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Comparative Phylogeny of the Genus Bordetella Using Sequence Analysis of 16S Rrna and Ompa Genes
J Med Bacteriol. Vol. 6, No. 3, 4 (2017): pp.1-13 jmb.tums.ac.ir Comparative Phylogeny of the Genus Bordetella Using Sequence Analysis of 16S rRNA and ompA Genes Ali Badamchi 1, Moslem Papizadeh 2* 1 Children's Medical Center Hospital, Tehran University of Medical Sciences, Tehran, Iran. 2 Department of Microbiology, Pasteur Institute of Iran (IPI), Tehran, Iran. ARTICLE INFO ABSTRACT Article type: Background: The genus Bordetella harbors 16 species; three of them are well-known for their high Original Article medical importance. The phylogenetic diversity of the genus is currently not very well investigated. Methods: In this study, 16S rRNA gene sequence of 16 type strains of the Bordetella species were Article history: analyzed. Also, phylogenies conducted on the same gene of 247 isolates of Bordetella species, Received: 19 Jan 2017 comprising a wide physiological as well as ecological diversity and encompassing ex-type Revised: Jun Mar 2017 representatives of the 16 Bordetella species, were analyzed. Accepted: 11 Sep 2017 Results: It was found that the phylogenetic diversity of the genus may be very different from that is Published: 15 Oct 2017 currently assumed. Interestingly, the 16S rRNA gene signals could not resolve some species with Keywords: promising bootstrap and posterior probability values as our phylogenies, using maximum likelihood Alcaligenaceae, and Bayesian inference methods, showed. Biogeography, Bordetella Conclusion: Our results indicate a probable need for additional phylogenetic signals which can be species, Ecological provided by coding genes. Therefore, sequence data of ompA gene of Bordetella species, a critically distribution, Phylogenetic significant genomic region in pathogenesis, was here analyzed, phylogenetically. -
Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells. -
Eelgrass Sediment Microbiome As a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan
Microbes Environ. Vol. 34, No. 1, 13-22, 2019 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME18103 Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan TATSUNORI NAKAGAWA1*, YUKI TSUCHIYA1, SHINGO UEDA1, MANABU FUKUI2, and REIJI TAKAHASHI1 1College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252–0880, Japan; and 2Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060–0819, Japan (Received July 16, 2018—Accepted October 22, 2018—Published online December 1, 2018) Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. -
Fluviicola Taffensis Type Strain (RW262)
Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262). Permalink https://escholarship.org/uc/item/9tc6n0sm Journal Standards in genomic sciences, 5(1) ISSN 1944-3277 Authors Woyke, Tanja Chertkov, Olga Lapidus, Alla et al. Publication Date 2011-10-01 DOI 10.4056/sigs.2124912 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2011) 5:21-29 DOI:10.4056/sigs.2124912 Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262T) Tanja Woyke1, Olga Chertkov1, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Tijana Glavina Del Rio1, Hope Tice1, Jan-Fang Cheng1, Roxanne Tapia1,2, Cliff Han1,2, Lynne Goodwin1,2, Sam Pitluck1, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Marcel Huntemann1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Amy Chen3, Krishna Palaniappan3, Miriam Land1,4, Loren Hauser1,4, Evelyne-Marie Brambilla5, Manfred Rohde6, Romano Mwirichia7, Johannes Sikorski5, Brian J. Tindall5, Markus Göker5, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1,9, Hans-Peter Klenk5, 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 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 Jomo Kenyatta University of Agriculture and Technology, Kenya 8 University of California Davis Genome Center, Davis, California, USA 9 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Nikos C. -
Bridging the Gap Between Genomics- and Metabolomics-Based Perspectives of Myxobacterial Secondary Metabolite Production Capabili
