DOCSLIB.ORG

Multi-Locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level11

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Multi-Locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level11 CHAPTER Multi-locus Sequence Analysis: Taking Prokaryotic Systematics to the Next Level11 Xiaoying Rong, Ying Huang1 State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P.R. China 1Corresponding author: e-mail address: [email protected] 1 INTRODUCTION The study of genetic variation among prokaryotes is fundamental for understanding their evolution, and untangling their ecology and evolutionary theory-based system- atics. Recently, advances in DNA sequencing technology, the exploration of neglected habitats and the discovery of new species and products have forced micro- bial systematists to undertake comprehensive analyses of genetic variation within and between species and determine its impact on evolutionary relationships. 16S rRNA gene sequence analyses have enhanced our understanding of prokaryotic diversity and phylogeny, including that of non-culturable microorganisms (Doolittle, 1999; Head, Saunders, & Pickup, 1998; Mason et al., 2009). However, 16S rRNA gene phy- logenetic analyses have major drawbacks, notably providing insufficient resolution, especially for distinguishing between closely related species. In addition, there are well-documented cases in which individual prokaryotic organisms have been found to contain divergent 16S rRNA genes, thereby suggesting the potential for horizontal exchange of rRNA genes; such problems pose a challenge for reconstructing the evolutionary history of prokaryotic species and complicate efforts to classify them (Acinas, Marcelino, Klepac-Ceraj, & Polz, 2004; Cilia, Lafay, & Christen, 1996; Michon et al., 2010; Pei et al., 2010; Rokas, Williams, King, & Carroll, 2003). Multi-locus sequence analysis/typing (MLSA/MLST) is a nucleotide sequence- based approach for the unambiguous characterization of prokaryotes via the Internet, which directly characterizes DNA sequence variations in a set of housekeeping genes and evaluates relationships between strains based on their unique allelic profiles or sequences (Maiden, 2006). The method has been extensively used in the classification and identification of diverse bacteria, to determine the extent of gene exchange within and between species and to establish the relative importance of recombination in pop- ulation genetics (Doroghazi & Buckley, 2010; Alvarez-Perez, de Vega, & Herrera, 2013; Freel, Millan-Aguinaga, & Jensen, 2013). MLSA is providing new opportuni- ties to evaluate the status of bacterial taxa using patterns of genetic variation. Methods in Microbiology, Volume 41, ISSN 0580-9517, http://dx.doi.org/10.1016/bs.mim.2014.10.001 221 © 2014 Elsevier Ltd. All rights reserved. 222 CHAPTER 11 Multi-locus Sequence Analysis Actinobacteria are well known for their ability to produce diverse bioactive me- tabolites of commercial significance and to produce signalling molecules of ecolog- ical value (Be´rdy, 2005, 2012; Vetsigian, Jajoo, & Kishony, 2011). Although once considered primarily as soil bacteria, it is now known that actinobacteria are widely distributed in diverse natural habitats where they show a high degree of species and functional diversity (Bull, 2010). Since the discovery of streptomycin from Strepto- myces griseus (Schatz, Bugie, & Waksman, 1944), actinobacteria, notably strepto- mycetes, have been isolated from innumerable habitats and screened for bioactive compounds. In the case of the genus Streptomyces, such studies have led to the pub- lication of over 600 validly named species that pose significant taxonomic chal- lenges (Ka¨mpfer, 2012; Labeda et al., 2012). In this chapter, we summarize the practical procedures and the implementation of MLSA to species assignments of representative taxa within the genus Streptomyces of the phylum Actinobacteria, and how MLSA results are compared with and vali- dated against the current benchmark of DNA–DNA hybridization (DDH) values. We also describe how MLSA could be used to construct a sound framework that bridges taxonomic relationships and ecotype-level functional diversity within prokaryotic species. 