CONSENSUS
Consensus on standard biobanking of gut microbiota
Yi Chao Shi,
Zi Kai Wang,
Yun Sheng Yang,
on behalf of Biobank Branch China Medicinal Biotech Association, the Digestive Biobanking Committee China Association of Medical Equipment, the Gut Microbiome Committee China Society of Gastroenterology,
Yi Chao Shi
Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
Search for more papers by this authorZi Kai Wang
Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
Search for more papers by this authorCorresponding Author
Yun Sheng Yang
Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
Correspondence
Yun Sheng Yang, Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853, China.
Email: [email protected]
Search for more papers by this authoron behalf of Biobank Branch China Medicinal Biotech Association, the Digestive Biobanking Committee China Association of Medical Equipment, the Gut Microbiome Committee China Society of Gastroenterology
Search for more papers by this authorYi Chao Shi,
Zi Kai Wang,
Yun Sheng Yang,
on behalf of Biobank Branch China Medicinal Biotech Association, the Digestive Biobanking Committee China Association of Medical Equipment, the Gut Microbiome Committee China Society of Gastroenterology,
Yi Chao Shi
Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
Search for more papers by this authorZi Kai Wang
Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
Search for more papers by this authorCorresponding Author
Yun Sheng Yang
Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, Beijing, China
Correspondence
Yun Sheng Yang, Department of Gastroenterology and Hepatology, Institute of Digestive Diseases, Chinese PLA General Hospital, 28 Fuxing Road, Beijing 100853, China.
Email: [email protected]
Search for more papers by this authoron behalf of Biobank Branch China Medicinal Biotech Association, the Digestive Biobanking Committee China Association of Medical Equipment, the Gut Microbiome Committee China Society of Gastroenterology
Search for more papers by this authorThis expert consensus has been published in Chinese on the Chinese Journal of Gastroenterology 2018; 23(6):356-362.
CONFLICT OF INTEREST
None.
REFERENCES
- 1Hollister EB, Gao C, Versalovic J. Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Gastroenterology. 2014; 146(6): 1449-1458.
- 2Yang YS. Focus and prospect of gut microbiota research. Chin J Intern Med. 2015; 54(5): 396-398.
- 3Guo Y, Li SH, Kuang YS, et al. Effect of short-term room temperature storage on the microbial community in infant fecal samples. Sci Rep. 2016; 6:26648. https://doi.org/10.1038/srep26648.
- 4Guo YC. Clinical Biobank. China: Science Press, 2014. [in Chinese].
- 5 Tentative biobanking standard of China Medical Biotechnology Association. Chin Med Biotechnol. 2011; 6(1): 71-79. [in Chinese].
- 6Campbell LD, Astrin JJ, DeSouza Y, et al. The 2018 revision of the ISBER Best Practices: Summary of changes and the editorial team's development process. Biopreserv Biobank. 2018; 16(1): 3-6.
- 7 National Health and Family Planning Commission of the People's Republic of China. Ethical review of biomedical research involving humans: 2016. Order No. 11. National Health and Family Planning Commission of the People's Republic of China; 2016. [in Chinese].
- 8 World Medical Association. World Medical Association Declaration of Helsinki: ethical principles for medical research involving human subjects. JAMA. 2013; 310(20): 2191-2194.
- 9 International Ethical Guidelines for Biomedical Research Involving Human Subjects. Bulletin of medical ethics. 2002;(182):17-23.
- 10 National Standardization Administration of the People's Republic of China. National standards of the People's Republic of China. Available from: http://www.gb688.cn/bzgk/gb/index [in Chinese].
- 11 China National Accreditation Service for Conformity Assessment. Accreditation criteria for laboratory bio-safety (2015). Available from: https://www.cnas.org.cn/images/rkgf/sysrk/jbzz/2015/06/04/82FDF809FB8C3413A76E70BF8F008B71.pdf [in Chinese]
- 12 National Health Commission of the People's Republic of China. Performance verification of vacuum tubes for venous blood specimen (2018). Available from: http://www.moh.gov.cn/zwgkzt/pwsbz/wsbz.shtml [in Chinese].
- 13 World Health Organization. Laboratory biosafety manual. 3rd ed. Geneva: World Health Organization, 2004. Available from. https://www.who.int/csr/delibepidemics/WHO_CDS_CSR_LYO_2004_11/en/.
- 14Ma Y, Chen H, Lan C, Ren J. Help, hope and hype: ethical considerations of human microbiome research and applications. Protein Cell. 2018; 9(5): 404-415.
- 15Ma Y, Chen H, Lei R, Ren J. Biobanking for human microbiome research: promise, risks, and ethics. Asian Bioethics Rev. 2017; 9(4): 311-324.
10.1007/s41649-017-0033-9 Google Scholar
- 16Spor A, Koren O, Ley R. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol. 2011; 9(4): 279-290.
- 17Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ. Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences. Eur J Clin Invest. 2012; 42(8): 855-863.
- 18 Human Microbiome Project Consortium. A framework for human microbiome research. Nature. 2012; 486(7402): 215-221.
- 19Wu WK, Chen CC, Panyod S, et al. Optimization of fecal sample processing for microbiome study — The journey from bathroom to bench [Published online ahead of print February 25, 2018]. J Formos Med Assoc. https://doi.org/10.1016/j.jfma.2018.02.005.
