Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing
Publication Date
May 12, 2016
Journal
PLOS ONE
Authors
Emily Vogtmann, Xing Hua, Georg Zeller, Shinichi Sunagawa, et al
Volume
11
Issue
5
Pages
e0155362
DOI
https://dx.plos.org/10.1371/journal.pone.0155362
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0155362
Web of Science
000376588600028
Scopus
84969888744
Mendeley
http://www.mendeley.com/research/colorectal-cancer-human-gut-microbiome-reproducibility-wholegenome-shotgun-sequencing
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Mendeley | Further Information

{"title"=>"Colorectal cancer and the human gut microbiome: Reproducibility with whole-genome shotgun sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Emily", "last_name"=>"Vogtmann", "scopus_author_id"=>"36629538700"}, {"first_name"=>"Xing", "last_name"=>"Hua", "scopus_author_id"=>"55203061100"}, {"first_name"=>"Georg", "last_name"=>"Zeller", "scopus_author_id"=>"23974032000"}, {"first_name"=>"Shinichi", "last_name"=>"Sunagawa", "scopus_author_id"=>"24468849800"}, {"first_name"=>"Anita Y.", "last_name"=>"Voigt", "scopus_author_id"=>"37038854700"}, {"first_name"=>"Rajna", "last_name"=>"Hercog", "scopus_author_id"=>"55850794200"}, {"first_name"=>"James J.", "last_name"=>"Goedert", "scopus_author_id"=>"7103299277"}, {"first_name"=>"Jianxin", "last_name"=>"Shi", "scopus_author_id"=>"57125155100"}, {"first_name"=>"Peer", "last_name"=>"Bork", "scopus_author_id"=>"7103061421"}, {"first_name"=>"Rashmi", "last_name"=>"Sinha", "scopus_author_id"=>"7402857340"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84969888744", "sgr"=>"84969888744", "pui"=>"610398049", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"27171425", "doi"=>"10.1371/journal.pone.0155362"}, "id"=>"a587d39c-8fec-36e9-b4e3-fa6f3ab9cf68", "abstract"=>"Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons and for potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment colorectal cancer cases and 52 matched controls from Washington, DC. We compared findings from a previously published 16S rRNA study to the metagenomics-derived taxonomy within the same population. In addition, metagenome-predicted genes, modules, and pathways in the Washington, DC cases and controls were compared to cases and controls recruited in France whose specimens were processed using the same platform. Associations between the presence of fecal Fusobacteria, Fusobacterium, and Porphyromonas with colorectal cancer detected by 16S rRNA were reproduced by metagenomics, whereas higher relative abundance of Clostridia in cancer cases based on 16S rRNA was merely borderline based on metagenomics. This demonstrated that within the same sample set, most, but not all taxonomic associations were seen with both methods. Considering significant cancer associations with the relative abundance of genes, modules, and pathways in a recently published French metagenomics dataset, statistically significant associations in the Washington, DC population were detected for four out of 10 genes, three out of nine modules, and seven out of 17 pathways. In total, colorectal cancer status in the Washington, DC study was associated with 39% of the metagenome-predicted genes, modules, and pathways identified in the French study. More within and between population comparisons are needed to identify sources of variation and disease associations that can be reproduced despite these variations. Future studies should have larger sample sizes or pool data across studies to have sufficient power to detect associations that are reproducible and significant after correction for multiple testing.", "link"=>"http://www.mendeley.com/research/colorectal-cancer-human-gut-microbiome-reproducibility-wholegenome-shotgun-sequencing", "reader_count"=>104, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>30, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>4, "Student > Master"=>14, "Other"=>6, "Student > Bachelor"=>14, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>30, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>4, "Student > Master"=>14, "Other"=>6, "Student > Bachelor"=>14, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>21, "Agricultural and Biological Sciences"=>51, "Medicine and Dentistry"=>9, "Neuroscience"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>12}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>12}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>51}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>21}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>2, "Norway"=>1, "China"=>1, "Japan"=>1, "Brazil"=>3, "South Africa"=>1, "United Kingdom"=>1, "Germany"=>1}, "group_count"=>3}

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Scopus | Further Information

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