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Identification of 16S Rrna and Virulence-Associated Genes Of
pathogens Article Identification of 16S rRNA and Virulence-Associated Genes of Arcobacter in Water Samples in the Kathmandu Valley, Nepal Rajani Ghaju Shrestha 1,2 , Yasuhiro Tanaka 3, Jeevan B. Sherchand 4 and Eiji Haramoto 2,* 1 Division of Sustainable Energy and Environmental Engineering, Osaka University, Suita, Osaka 565-0871, Japan 2 Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan 3 Department of Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan 4 Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu 1524, Nepal * Correspondence: [email protected]; Tel.: +81-55-220-8725 Received: 8 July 2019; Accepted: 25 July 2019; Published: 26 July 2019 Abstract: This study aimed to determine the prevalence of Arcobacter and five associated virulence genes (cadF, ciaB, mviN, pldA, and tlyA) in water samples in the Kathmandu Valley, Nepal. A total of 286 samples were collected from deep tube wells (n = 30), rivers (n = 14), a pond (n = 1), shallow dug wells (n = 166), shallow tube wells (n = 33), springs (n = 21), and stone spouts (n = 21) in February and March (dry season) and August (wet season), 2016. Bacterial DNA was extracted from the water samples and subjected to SYBR Green-based quantitative PCR for 16S rRNA and virulence genes of Arcobacter. The 16S rRNA gene of Arcobacter was detected in 36% (40/112) of samples collected in the dry season, at concentrations ranging from 5.7 to 10.2 log copies/100 mL, and 34% (59/174) of samples collected in the wet season, at concentrations of 5.4–10.8 log copies/100 mL. -
APP201895 APP201895__Appli
APPLICATION FORM DETERMINATION Determine if an organism is a new organism under the Hazardous Substances and New Organisms Act 1996 Send by post to: Environmental Protection Authority, Private Bag 63002, Wellington 6140 OR email to: [email protected] Application number APP201895 Applicant Neil Pritchard Key contact NPN Ltd www.epa.govt.nz 2 Application to determine if an organism is a new organism Important This application form is used to determine if an organism is a new organism. If you need help to complete this form, please look at our website (www.epa.govt.nz) or email us at [email protected]. This application form will be made publicly available so any confidential information must be collated in a separate labelled appendix. The fee for this application can be found on our website at www.epa.govt.nz. This form was approved on 1 May 2012. May 2012 EPA0159 3 Application to determine if an organism is a new organism 1. Information about the new organism What is the name of the new organism? Briefly describe the biology of the organism. Is it a genetically modified organism? Pseudomonas monteilii Kingdom: Bacteria Phylum: Proteobacteria Class: Gamma Proteobacteria Order: Pseudomonadales Family: Pseudomonadaceae Genus: Pseudomonas Species: Pseudomonas monteilii Elomari et al., 1997 Binomial name: Pseudomonas monteilii Elomari et al., 1997. Pseudomonas monteilii is a Gram-negative, rod- shaped, motile bacterium isolated from human bronchial aspirate (Elomari et al 1997). They are incapable of liquefing gelatin. They grow at 10°C but not at 41°C, produce fluorescent pigments, catalase, and cytochrome oxidase, and possesse the arginine dihydrolase system. -
Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg -
Resilience of Microbial Communities After Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
microorganisms Article Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms Tim Piel 1,†, Giovanni Sandrini 1,†,‡, Gerard Muyzer 1 , Corina P. D. Brussaard 1,2 , Pieter C. Slot 1, Maria J. van Herk 1, Jef Huisman 1 and Petra M. Visser 1,* 1 Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; [email protected] (T.P.); [email protected] (G.S.); [email protected] (G.M.); [email protected] (C.P.D.B.); [email protected] (P.C.S.); [email protected] (M.J.v.H.); [email protected] (J.H.) 2 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands * Correspondence: [email protected]; Tel.: +31-20-5257073 † These authors have contributed equally to this work. ‡ Current address: Department of Technology & Sources, Evides Water Company, 3006 AL Rotterdam, The Netherlands. Abstract: Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little Citation: Piel, T.; Sandrini, G.; is known about the impacts of these H2O2 treatments on other members of the microbial com- Muyzer, G.; Brussaard, C.P.D.; Slot, munity. In this study, we investigated changes in microbial community composition during two P.C.; van Herk, M.J.; Huisman, J.; −1 lake treatments with low H2O2 concentrations (target: 2.5 mg L ) and in two series of controlled Visser, P.M. -
