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.
authors.affiliation: Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA.|Department of Medicine, Division of Hematology and Medical Oncology, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA.
authors.forename: Chao
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Department of Medicine, Division of Hematology and Medical Oncology, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA.
authors.forename: Kyle
authors.initials: K
authors.lastname: Cleveland
authors.affiliation: Department of Medicine, Division of Hematology and Medical Oncology, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA.|The Jay Monahan Center for Gastrointestinal Health, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA.
authors.forename: Felice
authors.initials: F
authors.lastname: Schnoll-Sussman
authors.affiliation: Center for Advanced Digestive Care, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA.
authors.forename: Bridget
authors.initials: B
authors.lastname: McClure
authors.affiliation: The Jay Monahan Center for Gastrointestinal Health, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA.
authors.forename: Michelle
authors.initials: M
authors.lastname: Bigg
authors.affiliation: Department of Medicine, Division of Hematology and Medical Oncology, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA.
authors.forename: Prashant
authors.initials: P
authors.lastname: Thakkar
authors.affiliation: Kravis Center for Molecular Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.|Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Schultz
authors.affiliation: Department of Medicine, Division of Hematology and Medical Oncology, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA. mas9313@med.cornell.edu.|Center for Advanced Digestive Care, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA. mas9313@med.cornell.edu.
authors.forename: Manish A
authors.initials: MA
authors.lastname: Shah
authors.affiliation: Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021, USA. dob2014@med.cornell.edu.|Department of Medicine, Division of Hematology and Medical Oncology, New York-Presbyterian Hospital/Weill Cornell Medicine, New York, NY, 10021, USA. dob2014@med.cornell.edu.
authors.forename: Doron
authors.initials: D
authors.lastname: Betel
mesh_terms: D001706:Biopsy; D015894:Genome, Human; D060148:HapMap Project; D016480:Helicobacter pylori / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D064307:Microbiota / Q000235:genetics*; D013274:Stomach Neoplasms / Q000235:genetics* / Q000382:microbiology / Q000473:pathology