DOCSLIB.ORG

Nomenclature of Bacteria with Special Reference to the Order Actinomycetales'

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
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. For the past clature to follow and on a common language to several years I have been engaged in a practical describe new taxa. application of the International Code of (iii) Agreement on generic names to be used. Nomenclature of Bacteria (hereinafter referred (iv) Check of type strains and their recharac- to as the Code). My results have been informa- t erization by contemporary met hods. tive, yet disappointing, frustrating, and men- (v) Assignment of numbers to each im- tally exhausting. My experience is an indict- portant named or unnamed strain reported in ment against departments of bacteriology, the literature. microbiology, and biology the world over. (vi) Agreement on designation of a minimum Although I speak primarily to actinomycetolo- set of substrata and tests for characterization of gists, unquestionably my remarks apply to strains. other subdisciplines within microbiology. Too (vii) Determination of ranges of variation many of us either do not know about the Code, within particular taxa, if possible. do not understand it, or simply choose to (viii) Provision for adequate preservation of ignore it. On the other hand, those concerned cultures of type strains. with the development of the Code may not In the ensuing years, considerable advance- have fully realized the impact of applied micro- ment has been made on some of these sug- biology or of the teamwork approach in solving gestions. Actinomycetologists have agreed ( 1) microbiological problems. Applied micro- on using the International Code of Nomencla- biology and the research team present many new problems to the nomenclature of micro- Presented at a round table on Nomenclature of organisms, particularly the A ctinomycetales Actinornycetales at the 10th International Congress and other taxa of industrial-economic interest. I for Microbiology, Mexico, D.F., 9-1 5 August 1970. daresay that a majority of the new taxa which This is a laboratory of the Northern Marketing and Nutrition Research Division, Agricultural Re- confront us now have come from applied search Service, US. Department of Agriculture. microbiology. Therefore its stake in nomencla- 197 198 PRIDHAM INT. J. SYST. BACTERIOL. ture is high. I am particularly concerned be- Only by taking certain liberties can one arrive cause classification and nomenclature seem to at any reasonably accurate contemporary pic- move along separate pathways. Taxonomists ture of the Order as it is known from a should apply the correct names to their taxa. taxonomic viewpoint. The taxonomic informa- Hence, the relationship between the two discip- tion is there, but there are problems associated lines should be closer. with communicating this information through As shown in Table 1, the number of names nomenclature. of streptomycetes in the scientific literature Perhaps we have lost sight of the principal now is exceeded only by the number of names reason for naming a microorganism, i.e., to of organisms placed in the genera Bacillus Cohn facilitate communication. In virtually every 1872 and Bacterium Ehrenberg. (The name of microbiological operation one ultimate ques- the latter genus has been placed on the list of tion that arises is, “What is the name of the rejected names.) organism?” The accuracy of this determination The genus Streptomyces Waksman and eventually reflects the state of the discipline Henrici 1943, when combined with the genus and its progress. Despite the fundamental dis- Actinomyces Harz 1877, most of which are coveries that have come out of pure taxonomy streptomycetes or streptoverticillia anyway, and despite the excellent chemical work result- may well rank in first place as far as number of ing from studies of secondary metabolites, our named species and subspecies is concerned if means of communicating in terms of the those in the patent and quasiscientific literature microorganisms involved is in a sad state be- are included. The overwhelming number of cause of failures to follow the Code. Or, names, lack of a precise definition of a species perhaps from another viewpoint, the Code may or subspecies, lack of type or neotype strains, be too involved and restrictive. Because of its and lack of essential details associated with complex nature, it may present too many particular names have brought about questions obstacles for practical application. Only in in assessing the status of many names. Principle 8 of the Code do I find reference to My task was a frustrating one complicated an explanation of why microorganisms are initially by translation, the Actinomyces versus named: “. ..to supply a means of referring to Streptomyces, and patent problems. I will taxa.” Savory (34) gives a fuller discussion in discuss some of these and present a simple his interesting little book on nomenclature. Of format that may help to alleviate the situation course, to aid communication any kind of in the future. Unless more attention is paid to system or supplement would suffice, provided the Code, I predict continuing confusion and it is acceptable. Suggestions toward this end much busy work in the years to come, have been made (13, 39), but the binary system especially if one considers the multitude of new supplemented with strain designations still names that might be proposed through applica- appears to be the most acceptable, at least to tion of a typological-nominalistic kind of me, for the Actinomycetales. species concept. The information I have Scientists require that a name be correct gathered suggests that literal interpretation of according to certain rules. However, because of the Code would result in a rather short list of the impact of applied microbiology, we are in a names of organisms belonging to the order position where scientific law and the much Actinomycetales that are scientifically correct. older juridicial law (10) are opposed in certain No. of pages Genus IBa IB-1 IB-2 IB-3 Total Bacillus ............................... 