A guide to human microbiome research: study design, sample collection, and bioinformatics analysis.
10.1097/CM9.0000000000000871
- VernacularTitle:A guide to human microbiome research: study design, sample collection, and bioinformatics analysis
- Author:
Xu-Bo QIAN
1
;
Tong CHEN
2
;
Yi-Ping XU
1
;
Lei CHEN
3
;
Fu-Xiang SUN
4
;
Mei-Ping LU
1
;
Yong-Xin LIU
5
Author Information
1. Department of Rheumatology Immunology & Allergy, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China.
2. National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Scienc?\ es, Beijing 100700, China.
3. Department of Vascular Surgery, Fu Xing Hospital, Capital Medical University, Beijing 100045, China.
4. EHBIO Gene Technology (Beijing) Co., Ltd, Beijing 100009, China.
5. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
- Publication Type:Journal Article
- From:
Chinese Medical Journal
2020;133(15):1844-1855
- CountryChina
- Language:English
-
Abstract:
The purpose of this review is to provide medical researchers, especially those without a bioinformatics background, with an easy-to-understand summary of the concepts and technologies used in microbiome research. First, we define primary concepts such as microbiota, microbiome, and metagenome. Then, we discuss study design schemes, the methods of sample size calculation, and the methods for improving the reliability of research. We emphasize the importance of negative and positive controls in this section. Next, we discuss statistical analysis methods used in microbiome research, focusing on problems with multiple comparisons and ways to compare β-diversity between groups. Finally, we provide step-by-step pipelines for bioinformatics analysis. In summary, the meticulous study design is a key step to obtaining meaningful results, and appropriate statistical methods are important for accurate interpretation of microbiome data. The step-by-step pipelines provide researchers with insights into newly developed bioinformatics analysis methods.
