Literature DB >> 24141494

Metagenomic species profiling using universal phylogenetic marker genes.

Shinichi Sunagawa1, Daniel R Mende, Georg Zeller, Fernando Izquierdo-Carrasco, Simon A Berger, Jens Roat Kultima, Luis Pedro Coelho, Manimozhiyan Arumugam, Julien Tap, Henrik Bjørn Nielsen, Simon Rasmussen, Søren Brunak, Oluf Pedersen, Francisco Guarner, Willem M de Vos, Jun Wang, Junhua Li, Joël Doré, S Dusko Ehrlich, Alexandros Stamatakis, Peer Bork.   

Abstract

To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

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Year:  2013        PMID： 24141494     DOI： 10.1038/nmeth.2693

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  33 in total

1.  Highlighting new phylogenetic specificities of Crohn's disease microbiota.

Authors:  S Mondot; S Kang; J P Furet; D Aguirre de Carcer; C McSweeney; M Morrison; P Marteau; J Doré; M Leclerc
Journal:  Inflamm Bowel Dis       Date:  2010-08-18       Impact factor: 5.325

2.  Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria.

Authors:  Chin Wen Png; Sara K Lindén; Kristen S Gilshenan; Erwin G Zoetendal; Chris S McSweeney; Lindsay I Sly; Michael A McGuckin; Timothy H J Florin
Journal:  Am J Gastroenterol       Date:  2010-07-20       Impact factor: 10.864

3.  Quantitative phylogenetic assessment of microbial communities in diverse environments.

Authors:  C von Mering; P Hugenholtz; J Raes; S G Tringe; T Doerks; L J Jensen; N Ward; P Bork
Journal:  Science       Date:  2007-02-01       Impact factor: 47.728

4.  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

5.  Aligning short reads to reference alignments and trees.

Authors:  Simon A Berger; Alexandros Stamatakis
Journal:  Bioinformatics       Date:  2011-06-02       Impact factor: 6.937

6.  Dominant and diet-responsive groups of bacteria within the human colonic microbiota.

Authors:  Alan W Walker; Jennifer Ince; Sylvia H Duncan; Lucy M Webster; Grietje Holtrop; Xiaolei Ze; David Brown; Mark D Stares; Paul Scott; Aurore Bergerat; Petra Louis; Freda McIntosh; Alexandra M Johnstone; Gerald E Lobley; Julian Parkhill; Harry J Flint
Journal:  ISME J       Date:  2010-08-05       Impact factor: 10.302

7.  A metagenome-wide association study of gut microbiota in type 2 diabetes.

Authors:  Junjie Qin; Yingrui Li; Zhiming Cai; Shenghui Li; Jianfeng Zhu; Fan Zhang; Suisha Liang; Wenwei Zhang; Yuanlin Guan; Dongqian Shen; Yangqing Peng; Dongya Zhang; Zhuye Jie; Wenxian Wu; Youwen Qin; Wenbin Xue; Junhua Li; Lingchuan Han; Donghui Lu; Peixian Wu; Yali Dai; Xiaojuan Sun; Zesong Li; Aifa Tang; Shilong Zhong; Xiaoping Li; Weineng Chen; Ran Xu; Mingbang Wang; Qiang Feng; Meihua Gong; Jing Yu; Yanyan Zhang; Ming Zhang; Torben Hansen; Gaston Sanchez; Jeroen Raes; Gwen Falony; Shujiro Okuda; Mathieu Almeida; Emmanuelle LeChatelier; Pierre Renault; Nicolas Pons; Jean-Michel Batto; Zhaoxi Zhang; Hua Chen; Ruifu Yang; Weimou Zheng; Songgang Li; Huanming Yang; Jian Wang; S Dusko Ehrlich; Rasmus Nielsen; Oluf Pedersen; Karsten Kristiansen; Jun Wang
Journal:  Nature       Date:  2012-09-26       Impact factor: 49.962