2 MULTI-LOCUS SEQUENCE ANALYSIS 2.1 UNDERLYING CONCEPTS MLSA was developed from the application of the MLST method in order to recon- struct evolutionary relationships between prokaryotes (Sawabe, Kita-Tsukamoto, & Thompson, 2007; Vinuesa et al., 2008; Wagner, Varghese, Hemme, & Wiegel, 2013). Comparative MLST is based on sequencing 450–500 bp fragments of five to seven housekeeping genes that provide information on the spread of nucleotide divergence across the chromosomes of sampled populations. Sequences that differ by even a single nucleotide for each gene are assigned as different alleles, thus mak- ing MLSA highly suitable for detecting genetic changes within and between species. Phylogenetic analysis using multi-locus sequences involves several steps: (1) se- lection of strains and housekeeping genes, (2) generation of sequences (polymerase chain reaction (PCR) amplification and DNA sequencing), (3) data analysis to iden- tify homologous sites within each gene and (4) MLSA using concatenated sequences or allelic profiles (the latter are usually used for population genetics). In step 1, the most important factors to consider are the clock-like behaviour and phylogenetic range of the gene sequences; the availability of complete genomes makes it easier to establish new MLSA schemes. The amplicon of each gene needs to be based on accurate sequence information from both strands hence high-quality sequencing chromatograms are at a premium. In data analysis, definitive identification of vari- ation is obtained by nucleotide sequence determination of gene fragments, with no weight given to the number of nucleotide differences between alleles when assigning 2 Multi-Locus Sequence Analysis 223 sequence types (STs), as it is not possible to determine whether differences at mul- tiple nucleotide sites are due to multiple point mutations or to single recombination events (Maiden, 2006). Finally, relatedness between strains in MLSA is obtained by comparing concatenated sequences or allelic profiles (also STs). Those undertaking population genetics or phylogenetic adaptation studies may compare expanded can- didate functional gene sequences (Tankouo-Sandjong et al., 2007; Parker, Havird, & De La Fuente, 2012; Stefanic et al., 2012). 2.2 SELECTION OF GENE LOCI The housekeeping genes selected for MLSA analyses should be single copies, ortho- logous and ubiquitous among all of the sampled strains. They should also be highly conserved, have no linkage disequilibrium on the chromosome but should contain sufficient varying nucleotide positions to accurately establish relationships between closely related strains. To strike a balance among acceptable identification power, time and cost for strain typing, about five to seven housekeeping genes are com- monly used. The five housekeeping genes that we have used in our Streptomyces MLSA scheme are atpD (ATP synthase F1, b-subunit), gyrB (DNA gyrase, B subunit), recA (recombinase A), rpoB (RNA polymerase, b-subunit) and trpB (tryptophan synthase, b-subunit); the physical distance between any two of these genes is greater than 30 kb in a single Streptomyces genome, thereby avoiding hitchhiking effects (Guo, Zheng, Rong, & Huang, 2008; Rong & Huang, 2012). However, it is not uncommon to use up to 10 housekeeping genes, as exemplified in the case of the genus Nocardia where 14 protein-coding genes were examined (Tamura et al., 2012). Thus, both the number and type of housekeeping genes inter- rogated by MLSA may differ from genus to genus. 