DOCSLIB.ORG

Analysis of Intestinal Bacterial Community Diversity of Adult Dastarcus Helophoroides Author(S): Z

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Analysis of Intestinal Bacterial Community Diversity of Adult Dastarcus Helophoroides Author(S): Z Analysis of Intestinal Bacterial Community Diversity of Adult Dastarcus helophoroides Author(s): Z. Q. Zhang, C. He, M. L. Li Source: Journal of Insect Science, 14(114):1-13. 2014. Published By: Entomological Society of America DOI: http://dx.doi.org/10.1673/031.014.114 URL: http://www.bioone.org/doi/full/10.1673/031.014.114 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Journal of Insect Science: Vol. 14 | Article 114 Zhang et al. Analysis of intestinal bacterial community diversity of adult Dastarcus helophoroides Z. Q. Zhang1a, C. He2b, M. L. Li1c* 1Laboratory of Forestry Pests Biological Control, College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, 712100, China 2Wuwei academy of Forestry Sciences, WuWei, Gansu, 733000, China Abstract Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), and a culture- dependent technique were used to study the diversity of the intestinal bacterial community in adult Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae). Universal bacterial pri- mers targeting 200 bp regions of the 16S rDNA gene were used in the PCR-DGGE assay, and 14 bright bands were obtained. The intestinal bacteria detected by PCR-DGGE were classified to Enterococcus (Lactobacillales: Enterococcaceae), Bacillus (Bacillales: Bacillaceae), Cellvibrio (Pseudomonadales: Pseudomonadaceae), Caulobacter (Caulobacterales: Caulobacteraceae), and uncultured bacteria, whereas those isolated by the culture-dependent technique belonged to Staphylococcus (Bacillales: Staphylococcaceae), Pectobacterium Enterobacteriales: Enterobacte- riaceae), and Enterobacter (Enterobacteriales: Enterobacteriaceae). These intestinal bacteria represented the groups Lactobacillales (Enterococcus), Pseudomonadales (Cellvibrio), Caulobac- terales (Caulobacter), Bacilli (Bacillus and Staphylococcus), and Gammaproteobacteria (Pectobacterium and Enterobacter). Our results demonstrated that PCR-DGGE analysis and the culture-dependent technique were useful in determining the intestinal bacteria of D. helophoroid- es and the two methods should be integrated to characterize the microbial community and diversity. Keywords: PCR-DGGE assay, culture-dependent technique Correspondence: a [email protected], b [email protected], c [email protected], *Corresponding author Editor: Allen Cohen was editor of this paper. Received: 8 October 2012 Accepted: 20 February 2013 Published: 12 August 2014 Copyright: This is an open access paper. We use the Creative Commons Attribution 3.0 license that permits unrestricted use, provided that the paper is properly attributed. ISSN: 1536-2442 | Vol. 14, Number 114 Cite this paper as: Zhang ZQ, He C, Li ML. 2014. Analysis of intestinal bacterial community diversity of adult Dastarcus helophoroides. Journal of Insect Science 14(114). Available online: http://www.insectscience.org/14.114 Journal of Insect Science | http://www.insectscience.org 1 Journal of Insect Science: Vol. 14 | Article 114 Zhang et al. Introduction tus Kollbe (Isoptera: Rhinotermitidae) (Hongoh et al. 2003), Hepialus gonggaensis Many insects are inhabited by diverse com- Fu & Huang (Lepidoptera: Hepialidae) (Zhuo munities of microorganisms. It is possible that 2005), Bombyx mori L. (Lepidoptera: Bomby- the number of microbes in most insects is cidae) (Xiang et al. 2007), Anopheles sinensis larger than the number of somatic cells Wiedemann (Diptera: Culicidae) (Wang (Campbell 1990). The intestinal microbial 2008), and Costelytra zealandica (White) bacteria in insects have been shown to play (Coleoptera: Melolonthidae) (Zhang and Jack- important roles, such as providing vitamins, son 2008), but few reports are available on the aiding in fat and carbohydrate metabolism, intestinal bacteria of Dastarcus helophoroides preventing the invasion of external bacteria, (= longulus) (Fairmaire) (Coleoptera: Both- and promoting the function of the immune rideridae). This parasitic beetle is an important system (Eutick et al. 1978, Abe et al. 2000, natural enemy of long-horned beetles (Ogura Suchodolski and Ruaux 2004). Insects’ guts et al. 1999) and is therefore an important ex- offer many niches for bacteria, while the in- perimental insect. sects take advantage of the bacterial metabolism and the adaptability of prokary- Amann et al. (1995) indicated that only 0.1– otes (Dillon and Dillon 2004). For example, 15% of microbes from natural environments extensive research has revealed the symbiotic could grow in artificial media. Hence, results relationship between termites and bacteria. from culture-dependent methods only partially Microbes provide carbon, nitrogen, and other reflected the real microbial communities and nutrient sources to their host termites, and restricted our past knowledge of microbial termites can no longer live without them ecology. For example, when culture- (Hongoh et al. 2003). The analysis of intesti- dependent methods were applied to assay the nal bacteria was performed by culture- gut microbial community of H. gonggaensis dependent and molecular methods. The cul- larvae, 12 bacteria were isolated (Zhuo et al. ture-dependent technique defined the gut 2004). In contrast, by using a PCR-DGGE as- microbes by phenotypic characterization say, Zhuo (2005) separated 76 bands that all (morphology, immunology, and physiologi- represented different bacteria from this insect. cal-biochemical reaction), but unculturable Muyzer et al. (1993) were among the first re- bacteria were largely ignored (Lysenko 1985). searchers who used DGGE to analyze the Molecular biology methods allowed extract- genetic diversity of microorganisms in algal- ing the total genomic DNA of bacteria directly fungal and bacterial biofilms, and their results from samples and then sequencing and ana- indicated that this technique offered ad- lyzing the DNA to characterize the bacteria vantages over culture-dependent methods in species composition and abundance (Yu et al. revealing natural microbial communities. 2008). The aim of this study was to analyze the di- Coupled polymerase chain reaction and dena- versity of the intestinal bacterial community turing gradient gel electrophoresis (PCR- in adult D. helophoroides by using culture- DGGE) and other modern molecular biologi- dependent and PCR-DGGE techniques and to cal technologies have been applied to study compare the results obtained by both methods. the microbial diversity and dominant species in many insects, such as Reticulitermes spera- Journal of Insect Science | http://www.insectscience.org 2 Journal of Insect Science: Vol. 14 | Article 114 Zhang et al. Materials and Methods 50 µL, consisting of 25 µL 2× Es Taq Master Mix (with dye; CWBIO, Sample collection www.cwbiotech.com), 19 µL RNase-free Adults of D. helophoroides were obtained H2O, 2 µL of each primer, and 2 µL template from the Laboratory of Forest Pest Biological DNA. The PCR was performed in a DNA En- Control, College of Forestry, Northwest Agri- gine Dyas Peltier Thermal Cycler (Bio-Rad culture and Forestry University, China. All Life Science Product, Hercules, CA). The am- insects were maintained and reared in con- plification program (designed by lab trolled incubators at 25 ± 1°C, 50-70% members) was as follows: an initial denatura- relative humidity (RH), and a photoperiod of tion at 95°C for 5 min; 29 cycles of 10:14 (L:D) on an artificial diet (Zhang et al. denaturation at 94°C for 1 min, annealing at 2014). The adult beetles were starved for 12 55°C for 30 sec, extension at 72°C for 90 sec, hr to allow elimination of the food bolus. The and a final extension at 72°C for 10 min. The digestive tracts were carefully removed from amplification products were purified with a the abdomen by using sterile dissecting nee- universal DNA purification kit (TIANGEN dles, and five guts were pooled and crushed Biotech, Beijing, China). gently with a pestle in liquid nitrogen. DGGE analysis Genomic DNA extraction