DOCSLIB.ORG

16S Rdna Sequencing Analysis of Upper Respiratory Tract flora in Patients with Influenza H1N1 Virus Infection

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
16S Rdna Sequencing Analysis of Upper Respiratory Tract flora in Patients with Influenza H1N1 Virus Infection Frontiers in Laboratory Medicine xxx (2017) xxx–xxx Contents lists available at ScienceDirect Frontiers in Laboratory Medicine journal homepage: www.keaipublishing.com/en/journals/frontiers-in-laboratory-medicine 16S rDNA sequencing analysis of upper respiratory tract flora in patients with influenza H1N1 virus infection Yanhua Li a,1, Jianbing Ding b,1, Yunfeng Xiao c, Bin Xu d, Wenfang He a, Yuqi Yang a, Liu Yang a, ⇑ ⇑ Mingquan Su a, Xiaoke Hao a, , Yueyun Ma a, a Department of Clinical Laboratory Medicine, Xijing Hospital, The Fourth Military Medical University, Xi’an, Shaanxi 710032, PR China b Department of Immunology, Xinjiang Medical University, Urumqi, Xinjiang, 810034, PR China c Department of Pharmacy, Tangdu Hospital, The Fourth Military Medical University, Xi’an, Shaanxi 710038, PR China d Shandong International Trust Co., Ltd, Jinan, Shandong 250013, PR China article info abstract Article history: Background: We analyzed respiratory tract bacterial flora in patients with influenza H1N1 virus infection, Received 13 December 2016 and investigated the role of H1N1 virus in secondary bacterial infection. Received in revised form 13 January 2017 Method: A total of 12,766 operational taxonomic units (OTUs) were obtained, of which, 12,127 were Accepted 17 January 2017 identified to phylum level and 10,494 to genus level. We used next-generation sequencing technology Available online xxxx to evaluate bacterial abundance in swab specimens from patients infected with influenza H1N1 virus or Non-H1N1 influenza and from healthy controls. Data analysis was carried out by using alpha analysis Keywords: (Shannon-Wiener index and Rarefaction-Curve), beta analysis [UniFrac(abundance) and Metastats 16S rDNA analysis], and Community-and-Phylogenesis analysis. Influenza H1N1 Upper respiratory tract flora Results: At phylum level, Proteobacteria in patients with H1N1 virus infection (99.928 ± 0.008%) and Next-generation sequencing common cold (89.019 ± 1.845%) were significantly higher than in healthy controls (26.103 ± 2.495%) (p < 0.01). In contrast, proportions of Firmicutes, Bacteroidetes, Actinobacteria, Candidate division TM7, Fusobacteria and SR1 were down-regulated (p < 0.01) in patients with H1N1 virus infection. At genus level, Pseudomonas increased >500-fold in patients with H1N1 virus infection compared with healthy controls. Ochrobactrum, Brevundimonas, Caulobacter, Aquabacterium and Serratia also increased signifi- cantly in H1N1 virus infection, while Neisseria, Prevotella, Veillonella, Actinomyces, Porphyromonas, Streptococcus, Haemophilus and Acinetobacter decreased. Conclusion: Our data indicated that microbial abundance of the upper respiratory tract decreased in patients with H1N1 virus infection. Pseudomonas was the dominant genus among the upper respiratory tract bacterial flora in H1N1-infected patients. The changes in upper respiratory tract flora probably be closely related to the occurrence and progression of secondary bacterial infection. Ó 2017 Published by Elsevier B.V. on behalf of Laboratorial Medicine Committee of the Chinese Research Hospital Association. This is an open access article under the CC BY-NC-ND license (http://creativecom- mons.org/licenses/by-nc-nd/4.0/). Introduction that has a serious negative impact on economic development and human health. The early symptoms of H1N1 influenza are similar Influenza A virus subtype H1N1 [denoted as A(H1N1) or H1N1] to Non-H1N1 influenza, however, progression is rapid and may is one of the most commonly found influenza viruses in humans.26 lead to secondary and severe bacterial pneumonia, respiratory fail- Epidemic H1N1 