Physiology of Dimethylsulfoniopropionate Metabolism
PHYSIOLOGY OF DIMETHYLSULFONIOPROPIONATE METABOLISM IN A MODEL MARINE ROSEOBACTER, Silicibacter pomeroyi by JAMES R. HENRIKSEN (Under the direction of William B. Whitman) ABSTRACT Dimethylsulfoniopropionate (DMSP) is a ubiquitous marine compound whose degradation is important in carbon and sulfur cycles and influences global climate due to its degradation product dimethyl sulfide (DMS). Silicibacter pomeroyi, a member of the a marine Roseobacter clade, is a model system for the study of DMSP degradation. S. pomeroyi can cleave DMSP to DMS and carry out demethylation to methanethiol (MeSH), as well as degrade both these compounds. Dif- ferential display proteomics was used to find proteins whose abundance increased when chemostat cultures of S. pomeroyi were grown with DMSP as the sole carbon source. Bioinformatic analysis of these genes and their gene clusters suggested roles in DMSP metabolism. A genetic system was developed for S. pomeroyi that enabled gene knockout to confirm the function of these genes. INDEX WORDS: Silicibacter pomeroyi, Ruegeria pomeroyi, dimethylsulfoniopropionate, DMSP, roseobacter, dimethyl sulfide, DMS, methanethiol, MeSH, marine, environmental isolate, proteomics, genetic system, physiology, metabolism PHYSIOLOGY OF DIMETHYLSULFONIOPROPIONATE METABOLISM IN A MODEL MARINE ROSEOBACTER, Silicibacter pomeroyi by JAMES R. HENRIKSEN B.S. (Microbiology), University of Oklahoma, 2000 B.S. (Biochemistry), University of Oklahoma, 2000 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ATHENS, GEORGIA 2008 cc 2008 James R. Henriksen Some Rights Reserved Creative Commons License Version 3.0 Attribution-Noncommercial-Share Alike PHYSIOLOGY OF DIMETHYLSULFONIOPROPIONATE METABOLISM IN A MODEL MARINE ROSEOBACTER, Silicibacter pomeroyi by JAMES R. -
Identification by 16S Ribosomal RNA Gene Sequencing of Arcobacter
182 ORIGINAL ARTICLE Identification by 16S ribosomal RNA gene sequencing of Mol Path: first published as 10.1136/mp.55.3.182 on 1 June 2002. Downloaded from Arcobacter butzleri bacteraemia in a patient with acute gangrenous appendicitis SKPLau,PCYWoo,JLLTeng, K W Leung, K Y Yuen ............................................................................................................................. J Clin Pathol: Mol Pathol 2002;55:182–185 Aims: To identify a strain of Gram negative facultative anaerobic curved bacillus, concomitantly iso- lated with Escherichia coli and Streptococcus milleri, from the blood culture of a 69 year old woman with acute gangrenous appendicitis. The literature on arcobacter bacteraemia and arcobacter infections associated with appendicitis was reviewed. Methods: The isolate was phenotypically investigated by standard biochemical methods using conventional biochemical tests. Genotypically, the 16S ribosomal RNA (rRNA) gene of the bacterium was amplified by the polymerase chain reaction (PCR) and sequenced. The sequence of the PCR prod- uct was compared with known 16S rRNA gene sequences in the GenBank by multiple sequence align- ment. Literature review was performed by MEDLINE search (1966–2000). Results: The bacterium grew on blood agar, chocolate agar, and MacConkey agar to sizes of 1 mm in diameter after 24 hours of incubation at 37°C in 5% CO2. It grew at 15°C, 25°C, and 37°C; it also grew in a microaerophilic environment, and was cytochrome oxidase positive and motile, typically a member of the genus arcobacter. Furthermore, phenotypic testing showed that the biochemical profile See end of article for of the isolate did not fit into the pattern of any of the known arcobacter species. -
