm installation of L. monocytogenes strain grown on AISI 304 stainless steel slides. The treatment of stainless steel with nisin (1 mg. ml-1 or 16 mg. ml-1) diminished the cell numbers by about 2 logs CFU. ml-1, preventing therefore the biofilm formation by L. monocytogenes 162 or by its nisin-resistant variant L. monocytogenes 162R. Further combination of nisin and B3A-B3B enterocin reduced the MIC value needed to inhibit this pathogen about 2 logs CFU. ml-1. To gain insights on the probiotic profile of the E. faecalis B3A-B3B strain, the whole genome was sequenced and in silico analysis was performed and compared with those of clinical strains as E. faecalis MMH594, E. faecalis V583, and E. faecalis OG1RF from humans, and also compared to that of the well-known probiotic E. faecalis Symbioflor1 strain. Even harboring gelE, cpd, efaAfm, ccf, agg, and cob coding for virulence factors, the B3A-B3B strain resulted to be sensitive to most antibiotics tested here, non-cytotoxic, non-hemolytic, and devoid of inflammatory effects. Moreover, B3A-B3B strain showed remarkable hydrophobicity, auto- aggregation, adhesion to human Caco-2 cells, viability in simulated GIT conditions, and cholesterol assimilation. These features together introduce the E. faecalis B3A- B3B strain as an interesting probiotic candidate. VI RESUME Dans cette étude, nous avons isolé des levures et des bactéries lactiques (BL) potentiellement probiotiques, à partir de différents écosystèmes microbiens. Quatre- vingt-une (81) levures, et soixante-dix (70) BL, ont été isolées et identifiées à partir de matières fécales animales (poulet) et humaines (enfants Irakiens en bonne santé). Ainsi, les souches de levures ont été isolées à partir de matières fécales de poulets, dans une ferme située dans la région de Lille (France). Elles ont été regroupées en 22 groupes par la technique de Rep-PCR utilisant une amorce unique 5'- GTG5-3', puis identifiées comme appartenant à l’espèce Debaryomyces hansenii (téléomorphe de Candida famata) en utilisant des méthodes biochimique (système ID- 32C) et moléculaire (séquençage de l'ADNr 26S et les régions ITS1-5.8-ITS2 de l’ADNr).
Load more

Recommended publications
  • Molecular Epidemiology of Clinical Enterococcus Faecium Hanna
    From the Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden Molecular Epidemiology of Clinical Enterococcus faecium Hanna Billström Stockholm 2008 1 All previously published papers were reproduced with permission from the publisher. Published by Karolinska Institutet. Printed by Larserics Digital Print AB. © Hanna Billström, 2008 ISBN 978-91-7409-257-8 2 Till min fantastiska Familj 3 ABSTRACT Enterococci are today the third most commonly isolated species from blood- stream infections, and problems with ampicillin and vancomycin resistance are increasing. Some putative virulence factors such as the enterococcal surface protein (Esp) and hyaluronidase (Hyl) have been described in Enterococcus faecium. Multilocus sequence typing (MLST) has revealed the existence of a genetic lineage, denoted clonal complex 17 (CC17), associated with hospital outbreaks and nosocomial infections worldwide. The general aim of the present study was to investigate if blood-stream infections caused by E. faecium were of endogenous origin or the result of nosocomial transmission, and also to determine the conjugation ability, presence of virulence determinants, antibiotic resistance, and to clarify if the globally spread CC17 occurred in Sweden. A total of 596 clinical E. faecium isolates consecutively collected during year 2000 to 2007 were included. All isolates originated from a blood-culture collection at the Karolinska University Hospital Huddinge, Sweden, deriving from hospitalized patients with blood-stream infections in the southern part of Stockholm. The conjugation ability was tested using in vitro filter mating. The genetic relatedness between isolates was analyzed using pulsed-field gel electrophoresis (PFGE), multiple-locus variable-number tandem repeat analysis (MLVA) and MLST.
