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Genomic Homogeneity Between Mycobacterium Avium Subsp. Avium and Mycobacterium Avium Subsp
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Department of Agriculture: Agricultural Publications from USDA-ARS / UNL Faculty Research Service, Lincoln, Nebraska 2003 Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates John P. Bannantine ARS-USDA, [email protected] Qing Zhang 2University of Minnesota, Minneapolis, [email protected] Ling-Ling Li University of Minnesota, Minneapolis, [email protected] Vivek Kapur University of Minnesota, Minneapolis, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/usdaarsfacpub Bannantine, John P.; Zhang, Qing; Li, Ling-Ling; and Kapur, Vivek, "Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their divergent growth rates" (2003). Publications from USDA-ARS / UNL Faculty. 2372. https://digitalcommons.unl.edu/usdaarsfacpub/2372 This Article is brought to you for free and open access by the U.S. Department of Agriculture: Agricultural Research Service, Lincoln, Nebraska at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Publications from USDA-ARS / UNL Faculty by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. BMC Microbiology BioMed Central Research article Open Access Genomic homogeneity between Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis belies their -
Nomenclature of Bacteria with Special Reference to the Order Actinomycetales'
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY VOL. 21, No. 2 April 1971, pp. 197-206 Printed in U.S.A. Copyright 0 1971 International Association of Microbiological Societies Nomenclature of Bacteria with Special Reference to the Order Actinomycetales' THOMAS G. PRIDHAM Northern Regional Research Laboratory,z Peoria, Illinois 61604 The number of names for streptomycetes that is in the scientific literature now is exceeded only by those for organisms placed in the genus Bacillus Cohn 1872. The genus Streptomyces Waksman and Henrici 1943 may well rank in first place if names in the patent and quasiscientific literature are included. The overwhelming number of names and the lack of a precise definition of a particular species or subspecies, of type or neotype strains, and of certain essential details have brought about problems in assessing the status of many names. The major problems encountered in a 2-year study are discussed, and a simple format is suggested, use of which may help to clarify future nomenclature. Twelve years ago, I presented (29) before ture of Bacteria (20); type strains, where these the First Latin-American Congress for Micro- can be located and obtained, are being as- biology held at Mexico, D.F., some suggestions sembled and recharacterized (35 -38) through on establishing a logical order in streptomycete the International Streptomyces Project, and a classification. minumum set of substrata and tests have been (i) Compilation and evaluation of available recommended for description of A ctino- literature on nomenclature and characterization mycetales in patents (1 1, 12). of streptomycetes. One item upon which insufficient attention (ii) Decision on the proper code of nomen- has been focused is nomenclature. -
Glycomyces, a New Genus of the Actinomycetales D
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Oct. 1985, p. 417-421 Vol. 35, No. 4 0020-7713/85/040417-05$02.00/0 Glycomyces, a New Genus of the Actinomycetales D. P. LABEDA,l* R. T. TESTA,2 M. P. LECHEVALIER,3 AND H. A. LECHEVALIER3 U. S. Department of Agriculture, Agricultural Research Sewice, Northern Regional Research Center, Peoria, Illinois 61604'; Medical Research Division, American Cyanamid Co., Pearl River, New York 109652; and Waksman Institute of Microbiology, Rutgers, The State University, Piscataway, New Jersey 088543 We describe two species of the new genus Glycomyces, Glycomyces harbinensis sp. nov. and Glycomyces rutgersensis sp. nov. Members of this genus are aerobic, produce nonfragmenting vegetative hyphae, and form chains of conidia on aerial sporophores. The cell walls are type I1 (rneso-diaminopimelic acid and glycine are present), and the whole-cell sugar patterns are type D (xylose and arabinose are present). The phospholipid pattern of both