TYGS Is an Automated High-Throughput Platform for State-Of-The-Art Genome-Based Taxonomy
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The Coliform Kind: E. Coli and Its “Cousins” the Good, the Bad, and the Deadly
Scholars Crossing Faculty Publications and Presentations Department of Biology and Chemistry 10-3-2018 The Coliform Kind: E. coli and Its “Cousins” The Good, the Bad, and the Deadly Alan L. Gillen Liberty University, [email protected] Matthew Augusta Follow this and additional works at: https://digitalcommons.liberty.edu/bio_chem_fac_pubs Part of the Biology Commons Recommended Citation Gillen, Alan L. and Augusta, Matthew, "The Coliform Kind: E. coli and Its “Cousins” The Good, the Bad, and the Deadly" (2018). Faculty Publications and Presentations. 125. https://digitalcommons.liberty.edu/bio_chem_fac_pubs/125 This Article is brought to you for free and open access by the Department of Biology and Chemistry at Scholars Crossing. It has been accepted for inclusion in Faculty Publications and Presentations by an authorized administrator of Scholars Crossing. For more information, please contact [email protected]. The Coliform Kind: E. coli and Its “Cousins” The Good, the Bad, and the Deadly by Dr. Alan L. Gillen and Matthew Augusta on October 3, 2018 Abstract Even though some intestinal bacteria strains are pathogenic and even deadly, most coliforms strains still show evidence of being one of God’s “very good” creations. In fact, bacteria serve an intrinsic role in the colon of the human body. These bacteria aid in the early development of the immune system and stimulate up to 80% of immune cells in adults. In addition, digestive enzymes, Vitamins K and B12, are produced byEscherichia coli and other coliforms. E. coli is the best-known bacteria that is classified as coliforms. The term “coliform” name was historically attributed due to the “Bacillus coli-like” forms. -
Citrobacter Braakii
& M cal ed ni ic li a l C G f e Trivedi et al., J Clin Med Genom 2015, 3:1 o n l o a m n r DOI: 10.4172/2472-128X.1000129 i u c s o Journal of Clinical & Medical Genomics J ISSN: 2472-128X ResearchResearch Article Article OpenOpen Access Access Phenotyping and 16S rDNA Analysis after Biofield Treatment on Citrobacter braakii: A Urinary Pathogen Mahendra Kumar Trivedi1, Alice Branton1, Dahryn Trivedi1, Gopal Nayak1, Sambhu Charan Mondal2 and Snehasis Jana2* 1Trivedi Global Inc., Eastern Avenue Suite A-969, Henderson, NV, USA 2Trivedi Science Research Laboratory Pvt. Ltd., Chinar Fortune City, Hoshangabad Rd., Madhya Pradesh, India Abstract Citrobacter braakii (C. braakii) is widespread in nature, mainly found in human urinary tract. The current study was attempted to investigate the effect of Mr. Trivedi’s biofield treatment on C. braakii in lyophilized as well as revived state for antimicrobial susceptibility pattern, biochemical characteristics, and biotype number. Lyophilized vial of ATCC strain of C. braakii was divided into two parts, Group (Gr.) I: control and Gr. II: treated. Gr. II was further subdivided into two parts, Gr. IIA and Gr. IIB. Gr. IIA was analysed on day 10 while Gr. IIB was stored and analysed on day 159 (Study I). After retreatment on day 159, the sample (Study II) was divided into three separate tubes. First, second and third tube was analysed on day 5, 10 and 15, respectively. All experimental parameters were studied using automated MicroScan Walk-Away® system. The 16S rDNA sequencing of lyophilized treated sample was carried out to correlate the phylogenetic relationship of C. -
Escherichia Coli and Shigella Species M
INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, Apr. 1988, p. 201-206 Vol. 38. No. 2 0020-7713/88/040201-06$02.OO/O Specificity of a Monoclonal Antibody for Alkaline Phosphatase in Escherichia coli and Shigella Species M. 0. HUSSON,1*2*P. A. TRINELY2C. MIELCAREK,2 F. GAVINI,2 C. CARON,lq2D. IZARD,l AND H. LECLERC' Faculte' de Me'decine, Laboratoire de Bacte'riologie A, 59045 Lille Cedex, France' and Unite' Institut National de la Sante' et de la Recherche Me'dicale 146, Domaine dir CERTIA, 59650 Villeneuve-d'Ascq Cedex, France2 The specificity of monoclonal antibody 2E5 for the alkaline phosphatase of Escherichia coli was studied against the alkaline phosphatases of 251 other bacterial strains. The organisms used included members of the six species of the genus Escherichia (E. coli, E. fergusonii, E. hermannii, E. blattae, E. vulneris, E. adecarboxylata), 41 species representing the family Enterobacteriaceae, and, in addition, Pseudomonas aeruginosa, Aeromonas spp., Plesiomonas shigelloides, Acinetobacter calcoaceticus, and Vibrio cholerae non-01. Three methods were used. An enzyme-linked immunosorbent assay was performed against 21U of alkaline phosphatase per ml; immunofluorescence against bacterial cells and Western blotting against periplasmic proteins were also used. All of our experiments demonstrated the high specificity of monoclonal antibody 2E5. This antibody recognized only E. coli (118 strains tested) and the four species of the genus Shigella (S. sonnei, S. flexneri, S. boydii, S. dysenteriae; 12 strains tested). Since the description of hybridoma production by Kohler mouse immunized with purified Escherichia coli ATCC and Milstein in 1975 (14), many monoclonal antibodies 10536 alkaline phosphatase as described elsewhere (12). -
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’. -
Isolation and Characterization of an Arsenate-Reducing Bacterium and Its Application for Arsenic Extraction from Contaminated Soil
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Muroran-IT Academic Resource Archive Isolation and characterization of an arsenate-reducing bacterium and its application for arsenic extraction from contaminated soil 著者 CHANG Young-Cheol, NAWATA Akinori, JUNG Kweon, KIKUCHI Shintaro journal or Journal of Industrial Microbiology & publication title Biotechnology volume 39 number 1 page range 37-44 year 2011-06-17 URL http://hdl.handle.net/10258/666 doi: info:doi/10.1007/s10295-011-0996-6 Isolation and characterization of an arsenate-reducing bacterium and its application for arsenic extraction from contaminated soil 著者 CHANG Young-Cheol, NAWATA Akinori, JUNG Kweon, KIKUCHI Shintaro journal or Journal of Industrial Microbiology & publication title Biotechnology volume 39 number 1 page range 37-44 year 2011-06-17 URL http://hdl.handle.net/10258/666 doi: info:doi/10.1007/s10295-011-0996-6 1 Isolation and characterization of an arsenate-reducing bacterium and its application for 2 arsenic extraction from contaminated soil 3 4 Young C. Chang1*, Akinori Nawata1, Kweon Jung2 and Shintaro Kikuchi2 5 1Biosystem Course, Division of Applied Sciences, Muroran Institute of Technology, 27-1 6 Mizumoto, Muroran 050-8585, Japan, 2Seoul Metropolitan Government Research Institute of 7 Public Health and Environment, Yangjae-Dong, Seocho-Gu, Seoul 137-734, Republic of 8 Korea 9 10 *Corresponding author: 11 Phone: +81-143-46-5757; Fax: +81-143-46-5757; E-mail: [email protected] 12 1 13 Abstract 14 A gram-negative anaerobic bacterium, Citrobacter sp. NC-1, was isolated from soil 15 contaminated with arsenic at levels as high as 5000 mg As kg-1. -
Intrahepatic Bacterial Metataxonomic Signature in Non-Alcoholic Fatty Liver
Hepatology ORIGINAL RESEARCH Intrahepatic bacterial metataxonomic signature in Gut: first published as 10.1136/gutjnl-2019-318811 on 2 January 2020. Downloaded from non- alcoholic fatty liver disease Silvia Sookoian ,1,2 Adrian Salatino,1,3 Gustavo Osvaldo Castaño,4 Maria Silvia Landa,1,3 Cinthia Fijalkowky,1,3 Martin Garaycoechea,5 Carlos Jose Pirola 1,3 ► Additional material is ABSTRact published online only. To view Objective We aimed to characterise the liver tissue Significance of this study please visit the journal online bacterial metataxonomic signature in two independent (http:// dx. doi. org/ 10. 