influenza spreads rapidly in autumn and winter in ure and multiple organ injury and even death. Secondary bacterial the Northern Hemisphere, such as North America, Europe and infection accounted for 26–33% of deaths caused by H1N1 virus Asia.22,25 This has become a major social and public health problem infection,13,20,28,41,8 and 30–33% of patients with H1N1 virus in intensive care might have secondary bacterial infection.35,36 ⇑ H1N1 virus was the leading main cause of death in the three large Corresponding authors at: Department of Clinical Laboratory, Xijing Hospital, 30 The Fourth Military Medical University, 169 Changle West Road, Xi’an, Shaanxi influenza pandemics in 1918, 1957 and 1968. 710032, PR China. Secondary bacterial infection is attributed to the capacity of E-mail addresses: [email protected] (X. Hao), [email protected] H1N1 virus to replicate in the lower airways, causing extensive (Y. Ma). epithelial destruction, viral pneumonia, and secondary bacterial 1 These authors contributed equally to this study. http://dx.doi.org/10.1016/j.flm.2017.02.005 2542-3649/Ó 2017 Published by Elsevier B.V. on behalf of Laboratorial Medicine Committee of the Chinese Research Hospital Association. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Please cite this article in press as: Li Y., et al. 16S rDNA sequencing analysis of upper respiratory tract flora in patients with influenza H1N1 virus infection Frontiers in Laboratory Medicine (2017), http://dx.doi.org/10.1016/j.flm.2017.02.005 2 Y. Li et al. / Frontiers in Laboratory Medicine xxx (2017) xxx–xxx infections with increased lethality.22 Viral infection may enhance Guangzhou, China) and criteria for influenza infection were simul- bacterial pathogenesis and include impairment of mucociliary taneously met. According to the examination results, patients were clearance and increased bacterial adherence to epithelial cells. divided into two groups: G1, infection with H1N1 (n = 100), and Virus-induced epithelial damage facilitates bacterial translocation G2, infection without H1N1 but other type of influenza infection and dissemination and/or inhibition of antibacterial immune (Flu group or other influenza group) (n = 72). And the clinical fea- response. The healthy nose/nasopharynx has a bacterial tures are summarized in Table 1. community dominated by Actinobacteria, Firmicutes and Thirty healthy individuals were chosen as the normal control Proteobacteria.6 Secondary bacterial pneumonia is usually (N) group, whose average age was 26.5 years. Inclusion criteria: caused by Haemophilus influenzae, Pseudomonas aeruginosa, Staphy- despite their regular physical examinations, they were normal or lococcus epidermidis, Staphylococcus aureus and Corynebacterium healthy, without upper respiratory tract infection within the past tuberculostearicum.38,15,1,12,25 3 months. Exclusion criteria: same as for influenza. The occurrence and development of many human diseases are Pharyngeal swab specimens were collected with Copan 480CE usually closely related to changes in their bacterial flora.33,11 The (Copan, Brescia, Italy). In addition, we used five standard strains normal flora in the respiratory mucous membrane can be involved as positive controls: Streptococcus pneumoniae (ATCC 49619), in the regulation of adaptive immune response against influenza Escherichia coli (ATCC25922), P. aeruginosa (ATCC 27853), S. aureus virus.43,17,2 It can maintain a high tolerance threshold to modulate (ATCC 25923), and H. influenzae (ATCC 49247). the inflammatory response.29,37,23 So, it is reasonable to hypothe- size that the changes in respiratory tract flora caused by acute DNA extraction and PCR amplification H1N1 virus infection stimulate secondary and severe bacterial pneumonia, but the mechanisms are still not clear. The swabs were transferred to new 1.5-mL centrifuge tubes, The gold standard of identification by bacterial culture has been dissolved in PBS buffer by stirring, and centrifuged for 3 min at unable to meet the demand of bacterial diversity analysis, because 20,000g. The supernatant was discarded and 100–200 mL suspen- 34 >90% of the clinical bacteria cannot be cultured. Next-generation sion was left. Microbial DNA was extracted from swab samples sequencing (NGS) provides a new technology to study the micro- using the E.Z.N.A.