Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench
Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optim...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-02-01
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| Series: | Journal of the Formosan Medical Association |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0929664617308574 |
| _version_ | 1811235020342296576 |
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| author | Wei-Kai Wu Chieh-Chang Chen Suraphan Panyod Rou-An Chen Ming-Shiang Wu Lee-Yan Sheen Shan-Chwen Chang |
| author_facet | Wei-Kai Wu Chieh-Chang Chen Suraphan Panyod Rou-An Chen Ming-Shiang Wu Lee-Yan Sheen Shan-Chwen Chang |
| author_sort | Wei-Kai Wu |
| collection | DOAJ |
| description | Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP). Third, we provide a useful information of collection kit with DNA stabilization buffers and compare their pros and cons for multi-omic study. Fourth, we offer technical strategies as well as information of novel tools for sample aliquoting before long-term storage. Fifth, we discuss the substantial impact of different DNA extraction protocols on technical variations of metagenomic analysis. And lastly, we point out the limitation of current methods and the unmet needs for better quality control of metagenomic analysis. We hope the information provided here will help investigators in this exciting field to advance their studies while avoiding experimental artifacts. Keywords: Gut microbiome, Stool collection, Sample processing, Storage condition, Standardization |
| first_indexed | 2024-04-12T11:45:11Z |
| format | Article |
| id | doaj.art-86dad71b546b4703b86a1a24d1a5bb5c |
| institution | Directory Open Access Journal |
| issn | 0929-6646 |
| language | English |
| last_indexed | 2024-04-12T11:45:11Z |
| publishDate | 2019-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of the Formosan Medical Association |
| spelling | doaj.art-86dad71b546b4703b86a1a24d1a5bb5c2022-12-22T03:34:24ZengElsevierJournal of the Formosan Medical Association0929-66462019-02-011182545555Optimization of fecal sample processing for microbiome study — The journey from bathroom to benchWei-Kai Wu0Chieh-Chang Chen1Suraphan Panyod2Rou-An Chen3Ming-Shiang Wu4Lee-Yan Sheen5Shan-Chwen Chang6Department of Internal Medicine, National Taiwan University Hospital Bei-Hu Branch, Taipei, Taiwan; Institute of Food Science and Technology, National Taiwan University, Taipei, TaiwanDepartment of Internal Medicine, National Taiwan University Hospital, Taipei, TaiwanInstitute of Food Science and Technology, National Taiwan University, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, TaiwanInstitute of Food Science and Technology, National Taiwan University, Taipei, TaiwanDepartment of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, TaiwanInstitute of Food Science and Technology, National Taiwan University, Taipei, Taiwan; Corresponding author.Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; College of Medicine, National Taiwan University, Taipei, Taiwan; Corresponding author. Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, No 7 Chung-Shan South Road, Taipei, Taiwan. Fax: +886 02 23947899.Although great interest has been displayed by researchers in the contribution of gut microbiota to human health, there is still no standard protocol with consensus to guarantee the sample quality of metagenomic analysis. Here we reviewed existing methodology studies and present suggestions for optimizing research pipeline from fecal sample collection to DNA extraction. First, we discuss strategies of clinical metadata collection as common confounders for microbiome research. Second, we propose general principles for freshly collected fecal sample and its storage and share a DIY stool collection kit protocol based on the manual procedure of Human Microbiome Project (HMP). Third, we provide a useful information of collection kit with DNA stabilization buffers and compare their pros and cons for multi-omic study. Fourth, we offer technical strategies as well as information of novel tools for sample aliquoting before long-term storage. Fifth, we discuss the substantial impact of different DNA extraction protocols on technical variations of metagenomic analysis. And lastly, we point out the limitation of current methods and the unmet needs for better quality control of metagenomic analysis. We hope the information provided here will help investigators in this exciting field to advance their studies while avoiding experimental artifacts. Keywords: Gut microbiome, Stool collection, Sample processing, Storage condition, Standardizationhttp://www.sciencedirect.com/science/article/pii/S0929664617308574 |
| spellingShingle | Wei-Kai Wu Chieh-Chang Chen Suraphan Panyod Rou-An Chen Ming-Shiang Wu Lee-Yan Sheen Shan-Chwen Chang Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench Journal of the Formosan Medical Association |
| title | Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench |
| title_full | Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench |
| title_fullStr | Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench |
| title_full_unstemmed | Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench |
| title_short | Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench |
| title_sort | optimization of fecal sample processing for microbiome study the journey from bathroom to bench |
| url | http://www.sciencedirect.com/science/article/pii/S0929664617308574 |
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