2.3 GENERATING SEQUENCES The PCR is commonly used to generate sequence fragments. Conserved profiles of protein-coding genes provide highly conserved islands that can be used to design am- plification and sequencing primers that have broad specificity with respect to phy- logenetic diversity. Commonly used primer design tools include Primer Premier (Premier Biosoft International) and OLIGO Primer Analysis software (Molecular Biology Insights), web tools such as Primer3 (http://biotools.umassmed.edu/bioapps/ primer3_www.cgi)andBLAST(http://www.ncbi.nlm.nih.gov/tools/primer-blast/)for finding primers specific to PCR templates. DANMAN software (Molecular Biology Insights) can be used to evaluate the resultant primers, e.g. by checking the minimum free energy of the primer structure and if dimers (including self- and cross-dimers), hairpin and GC clamps exist. It is essential that dimers are situated well away from the 30 ends of the primers and continuous cross-dimers between the forward and reverse primers are to be avoided. The genes and primers used in our streptomycete MLSA scheme are shown in Table 1. The suggested primer set for each gene covers more than the 400 bp internal Table 1 Genes and Primers Used in the Streptomyces MLSA Scheme Chromosomal Gene Function Direction Primer Sequence (50–30)a Positionb Locationb atpD Amplification F atpDPF-GTCGGCGACTTCACCAAGGGCAAGGTGTTC 283–318 5842699-5844135 AACACC R atpDPR-GTGAACTGCTTGGCGACGTGGGTGTTCTGG 1243–1280 GACAGGAA Sequencing F atpDF-ACCAAGGGCAAGGTGTTCAA 295–314 R atpDR-GCCGGGTAGATGCCCTTCTC 1027–1046 gyrB Amplification F gyrBPFA-CTCGAGGGTCTGGACGCGGTCCGCAAGCGA 121–161 c4265438-4263378 CCCGGTATGTA R gyrBPRA-GAAGGTCTTCACCTCGGTGTTGCCCAGCTT 1150–1185 CGTCTT Sequencing F gyrBFA-GCAAGCGACCCGGTATGTAC 143–162 R gyrBRA-GAGGTTGTCGTCCTTCTCGC 1052–1071 recA Amplification* F recAPFA-GABSCCGCDCTCGCNCAGATYGARCG 31–56 6306654-6307778 R recAPRA-GGAAGTTGCGSGCGTTCTCCTTGC 902–925 Sequencing F recAF-ACAGATTGAACGGCAATTCG
Load more

Recommended publications
  • Estimation of Antimicrobial Activities and Fatty Acid Composition Of
    Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia Irina V. Voytsekhovskaya1,*, Denis V. Axenov-Gribanov1,2,*, Svetlana A. Murzina3, Svetlana N. Pekkoeva3, Eugeniy S. Protasov1, Stanislav V. Gamaiunov2 and Maxim A. Timofeyev1 1 Irkutsk State University, Irkutsk, Russia 2 Baikal Research Centre, Irkutsk, Russia 3 Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, Petrozavodsk, Karelia, Russia * These authors contributed equally to this work. ABSTRACT Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Acti- nobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against Submitted 23 May 2018 bacteria and fungi. It was shown that representatives of the genera Nocardia and Accepted 24 September 2018 Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic Published 25 October 2018 properties. However, despite the lack of antimicrobial and fungicidal activity of Corresponding author Nocardia extracts, those strains are specific in terms of their fatty acid spectrum.
    [Show full text]
  • UNIVERSITY of CALIFORNIA, SAN DIEGO the Genus Salinispora As A
    UNIVERSITY OF CALIFORNIA, SAN DIEGO The genus Salinispora as a model organism for species concepts and natural products discovery A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Natalie Millán Aguiñaga Committee in charge: Paul R. Jensen, Chair Eric E. Allen William Fenical Joseph Pogliano Gregory W. Rouse 2016 Copyright Natalie Millán Aguiñaga, 2016 All rights reserved The dissertation of Natalie Millán Aguiñaga is approved, and it is acceptable in quality and form for publication on microfilm and electronically: __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ __________________________________________________________________ Chair University of California, San Diego 2016 iii DEDICATION To my parents Roberto and Yolanda. Thanks for sharing this dream come true and for continuing to support me in the dreams I still want to achieve. iv TABLE OF CONTENTS Signature Page ...................................................................................................... iii Dedication ............................................................................................................. iv Table of Contents ................................................................................................ v List of Figures .....................................................................................................