Ò DNA Kit (Omega Bio-tek, Norcross, GA, USA). 16 biota and pathogenic mechanisms. The V3–V4 region of the bacterial 16S rDNA was amplified by 16S rDNA sequencing is a powerful tool for researching taxon- PCR (95 °C for 2 min, followed by 25 cycles at 95 °C for 30 s, omy and phylogeny of samples from a complex microorganism 55 °C for 30 s, and 72 °C for 30 s and a final extension at 72 °C for or environment. The generated operational taxonomic units 5 min) using primers 338F 50-barcode-ACTCCTACGGGAGG (OTUs) can be analyzed at seven levels: kingdom, phylum, class, CAGCA)-30 and 806R 50-GGACTACHVGGGTWTCTAAT-30, where 32 order, family, genus and species. Nasidze et al. found 39 bacteria barcode is an eight-base sequence unique to each sample. PCRs that have never been reported in the mouth through 16S rDNA were performed in triplicate with a 20-lL mixture containing 45 sequencing. Yang et al. analyzed salivary microorganisms in 19 4 lL5Â FastPfu Buffer, 2 lL 2.5 mM dNTPs, 0.8 lL each primer individuals with active caries and 26 without caries with 16S rRNA (5 lM), 0.4 lL FastPfu Polymerase, and 10 ng template DNA. and whole genome sequencing technology. They found that the microbial changes were greater in patients with active caries. The present study applied NGS of 16S rDNA sequencing and Illumina MiSeq sequencing bioinformatics to analyze variation of the microbiome during H1N1 virus infection and might show how respiratory tract flora Amplicons were extracted from 2% agarose gels and purified changes cause severe secondary pulmonary infection
Load more

Recommended publications
  • Contamination of Sulfonamide Antibiotics and Sulfamethazine-Resistant Bacteria in the Downstream and Estuarine Areas of Jiulong River in Southeast China
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Crossref Environ Sci Pollut Res (2015) 22:12104–12113 DOI 10.1007/s11356-015-4473-z RESEARCH ARTICLE Contamination of sulfonamide antibiotics and sulfamethazine-resistant bacteria in the downstream and estuarine areas of Jiulong River in Southeast China Danyun Ou1 & Bin Chen1 & Renao Bai 1 & Puqing Song1 & Heshan Lin1 Received: 28 December 2014 /Accepted: 30 March 2015 /Published online: 16 April 2015 # The Author(s) 2015. This article is published with open access at Springerlink.com Abstract Surface water samples from downstream and estu- Introduction arine areas of Jiulong River were collected in August 2011 and May 2012 for detecting sulfonamide antibiotic residues The occurrence of antibiotics in aquatic environments is of and isolating sulfamethazine-resistant bacteria. ecotoxicological concern because of potential ecosystem al- Sulfamethazine was detected in all samples in May 2012 at teration. Prolonged exposure to low doses of antibiotics leads an average concentration of 78.3 ng L−1, which was the to selective proliferation of resistant bacteria, which could highest among the nine sulfonamide antibiotics determined. transfer antimicrobial resistance genes to other bacterial spe- Sulfamethazine-resistant bacteria (SRB) were screened using cies (Dantas et al. 2008;LevyandMarshall2004)with antibiotic-containing agar plates. The SRB average abundance difficult-to-predict consequences on human health (Martínez in the samples was 3.69×104 and 2.17×103 CFUs mL−1 in 2008). The potential of these low antibiotic concentrations to August 2011 and May 2012, respectively, and was positively promote antimicrobial resistance has been substantiated by the correlated to sulfamethazine concentration in May 2012.