Bridging the gap between genomics - and metabolomics - based perspectives of myxobacterial secondary metabolite production capability Dissertation zur Erlangung des Grades des Doktors der Naturwissenschaften der Naturwissenschaftlich - T echnischen Fakultät der Universität des Saarlandes. von Fabian Panter Saarbrücken 2018 2 Tag des Kolloquiums: 01.04.2019 Dekan : Prof. Dr. Guido Kickelbick Berichterstatter: Prof. Dr. Rolf Müller Prof. Dr. Christian Ducho Prof. Dr. Tobias Gulder Vorsitz: Prof. Dr. Uli Kazmaier Akad. Mitarbeiter : Dr. Judith Becker 3 Diese Arbeit entstand unter der Anleitung von Prof. Dr. Rolf Müller am Institut für Pharmazeutische Biotechnologie der Naturwissenschaftlich - Technischen Fakultät der Universität des Saarlandes von Dezember 2014 bis November 2018 . 4 Ο ἶ δα ο ὐ κ ε ἰ δώς Ich weiß, dass ich unwissend bin . entlehnt aus der Apologie des Sokrates, V olksgericht von Athen 399 v. Chr . 5 Danksagung Als erstes möchte ich mich bei meinem Doktorvater Prof. Dr. Rolf Müller für die Möglichkeit be danken , meine Dissertation in dieser Arbeitsgruppe durchzuführen. Das entgegengebrachte Vertrauen für die Bearbeitung anspruchsvoller Themen im Bereich des bakteriellen Sekundärstoffwechsels und die immerwährende Unterstützung im Rahmen wissenschaftlicher Diskus sionen waren sehr hilfreich und motivierend. Zudem möchte ich mich bei Prof. Dr. Christian Ducho für die Annahme des Co - Referats und Unterstützung als wissenschaftlicher Begleiter bedanken. Zudem möchte ich mich bei meinem Betreuer Dr. Daniel Krug für die tatkräftige Unterstützung meiner Dissertation, durch wissenschaftliche Diskussionen und innovative Lösungsansätze für Probleme meiner Doktorarbeit, sowie für kritische Überarbeitung meiner Manuskripte bedanken. Darüber hinaus möchte ich mich bei allen beda nken die mir in den vergangenen fast 4 Jahren mit Rat und Tat zur Seite standen und es mir ermöglichten in sehr vielen Bereichen der Naturstoffforschung dazu zu lernen. -
Bordetella Petrii Clinical Isolate Isolates of This Species Have Been Previously Reported from 4
routine laboratory protocols. Initial susceptibility testing Bordetella petrii using disk diffusion indicated apparent susceptibility of the isolate to erythromycin, gentamicin, ceftriaxone, and Clinical Isolate piperacillin/tazobactam. The isolate was resistant to amox- icillin, co-amoxiclav, tetracycline, clindamycin, ciproflo- Norman K. Fry,* John Duncan,* Henry Malnick,* xacin, and metronidazole. After initial sensitivity results, a Marina Warner,* Andrew J. Smith,† 6-week course of oral clarithromycin (500 mg, 8 hourly) Margaret S. Jackson,† and Ashraf Ayoub† was begun. We describe the first clinical isolate of Bordetella petrii At follow-up appointments 3 months and 6 months from a patient with mandibular osteomyelitis. The only pre- after antimicrobial drug therapy ceased, clinical and radi- viously documented isolation of B. petrii occurred after the ographic findings were not unusual, and the infected area initial culture of a single strain from an environmental healed successfully. Despite the successful clinical out- source. come, the isolate was subsequently shown to be resistant to clarithromycin in vitro (Table). Improvement of the 67-year-old man visited an emergency dental clinic, osteomyelitis may also have been facilitated by the biopsy Awhere he complained of toothache in the lower right procedure, during which a sequestrum of bone was mandibular quadrant. Examination showed a root-filled removed. lower right canine tooth that was mobile and tender to per- The gram-negative bacillus (designated strain cussion. The tooth was extracted uneventfully under local GDH030510) was submitted to the Health Protection anesthesia. The patient returned after several days with Agency, Centre for Infections, London, for identification. pain at the extraction site. A localized alveolar osteitis was Preliminary tests results were consistent with those diagnosed, and local debridement measures were institut- described for members of the genus Bordetella. -
Community Structure Analysis 9
