Title |
Optimizing methods and dodging pitfalls in microbiome research
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Published in |
Microbiome, May 2017
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DOI | 10.1186/s40168-017-0267-5 |
Pubmed ID | |
Authors |
Dorothy Kim, Casey E. Hofstaedter, Chunyu Zhao, Lisa Mattei, Ceylan Tanes, Erik Clarke, Abigail Lauder, Scott Sherrill-Mix, Christel Chehoud, Judith Kelsen, Máire Conrad, Ronald G. Collman, Robert Baldassano, Frederic D. Bushman, Kyle Bittinger |
Abstract |
Research on the human microbiome has yielded numerous insights into health and disease, but also has resulted in a wealth of experimental artifacts. Here, we present suggestions for optimizing experimental design and avoiding known pitfalls, organized in the typical order in which studies are carried out. We first review best practices in experimental design and introduce common confounders such as age, diet, antibiotic use, pet ownership, longitudinal instability, and microbial sharing during cohousing in animal studies. Typically, samples will need to be stored, so we provide data on best practices for several sample types. We then discuss design and analysis of positive and negative controls, which should always be run with experimental samples. We introduce a convenient set of non-biological DNA sequences that can be useful as positive controls for high-volume analysis. Careful analysis of negative and positive controls is particularly important in studies of samples with low microbial biomass, where contamination can comprise most or all of a sample. Lastly, we summarize approaches to enhancing experimental robustness by careful control of multiple comparisons and to comparing discovery and validation cohorts. We hope the experimental tactics summarized here will help researchers in this exciting field advance their studies efficiently while avoiding errors. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 35 | 31% |
United Kingdom | 10 | 9% |
Canada | 5 | 4% |
Australia | 5 | 4% |
Spain | 4 | 4% |
Netherlands | 4 | 4% |
Sweden | 3 | 3% |
Austria | 2 | 2% |
Denmark | 2 | 2% |
Other | 11 | 10% |
Unknown | 32 | 28% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 59 | 52% |
Members of the public | 53 | 47% |
Practitioners (doctors, other healthcare professionals) | 1 | <1% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Netherlands | 1 | <1% |
Sweden | 1 | <1% |
Estonia | 1 | <1% |
Germany | 1 | <1% |
Unknown | 831 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 195 | 23% |
Researcher | 160 | 19% |
Student > Master | 110 | 13% |
Student > Bachelor | 54 | 6% |
Other | 44 | 5% |
Other | 111 | 13% |
Unknown | 161 | 19% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 206 | 25% |
Biochemistry, Genetics and Molecular Biology | 167 | 20% |
Immunology and Microbiology | 85 | 10% |
Medicine and Dentistry | 63 | 8% |
Environmental Science | 16 | 2% |
Other | 98 | 12% |
Unknown | 200 | 24% |