    [Show full text]
  • Control of Phytopathogenic Microorganisms with Pseudomonas Sp. and Substances and Compositions Derived Therefrom
    (19) TZZ Z_Z_T (11) EP 2 820 140 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: A01N 63/02 (2006.01) A01N 37/06 (2006.01) 10.01.2018 Bulletin 2018/02 A01N 37/36 (2006.01) A01N 43/08 (2006.01) C12P 1/04 (2006.01) (21) Application number: 13754767.5 (86) International application number: (22) Date of filing: 27.02.2013 PCT/US2013/028112 (87) International publication number: WO 2013/130680 (06.09.2013 Gazette 2013/36) (54) CONTROL OF PHYTOPATHOGENIC MICROORGANISMS WITH PSEUDOMONAS SP. AND SUBSTANCES AND COMPOSITIONS DERIVED THEREFROM BEKÄMPFUNG VON PHYTOPATHOGENEN MIKROORGANISMEN MIT PSEUDOMONAS SP. SOWIE DARAUS HERGESTELLTE SUBSTANZEN UND ZUSAMMENSETZUNGEN RÉGULATION DE MICRO-ORGANISMES PHYTOPATHOGÈNES PAR PSEUDOMONAS SP. ET DES SUBSTANCES ET DES COMPOSITIONS OBTENUES À PARTIR DE CELLE-CI (84) Designated Contracting States: • O. COUILLEROT ET AL: "Pseudomonas AL AT BE BG CH CY CZ DE DK EE ES FI FR GB fluorescens and closely-related fluorescent GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO pseudomonads as biocontrol agents of PL PT RO RS SE SI SK SM TR soil-borne phytopathogens", LETTERS IN APPLIED MICROBIOLOGY, vol. 48, no. 5, 1 May (30) Priority: 28.02.2012 US 201261604507 P 2009 (2009-05-01), pages 505-512, XP55202836, 30.07.2012 US 201261670624 P ISSN: 0266-8254, DOI: 10.1111/j.1472-765X.2009.02566.x (43) Date of publication of application: • GUANPENG GAO ET AL: "Effect of Biocontrol 07.01.2015 Bulletin 2015/02 Agent Pseudomonas fluorescens 2P24 on Soil Fungal Community in Cucumber Rhizosphere (73) Proprietor: Marrone Bio Innovations, Inc.
    [Show full text]
  • D 6.1 EMBRIC Showcases
    Grant Agreement Number: 654008 EMBRIC European Marine Biological Research Infrastructure Cluster to promote the Blue Bioeconomy Horizon 2020 – the Framework Programme for Research and Innovation (2014-2020), H2020-INFRADEV-1-2014-1 Start Date of Project: 01.06.2015 Duration: 48 Months Deliverable D6.1 b EMBRIC showcases: prototype pipelines from the microorganism to product discovery (Revised 2019) HORIZON 2020 - INFRADEV Implementation and operation of cross-cutting services and solutions for clusters of ESFRI 1 Grant agreement no.: 654008 Project acronym: EMBRIC Project website: www.embric.eu Project full title: European Marine Biological Research Infrastructure cluster to promote the Bioeconomy (Revised 2019) Project start date: June 2015 (48 months) Submission due date: May 2019 Actual submission date: Apr 2019 Work Package: WP 6 Microbial pipeline from environment to active compounds Lead Beneficiary: CABI [Partner 15] Version: 1.0 Authors: SMITH David [CABI Partner 15] GOSS Rebecca [USTAN 10] OVERMANN Jörg [DSMZ Partner 24] BRÖNSTRUP Mark [HZI Partner 18] PASCUAL Javier [DSMZ Partner 24] BAJERSKI Felizitas [DSMZ Partner 24] HENSLER Michael [HZI Partner 18] WANG Yunpeng [USTAN Partner 10] ABRAHAM Emily [USTAN Partner 10] FIORINI Federica [HZI Partner 18] Project funded by the European Union’s Horizon 2020 research and innovation programme (2015-2019) Dissemination Level PU Public X PP Restricted to other programme participants (including the Commission Services) RE Restricted to a group specified by the consortium (including the Commission Services) CO Confidential, only for members of the consortium (including the Commission Services 2 Abstract Deliverable D6.1b replaces Deliverable 6.1 EMBRIC showcases: prototype pipelines from the microorganism to product discovery with the specific goal to refine technologies used but more specifically deliver results of the microbial discovery pipeline.