Biodegradation of Polystyrene Foam by the Microorganisms from Landfill Pat Pataranutaporn ! Assistant prof. Savaporn Supaphol prof. Amornrat Phongdara Sureeporn Nualkaew Hi, I would like to invite you to take a look on my research Pat Introduction !3 “Styrofoam” Polystyrene Disadvantage Physical Properties ! • chemical formula is (C8H8)n • Non-biodegradable in the environment • monomer styrene • Made from non-renewable petroleum products • Thermoplastic • Chronic, low-level exposure risks undetermined • blowing agents Introduction !4 Bacteria nutritional requirements ! ‣ Energy source Biodegradation ‣ Carbon source Possibly work? ‣ Nitrogen source ‣ Minerals ‣ Water ‣ Growth factors Polystyrene structure http://faculty.ccbcmd.edu/courses/bio141/ lecguide/unit6/metabolism/growth/factors.html Introduction !5 Aims of the research ‣To identify the microbe that able to growth in the condition that polystyrene is a sole carbon source ! ‣To study the changing of microbe community structure in the selective culture which polystyrene is a sole carbon source ! ‣To observe the biodegradability of polystyrene To analyse the by product of polystyrene after degradation Methodology Methodology !7 Agar cultivation Community fingerprint 2 16s Ribosomal RNA Microbe Screening months later identification sampling Cultivation Molecular cloning Phylogenetic tree Degradability observation (SEM) Methodology Microbe sampling & cultivation !8 Agar cultivation Community fingerprint 2 16s Ribosomal RNA Microbe Screening months later identification sampling Cultivation -
Drylands Soil Bacterial Community Is Affected by Land Use Change and Different Irrigation Practices in the Mezquital Valley
www.nature.com/scientificreports OPEN Drylands soil bacterial community is afected by land use change and diferent irrigation practices in the Received: 23 June 2017 Accepted: 3 January 2018 Mezquital Valley, Mexico Published: xx xx xxxx Kathia Lüneberg1, Dominik Schneider2, Christina Siebe1 & Rolf Daniel 2 Dryland agriculture nourishes one third of global population, although crop irrigation is often mandatory. As freshwater sources are scarce, treated and untreated wastewater is increasingly used for irrigation. Here, we investigated how the transformation of semiarid shrubland into rainfed farming or irrigated agriculture with freshwater, dam-stored or untreated wastewater afects the total (DNA-based) and active (RNA-based) soil bacterial community composition, diversity, and functionality. To do this we collected soil samples during the dry and rainy seasons and isolated DNA and RNA. Soil moisture, sodium content and pH were the strongest drivers of the bacterial community composition. We found lineage-specifc adaptations to drought and sodium content in specifc land use systems. Predicted functionality profles revealed gene abundances involved in nitrogen, carbon and phosphorous cycles difered among land use systems and season. Freshwater irrigated bacterial community is taxonomically and functionally susceptible to seasonal environmental changes, while wastewater irrigated ones are taxonomically susceptible but functionally resistant to them. Additionally, we identifed potentially harmful human and phytopathogens. The analyses of 16 S rRNA genes, its transcripts and deduced functional profles provided extensive understanding of the short- term and long-term responses of bacterial communities associated to land use, seasonality, and water quality used for irrigation in drylands. Drylands are defned as regions with arid, semi-arid, and dry sub humid climate with an annual precipitation/ evapotranspiration potential ratio (P/PET)1 ranging from 0.05 to 0.652. -
Which Organisms Are Used for Anti-Biofouling Studies
Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E. -
Candidatus Prosiliicoccus Vernus, a Spring Phytoplankton Bloom
Systematic and Applied Microbiology 42 (2019) 41–53 Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae ∗ T. Ben Francis, Karen Krüger, Bernhard M. Fuchs, Hanno Teeling, Rudolf I. Amann Max Planck Institute for Marine Microbiology, Bremen, Germany a r t i c l e i n f o a b s t r a c t Keywords: Microbial degradation of algal biomass following spring phytoplankton blooms has been characterised as Metagenome assembled genome a concerted effort among multiple clades of heterotrophic bacteria. Despite their significance to overall Helgoland carbon turnover, many of these clades have resisted cultivation. One clade known from 16S rRNA gene North Sea sequencing surveys at Helgoland in the North Sea, was formerly identified as belonging to the genus Laminarin Ulvibacter. This clade rapidly responds to algal blooms, transiently making up as much as 20% of the Flow cytometric sorting free-living bacterioplankton. Sequence similarity below 95% between the 16S rRNA genes of described Ulvibacter species and those from Helgoland suggest this is a novel genus. Analysis of 40 metagenome assembled genomes (MAGs) derived from samples collected during spring blooms at Helgoland support this conclusion. These MAGs represent three species, only one of which appears to bloom in response to phytoplankton. MAGs with estimated completeness greater than 90% could only be recovered for this abundant species. Additional, less complete, MAGs belonging to all three species were recovered from a mini-metagenome of cells sorted via flow cytometry using the genus specific ULV995 fluorescent rRNA probe. -
