Comparison of in Clinic-Based Fecal Microbiome Collection Techniques for Increase in Study Participation and Utilization of Microbiome Analysis

作     者：Benjamin D. Besasie Dimpy P. Shah Robin J. Leach Michael A. Liss 

作者机构：Department of Urology UT Health San Antonio San Antonio TX USA Department of Epidemiology and Biostatistics UT Health San Antonio San Antonio TX USA 

出 版 物：《Open Journal of Urology》 (泌尿学期刊（英文）)

年 卷 期：2019年第9卷第3期

页      面：51-61页

学科分类：1002[医学-临床医学] 100214[医学-肿瘤学] 10[医学] 

主　　题：Fecal Microbiome Stool Collection Technique Swab Glove Urology Digital Rectal Exam 16S rRNA Gene Sequencing 

摘      要：We compared the collection techniques of fecal specimens for DNA extraction and fecal microbiome analysis by utilizing the glove from a standard-of-care digital rectal exam (DRE) and the rectal swab from a pre-prostate biopsy bacterial rectal culture collected in clinical care settings. DNA yield from the swab technique compared to the glove technique yielded similar amounts of DNA (18.1 vs. 13.1 ng/μL, p = 0.06), slightly favoring the swab technique. However, utilizing DNA yield cutoffs of 15 ng/μL (37% vs. 29%, p = 0.18) and 30 ng/μL (15% and 9%, p = 0.16), we identified no differences in yield between the swab versus glove technique, respectively. Absorbance values for overall DNA quality were significantly different in favor of the glove technique (mean 1.6 vs. 2.0, p 0.001). Using an absorbance value of 1.5 as an indication of DNA quality, only 26% (19/91) met the cutoff value using the swab group compared to 47.3% (53/112) if the glove technique was used (p 0.001). Similar results occurred for the RNA quality with an absorbance value cutoff of 2.0 (2.2% vs. 30.4%, p 0.001). To increase sampling feasibility and improve population sampling, gloves used from a DRE may be utilized as a consistent and efficient fecal DNA collection technique for fecal microbiome analysis. DNA yield and quality from the glove technique are comparable to—if not better than—rectal swab collection.