Environmental Chemistry MICROBIAL TRANSFORMATION of PYRETHROID INSECTICIDES in AQUEOUS and SEDIMENT PHASES
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Succession and Persistence of Microbial Communities and Antimicrobial Resistance Genes Associated with International Space Stati
Singh et al. Microbiome (2018) 6:204 https://doi.org/10.1186/s40168-018-0585-2 RESEARCH Open Access Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces Nitin Kumar Singh1, Jason M. Wood1, Fathi Karouia2,3 and Kasthuri Venkateswaran1* Abstract Background: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms. Results: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii,andAspergillus lentulus.EventhoughRhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. -
Supplementary Information
doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
A Case Series of Diarrheal Diseases Associated with Yersinia Frederiksenii
Article A Case Series of Diarrheal Diseases Associated with Yersinia frederiksenii Eugene Y. H. Yeung Department of Medical Microbiology, The Ottawa Hospital General Campus, The University of Ottawa, Ottawa, ON K1H 8L6, Canada; [email protected] Abstract: To date, Yersinia pestis, Yersinia enterocolitica, and Yersinia pseudotuberculosis are the three Yersinia species generally agreed to be pathogenic in humans. However, there are a limited number of studies that suggest some of the “non-pathogenic” Yersinia species may also cause infections. For instance, Yersinia frederiksenii used to be known as an atypical Y. enterocolitica strain until rhamnose biochemical testing was found to distinguish between these two species in the 1980s. From our regional microbiology laboratory records of 18 hospitals in Eastern Ontario, Canada from 1 May 2018 to 1 May 2021, we identified two patients with Y. frederiksenii isolates in their stool cultures, along with their clinical presentation and antimicrobial management. Both patients presented with diarrhea, abdominal pain, and vomiting for 5 days before presentation to hospital. One patient received a 10-day course of sulfamethoxazole-trimethoprim; his Y. frederiksenii isolate was shown to be susceptible to amoxicillin-clavulanate, ceftriaxone, ciprofloxacin, and sulfamethoxazole- trimethoprim, but resistant to ampicillin. The other patient was sent home from the emergency department and did not require antimicrobials and additional medical attention. This case series illustrated that diarrheal disease could be associated with Y. frederiksenii; the need for antimicrobial treatment should be determined on a case-by-case basis. Keywords: Yersinia frederiksenii; Yersinia enterocolitica; yersiniosis; diarrhea; microbial sensitivity tests; Citation: Yeung, E.Y.H. A Case stool culture; sulfamethoxazole-trimethoprim; gastroenteritis Series of Diarrheal Diseases Associated with Yersinia frederiksenii. -
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’. -
Insights Into the Evolution of Sialic Acid Catabolism Among Bacteria Salvador Almagro-Moreno1,2 and E Fidelma Boyd*1
BMC Evolutionary Biology BioMed Central Research article Open Access Insights into the evolution of sialic acid catabolism among bacteria Salvador Almagro-Moreno1,2 and E Fidelma Boyd*1 Address: 1Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA and 2Department of Microbiology, National University of Ireland, University College Cork, Cork, Ireland Email: Salvador Almagro-Moreno - [email protected]; E Fidelma Boyd* - [email protected] * Corresponding author Published: 26 May 2009 Received: 16 September 2008 Accepted: 26 May 2009 BMC Evolutionary Biology 2009, 9:118 doi:10.1186/1471-2148-9-118 This article is available from: http://www.biomedcentral.com/1471-2148/9/118 © 2009 Almagro-Moreno and Boyd; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Sialic acids comprise a family of nine-carbon amino sugars that are prevalent in mucus rich environments. Sialic acids from the human host are used by a number of pathogens as an energy source. Here we explore the evolution of the genes involved in the catabolism of sialic acid. Results: The cluster of genes encoding the enzymes N-acetylneuraminate lyase (NanA), epimerase (NanE), and kinase (NanK), necessary for the catabolism of sialic acid (the Nan cluster), are confined 46 bacterial species, 42 of which colonize mammals, 33 as pathogens and 9 as gut commensals. We found a putative sialic acid transporter associated with the Nan cluster in most species. -
Aerobic Gram-Positive Bacteria
