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

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. Background The human microbiome is a critical constituent of nor-mal human physiology as well as in the pathogenesis of disease [1, 2], including malignancy [3–6]. Conservative estimates are that greater than 15 % of all malignancies may be attributed to microbiota [7], though the mecha-nisms by which the human microbiome contribute t