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Detection of a Bacterial Group Within the Phylum Chloroflexi And
Microbes Environ. Vol. 21, No. 3, 154–162, 2006 http://wwwsoc.nii.ac.jp/jsme2/ Detection of a Bacterial Group within the Phylum Chloroflexi and Reductive-Dehalogenase-Homologous Genes in Pentachlorobenzene- Dechlorinating Estuarine Sediment from the Arakawa River, Japan KYOSUKE SANTOH1, ATSUSHI KOUZUMA1, RYOKO ISHIZEKI2, KENICHI IWATA1, MINORU SHIMURA3, TOSHIO HAYAKAWA3, TOSHIHIRO HOAKI4, HIDEAKI NOJIRI1, TOSHIO OMORI2, HISAKAZU YAMANE1 and HIROSHI HABE1*† 1 Biotechnology Research Center, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113–8657, Japan 2 Department of Industrial Chemistry, Faculty of Engineering, Shibaura Institute of Technology, Minato-ku, Tokyo 108–8548, Japan 3 Environmental Biotechnology Laboratory, Railway Technical Research Institute, 2–8–38 Hikari-cho, Kokubunji-shi, Tokyo 185–8540, Japan 4 Technology Research Center, Taisei Corporation, 344–1 Nase, Totsuka-ku, Yokohama 245–0051, Japan (Received April 21, 2006—Accepted June 12, 2006) We enriched a pentachlorobenzene (pentaCB)-dechlorinating microbial consortium from an estuarine-sedi- ment sample obtained from the mouth of the Arakawa River. The sediment was incubated together with a mix- ture of four electron donors and pentaCB, and after five months of incubation, the microbial community structure was analyzed. Both DGGE and clone library analyses showed that the most expansive phylogenetic group within the consortium was affiliated with the phylum Chloroflexi, which includes Dehalococcoides-like bacteria. PCR using a degenerate primer set targeting conserved regions in reductive-dehalogenase-homologous (rdh) genes from Dehalococcoides species revealed that DNA fragments (approximately 1.5–1.7 kb) of rdh genes were am- plified from genomic DNA of the consortium. The deduced amino acid sequences of the rdh genes shared sever- al characteristics of reductive dehalogenases. -
Morbidity and Mortality Weekly Report Weekly March 20, 2009 / Vol
Morbidity and Mortality Weekly Report www.cdc.gov/mmwr Weekly March 20, 2009 / Vol. 58 / No. 10 Trends in Tuberculosis — World TB Day — March 24, 2009 United States, 2008 World TB Day is observed each year on March 24 to commemorate the date in 1882 when Dr. Robert Koch In 2008, a total of 12,898 incident tuberculosis (TB) cases announced the discovery of Mycobacterium tuberculosis, the were reported in the United States; the TB rate declined 3.8% bacterium that causes tuberculosis (TB). Worldwide, TB from 2007 to 4.2 cases per 100,000 population, the lowest remains one of the leading causes of death from infectious rate recorded since national reporting began in 1953. This disease. An estimated 2 billion persons are infected with report summarizes provisional 2008 data from the National M. tuberculosis (1). In 2006, approximately 9.2 million TB Surveillance System and describes trends since 1993. persons became ill from TB, and 1.7 million died from Despite this overall improvement, progress has slowed in the disease (1). World TB Day provides an opportunity recent years; the average annual percentage decline in the TB for TB programs, nongovernmental organizations, and rate decreased from 7.3% per year during 1993–2000 to 3.8% other partners to describe problems and solutions related during 2000–2008.* Foreign-born persons and racial/ethnic to the TB pandemic and to support worldwide TB minorities continued to bear a disproportionate burden of TB control efforts. The U.S. theme for this year’s observance disease in the United States. In 2008, the TB rate in foreign- is Partnerships for TB Elimination. -
2012 Case Definitions Infectious Disease
Arizona Department of Health Services Case Definitions for Reportable Communicable Morbidities 2012 TABLE OF CONTENTS Definition of Terms Used in Case Classification .......................................................................................................... 6 Definition of Bi-national Case ............................................................................................................................................. 7 ------------------------------------------------------------------------------------------------------- ............................................... 7 AMEBIASIS ............................................................................................................................................................................. 