期刊
GENOME BIOLOGY
卷 16, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s13059-015-0821-z
关键词
-
资金
- Applied Bioinformatics Core at Weill Cornell
- DeGregorio Family Foundation for Gastroesophageal Malignancies
- internal grant from the Center for Advanced Digestive Care at Weill Cornell Medical College
Identifying the microbiome composition from primary tissues directly affords an opportunity to study the causative relationships between the host microbiome and disease. However, this is challenging due the low abundance of microbial DNA relative to the host. We present a systematic evaluation of microbiome profiling directly from endoscopic biopsies by whole genome sequencing. We compared our methods with other approaches on datasets with previously identified microbial composition. We applied this approach to identify the microbiome from 27 stomach biopsies, and validated the presence of Helicobacter pylori by quantitative PCR. Finally, we profiled the microbial composition in The Cancer Genome Atlas gastric adenocarcinoma cohort.
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