Bordetella Trematum Infection: Case Report and Review of Previous Cases
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Microbial Community Structure Dynamics in Ohio River Sediments During Reductive Dechlorination of Pcbs
University of Kentucky UKnowledge University of Kentucky Doctoral Dissertations Graduate School 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS Andres Enrique Nunez University of Kentucky Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Nunez, Andres Enrique, "MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS" (2008). University of Kentucky Doctoral Dissertations. 679. https://uknowledge.uky.edu/gradschool_diss/679 This Dissertation is brought to you for free and open access by the Graduate School at UKnowledge. It has been accepted for inclusion in University of Kentucky Doctoral Dissertations by an authorized administrator of UKnowledge. For more information, please contact [email protected]. ABSTRACT OF DISSERTATION Andres Enrique Nunez The Graduate School University of Kentucky 2008 MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS ABSTRACT OF DISSERTATION A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the College of Agriculture at the University of Kentucky By Andres Enrique Nunez Director: Dr. Elisa M. D’Angelo Lexington, KY 2008 Copyright © Andres Enrique Nunez 2008 ABSTRACT OF DISSERTATION MICROBIAL COMMUNITY STRUCTURE DYNAMICS IN OHIO RIVER SEDIMENTS DURING REDUCTIVE DECHLORINATION OF PCBS The entire stretch of the Ohio River is under fish consumption advisories due to contamination with polychlorinated biphenyls (PCBs). In this study, natural attenuation and biostimulation of PCBs and microbial communities responsible for PCB transformations were investigated in Ohio River sediments. Natural attenuation of PCBs was negligible in sediments, which was likely attributed to low temperature conditions during most of the year, as well as low amounts of available nitrogen, phosphorus, and organic carbon. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Structural and Functional Effects of Bordetella Avium Infection in the Turkey Respiratory Tract William George Van Alstine Iowa State University
Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1987 Structural and functional effects of Bordetella avium infection in the turkey respiratory tract William George Van Alstine Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Animal Sciences Commons, and the Veterinary Medicine Commons Recommended Citation Van Alstine, William George, "Structural and functional effects of Bordetella avium infection in the turkey respiratory tract " (1987). Retrospective Theses and Dissertations. 11655. https://lib.dr.iastate.edu/rtd/11655 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS While the most advanced technology has been used to photograph and reproduce this manuscript, the quality of the reproduction is heavily dependent upon the quality of the material submitted. For example: • Manuscript pages may have indistinct print. In such cases, the best available copy has been filmed. • Manuscripts may not always be complete. In such cases, a note will indicate that it is not possible to obtain missing pages. • Copyrighted material may have been removed from the manuscript. In such cases, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, and charts) are photographed by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. -
Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): from Uptake to Pathogenicity
This is a repository copy of Tripartite ATP-independent periplasmic (TRAP) transporters and tripartite tricarboxylate transporters (TTT): From uptake to pathogenicity. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/127518/ Version: Published Version Article: Rosa, Leonardo T., Bianconi, Matheus E., Thomas, Gavin Hugh orcid.org/0000-0002- 9763-1313 et al. (1 more author) (2018) Tripartite ATP-independent periplasmic (TRAP) transporters and tripartite tricarboxylate transporters (TTT): From uptake to pathogenicity. Frontiers in Microbiology. 33. ISSN 1664-302X https://doi.org/10.3389/fcimb.2018.00033 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ REVIEW published: 12 February 2018 doi: 10.3389/fcimb.2018.00033 Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): From Uptake to Pathogenicity Leonardo T. Rosa 1, Matheus E. Bianconi 2, Gavin H. Thomas 3 and David J. Kelly 1* 1 Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom, 2 Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom, 3 Department of Biology, University of York, York, United Kingdom The ability to efficiently scavenge nutrients in the host is essential for the viability of any pathogen. -