    [Show full text]
  • Genome Mining Coupled with OSMAC-Based Cultivation Reveal Differential Production of Surugamide a by the Marine Sponge Isolate Streptomyces Sp
    microorganisms Article Genome Mining Coupled with OSMAC-Based Cultivation Reveal Differential Production of Surugamide A by the Marine Sponge Isolate Streptomyces sp. SM17 When Compared to Its Terrestrial Relative S. albidoflavus J1074 Eduardo L. Almeida 1 , Navdeep Kaur 2, Laurence K. Jennings 2 , Andrés Felipe Carrillo Rincón 1, Stephen A. Jackson 1,3 , Olivier P. Thomas 2 and Alan D.W. Dobson 1,3,* 1 School of Microbiology, University College Cork, T12 YN60 Cork, Ireland; [email protected] (E.L.A.); [email protected] (A.F.C.R.); [email protected] (S.A.J.) 2 Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33 Galway, Ireland; [email protected] (N.K.); [email protected] (L.K.J.); [email protected] (O.P.T.) 3 Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland * Correspondence: [email protected] Received: 12 August 2019; Accepted: 24 September 2019; Published: 26 September 2019 Abstract: Much recent interest has arisen in investigating Streptomyces isolates derived from the marine environment in the search for new bioactive compounds, particularly those found in association with marine invertebrates, such as sponges. Among these new compounds recently identified from marine Streptomyces isolates are the octapeptidic surugamides, which have been shown to possess anticancer and antifungal activities. By employing genome mining followed by an one strain many compounds (OSMAC)-based approach, we have identified the previously unreported capability of a marine sponge-derived isolate, namely Streptomyces sp. SM17, to produce surugamide A.
    [Show full text]
  • Schneider-Dissertation-2019
    Biosynthetic Investigation, Synthesis, and Bioactivity Evaluation of Putative Peptide Aldehyde Natural Products From the Human Gut Microbiota The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Schneider, Benjamin Aaron. 2019. Biosynthetic Investigation, Synthesis, and Bioactivity Evaluation of Putative Peptide Aldehyde Natural Products From the Human Gut Microbiota. Doctoral dissertation, Harvard University, Graduate School of Arts & Sciences. Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:42029686 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use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
    [Show full text]
  • Deanship of Graduate Studies Al-Quds University Antimicrobial
    Deanship of Graduate Studies Al-Quds University Antimicrobial activity of a Number of Streptomyces species Ibtehal Mahmoud Rabie Ayyad M.Sc. Thesis Jerusalem - Palestine 1437 -2016 Antimicrobial activity of a Number of Streptomyces species Prepared by: Ibtehal Mahmoud Rabie Ayyad B.Sc Degree in Biology from Alquds University palestine Supervisor: Dr. Sameer A. Barghouthi A thesis submitted in partial fulfillment of requirements for the degree of Master of Medical Laboratory Sciences Department of Medical Laboratory Sciences / Al-Quds University . 1437 – 2016 Deanship of Graduate Studies Al-Quds University Medical Laboratory Science Thesis Approval Antimicrobial activity of a Number of Streptomyces species Prepared by: Ibtehal Mahmoud Rabie Ayyad Registration No: 20913376 Supervisor: Dr. Sameer A. Barghouthi Master Thesis Submission and acceptance date: 17/5/2016. The names and signatures of examining committee members are as Follows: 1. Head of committee Dr. Sameer A. Barghouthi 2. The internal examiner Dr. Ibrahim Abassi 3. The external examiner Dr. Robin Abu Ghazaleh Jerusalem – Palestine 1437- 2016 Dedication: I dedicate my work to those dearest to me. To my husband, who faced a great deal of time and difficulties for the sake of my success, Ahmad I could not have done it without your support. To my lovely daughters Zeinab, Jana and ro’aa. And finally to my precious family and friends. Ibtehal Mahmoud Rabie Ayyad. i Acknowledgments I offer my deepest feelings of gratitude and acknowledgment to my supervisor Dr. Sameer A. Barghouthi for his sincere efforts in my training, supervision, and guidance. The study was conducted in the research lab of the faculty of health professions in Al-Quds University.
