Research Progress of Intestinal Microbiome Detection Method_Journal of Biomedical Engineering

Authors：

ZHAORui ,  CHENMaowei

Department of Infectious Diseases, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China;

Corresponding author：

CHENMaowei, Email: chenmaowei2008@163.com

Keywords：

microbiome; gene library; genetic fingerprinting; hybridization; DNA sequencing

DOI：

10.7507/1001-5515.20150204

Video：

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Microorganism distributes in the organs of human body which connect with external environment, especially those organs in the gastrointestinal tracts, and it also plays a fundamental role in the physiopathology of the host's body. Because the microorganism is very small and has a great variety, it is difficult to reveal the significance of microorganism in the human physiopathology comprehensively and deeply. With the development of molecular biology, genomics, bioinformatics and other disciplines, the microbiome research will be more possible and easier. There are two key contents of microecology. One of these is to identify and quantify the diversity of microorganism, and the other is to reveal activity and the physiopathological function of microorganism in the host. Microbiome research methods, therefore, can be summarized as the traditional detection methods, construction of gene library, the genetic fingerprint analysis and molecular hybridization techniques and so on.

Citation： ZHAORui, CHENMaowei. Research Progress of Intestinal Microbiome Detection Method. Journal of Biomedical Engineering, 2015, 32(5): 1150-1154. doi: 10.7507/1001-5515.20150204 Copy

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1. SERINO M, LUCHE E, GRES S, et al. Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota[J]. Gut, 2012, 61(4):543-553.
2. SWARTZ T D, SAKAR Y, DUCA F A, et al. Preserved adiposity in the Fischer 344 rat devoid of gut microbiota[J]. FASEB J, 2013, 27(4):1701-1710.
3. ROUND J L, LEE S M, LI J, et al. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota[J]. Science, 2011, 332(6032):974-977.
4. MOORE W E C, HOLDEMAN L V. Human fecal flora:the normal flora of 20 Japanese-Hawaiians[J]. Appl Microbiol, 1974, 27(5):961-979.
5. KOENIG J E, SPOR A, SCALFONE N, et al. Succession of microbial consortia in the developing infant gut microbiome[J]. Proc Natl Acad Sci U S A, 2011, 108(Suppl 1):4578-4585.
6. RAVEL J, GAJER P, ABDO Z, et al. Vaginal microbiome of reproductive-age women[J]. Proc Natl Acad Sci U S A, 2011, 108(Suppl 1):4680-4687.
7. YANG Fang, ZENG Xiaowei, NING Kang, et al. Saliva microbiomes distinguish caries-active from healthy human populations[J]. ISME J, 2012, 6(1):1-10.
8. GILL S R, POP M, DEBOY R T, et al. Metagenomic analysis of the human distal gut microbiome[J]. Science, 2006, 312(5778):1355-1359.
9. QIN Junjie, LI Yingrui, CAI Zhiming, et al. A metagenome-wide association study of gut microbiota in type 2 diabetes[J]. Nature, 2012, 490(7418):55-60.
10. SHEN Q, TUOHY K M, GIBSON G R, et al. In vitro measurement of the impact of human milk oligosaccharides on the faecal microbiota of weaned formula-fed infants compared to a mixture of prebiotic fructooligosaccharides and galactooligosaccharides[J]. Lett Appl Microbiol, 2011, 52(4):337-343.
11. MARTÍN V, MALDONADO-BARRAGÁN A, MOLES L, et al. Sharing of bacterial strains between breast milk and infant feces[J]. J Hum Lact, 2012, 28(1):36-44.
12. ALBESHARAT R, EHRMANN M A, KORAKLI M, et al. Phenotypic and genotypic analyses of lactic acid bacteria in local fermented food, breast milk and faeces of mothers and their babies[J]. Syst Appl Microbiol, 2011, 34(2):148-155.
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14. SAWAMURA H, YAMADA M, ENDO K, et al. Characterization of microorganisms at different landfill depths using carbon-utilization patterns and 16S rRNA gene based T-RFLP[J]. J Biosci Bioeng, 2010, 109(2):130-137.
15. ROGER L C, MCCARTNEY A L. Longitudinal investigation of the faecal microbiota of healthy full-term infants using fluorescence in situ hybridization and denaturing gradient gel electrophoresis[J]. Microbiology, 2010, 156(Pt 11):3317-3328.
16. SOKOL H, VASQUEZ N, HOYEAU-IDRISSI N, et al. Crypt abscess-associated microbiota in inflammatory bowel disease and acute self-limited colitis[J]. World J Gastroenterol, 2010, 16(5):583-587.
17. YANG Yunfeng, WU Linwei, LIN Qiaoyan, et al. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland[J]. Glob Chang Biol, 2013, 19(2):637-648.
18. LIANG Yuting, VAN NOSTRAND J D, DENG Ye, et al. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China[J]. ISME J, 2011, 5(3):403-413.
19. XIE Jianping, HE Zhili, LIU Xinxing, et al. GeoChip-based analysis of the functional gene diversity and metabolic potential of microbial communities in acid mine drainage[J]. Appl Environ Microbiol, 2011, 77(3):991-999.
20. HE Zhili, DENG Ye, ZHOU Jizhong. Development of functional gene microarrays for microbial community analysis[J]. Curr Opin Biotechnol, 2012, 23(1):49-55.
21. HE Zhili, VAN NOSTRAND J D, ZHOU Jizhong, Applications of functional gene microarrays for profiling microbial communities[J]. Curr Opin Biotechnol, 2012, 23(3):460-466.
22. Human Microbiome Project Consortium. A framework for human microbiome research[J]. Nature, 2012, 486(7402):215-221.
23. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome[J]. Nature, 2012, 486(7402):207-214.
24. GOSALBES M J, DURBÁN A, PIGNATELLI M, et al. Metatranscriptomic approach to analyze the functional human gut microbiota[J]. PLoS One, 2011, 6(3):e17447.
25. SPOR A, KOREN O, LEY R. Unravelling the effects of the environment and host genotype on the gut microbiome[J]. Nat Rev Microbiol, 2011, 9(4):279-290.
26. BARTRAM A K, LYNCH M D J, STEARNS J C, et al. Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads[J]. Appl Environ Microbiol, 2011, 77(11):3846-3852.
27. LUO Chengwei, TSEMENTZI D, KYRPIDES N, et al. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample[J]. PLoS One, 2012, 7(2):e30087.

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