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Isolation, characterization and genome sequencing of a soil-borne Citrobacter freundii strain capable of detoxifying trichothecene mycotoxins by Rafiqul Islam A Thesis Presented to The University of Guelph In Partial Fulfilment of Requirements for the Degree of Doctor of Philosophy in Plant Agriculture Guelph, Ontario, Canada © Rafiqul Islam, April, 2012 ABSTRACT ISOLATION, CHARACTERIZATION AND GENOME SEQUENCING OF A SOIL- BORNE CITROBACTER FREUNDII STRAIN CAPABLE OF DETOXIFIYING TRICHOTHECENE MYCOTOXINS Rafiqul Islam Advisors: University of Guelph, 2012 Dr. K. Peter Pauls Dr. Ting Zhou Cereals are frequently contaminated with tricthothecene mycotoxins, like deoxynivalenol (DON, vomitoxin), which are toxic to humans, animals and plants. The goals of the research were to discover and characterize microbes capable of detoxifying DON under aerobic conditions and moderate temperatures. To identify microbes capable of detoxifying DON, five soil samples collected from Southern Ontario crop fields were tested for the ability to convert DON to a de-epoxidized derivative. One soil sample showed DON de-epoxidation activity under aerobic conditions at 22-24°C. To isolate the microbes responsible for DON detoxification (de-epoxidation) activity, the mixed culture was grown with antibiotics at 50ºC for 1.5 h and high concentrations of DON. The treatments resulted in the isolation of a pure DON de-epoxidating bacterial strain, ADS47, and phenotypic and molecular analyses identified the bacterium as Citrobacter freundii. The bacterium was also able to de-epoxidize and/or de-acetylate 10 other food-contaminating trichothecene mycotoxins. A fosmid genomic DNA library of strain ADS47 was prepared in E. coli and screened for DON detoxification activity. However, no library clone was found with DON detoxification activity. -
From Genotype to Phenotype: Inferring Relationships Between Microbial Traits and Genomic Components
From genotype to phenotype: inferring relationships between microbial traits and genomic components Inaugural-Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakult¨at der Heinrich-Heine-Universit¨atD¨usseldorf vorgelegt von Aaron Weimann aus Oberhausen D¨usseldorf,29.08.16 aus dem Institut f¨urInformatik der Heinrich-Heine-Universit¨atD¨usseldorf Gedruckt mit der Genehmigung der Mathemathisch-Naturwissenschaftlichen Fakult¨atder Heinrich-Heine-Universit¨atD¨usseldorf Referent: Prof. Dr. Alice C. McHardy Koreferent: Prof. Dr. Martin J. Lercher Tag der m¨undlichen Pr¨ufung: 24.02.17 Selbststandigkeitserkl¨ arung¨ Hiermit erkl¨areich, dass ich die vorliegende Dissertation eigenst¨andigund ohne fremde Hilfe angefertig habe. Arbeiten Dritter wurden entsprechend zitiert. Diese Dissertation wurde bisher in dieser oder ¨ahnlicher Form noch bei keiner anderen Institution eingereicht. Ich habe bisher keine erfolglosen Promotionsversuche un- ternommen. D¨usseldorf,den . ... ... ... (Aaron Weimann) Statement of authorship I hereby certify that this dissertation is the result of my own work. No other person's work has been used without due acknowledgement. This dissertation has not been submitted in the same or similar form to other institutions. I have not previously failed a doctoral examination procedure. Summary Bacteria live in almost any imaginable environment, from the most extreme envi- ronments (e.g. in hydrothermal vents) to the bovine and human gastrointestinal tract. By adapting to such diverse environments, they have developed a large arsenal of enzymes involved in a wide variety of biochemical reactions. While some such enzymes support our digestion or can be used for the optimization of biotechnological processes, others may be harmful { e.g. mediating the roles of bacteria in human diseases. -
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’. -
Diverse Endophytic Bacteria Isolated from a Leguminous Tree Conzattia Multixora Grown in Mexico