    [Show full text]
  • Contributions of Ancestral Inter-Species Recombination to the Genetic Diversity of Extant Streptomyces Lineages
    The ISME Journal (2016) 10, 1731–1741 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 www.nature.com/ismej ORIGINAL ARTICLE Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages Cheryl P Andam, Mallory J Choudoir, Anh Vinh Nguyen, Han Sol Park and Daniel H Buckley Soil and Crop Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY USA Streptomyces species produce many important antibiotics and have a crucial role in soil nutrient cycling. However, their evolutionary history remains poorly characterized. We have evaluated the impact of homologous recombination on the evolution of Streptomyces using multi-locus sequence analysis of 234 strains that represent at least 11 species clusters. Evidence of inter-species recombination is widespread but not uniform within the genus and levels of mosaicism vary between species clusters. Most phylogenetically incongruent loci are monophyletic at the scale of species clusters and their subclades, suggesting that these recombination events occurred in shared ancestral lineages. Further investigation of two mosaic species clusters suggests that genes acquired by inter-species recombination may have become fixed in these lineages during periods of demographic expansion; implicating a role for phylogeography in determining contemporary patterns of genetic diversity. Only by examining the phylogeny at the scale of the genus is apparent that widespread phylogenetically incongruent loci in Streptomyces are derived from a far smaller number of ancestral inter-species recombination events. The ISME Journal (2016) 10, 1731–1741; doi:10.1038/ismej.2015.230; published online 9 February 2016 Introduction 2009; Caro-Quintero and Konstantinidis, 2012; Segerman, 2012).
    [Show full text]
  • 7E232d5e0e3a6c39f74394138a
    Journal of Antibiotics Research Volume 1 | Issue 1 ISSN: 2574-5980 Research Article Open Access Isolation, Identification, and Characterization of the Novel Antibacterial Agent Methoxyphenyl-Oxime from Streptomyces pratensis QUBC97 Isolate Barghouthi SA*1, Ayyad I1, Ayesh M1, and Abu-Lafi S2 1Medical Laboratory Sciences, Faculty of Health Professions, Jerusalem, Palestine 2Faculty of Pharmacy, Al-Quds University, Jerusalem, Palestine *Corresponding author: Barghouthi SA, Medical Laboratory Sciences, Faculty of Health Professions, Jerusalem, Palestine, Fax: +972-2-2791234, Tel: +972-599-379561, E-mail: [email protected] Citation: Barghouthi SA, Ayyad I, Ayesh M, Abu-Lafi S (2017) Isolation, Identification, and Characteriza- tion of the Novel Antibacterial Agent Methoxyphenyl-Oxime from Streptomyces pratensis QUBC97 Isolate. J Antibio Res 1(1): 105. doi: 10.15744/2574-5980.1.105 Received Date: January 11, 2017 Accepted Date: February 28, 2017 Published Date: March 03, 2017 Abstract Introduction: Streptomyces species are medically, industrially, and microbiologically important bacteria that are found in soils and other habitats. Methods: Streptomyces isolates and QUBC97 were cultured on a new medium (CCG). Agar plug diffusion test showed antibacterial activity. N-butanol extracts analysed by silica thin layer chromatography (TLC), HPLC purified, and identified by MS analysis. QUBC97 was identified based on morphology, PCR, and DNA sequencing of two loci. Results: CCG medium allowed Streptomyces isolation, growth, and antibacterial agent production. QUBC97 was identified as Streptomyces pratensis. In CCG broth, it produced two distinguishable antibacterial compounds; a one-week fresh compound (FCm) or a 6-week old compound (OCm). Agar cultures showed a mixture of both compounds. Split peak absorptions (426/442 nm) was observed for FCm and (428/442 nm) for OCm.
    [Show full text]
  • Atmospheric Precipitations, Hailstone and Rainwater, As a Novel Source of Streptomyces Producing Bioactive Natural Products
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Repositorio Institucional de la Universidad de Oviedo ORIGINAL RESEARCH published: 23 April 2018 doi: 10.3389/fmicb.2018.00773 Atmospheric Precipitations, Hailstone and Rainwater, as a Novel Source of Streptomyces Producing Bioactive Natural Products Aida Sarmiento-Vizcaíno 1, Julia Espadas 1, Jesús Martín 2, Alfredo F. Braña 1, Fernando Reyes 2, Luis A. García 3 and Gloria Blanco 1* 1 Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain, 2 Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Granada, Spain, 3 Departamento de Ingeniería Química y Tecnología del Medio Ambiente, Área de Ingeniería Química, Universidad de Oviedo, Oviedo, Spain A cultivation-dependent approach revealed that highly diverse populations of Streptomyces were present in atmospheric precipitations from a hailstorm event sampled in February 2016 in the Cantabrian Sea coast, North of Spain. A total of 29 bioactive Streptomyces strains isolated from small samples of hailstone and rainwater, collected Edited by: Pierre Amato, from this hailstorm event, were studied here. Taxonomic identification by 16S rRNA UMR6296 Institut de Chimie de sequencing revealed more than 20 different Streptomyces species, with their closest Clermont-Ferrand, France homologs displaying mainly oceanic but also terrestrial origins. Backward trajectory Reviewed by: analysis revealed that the air-mass sources of the hailstorm event, with North Western Atsuko Matsumoto, Kitasato University, Japan winds, were originated in the Arctic Ocean (West Greenland and North Iceland) and Learn-Han Lee, Canada (Labrador), depending on the altitude.