Unveiling Bacterial Interactions Through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P
www.nature.com/scientificreports OPEN Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling Received: 06 May 2015 Pedro Dorado-Morales1, Cristina Vilanova1, Carlos P. Garay3, Jose Manuel Martí3 Accepted: 17 November 2015 & Manuel Porcar1,2 Published: 16 December 2015 We propose a new strategy to identify and visualize bacterial consortia by conducting replicated culturing of environmental samples coupled with high-throughput sequencing and multidimensional scaling analysis, followed by identification of bacteria-bacteria correlations and interactions. We conducted a proof of concept assay with pine-tree resin-based media in ten replicates, which allowed detecting and visualizing dynamical bacterial associations in the form of statistically significant and yet biologically relevant bacterial consortia. There is a growing interest on disentangling the complexity of microbial interactions in order to both optimize reactions performed by natural consortia and to pave the way towards the development of synthetic consor- tia with improved biotechnological properties1,2. Despite the enormous amount of metagenomic data on both natural and artificial microbial ecosystems, bacterial consortia are not necessarily deduced from those data. In fact, the flexibility of the bacterial interactions, the lack of replicated assays and/or biases associated with differ- ent DNA isolation technologies and taxonomic bioinformatics tools hamper the clear identification of bacterial consortia. We propose here a holistic approach aiming at identifying bacterial interactions in laboratory-selected microbial complex cultures. The method requires multi-replicated taxonomic data on independent subcultures, and high-throughput sequencing-based taxonomic data. From this data matrix, randomness of replicates can be verified, linear correlations can be visualized and interactions can emerge from statistical correlations. -
Reviewed Scientific Articles and P
Notes Notes from the Group of Editors This version of Scientifur, which is the third issue of Please note that the papers in the proceedings have volume 28, contains the proceedings of the VIII been divided into the following two groups: International Scientific Congress in Fur Animal Production, held in ‘s-Hertogenbosch, The RP – reviewed scientific articles and Netherlands, 15 – 18 September 2004. P – short communications On behalf of the Group of Editors Birthe Damgaard Erratum Erratum to table 5, page 124, in the article “Ideal Protein for Mink (Mustela vison) in the Growing and Furring Periods” Peter Sandbol, T.N. Clausen and C. Hejlesen. Scientifur, Vol 28, No 3, proceedings, VIII International Scientific Congress in Fur Animal Production, ’s-Hertogenbosch, The Netherlands, 15-18 September 2004, Due to faulty conversion from g/100 kcal ME to g/MJ, the whole table in the publication shows incorrect values. However this does not change anything else in the publication. The correct figures are as shown below: Table 5. Estimated content of amino acids in gram/MJ during the growing period, compared to an Ideal Protein (IP) and the present norm. 22 ME from protein, → → → → → Present % 32 28 24 20 16 30 26 22 18 14 IP Norm Met incl, MHA* 0.62 0.53 0.46 0.38 0.31 0.57 0.50 0.43 0.34 0.26 0.38 0.38 Met 0.34 0.30 0.25 0.21 0.17 0.31 0.28 0.23 0.19 0.15 0.38 0.38 Cys 0.23 0.20 0.17 0.14 0.11 0.22 0.19 0.16 0.13 0.10 0.14 0.14 Lys 1.03 0.91 0.77 0.65 0.53 0.98 0.83 0.72 0.57 0.46 0.65 0.65 Thr 0.72 0.65 0.55 0.46 0.36 0.67 0.60 0.50 0.41 0.31 -
Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax As Acidovorax Avenae Subsp
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Jan. 1992, p. 107-119 Vol. 42, No. 1 0020-7713/92/010107-13$02 .OO/O Copyright 0 1992, International Union of Microbiological Societies Transfer of Several Phytopathogenic Pseudomonas Species to Acidovorax as Acidovorax avenae subsp. avenae subsp. nov., comb. nov. , Acidovorax avenae subsp. citrulli, Acidovorax avenae subsp. cattleyae, and Acidovorax konjaci A. WILLEMS,? M. GOOR, S. THIELEMANS, M. GILLIS,” K. KERSTERS, AND J. DE LEY Laboratorium voor Microbiologie en microbiele Genetica, Rijksuniversiteit Gent, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium DNA-rRNA hybridizations, DNA-DNA hybridizations, polyacrylamide gel electrophoresis of whole-cell proteins, and a numerical analysis of carbon assimilation tests were carried out to determine the relationships among the phylogenetically