1136/ What is already known on this subject? gutjnl- 2019- 318811). cohorts of patients with biopsy- proven non- alcoholic fatty liver disease (NAFLD) diagnosis, as differences in ► The natural history of non- alcoholic fatty liver For numbered affiliations see disease (NAFLD) is modulated by genetic and end of article. the host phenotypic features—from moderate to severe obesity—may be associated with significant changes in environmental factors. ► Recent discoveries revealed the role of the Correspondence to the microbial DNA profile. Dr Silvia Sookoian, Institute Design and methods Liver tissue samples from 116 gut microbiota in human health and disease, of Medical Research A Lanari, individuals, comprising of 47 NAFLD overweight or including NAFLD. However, the impact of the University of Buenos Aires moderately obese patients, 50 NAFLD morbidly obese liver tissue microbial DNA profiling on the Faculty of Medicine, Buenos disease biology remains unknown. Aires, 10109 CABA, Argentina; patients elected for bariatric surgery and 19 controls, ssookoian@ intramed. net were analysed using high- throughput 16S rRNA gene What are the new findings? Dr Carlos Jose Pirola; sequencing. -
Isolation and Identification of Some Pathogenic Bacteria Species from Contaminated Ambient with Oily Hydrocarbons
Journal of Bacteriology & Mycology: Open Access Research Article Open Access Isolation and identification of some pathogenic bacteria species from contaminated ambient with oily hydrocarbons Abstract Volume 8 Issue 4 - 2020 Pathogenic species may naturally at nature in different conditions, at fields of petrol and contaminated area. The pathogenic species Citrobacter amalonaticus which is a genus Ahmed Ibrahim Jessim, Rasha Kifah Hassan, of coliform bacteria that is a gram-negative within the family of intestinal bacteria, were Ammar Salim Salman isolated from water samples 3, 4, and 5 of Al-Ahdab field in addition of presence Bacillus Ministry of Science and Technology, Center for research and subtilis, but pathogenic gram-negative species Sphingomonas paucimobilis bacteria found evaluation, Directorate of Treatment and disposal of chemical, as a biodegradable organism was identified and isolated from samples of soil from a Al- biological and military hazardous wastes, Iraq Ahdad filed 1 and 2, In addition of presence Pseudomonas aeruginosa in a soil sample Correspondence: Ahmed Ibrahim Jessim, Ministry of Science of Al-Gharaaf field at Al-Nnasiriyah in Iraq. These results were different from municipal and Technology, Center for research and evaluation, Directorate fuel of Al-Sidiyeh station, Brother’s station, and Al-Amel station for calibration, which of Treatment and disposal of chemical, biological and military shown just Bacillus spp., B. cereus, in general especially in polluted soil with diesel with no hazardous wastes, Iraq, Tel +9647713659713, presence of C. amalonaticus, and S. paucimobilis. Isolation and identification of bacterial Email depended on morphology using triple light microscope and biochemical tests. Furthermore we can use pathogenic microorganisms in biodegradation. -
Environment Canada and Health Canada
Évaluation préalable finale de la souche ATCC 700368 d’Escherichia hermannii Environnement Canada Santé Canada Août 2015 No de cat. : En14-227/2015F-PDF ISBN 978-0-660-02213-0 Le contenu de cette publication ou de ce produit peut être reproduit en tout ou en partie, et par quelque moyen que ce soit, sous réserve que la reproduction soit effectuée uniquement à des fins personnelles ou publiques mais non commerciales, sans frais ni autre permission, à moins d’avis contraire. On demande seulement : • de faire preuve de diligence raisonnable en assurant l’exactitude du matériel reproduit; • d’indiquer le titre complet du matériel reproduit et l’organisation qui en est l’auteur; • d’indiquer que la reproduction est une copie d’un document officiel publié par le gouvernement du Canada et que la reproduction n’a pas été faite en association avec le gouvernement du Canada ni avec l’appui de celui-ci. La reproduction et la distribution à des fins commerciales est interdite, sauf avec la permission écrite de l’auteur. Pour de plus amples renseignements, veuillez communiquer avec l’informathèque d'Environnement Canada au 1-800-668-6767 (au Canada seulement) ou 819-997-2800 ou par courriel à [email protected]. © Sa Majesté la Reine du chef du Canada, représentée par le ministre de l’environnement, 2015. Also available in English ii Sommaire Conformément à l’alinéa 74b) de la Loi canadienne sur la protection de l'environnement (1999) (LCPE (1999)), la ministre de l'Environnement et la ministre de la Santé ont procédé à une évaluation préalable de la souche ATCC 700368 d’Escherichia hermannii. -