    [Show full text]
  • A002 Methylobacterium Carri Sp. Nov., Isolated from Automotive Air
    A002 Methylobacterium carri sp. nov., Isolated from Automotive Air Conditioning System Jigwan Son and Jong-Ok Ka* Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University A bacterial strain, designated DB0501T, with Gram-stain-negative, aerobic, motile, and rod-shaped cell, was isolated from an automotive air conditioning system collected in the Republic of Korea. 16S rRNA gene sequence analysis indicated that the strain DB0501T grouped in the genus Methylobacterium and closely related to Methylobacterium platani PMB02T (98.8%), Methylobacterium currus PR1016AT (97.7%), Methylobacterium variabile DSM 16961T (97.7%), Methylobacterium aquaticum DSM 16371T (97.6%), Methylobacterium tarhaniae N4211T (97.4%) and Methylobacterium frigidaeris IER25-16T (97.2%). Genomic relatedness between strain DB0501T and its closest relatives was evaluated using average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity with values of 86.4–90.8%, 39.3 ± 2.6–48.2 ± 5.0% and 87.8–89.5% respectively. The strain grew 15-30°C , pH 5.5-8.0 and in 0–1.0% w/v NaCl. Summed feature 3 (C16:1 7c and/or C16:1 6c) and summed feature 8 (C18:1 ω7c T and/or C18:1 ω6c) were the predominant cellular fatty acids in strain DB0501 . Q-10 was the major ubiquinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylcholine. The DNA G+C content of strain DB0501T was 70.8 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain DB0501T represents a novel species of the genus Methylobacterium, for which the name Methylobacterium carri sp.
    [Show full text]
  • Microbial Reduction of Uranium(VI)
    Applied Geochemistry 51 (2014) 55–64 Contents lists available at ScienceDirect Applied Geochemistry journal homepage: www.elsevier.com/locate/apgeochem Microbial reduction of uranium(VI) in sediments of different lithologies collected from Sellafield ⇑ Laura Newsome a, , Katherine Morris a, Divyesh Trivedi b, Nick Atherton c, Jonathan R. Lloyd a,b a Research Centre for Radwaste and Decommissioning and Williamson Research Centre for Molecular Environmental Science, School of Earth, Atmospheric and Environmental Sciences, University of Manchester, Manchester M13 9PL, UK b National Nuclear Laboratory, Chadwick House, Birchwood Park, Warrington WA3 6AE, UK c Sellafield Ltd., Land Quality, Sellafield, Seascale, Cumbria CA20 1PG, UK article info abstract Article history: The presence of uranium in groundwater at nuclear sites can be controlled by microbial processes. Here Available online 28 September 2014 we describe the results from stimulating microbial reduction of U(VI) in sediment samples obtained from Editorial handling by M. Kersten a nuclear-licensed site in the UK. A variety of different lithology sediments were selected to represent the heterogeneity of the subsurface at a site underlain by glacial outwash deposits and sandstone. The nat- ural sediment microbial communities were stimulated via the addition of an acetate/lactate electron donor mix and were monitored for changes in geochemistry and molecular ecology. Most sediments facilitated the removal of 12 ppm U(VI) during the onset of Fe(III)-reducing conditions; this was reflected by an increase in the proportion of known Fe(III)- and U(VI)-reducing species. However U(VI) remained in solution in two sediments and Fe(III)-reducing conditions did not develop.
