Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Hong, Xutao ^a,b   Chen, Jing ^c   Liu, Lin ^d   Wu, Huan ^c   Tan, Haiqin ^a   Xie, Guangfa ^e   Xu, Qian ^c   Zou, Huijun ^e   Yu, Wenjing ^a   Wang, Lan ^d   Qin, Nan ^d  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c Realbio Genomics Institute   (China)

^d ZHEJIANG UNIVERSITY   (China)

^e Zhejiang Guvuelongshan Shaoxing Wine Company   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA SEQUENCE; FOOD CONTROL; GENETICS; LACTOBACILLUS; METAGENOME; MICROBIOLOGY; MICROFLORA; WINE;

FOOD MICROBIOLOGY; LACTOBACILLUS; METAGENOME; MICROBIOTA; SEQUENCE ANALYSIS, DNA; WINE;

EID: 84973365189     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep26621     Document Type: Article

References (41)

1. Zhang, Z. & Wu, G. The brewing technology development of yellow wine. Liquor Making 13, 45-47 (1999).
2. Xie, G. et al. Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing. J Sci Food Agric 93, 3121-5 (2013).
3. Lu, Y. et al. A survey of biogenic amines in Chinese rice wines. Food Chemistry 100, 1424-1428 (2007).
4. Que, F., Mao, L. & Pan, X. Antioxidant activities of five Chinese rice wines and the involvement of phenolic compounds. Food Research International 39, 581-587 (2006).
5. Tan, Y., Hu, P. & Xie, H. Present Research Status and Prospects of the Diversity of Liquor-making Microbes in China. Liquor-making Science & Technology 11, 033 (2011).
6. Xing, G., Zonghua, A. & Bo, D. Research & Detection Progress of Microbes in Daqu. Liquor-making science & Technology 12, 86-89 (2012).
7. Shi, S. et al. Application of DGGE in the Analysis of Microflora Structure of Xijiu Fermented Grains in Summer. Liquor-making science & Technology 3, 51-53 (2010).
8. Pan, Q. et al. Analysis of Bacterial Community Structures in Fenjiu Daqu by PCR-DGGE. Liquor-Making Science & Technology 6, 95-99 (2011).
9. Roh, S. W. et al. Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing. ISME J 4, 1-16 (2010).
10. Ye, L., Shao, M. F., Zhang, T., Tong, A. H. & Lok, S. Analysis of the bacterial community in a laboratory-scale nitrification reactor and a wastewater treatment plant by 454-pyrosequencing. Water Res 45, 4390-4398 (2011).
11. Park, E. J. et al. Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing. Food Microbiol 30, 197-204 (2012).
12. Alexandre, H. & Charpentier, C. Biochemical aspects of stuck and sluggish fermentation in grape must. Journal of Industrial microbiology & biotechnology 20, 20-27 (1998).
13. Sami, M. et al. Hop-resistant Lactobacillus brevis contains a novel plasmid harboring a multidrug resistance-like gene. Journal of Fermentation and Bioengineering 84, 1-6 (1997).
14. Edwards, C. G., Reynolds, A. F., Rodriguez, A. V., Semon, M. J. & Mills, J. M. Implication of acetic acid in the induction of slow/stuck grape juice fermentations and inhibition of yeast by Lactobacillus sp. Am J Enol Vitic 50, 204-210 (1999).
15. Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
16. Schirmer, M. et al. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res 43, e37 (2015).
17. Brooks, J. P. et al. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol 15, 66 (2015).
18. O'Sullivan, D. M. et al. Assessing the accuracy of quantitative molecular microbial profiling. Int J Mol Sci 15, 21476-91 (2014).
19. Kraal, L., Abubucker, S., Kota, K., Fischbach, M. A. & Mitreva, M. The prevalence of species and strains in the human microbiome: a resource for experimental efforts. PLoS One 9, e97279 (2014).
20. Poretsky, R., Rodriguez, R. L., Luo, C., Tsementzi, D. & Konstantinidis, K. T. Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS One 9, e93827 (2014).
21. Filippidou, S. et al. Under-detection of endospore-forming Firmicutes in metagenomic data. Comput Struct Biotechnol J 13, 299-306 (2015).
22. Costello, P. J., Lee, T. H. & Henschke, P. H. Ability of lactic acid bacteria to produce N-heterocycles causing mousy off-flavour in wine. Australian Journal of Grape and Wine Research 7, 160-167 (2001).
23. Korkes, S., Campillo, A. D. & Ochoa, S. Biosynthesis of dicarboxylic acids by carbon dioxide fixation. Journal of Biological Chemistry 187, 891-905 (1950).
24. Kosseva, M., Beschkov, V., Kennedy, J. F. & Lloyd, L. L. Malolactic fermentation in Chardonnay wine by immobilised Lactobacillus casei cells. Process Biochemistry 33, 793-797 (1998).
25. Navarro, L., Zarazaga, M., Ruiz-Larrea, F., Torres, C. & Saenz, J. Bacteriocin production by lactic acid bacteria isolated from Rioja red wines. Journal of applied microbiology 88, 44-51 (2000).
26. Joyeux, A., Lafon-lafourcade, S. & Ribéreau-gayon, P. Evolution of Acetic Acid Bacteria During Fermentation and Storage of Wine. Applied and Environmental Microbiology 48, 153-156 (1984).
27. Li, H. et al. Simultaneous saccharification and fermentation of broken rice: an enzymatic extrusion liquefaction pretreatment for Chinese rice wine production. Bioprocess Biosyst Eng 36, 1141-1148 (2013).
28. Litvan, I. et al. Clinical research criteria for the diagnosis of progressive supranuclear palsy (Steele-Richardson-Olszewski syndrome): Report of the NINDS-SPSP International Workshop. Neurology 47, 1-9 (1996).
29. Ingledew, W. M. & Kunkee, R. E. Factors influencing sluggish fermentations of grape juice. American Journal of Enology and Viticulture 36, 65-76 (1985).
30. Davis, C. R., Wibowo, D., Eschenbruch, R., Lee, T. H. & Fleet, G. H. Practical implications of malolactic fermentation: a review. American Journal of Enology and Viticulture 36, 290-301 (1985).
31. Carreté, R., Vidal, M. T., Bordons, A. & Constanti, M. Inhibitory effect of sulfur dioxide and other stress compounds in wine on the ATPase activity of Oenococcus oeni. FEMS microbiology letters 211, 155-159 (2002).
32. Bohlscheid, J. C., Fellman, J. K., Wang, X. D., Ansen, D. & Edwards, C. G. The influence of nitrogen and biotin interactions on the performance of Saccharomyces in alcoholic fermentations. J Appl Microbiol 102, 390-400 (2007).
33. Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencingbased diversity studies. Nucleic Acids Res 41, e1 (2013).
34. Toju, H., Tanabe, A. S., Yamamoto, S. & Sato, H. High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmnental Samples. PLoS ONE 7, e40863 (2012).
35. Fadrosh, D. W. et al. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2, 1-7 (2014).
36. Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10, 996-988 (2013).
37. Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Applied and Environmental Microbiology 73, 5261-5267 (2007).
38. Qin, N. et al. Alterations of the human gut microbiome in liver cirrhosis. Nature 513, 59-64 (2014).
39. Forsberg, K. J. et al. Bacterial phylogeny structures soil resistomes across habitats. Nature 509, 612-616 (2014).
40. Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55-60 (2012).
41. Hu, Y. et al. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun 4, 2151 (2013).