title: Rectal swabs for analysis of the intestinal microbiota.
abstract: The composition of the gut microbiota is associated with various disease states, most notably inflammatory bowel disease, obesity and malnutrition. This underlines that analysis of intestinal microbiota is potentially an interesting target for clinical diagnostics. Currently, the most commonly used sample types are feces and mucosal biopsy specimens. Because sampling method, storage and processing of samples impact microbiota analysis, each sample type has its own limitations. An ideal sample type for use in routine diagnostics should be easy to obtain in a standardized fashion without perturbation of the microbiota. Rectal swabs may satisfy these criteria, but little is known about microbiota analysis on these sample types. In this study we investigated the characteristics and applicability of rectal swabs for gut microbiota profiling in a clinical routine setting in patients presenting with various gastro-intestinal disorders. We found that rectal swabs appeared to be a convenient means of sampling the human gut microbiota. Swabs can be performed on demand, whenever a patient presents; swab-derived microbiota profiles are reproducible, whether they are gathered at home by patients or by medical professionals in an outpatient setting and may be ideally suited for clinical diagnostics and large-scale studies.
authors.affiliation: Department of Medical Microbiology and Infection control, VU University medical center, Amsterdam, the Netherlands.
authors.forename: Andries E
authors.initials: AE
authors.lastname: Budding
authors.affiliation: Department of Gastroenterology and Hepatology, VU University medical center, Amsterdam, the Netherlands.
authors.forename: Matthijs E
authors.initials: ME
authors.lastname: Grasman
authors.affiliation: Department of Medical Microbiology and Infection control, VU University medical center, Amsterdam, the Netherlands.
authors.forename: Anat
authors.initials: A
authors.lastname: Eck
authors.affiliation: Department of Epidemiology and Biostatistics, VU University medical center, Amsterdam, the Netherlands.
authors.forename: Johannes A
authors.initials: JA
authors.lastname: Bogaards
authors.affiliation: Department of Medical Microbiology and Infection control, VU University medical center, Amsterdam, the Netherlands.
authors.forename: Christina M J E
authors.initials: CM
authors.lastname: Vandenbroucke-Grauls
authors.affiliation: Department of Gastroenterology and Hepatology, VU University medical center, Amsterdam, the Netherlands; Department of Internal Medicine, Gastroenterology and Geriatrics, ORBIS medical center, Sittard-Geleen, the Netherlands.
authors.forename: Adriaan A
authors.initials: AA
authors.lastname: van Bodegraven
authors.affiliation: Department of Medical Microbiology and Infection control, VU University medical center, Amsterdam, the Netherlands; Department of medical microbiology, Maastricht University medical center, Maastricht, the Netherlands.
authors.forename: Paul H M
authors.initials: PH
authors.lastname: Savelkoul
mesh_terms: D005243:Feces / Q000382:microbiology; D005260:Female; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology; D007422:Intestines / Q000382:microbiology*; D008297:Male; D064307:Microbiota; D013048:Specimen Handling / Q000379:methods*