دورية أكاديمية
أعرض في EDS

Comparison of rectal swab, glove tip, and participant-collected stool techniques for gut microbiome sampling.

التفاصيل البيبلوغرافية
العنوان: Comparison of rectal swab, glove tip, and participant-collected stool techniques for gut microbiome sampling.
المؤلفون: Short MI; University of Texas Health San Antonio, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA., Hudson R; Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA., Besasie BD; Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA., Reveles KR; The University of Texas at Austin, College of Pharmacy, Austin, TX, USA., Shah DP; Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX, USA., Nicholson S; Department of Surgery, University of Texas Health San Antonio, San Antonio, TX, USA., Johnson-Pais TL; Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA., Weldon K; University of Texas Health San Antonio, Genome Sequencing Facility, Greehey Children's Cancer Research Institute (GCCRI), San Antonio, TX, USA., Lai Z; University of Texas Health San Antonio, Genome Sequencing Facility, Greehey Children's Cancer Research Institute (GCCRI), San Antonio, TX, USA., Leach RJ; Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA.; Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA., Fongang B; University of Texas Health San Antonio, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA.; Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX, USA.; Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA., Liss MA; Department of Urology, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, 78229, USA. liss@uthscsa.edu.; The University of Texas at Austin, College of Pharmacy, Austin, TX, USA. liss@uthscsa.edu.
المصدر: BMC microbiology [BMC Microbiol] 2021 Jan 14; Vol. 21 (1), pp. 26. Date of Electronic Publication: 2021 Jan 14.
نوع المنشور: Comparative Study; Journal Article; Observational Study; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : BioMed Central, [2001-
مواضيع طبية MeSH: Bacteria/*classification , Feces/*microbiology , Gloves, Surgical/*microbiology , RNA, Ribosomal, 16S/*genetics , Rectum/*microbiology , Specimen Handling/*instrumentation, Aged ; Aged, 80 and over ; Bacteria/genetics ; Bacteria/isolation & purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Phylogeny ; Prospective Studies ; Sequence Analysis, DNA/methods ; Specimen Handling/methods
مستخلص: Background: Studies of the gut microbiome are becoming increasingly important. Such studies require stool collections that can be processed or frozen in a timely manner so as not to alter the microbial content. Due to the logistical difficulties of home-based stool collection, there has been a challenge in selecting the appropriate sample collection technique and comparing results from different microbiome studies. Thus, we compared stool collection and two alternative clinic-based fecal microbiome collection techniques, including a newer glove-based collection method.
Results: We prospectively enrolled 22 adult men from our prostate cancer screening cohort SABOR (San Antonio Biomarkers of Risk for prostate cancer) in San Antonio, TX, from 8/2018 to 4/2019. A rectal swab and glove tip sample were collected from each participant during a one-time visit to our clinics. A single stool sample was collected at the participant's home. DNA was isolated from the fecal material and 16 s rRNA sequencing of the V1-V2 and V3-V4 regions was performed. We found the gut microbiome to be similar in richness and evenness, noting no differences in alpha diversity among the collection methods. The stool collection method, which remains the gold-standard method for the gut microbiome, proved to have different community composition compared to swab and glove tip techniques (p< 0.001) as measured by Bray-Curtis and unifrac distances. There were no significant differences in between the swab and glove tip samples with regard to beta diversity (p> 0.05). Despite differences between home-based stool and office-based fecal collection methods, we noted that the distance metrics for the three methods cluster by participant indicating within-person similarities. Additionally, no taxa differed among the methods in a Linear Discriminant Analysis Effect Size (LEfSe) analysis comparing all-against-all sampling methods.
Conclusion: The glove tip method provides similar gut microbiome results as rectal swab and stool microbiome collection techniques. The addition of a new office-based collection technique could help easy and practical implementation of gut microbiome research studies and clinical practice.
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معلومات مُعتمدة: P30 CA054174 United States NH NIH HHS; RF1 AG061729 United States AG NIA NIH HHS; U01 CA086402 United States NH NIH HHS; P30 AG059305 United States AG NIA NIH HHS; P30 CA054174 United States CA NCI NIH HHS; R01 AG061729 United States AG NIA NIH HHS; P30 AG066546 United States AG NIA NIH HHS; P30 AG044271 United States AG NIA NIH HHS; U01 AG052409 United States AG NIA NIH HHS
فهرسة مساهمة: Keywords: 16 s rRNA gene sequencing; Digital rectal examination; Gut microbiome; Rectal swabs; Stool collection
المشرفين على المادة: 0 (DNA, Bacterial)
0 (DNA, Ribosomal)
0 (RNA, Ribosomal, 16S)
تواريخ الأحداث: Date Created: 20210115 Date Completed: 20211029 Latest Revision: 20240523
رمز التحديث: 20240523
مُعرف محوري في PubMed: PMC7809826
DOI: 10.1186/s12866-020-02080-3
PMID: 33446094
قاعدة البيانات: MEDLINE
الوصف
تدمد:1471-2180
DOI:10.1186/s12866-020-02080-3