    [Show full text]
  • A Report of 31 Unrecorded Bacterial Species in South Korea Belonging to the Class Gammaproteobacteria
    Journal188 of Species Research 5(1):188-200, 2016JOURNAL OF SPECIES RESEARCH Vol. 5, No. 1 A report of 31 unrecorded bacterial species in South Korea belonging to the class Gammaproteobacteria Yong-Taek Jung1, Jin-Woo Bae2, Che Ok Jeon3, Kiseong Joh4, Chi Nam Seong5, Kwang Yeop Jahng6, Jang-Cheon Cho7, Chang-Jun Cha8, Wan-Taek Im9, Seung Bum Kim10 and Jung-Hoon Yoon1,* 1Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Korea 2Department of Biology, Kyung Hee University, Seoul 02447, Korea 3Department of Life Science, Chung-Ang University, Seoul 06974, Korea 4Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Gyeonggi 17035, Korea 5Department of Biology, Sunchon National University, Suncheon 57922, Korea 6Department of Life Sciences, Chonbuk National University, Jeonju-si 54896, Korea 7Department of Biological Sciences, Inha University, Incheon 22212, Korea 8Department of Biotechnology, Chung-Ang University, Anseong 17546, Korea 9Department of Biotechnology, Hankyong National University, Anseong 17579, Korea 10Department of Microbiology, Chungnam National University, Daejeon 34134, Korea *Correspondent: [email protected] During recent screening to discover indigenous prokaryotic species in South Korea, a total of 31 bacterial strains assigned to the class Gammaproteobacteria were isolated from a variety of environmental samples including soil, tidal flat, freshwater, seawater, and plant roots. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of a robust
    [Show full text]
  • A Survey of Culturable Microbial Diversity from the Lycoming Creek. Kristen Collins, Allison Batties, Tyler Hoffman, Jeffrey D
    A Survey of Culturable Microbial Diversity from the Lycoming Creek. Kristen Collins, Allison Batties, Tyler Hoffman, Jeffrey D. Newman, Biology Department, Lycoming College, Williamsport, PA Abstract Survey Results Figure 2. Phylogenetic Tree of Organisms found in Lycoming Creek Yersinia massiliensis AAan-05 The purpose of our study was to survey the bacterial diversity of Lycoming Creek in Table 1. Types of Bacteria found in Lycoming Creek Yersinia massiliensis AArt-01 Obesumbacterium proteus AH-07 Lycoming County, PA with a systematic approach. We obtained a water and sediment Cronobacter dublinensis AAan-04 sample from Lycoming Creek near where it empties into the Susquehanna River and Group Number of Organisms Enterobacter asburiae AH-15 Gamma Proteobacteria Enterobacter hormaechei AH-16 Enterobacteriales grew bacteria on several types of media under different conditions, selecting for single Enterobacter asburiae AAan-07 Enterobacter hormaechei AE44-10 colonies. We then amplified the 16S rRNA genes from the organisms by PCR and Actinobacteria 2 Enterobacter asburiae AAan-08 Enterobacter asburiae AEM-17 analyzed their sequences to determine their identity. Here we present data showing Aeromonas ichthiosmia-veronii AEM-06 Aeromonas ichthiosmia-veronii AEM-14 the different types of organisms isolated from the same source using different types of Bacteriodes 2 Aeromonas ichthiosmia-veronii AH-03 Aeromonas allosaccharophila ALAm-01 growth media and incubation conditions. Our secondary purpose was to identify Aeromonas ichthiosmia-veronii
    [Show full text]
  • Gas Seepage Pockmark Microbiomes Suggest the Presence Of
    bioRxiv preprint doi: https://doi.org/10.1101/348011; this version posted September 5, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Gas seepage pockmark microbiomes suggest the presence of 2 sedimentary coal seams in the Öxarfjörður graben of NE-Iceland 3 4 Guðný Vala Þorsteinsdóttir1,2, Anett Blischke3, M. Auður Sigurbjörnsdóttir1, Finnbogi Óskarsson4, 5 Þórarinn Sveinn Arnarson5†, Kristinn P. Magnússon1,2,6, and Oddur Vilhelmsson1,6 6 7 1University of Akureyri, Faculty of Natural Resource Sciences, Borgir v. Nordurslod, 600 8 Akureyri, Iceland. 