Bacterial Bloodstream Infections in a Tertiary Infectious Diseases Hospital
Dat et al. BMC Infectious Diseases (2017) 17:493 DOI 10.1186/s12879-017-2582-7 RESEARCHARTICLE Open Access Bacterial bloodstream infections in a tertiary infectious diseases hospital in Northern Vietnam: aetiology, drug resistance, and treatment outcome Vu Quoc Dat1,2,3* , Hieu Ngoc Vu1, Hung Nguyen The1, Hoa Thi Nguyen1, Long Bao Hoang3, Dung Vu Tien Viet3, Chi Linh Bui1, Kinh Van Nguyen2, Trung Vu Nguyen1,2, Dao Tuyet Trinh2, Alessandro Torre3, H. Rogier van Doorn3,4, Behzad Nadjm3,4 and Heiman F.L. Wertheim3,4,5 Abstract Background: Bloodstream infections (BSIs) are associated with high morbidity and mortality worldwide. However their aetiology, antimicrobial susceptibilities and associated outcomes differ between developed and developing countries. Systematic data from Vietnam are scarce. Here we present aetiologic data on BSI in adults admitted to a large tertiary referral hospital for infectious diseases in Hanoi, Vietnam. Methods: A retrospective study was conducted at the National Hospital for Tropical Diseases between January 2011 and December 2013. Cases of BSI were determined from records in the microbiology department. Case records were obtained where possible and clinical findings, treatment and outcome were recorded. BSI were classified as community acquired if the blood sample was drawn ≤48 h after hospitalization or hospital acquired if >48 h. Results: A total of 738 patients with BSI were included for microbiological analysis. The predominant pathogens were: Klebsiella pneumoniae (17.5%), Escherichia coli (17.3%), Staphylococcus aureus (14.9%), Stenotrophomonas maltophilia (9.6%) and Streptococcus suis (7.6%). The overall proportion of extended spectrum beta-lactamase (ESBL) production among Enterobacteriaceae was 25.1% (67/267 isolates) and of methicillin-resistance in S. -
Activities and Prevalence of Proteobacteria Members Colonizing Echinacea Purpurea Fully Account for Macro- Phage Activation Exhibited by Extracts of This Botanical
1258 Original Papers Activities and Prevalence of Proteobacteria Members Colonizing Echinacea purpurea Fully Account for Macro- phage Activation Exhibited by Extracts of This Botanical Authors Mona H. Haron 1*, Heather L. Tyler 2, 3*, Nirmal D. Pugh 1, Rita M. Moraes1, Victor L. Maddox4, Colin R. Jackson 2, David S. Pasco1,5 Affiliations The affiliations are listed at the end of the article Key words Abstract highest potency for in vitro macrophage activa- l" Echinacea purpurea ! tion and were the most predominant taxa. Fur- l" Asteraceae Evidence supports the theory that bacterial com- thermore, the mean activity exhibited by the l" immunostimulatory munities colonizing Echinacea purpurea contrib- Echinacea extracts could be solely accounted for l" macrophage activation ute to the innate immune enhancing activity of by the activities and prevalence of Proteobacteria l" bacteria l" proteobacteria this botanical. Previously, we reported that only members comprising the plant-associated bacte- l" endophytes about half of the variation in in vitro monocyte rial community. The efficacy of E. purpurea mate- stimulating activity exhibited by E. purpurea ex- rial for use against respiratory infections may be tracts could be accounted for by total bacterial determined by the Proteobacterial community load within the plant material. In the current composition of this plant, since ingestion of bac- study, we test the hypothesis that the type of bac- teria (probiotics) is reported to have a protective teria, in addition to bacterial load, is necessary to effect against this health condition. fully account for extract activity. Bacterial com- munity composition within commercial and freshly harvested (wild and cultivated) E. -