Arch Microbiol (2006) 186:251–259 DOI 10.1007/s00203-006-0141-5 ORIGINAL PAPER Diverse endophytic bacteria isolated from a leguminous tree Conzattia multiXora grown in Mexico En Tao Wang · Zhi Yuan Tan · Xian Wu Guo · Rolando Rodríguez-Duran · Gisela Boll · Esperanza Martínez-Romero Received: 1 March 2006 / Revised: 18 May 2006 / Accepted: 24 May 2006 / Published online: 22 July 2006 © Springer-Verlag 2006 Abstract Conzattia multiXora is a leguminous tree Introduction present only in Mexico and Guatemala. There is no record about its symbiotic or pathogenic microbes. In The endophytes are microorganisms residing in the tis- this study, we found that numerous bacteria with sue of living plants and do not visibly harm the plants 104–106 individuals per gram of fresh epidermis were (Hallmann et al. 1997). These microorganisms are rela- distributed in the tissue of this plant. All the bacteria tively unstudied and are potential sources of novel nat- isolated from the Conzattia epidermis were Gram-neg- ural products for exploitation in medicine, agriculture, ative, facultative anaerobic rods and formed yellow or and industry (Strobel et al. 2004). In nature, each indi- colorless colonies. They were identiWed as endophytes vidual plant is the host to one or more kinds of endo- by inoculation tests. Some of the bacteria could signiW- phyte and only a handful of these plants (grass species) cantly promote the growth of Conzattia seedlings. Nine have been studied in regard to their endophytic biol- diVerent groups were deWned by PCR-based RFLP, ogy. Thus there is a great opportunity to Wnd new and which were classiWed as Pantoea, Erwinia, Salmonella, interesting endophytic microorganisms among myriad Enterobacter, Citrobacter and Klebsiella by the phylo- plants in diVerent settings and ecosystems (Strobel genetic analysis of 16S rRNA genes. -
Isolation and Characterization of an Arsenate-Reducing Bacterium and Its Application for Arsenic Extraction from Contaminated Soil
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Muroran-IT Academic Resource Archive Isolation and characterization of an arsenate-reducing bacterium and its application for arsenic extraction from contaminated soil 著者 CHANG Young-Cheol, NAWATA Akinori, JUNG Kweon, KIKUCHI Shintaro journal or Journal of Industrial Microbiology & publication title Biotechnology volume 39 number 1 page range 37-44 year 2011-06-17 URL http://hdl.handle.net/10258/666 doi: info:doi/10.1007/s10295-011-0996-6 Isolation and characterization of an arsenate-reducing bacterium and its application for arsenic extraction from contaminated soil 著者 CHANG Young-Cheol, NAWATA Akinori, JUNG Kweon, KIKUCHI Shintaro journal or Journal of Industrial Microbiology & publication title Biotechnology volume 39 number 1 page range 37-44 year 2011-06-17 URL http://hdl.handle.net/10258/666 doi: info:doi/10.1007/s10295-011-0996-6 1 Isolation and characterization of an arsenate-reducing bacterium and its application for 2 arsenic extraction from contaminated soil 3 4 Young C. Chang1*, Akinori Nawata1, Kweon Jung2 and Shintaro Kikuchi2 5 1Biosystem Course, Division of Applied Sciences, Muroran Institute of Technology, 27-1 6 Mizumoto, Muroran 050-8585, Japan, 2Seoul Metropolitan Government Research Institute of 7 Public Health and Environment, Yangjae-Dong, Seocho-Gu, Seoul 137-734, Republic of 8 Korea 9 10 *Corresponding author: 11 Phone: +81-143-46-5757; Fax: +81-143-46-5757; E-mail: [email protected] 12 1 13 Abstract 14 A gram-negative anaerobic bacterium, Citrobacter sp. NC-1, was isolated from soil 15 contaminated with arsenic at levels as high as 5000 mg As kg-1. -
Genomic and Phenotypic Insights Point to Diverse Ecological Strategies by Facultative Anaerobes Obtained from Subsurface Coal Seams Silas H
www.nature.com/scientificreports OPEN Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams Silas H. W. Vick1,2*, Paul Greenfeld2, Sasha G. Tetu 1, David J. Midgley2 & Ian T. Paulsen1 Microbes in subsurface coal seams are responsible for the conversion of the organic matter in coal to methane, resulting in vast reserves of coal seam gas. This process is important from both environmental and economic perspectives as coal seam gas is rapidly becoming a popular fuel source worldwide and is a less carbon intensive fuel than coal. Despite the importance of this process, little is known about the roles of individual bacterial taxa in the microbial communities carrying out this process. Of particular interest is the role of members of the genus Pseudomonas, a typically aerobic taxa which is ubiquitous in coal seam microbial communities worldwide and which has been shown to be abundant at early time points in studies of ecological succession on