Phage-Induced Lysis Enhances Biofilm Formation in Shewanella Oneidensis MR-1
The ISME Journal (2011) 5, 613–626 & 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11 www.nature.com/ismej ORIGINAL ARTICLE Phage-induced lysis enhances biofilm formation in Shewanella oneidensis MR-1 Julia Go¨deke, Kristina Paul, Ju¨ rgen Lassak and Kai M Thormann Department of Ecophysiology, Max-Planck-Institut fu¨r Terrestrische Mikrobiologie, Marburg, Germany Shewanella oneidensis MR-1 is capable of forming highly structured surface-attached communities. By DNase I treatment, we demonstrated that extracellular DNA (eDNA) serves as a structural component in all stages of biofilm formation under static and hydrodynamic conditions. We determined whether eDNA is released through cell lysis mediated by the three prophages LambdaSo, MuSo1 and MuSo2 that are harbored in the genome of S. oneidensis MR-1. Mutant analyses and infection studies revealed that all three prophages may individually lead to cell lysis. However, only LambdaSo and MuSo2 form infectious phage particles. Phage release and cell lysis already occur during early stages of static incubation. A mutant devoid of the prophages was significantly less prone to lysis in pure culture. In addition, the phage-less mutant was severely impaired in biofilm formation through all stages of development, and three-dimensional growth occurred independently of eDNA as a structural component. Thus, we suggest that in S. oneidensis MR-1 prophage-mediated lysis results in the release of crucial biofilm-promoting factors, in particular eDNA. The ISME Journal (2011) 5, 613–626; doi:10.1038/ismej.2010.153; published online 21 October 2010 Subject Category: microbe–microbe and microbe–host interactions Keywords: Shewanella; biofilm; eDNA; lysis; phage Introduction been demonstrated to adhere to various surfaces and form biofilms (Bagge et al., 2001; Thormann et al., Shewanella oneidensis MR-1 belongs to the Gram- 2004, 2005, 2006; Teal et al., 2006; McLean et al., negative g-proteobacteria and is characterized by an 2008a; Zhang et al., 2010). -
Fish Bacterial Flora Identification Via Rapid Cellular Fatty Acid Analysis
Fish bacterial flora identification via rapid cellular fatty acid analysis Item Type Thesis Authors Morey, Amit Download date 09/10/2021 08:41:29 Link to Item http://hdl.handle.net/11122/4939 FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS By Amit Morey /V RECOMMENDED: $ Advisory Committe/ Chair < r Head, Interdisciplinary iProgram in Seafood Science and Nutrition /-■ x ? APPROVED: Dean, SchooLof Fisheries and Ocfcan Sciences de3n of the Graduate School Date FISH BACTERIAL FLORA IDENTIFICATION VIA RAPID CELLULAR FATTY ACID ANALYSIS A THESIS Presented to the Faculty of the University of Alaska Fairbanks in Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE By Amit Morey, M.F.Sc. Fairbanks, Alaska h r A Q t ■ ^% 0 /v AlA s ((0 August 2007 ^>c0^b Abstract Seafood quality can be assessed by determining the bacterial load and flora composition, although classical taxonomic methods are time-consuming and subjective to interpretation bias. A two-prong approach was used to assess a commercially available microbial identification system: confirmation of known cultures and fish spoilage experiments to isolate unknowns for identification. Bacterial isolates from the Fishery Industrial Technology Center Culture Collection (FITCCC) and the American Type Culture Collection (ATCC) were used to test the identification ability of the Sherlock Microbial Identification System (MIS). Twelve ATCC and 21 FITCCC strains were identified to species with the exception of Pseudomonas fluorescens and P. putida which could not be distinguished by cellular fatty acid analysis. The bacterial flora changes that occurred in iced Alaska pink salmon ( Oncorhynchus gorbuscha) were determined by the rapid method.