188-112 2 11-112 1-114 203-114 Bacterium (illegal) ....................... 109 1-1/2 12-1/2 314 123-314 Actinomyces-Streptomyces ................ 77 2-112 8 2-112 90 Salmonella ............................ 8 1 0 0 0 81 Pseudomonas .......................... 37-314 2-114 0 0 40 Micrococcus ........................... 36 112 0 0 36-112 Q IB, reference 8; IB-1, reference 15; IB-2, reference 43; IB-3, reference 44. VOL. 21,1971 A CTINOMYCETALES NOMENCLATURE 199 areas, e.g., Rule 11 of the Code, wherein names taxonomic reports on nomenclature. This of bacteria published in patents are not recog- consequence can be fully appreciated only nized as valid. through study of the Code and implementation Of the three initial broad problems I en- of its “Principles, Rules, and Recommenda- countered, that of translation, though difficult, tions.” Resolving taxonomic problems also will is perhaps the simplest to solve. Lack of ultimately clarify some of the nomenclatural adequate services or capabilities for translating problems. a variety of languages leads to a considerable lag The third major problem I encountered or breach in communication simply because too revolves around Rule 11 of the Code and few people are adept in all foreign languages, concerns names of organisms published in taxonomic papers may not have high priority patents. I am fearful that this Rule may have for translation services, and translations are placed nomenclatural specialists in a position expensive. I am beginning to look with jaun- worse than before the Rule was promulgated. I diced eye on the time, effort, and expense of still am not certain as to the reason(s) for its obtaining translations when much of the infor- proposal. In the review of this manuscript, mation turns out to be of little or no real value. three reviewers offered the following as their Only through much perseverance
Load more

Recommended publications
  • 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
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Comparative Analyses of Whole-Genome Protein Sequences
    www.nature.com/scientificreports OPEN Comparative analyses of whole- genome protein sequences from multiple organisms Received: 7 June 2017 Makio Yokono 1,2, Soichirou Satoh3 & Ayumi Tanaka1 Accepted: 16 April 2018 Phylogenies based on entire genomes are a powerful tool for reconstructing the Tree of Life. Several Published: xx xx xxxx methods have been proposed, most of which employ an alignment-free strategy. Average sequence similarity methods are diferent than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole-genome trees. In this study, we developed a novel average sequence similarity method. Our method correctly reconstructs the phylogenetic tree of in silico evolved E. coli proteomes. We applied the method to reconstruct a whole-proteome phylogeny of 1,087 species from all three domains of life, Bacteria, Archaea, and Eucarya. Our tree was automatically reconstructed without any human decisions, such as the selection of organisms. The tree exhibits a concentric circle-like structure, indicating that all the organisms have similar total branch lengths from their common ancestor. Branching patterns of the members of each phylum of Bacteria and Archaea are largely consistent with previous reports. The topologies are largely consistent with those reconstructed by other methods. These results strongly suggest that this approach has sufcient taxonomic resolution and reliability to infer phylogeny, from phylum to strain, of a wide range of organisms. Te reconstruction of phylogenetic trees is a powerful tool for understanding organismal evolutionary processes. Molecular phylogenetic analysis using ribosomal RNA (rRNA) clarifed the phylogenetic relationship of the three domains, bacterial, archaeal, and eukaryotic1.
    [Show full text]
  • Type of the Paper (Article
    Supplementary Materials S1 Clinical details recorded, Sampling, DNA Extraction of Microbial DNA, 16S rRNA gene sequencing, Bioinformatic pipeline, Quantitative Polymerase Chain Reaction Clinical details recorded In addition to the microbial specimen, the following clinical features were also recorded for each patient: age, gender, infection type (primary or secondary, meaning initial or revision treatment), pain, tenderness to percussion, sinus tract and size of the periapical radiolucency, to determine the correlation between these features and microbial findings (Table 1). Prevalence of all clinical signs and symptoms (except periapical lesion size) were recorded on a binary scale [0 = absent, 1 = present], while the size of the radiolucency was measured in millimetres by two endodontic specialists on two- dimensional periapical radiographs (Planmeca Romexis, Coventry, UK). Sampling After anaesthesia, the tooth to be treated was isolated with a rubber dam (UnoDent, Essex, UK), and field decontamination was carried out before and after access opening, according to an established protocol, and shown to eliminate contaminating DNA (Data not shown). An access cavity was cut with a sterile bur under sterile saline irrigation (0.9% NaCl, Mölnlycke Health Care, Göteborg, Sweden), with contamination control samples taken. Root canal patency was assessed with a sterile K-file (Dentsply-Sirona, Ballaigues, Switzerland). For non-culture-based analysis, clinical samples were collected by inserting two paper points size 15 (Dentsply Sirona, USA) into the root canal. Each paper point was retained in the canal for 1 min with careful agitation, then was transferred to −80ºC storage immediately before further analysis. Cases of secondary endodontic treatment were sampled using the same protocol, with the exception that specimens were collected after removal of the coronal gutta-percha with Gates Glidden drills (Dentsply-Sirona, Switzerland).
