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Front Cell Infect Microbiol. 2017 Feb 24;7:51. doi: 10.3389/fcimb.2017.00051. eCollection 2017.

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research.

Author information

1
Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China; Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China.
2
Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital; Tianjin Medical University Tianjin, China.

Abstract

Identifying intestinal microbiota is arguably an important task that is performed to determine the pathogenesis of inflammatory bowel diseases (IBD); thus, it is crucial to collect and analyze intestinally-associated microbiota. Analyzing a single niche to categorize individuals does not enable researchers to comprehensively study the spatial variations of the microbiota. Therefore, characterizing the spatial community structures of the inflammatory bowel disease microbiome is critical for advancing our understanding of the inflammatory landscape of IBD. However, at present there is no universally accepted consensus regarding the use of specific sampling strategies in different biogeographic locations. In this review, we discuss the spatial distribution when screening sample collections in IBD microbiota research. Here, we propose a novel model, a three-dimensional spatial community structure, which encompasses the x-, y-, and z-axis distributions; it can be used in some sampling sites, such as feces, colonoscopic biopsy, the mucus gel layer, and oral cavity. On the basis of this spatial model, this article also summarizes various sampling and processing strategies prior to and after DNA extraction and recommends guidelines for practical application in future research.

KEYWORDS:

IBD microbiota research; colonoscopic biopsy; community structure; feces; mucus gel layer; oral cavity; sampling strategies

PMID:
28286741
PMCID:
PMC5323387
DOI:
10.3389/fcimb.2017.00051
[Indexed for MEDLINE]
Free PMC Article

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