and 16S rDNA The PCR products (30 μL) were separated and amplification analyzed by DGGE on an 8% polyacrylamide A modified cetyltrimethyl ammonium bro- gel with a denaturant-gradient of 35-60% mide method was used for genomic DNA (100% defined as 7 M solid urea and 40% de- TM extraction (Calderón-Cortés et al. 2010). The ionized formamide [v/v]) in a Dcodek extracted genomic DNA was electrophoresed Universal Mutation Detection System (Bio- through a 1.0% TAE (40 mM Tris, 20 mM Rad). The electrophoresis was carried out in acetic acid, 1.0 mM Na2-EDTA, 1.0% aga- 1× TAE buffer (40 mM Tris, 20 mM acetic rose) gel for detection of the extracted acid, 1.0 mM Na2-EDTA) at 35 V and 60°C genomic
Load more

Recommended publications
  • Analyzing the Early Stages of Clostridium Difficile Spore
    ANALYZING THE EARLY STAGES OF CLOSTRIDIUM DIFFICILE SPORE GERMINATION A Dissertation by MICHAEL FRANCIS Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Joseph A. Sorg Committee Members, James L. Smith Matthew S. Sachs Paul D. Straight Head of Department, Thomas D. McKnight May 2017 Major Subject: Microbiology Copyright 2017 Michael Francis ABSTRACT Infections caused by Clostridium difficile have increased steadily over the past several years. While studies on C. difficile virulence and physiology have been hindered, in the past, by lack of genetic approaches and suitable animal models, newly developed technologies and animal models allow for improved experimental detail. One such advance was the generation of a mouse-model of C. difficile infection. This system was an important step forward in the analysis of the genetic requirements for colonization and infection. Equally important is understanding the differences that exist between mice and humans. One of these differences is the natural bile acid composition. Bile acid-mediated spore germination, a process whereby a dormant spore returns to active, vegetative growth, is an important step during C. difficile colonization. Mice produce several different bile acids that are not found in humans (muricholic acids) that have the potential to impact C. difficile spore germination. In order to understand potential effects of these different bile acids on C. difficile physiology, we characterized their effects on C. difficile spore germination and growth of vegetative cells. We found that the mouse-derived muricholic acids affect germination similarly to a previously-described inhibitor of germination, chenodeoxycholic acid.
    [Show full text]
  • Insight Into the Genome of Staphylococcus Xylosus, a Ubiquitous Species Well Adapted to Meat Products Sabine Leroy, Aurore Vermassen, Geoffrey Ras, Régine Talon
    Insight into the genome of staphylococcus xylosus, a ubiquitous species well adapted to meat products Sabine Leroy, Aurore Vermassen, Geoffrey Ras, Régine Talon To cite this version: Sabine Leroy, Aurore Vermassen, Geoffrey Ras, Régine Talon. Insight into the genome of staphylo- coccus xylosus, a ubiquitous species well adapted to meat products. Microorganisms, MDPI, 2017, 5 (3), 10.3390/microorganisms5030052. hal-01607624 HAL Id: hal-01607624 https://hal.archives-ouvertes.fr/hal-01607624 Submitted on 25 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - ShareAlike| 4.0 International License microorganisms Review Insight into the Genome of Staphylococcus xylosus, a Ubiquitous Species Well Adapted to Meat Products Sabine Leroy, Aurore Vermassen, Geoffrey Ras and Régine Talon * Université Clermont-Auvergne, INRA, MEDIS, F-63000 Clermont-Ferrand, France; [email protected] (S.L.); [email protected] (A.V.); [email protected] (G.R.) * Correspondence: [email protected]; Tel.: +33-473-624-170 Received: 29 June 2017; Accepted: 25 August 2017; Published: 29 August 2017 Abstract: Staphylococcus xylosus belongs to the vast group of coagulase-negative staphylococci. It is frequently isolated from meat products, either fermented or salted and dried, and is commonly used as starter cultures in sausage manufacturing.
    [Show full text]
  • 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.