    [Show full text]
  • Bacteriophage of Enterococcus Species for Microbial Source Tracking
    Bacteriophage of Enterococcus species for microbial source tracking Sarah Elizabeth Purnell A thesis submitted in partial fulfilment of the requirements of the University of Brighton for the degree of Doctor of Philosophy 2012 School of Environment and Technology University of Brighton United Kingdom Abstract Contamination of surface waters with faeces may lead to increased public risk of human exposure to pathogens through drinking water supply, aquaculture, and recreational activities. Determining the source(s) of contamination is important for assessing the degree of risk to public health, and for selecting appropriate mitigation measures. Phage-based microbial source tracking (MST) techniques have been promoted as effective, simple and low-cost. The intestinal enterococci are a faecal “indicator of choice” in many parts of the world for determining water quality, and recently, phages capable of infecting Enterococcus faecalis have been proposed as a potential alternative indicator of human faecal contamination. The primary aim of this study was to evaluate critically the suitability and efficacy of phages infecting host strains of Enterococcus species as a low-cost tool for MST. In total, 390 potential Enterococcus hosts were screened for their ability to detect phage in reference faecal samples. Development and implementation of a tiered screening approach allowed the initial large number of enterococcal hosts to be reduced rapidly to a smaller subgroup suitable for phage enumeration and MST. Twenty-nine hosts were further tested using additional faecal samples of human and non-human origin. Their specificity and sensitivity were found to vary, ranging from 44 to 100% and from 17 to 83%, respectively. Most notably, seven strains exhibited 100% specificity to cattle, human, or pig samples.
    [Show full text]
  • Taxonomie a Ekologie Rodu Enterococcus
    ___________________________________________________________________________ MasarykovauniverzitavBrně Přírodovědeckáfakulta Ústavexperimentální biologie,Oddělenímikrobiologie Taxonomie a ekologie rodu Enterococcus (Bakalářská prácestudijníhoprogramuBiologie oboruObecná biologie –směrMikrobiologie) Hana Bryndová Brno,Českárepublika2008 ___________________________________________________________________________ 1 Za cenné rady,ochotnoupomoc a čas,kterými věnoval při vznikutétopráce,tímto děkuji RNDr.PavluŠvecovi,PhD.,podjehož vedením jsem bakalářskoupráci zpracovala na půděČeskésbírkymikroorganismů. 2 Obsah 1. Úvod...................................................................................................................................6 2. Cíl práce .............................................................................................................................6 3. Taxonomie rodu Enterococcus ...........................................................................................7 3.1 Historietaxonomierodu Enterococcus ......................................................................7 3.2 Současnátaxonomierodu Enterococcus ....................................................................7 3.3 Charakteristikarodu Enterococcus ............................................................................9 3.3.1 Fylogenetickézařazení rodu Enterococcus ............................................................9 3.3.2 Základnícharakteristika .........................................................................................9
    [Show full text]
  • Suppl Table 2
    Table S2. Large subunit rRNA gene sequences of Bacteria and Eukarya from V5. ["n" indicates information not specified in the NCBI GenBank database.] Accession number Q length Q start Q end e-value %-ident %-sim GI number Domain Phylum Family Genus / Species JQ997197 529 30 519 3E-165 89% 89% 48728139 Bacteria Actinobacteria Frankiaceae uncultured Frankia sp. JQ997198 732 17 128 2E-35 93% 93% 48728167 Bacteria Actinobacteria Frankiaceae uncultured Frankia sp. JQ997196 521 26 506 4E-95 81% 81% 48728178 Bacteria Actinobacteria Frankiaceae uncultured Frankia sp. JQ997274 369 8 54 4E-14 100% 100% 289551862 Bacteria Actinobacteria Mycobacteriaceae Mycobacterium abscessus JQ999637 486 5 321 7E-62 82% 82% 269314044 Bacteria Actinobacteria Mycobacteriaceae Mycobacterium immunoGenum JQ999638 554 17 509 0 92% 92% 44368 Bacteria Actinobacteria Mycobacteriaceae Mycobacterium kansasii JQ999639 552 18 455 0 93% 93% 196174916 Bacteria Actinobacteria Mycobacteriaceae Mycobacterium sHottsii JQ997284 598 5 598 0 90% 90% 2414571 Bacteria Actinobacteria Propionibacteriaceae Propionibacterium freudenreicHii JQ999640 567 14 560 8E-152 85% 85% 6714990 Bacteria Actinobacteria THermomonosporaceae Actinoallomurus spadix JQ997287 501 8 306 4E-119 93% 93% 5901576 Bacteria Actinobacteria THermomonosporaceae THermomonospora cHromoGena JQ999641 332 26 295 8E-115 95% 95% 291045144 Bacteria Actinobacteria Bifidobacteriaceae Bifidobacterium bifidum JQ999642 349 19 255 5E-82 90% 90% 30313593 Bacteria Bacteroidetes Bacteroidaceae Bacteroides caccae JQ997308 588 20 582 0 90%