8 ANTHRAX (β) ......................................................................................................................................................................... 9 ASEPTIC MENINGITIS (viral) ......................................................................................................................................... 11 BASIDIOBOLOMYCOSIS ................................................................................................................................................. 12 BOTULISM, FOODBORNE (β) ....................................................................................................................................... 13 BOTULISM, INFANT (β) ................................................................................................................................................... -
Ehrlichiosis and Anaplasmosis Are Tick-Borne Diseases Caused by Obligate Anaplasmosis: Intracellular Bacteria in the Genera Ehrlichia and Anaplasma
Ehrlichiosis and Importance Ehrlichiosis and anaplasmosis are tick-borne diseases caused by obligate Anaplasmosis: intracellular bacteria in the genera Ehrlichia and Anaplasma. These organisms are widespread in nature; the reservoir hosts include numerous wild animals, as well as Zoonotic Species some domesticated species. For many years, Ehrlichia and Anaplasma species have been known to cause illness in pets and livestock. The consequences of exposure vary Canine Monocytic Ehrlichiosis, from asymptomatic infections to severe, potentially fatal illness. Some organisms Canine Hemorrhagic Fever, have also been recognized as human pathogens since the 1980s and 1990s. Tropical Canine Pancytopenia, Etiology Tracker Dog Disease, Ehrlichiosis and anaplasmosis are caused by members of the genera Ehrlichia Canine Tick Typhus, and Anaplasma, respectively. Both genera contain small, pleomorphic, Gram negative, Nairobi Bleeding Disorder, obligate intracellular organisms, and belong to the family Anaplasmataceae, order Canine Granulocytic Ehrlichiosis, Rickettsiales. They are classified as α-proteobacteria. A number of Ehrlichia and Canine Granulocytic Anaplasmosis, Anaplasma species affect animals. A limited number of these organisms have also Equine Granulocytic Ehrlichiosis, been identified in people. Equine Granulocytic Anaplasmosis, Recent changes in taxonomy can make the nomenclature of the Anaplasmataceae Tick-borne Fever, and their diseases somewhat confusing. At one time, ehrlichiosis was a group of Pasture Fever, diseases caused by organisms that mostly replicated in membrane-bound cytoplasmic Human Monocytic Ehrlichiosis, vacuoles of leukocytes, and belonged to the genus Ehrlichia, tribe Ehrlichieae and Human Granulocytic Anaplasmosis, family Rickettsiaceae. The names of the diseases were often based on the host Human Granulocytic Ehrlichiosis, species, together with type of leukocyte most often infected. -
Ehrlichia Ewingii Sp. Nov., the Etiologic Agent of Canine Granulocytic Ehrlichiosis
INTERNATIONAL JOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1992, p. 299-302 Vol. 42, No. 2 0020-7713/92/020299-04$02.00/0 Copyright 0 1992, International Union of Microbiological Societies NOTES Ehrlichia ewingii sp. nov., the Etiologic Agent of Canine Granulocytic Ehrlichiosis BURT E. ANDERSON,l* CRAIG E. GREENE,2 DANA C. JONES,l AND JACQUELINE E. DAWSON’ viral and Rickettsial Zoonoses Branch, Division of viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control, Atlanta, Georgia 30333, and Department of Small Animal Medicine, College of Veterinaly Medicine, University of Georgia, Athens, Georgia 306022 The 16s rRNA gene was amplified, cloned, and sequenced from the blood of two dogs that were experimentally infected with the etiologic agent of canine granulocytic ehrlichiosis. The 16s rRNA sequence was found to be unique when it was compared with the sequences of other members of the genus Ehrlichia. The most closely related species were Ehrlichia canis (98.0% related) and the human ehrlichiosis agent (Ehrlichia chafeensis) (98.1% related); all other species in the genus were found to be phylogenetically much more distant. Our results, coupled with previous serologic data, provide conclusive evidence that the canine granulocytic ehrlichiosis agent is a new species of the genus Ehrlichia that is related to, but is distinct from, E. canis and all other members of the genus. We propose the name Ehrlichia ewingii sp. nov.; the Stillwater strain is the type strain. Ehrlichia canis, the type species of the genus Ehrlichia, human ehrlichiosis (Ehrlichia chafeensis) (1) is discussed was first described by Donatien and Lestoquard in 1935 (7). -