9 2Icelandic Institute of Natural History, Borgir v. Nordurslod, 600 Akureyri, Iceland 10 3Íslenskar orkurannsóknir / Iceland GeoSurvey (ISOR), Akureyri Branch, Rangarvollum, 600 11 Akureyri, Iceland 12 4Íslenskar orkurannsóknir / Iceland GeoSurvey (ISOR), Department of Geothermal 13 Engineering, Grensasvegi 9, 108 Reykjavik, Iceland 14 5Orkustofnun / The Icelandic Energy Authority, Grensasvegi 9, 108 Reykjavik, Iceland 15 (†Passed away) 16 6Biomedical Center, University of Iceland, Vatnsmyrarvegur 16, 101 Reykjavik, Iceland 17 18 Correspondence: Oddur Vilhelmsson, [email protected] 19 20 Abstract 21 Natural gas seepage pockmarks are found off and onshore in the Öxarfjörður graben, 22 NE Iceland. The bacterial communities of two onshore seepage sites were analysed by 23 amplicon sequencing of 16S rDNA, along with determining the geochemical 24 characteristics, hydrocarbon content and the carbon isotope composition of the sites. 25 While one site was found to be characterised by biogenic origin of methane gas, with 26 carbon isotope ratio δ¹³C [‰] = -63.2, high content of organic matter and complex 1 bioRxiv preprint doi: https://doi.org/10.1101/348011; this version posted September 5, 2018.
    [Show full text]
  • Production and Characterization of Alkaline Phosphatase from Psychrophilic Bacteria
    PRODUCTION AND CHARACTERIZATION OF ALKALINE PHOSPHATASE FROM PSYCHROPHILIC BACTERIA BASHIR AHMAD Department of Microbiology Quaid-i-Azam University Islamabad 2010 Production and Characterization of Alkaline Phosphatase from Psychrophilic Bacteria A thesis submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY In MICROBIOLOGY BASHIR AHMAD Department of Microbiology Quaid-i-Azam University Islamabad 2010 With the name of ALLAH, Beneficent, Merciful DEDICATION To ABBA G (Dost Muhammad) and AMMAN (Sakina Bibi) This little effort is the first fruit of prayers, struggle and wishes, which I have been receiving from you since last thirty years, and as an expression of gratitude, I beg to dedicate it to your name. I hope you will accept these pages with the same spirit as you did it on the day when BABA took me to school on his shoulders. You are the best parents ever Declaration The material contained in this thesis is my original work. I have not previously presented any part of this work elsewhere for any other degree. Bashir Ahmad CERTIFICATE This thesis, submitted by Bashir Ahmad is accepted in its present form by the Department of Microbiology, Quaid-i-Azam University, Islamabad as satisfying the thesis requirement for the degree of Doctor of Philosophy in Microbiology. Internal examiner _____________________ (Dr. Fariha Hasan) External examiner _____________________ External examiner _____________________ Chairman _____________________ (Prof. Dr. Abdul Hameed) Dated: August 30, 2010 TABLE OF CONTENTS Sr. No. Title Page No. I List of figures i II List of Tables iii III List of Abbreviations iv IV Acknowledgment vi V Abstract viii 1.
    [Show full text]
  • The Geomicrobiology of Cementitious Radioactive Waste
    The Geomicrobiology of Cementitious Radioactive Waste A thesis submitted to The University of Manchester for the degree of Doctor of Philosophy in the Faculty of Engineering and Physical Sciences 2014 Adam John Williamson School of Earth, Atmospheric and Environmental Sciences Table of Contents Table of Contents .............................................................................................................. 2 List of Figures ................................................................................................................... 8 List of Tables................................................................................................................... 13 Abbreviations .................................................................................................................. 16 Abstract ........................................................................................................................... 18 Declaration ...................................................................................................................... 19 Copyright Statement ....................................................................................................... 20 Acknowledgments .......................................................................................................... 21 The Author ..................................................................................................................... 22 1. Introduction and Thesis Content ...........................................................................