- 20 Chinese Medical Association. Operational specifications of clinical techniques: Pathology. Beijing: People's Military Medical Press; 2004.
- 21Shaw AG, Sim K, Powell E, et al. Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? Microbiome. 2016; 4(1): 40. https://doi.org/10.1186/s40168-016-0186-x.
- 22Carroll IM, Ringel-Kulka T, Siddle JP, Klaenhammer TR, Ringel Y. Characterization of the fecal microbiota using high-throughput sequencing reveals a stable microbial community during storage. PLoS One. 2012; 7(10): e46953. https://doi.org/10.1371/journal.pone.0046953.
- 23Fouhy F, Deane J, Rea MC, et al. The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations. PLoS One. 2015; 10(3): e0119355. https://doi.org/10.137/journal.pone.0119355.
- 24Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010; 464(7285): 59-65.
- 25Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature. 2009; 457(7228): 480-484.
- 26Nishimoto Y, Mizutani S, Nakajima T, et al. High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy. Gut. 2016; 65(9): 1574-1575.
- 27Wu GD, Lewis JD, Hoffmann C, et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol. 2010; 10: 206. https://doi.org/10.1186/1471-2180-10-206.
- 28Vogtmann E, Chen J, Amir A, et al. Comparison of collection methods for fecal samples in microbiome studies. Am J Epidemiol. 2017; 185(2): 115-123.
- 29Blekhman R, Tang K, Archie EA, et al. Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Sci Rep. 2016; 6:31519. https://doi.org/10.1038/srep31519.
- 30 Pathology Collaboration Group, Chinese Society of Digestive Endoscopology. Chinese expert consensus on endoscopic biopsy and pathology examination (draft). Chin J Dig. 2014; 31(9): 577-581. [in Chinese].
- 31Shanahan ER, Zhong L, Talley NJ, Morrison M, Holtmann G. Characterisation of the gastrointestinal mucosa-associated microbiota: a novel technique to prevent cross-contamination during endoscopic procedures. Aliment Pharmacol Ther. 2016; 43(11): 1186-1196.
- 32Watt E, Gemmell MR, Berry S, et al. Extending colonic mucosal microbiome analysis—assessment of colonic lavage as a proxy for endoscopic colonic biopsies. Microbiome. 2016; 4: 61. https://doi.org/10.1186/s40168-016-0207-9.
- 33Païssé S, Valle C, Servant F, et al. Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing. Transfusion. 2016; 56(5): 1138-1147.
- 34Merlini E, Bellistri GM, Tincati C, d'Arminio Monforte A, Marchetti G. Sequencing of bacterial microflora in peripheral blood: our experience with HIV-infected patients. J Vis Exp. 2011; 52: 2830. https://doi.org/10.3791/2830.
- 35Puri P, Liangpunsakul S, Christensen JE, et al. The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis. Hepatology. 2018; 67(4): 1284-1302.
- 36Amar J, Lange C, Payros G, et al. Blood microbiota dysbiosis is associated with the onset of cardiovascular events in a large general population: the D.E.S.I.R. study. PLoS One. 2013; 8(1): e54461. https://doi.org/10.1371/journal.pone.0054461.
- 37Wang L, Llorente C, Hartmann P, Yang AM, Chen P, Schnabl B. Methods to determine intestinal permeability and bacterial translocation during liver disease. J Immunol Methods. 2015; 421: 44-53.
- 38Bellot P, García-Pagán JC, Francés R, et al. Bacterial DNA translocation is associated with systemic circulatory abnormalities and intrahepatic endothelial dysfunction in patients with cirrhosis. Hepatology. 2010; 52(6): 2044-2052.
- 39Ono S, Tsujimoto H, Yamauchi A, Hiraki S, Takayama E, Mochizuki H. Detection of microbial DNA in the blood of surgical patients for diagnosing bacterial translocation. World J Surg. 2005; 29(4): 535-539.
- 40Serino M, Blasco-Baque V, Burcelin R. Microbes on-air: gut and tissue microbiota as targets in type 2 diabetes. J Clin Gastroenterol. 2012; 46(suppl): S27-S28.
- 41Perez PF, Doré J, Leclerc M, et al. Bacterial imprinting of the neonatal immune system: lessons from maternal cells? Pediatrics. 2007; 119(3): e724-e732.
- 42Jeon SJ, Cunha F, Vieira-Neto A, et al. Blood as a route of transmission of uterine pathogens from the gut to the uterus in cows. Microbiome. 2017; 5(1): 109. https://doi.org/10.1186/s40168-017-0328-9.
- 43Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014; 12: 87. https://doi.org/10.1186/s12915-014-0087-z.
- 44Vientós-Plotts AI, Ericsson AC, Rindt H, et al. Dynamic changes of the respiratory microbiota and its relationship to fecal and blood microbiota in healthy young cats. PLoS One. 2017; 12(3): e0173818. https://doi.org/10.1371/journal.pone.0173818.
- 45Mandal RK, Jiang T, Al-Rubaye AA, et al. An investigation into blood microbiota and its potential association with bacterial chondronecrosis with osteomyelitis (BCO) in boilers. Sci Rep. 2016; 6: 25882. https://doi.org/10.1038/srep25882.
- 46 Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486(7402): 207-214.
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