species is type P-I (no nitrogenous phospholipids). The guanine-plus-cytosine content of the deoxyribonucleic acid ranges from 71 to 73 mol%. The type strain of type species G. harbinensis is strain NRRL 15337 (= LL-D05139), and the type strain of G. rutgersensis is strain NRRL B-16106 (= LL-1-20). During the course of isolation of actinomycete strains Gordon et al. (8). Esculin hydrolysis was evaluated by the from soil for an antibiotic screening program, a novel isolate method of Williams et al. (27), and Tween 80 hydrolysis was was obtained from a soil sample from Harbin, People's evaluated by the method of Sierra (26). Phosphatase activity Republic of China. -
Biofilm Degradation of Nontuberculous Mycobacteria
processes Article Biofilm Degradation of Nontuberculous Mycobacteria Formed on Stainless Steel Following Treatment with Immortelle (Helichrysum italicum) and Common Juniper (Juniperus communis) Essential Oils Dolores Peruˇc 1,* , Dalibor Brozni´c 2 , Željka Maglica 3, Zvonimir Marijanovi´c 4, Ljerka Karleuša 5 and Ivana Gobin 1 1 Department of Microbiology and Parasitology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; [email protected] 2 Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; [email protected] 3 Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia; [email protected] 4 Department of Food Technology and Biotechnology, Faculty of Chemistry and Technology, University of Split, 21000 Split, Croatia; [email protected] 5 Department of Physiology and Immunology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia; [email protected] * Correspondence: [email protected]; Tel.: +385-(0)51-651-145; Fax: +385-(0)51-651-177 Abstract: Nontuberculous mycobacteria, like other opportunistic premise plumbing pathogens, pro- duce resistant biofilms on various surfaces in the plumbing system including pipes, tanks, and fittings. Citation: Peruˇc,D.; Brozni´c,D.; Since standard methods of water disinfection are ineffective in eradicating biofilms, research into new Maglica, Ž.; Marijanovi´c,Z.; Karleuša, agents is necessary. Essential oils (EOs) have great potential as anti-biofilm agents. Therefore, the pur- L.; Gobin, I. Biofilm Degradation of pose of this research was to investigate the potential anti-biofilm effect of common juniper (Juniperus Nontuberculous Mycobacteria communis) and immortelle (Helichrysum italicum) EOs. Minimum inhibitory concentrations (MIC), Formed on Stainless Steel Following Treatment with Immortelle minimum bactericidal concentrations (MBC), and minimum effective concentrations of EOs on My- (Helichrysum italicum) and Common cobacterium avium, M. -
Human Microbiota Network: Unveiling Potential Crosstalk Between the Different Microbiota Ecosystems and Their Role in Health and Disease
nutrients Review Human Microbiota Network: Unveiling Potential Crosstalk between the Different Microbiota Ecosystems and Their Role in Health and Disease Jose E. Martínez †, Augusto Vargas † , Tania Pérez-Sánchez , Ignacio J. Encío , Miriam Cabello-Olmo * and Miguel Barajas * Biochemistry Area, Department of Health Science, Public University of Navarre, 31008 Pamplona, Spain; [email protected] (J.E.M.); [email protected] (A.V.); [email protected] (T.P.-S.); [email protected] (I.J.E.) * Correspondence: [email protected] (M.C.-O.); [email protected] (M.B.) † These authors contributed equally to this work. Abstract: The human body is host to a large number of microorganisms which conform the human microbiota, that is known to play an important role in health and disease. Although most of the microorganisms that coexist with us are located in the gut, microbial cells present in other locations (like skin, respiratory tract, genitourinary tract, and the vaginal zone in women) also play a significant role regulating host health. The fact that there are different kinds of microbiota in different body areas does not mean they are independent. It is plausible that connection exist, and different studies have shown that the microbiota present in different zones of the human body has the capability of communicating through secondary metabolites. In this sense, dysbiosis in one body compartment Citation: Martínez, J.E.; Vargas, A.; may negatively affect distal areas and contribute to the development of diseases. Accordingly, it Pérez-Sánchez, T.; Encío, I.J.; could be hypothesized that the whole set of microbial cells that inhabit the human body form a Cabello-Olmo, M.; Barajas, M. -
