利用de novo测序分析蚕豆瓣酱醅微生物多样性
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摘要
【目的】分析蚕豆瓣醅微生物多样性并比较与过去采用16S、ITS等扩增子测序的差异。【方法】利用de novo测序方法研究微生物菌群多样性。【结果】嗜盐四联球菌(Tetragenococcus halophilus)是蚕豆瓣酱醅的优势微生物,相对丰度占一半以上(m OTUs方法为64.26%,Metaphlan2方法为50.80%),Metaphlan2方法发现破布子乳酸菌(Lactobacillus pobuzihii)也是优势菌株,其相对丰度为17.60%,另外,存在大量未分离到的微生物有待进一步研究。【结论】该方法能分析到蚕豆瓣醅微生物中种或菌株的水平,研究结果不仅为后续深入研究提供了技术支撑,而且对郫县豆瓣的微生物安全性评价提供了有效的方法。
【Objective】The study aimed to analyze the microbial diversity in Doubanjiang-meju using the de novo genome sequencing and compare with amplicon sequencing methods.【Method】de novo genome sequencing.【Result】The results showed that de novo method could analyze at species or strain level. Tetragenococcus halophilus was the predominant species( above 50 % relative abundance) and Lactobacillus pobuzihii was also predominant species( 17. 60 %). 【Conclusion】Previous amplicon sequencing methods,such as 16 S and ITS,of which accuracy is limited,often only to genus,while de novo sequencing has the ability to compensate for these shortcomings,with being accurate to species or strain level. The results not only provide technical support for further research,but also provide an effective method for assessment of microbial safety in Doubanjiang.
【Objective】The study aimed to analyze the microbial diversity in Doubanjiang-meju using the de novo genome sequencing and compare with amplicon sequencing methods.【Method】de novo genome sequencing.【Result】The results showed that de novo method could analyze at species or strain level. Tetragenococcus halophilus was the predominant species( above 50 % relative abundance) and Lactobacillus pobuzihii was also predominant species( 17. 60 %). 【Conclusion】Previous amplicon sequencing methods,such as 16 S and ITS,of which accuracy is limited,often only to genus,while de novo sequencing has the ability to compensate for these shortcomings,with being accurate to species or strain level. The results not only provide technical support for further research,but also provide an effective method for assessment of microbial safety in Doubanjiang.
引文
[1]李幼筠.“郫县豆瓣”剖析[J].中国酿造,2008,11:83-86.
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[8]Baba T,Kuwahara-Arai K,Uchiyama I,et al.Complete genome sequence of Macrococcus caseolyticus strain JSCS5402,reflecting the ancestral genome of the human-pathogenic staphylococci[J].Journal of Bacteriology,2009,191(4):1180-1190.
[9]Li Z,Rui J,Li X,et al.Bacterial community succession and metabolite changes during doubanjiang-meju fermentation,a Chinese traditional fermented broad bean(Vicia faba L.)paste[J].Food Chemistry,2017,218:534-542.
[2]李昂,崔迪,王继华,等.适用于第2代测序技术的宏基因组DNA提取方法[J].哈尔滨工业大学学报,2012(6):20-23.
[3]Sunagawa S,Mende D R,Zeller G,et al.Metagenomic species profiling using universal phylogenetic marker genes[J].Nature Methods,2013,10(12):1196-1199.
[4]李治华,黄驰,王自鹏,等.发酵豆瓣酱微生物宏基因组DNA提取研究[J].西南农业学报,2013,26(6):2663-2665.
[5]Truong D T,Franzosa E A,Tickle T L,et al.Meta Phl An2 for enhanced metagenomic taxonomic profiling[J].Nature Methods,2015,12(10):902-903.
[6]Satomi M,Furushita M,Oikawa H,et al.Diversity of plasmids encoding histidine decarboxylase gene in Tetragenococcus spp.isolated from Japanese fish sauce[J].International Journal of Food Microbiology,2011,148(1):60-65.
[7]Chen Y S,Miyashita M,Suzuki K,et al.Lactobacillus pobuzihii sp.nov.,isolated from pobuzihi(fermented cummingcordia)[J].International Journal of Systematic and Evolutionary Microbiology,2010,60(8):1914-1917.
[8]Baba T,Kuwahara-Arai K,Uchiyama I,et al.Complete genome sequence of Macrococcus caseolyticus strain JSCS5402,reflecting the ancestral genome of the human-pathogenic staphylococci[J].Journal of Bacteriology,2009,191(4):1180-1190.
[9]Li Z,Rui J,Li X,et al.Bacterial community succession and metabolite changes during doubanjiang-meju fermentation,a Chinese traditional fermented broad bean(Vicia faba L.)paste[J].Food Chemistry,2017,218:534-542.