Update on Modern Bacterial Taxonomy for Bench Microbiologists
11/5/2018 Update on Modern Bacterial Taxonomy for Bench Microbiologists J. Michael Janda Kern County Public Health Laboratory Bakersfield CA The “Name Game” Which Ones Different? Bacterial Taxonomy for Why is Taxonomy Important? Clinical Microbiologists • Think of it as a “LABEL” NOMENCLATURE CLASSIFICATION • We communicate with colleagues around the world regarding • Correct naming and use of • Determines where specific infectious diseases using a standardized communication bacterial names species or groups reside system, microbial taxonomy • Codified compared to others • Basic rules are in • Determines • We describe new diseases, disease outbreaks, epidemics, or pandemics, and emerging syndromes using a binomial name the “Red Book” phylogenetic • to indicate the infectious agent(s) Unlike classification, position relatively stable • Not codified • A lack of a standardized communication system can lead to: but subject to • Can change rapidly – Misidentifications change • What is accepted is – Inappropriate therapeutic decisions based upon common – Inability to determine disease prognosis, treatment and pathogenicity usage and acceptance by the – Identify important outbreaks and epidemics scientific community 1 11/5/2018 Description of a New Species [Idealized] Some Requirements for a Valid Species • Type strain must be identified and defined (etymology); deposited Bios in at least two recognized international culture collections Morpho & 16S • Properties of the taxon, including phenotypic characteristics must Physio NEW be described and compared to closest neighbors on both a phylogenetic as swell as phenotypic basis SPECIES – Cell shape, motility, color, Gram stain DDH, Chemo ANI – Physiologic properties: pH, temperature range Type • Strain G+C mol% • Full 16S rRNA gene sequence, DDH, and/or ANI Classification Pathways to Species Validation Enterobacter Cronobacter Proposed New sakazakii sakazakii Species (Farmer, 1980) (Iversen, 2008) C. -
Genomic and Phenotypic Insights Point to Diverse Ecological Strategies by Facultative Anaerobes Obtained from Subsurface Coal Seams Silas H
www.nature.com/scientificreports OPEN Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams Silas H. W. Vick1,2*, Paul Greenfeld2, Sasha G. Tetu 1, David J. Midgley2 & Ian T. Paulsen1 Microbes in subsurface coal seams are responsible for the conversion of the organic matter in coal to methane, resulting in vast reserves of coal seam gas. This process is important from both environmental and economic perspectives as coal seam gas is rapidly becoming a popular fuel source worldwide and is a less carbon intensive fuel than coal. Despite the importance of this process, little is known about the roles of individual bacterial taxa in the microbial communities carrying out this process. Of particular interest is the role of members of the genus Pseudomonas, a typically aerobic taxa which is ubiquitous in coal seam microbial communities worldwide and which has been shown to be abundant at early time points in studies of ecological succession on coal. The current study performed aerobic isolations of coal seam microbial taxa generating ten facultative anaerobic isolates from three coal seam formation waters across eastern Australia. Subsequent genomic sequencing and phenotypic analysis revealed a range of ecological strategies and roles for these facultative anaerobes in biomass recycling, suggesting that this group of organisms is involved in the degradation of accumulated biomass in coal seams, funnelling nutrients back into the microbial communities degrading coal to methane. Globally, coal represents a key fuel, accounting for almost ~25% of the world’s energy consumption (International Energy Agency). Te use of coal for power generation, however, is associated with signifcant environmental and health impacts1,2.