    [Show full text]
  • Significance of Donor Human Milk
    fmicb-09-01376 June 26, 2018 Time: 17:31 # 1 ORIGINAL RESEARCH published: 27 June 2018 doi: 10.3389/fmicb.2018.01376 Preterm Gut Microbiome Depending on Feeding Type: Significance of Donor Human Milk Anna Parra-Llorca1, María Gormaz1,2, Cristina Alcántara3, María Cernada1,2, Antonio Nuñez-Ramiro1,2, Máximo Vento1,2*† and Maria C. Collado3*† 1 Neonatal Research Group, Health Research Institute La Fe, University and Polytechnic Hospital La Fe, Valencia, Spain, 2 Division of Neonatology, University and Polytechnic Hospital La Fe, Valencia, Spain, 3 Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council, Valencia, Spain Preterm microbial colonization is affected by gestational age, antibiotic treatment, type of birth, but also by type of feeding. Breast milk has been acknowledged as the gold standard for human nutrition. In preterm infants breast milk has been associated with improved growth and cognitive development and a reduced risk of necrotizing enterocolitis and late onset sepsis. In the absence of their mother’s own milk (MOM), pasteurized donor human milk (DHM) could be the best available alternative due to its similarity to the former. However, little is known about the effect of DHM upon preterm Edited by: Sandra Torriani, microbiota and potential biological implications. Our objective was to determine the University of Verona, Italy impact of DHM upon preterm gut microbiota admitted in a referral neonatal intensive Reviewed by: care unit (NICU). A prospective observational cohort study in NICU of 69 neonates Carlotta De Filippo, <32 weeks of gestation and with a birth weight ≤1,500 g was conducted.
    [Show full text]
  • Guide to Turning an RDP File Into a Data Set
    Guide to Turning an RDP File into a Data Set Berkley Shands, Patricio S. La Rosa, Elena Deych, William Shannon July 5, 2017 Below we will define the basic steps required to generate a data set from an RDP file 1. Take an RDP file such as this example: ;Root:1.0;Bacteria:1.0;Firmicutes:1.0;Bacilli:1.0;Bacillales:1.0;Staphylococcaceae:1.0; ;Root:1.0;Bacteria:1.0;Firmicutes:1.0;Bacilli:1.0;Lactobacillales:1.0;Carnobacteriaceae:0.8; ;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Bacteroidales:1.0;Prevotellaceae:1.0; ;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Bacteroidales:1.0;Prevotellaceae:1.0; ;Root:1.0;Bacteria:1.0;Bacteroidetes:1.0;Bacteroidia:1.0;Unclassified:0.5;Unclassified:0.5; 2. Take the first entry and seperate each level into its own row, while seper- ating levels by a period: Root, 1 Root.Bacteria, 1 Root.Bacteria.Firmicutes, 1 Root.Bacteria.Firmicutes.Bacilli, 1 Root.Bacteria.Firmicutes.Bacilli.Bacillales, 1 Root.Bacteria.Firmicutes.Bacilli.Bacillales.Staphylococcaceae, 1 3. Do the same with each following row, adding to the number at the end if it is the same: Root, 5 Root.Bacteria, 5 Root.Bacteria.Firmicutes, 2 Root.Bacteria.Firmicutes.Bacilli, 2 Root.Bacteria.Firmicutes.Bacilli.Bacillales, 1 Root.Bacteria.Firmicutes.Bacilli.Bacillales.Staphylococcaceae, 1 Root.Bacteria.Firmicutes.Bacilli.Lactobacillales, 1 Root.Bacteria.Firmicutes.Bacilli.Lactobacillales.Carnobacteriaceae, .8 Root.Bacteria.Bacteroidetes, 3 Root.Bacteria.Bacteroidetes.Bacteroidia, 3 Root.Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales, 2 Root.Bacteria.Bacteroidetes.Bacteroidia.Bacteroidales.Prevotellaceae, 2 Root.Bacteria.Bacteroidetes.Bacteroidia.Unclassified, .5 Root.Bacteria.Bacteroidetes.Bacteroidia.Unclassified.Unclassified, .5 4.
