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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.   Electronic supplementary material  The online version of this article (doi:10.1186/s13059-015-0821-z) contains supplementary material, which is available to authorized users.

Identification of low abundance microbiome in clinical samples using whole genome sequencing