Reactor Performance and Microbial Analysis
www.nature.com/scientificreports OPEN Investigation of foaming causes in three mesophilic food waste digesters: reactor performance and Received: 24 March 2017 Accepted: 9 October 2017 microbial analysis Published: xx xx xxxx Qin He, Lei Li, Xiaofei Zhao, Li Qu, Di Wu & Xuya Peng Foaming negatively afects anaerobic digestion of food waste (FW). To identify the causes of foaming, reactor performance and microbial community dynamics were investigated in three mesophilic digesters treating FW. The digesters were operated under diferent modes, and foaming was induced with several methods. Proliferation of specifc bacteria and accumulation of surface active materials may be the main causes of foaming. Volatile fatty acids (VFAs) and total ammonia nitrogen (TAN) accumulated in these reactors before foaming, which may have contributed to foam formation by decreasing the surface tension of sludge and increasing foam stability. The relative abundance of acid- producing bacteria (Petrimonas, Fastidiosipila, etc.) and ammonia producers (Proteiniphilum, Gelria, Aminobacterium, etc.) signifcantly increased after foaming, which explained the rapid accumulation + of VFAs and NH4 after foaming. In addition, the proportions of microbial genera known to contribute to foam formation and stabilization signifcantly increased in foaming samples, including bacteria containing mycolic acid in cell walls (Actinomyces, Corynebacterium, etc.) and those capable of producing biosurfactants (Corynebacterium, Lactobacillus, 060F05-B-SD-P93, etc.). These fndings improve the understanding of foaming mechanisms in FW digesters and provide a theoretical basis for further research on efective suppression and early warning of foaming. Anaerobic digestion is the most feasible method for treating food waste (FW) and recovering renewable energy due to its high organic and moisture contents and low calorifc value compared with traditional treatments such as incineration or landflls1. -
Piscine Mycobacteriosis
Piscine Importance The genus Mycobacterium contains more than 150 species, including the obligate Mycobacteriosis pathogens that cause tuberculosis in mammals as well as environmental saprophytes that occasionally cause opportunistic infections. At least 20 species are known to Fish Tuberculosis, cause mycobacteriosis in fish. They include Mycobacterium marinum, some of its close relatives (e.g., M. shottsii, M. pseudoshottsii), common environmental Piscine Tuberculosis, organisms such as M. fortuitum, M. chelonae, M. abscessus and M. gordonae, and Swimming Pool Granuloma, less well characterized species such as M. salmoniphilum and M. haemophilum, Fish Tank Granuloma, among others. Piscine mycobacteriosis, which has a range of outcomes from Fish Handler’s Disease, subclinical infection to death, affects a wide variety of freshwater and marine fish. It Fish Handler’s Nodules has often been reported from aquariums, research laboratories and fish farms, but outbreaks also occur in free-living fish. The same organisms sometimes affect other vertebrates including people. Human infections acquired from fish are most often Last Updated: November 2020 characterized by skin lesions of varying severity, which occasionally spread to underlying joints and tendons. Some lesions may be difficult to cure, especially in those who are immunocompromised. Etiology Mycobacteriosis is caused by members of the genus Mycobacterium, which are Gram-positive, acid fast, pleomorphic rods in the family Mycobacteriaceae and order Actinomycetales. This genus is traditionally divided into two groups: the members of the Mycobacterium tuberculosis complex (e.g., M. tuberculosis, M. bovis, M. caprae, M. pinnipedii), which cause tuberculosis in mammals, and the nontuberculous mycobacteria. The organisms in the latter group include environmental saprophytes, which sometimes cause opportunistic infections, and other species such as M. -
Mycobacterium Kansasii, Strain 824 Catalog No. NR-44269 For