    [Show full text]
  • The Ecology, Epidemiology and Virulence of Enterococcus
    Microbiology (2009), 155, 1749–1757 DOI 10.1099/mic.0.026385-0 Review The ecology, epidemiology and virulence of Enterococcus Katie Fisher and Carol Phillips Correspondence University of Northampton, School of Health, Park Campus, Boughton Green Road, Northampton Katie Fisher NN2 7AL, UK [email protected] Enterococci are Gram-positive, catalase-negative, non-spore-forming, facultative anaerobic bacteria, which usually inhabit the alimentary tract of humans in addition to being isolated from environmental and animal sources. They are able to survive a range of stresses and hostile environments, including those of extreme temperature (5–65 6C), pH (4.5”10.0) and high NaCl concentration, enabling them to colonize a wide range of niches. Virulence factors of enterococci include the extracellular protein Esp and aggregation substances (Agg), both of which aid in colonization of the host. The nosocomial pathogenicity of enterococci has emerged in recent years, as well as increasing resistance to glycopeptide antibiotics. Understanding the ecology, epidemiology and virulence of Enterococcus speciesisimportant for limiting urinary tract infections, hepatobiliary sepsis, endocarditis, surgical wound infection, bacteraemia and neonatal sepsis, and also stemming the further development of antibiotic resistance. Introduction Taxonomy For many years Enterococcus species were believed to be The genus Enterococcus consists of Gram-positive, catalase- harmless to humans and considered unimportant med- negative, non-spore-forming, facultative anaerobic bacteria ically. Because they produce bacteriocins, Enterococcus that can occur both as single cocci and in chains. species have been used widely over the last decade in the Enterococci belong to a group of organisms known as food industry as probiotics or as starter cultures (Foulquie lactic acid bacteria (LAB) that produce bacteriocins Moreno et al., 2006).
    [Show full text]
  • The Ecology, Epidemiology and Virulence of Enterococcus
    Microbiology (2009), 155, 1749–1757 DOI 10.1099/mic.0.026385-0 Review The ecology, epidemiology and virulence of Enterococcus Katie Fisher and Carol Phillips Correspondence University of Northampton, School of Health, Park Campus, Boughton Green Road, Northampton Katie Fisher NN2 7AL, UK [email protected] Enterococci are Gram-positive, catalase-negative, non-spore-forming, facultative anaerobic bacteria, which usually inhabit the alimentary tract of humans in addition to being isolated from environmental and animal sources. They are able to survive a range of stresses and hostile environments, including those of extreme temperature (5–65 6C), pH (4.5”10.0) and high NaCl concentration, enabling them to colonize a wide range of niches. Virulence factors of enterococci include the extracellular protein Esp and aggregation substances (Agg), both of which aid in colonization of the host. The nosocomial pathogenicity of enterococci has emerged in recent years, as well as increasing resistance to glycopeptide antibiotics. Understanding the ecology, epidemiology and virulence of Enterococcus speciesisimportant for limiting urinary tract infections, hepatobiliary sepsis, endocarditis, surgical wound infection, bacteraemia and neonatal sepsis, and also stemming the further development of antibiotic resistance. Introduction Taxonomy For many years Enterococcus species were believed to be The genus Enterococcus consists of Gram-positive, catalase- harmless to humans and considered unimportant med- negative, non-spore-forming, facultative anaerobic bacteria ically. Because they produce bacteriocins, Enterococcus that can occur both as single cocci and in chains. species have been used widely over the last decade in the Enterococci belong to a group of organisms known as food industry as probiotics or as starter cultures (Foulquie lactic acid bacteria (LAB) that produce bacteriocins Moreno et al., 2006).
