Funding

This work was primarily supported by Lega Italiana per La Lotta contro i Tumori to Nicola Segata, Francesca Cordero and Alessio Naccarati, and by Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP, grant No. 16/23527-2) to Andrew Malthez Thomas.

Two new Italian CRC metagenomic cohorts

For the paper "Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation", we considered 9 Whole-Genome-Shotgun metagenomic cohorts, for a total of 982 fecal metagenomes. Clinical metadata are listed here together with the species-level taxonomical profiles. Cohorts are named: ZellerG_2014 (France), YuJ_2015 (China), FengQ_2015 (Austria), VogtmannE_2016 (USA), HanniganGD_2017 (USA, Canada), WirbelJ_2018 (Germany), ThomasAM_2019_a (Italy), ThomasAM_2019_b (Italy), ThomasAM_2019_c (Japan). The first 5 cohorts of this list have been published originally by previous studies. Wirbel et al cohort has been published in the companion paper (see below), Thomas cohorts a and b have been published in this study, while the cohort named Thomas c has been sequenced as a validaton cohort used in both the studies.

 

Data repository

The 9 cohorts Metaphlan2 Species-Level profiles

Citation

If you find the resource useful in your research, please cite our papers:

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort mucrobial diagnostic signature and a link with choline degradation

A.T. Malthez P. Manghi F. Asnicar E. Pasolli F. Armanini M. Zolfo F. Beghini S. Manara N. Karcher C. Pozzi S. Gandini S. Serrano S. Tarallo A. Francavilla G. Gallo M. Trompetto G. Ferrero S. Mizutani H. Shiroma S. Shiba T. Shibata S. Yachida T. Yamada J. Wirbel P. Schrotz-King C.M. Ulrich H. Brenner M. Arumugam P. Bork G. Zeller F. Cordero E. Dias-Neto J.C. Setubal A. Tett B. Pardini M. Rescigno L. Waldron A. Naccarati N. Segata

Nature Medicine 2019 10.1038/s41591-019-0405-7

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

Jakob Wirbel Paul Theodor Pyl  Ece Kartal Konrad Zych Alireza Kashani Alessio Milanese Jonas S. Fleck Anita Y. Voigt Albert Palleja Ruby Ponnudurai Shinichi Sunagawa Luis Pedro Coelho Petra Schrotz-King Emily Vogtmann Nina Habermann Emma Niméus Andrew M. Thomas Paolo Manghi Sara Gandini Davide Serrano Sayaka Mizutani Hirotsugu Shiroma Satoshi Shiba Tatsuhiro Shibata Shinichi Yachida Takuji Yamada Levi Waldron Alessio Naccarati Nicola Segata Rashmi Sinha Cornelia M. Ulrich Hermann Brenner Manimozhiyan Arumugam Peer Bork Georg Zeller

Nature Medicine 2019 10.1038/s41591-019-0406-6