misnamed phytopathogenic taxa Pseudomonas avenue, Pseudomonas rubrilineans, “Pseudomonas setariae, ” Pseudomonas cattleyae, Pseudomonas pseudoalcaligenes subsp. citrulli, and Pseudo- monas pseudoalcaligenes subsp. konjaci. These organisms are all members of the family Comamonadaceae, within which they constitute a separate rRNA branch. Only P. pseudoalcaligenes subsp. konjaci is situated on the lower part of this rRNA branch; all of the other taxa cluster very closely around the type strain of P. avenue. When they are compared phenotypically, all of the members of this rRNA branch can be differentiated from each other, and they are, as a group, most closely related to the genus Acidovorax. DNA-DNA hybridization experiments showed that these organisms constitute two genotypic groups. We propose that the generically misnamed phytopathogenic Pseudomonas species should be transferred to the genus Acidovorax as Acidovorax avenue and Acidovorax konjaci. Within Acidovorax avenue we distinguished the following three subspecies: Acidovorax avenue subsp. -
Physiological and Genomic Features of Highly Alkaliphilic Hydrogen-Utilizing Betaproteobacteria from a Continental Serpentinizing Site
ARTICLE Received 17 Dec 2013 | Accepted 16 Apr 2014 | Published 21 May 2014 DOI: 10.1038/ncomms4900 OPEN Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site Shino Suzuki1, J. Gijs Kuenen2,3, Kira Schipper1,3, Suzanne van der Velde2,3, Shun’ichi Ishii1, Angela Wu1, Dimitry Y. Sorokin3,4, Aaron Tenney1, XianYing Meng5, Penny L. Morrill6, Yoichi Kamagata5, Gerard Muyzer3,7 & Kenneth H. Nealson1,2 Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging environments for life in continental sites due to the combination of extremely high pH, low salinity and lack of obvious electron acceptors and carbon sources. Nevertheless, certain Betaproteobacteria have been frequently observed in such environments. Here we describe physiological and genomic features of three related Betaproteobacterial strains isolated from highly alkaline (pH 11.6) serpentinizing springs at The Cedars, California. All three strains are obligate alkaliphiles with an optimum for growth at pH 11 and are capable of autotrophic growth with hydrogen, calcium carbonate and oxygen. The three strains exhibit differences, however, regarding the utilization of organic carbon and electron acceptors. Their global distribution and physiological, genomic and transcriptomic characteristics indicate that the strains are adapted to the alkaline and calcium-rich environments represented by the terrestrial serpentinizing ecosystems. We propose placing these strains in a new genus ‘Serpentinomonas’. 1 J. Craig Venter Institute, 4120 Torrey Pines Road, La Jolla, California 92037, USA. 2 University of Southern California, 835 W. 37th St. SHS 560, Los Angeles, California 90089, USA. 3 Delft University of Technology, Julianalaan 67, Delft, 2628BC, The Netherlands. -
Orrella Amnicola Sp. Nov., Isolated from a Freshwater River, Reclassification of Algicoccus Marinus As Orrella Marina Comb
Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella Shih-Yi Sheu, Li-Chu Chen, Che-Chia Yang, Aurélien Carlier, Wen-Ming Chen To cite this version: Shih-Yi Sheu, Li-Chu Chen, Che-Chia Yang, Aurélien Carlier, Wen-Ming Chen. Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella. International Journal of Systematic and Evo- lutionary Microbiology, Microbiology Society, 2020, 70 (12), pp.6381-6389. 10.1099/ijsem.0.004538. hal-03151291 HAL Id: hal-03151291 https://hal.inrae.fr/hal-03151291 Submitted on 24 Feb 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. TAXONOMIC DESCRIPTION Sheu et al., Int. J. Syst. Evol. Microbiol. 2020;70:6381–6389 DOI 10.1099/ijsem.0.004538 Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella Shih- Yi Sheu1, Li- Chu Chen1, Che- Chia Yang1, Aurelien Carlier2,3 and Wen- Ming Chen4,* Abstract A novel Gram- negative, aerobic, non- motile, ovoid to rod- shaped bacterium, designated NBD-18T, was isolated from a freshwa- ter river in Taiwan. -
UK SMI ID 05: Identification of Bordetella Species
