title: The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters.
abstract: The Human Microbiome Project used rigorous good clinical practice standards to complete comprehensive body site sampling in healthy 18- to 40-yr-old adults, creating an unparalleled reference set of microbiome specimens. To ensure that specimens represented minimally perturbed microbiomes, we first screened potential participants using exclusion criteria based on health history, including the presence of systemic diseases (e.g., hypertension, cancer, or immunodeficiency or autoimmune disorders), use of potential immunomodulators, and recent use of antibiotics or probiotics. Subsequent physical examinations excluded individuals based on body mass index (BMI), cutaneous lesions, and oral health. We screened 554 individuals to enroll 300 (149 men and 151 women, mean age 26 yr, mean BMI 24 kg/m, 20.0% racial minority, and 10.7% Hispanic). We obtained specimens from the oral cavity, nares, skin, gastrointestinal tract, and vagina (15 specimens from men and 18 from women). The study evaluated longitudinal changes in an individual's microbiome by sampling 279 participants twice (mean 212 d after the first sampling; range 30-359 d) and 100 individuals 3 times (mean 72 d after the second sampling; range 30-224 d). This sampling strategy yielded 11,174 primary specimens, from which 12,479 DNA samples were submitted to 4 centers for metagenomic sequencing. Our clinical design and well-defined reference cohort has laid a foundation for microbiome research.
authors.affiliation: Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA. aagaardt@bcm.edu
authors.forename: Kjersti
authors.initials: K
authors.lastname: Aagaard
authors.forename: Joseph
authors.initials: J
authors.lastname: Petrosino
authors.forename: Wendy
authors.initials: W
authors.lastname: Keitel
authors.forename: Mark
authors.initials: M
authors.lastname: Watson
authors.forename: James
authors.initials: J
authors.lastname: Katancik
authors.forename: Nathalia
authors.initials: N
authors.lastname: Garcia
authors.forename: Shital
authors.initials: S
authors.lastname: Patel
authors.forename: Mary
authors.initials: M
authors.lastname: Cutting
authors.forename: Tessa
authors.initials: T
authors.lastname: Madden
authors.forename: Holli
authors.initials: H
authors.lastname: Hamilton
authors.forename: Emily
authors.initials: E
authors.lastname: Harris
authors.forename: Dirk
authors.initials: D
authors.lastname: Gevers
authors.forename: Gina
authors.initials: G
authors.lastname: Simone
authors.forename: Pamela
authors.initials: P
authors.lastname: McInnes
authors.forename: James
authors.initials: J
authors.lastname: Versalovic
mesh_terms: D000293:Adolescent; D000328:Adult; D015992:Body Mass Index; D005260:Female; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D008297:Male; D054892:Metagenome; D009055:Mouth / Q000382:microbiology*; D012867:Skin / Q000382:microbiology*; D013048:Specimen Handling / Q000379:methods*; D014621:Vagina / Q000382:microbiology*