    [Show full text]
  • Molecular Identification and Probiotic Potential Characterization of Lactic Acid Bacteria Isolated from Human Vaginal Microbiota
    Advanced Adv Pharm Bull, 2018, 8(4), 683-695 Pharmaceutical doi: 10.15171/apb.2018.077 Bulletin http://apb.tbzmed.ac.ir Research Article Molecular Identification and Probiotic Potential Characterization of Lactic Acid Bacteria Isolated from Human Vaginal Microbiota Yousef Nami1* , Babak Haghshenas2, Ahmad Yari Khosroushahi3,4 1 Department of Food Biotechnology, Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran. 2 Regenerative Medicine Research Center (RMRC), Kermanshah University of Medical Sciences, Kermanshah, Iran. 3 Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran. 4 Department of Pharmacognosy, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran. Article info Abstract Article History: Purpose: The increased demand for probiotics because of their health purposes provides the Received: 22 November 2017 context for this study, which involves the molecular identification of lactic acid bacteria Revised: 28 July 2018 (LAB) obtained from the vaginal microbiota of healthy fertile women. The isolates were Accepted: 15 August 2018 subjected for examination to prove their probiotic potential. In particular, the isolates were ePublished: 29 November 2018 subjected to various tests, including acid/bile tolerance, antimicrobial activity, antibiotic susceptibility, Gram staining, and catalase enzyme activity assessment. Keywords: Methods: Several methods were utilized for the molecular identification of the isolates, Molecular identification including ARDRA, (GTG)5-PCR fingerprinting, and the PCR sequencing of 16S-rDNA Probiotic characterization amplified fragments. Disc diffusion and well diffusion methods were used to assess (GTG)5-fingerprinting antibiotic susceptibility and antibacterial activity of isolates. Tolerance to acid and bile was Lactic acid bacteria performed at pH 2.5 and 0.3% bile oxgall.
    [Show full text]
  • Resistance Mechanisms and Inflammatory Bowel Disease 10.1515/Med-2020-0032 Present Multi-Resistant E
    Open Med. 2020; 15: 211-224 Research Article Michaela Růžičková, Monika Vítězová, Ivan Kushkevych* The characterization of Enterococcus genus: resistance mechanisms and inflammatory bowel disease https://doi.org/ 10.1515/med-2020-0032 present multi-resistant E. faecium belongs to a different received September 18, 2019; accepted February 5, 2020 taxon than the original strains isolated from animals. This separation must have happened around 75 years ago and Abstract: The constantly growing bacterial resistance is being connected to antibiotic usage in clinical practice. against antibiotics is recently causing serious problems This clade can be distinguished by its increased number in the field of human and veterinary medicine as well as of mobile genetic elements, metabolic alternations and in agriculture. The mechanisms of resistance formation hypermutability [1]. All of these attributes led to the devel- and its preventions are not well explored in most bacterial opment of a flexible genome, which is now able to easily genera. The aim of this review is to analyse recent litera- adapt to the changes of the surroundings [2,3]. ture data on the principles of antibiotic resistance forma- It is also necessary to mention some basic informa- tion in bacteria of the Enterococcus genus. Furthermore, tion about morphological diversity, physiological and bio- the habitat of the Enterococcus genus, its pathogenicity chemical characteristics and taxonomy in order to under- and pathogenicity factors, its epidemiology, genetic and stand the resistance mechanisms completely. Biochemical molecular aspects of antibiotic resistance, and the rela- features must especially be mentioned since they play a tionship between these bacteria and bowel diseases are huge role in the high increase of resistance in these bac- discussed.
    [Show full text]
  • Environment Or Kin: Whence Do Bees Obtain Acidophilic Bacteria?