    [Show full text]
  • Workshop on Mycobacterium Avium Subsp
    Workshop on Mycobacterium avium subsp. paratuberculosis in North American Bison (Bison bison) PROCEEDINGS AND WORKSHOP REPORT Alberta Cooperative Conservation Research Unit National (Canadian) Wood Bison (ACCRU) Recovery Team Editors: Murray Woodbury, Elena Garde, Helen Schwantje, John Nishi, and Brett Elkin with contributions from Michelle Oakley, Jenny Powers, Jennifer Sibley and workshop participants. Department of Resources, Wildlife and Economic Development Government of the Northwest Territories Yellowknife, NT 2006 Manuscript Report No. 170 The contents of this paper are the sole responsibility of the author ii iii ABSTRACT Many of the emerging diseases worldwide are shared between domestic livestock, free ranging wildlife, and humans. Infection by mycobacterial organisms is not a recent or newly emerging issue, but the increasing frequency of disease caused by Mycobacterium species, where wildlife, domestic livestock, and humans are epidemiologically linked is cause for concern for wildlife management, agricultural and public health agencies alike. Human tuberculosis, including that caused by Mycobacterium bovis, once thought to be a well understood disease of lifestyle and socioeconomic consequences is once again a global concern. Johne’s disease (Mycobacterium avium subspecies paratuberculosis infection), previously considered a production limiting disease important only in domestic ruminants, has recently been implicated in the pathogenesis of Crohn’s disease in humans. Furthermore, wildlife and livestock reservoirs of infection
    [Show full text]
  • Microbial Diversity of Thermophiles with Biomass Deconstruction Potential in a Foliage-­Rich Hot Spring
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Universiti Teknologi Malaysia Institutional Repository Received: 9 December 2017 | Revised: 29 January 2018 | Accepted: 12 February 2018 DOI: 10.1002/mbo3.615 ORIGINAL RESEARCH Microbial diversity of thermophiles with biomass deconstruction potential in a foliage- rich hot spring Li Sin Lee1 | Kian Mau Goh2 | Chia Sing Chan2 | Geok Yuan Annie Tan1 | Wai-Fong Yin1 | Chun Shiong Chong2 | Kok-Gan Chan1,3 1ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Abstract Lumpur, Malaysia The ability of thermophilic microorganisms and their enzymes to decompose biomass 2 Faculty of Biosciences and Medical have attracted attention due to their quick reaction time, thermostability, and de- Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia creased risk of contamination. Exploitation of efficient thermostable glycoside hy- 3Jiangsu University, Zhenjiang, China drolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for Correspondence Kok-Gan Chan, International Genome biomass degradation at high temperatures have not yet been thoroughly studied. We Centre, Jiangsu University, Zhenjiang, China. examined a Malaysian Y- shaped Sungai Klah hot spring located within a wooded area. Email: [email protected] The fallen foliage that formed a thick layer of biomass bed under the heated water of Funding information the Y- shaped Sungai Klah hot spring was an ideal environment for the discovery and Postgraduate Research Fund grant, Grant/ Award Number: PG124-2016A; University analysis of microbial biomass decay communities. We sequenced the hypervariable of Malaya, Grant/Award Number: GA001- regions of bacterial and archaeal 16S rRNA genes using total community DNA ex- 2016 and GA002-2016; Universiti Teknologi Malaysia GUP, Grant/Award Number: tracted from the hot spring.
