Identification of low abundance microbiome in clinical samples using whole genome sequencing Journal Article
| Authors: | Zhang, C.; Cleveland, K.; Schnoll-Sussman, F.; McClure, B.; Bigg, M.; Thakkar, P.; Schultz, N.; Shah, M. A.; Betel, D. |
| Article Title: | Identification of low abundance microbiome in clinical samples using whole genome sequencing |
| Abstract: | 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. © 2015 Zhang et al. |
| Keywords: | controlled study; sequence analysis; nonhuman; validation process; polymerase chain reaction; genome analysis; blood sampling; quantitative analysis; intermethod comparison; endoscopic biopsy; bacterium identification; helicobacter pylori; epstein barr virus; virus identification; epstein barr virus infection; stomach biopsy; microbiome; article; whole genome sequencing; population abundance |
| Journal Title: | Genome Biology |
| Volume: | 16 |
| ISSN: | 1465-6906 |
| Publisher: | Biomed Central Ltd |
| Date Published: | 2015-11-27 |
| Start Page: | 265 |
| Language: | English |
| DOI: | 10.1186/s13059-015-0821-z |
| PROVIDER: | scopus |
| PMCID: | PMC4661937 |
| PUBMED: | 26614063 |
| DOI/URL: | |
| Notes: | Article -- Art. No. 265 -- Export Date: 7 January 2016 -- Source: Scopus |
