Literature DB >> 25000402

Metagenomic small molecule discovery methods.

Zachary Charlop-Powers1, Aleksandr Milshteyn1, Sean F Brady2.   

Abstract

Metagenomic approaches to natural product discovery provide the means to harvest bioactive small molecules synthesized by environmental bacteria without the requirement of first culturing these organisms. Advances in sequencing technologies and general metagenomic methods are beginning to provide the tools necessary to unlock the unexplored biosynthetic potential encoded by the genomes of uncultured environmental bacteria. Here, we highlight recent advances in sequence-based and functional-based metagenomic approaches that promise to facilitate antibiotic discovery from diverse environmental microbiomes.
Copyright © 2014 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 25000402      PMCID: PMC4135586          DOI: 10.1016/j.mib.2014.05.021

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN: 1369-5274            Impact factor:   7.934


  70 in total

1.  Expression and isolation of antimicrobial small molecules from soil DNA libraries.

Authors:  I A MacNeil; C L Tiong; C Minor; P R August; T H Grossman; K A Loiacono; B A Lynch; T Phillips; S Narula; R Sundaramoorthi; A Tyler; T Aldredge; H Long; M Gilman; D Holt; M S Osburne
Journal:  J Mol Microbiol Biotechnol       Date:  2001-04

2.  Fluorescence in situ hybridization-flow cytometry-cell sorting-based method for separation and enrichment of type I and type II methanotroph populations.

Authors:  Marina G Kalyuzhnaya; Rebecca Zabinsky; Sarah Bowerman; David R Baker; Mary E Lidstrom; Ludmila Chistoserdova
Journal:  Appl Environ Microbiol       Date:  2006-06       Impact factor: 4.792

3.  Pederin-type pathways of uncultivated bacterial symbionts: analysis of o-methyltransferases and generation of a biosynthetic hybrid.

Authors:  Katrin Zimmermann; Marianne Engeser; John W Blunt; Murray H G Munro; Jörn Piel
Journal:  J Am Chem Soc       Date:  2009-03-04       Impact factor: 15.419

4.  Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules.

Authors:  Joel Pel; David Broemeling; Laura Mai; Hau-Ling Poon; Giorgia Tropini; René L Warren; Robert A Holt; Andre Marziali
Journal:  Proc Natl Acad Sci U S A       Date:  2009-08-17       Impact factor: 11.205

5.  Deep sequencing of non-ribosomal peptide synthetases and polyketide synthases from the microbiomes of Australian marine sponges.

Authors:  Jason N Woodhouse; Lu Fan; Mark V Brown; Torsten Thomas; Brett A Neilan
Journal:  ISME J       Date:  2013-04-18       Impact factor: 10.302

6.  Exploiting the natural diversity of microviridin gene clusters for discovery of novel tricyclic depsipeptides.

Authors:  Nadine Ziemert; Keishi Ishida; Annika Weiz; Christian Hertweck; Elke Dittmann
Journal:  Appl Environ Microbiol       Date:  2010-04-02       Impact factor: 4.792

7.  Analysis of the integration function of the streptomycete bacteriophage phi C31.

Authors:  S Kuhstoss; R N Rao
Journal:  J Mol Biol       Date:  1991-12-20       Impact factor: 5.469

8.  A global assembly line for cyanobactins.

Authors:  Mohamed S Donia; Jacques Ravel; Eric W Schmidt
Journal:  Nat Chem Biol       Date:  2008-04-20       Impact factor: 15.040

9.  Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening.

Authors:  Fang-Yuan Chang; Sean F Brady
Journal:  Proc Natl Acad Sci U S A       Date:  2013-01-09       Impact factor: 11.205

10.  Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules.

Authors:  Sean F Brady
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

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  31 in total

Review 1.  Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and other actinomycetes.

Authors:  Richard H Baltz
Journal:  J Ind Microbiol Biotechnol       Date:  2015-09-12       Impact factor: 3.346

Review 2.  Natural product discovery from the human microbiome.

Authors:  Matthew R Wilson; Li Zha; Emily P Balskus
Journal:  J Biol Chem       Date:  2017-04-07       Impact factor: 5.157

3.  Endless Resistance. Endless Antibiotics?

Authors:  Jed F Fisher; Shahriar Mobashery
Journal:  Medchemcomm       Date:  2015-11-03       Impact factor: 3.597

4.  Actinoramide A Identified as a Potent Antimalarial from Titration-Based Screening of Marine Natural Product Extracts.

Authors:  Ken Chih-Chien Cheng; Shugeng Cao; Avi Raveh; Ryan MacArthur; Patricia Dranchak; George Chlipala; Matthew T Okoneski; Rajarshi Guha; Richard T Eastman; Jing Yuan; Pamela J Schultz; Xin-Zhuan Su; Giselle Tamayo-Castillo; Teatulohi Matainaho; Jon Clardy; David H Sherman; James Inglese
Journal:  J Nat Prod       Date:  2015-10-14       Impact factor: 4.050

5.  Unique amalgamation of primary and secondary structural elements transform peptaibols into potent bioactive cell-penetrating peptides.