Aerobic Gram-Positive Bacteria Abiotrophia defectiva Corynebacterium xerosisB Micrococcus lylaeB Staphylococcus warneri Aerococcus sanguinicolaB Dermabacter hominisB Pediococcus acidilactici Staphylococcus xylosusB Aerococcus urinaeB Dermacoccus nishinomiyaensisB Pediococcus pentosaceusB Streptococcus agalactiae Aerococcus viridans Enterococcus avium Rothia dentocariosaB Streptococcus anginosus Alloiococcus otitisB Enterococcus casseliflavus Rothia mucilaginosa Streptococcus canisB Arthrobacter cumminsiiB Enterococcus durans Rothia aeriaB Streptococcus equiB Brevibacterium caseiB Enterococcus faecalis Staphylococcus auricularisB Streptococcus constellatus Corynebacterium accolensB Enterococcus faecium Staphylococcus aureus Streptococcus dysgalactiaeB Corynebacterium afermentans groupB Enterococcus gallinarum Staphylococcus capitis Streptococcus dysgalactiae ssp dysgalactiaeV Corynebacterium amycolatumB Enterococcus hiraeB Staphylococcus capraeB Streptococcus dysgalactiae spp equisimilisV Corynebacterium aurimucosum groupB Enterococcus mundtiiB Staphylococcus carnosusB Streptococcus gallolyticus ssp gallolyticusV Corynebacterium bovisB Enterococcus raffinosusB Staphylococcus cohniiB Streptococcus gallolyticusB Corynebacterium coyleaeB Facklamia hominisB Staphylococcus cohnii ssp cohniiV Streptococcus gordoniiB Corynebacterium diphtheriaeB Gardnerella vaginalis Staphylococcus cohnii ssp urealyticusV Streptococcus infantarius ssp coli (Str.lutetiensis)V Corynebacterium freneyiB Gemella haemolysans Staphylococcus delphiniB Streptococcus infantarius -
A New Evaluation Method for Antibiotic-Resistant Bacterial Groups in Environment
Advances in Microbiology, 2016, 6, 133-151 Published Online March 2016 in SciRes. http://www.scirp.org/journal/aim http://dx.doi.org/10.4236/aim.2016.63014 A New Evaluation Method for Antibiotic-Resistant Bacterial Groups in Environment Katsuji Watanabe1*, Naoto Horinishi1, Kunimasa Matsumoto1, Akihiro Tanaka2, Kenichi Yakushido3 1Department of Life, Environment and Materials Science, Fukuoka Institute of technology, Fukuoka, Japan 2National Agricultural Research Center for Kyushu-Okinawa Region, National Agriculture and Food Research Organization, Kumamoto, Japan 3National Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Japan Received 31 January 2016; accepted 8 March 2016; published 11 March 2016 Copyright © 2016 by authors and Scientific Research Publishing Inc. This work is licensed under the Creative Commons Attribution International License (CC BY). http://creativecommons.org/licenses/by/4.0/ Abstract In the present manuscript it was presented whether spreading of antibiotic resistant bacterial groups in environment could be monitored by our newly developed method by enumerating anti- biotic resistant bacterial groups in various biological wastes and composts. Although the numbers were not so high, diverse kinds of colistin resistant bacteria (25 mg∙L−1) were included in row cat- tle feces (1.78 × 104 MPN g−1) and cattle feces manure (>3.84 × 104 MPN g−1). Compost originated from leftover food (>44.8 × 104 MPN g−1) and shochu lee (>320 × 104 MPN g−1) included higher numbers of chlortetracycline resistant Pseudomonas sp., (25 mg∙L−1), and row cattle feces included higher numbers of chlortetracycline resistant Enterobacteriacea (15.7 × 104 MPN g−1), which mostly consisted from Pantoea sp. -
Parallel Independent Evolution of Pathogenicity Within the Genus Yersinia
Parallel independent evolution of pathogenicity within the genus Yersinia Sandra Reutera,b,1, Thomas R. Connorb,c,1, Lars Barquistb, Danielle Walkerb, Theresa Feltwellb, Simon R. Harrisb, Maria Fookesb, Miquette E. Halla, Nicola K. Pettyb,d, Thilo M. Fuchse, Jukka Coranderf, Muriel Dufourg, Tamara Ringwoodh, Cyril Savini, Christiane Bouchierj, Liliane Martini, Minna Miettinenf, Mikhail Shubinf, Julia M. Riehmk, Riikka Laukkanen-Niniosl, Leila M. Sihvonenm, Anja Siitonenm, Mikael Skurnikn, Juliana Pfrimer Falcãoo, Hiroshi Fukushimap, Holger C. Scholzk, Michael B. Prenticeh, Brendan W. Wrenq, Julian Parkhillb, Elisabeth Carnieli, Mark Achtmanr,s, Alan McNallya, and Nicholas R. Thomsonb,q,2 aPathogen Research Group, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom; bPathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, United Kingdom; cCardiff University School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, United Kingdom; dThe ithree institute, University of Technology, Sydney, NSW 2007, Australia; eZentralinstitut für Ernährungs- und Lebensmittelforschung, Technische Universität München, D-85350 Freising, Germany; fDepartment