Product Information Sheet for NR-44269 Mycobacterium kansasii, Strain 824 at -60°C or colder immediately upon arrival. For long-term storage, the vapor phase of a liquid nitrogen freezer is recommended. Freeze-thaw cycles should be avoided. Catalog No. NR-44269 Growth Conditions: For research use only. Not for human use. Media: Middlebrook 7H9 broth with ADC enrichment or equivalent Contributor: Middlebrook 7H10 agar with OADC enrichment or Diane Ordway, Ph.D., Assistant Professor, Department of Lowenstein-Jensen agar or equivalent Microbiology, Immunology and Pathology, Colorado State Incubation: University, Fort Collins, Colorado, USA and National Institute Temperature: 37°C of Allergy and Infectious Diseases (NIAID), National Institutes Atmosphere: Aerobic with 5% CO2 of Health (NIH), Bethesda, Maryland, USA Propagation: 1. Keep vial frozen until ready for use; then thaw. Manufacturer: 2. Transfer the entire thawed aliquot into a single tube of BEI Resources broth. 3. Use several drops of the suspension to inoculate an agar Product Description: slant and/or plate. Bacteria Classification: Mycobacteriaceae, Mycobacterium 4. Incubate the tube, slant and/or plate at 37°C for 1 to 6 Species: Mycobacterium kansasii weeks. Strain: 824 Original Source: Mycobacterium kansasii (M. kansasii), strain Citation: 824 was isolated in 2012 from human sputum at the Acknowledgment for publications should read “The following University of Texas Health Science Center at Tyler, Tyler, reagent was obtained through BEI Resources, NIAID, NIH: 1 Texas, USA. Mycobacterium kansasii, Strain 824, NR-44269.” Comment: M. kansasii, strain 824 is part of the Top Priority Nontuberculous Mycobacteria Whole Genome Sequencing Biosafety Level: 2 Project at the Genomic Sequencing Center for Infectious Appropriate safety procedures should always be used with this Diseases (GSCID) at University of Maryland School of material. -
Composition of the Adult Digestive Tract Bacterial Microbiome Based On
Segata et al. Genome Biology 2012, 13:R42 http://genomebiology.com/2012/13/6/R42 RESEARCH Open Access Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples Nicola Segata1, Susan Kinder Haake2,3†, Peter Mannon4†, Katherine P Lemon5,6†, Levi Waldron1, Dirk Gevers7, Curtis Huttenhower1 and Jacques Izard5,8* Abstract Background: To understand the relationship between our bacterial microbiome and health, it is essential to define the microbiome in the absence of disease. The digestive tract includes diverse habitats and hosts the human body’s greatest bacterial density. We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites. Results: The microbiota of these diverse habitats formed four groups based on similar community compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils, throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from environmental samples were detected throughout this population, primarily TM7, SR1, and Synergistetes. Genera with pathogenic members were well-represented among this disease-free cohort. Tooth-associated communities were distinct, but not entirely dissimilar, from other oral surfaces. The Porphyromonadaceae, Veillonellaceae and Lachnospiraceae families were common to all sites, but the distributions of their genera varied significantly. Most metabolic processes were distributed widely throughout the digestive tract microbiota, with variations in metagenomic abundance between body habitats. These included shifts in sugar transporter types between the supragingival plaque, other oral surfaces, and stool; hydrogen and hydrogen sulfide production were also differentially distributed. -
Genomics of Atlantic Forest Mycobacteriaceae Strains Unravels a Mobilome Diversity with a Novel Integrative Conjugative Element and Plasmids Harbouring T7SS