Yu-Chen Ling and John W. Moreau
Microbial Distribution and Activity in a Coastal Acid Sulfate Soil System Introduction: Bioremediation in Yu-Chen Ling and John W. Moreau coastal acid sulfate soil systems Method A Coastal acid sulfate soil (CASS) systems were School of Earth Sciences, University of Melbourne, Melbourne, VIC 3010, Australia formed when people drained the coastal area Microbial distribution controlled by environmental parameters Microbial activity showed two patterns exposing the soil to the air. Drainage makes iron Microbial structures can be grouped into three zones based on the highest similarity between samples (Fig. 4). Abundant populations, such as Deltaproteobacteria, kept constant activity across tidal cycling, whereas rare sulfides oxidize and release acidity to the These three zones were consistent with their geological background (Fig. 5). Zone 1: Organic horizon, had the populations changed activity response to environmental variations. Activity = cDNA/DNA environment, low pH pore water further dissolved lowest pH value. Zone 2: surface tidal zone, was influenced the most by tidal activity. Zone 3: Sulfuric zone, Abundant populations: the heavy metals. The acidity and toxic metals then Method A Deltaproteobacteria Deltaproteobacteria this area got neutralized the most. contaminate coastal and nearby ecosystems and Method B 1.5 cause environmental problems, such as fish kills, 1.5 decreased rice yields, release of greenhouse gases, Chloroflexi and construction damage. In Australia, there is Gammaproteobacteria Gammaproteobacteria about a $10 billion “legacy” from acid sulfate soils, Chloroflexi even though Australia is only occupied by around 1.0 1.0 Cyanobacteria,@ Acidobacteria Acidobacteria Alphaproteobacteria 18% of the global acid sulfate soils. Chloroplast Zetaproteobacteria Rare populations: Alphaproteobacteria Method A log(RNA(%)+1) Zetaproteobacteria log(RNA(%)+1) Method C Method B 0.5 0.5 Cyanobacteria,@ Bacteroidetes Chloroplast Firmicutes Firmicutes Bacteroidetes Planctomycetes Planctomycetes Ac8nobacteria Fig. -
1471-2164-13-670.Pdf
Hobley et al. BMC Genomics 2012, 13:670 http://www.biomedcentral.com/1471-2164/13/670 RESEARCH ARTICLE Open Access Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria Laura Hobley1,3, Thomas R Lerner1,4, Laura E Williams2, Carey Lambert1, Rob Till1, David S Milner1, Sarah M Basford1, Michael J Capeness1, Andrew K Fenton1,5, Robert J Atterbury1,6, Maximilian ATS Harris1 and R Elizabeth Sockett1* Abstract Background: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as “obligate predators” because only by mutations, often in gene bd0108, are 1 in ~1x107 of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome. Results: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. -
Being Aquifex Aeolicus: Untangling a Hyperthermophile's Checkered Past
GBE Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past Robert J.M. Eveleigh1,2, Conor J. Meehan1,2,JohnM.Archibald1, and Robert G. Beiko2,* 1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada 2Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada *Corresponding author: E-mail: [email protected]. Accepted: November 22, 2013 Abstract Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyper- thermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic analyses focused on Aquifex aeolicus identified Thermotogae and Downloaded from Aquificae either as successive early branches or sisters in a rooted bacterial phylogeny, but many phylogenies and cellular traits have suggested a stronger affiliation with the Epsilonproteobacteria. Different scenarios for the evolution of the Aquificae yield different phylogenetic predictions. Here, we outline these scenarios and consider the fit of the available data, including three sequenced Aquificae genomes, to different sets of predictions. Evidence from phylogenetic profiles and trees suggests that the Epsilonproteobacteria have the strongest affinities with the three Aquificae analyzed. However, this pattern is shown by only a http://gbe.oxfordjournals.org/ minority of encoded proteins, and the Archaea, many lineages of thermophilic bacteria, and members of genus Clostridium and class Deltaproteobacteria also show strong connections to the Aquificae. The phylogenetic affiliations of different functional subsystems showed strong biases: Most but not all genes implicated in the core translational apparatus tended to group Aquificae with Thermotogae, whereas a wide range of metabolic and cellular processes strongly supported the link between Aquificae and Epsilonproteobacteria. -