    [Show full text]
  • 167 Sustainable Feed Technology and Nutrient Input Systems/Experiment/16SFT02NC
    Research Project Investigations: Sustainable Feed Technology and Nutrient Input Systems NUTRITIONAL CONDITIONING DURING LARVAL DEVELOPMENT TO IMPROVE PRODUCTION AND FEED EFFICIENCY AND ESTABLISHMENT OF BENEFICIAL GUT FLORA IN TILAPIA CULTURE Sustainable Feed Technology and Nutrient Input Systems/Experiment/16SFT02NC Scott A. Salger1, Kaniz Fatema2, Courtney A. Deck1, Nusrat Hossain Nushy2, Md Mehedi Hasan2, Jakir Hossain2, , Hannah M. Reynolds1, Peter R. Ferket3, Md Abdul Wahab2, S. Mahean Haque2, and Russell J. Borski1 1Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA 2Department of Fisheries Management, Bangladesh Agricultural University, Mymensingh, Bangladesh 3Department of Poultry Sciences, North Carolina State University, Raleigh, NC, USA ABSTRACT Feed constitutes 60-80% of total production costs of tilapia (Oreochromis spp.) with high quality protein being the most expensive component. Studies in mammals have demonstrated that early nutrient contributions can influence growth and other key physiological processes. This phenomenon, known as nutritional conditioning, was also shown in chickens and fish where limiting a nutrient in the early stages of development led to enhanced uptake and utilization later in life. We evaluated if this process could be applied to tilapia culture in the form of protein-restriction as this could reduce the cost of feed and thus production of tilapia for small-scale rural farmers in Bangladesh. It has yet to be determined in fish if protein restriction early in life might lead to improved growth later on. We first performed a tank trial to determine the effectiveness of protein-restriction in tilapia culture. Post-yolk sac fry were fed a 25% crude protein (CP) starter diet for 7, 14, or 21 days or a typical 48% CP diet for 21 days after which half the tanks from each treatment were fed a reduced 25% CP growout diet while the other half received a typical 38% CP growout diet.
    [Show full text]
  • High-Throughput Sequencing Techniques to Analyze Microbial Communities in the Gastrointestinal Tract of Broiler Chickens
    High-throughput sequencing techniques to analyze microbial communities in the gastrointestinal tract of broiler chickens Daniel Enrique, Borda Molina FACULTY OF AGRICULTURAL SCIENCES Institute of Animal Science – University of Hohenheim Livestock Microbial Ecology Jun.-Prof. Dr. rer. nat. Amélia Camarinha Silva HIGH-THROUGHPUT SEQUENCING TECHNIQUES TO ANALYZE MICROBIAL COMMUNITIES IN THE GASTROINTESTINAL TRACT OF BROILER CHICKENS DISSERTATION submitted in fulfilment of the requirements for the degree “Doktor der Agrarwissenschaften” (Dr. sc. agr. / PhD in Agricultural Sciences) to the Faculty of Agricultural Sciences presented by Daniel Enrique, Borda Molina (M.Sc. – Microbiologist) born on 17.07.1987 in Bogotá, Colombia Stuttgart-Hohenheim, 2018 The presented studies were realized at the Institute of Animal Science and at the Agricultural Research Station Lindenhöfe (72800, Eningen), of the University of Hohenheim in Stuttgart, Germany. The animal experiments were performed in February 2015 and April 2016 under the supervision of Jun.-Prof. Dr. Amélia Camarinha Silva (University of Hohenheim, Head of the “Livestock Microbial Ecology”) and the co- supervision of Prof. Dr. Markus Rodehutscord (University of Hohenheim, Head of the “Animal Nutrition”). University of Hohenheim, Faculty of Agricultural Science, December 2018 Dean of the Faculty of Agricultural Sciences: Prof. Dr. Ralf T. Vögele Date of examination: 10th December 2018 Chair of the committee: Prof. Dr. J. Bennewitz First Reviewer, First Examiner: Jun.-Prof. Dr. rer. Nat. A.
    [Show full text]