Complete Genome Sequence of Arcobacter Nitrofigilis Type Strain (CIT)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Arcobacter nitrofigilis type strain (CI). Permalink https://escholarship.org/uc/item/4kk473v4 Journal Standards in genomic sciences, 2(3) ISSN 1944-3277 Authors Pati, Amrita Gronow, Sabine Lapidus, Alla et al. Publication Date 2010-06-15 DOI 10.4056/sigs.912121 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:300-308 DOI:10.4056/sigs.912121 Complete genome sequence of Arcobacter nitrofigilis type strain (CIT) Amrita Pati1, Sabine Gronow3, Alla Lapidus1, Alex Copeland1, Tijana Glavina Del Rio1, Matt Nolan1, Susan Lucas1, Hope Tice1, Jan-Fang Cheng1, Cliff Han1,2, Olga Chertkov1,2, David Bruce1,2, Roxanne Tapia1,2, Lynne Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Natalia Ivanova1, Konstantinos Mavromatis1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, John C. Detter1,2, Manfred Rohde6, Markus Göker3, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1, Hans-Peter Klenk3, and Nikos C. Kyrpides1* 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C. Kyrpides Keywords: symbiotic, Spartina alterniflora Loisel, nitrogen fixation, micro-anaerophilic, mo- tile, Campylobacteraceae, GEBA Arcobacter nitrofigilis (McClung et al. -
The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment. -
Aliarcobacter Butzleri from Water Poultry: Insights Into Antimicrobial Resistance, Virulence and Heavy Metal Resistance
G C A T T A C G G C A T genes Article Aliarcobacter butzleri from Water Poultry: Insights into Antimicrobial Resistance, Virulence and Heavy Metal Resistance Eva Müller, Mostafa Y. Abdel-Glil * , Helmut Hotzel, Ingrid Hänel and Herbert Tomaso Institute of Bacterial Infections and Zoonoses (IBIZ), Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 07743 Jena, Germany; Eva.Mueller@fli.de (E.M.); Helmut.Hotzel@fli.de (H.H.); [email protected] (I.H.); Herbert.Tomaso@fli.de (H.T.) * Correspondence: Mostafa.AbdelGlil@fli.de Received: 28 July 2020; Accepted: 16 September 2020; Published: 21 September 2020 Abstract: Aliarcobacter butzleri is the most prevalent Aliarcobacter species and has been isolated from a wide variety of sources. This species is an emerging foodborne and zoonotic pathogen because the bacteria can be transmitted by contaminated food or water and can cause acute enteritis in humans. Currently, there is no database to identify antimicrobial/heavy metal resistance and virulence-associated genes specific for A. butzleri. The aim of this study was to investigate the antimicrobial susceptibility and resistance profile of two A. butzleri isolates from Muscovy ducks (Cairina moschata) reared on a water poultry farm in Thuringia, Germany, and to create a database to fill this capability gap. The taxonomic classification revealed that the isolates belong to the Aliarcobacter gen. nov. as A. butzleri comb. nov. The antibiotic susceptibility was determined using the gradient strip method. While one of the isolates was resistant to five antibiotics, the other isolate was resistant to only two antibiotics. The presence of antimicrobial/heavy metal resistance genes and virulence determinants was determined using two custom-made databases. -
Fate of Arcobacter Spp. Upon Exposure to Environmental
FATE OF ARCOBACTER SPP. UPON EXPOSURE TO ENVIRONMENTAL STRESSES AND PREDICTIVE MODEL DEVELOPMENT by ELAINE M. D’SA (Under the direction of Dr. Mark A. Harrison) ABSTRACT Growth and survival characteristics of two species of the ‘emerging’ pathogenic genus Arcobacter were determined. The optimal pH growth range of most A. butzleri (4 strains) and A. cryaerophilus (2 strains) was 6.0-7.0 and 7.0-7.5 respectively. The optimal NaCl growth range was 0.09-0.5 % (A. butzleri) and 0.5-1.0% (A. cryaerophilus), while growth limits were 0.09-3.5% and 0.09-3.0% for A. butzleri and A. cryaerophilus, respectively. A. butzleri 3556, 3539 and A. cryaerophilus 1B were able to survive at NaCl concentrations of up to 5% for 48 h at 25°C, but the survival limit dropped to 3.5-4.0% NaCl after 96 h. Thermal tolerance studies on three strains of A. butzleri determined that the D-values at pH 7.3 had a range of 0.07-0.12 min (60°C), 0.38-0.76 min (55°C) and 5.12-5.81 min (50°C). At pH 5.5, thermotolerance decreased under the synergistic effects of heat and acidity. D-values decreased for strains 3556 and 3257 by 26-50% and 21- 66%, respectively, while the reduction for strain 3494 was lower: 0-28%. Actual D- values of the three strains at pH 5.5 had a range of 0.03-0.11 (60°C), 0.30-0.42 (55°C) and 1.97-4.42 (50°C). -