    [Show full text]
  • Intraspecies Comparison of Streptomyces Pratensis Genomes
    Doroghazi and Buckley BMC Genomics 2014, 15:970 http://www.biomedcentral.com/1471-2164/15/970 RESEARCH ARTICLE Open Access Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin James R Doroghazi1 and Daniel H Buckley2* Abstract Background: Streptomyces are widespread bacteria that contribute to the terrestrial carbon cycle and produce the majority of clinically useful antibiotics. While interspecific genomic diversity has been investigated among Streptomyces, information is lacking on intraspecific genomic diversity. Streptomyces pratensis has high rates of homologous recombination but the impact of such gene exchange on genome evolution and the evolution of natural product gene clusters remains uncharacterized. Results: We report draft genome sequences of four S. pratensis strains and compare to the complete genome of Streptomyces flavogriseus IAF-45-CD (=ATCC 33331), a strain recently reclassified to S. pratensis. Despite disparate geographic origins, the genomes are highly similar with 85.9% of genes present in the core genome and conservation of all natural product gene clusters. Natural products include a novel combination of carbapenem and beta-lactamase inhibitor gene clusters. While high intraspecies recombination rates abolish the phylogenetic signal across the genome, intraspecies recombination is suppressed in two genomic regions. The first region is centered on an insertion/deletion polymorphism and the second on a hybrid NRPS-PKS gene. Finally, two gene families accounted for over 25% of the divergent genes in the core genome. The first includes homologs of bldB (required for spore development and antibiotic production) while the second includes homologs of an uncharacterized protein with a helix-turn-helix motif (hpb).
    [Show full text]
  • Insights Into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea Against ESKAPE and Ovarian Cancer
    marine drugs Article Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer Edna M. Sabido 1 , Chuckcris P. Tenebro 2 , Dana Joanne Von L. Trono 2 , Carmela Vannette B. Vicera 2 , Sheeny Fane L. Leonida 1, Jose Jeffrey Wayne B. Maybay 1 , Rikka Reyes-Salarda 2,3 , Diana S. Amago 1 , Angelica Marie V. Aguadera 1 , May C. Octaviano 1, Jonel P. Saludes 1,4,5,6,* and Doralyn S. Dalisay 2,3,5,6,* 1 Center for Natural Drug Discovery and Development (CND3), University of San Agustin, Iloilo City 5000, Philippines; [email protected] (E.M.S.); sfl[email protected] (S.F.L.L.); [email protected] (J.J.W.B.M.); [email protected] (D.S.A.); [email protected] (A.M.V.A.); [email protected] (M.C.O.) 2 Center for Chemical Biology and Biotechnology (C2B2), University of San Agustin, Iloilo City 5000, Philippines; [email protected] (C.P.T.); [email protected] (D.J.V.L.T.); [email protected] (C.V.B.V.); [email protected] (R.R.-S.) 3 Department of Biology, College of Liberal Arts, Sciences, and Education, University of San Agustin, Iloilo City 5000, Philippines 4 Department of Chemistry, College of Liberal Arts, Sciences, and Education, University of San Agustin, Citation: Sabido, E.M.; Tenebro, C.P.; Iloilo City 5000, Philippines 5 Trono, D.J.V.L.; Vicera, C.V.B.; Tuklas Lunas Development Center, University of San Agustin, Iloilo City 5000, Philippines 6 Balik Scientist Program, Department of Science and Technology, Philippine Council for Health Research and Leonida, S.F.L.; Maybay, J.J.W.B.; Development (PCHRD), Bicutan, Taguig City 1631, Philippines Reyes-Salarda, R.; Amago, D.S.; * Correspondence: [email protected] (J.P.S.); [email protected] (D.S.D.); Aguadera, A.M.V.; Tel.: +63-33-503-6887 (J.P.S.); +63-33-501-0350 (D.S.D.) Octaviano, M.C.; et al.