of Mathematics and Statistics, and lDepartment of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, FIN-00014 Helsinki, Finland; gInstitute of Environmental Science and Research, Wallaceville, Upper Hutt 5140, New Zealand; hDepartment of Microbiology and rEnvironmental Research Institute, University College Cork, Cork, Ireland; iYersinia Research Unit, jGenomics Platform, Institut Pasteur, 75724 Paris, France; kDepartment of Bacteriology, Bundeswehr Institute of Microbiology, D-80937 Munich, Germany; mBacteriology Unit, National Institute for Health and Welfare (THL), FIN-00271 Helsinki, Finland; nDepartment of Bacteriology and Immunology, Haartman Institute, University of Helsinki and Helsinki University Central Hospital Laboratory Diagnostics, FIN-00014 Helsinki, Finland; oBrazilian Reference Center on Yersinia spp. -
Table of Contents
APRIL 2012 • VOLUME 194 • NO. 8 TABLE OF CONTENTS ARTICLES Transcriptional and Posttranscriptional Events Control Copper- Corinna Rademacher, Roman Moser, 1849–1859 Responsive Expression of a Rhodobacter capsulatus Multicopper Jan-Wilm Lackmann, Birgit Klinkert, Oxidase Franz Narberhaus, and Bernd Masepohl Spontaneous Excision of the O-Polysaccharide wbkA Marcos Mancilla, Clara M. Marín, José 1860–1867 Glycosyltranferase Gene Is a Cause of Dissociation of Smooth to M. Blasco, Ana María Zárraga, Ignacio Rough Brucella Colonies López-Goñi, and Ignacio Moriyón Biochemical Characterization of the CDP-D-Arabinitol Quan Wang, Yanli Xu, Andrei V. 1868–1874 Biosynthetic Pathway in Streptococcus pneumoniae 17F Perepelov, Yuriy A. Knirel, Peter R. Reeves, Alexander S. Shashkov, Xi Guo, Peng Ding, and Lu Feng Role of a SpoVA Protein in Dipicolinic Acid Uptake into Yunfeng Li, Andrew Davis, George 1875–1884 Developing Spores of Bacillus subtilis Korza, Pengfei Zhang, Yong-qing Li, Barbara Setlow, Peter Setlow, and Bing Hao Escherichia coli Serotype O55:H7 Diversity Supports Parallel Jennifer L. Kyle, Craig A. Cummings, 1885–1896 Acquisition of Bacteriophage at Shiga Toxin Phage Insertion Craig T. Parker, Beatriz Quiñones, Sites during Evolution of the O157:H7 Lineage Paolo Vatta, Elizabeth Newton, Steven Huynh, Michelle Swimley, Lovorka Degoricija, Melissa Barker, Samar Fontanoz, Kimberly Nguyen, Ronak Patel, Rixun Fang, Robert Tebbs, Olga Petrauskene, Manohar Furtado, and Robert E. Mandrell The TonB3 System in the Human Pathogen Vibrio vulnificus Is Alejandro F. Alice and Jorge H. Crosa 1897–1911 under the Control of the Global Regulators Lrp and Cyclic AMP Receptor Protein The PduM Protein Is a Structural Component of the Sharmistha Sinha, Shouqiang Cheng, 1912–1918 Microcompartments Involved in Coenzyme B12-Dependent 1,2- Chenguang Fan, and Thomas A. -
CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata
report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations. -
Dynamic Evolution of Selenocysteine Utilization in Bacteria: a Balance Between Selenoprotein Loss and Evolution of Selenocysteine from Redox Active Cysteine Residues
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Vadim Gladyshev Publications Biochemistry, Department of October 2006 Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues Yan Zhang University of Nebraska-Lincoln, [email protected] Hector Romero Instituto de Biología, Facultad de Ciencias, Uruguay Gustavo Salinas Instituto de Higiene, Avda A Navarro 3051, Montevideo, CP 11600, Uruguay Vadim Gladyshev University of Nebraska-Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/biochemgladyshev Part of the Biochemistry, Biophysics, and Structural Biology Commons Zhang, Yan; Romero, Hector; Salinas, Gustavo; and Gladyshev, Vadim, "Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues" (2006). Vadim Gladyshev Publications. 6. https://digitalcommons.unl.edu/biochemgladyshev/6 This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Vadim Gladyshev Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Open Access Research2006ZhangetVolume al. 7, Issue 10, Article R94 Dynamic evolution of selenocysteine utilization in bacteria: a comment balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues Yan Zhang*, Hector Romero†, Gustavo Salinas‡ and Vadim N Gladyshev* Addresses: *Department of Biochemistry, University of Nebraska, 1901 Vine street, Lincoln, NE 68588-0664, USA. †Laboratorio de Organización y Evolución del Genoma, Laboratorio de Organización y Evolución del Genoma, Dpto de Biología Celular y Molecular, Instituto ‡ de Biología, Facultad de Ciencias, Iguá 4225, Montevideo, CP 11400, Uruguay.