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Literature DB >> 26999001

Strain-level microbial epidemiology and population genomics from shotgun metagenomics.

Matthias Scholz¹, Doyle V Ward², Edoardo Pasolli¹, Thomas Tolio¹, Moreno Zolfo¹, Francesco Asnicar¹, Duy Tin Truong¹, Adrian Tett¹, Ardythe L Morrow³, Nicola Segata¹.

Abstract

Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.

Entities: Species

Mesh：

Year: 2016 PMID： 26999001 DOI： 10.1038/nmeth.3802

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

49 in total

1. Fast gapped-read alignment with Bowtie 2.

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Journal: Nat Methods Date: 2012-03-04 Impact factor: 28.547

2. Prokka: rapid prokaryotic genome annotation.

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3. Relating the metatranscriptome and metagenome of the human gut.

Authors: Eric A Franzosa; Xochitl C Morgan; Nicola Segata; Levi Waldron; Joshua Reyes; Ashlee M Earl; Georgia Giannoukos; Matthew R Boylan; Dawn Ciulla; Dirk Gevers; Jacques Izard; Wendy S Garrett; Andrew T Chan; Curtis Huttenhower
Journal: Proc Natl Acad Sci U S A Date: 2014-05-19 Impact factor: 11.205

4. 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

5. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors: Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal: Proc Natl Acad Sci U S A Date: 2005-09-30 Impact factor: 11.205

6. Richness of human gut microbiome correlates with metabolic markers.

Authors: Emmanuelle Le Chatelier; Trine Nielsen; Junjie Qin; Edi Prifti; Falk Hildebrand; Gwen Falony; Mathieu Almeida; Manimozhiyan Arumugam; Jean-Michel Batto; Sean Kennedy; Pierre Leonard; Junhua Li; Kristoffer Burgdorf; Niels Grarup; Torben Jørgensen; Ivan Brandslund; Henrik Bjørn Nielsen; Agnieszka S Juncker; Marcelo Bertalan; Florence Levenez; Nicolas Pons; Simon Rasmussen; Shinichi Sunagawa; Julien Tap; Sebastian Tims; Erwin G Zoetendal; Søren Brunak; Karine Clément; Joël Doré; Michiel Kleerebezem; Karsten Kristiansen; Pierre Renault; Thomas Sicheritz-Ponten; Willem M de Vos; Jean-Daniel Zucker; Jeroen Raes; Torben Hansen; Peer Bork; Jun Wang; S Dusko Ehrlich; Oluf Pedersen
Journal: Nature Date: 2013-08-29 Impact factor: 49.962

7. 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

8. Potential of fecal microbiota for early-stage detection of colorectal cancer.

Authors: Georg Zeller; Julien Tap; Anita Y Voigt; Shinichi Sunagawa; Jens Roat Kultima; Paul I Costea; Aurélien Amiot; Jürgen Böhm; Francesco Brunetti; Nina Habermann; Rajna Hercog; Moritz Koch; Alain Luciani; Daniel R Mende; Martin A Schneider; Petra Schrotz-King; Christophe Tournigand; Jeanne Tran Van Nhieu; Takuji Yamada; Jürgen Zimmermann; Vladimir Benes; Matthias Kloor; Cornelia M Ulrich; Magnus von Knebel Doeberitz; Iradj Sobhani; Peer Bork
Journal: Mol Syst Biol Date: 2014-11-28 Impact factor: 11.429

9. Roary: rapid large-scale prokaryote pan genome analysis.

Authors: Andrew J Page; Carla A Cummins; Martin Hunt; Vanessa K Wong; Sandra Reuter; Matthew T G Holden; Maria Fookes; Daniel Falush; Jacqueline A Keane; Julian Parkhill
Journal: Bioinformatics Date: 2015-07-20 Impact factor: 6.937

10. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis.

Authors: Jose U Scher; Andrew Sczesnak; Randy S Longman; Nicola Segata; Carles Ubeda; Craig Bielski; Tim Rostron; Vincenzo Cerundolo; Eric G Pamer; Steven B Abramson; Curtis Huttenhower; Dan R Littman
Journal: Elife Date: 2013-11-05 Impact factor: 8.140

137 in total

1. Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis.

Authors: Matthew Thoendel; Patricio Jeraldo; Kerryl E Greenwood-Quaintance; Janet Yao; Nicholas Chia; Arlen D Hanssen; Matthew P Abdel; Robin Patel
Journal: J Clin Microbiol Date: 2017-03-29 Impact factor: 5.948

2. Strain-Level Diversity Analysis of Pseudomonas fragi after In Situ Pangenome Reconstruction Shows Distinctive Spoilage-Associated Metabolic Traits Clearly Selected by Different Storage Conditions.

Authors: Francesca De Filippis; Antonietta La Storia; Francesco Villani; Danilo Ercolini
Journal: Appl Environ Microbiol Date: 2018-12-13 Impact factor: 4.792

3. Mesophilic Sporeformers Identified in Whey Powder by Using Shotgun Metagenomic Sequencing.

Authors: Aoife J McHugh; Conor Feehily; John T Tobin; Mark A Fenelon; Colin Hill; Paul D Cotter
Journal: Appl Environ Microbiol Date: 2018-10-01 Impact factor: 4.792

Review 4. Diversity within species: interpreting strains in microbiomes.

Authors: Thea Van Rossum; Pamela Ferretti; Oleksandr M Maistrenko; Peer Bork
Journal: Nat Rev Microbiol Date: 2020-06-04 Impact factor: 60.633

5. Microbiology: the road to strain-level identification.

Authors: Vivien Marx
Journal: Nat Methods Date: 2016-04-28 Impact factor: 28.547

6. Uncovering oral Neisseria tropism and persistence using metagenomic sequencing.

Authors: Claudio Donati; Moreno Zolfo; Davide Albanese; Duy Tin Truong; Francesco Asnicar; Valerio Iebba; Duccio Cavalieri; Olivier Jousson; Carlotta De Filippo; Curtis Huttenhower; Nicola Segata
Journal: Nat Microbiol Date: 2016-05-27 Impact factor: 17.745