    [Show full text]
  • Description of Unrecorded Bacterial Species Belonging to the Phylum Actinobacteria in Korea
    Journal of Species Research 10(1):23­45, 2021 Description of unrecorded bacterial species belonging to the phylum Actinobacteria in Korea Mi­Sun Kim1, Seung­Bum Kim2, Chang­Jun Cha3, Wan­Taek Im4, Won­Yong Kim5, Myung­Kyum Kim6, Che­Ok Jeon7, Hana Yi8, Jung­Hoon Yoon9, Hyung­Rak Kim10 and Chi­Nam Seong1,* 1Department of Biology, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology, Chungnam National University, Daejeon 34134, Republic of Korea 3Department of Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 4Department of Biotechnology, Hankyong National University, Anseong 17579, Republic of Korea 5Department of Microbiology, College of Medicine, Chung-Ang University, Seoul 06974, Republic of Korea 6Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, Seoul 01797, Republic of Korea 7Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea 8School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea 9Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon 16419, Republic of Korea 10Department of Laboratory Medicine, Saint Garlo Medical Center, Suncheon 57931, Republic of Korea *Correspondent: [email protected] For the collection of indigenous prokaryotic species in Korea, 77 strains within the phylum Actinobacteria were isolated from various environmental samples, fermented foods, animals and clinical specimens in 2019. Each strain showed high 16S rRNA gene sequence similarity (>98.8%) and formed a robust phylogenetic clade with actinobacterial species that were already defined and validated with nomenclature. There is no official description of these 77 bacterial species in Korea.
    [Show full text]
  • Antibiotic Activity of Actinobacteria from the Digestive Tract of Millipede Nedyopus Dawydoffiae (Diplopoda)
    antibiotics Article Antibiotic Activity of Actinobacteria from the Digestive Tract of Millipede Nedyopus dawydoffiae (Diplopoda) Alla A. Glukhova 1, Anna A. Karabanova 1,2, Andrey V. Yakushev 2, Irina I. Semenyuk 3,4, Yuliya V. Boykova 1, Natalia D. Malkina 1, Tatiana A. Efimenko 1 , Tatiana D. Ivankova 1, Larissa P. Terekhova 1 and Olga V. Efremenkova 1,* 1 Gause Institute of New Antibiotics, 119021 Moscow, Russia; [email protected] (A.A.G.); [email protected] (A.A.K.); [email protected] (Y.V.B.); [email protected] (N.D.M.); efi[email protected] (T.A.E.); [email protected] (T.D.I.); [email protected] (L.P.T.) 2 Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia; [email protected] 3 A.N. Severtsova Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; [email protected] 4 Joint Russian-Vietnamese Tropical Center, Ho Chi Minh City, Vietnam * Correspondence: [email protected]; Tel.: +7-916-596-9618 Received: 10 September 2018; Accepted: 24 October 2018; Published: 29 October 2018 Abstract: Because of the spread of drug resistance, it is necessary to look for new antibiotics that are effective against pathogenic microorganisms. The purpose of this study was to analyse the species composition of actinobacteria isolated from the digestive tract of the millipedes Nedyopus dawydoffiae and to determine their antimicrobial properties. Species identification was carried out on the basis of the morphological and culture properties and the sequence of the 16S rRNA gene. Actinobacteria were grown in different liquid media. Antibiotic properties were determined against some Gram-positive and Gram-negative bacteria as well as fungi.
    [Show full text]