Literature DB >> 24476823

An environmental bacterial taxon with a large and distinct metabolic repertoire.

Micheal C Wilson1, Tetsushi Mori2, Christian Rückert3, Agustinus R Uria4, Maximilian J Helf4, Kentaro Takada5, Christine Gernert6, Ursula A E Steffens7, Nina Heycke7, Susanne Schmitt8, Christian Rinke9, Eric J N Helfrich4, Alexander O Brachmann10, Cristian Gurgui7, Toshiyuki Wakimoto11, Matthias Kracht7, Max Crüsemann7, Ute Hentschel6, Ikuro Abe11, Shigeki Matsunaga5, Jörn Kalinowski3, Haruko Takeyama12, Jörn Piel4.   

Abstract

Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such 'talented' producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus 'Entotheonella' with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. 'Entotheonella' spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum 'Tectomicrobia'. The pronounced bioactivities and chemical uniqueness of 'Entotheonella' compounds provide significant opportunities for ecological studies and drug discovery.

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Year:  2014        PMID: 24476823     DOI: 10.1038/nature12959

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  61 in total

1.  ARB: a software environment for sequence data.

Authors:  Wolfgang Ludwig; Oliver Strunk; Ralf Westram; Lothar Richter; Harald Meier; Arno Buchner; Tina Lai; Susanne Steppi; Gangolf Jobb; Wolfram Förster; Igor Brettske; Stefan Gerber; Anton W Ginhart; Oliver Gross; Silke Grumann; Stefan Hermann; Ralf Jost; Andreas König; Thomas Liss; Ralph Lüssmann; Michael May; Björn Nonhoff; Boris Reichel; Robert Strehlow; Alexandros Stamatakis; Norbert Stuckmann; Alexander Vilbig; Michael Lenke; Thomas Ludwig; Arndt Bode; Karl-Heinz Schleifer
Journal:  Nucleic Acids Res       Date:  2004-02-25       Impact factor: 16.971

Review 2.  Bioactive microbial metabolites.

Authors:  János Bérdy
Journal:  J Antibiot (Tokyo)       Date:  2005-01       Impact factor: 2.649

3.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.

Authors:  Alexandros Stamatakis
Journal:  Bioinformatics       Date:  2006-08-23       Impact factor: 6.937

Review 4.  Compartmentalized function through cell differentiation in filamentous cyanobacteria.

Authors:  Enrique Flores; Antonia Herrero
Journal:  Nat Rev Microbiol       Date:  2010-01       Impact factor: 60.633

5.  FastTree 2--approximately maximum-likelihood trees for large alignments.

Authors:  Morgan N Price; Paramvir S Dehal; Adam P Arkin
Journal:  PLoS One       Date:  2010-03-10       Impact factor: 3.240

6.  Insights into the biosynthesis of hormaomycin, an exceptionally complex bacterial signaling metabolite.

Authors:  Ivonne Höfer; Max Crüsemann; Markus Radzom; Bernadette Geers; Daniel Flachshaar; Xiaofeng Cai; Axel Zeeck; Jörn Piel
Journal:  Chem Biol       Date:  2011-03-25

7.  Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting.

Authors:  Katja M Fisch; Cristian Gurgui; Nina Heycke; Sonia A van der Sar; Sally A Anderson; Victoria L Webb; Stefan Taudien; Matthias Platzer; Brent K Rubio; Sarah J Robinson; Phillip Crews; Jörn Piel
Journal:  Nat Chem Biol       Date:  2009-07       Impact factor: 15.040

8.  Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage.

Authors:  Rashel V Grindberg; Thomas Ishoey; Dumitru Brinza; Eduardo Esquenazi; R Cameron Coates; Wei-ting Liu; Lena Gerwick; Pieter C Dorrestein; Pavel Pevzner; Roger Lasken; William H Gerwick
Journal:  PLoS One       Date:  2011-04-12       Impact factor: 3.240

9.  SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

Authors:  Elmar Pruesse; Jörg Peplies; Frank Oliver Glöckner
Journal:  Bioinformatics       Date:  2012-05-03       Impact factor: 6.937

10.  r2cat: synteny plots and comparative assembly.

Authors:  Peter Husemann; Jens Stoye
Journal:  Bioinformatics       Date:  2009-12-16       Impact factor: 6.937

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  199 in total

Review 1.  Leveraging ecological theory to guide natural product discovery.

Authors:  Michael J Smanski; Daniel C Schlatter; Linda L Kinkel
Journal:  J Ind Microbiol Biotechnol       Date:  2015-10-05       Impact factor: 3.346

Review 2.  Culture-independent discovery of natural products from soil metagenomes.

Authors:  Micah Katz; Bradley M Hover; Sean F Brady
Journal:  J Ind Microbiol Biotechnol       Date:  2015-11-19       Impact factor: 3.346

Review 3.  Antibacterial drug discovery in the resistance era.

Authors:  Eric D Brown; Gerard D Wright
Journal:  Nature       Date:  2016-01-21       Impact factor: 49.962

4.  Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome.

Authors:  Eric J N Helfrich; Christine M Vogel; Reiko Ueoka; Martin Schäfer; Florian Ryffel; Daniel B Müller; Silke Probst; Markus Kreuzer; Jörn Piel; Julia A Vorholt
Journal:  Nat Microbiol       Date:  2018-07-23       Impact factor: 17.745

Review 5.  Cyclic azole-homologated peptides from Marine sponges.

Authors:  Tadeusz F Molinski
Journal:  Org Biomol Chem       Date:  2017-12-19       Impact factor: 3.876

6.  Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.

Authors:  Cintia P J Rua; Louisi S de Oliveira; Adriana Froes; Diogo A Tschoeke; Ana Carolina Soares; Luciana Leomil; Gustavo B Gregoracci; Ricardo Coutinho; Eduardo Hajdu; Cristiane C Thompson; Roberto G S Berlinck; Fabiano L Thompson
Journal:  Microb Ecol       Date:  2018-03-15       Impact factor: 4.552

Review 7.  Toward Accurate and Quantitative Comparative Metagenomics.

Authors:  Stephen Nayfach; Katherine S Pollard
Journal:  Cell       Date:  2016-08-25       Impact factor: 41.582

Review 8.  Recent advances in genomic DNA sequencing of microbial species from single cells.

Authors:  Roger S Lasken; Jeffrey S McLean
Journal:  Nat Rev Genet       Date:  2014-08-05       Impact factor: 53.242

9.  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

10.  Computational approaches to natural product discovery.

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

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