8.  Enterotypes of the human gut microbiome.

Authors:  Manimozhiyan Arumugam; Jeroen Raes; Eric Pelletier; Denis Le Paslier; Takuji Yamada; Daniel R Mende; Gabriel R Fernandes; Julien Tap; Thomas Bruls; Jean-Michel Batto; Marcelo Bertalan; Natalia Borruel; Francesc Casellas; Leyden Fernandez; Laurent Gautier; Torben Hansen; Masahira Hattori; Tetsuya Hayashi; Michiel Kleerebezem; Ken Kurokawa; Marion Leclerc; Florence Levenez; Chaysavanh Manichanh; H Bjørn Nielsen; Trine Nielsen; Nicolas Pons; Julie Poulain; Junjie Qin; Thomas Sicheritz-Ponten; Sebastian Tims; David Torrents; Edgardo Ugarte; Erwin G Zoetendal; Jun Wang; Francisco Guarner; Oluf Pedersen; Willem M de Vos; Søren Brunak; Joel Doré; María Antolín; François Artiguenave; Hervé M Blottiere; Mathieu Almeida; Christian Brechot; Carlos Cara; Christian Chervaux; Antonella Cultrone; Christine Delorme; Gérard Denariaz; Rozenn Dervyn; Konrad U Foerstner; Carsten Friss; Maarten van de Guchte; Eric Guedon; Florence Haimet; Wolfgang Huber; Johan van Hylckama-Vlieg; Alexandre Jamet; Catherine Juste; Ghalia Kaci; Jan Knol; Omar Lakhdari; Severine Layec; Karine Le Roux; Emmanuelle Maguin; Alexandre Mérieux; Raquel Melo Minardi; Christine M'rini; Jean Muller; Raish Oozeer; Julian Parkhill; Pierre Renault; Maria Rescigno; Nicolas Sanchez; Shinichi Sunagawa; Antonio Torrejon; Keith Turner; Gaetana Vandemeulebrouck; Encarna Varela; Yohanan Winogradsky; Georg Zeller; Jean Weissenbach; S Dusko Ehrlich; Peer Bork
Journal:  Nature       Date:  2011-04-20       Impact factor: 49.962

9.  Phylogenetic analysis of dysbiosis in ulcerative colitis during remission.

Authors:  Mirjana Rajilić-Stojanović; Fergus Shanahan; Francisco Guarner; Willem M de Vos
Journal:  Inflamm Bowel Dis       Date:  2013-03       Impact factor: 5.325

10.  Metagenomic microbial community profiling using unique clade-specific marker genes.

Authors:  Nicola Segata; Levi Waldron; Annalisa Ballarini; Vagheesh Narasimhan; Olivier Jousson; Curtis Huttenhower
Journal:  Nat Methods       Date:  2012-06-10       Impact factor: 28.547
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  200 in total

1.  MetaPhlAn2 for enhanced metagenomic taxonomic profiling.

Authors:  Duy Tin Truong; Eric A Franzosa; Timothy L Tickle; Matthias Scholz; George Weingart; Edoardo Pasolli; Adrian Tett; Curtis Huttenhower; Nicola Segata
Journal:  Nat Methods       Date:  2015-10       Impact factor: 28.547

2.  Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.

Authors:  Jiarong Guo; James R Cole; Qingpeng Zhang; C Titus Brown; James M Tiedje
Journal:  Appl Environ Microbiol       Date:  2015-10-16       Impact factor: 4.792

3.  Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples.

Authors:  Lucas Czech; Alexandros Stamatakis
Journal:  PLoS One       Date:  2019-05-28       Impact factor: 3.240

4.  NetCoMi: network construction and comparison for microbiome data in R.

Authors:  Stefanie Peschel; Christian L Müller; Erika von Mutius; Anne-Laure Boulesteix; Martin Depner
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622

5.  Challenges in benchmarking metagenomic profilers.

Authors:  Zheng Sun; Shi Huang; Meng Zhang; Qiyun Zhu; Niina Haiminen; Anna Paola Carrieri; Yoshiki Vázquez-Baeza; Laxmi Parida; Ho-Cheol Kim; Rob Knight; Yang-Yu Liu
Journal:  Nat Methods       Date:  2021-05-13       Impact factor: 28.547

6.  Accurate read-based metagenome characterization using a hierarchical suite of unique signatures.

Authors:  Tracey Allen K Freitas; Po-E Li; Matthew B Scholz; Patrick S G Chain
Journal:  Nucleic Acids Res       Date:  2015-03-12       Impact factor: 16.971

Review 7.  Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.

Authors:  Eric A Franzosa; Tiffany Hsu; Alexandra Sirota-Madi; Afrah Shafquat; Galeb Abu-Ali; Xochitl C Morgan; Curtis Huttenhower
Journal:  Nat Rev Microbiol       Date:  2015-04-27       Impact factor: 60.633

Review 8.  Ancient and modern environmental DNA.

Authors:  Mikkel Winther Pedersen; Søren Overballe-Petersen; Luca Ermini; Clio Der Sarkissian; James Haile; Micaela Hellstrom; Johan Spens; Philip Francis Thomsen; Kristine Bohmann; Enrico Cappellini; Ida Bærholm Schnell; Nathan A Wales; Christian Carøe; Paula F Campos; Astrid M Z Schmidt; M Thomas P Gilbert; Anders J Hansen; Ludovic Orlando; Eske Willerslev
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2015-01-19       Impact factor: 6.237

9.  APPLES: Scalable Distance-Based Phylogenetic Placement with or without Alignments.

Authors:  Metin Balaban; Shahab Sarmashghi; Siavash Mirarab
Journal:  Syst Biol       Date:  2020-05-01       Impact factor: 15.683

Review 10.  Toward Accurate and Quantitative Comparative Metagenomics.

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