    [Show full text]
  • Diversity of the Human Gastrointestinal Microbiota Novel Perspectives from High Throughput Analyses
    Diversity of the Human Gastrointestinal Microbiota Novel Perspectives from High Throughput Analyses Mirjana Rajilić-Stojanović Promotor Prof. Dr W. M. de Vos Hoogleraar Microbiologie Wageningen Universiteit Samenstelling Promotiecommissie Prof. Dr T. Abee Wageningen Universiteit Dr J. Doré INRA, France Prof. Dr G. R. Gibson University of Reading, UK Prof. Dr S. Salminen University of Turku, Finland Dr K. Venema TNO Quality for life, Zeist Dit onderzoek is uitgevoerd binnen de onderzoekschool VLAG. Diversity of the Human Gastrointestinal Microbiota Novel Perspectives from High Throughput Analyses Mirjana Rajilić-Stojanović Proefschrift Ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof. dr. M. J. Kropff, in het openbaar te verdedigen op maandag 11 juni 2007 des namiddags te vier uur in de Aula Mirjana Rajilić-Stojanović, Diversity of the Human Gastrointestinal Microbiota – Novel Perspectives from High Throughput Analyses (2007) PhD Thesis, Wageningen University and Research Centre, Wageningen, The Netherlands – with Summary in Dutch – 214 p. ISBN: 978-90-8504-663-9 Abstract The human gastrointestinal tract is densely populated by hundreds of microbial (primarily bacterial, but also archaeal and fungal) species that are collectively named the microbiota. This microbiota performs various functions and contributes significantly to the digestion and the health of the host. It has previously been noted that the diversity of the gastrointestinal microbiota is disturbed in relation to several intestinal and not intestine related diseases. However, accurate and detailed defining of such disturbances is hampered by the fact that the diversity of this ecosystem is still not fully described, primarily because of its extreme complexity, and high inter-individual variability.
    [Show full text]
  • Mycobacteriosis in Australian Birds Dec 2013
    Mycobacteriosis in Australian birds Fact sheet Introductory statement Multiple species of mycobacteria can cause disease in birds. The most common species, however, are Mycobacterium avium subspecies avium and M. genavense. Mycobacteria cause a slowly progressive and, in the end, fatal disease in the birds they infect. Infection in wild birds occurs sporadically. However, in certain species of captive birds and in certain collections of captive birds, infection prevalence is high. A lack of genetic diversity, insufficient hygiene, and an increased persistence of these bacteria in the environment are likely to be predisposing conditions to infection in captive birds. Although essentially eradicated with the onset of intensive raising processes in the chicken industry, the return to free-range farming of chickens may result in a re-emergence of mycobacterial infections. The role of captive birds in spill over to native Australian wild birds is not known. Aetiology Order (Actinomycetales), family (Mycobacteriaceae), genus (Mycobacterium). Mycobacteria are small rod-shaped bacteria that grow inside of the host’s cells. They do not stain with the Gram’s stain or do so faintly. They are difficult to see in haematoxyln and eosin stained tissue sections and only stain with the acid fast or Ziehl-Neelsen stain. They stain red with this stain and are referred to as acid- fast organisms (reviewed in Saggese et al. 2010). The two most common species of mycobacteria detected in diseased birds are Mycobacterium avium subspecies avium (MAA) and M. genavense (MG) and they are the focus of this fact sheet (Hoop et al. 1993; Feizabad et al. 1996; Saggese et al.
    [Show full text]
  • Bacterial Pseudomycoses of the Skin: a Case Report
    Bacterial Pseudomycoses of the Skin: A Case Report Robert Lin, DO,* Alpesh Desai, DO, FAOCD** *2nd-year resident, South Texas Osteopathic Dermatology Residency Program, Houston, TX **Program Director, South Texas Osteopathic Dermatology Residency Program, Houston, TX Abstract Clinicians in all scopes of medicine are no strangers to misnomers. The inaccurate naming of diseases and organisms oftentimes results from their resemblance to other entities and has been known to mislead physicians regarding etiologies and histopathologies. In the field of dermatology, certain skin infections have been mislabeled to be fungal when they are actually bacterial in nature. In order to further understand the origins and development of these infectious misnomers, we present a patient diagnosed with an unusual condition involving three different pseudomycotic skin infections. We also discuss the clinical features shared between these three bacterial pseudomycoses and identify the features that differentiate them from one another histopathologically. Introduction Histologic findings of these specimens were the diagnosis of actinomycetoma, actinomycosis, Pseudomycotic infections of the skin are a subset consistent with the diagnoses of botryomycosis, and botryomycosis, all are infections of the of bacterial infections that produces lesions with actinomycosis, and actinomycetoma pending the skin caused by specific types of bacteria. These clinically fungal features.1 Often, additional results of the tissue culture. conditions are differentiated from one
    [Show full text]