coal. The current study performed aerobic isolations of coal seam microbial taxa generating ten facultative anaerobic isolates from three coal seam formation waters across eastern Australia. Subsequent genomic sequencing and phenotypic analysis revealed a range of ecological strategies and roles for these facultative anaerobes in biomass recycling, suggesting that this group of organisms is involved in the degradation of accumulated biomass in coal seams, funnelling nutrients back into the microbial communities degrading coal to methane. Globally, coal represents a key fuel, accounting for almost ~25% of the world’s energy consumption (International Energy Agency). Te use of coal for power generation, however, is associated with signifcant environmental and health impacts1,2. -
Evidence of an Epidemic Spread of KPC-Producing Enterobacterales In
www.nature.com/scientificreports OPEN Evidence of an epidemic spread of KPC‑producing Enterobacterales in Czech hospitals Lucie Kraftova1,2, Marc Finianos1,2, Vendula Studentova1,2, Katerina Chudejova1,2, Vladislav Jakubu3,4, Helena Zemlickova3,4, Costas C. Papagiannitsis5,6*, Ibrahim Bitar1,2,6* & Jaroslav Hrabak1,2 The aim of the present study is to describe the ongoing spread of the KPC‑producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018–2019, a total of 108 KPC‑ producing Enterobacterales were recovered from 20 hospitals. Analysis of long‑read sequencing data revealed the presence of several types of blaKPC‑carrying plasmids; 19 out of 25 blaKPC‑carrying plasmids could be assigned to R (n = 12), N (n = 5), C (n = 1) and P6 (n = 1) incompatibility (Inc) groups. Five of the remaining blaKPC‑carrying plasmids were multireplicon, while one plasmid couldn’t be typed. Additionally, phylogenetic analysis confrmed the spread of blaKPC‑carrying plasmids among diferent clones of diverse Enterobacterales species. Our fndings demonstrated that the increased prevalence of KPC‑producing isolates was due to plasmids spreading among diferent species. In some districts, the local dissemination of IncR and IncN plasmids was observed. Additionally, the ongoing evolution of blaKPC‑carrying plasmids, through genetic rearrangements, favours the preservation and further dissemination of these mobile genetic elements. Therefore, the situation should be monitored, and immediate infection control should be implemented in hospitals reporting KPC‑producing strains. Carbapenem-resistant Enterobacterales (CRE) incidence have increased, causing worldwide public-health con- cern due to their rapid global dissemination and limited treatment options. -
University of Groningen Description Of
University of Groningen Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples Oberhettinger, Philipp; Schüle, Leonard; Marschal, Matthias; Bezdan, Daniela; Ossowski, Stephan; Dörfel, Daniela; Vogel, Wichard; Rossen, John W; Willmann, Matthias; Peter, Silke Published in: International Journal of Systematic and Evolutionary Microbiology DOI: 10.1099/ijsem.0.004100 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2020 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Oberhettinger, P., Schüle, L., Marschal, M., Bezdan, D., Ossowski, S., Dörfel, D., Vogel, W., Rossen, J. W., Willmann, M., & Peter, S. (2020). Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples. International Journal of Systematic and Evolutionary Microbiology, 70(5), 2998- 3003. [004100]. https://doi.org/10.1099/ijsem.0.004100 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy 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. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. -
Description of Citrobacter Cronae Sp. Nov., Isolated from Human Rectal
University of Groningen Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples Oberhettinger, Philipp; Schüle, Leonard; Marschal, Matthias; Bezdan, Daniela; Ossowski, Stephan; Dörfel, Daniela; Vogel, Wichard; Rossen, John W; Willmann, Matthias; Peter, Silke Published in: International Journal of Systematic and Evolutionary Microbiology DOI: 10.1099/ijsem.0.004100 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2020 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Oberhettinger, P., Schüle, L., Marschal, M., Bezdan, D., Ossowski, S., Dörfel, D., Vogel, W., Rossen, J. W., Willmann, M., & Peter, S. (2020). Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples. International Journal of Systematic and Evolutionary Microbiology, 70(5), 2998- 3003. [004100]. https://doi.org/10.1099/ijsem.0.004100 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy 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. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. -