    [Show full text]
  • The Genera Staphylococcus and Macrococcus
    Prokaryotes (2006) 4:5–75 DOI: 10.1007/0-387-30744-3_1 CHAPTER 1.2.1 ehT areneG succocolyhpatS dna succocorcMa The Genera Staphylococcus and Macrococcus FRIEDRICH GÖTZ, TAMMY BANNERMAN AND KARL-HEINZ SCHLEIFER Introduction zolidone (Baker, 1984). Comparative immu- nochemical studies of catalases (Schleifer, 1986), The name Staphylococcus (staphyle, bunch of DNA-DNA hybridization studies, DNA-rRNA grapes) was introduced by Ogston (1883) for the hybridization studies (Schleifer et al., 1979; Kilp- group micrococci causing inflammation and per et al., 1980), and comparative oligonucle- suppuration. He was the first to differentiate otide cataloguing of 16S rRNA (Ludwig et al., two kinds of pyogenic cocci: one arranged in 1981) clearly demonstrated the epigenetic and groups or masses was called “Staphylococcus” genetic difference of staphylococci and micro- and another arranged in chains was named cocci. Members of the genus Staphylococcus “Billroth’s Streptococcus.” A formal description form a coherent and well-defined group of of the genus Staphylococcus was provided by related species that is widely divergent from Rosenbach (1884). He divided the genus into the those of the genus Micrococcus. Until the early two species Staphylococcus aureus and S. albus. 1970s, the genus Staphylococcus consisted of Zopf (1885) placed the mass-forming staphylo- three species: the coagulase-positive species S. cocci and tetrad-forming micrococci in the genus aureus and the coagulase-negative species S. epi- Micrococcus. In 1886, the genus Staphylococcus dermidis and S. saprophyticus, but a deeper look was separated from Micrococcus by Flügge into the chemotaxonomic and genotypic proper- (1886). He differentiated the two genera mainly ties of staphylococci led to the description of on the basis of their action on gelatin and on many new staphylococcal species.
    [Show full text]
  • Bacterial Flora on the Mammary Gland Skin of Sows and in Their Colostrum
    Brief communication Peer reviewed Bacterial flora on the mammary gland skin of sows and in their colostrum Nicole Kemper, Prof, Dr med vet; Regine Preissler, DVM Summary Resumen - La flora bacteriana en la piel de Résumé - Flore bactérienne cutanée de la Mammary-gland skin swabs and milk la glándula mamaria de las hembras y en su glande mammaire de truies et de leur lait calostro samples were analysed bacteriologically. All Des écouvillons de la peau de la glande skin samples were positive, with 5.2 isolates Se analizaron bacteriológicamente hisopos de mammaire ainsi que des échantillons de lait on average, Staphylococcaceae being the la piel de la glándula mamaria y muestras de ont été soumis à une analyse bactériologique. dominant organisms. In 20.8% of milk leche. Todas las muestras de piel resultaron Tous les échantillons provenant de la peau samples, no bacteria were detected. Two iso- positivas, con 5.2 aislados en promedio, étaient positifs, avec en moyenne 5.2 isolats lates on average, mainly Staphylococcaceae siendo los Staphylococcaceae los organismos bactériens, les Staphylococcaceae étant de loin and Streptococcaceae, were isolated from the dominantes. En 20.8% de las muestras de les micro-organismes dominants. Aucune positive milk samples. leche, no se detectaron bacterias. De las bactérie ne fut détectée dans 20.8% des Keywords: swine, bacteria, colostrum, muestras de leche positivas, se aislaron échantillons de lait. En moyenne, on trouvait mammary gland, skin dos aislados en promedio, principalmente deux isolats bactériens par échantillon de lait Staphylococcaceae y los Streptococcaceae. positif, et ceux-ci étaient principalement des Received: April 7, 2010 Staphylococcaceae et des Streptococcaceae.