    Molecular Ecology (2012) doi: 10.1111/j.1365-294X.2012.05496.x Environment or kin: whence do bees obtain acidophilic bacteria? QUINN S. MC FREDERICK,* WILLIAM T. WCISLO,† DOUGLAS R. TAYLOR,‡ HEATHER D. ISHAK,* SCOT E. DOWD§ and ULRICH G. MUELLER* *Section of Integrative Biology, University of Texas at Austin, 2401 Speedway Drive #C0930. Austin, TX 78712, USA, †Smithsonian Tropical Research Institute, Box 0843-03092, Balboa, Ancon, Republic of Panama, ‡Department of Biology, University of Virginia, Charlottesville, VA 22904-4328, USA, §MR DNA (Molecular Research), 503 Clovis Rd., Shallowater, TX 79363, USA Abstract As honey bee populations decline, interest in pathogenic and mutualistic relationships between bees and microorganisms has increased. Honey bees and bumble bees appear to have a simple intestinal bacterial fauna that includes acidophilic bacteria. Here, we explore the hypothesis that sweat bees can acquire acidophilic bacteria from the environment. To quantify bacterial communities associated with two species of North American and one species of Neotropical sweat bees, we conducted 16S rDNA amplicon 454 pyrosequencing of bacteria associated with the bees, their brood cells and their nests. Lactobacillus spp. were the most abundant bacteria in many, but not all, of the samples. To determine whether bee-associated lactobacilli can also be found in the environment, we reconstructed the phylogenetic relationships of the genus Lactobacillus. Previously described groups that associate with Bombus and Apis appeared relatively specific to these genera. Close relatives of several bacteria that have been isolated from flowers, however, were isolated from bees. Additionally, all three sweat bee species associated with lactobacilli related to flower-associated lactobacilli.
    [Show full text]
  • Evaluation of FISH for Blood Cultures Under Diagnostic Real-Life Conditions
    Original Research Paper Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions Annalena Reitz1, Sven Poppert2,3, Melanie Rieker4 and Hagen Frickmann5,6* 1University Hospital of the Goethe University, Frankfurt/Main, Germany 2Swiss Tropical and Public Health Institute, Basel, Switzerland 3Faculty of Medicine, University Basel, Basel, Switzerland 4MVZ Humangenetik Ulm, Ulm, Germany 5Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany 6Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany Received: 04 September 2018; accepted: 18 September 2018 Background: The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. Methods: Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. Results: A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a spec- ificity of >95% in all instances.
    [Show full text]
  • Age-Related Differences in the Cloacal Microbiota of a Wild Bird Species
    van Dongen et al. BMC Ecology 2013, 13:11 http://www.biomedcentral.com/1472-6785/13/11 RESEARCH ARTICLE Open Access Age-related differences in the cloacal microbiota of a wild bird species Wouter FD van Dongen1*, Joël White1,2, Hanja B Brandl1, Yoshan Moodley1, Thomas Merkling2, Sarah Leclaire2, Pierrick Blanchard2, Étienne Danchin2, Scott A Hatch3 and Richard H Wagner1 Abstract Background: Gastrointestinal bacteria play a central role in the health of animals. The bacteria that individuals acquire as they age may therefore have profound consequences for their future fitness. However, changes in microbial community structure with host age remain poorly understood. We characterised the cloacal bacteria assemblages of chicks and adults in a natural population of black-legged kittiwakes (Rissa tridactyla), using molecular methods. Results: We show that the kittiwake cloaca hosts a diverse assemblage of bacteria. A greater number of total bacterial OTUs (operational taxonomic units) were identified in chicks than adults, and chicks appeared to host a greater number of OTUs that were only isolated from single individuals. In contrast, the number of bacteria identified per individual was higher in adults than chicks, while older chicks hosted more OTUs than younger chicks. Finally, chicks and adults shared only seven OTUs, resulting in pronounced differences in microbial assemblages. This result is surprising given that adults regurgitate food to chicks and share the same nesting environment. Conclusions: Our findings suggest that chick gastrointestinal tracts are colonised by many transient species and that bacterial assemblages gradually transition to a more stable adult state. Phenotypic differences between chicks and adults may lead to these strong differences in bacterial communities.
    [Show full text]
  • Microbial Changes and Safety of Lightly Preserved Seafood
    Downloaded from orbit.dtu.dk on: Oct 06, 2021 Microbial changes and safety of lightly preserved seafood Mejlholm, Ole Publication date: 2007 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Mejlholm, O. (2007). Microbial changes and safety of lightly preserved seafood. DIFRES, DTU. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Microbial Changes and Safety of Lightly Preserved Seafood By Ole Mejlholm Danish Institute for Fisheries Research, Department of Seafood Research, Technical University of Denmark Preface The present Ph.D.-project has been carried out at the Danish Institute for Fisheries Research (DIFRES) in Kgs. Lyngby, Denmark under the supervision of senior scientist Paw Dalgaard. The presented work was financed by the Danish Directorate for Food, Fisheries and Agri Business. I wish to thank Paw Dalgaard for his support and many valuable discussions, and for introducing me to predictive microbiology.
    [Show full text]