Exploration of Tick-Borne Pathogens and Microbiota of Dog Ticks Collected at Potchefstroom Animal Welfare Society
Exploration of tick-borne pathogens and microbiota of dog ticks collected at Potchefstroom Animal Welfare Society C Van Wyk orcid.org 0000-0002-5971-4396 Dissertation submitted in fulfilment of the requirements for the degree Master of Science in Environmental Sciences at the North-West University Supervisor: Prof MMO Thekisoe Co-supervisor: Ms K Mtshali Graduation May 2019 24263524 DEDICATION This thesis is dedicated to the late Nettie Coetzee. For her inspiration and lessons to overcome any obstacle that life may present. God called home another angel we all love and miss you. “We are the scientists, trying to make sense of the stars inside us.” -Christopher Poindexter i ACKNOWLEDGEMENTS My sincerest appreciation goes out to my supervisor, Prof. Oriel M.M. Thekisoe, for his support, motivation, guidance, and insightfulness during the duration of this project and been there every step of the way. I would also like to thank my co-supervisor, Ms. Khethiwe Mtshali, for her patience and insightfulness towards the corrections of this thesis. I would like to thank Dr. Stalone Terera and the staff members at PAWS for their aid towards the collection of tick specimens. For the sequencing on the Illumina MiSeq platform and metagenomic data analysis I would like to thank Dr. Moeti O. Taioe, Dr. Charlotte M.S. Mienie, Dr. Danie C. La Grange, and Dr. Marlin J. Mert. I would like to thank the National Research Foundation (NRF) for their financial support by awarding me the S&F- Innovation Masters Scholarship and the North-West University (NWU) for the use of their laboratories. -
Petroleum Hydrocarbon Rich Oil Refinery Sludge of North-East India
Roy et al. BMC Microbiology (2018) 18:151 https://doi.org/10.1186/s12866-018-1275-8 RESEARCHARTICLE Open Access Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations Ajoy Roy1, Pinaki Sar2, Jayeeta Sarkar2, Avishek Dutta2,3, Poulomi Sarkar2, Abhishek Gupta2, Balaram Mohapatra2, Siddhartha Pal1 and Sufia K Kazy1* Abstract Background: Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on- site bioremediation. Results: All sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea -
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. -
Canine Ehrlichiosis: Update
Canine Ehrlichiosis: Update Barbara Qurollo, MS, DVM ([email protected]) Vector-Borne Disease Diagnostic Laboratory Dep. Clinical Sciences-College of Veterinary Medicine North Carolina State University Overview Ehrlichia species are tick-transmitted, obligate intracellular bacteria that can cause granulocytic or monocytic ehrlichiosis. Ehlrichia species that have been detected in the blood and tissues of clinically ill dogs in North America include Ehrlichia canis, E. chaffeenis, E. ewingii, E. muris and Panola Mountain Ehrlichia species (Table 1). Clinicopathologic abnormalities reported in dogs with ehrlichiosis vary depending on the species of Ehrlichia, strain variances and the immune or health status of the dog. The course of disease may present as subclinical, acute, chronic or even result in death (Table 1). E. canis and E. ewingii are the most prevalent and frequently described Ehrlichia infections in dogs. E. canis: Transmitted by Rhipicephalus sanguineus, E. canis is found world-wide. Within North America, the highest seroprevalence rates have been reported in the Southern U. S.2, 12 E. canis typically infects canine mononuclear cells. Canine monocytic ehrlichiosis (CME) is characterized by 3 stages: acute, subclinical and chronic. Following an incubation period of 1-3 weeks, infected dogs may remain subclinical or present with nonspecific signs including fever, lethargy, lymphadenopathy, splenomegaly, lameness, edema, bleeding disorders and mucopurulent ocular discharge. Less commonly reported nonspecific signs include vomiting, diarrhea, coughing and dyspnea. Bleeding disorders can include epistaxis, petechiae, ecchymoses, gingival bleeding and melena. Ocular abnormalities identified in E. canis infected dogs have included anterior uveitis, corneal opacity, retinal hemorrhage, hyphema, chorioretinal lesions and tortuous retinal vessels.8 Following an acute phase (2-4 weeks), clinical signs may resolve without treatment and the dog could remain subclinically infected indefinitely or naturally clear the pathogen.