    [Show full text]
  • Enzymatic Potential of Bacteria and Fungi Isolates from the Sewage Sludge Composting Process
    applied sciences Article Enzymatic Potential of Bacteria and Fungi Isolates from the Sewage Sludge Composting Process 1,2, 1,2 1,2, Tatiana Robledo-Mahón y , Concepción Calvo and Elisabet Aranda * 1 Institute of Water Research, University of Granada, Ramón y Cajal 4, 18071 Granada, Spain; [email protected] (T.R.-M.); [email protected] (C.C.) 2 Department of Microbiology, Pharmacy Faculty, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain * Correspondence: [email protected] Current address: Department of Agro-Environmental Chemistry and Plant Nutrition, y Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, 16500 Prague 6-Suchdol, Czech Republic. Received: 6 October 2020; Accepted: 2 November 2020; Published: 3 November 2020 Featured Application: Screening of suitable microorganisms adapted to environmental conditions are the challenges for the optimization of biotechnological processes in the current and near future. Some of the isolated microorganisms in this study possess biotechnological desirable features which could be employed in different processes, such as biorefinery, bioremediation, or in the food industry. Abstract: The aim of this study was the isolation and characterisation of the fungi and bacteria during the composting process of sewage sludge under a semipermeable membrane system at full scale, in order to find isolates with enzymatic activities of biotechnological interest. A total of 40 fungi were isolated and enzymatically analysed. Fungal culture showed a predominance of members of Ascomycota and Basidiomycota division and some representatives of Mucoromycotina subdivision. Some noticeable fungi isolated during the mesophilic and thermophilic phase were Aspergillus, Circinella, and Talaromyces.
    [Show full text]
  • Type of the Paper (Article
    Supplementary Materials S1 Clinical details recorded, Sampling, DNA Extraction of Microbial DNA, 16S rRNA gene sequencing, Bioinformatic pipeline, Quantitative Polymerase Chain Reaction Clinical details recorded In addition to the microbial specimen, the following clinical features were also recorded for each patient: age, gender, infection type (primary or secondary, meaning initial or revision treatment), pain, tenderness to percussion, sinus tract and size of the periapical radiolucency, to determine the correlation between these features and microbial findings (Table 1). Prevalence of all clinical signs and symptoms (except periapical lesion size) were recorded on a binary scale [0 = absent, 1 = present], while the size of the radiolucency was measured in millimetres by two endodontic specialists on two- dimensional periapical radiographs (Planmeca Romexis, Coventry, UK). Sampling After anaesthesia, the tooth to be treated was isolated with a rubber dam (UnoDent, Essex, UK), and field decontamination was carried out before and after access opening, according to an established protocol, and shown to eliminate contaminating DNA (Data not shown). An access cavity was cut with a sterile bur under sterile saline irrigation (0.9% NaCl, Mölnlycke Health Care, Göteborg, Sweden), with contamination control samples taken. Root canal patency was assessed with a sterile K-file (Dentsply-Sirona, Ballaigues, Switzerland). For non-culture-based analysis, clinical samples were collected by inserting two paper points size 15 (Dentsply Sirona, USA) into the root canal. Each paper point was retained in the canal for 1 min with careful agitation, then was transferred to −80ºC storage immediately before further analysis. Cases of secondary endodontic treatment were sampled using the same protocol, with the exception that specimens were collected after removal of the coronal gutta-percha with Gates Glidden drills (Dentsply-Sirona, Switzerland).
    [Show full text]
  • Updates on the Sporulation Process in Clostridium Species
    Updates on the sporulation process in Clostridium species Talukdar, P. K., Olguín-Araneda, V., Alnoman, M., Paredes-Sabja, D., & Sarker, M. R. (2015). Updates on the sporulation process in Clostridium species. Research in Microbiology, 166(4), 225-235. doi:10.1016/j.resmic.2014.12.001 10.1016/j.resmic.2014.12.001 Elsevier Accepted Manuscript http://cdss.library.oregonstate.edu/sa-termsofuse *Manuscript 1 Review article for publication in special issue: Genetics of toxigenic Clostridia 2 3 Updates on the sporulation process in Clostridium species 4 5 Prabhat K. Talukdar1, 2, Valeria Olguín-Araneda3, Maryam Alnoman1, 2, Daniel Paredes-Sabja1, 3, 6 Mahfuzur R. Sarker1, 2. 7 8 1Department of Biomedical Sciences, College of Veterinary Medicine and 2Department of 9 Microbiology, College of Science, Oregon State University, Corvallis, OR. U.S.A; 3Laboratorio 10 de Mecanismos de Patogénesis Bacteriana, Departamento de Ciencias Biológicas, Facultad de 11 Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile. 12 13 14 Running Title: Clostridium spore formation. 15 16 17 Key Words: Clostridium, spores, sporulation, Spo0A, sigma factors 18 19 20 Corresponding author: Dr. Mahfuzur Sarker, Department of Biomedical Sciences, College of 21 Veterinary Medicine, Oregon State University, 216 Dryden Hall, Corvallis, OR 97331. Tel: 541- 22 737-6918; Fax: 541-737-2730; e-mail: [email protected] 23 1 24 25 Abstract 26 Sporulation is an important strategy for certain bacterial species within the phylum Firmicutes to 27 survive longer periods of time in adverse conditions. All spore-forming bacteria have two phases 28 in their life; the vegetative form, where they can maintain all metabolic activities and replicate to 29 increase numbers, and the spore form, where no metabolic activities exist.