Draft Genome Sequence of Thalassobius Mediterraneus CECT 5383T, a Poly-Beta-Hydroxybutyrate Producer
Genomics Data 7 (2016) 237–239 Contents lists available at ScienceDirect Genomics Data journal homepage: www.elsevier.com/locate/gdata Data in Brief Draft genome sequence of Thalassobius mediterraneus CECT 5383T, a poly-beta-hydroxybutyrate producer Lidia Rodrigo-Torres, María J. Pujalte, David R. Arahal ⁎ Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universidad de Valencia, Valencia, Spain article info abstract Article history: Thalassobius mediterraneus is the type species of the genus Thalassobius and a member of the Roseobacter clade, an Received 23 December 2015 abundant representative of marine bacteria. T. mediterraneus XSM19T (=CECT 5383T) was isolated from the Received in revised form 8 January 2016 Western Mediterranean coast near Valencia (Spain) in 1989. We present here the draft genome sequence and Accepted 14 January 2016 annotation of this strain (ENA/DDBJ/NCBI accession number CYSF00000000), which is comprised of Available online 15 January 2016 3,431,658 bp distributed in 19 contigs and encodes 10 rRNA genes, 51 tRNA genes and 3276 protein coding fi Keywords: genes. Relevant ndings are commented, including the complete set of genes required for poly-beta- Rhodobacteraceae hydroxybutyrate (PHB) synthesis and genes related to degradation of aromatic compounds. Roseobacter clade © 2016 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license PHB (http://creativecommons.org/licenses/by-nc-nd/4.0/). Aromatic compounds 1. Direct link to deposited data has not been yet validated, and even more recently T. abysii has been Specifications also proposed [6]. Organism/cell line/tissue Thalassobius mediterraneus Strain CECT 5383T Sequencer or array type Illumina MiSeq 2. -
Comparative Analysis of Four Campylobacterales
REVIEWS COMPARATIVE ANALYSIS OF FOUR CAMPYLOBACTERALES Mark Eppinger*§,Claudia Baar*§,Guenter Raddatz*, Daniel H. Huson‡ and Stephan C. Schuster* Abstract | Comparative genome analysis can be used to identify species-specific genes and gene clusters, and analysis of these genes can give an insight into the mechanisms involved in a specific bacteria–host interaction. Comparative analysis can also provide important information on the genome dynamics and degree of recombination in a particular species. This article describes the comparative genomic analysis of representatives of four different Campylobacterales species — two pathogens of humans, Helicobacter pylori and Campylobacter jejuni, as well as Helicobacter hepaticus, which is associated with liver cancer in rodents and the non-pathogenic commensal species, Wolinella succinogenes. ε CHEMOLITHOTROPHIC The -subdivision of the Proteobacteria is a large group infection can lead to gastric cancer in humans 9–11 An organism that is capable of of CHEMOLITHOTROPHIC and CHEMOORGANOTROPHIC microor- and liver cancer in rodents, respectively .The using CO, CO2 or carbonates as ganisms with diverse metabolic capabilities that colo- Campylobacter representative C. jejuni is one of the the sole source of carbon for cell nize a broad spectrum of ecological habitats. main causes of bacterial food-borne illness world- biosynthesis, and that derives Representatives of the ε-subgroup can be found in wide, causing acute gastroenteritis, and is also energy from the oxidation of reduced inorganic or organic extreme marine and terrestrial environments ranging the most common microbial antecedent of compounds. from oceanic hydrothermal vents to sulphidic cave Guillain–Barré syndrome12–15.Besides their patho- springs. Although some members are free-living, others genic potential in humans, C.