RESEARCH ARTICLE Morgado and Paulo Vicente, Microbial Genomics 2020;6 DOI 10.1099/mgen.0.000382 Genomics of Atlantic Forest Mycobacteriaceae strains unravels a mobilome diversity with a novel integrative conjugative element and plasmids harbouring T7SS Sergio Mascarenhas Morgado* and Ana Carolina Paulo Vicente Abstract Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs in prokaryotes, mainly plasmids and integrative conjugative elements. Nev- ertheless, many mobilomes, particularly those from environmental bacteria, remain underexplored despite their representing a reservoir of genes that can later emerge in the clinic. Here, we explored the mobilome of the Mycobacteriaceae family, focus- ing on strains from Brazilian Atlantic Forest soil. Novel Mycolicibacterium and Mycobacteroides strains were identified, with the former ones harbouring linear and circular plasmids encoding the specialized type- VII secretion system (T7SS) and mobility- associated genes. In addition, we also identified a T4SS- mediated integrative conjugative element (ICEMyc226) encoding two T7SSs and a number of xenobiotic degrading genes. Our study uncovers the diversity of the Mycobacteriaceae mobilome, pro- viding the evidence of an ICE in this bacterial family. Moreover, the presence of T7SS genes in an ICE, as well as plasmids, highlights the role of these mobile genetic elements in the dispersion of T7SS. Data SUMMARY Conjugative elements, such as conjugative plasmids and Genomic data analysed in this work are available in GenBank integrative conjugative elements (ICEs), mediate their own and listed in Tables S1 and S2 (available in the online version transfer to other organisms, often carrying cargo genes. -
(Gid ) Genes Coding for Putative Trna:M5u-54 Methyltransferases in 355 Bacterial and Archaeal Complete Genomes
Table S1. Taxonomic distribution of the trmA and trmFO (gid ) genes coding for putative tRNA:m5U-54 methyltransferases in 355 bacterial and archaeal complete genomes. Asterisks indicate the presence and the number of putative genes found. Genomes Taxonomic position TrmA Gid Archaea Crenarchaea Aeropyrum pernix_K1 Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae Cenarchaeum symbiosum Crenarchaeota; Thermoprotei; Cenarchaeales; Cenarchaeaceae Pyrobaculum aerophilum_str_IM2 Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae Sulfolobus acidocaldarius_DSM_639 Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus solfataricus Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Sulfolobus tokodaii Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae Euryarchaea Archaeoglobus fulgidus Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae Haloarcula marismortui_ATCC_43049 Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Halobacterium sp Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloarcula Haloquadratum walsbyi Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloquadra Methanobacterium thermoautotrophicum Euryarchaeota; Methanobacteria; Methanobacteriales; Methanobacteriaceae Methanococcoides burtonii_DSM_6242 Euryarchaeota; Methanomicrobia; Methanosarcinales; Methanosarcinaceae Methanococcus jannaschii Euryarchaeota; Methanococci; Methanococcales; Methanococcaceae Methanococcus maripaludis_S2 Euryarchaeota; Methanococci; -
Mycobacterium Avium Subsp
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Veterinary and Biomedical Sciences, Papers in Veterinary and Biomedical Science Department of July 2001 Mycobacterium avium subsp. paratuberculosis in Veterinary Medicine N. Beth Harris University of Nebraska - Lincoln Raul G. Barletta University of Nebraska - Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/vetscipapers Part of the Veterinary Medicine Commons Harris, N. Beth and Barletta, Raul G., "Mycobacterium avium subsp. paratuberculosis in Veterinary Medicine" (2001). Papers in Veterinary and Biomedical Science. 5. https://digitalcommons.unl.edu/vetscipapers/5 This Article is brought to you for free and open access by the Veterinary and Biomedical Sciences, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Papers in Veterinary and Biomedical Science by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. CLINICAL MICROBIOLOGY REVIEWS, July 2001, p. 489–512 Vol. 14, No. 3 0893-8512/01/$04.00ϩ0 DOI: 10.1128/CMR.14.3.489–512.2001 Copyright © 2001, American Society for Microbiology. All Rights Reserved. Mycobacterium avium subsp. paratuberculosis in Veterinary Medicine N. BETH HARRIS AND RAU´ L G. BARLETTA* Department of Veterinary and Biomedical Sciences, University of Nebraska—Lincoln, Lincoln, Nebraska 68583-0905 INTRODUCTION .......................................................................................................................................................489