    [Show full text]
  • Characterization of Ureolytic Bacteria Isolated from Limestone Caves of Sarawak and Evaluation of Their Efficiency in Biocementation
    CHARACTERIZATION OF UREOLYTIC BACTERIA ISOLATED FROM LIMESTONE CAVES OF SARAWAK AND EVALUATION OF THEIR EFFICIENCY IN BIOCEMENTATION By ARMSTRONG IGHODALO OMOREGIE A thesis presented in fulfilment of the requirements for the degree of Master of Science (Research) Faculty of Engineering, Computing and Science SWINBURNE UNIVERSITY OF TECHNOLOGY 2016 ABSTRACT The aim of this study was to isolate, identify and characterise bacteria that are capable of producing urease enzyme, from limestone cave samples of Sarawak. Little is known about the diversity of bacteria inhabiting Sarawak’s limestone caves with the ability of hydrolyzing urea substrate through urease for microbially induced calcite precipitation (MICP) applications. Several studies have reported that the majority of ureolytic bacterial species involved in calcite precipitation are pathogenic. However, only a few non-pathogenic urease-producing bacteria have high urease activities, essential in MICP treatment for improvement of soil’s shear strength and stiffness. Enrichment culture technique was used in this study to target highly active urease- producing bacteria from limestone cave samples of Sarawak collected from Fairy and Wind Caves Nature Reserves. These isolates were subsequently subjected to an increased urea concentration for survival ability in conditions containing high urea substrates. Urea agar base media was used to screen for positive urease producers among the bacterial isolates. All the ureolytic bacteria were identified with the use of phenotypic and molecular characterizations. For determination of their respective urease activities, conductivity method was used and the highly active ureolytic bacteria isolated comparable with control strain used in this study were selected and used for the next subsequent experiments in this study.
    [Show full text]
  • Sporulation and Germination in Clostridial Pathogens AIMEE SHEN,1 ADRIANNE N
    Sporulation and Germination in Clostridial Pathogens AIMEE SHEN,1 ADRIANNE N. EDWARDS,2 MAHFUZUR R. SARKER,3,4 and DANIEL PAREDES-SABJA5 1Department of Molecular Biology and Microbiology, Tufts University Medical School, Boston, MA 2Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 3Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR; 4Department of Microbiology, College of Science, Oregon State University, Corvallis, OR 5Department of Gut Microbiota and Clostridia Research Group, Departamento de Ciencias Biolo gicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile ABSTRACT As obligate anaerobes, clostridial pathogens IMPORTANCE OF SPORES TO depend on their metabolically dormant, oxygen-tolerant spore CLOSTRIDIAL PATHOGENESIS form to transmit disease. However, the molecular mechanisms Disease transmission by clostridial pathogens depends by which those spores germinate to initiate infection and then form new spores to transmit infection remain poorly on their ability to form aerotolerant, metabolically understood. While sporulation and germination have been well dormant spores before exiting their hosts (6). Since characterized in Bacillus subtilis and Bacillus anthracis, striking spores are highly resistant to extreme temperature and differences in the regulation of these processes have been pressure changes, radiation, enzymatic digestion, and observed between the bacilli and the clostridia, with even some oxidizing agents (7), they can persist for long periods of conserved proteins exhibiting differences in their requirements time and serve as environmental reservoirs for these and functions. Here, we review our current understanding of fi organisms (8). Spores from C. perfringens, C. botuli- how clostridial pathogens, speci cally Clostridium perfringens, fi Clostridium botulinum, and Clostridioides difficile, induce num, and C.
    [Show full text]