Molecular Characterization of Phenanthrene-Degrading Methanogenic Communities in Leachate-Contaminated Aquifer Sediment
Int. J. Environ. Sci. Technol. (2012) 9:705–712 DOI 10.1007/s13762-012-0098-7 ORIGINAL PAPER Molecular characterization of phenanthrene-degrading methanogenic communities in leachate-contaminated aquifer sediment S. Y. Zhang • Q. F. Wang • S. G. Xie Received: 21 April 2011 / Revised: 4 October 2011 / Accepted: 12 December 2011 / Published online: 18 July 2012 Ó CEERS, IAU 2012 Abstract The existence of polycyclic aromatic hydro- Introduction carbons in the various environments has aroused great environmental concerns due to their potential hazards to Polycyclic aromatic hydrocarbons (PAHs) are mainly human health. The presence of polycyclic aromatic hydro- produced from incomplete combustion of organic materials carbons in aquifer is particularly sensitive where ground- and fossil fuels in various industrial activities, such as water is used as a source of potable water. Anaerobic coking plants, thermo-power plants and refinery plants. The biodegradation of polycyclic aromatic hydrocarbons is an existence of PAHs in the various environments has aroused attractive option for remediation of contaminated aquifer great environmental concerns. The United States Envi- sediment. Bacterial and archaeal community structures of ronmental Protection Agency has listed 16 typical PAHs as phenanthrene-degrading aquifer sediment under methano- the priority pollutants. The presence of PAHs in aquifer is genic condition were investigated using clone library anal- particularly sensitive where groundwater is used as a ysis in combination with microcosm study. The bacterial source of potable water. The major process for successful members were all affiliated with c-Proteobacteria. Phylum removal of PAHs from contaminated sites is biological Euryarchaeota was the predominant archaeal group, repre- degradation (Yuan et al. -
Citrobacter Freundii Fitness During Bloodstream Infection
www.nature.com/scientificreports OPEN Citrobacter freundii ftness during bloodstream infection Mark T. Anderson1, Lindsay A. Mitchell1, Lili Zhao2 & Harry L. T. Mobley1 Sepsis resulting from microbial colonization of the bloodstream is a serious health concern associated Received: 2 May 2018 with high mortality rates. The objective of this study was to defne the physiologic requirements Accepted: 24 July 2018 of Citrobacter freundii in the bloodstream as a model for bacteremia caused by opportunistic Published: xx xx xxxx Gram-negative pathogens. A genetic screen in a murine host identifed 177 genes that contributed signifcantly to ftness, the majority of which were broadly classifed as having metabolic or cellular maintenance functions. Among the pathways examined, the Tat protein secretion system conferred the single largest ftness contribution during competition infections and a putative Tat-secreted protein, SufI, was also identifed as a ftness factor. Additional work was focused on identifying relevant metabolic pathways for bacteria in the bloodstream environment. Mutations that eliminated the use of glucose or mannitol as carbon sources in vitro resulted in loss of ftness in the murine model and similar results were obtained upon disruption of the cysteine biosynthetic pathway. Finally, the conservation of identifed ftness factors was compared within a cohort of Citrobacter bloodstream isolates and between Citrobacter and Serratia marcescens, the results of which suggest the presence of conserved strategies for bacterial survival and replication in the bloodstream environment. Septicemia is consistently among the 15 leading causes of all death in the United States, with greater than 40,000 deaths attributed in the most recently recorded year1. -
C G M 2 0 1 8 [0 4 on D Er Z O E K S R a Pp O
Update of the bacterial the of bacterial Update intaxonomy the classification lists of COGEM CGM 2018 - 04 ONDERZOEKSRAPPORT report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly.