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Bacterial Communities of the Upper Respiratory Tract of Turkeys
www.nature.com/scientificreports OPEN Bacterial communities of the upper respiratory tract of turkeys Olimpia Kursa1*, Grzegorz Tomczyk1, Anna Sawicka‑Durkalec1, Aleksandra Giza2 & Magdalena Słomiany‑Szwarc2 The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplifcation of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identifed in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Diferences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identifed, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey focks. Next-generation sequencing has resulted in a marked increase in culture-independent studies characterizing the microbiome of humans and animals1–6. Much of these works have been focused on the gut microbiome of humans and other production animals 7–11. -
A Rubber-Degrading Organism Growing from a Human Body
International Journal of Infectious Diseases (2010) 14, e75—e76 http://intl.elsevierhealth.com/journals/ijid CASE REPORT A rubber-degrading organism growing from a human body Mohit Gupta *, Deepali Prasad, Harshit S. Khara, David Alcid Department of Internal Medicine, Drexel University College of Medicine — Saint Peter’s University Hospital, 254 Easton Avenue, New Brunswick, NJ 08901, USA Received 24 October 2008; received in revised form 27 February 2009; accepted 3 March 2009 Corresponding Editor: Timothy Barkham, Tan Tock Seng, Singapore KEYWORDS Summary Patients with hematological malignancies are susceptible to unusual infections, Gordonia because of the use of broad-spectrum anti-infective agents, invasive procedures, and other polyisoprenivorans; immunocompromising procedures and medications. Gordonia polyisoprenivorans, a ubiquitous Pneumonia; environmental aerobic actinomycete belonging to the family of Gordoniaceae in the order Rubber-degrading Actinomycetales, is a very rare cause of bacteremia in these patients. We report the first case organism; of pneumonia with associated bacteremia due to this organism, which was initially described in Bacteremia; 1999 as a rubber-degrading bacterium following isolation from stagnant water inside a deterio- Leukemia rated automobile tire. We believe that hematologically immunocompromised patients on broad- spectrum antibiotics and with long-term central catheters select the possibility of infection with G. polyisoprenivorans. These infections can be prevented by handling catheters under aseptic conditions. We propose that blood cultures of persistently febrile neutropenic patients should be incubated for at least 4 weeks. Being a rare infection, there are no data available on treatment other than early removal of the foreign bodies. # 2009 International Society for Infectious Diseases. Published by Elsevier Ltd. -
Alpine Soil Bacterial Community and Environmental Filters Bahar Shahnavaz
Alpine soil bacterial community and environmental filters Bahar Shahnavaz To cite this version: Bahar Shahnavaz. Alpine soil bacterial community and environmental filters. Other [q-bio.OT]. Université Joseph-Fourier - Grenoble I, 2009. English. tel-00515414 HAL Id: tel-00515414 https://tel.archives-ouvertes.fr/tel-00515414 Submitted on 6 Sep 2010 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. THÈSE Pour l’obtention du titre de l'Université Joseph-Fourier - Grenoble 1 École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Par Bahar SHAHNAVAZ Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. Thierry HEULIN Rapporteur Dr. Christian JEANTHON Rapporteur Dr. Sylvie NAZARET Examinateur Dr. Jean MARTIN Examinateur Dr. Yves JOUANNEAU Président du jury Dr. Roberto GEREMIA Directeur de thèse Thèse préparée au sien du Laboratoire d’Ecologie Alpine (LECA, UMR UJF- CNRS 5553) THÈSE Pour l’obtention du titre de Docteur de l’Université de Grenoble École Doctorale : Chimie et Sciences du Vivant Spécialité : Biodiversité, Écologie, Environnement Communautés bactériennes de sols alpins et filtres environnementaux Bahar SHAHNAVAZ Directeur : Roberto GEREMIA Soutenue devant jury le 25 Septembre 2009 Composition du jury Dr. -
Identification of Pasteurella Species and Morphologically Similar Organisms
UK Standards for Microbiology Investigations Identification of Pasteurella species and Morphologically Similar Organisms Issued by the Standards Unit, Microbiology Services, PHE Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 1 of 28 © Crown copyright 2015 Identification of Pasteurella species and Morphologically Similar Organisms Acknowledgments UK Standards for Microbiology Investigations (SMIs) are developed under the auspices of Public Health England (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. 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. For further information please contact us at: Standards Unit Microbiology Services Public Health England 61 Colindale Avenue London NW9 5EQ E-mail: [email protected] Website: https://www.gov.uk/uk-standards-for-microbiology-investigations-smi-quality- and-consistency-in-clinical-laboratories UK Standards for Microbiology Investigations are produced in association with: Logos correct at time of publishing. Bacteriology – Identification | ID 13 | Issue no: 3 | Issue date: 04.02.15 | Page: 2 of 28 UK Standards for Microbiology Investigations | Issued by the Standards Unit, Public Health England Identification of Pasteurella species and Morphologically Similar Organisms Contents ACKNOWLEDGMENTS ......................................................................................................... -
WO 2018/064165 A2 (.Pdf)
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/064165 A2 05 April 2018 (05.04.2018) W !P O PCT (51) International Patent Classification: Published: A61K 35/74 (20 15.0 1) C12N 1/21 (2006 .01) — without international search report and to be republished (21) International Application Number: upon receipt of that report (Rule 48.2(g)) PCT/US2017/053717 — with sequence listing part of description (Rule 5.2(a)) (22) International Filing Date: 27 September 2017 (27.09.2017) (25) Filing Language: English (26) Publication Langi English (30) Priority Data: 62/400,372 27 September 2016 (27.09.2016) US 62/508,885 19 May 2017 (19.05.2017) US 62/557,566 12 September 2017 (12.09.2017) US (71) Applicant: BOARD OF REGENTS, THE UNIVERSI¬ TY OF TEXAS SYSTEM [US/US]; 210 West 7th St., Austin, TX 78701 (US). (72) Inventors: WARGO, Jennifer; 1814 Bissonnet St., Hous ton, TX 77005 (US). GOPALAKRISHNAN, Vanch- eswaran; 7900 Cambridge, Apt. 10-lb, Houston, TX 77054 (US). (74) Agent: BYRD, Marshall, P.; Parker Highlander PLLC, 1120 S. Capital Of Texas Highway, Bldg. One, Suite 200, Austin, TX 78746 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. -
Mycobacterium Tuberculosis Rv0366c-Rv0367c Encodes a Non
www.nature.com/scientificreports OPEN Mycobacterium tuberculosis Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin- Received: 3 August 2018 Accepted: 27 November 2018 antitoxin pair Published: xx xx xxxx Himani Tandon 1, Arun Sharma2, Sankaran Sandhya1, Narayanaswamy Srinivasan1 & Ramandeep Singh2 Toxin-antitoxin (TA) systems are ubiquitously existing addiction modules with essential roles in bacterial persistence and virulence. The genome of Mycobacterium tuberculosis encodes approximately 79 TA systems. Through computational and experimental investigations, we report for the frst time that Rv0366c-Rv0367c is a non-canonical PezAT-like toxin-antitoxin system in M. tuberculosis. Homology searches with known PezT homologues revealed that residues implicated in nucleotide, antitoxin-binding and catalysis are conserved in Rv0366c. Unlike canonical PezA antitoxins, the N-terminal of Rv0367c is predicted to adopt the ribbon-helix-helix (RHH) motif for deoxyribonucleic acid (DNA) recognition. Further, the modelled complex predicts that the interactions between PezT and PezA involve conserved residues. We performed a large-scale search in sequences encoded in 101 mycobacterial and 4500 prokaryotic genomes and show that such an atypical PezAT organization is conserved in 20 other mycobacterial organisms and in families of class Actinobacteria. We also demonstrate that overexpression of Rv0366c induces bacteriostasis and this growth defect could be restored upon co-expression of cognate antitoxin, Rv0367c. Further, we also observed that inducible expression of Rv0366c in Mycobacterium smegmatis results in decreased cell-length and enhanced tolerance against a front-line tuberculosis (TB) drug, ethambutol. Taken together, we have identifed and functionally characterized a novel non-canonical TA system from M. tuberculosis. Bacterial toxin-antitoxin (TA) systems are plasmid or chromosome-encoded, mobile genetic elements expressed as part of the same operon1–3. -
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 -
Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile
ORIGINAL RESEARCH published: 19 July 2016 doi: 10.3389/fmicb.2016.01135 Exploring the Diversity and Antimicrobial Potential of Marine Actinobacteria from the Comau Fjord in Northern Patagonia, Chile Agustina Undabarrena 1, Fabrizio Beltrametti 2, Fernanda P. Claverías 1, Myriam González 1, Edward R. B. Moore 3, 4, Michael Seeger 1 and Beatriz Cámara 1* 1 Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile, 2 Actygea S.r.l., Gerenzano, Italy, 3 Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden, 4 Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden Edited by: Bioprospecting natural products in marine bacteria from fjord environments are attractive Learn-Han Lee, due to their unique geographical features. Although, Actinobacteria are well known Monash University Malaysia Campus, Malaysia for producing a myriad of bioactive compounds, investigations regarding fjord-derived Reviewed by: marine Actinobacteria are scarce. In this study, the diversity and biotechnological Atte Von Wright, potential of Actinobacteria isolated from marine sediments within the Comau University of Eastern Finland, Finland fjord, in Northern Chilean Patagonia, were assessed by culture-based approaches. Polpass Arul Jose, Central Salt and Marine Chemicals The 16S rRNA gene sequences revealed that members phylogenetically related Research Institute, India to the Micrococcaceae, Dermabacteraceae, Brevibacteriaceae, Corynebacteriaceae, *Correspondence: Microbacteriaceae, Dietziaceae, Nocardiaceae, and Streptomycetaceae families were Beatriz Cámara [email protected] present at the Comau fjord. A high diversity of cultivable Actinobacteria (10 genera) was retrieved by using only five different isolation media. -
Williamsia Soli Sp. Nov., Isolated from Thermal Power Plant in Yantai
Williamsia soli sp. nov., Isolated from Thermal Power Plant in Yantai Ming-Jing Zhang ShanDong University Xue-Han Li ShanDong University Li-Yang Peng ShanDong University Shuai-Ting Yun ShanDong University Zhuo-Cheng Liu ShanDong University Yan-Xia Zhou ( [email protected] ) Shandong University https://orcid.org/0000-0003-0393-8136 Research Article Keywords: Aerobic, Genomic Analysis, Predominant fatty acid, Soil, Thermal power plant, Williamsia soli sp. nov Posted Date: June 10th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-594776/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License 1 Williamsia soli sp. nov., isolated from thermal power plant in Yantai 2 Ming-Jing Zhang · Xue-Han Li · Li-Yang Peng · Shuai-Ting Yun · Zhuo-Cheng 3 Liu · Yan-Xia Zhou* 4 Marine College, Shandong University, Weihai 264209, China 5 *Correspondence: Yan-Xia Zhou; Email: [email protected] 6 Abstract 7 Strain C17T, a novel strain belonging to the phylum Actinobacteria, was isolated from 8 thermal power plant in Yantai, Shandong Province, China. Cells of strain C17T were 9 Gram-stain-positive, aerobic, pink, non-motile and round with neat edges. Strain C17T 10 was able to grow at 4–42 °C (optimum 28 °C), pH 5.5–9.5 (optimum 7.5) and with 11 0.0–5.0% NaCl (optimum 1.0%, w/v). Phylogenetically, the strain was a member of 12 the family Gordoniaceae, order Mycobacteriales, class Actinobacteria. Phylogenetic 13 analysis based on 16S rRNA gene sequence comparisons revealed that the closest 14 relative was the type strain of Williamsia faeni JCM 17784T with pair-wise sequence 15 similarity of 98.4%. -
Pasteurellaceae: P. Multocida, Avibacterium Gallinarum, A
Pasteurellaceae: P. Multocida, Avibacterium gallinarum, A. paragallinarum All the members of the family Pasteurellaceae are gram negative coccobacilli. They are facultative anaerobes, and typically oxidase-positive (which sets them apart from members of the family Enterobacteriaceae). Morphology and Staining Members of the genera Avibacterium, and Pasteurella are gram-negative coccobacilli. Bipolarity, that is, the staining of only the tips of cells, may be demonstrable with polychrome stains (e.g., Wright’s stain). Cell structure Adhesins. Some and probably all members of the family Pasteurellaceae produce adhesins (and possibly more than one kind). A type 4 fimbria (adhesin) has been described for avian strains of P. Multocida. Capsule. The hyaluronic acid capsule of type A strains P. multocida serves as an adhesin. The hyaluronic acid is similar (if not identical) to host tissue components, and is thus poorly antigenic; they also bind complement components poorly (and is therefore antiphagocytic).The hyaluronic acid capsule also serves as an adhesin for respiratory tract epithelial cells as in the case of capsule type A strains of P. Multocida Exotoxin. Pasteurella produce a number of proteins with toxic activity. At least two of these are important in the pathogenesis of disease: RTX and Rho toxin Growth Characteristics Avibacterium and Pasteurella grow best in the presence of serum or blood. After overnight incubation (35–37 ◦C), colonies are up to 2 mm in diameter, clear to 1 grayish, and smooth or mucoid. All are gram-negative, nonmotile coccobacilli. They are facultative anaerobes, typically oxidase-positive. Variability P. multocida consists of 5 capsular serogroups (A, B, D, E, and F) and 16 somatic serotypes (1–16). -
Mapping the Bacterial Ecology on the Phyllosphere Of
bioRxiv preprint doi: https://doi.org/10.1101/494799; this version posted December 12, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Mapping the bacterial ecology on the phyllosphere of grass hay and the 2 potential hazards of soaking fodder for horse gut health 3 Meriel JS Moore-Colyer1, Annette Longland2, Patricia Harris3, Susan Crosthwaite4 4 1 Royal Agricultural University, Cirencester Gloucestershire, UK GL7 6JS. 5 2Equine and Livestock Nutrition Services, Pantafallen Fach, Tregaron, Ceredigion, Wales. SY25 6NF 6 3Mars Horsecare UK LTD; Equine Studies Group, Waltham Centre for Pet Nutrition, Waltham-on-the Wolds, 7 Leicestershire, UK. LE14 4RT 8 4 Faculty of Biology, Medicine and Health, University of Manchester, UK M13 9PT. 9 10 Corresponding author: *[email protected] ORCID 0000-0002-9172-9862 11 12 Short title: The bacterial ecology on the phyllosphere of dry and post-soaked grass hay for 13 horses 14 bioRxiv preprint doi: https://doi.org/10.1101/494799; this version posted December 12, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 15 Abstract 16 Globally hay is the preferred forage for stabled horses. Variable nutritional and hygienic quality stimulates pre- 17 feeding soaking to reduce dust and nutrients to reduce respiratory and metabolic disorders in horses. -
Marine Rare Actinomycetes: a Promising Source of Structurally Diverse and Unique Novel Natural Products
Review Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products Ramesh Subramani 1 and Detmer Sipkema 2,* 1 School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji; [email protected] 2 Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands * Correspondence: [email protected]; Tel.: +31-317-483113 Received: 7 March 2019; Accepted: 23 April 2019; Published: 26 April 2019 Abstract: Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.