UK Standards for Microbiology Investigations Identification of Bordetella species This publication was created by Public Health England (PHE) in partnership with the NHS. Identification | ID 5 | Issue no: 4 | Issue date: 10.08.2020 | Page: 1 of 18 © Crown copyright 2020 Identification of Bordetella species Acknowledgments UK Standards for Microbiology Investigations (UK SMIs) are developed under the auspices of PHE working in partnership with the National Health Service (NHS), Public Health Wales and with the professional organisations whose logos are displayed below and listed on the website https://www.gov.uk/uk-standards-for-microbiology- investigations-smi-quality-and-consistency-in-clinical-laboratories. UK SMIs are developed, reviewed and revised by various working groups which are overseen by a steering committee (see https://www.gov.uk/government/groups/standards-for- microbiology-investigations-steering-committee). The contributions of many individuals in clinical, specialist and reference laboratories who have provided information and comments during the development of this document are acknowledged. We are grateful to the medical editors for editing the medical content. PHE publications gateway number: GW-983 UK Standards for Microbiology Investigations are produced in association with: Identification | ID 5 | Issue no: 4 | Issue date: 10.08.2020 | Page: 2 of 18 Identification of Bordetella species Contents Acknowledgments ................................................................................................................ -
Emended Descriptions of the Genus Alcaligenes and of Alcaligenes
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY Vol. 24, No. 4 Oct. 1974, p. 534-550 Printed in U.S.A. Copyright 0 1914 International Association of Microbiological Societies Emended Descriptions of the Genus Alcaligenes and of Alcaligenes faecalis and Proposal That tfie Generic Name Achromobacter be Rejected: Status of the Named Species of Alcaligenes and A c h romo bac ter Request for an Opinion MARGARET S. HENDRIE, A. J. HOLDING, and J. M. SHEWAN Torry Research Station, Aberdeen, Scotland, United Kingdom, and Department of Microbiology, University of' Edinburgh, Scotland, United Kingdom The descriptions of the genus Alcaligenes Castellani and Chalmers and Alcaligenes faecalis Castellani and Chalmers have been emended. It is requested that the Judicial Commission issue an Opinion rejecting the name Achromobacter Bergey et al. as a nomen dubium. It is proposed, on the basis of a comparison of type and reference strains, that Alcaligenes denitrificans Leifson and Hugh, Achromobacter arsenoxy- dans-tres Turner, and Alcaligenes odorans (Mhlek and Kazdovii-KoiiSkovii) MBlek et al. be considered as subjective synonyms of A.faecalis. The proposed taxonomic status of all known previously described species of the genera Alcaligenes and Achromobacter is indicated in appendixes. Emendation of description of the genus Aha- Rods or coccoid cells, 0.5 to.0.6 by 1.2 to 2.6 ligenes Castellani and Chalmers. Extensive stud- gm, usually occurring singly. Motile by means of ies on the morphology and physiology of the one to four (occasionally up to eight) flagella; the gram-negative asporogenous rods have been un- flagella may be degenerate. Cells are peritrichous. -
Microorganisms Overwinter Within the Ice Column of a Coastal Antarctic Lake
RESEARCH ARTICLE When a habitat freezes solid: microorganisms over-winter within the ice column ofa coastal Antarctic lake Christine M. Foreman1, Markus Dieser1, Mark Greenwood2, Rose M. Cory3, Johanna Laybourn-Parry4, John T. Lisle5, Christopher Jaros3, Penney L. Miller6, Yu-Ping Chin7 & Diane M. McKnight3 1Department of Land Resources and Environmental Sciences, Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA; 2Department of Mathematical Sciences, Montana State University, Bozeman, MT, USA; 3INSTAAR, University of Colorado, Boulder, CO, USA; 4Bristol Glaciology Centre, University of Bristol, Bristol, UK; 5USGS, Center for Coastal and Watershed Studies, St. Petersburg, FL, USA; 6Department of 7 Chemistry, Rose-Hulman Institute of Technology, Terre Haute, IN, USA; and 285 Mendenhall Laboratory, the Ohio State University, School of Earth Downloaded from https://academic.oup.com/femsec/article/76/3/401/486873 by guest on 27 September 2021 Sciences, Columbus, OH, USA Correspondence: Christine M. Foreman, Abstract Department of Land Resources and Environmental Sciences, Center for Biofilm A major impediment to understanding the biology of microorganisms inhabiting Engineering, Montana State University, 366 Antarctic environments is the logistical constraint of conducting field work EPS Building, Bozeman, MT 59717, USA. primarily during the summer season. However, organisms that persist throughout Tel.: 11 406 994 7361; fax: 11 406 994 the year encounter severe environmental changes between seasons. In an attempt 6098; e-mail: [email protected] to bridge this gap, we collected ice core samples from Pony Lake in early November 2004 when the lake was frozen solid to its base, providing an archive for the Present address: Rose M.