Authors:  Lin Du; April L Risinger; Carter A Mitchell; Jianlan You; Blake W Stamps; Ning Pan; Jarrod B King; Jean C Bopassa; Susan I V Judge; Zhibo Yang; Bradley S Stevenson; Robert H Cichewicz
Journal:  Proc Natl Acad Sci U S A       Date:  2017-10-10       Impact factor: 11.205

6.  Reinvigorating natural product combinatorial biosynthesis with synthetic biology.

Authors:  Eunji Kim; Bradley S Moore; Yeo Joon Yoon
Journal:  Nat Chem Biol       Date:  2015-09       Impact factor: 15.040

7.  Minimum Information about a Biosynthetic Gene cluster.

Authors:  Marnix H Medema; Renzo Kottmann; Pelin Yilmaz; Matthew Cummings; John B Biggins; Kai Blin; Irene de Bruijn; Yit Heng Chooi; Jan Claesen; R Cameron Coates; Pablo Cruz-Morales; Srikanth Duddela; Stephanie Düsterhus; Daniel J Edwards; David P Fewer; Neha Garg; Christoph Geiger; Juan Pablo Gomez-Escribano; Anja Greule; Michalis Hadjithomas; Anthony S Haines; Eric J N Helfrich; Matthew L Hillwig; Keishi Ishida; Adam C Jones; Carla S Jones; Katrin Jungmann; Carsten Kegler; Hyun Uk Kim; Peter Kötter; Daniel Krug; Joleen Masschelein; Alexey V Melnik; Simone M Mantovani; Emily A Monroe; Marcus Moore; Nathan Moss; Hans-Wilhelm Nützmann; Guohui Pan; Amrita Pati; Daniel Petras; F Jerry Reen; Federico Rosconi; Zhe Rui; Zhenhua Tian; Nicholas J Tobias; Yuta Tsunematsu; Philipp Wiemann; Elizabeth Wyckoff; Xiaohui Yan; Grace Yim; Fengan Yu; Yunchang Xie; Bertrand Aigle; Alexander K Apel; Carl J Balibar; Emily P Balskus; Francisco Barona-Gómez; Andreas Bechthold; Helge B Bode; Rainer Borriss; Sean F Brady; Axel A Brakhage; Patrick Caffrey; Yi-Qiang Cheng; Jon Clardy; Russell J Cox; René De Mot; Stefano Donadio; Mohamed S Donia; Wilfred A van der Donk; Pieter C Dorrestein; Sean Doyle; Arnold J M Driessen; Monika Ehling-Schulz; Karl-Dieter Entian; Michael A Fischbach; Lena Gerwick; William H Gerwick; Harald Gross; Bertolt Gust; Christian Hertweck; Monica Höfte; Susan E Jensen; Jianhua Ju; Leonard Katz; Leonard Kaysser; Jonathan L Klassen; Nancy P Keller; Jan Kormanec; Oscar P Kuipers; Tomohisa Kuzuyama; Nikos C Kyrpides; Hyung-Jin Kwon; Sylvie Lautru; Rob Lavigne; Chia Y Lee; Bai Linquan; Xinyu Liu; Wen Liu; Andriy Luzhetskyy; Taifo Mahmud; Yvonne Mast; Carmen Méndez; Mikko Metsä-Ketelä; Jason Micklefield; Douglas A Mitchell; Bradley S Moore; Leonilde M Moreira; Rolf Müller; Brett A Neilan; Markus Nett; Jens Nielsen; Fergal O'Gara; Hideaki Oikawa; Anne Osbourn; Marcia S Osburne; Bohdan Ostash; Shelley M Payne; Jean-Luc Pernodet; Miroslav Petricek; Jörn Piel; Olivier Ploux; Jos M Raaijmakers; José A Salas; Esther K Schmitt; Barry Scott; Ryan F Seipke; Ben Shen; David H Sherman; Kaarina Sivonen; Michael J Smanski; Margherita Sosio; Evi Stegmann; Roderich D Süssmuth; Kapil Tahlan; Christopher M Thomas; Yi Tang; Andrew W Truman; Muriel Viaud; Jonathan D Walton; Christopher T Walsh; Tilmann Weber; Gilles P van Wezel; Barrie Wilkinson; Joanne M Willey; Wolfgang Wohlleben; Gerard D Wright; Nadine Ziemert; Changsheng Zhang; Sergey B Zotchev; Rainer Breitling; Eriko Takano; Frank Oliver Glöckner
Journal:  Nat Chem Biol       Date:  2015-09       Impact factor: 15.040

8.  Computational approaches to natural product discovery.

Authors:  Marnix H Medema; Michael A Fischbach
Journal:  Nat Chem Biol       Date:  2015-09       Impact factor: 15.040

9.  Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist.

Authors:  Louis J Cohen; Hahk-Soo Kang; John Chu; Yun-Han Huang; Emma A Gordon; Boojala Vijay B Reddy; Melinda A Ternei; Jeffrey W Craig; Sean F Brady
Journal:  Proc Natl Acad Sci U S A       Date:  2015-08-17       Impact factor: 11.205

10.  Synthetic-Bioinformatic Natural Product Antibiotics with Diverse Modes of Action.

Authors:  John Chu; Bimal Koirala; Nicholas Forelli; Xavier Vila-Farres; Melinda A Ternei; Thahmina Ali; Dominic A Colosimo; Sean F Brady
Journal:  J Am Chem Soc       Date:  2020-08-11       Impact factor: 15.419

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