Next-generation sequencing reveals significant bacterial diversity of botrytized wine.
Next-generation sequencing reveals significant bacterial diversity of botrytized wine.
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DOI：
10.1371/journal.pone.0036357
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Mills DA
中科院分区：
文献类型：
--
作者：
Bokulich NA;Joseph CM;Allen G;Benson AK;Mills DA
虽然葡萄酒发酵长期以来一直被认为涉及复杂的微生物群落，但除了一组选定的乳酸菌（LAB）之外，细菌的组成和作用通常被认为是可忽略的或有害的。这项研究作为一个试点研究，使用条形码扩增子下一代测序，以配置文件在葡萄酒和葡萄汁中的细菌群落结构，比较通过测序两个不同的结构域的原核16 S rDNA（V4和V5）的分类深度。本研究的目的有两个：1）比较细菌16 SrDNA的V4和V5结构域与乳酸菌群落的末端限制性片段长度多态性（TRFLP），以经验性地确定用于葡萄酒条形码扩增子测序的最具分类学信息的16 SrDNA靶区域;以及2）探索葡萄酒发酵的细菌群落，以更好地了解葡萄酒的生物多样性，这是以前使用其他技术无法达到的深度。从V4和V5的扩增子的分析提供了类似的意见，葡萄酒发酵的细菌群落，揭示了广泛的多样性，传统上不与葡萄酒，以及非典型的LAB社区最初检测到的TRFLP低丰度类群。V4域被确定为更适合葡萄酒生态学研究的读数，因为它为分析LAB群落提供了更大的分类学深度。此外，靶向富集用于从成品发酵中分离两种α变形菌。接种和未接种样品之间多样性的显着差异表明酵母菌接种对这些发酵中的细菌多样性施加选择压力，最显着的是抑制醋酸菌的丰度。这些结果确定了葡萄酒的细菌多样性远远高于以前认识到的，提供了进一步了解这些葡萄酒的发酵动力学，并证明了下一代测序葡萄酒生态学研究的实用性。
While wine fermentation has long been known to involve complex microbial communities, the composition and role of bacteria other than a select set of lactic acid bacteria (LAB) has often been assumed either negligible or detrimental. This study served as a pilot study for using barcoded amplicon next-generation sequencing to profile bacterial community structure in wines and grape musts, comparing the taxonomic depth achieved by sequencing two different domains of prokaryotic 16S rDNA (V4 and V5). This study was designed to serve two goals: 1) to empirically determine the most taxonomically informative 16S rDNA target region for barcoded amplicon sequencing of wine, comparing V4 and V5 domains of bacterial 16S rDNA to terminal restriction fragment length polymorphism (TRFLP) of LAB communities; and 2) to explore the bacterial communities of wine fermentation to better understand the biodiversity of wine at a depth previously unattainable using other techniques. Analysis of amplicons from the V4 and V5 provided similar views of the bacterial communities of botrytized wine fermentations, revealing a broad diversity of low-abundance taxa not traditionally associated with wine, as well as atypical LAB communities initially detected by TRFLP. The V4 domain was determined as the more suitable read for wine ecology studies, as it provided greater taxonomic depth for profiling LAB communities. In addition, targeted enrichment was used to isolate two species of Alphaproteobacteria from a finished fermentation. Significant differences in diversity between inoculated and uninoculated samples suggest that Saccharomyces inoculation exerts selective pressure on bacterial diversity in these fermentations, most notably suppressing abundance of acetic acid bacteria. These results determine the bacterial diversity of botrytized wines to be far higher than previously realized, providing further insight into the fermentation dynamics of these wines, and demonstrate the utility of next-generation sequencing for wine ecology studies.
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影响因子：
5.3
作者：
Andorra, Imma;Landi, Sara;Esteve-Zarzoso, Braulio
通讯作者：
Esteve-Zarzoso, Braulio
影响因子：
5.9
作者：
FAITH, DP
通讯作者：
FAITH, DP
影响因子：
14.9
作者：
Liu Z;Lozupone C;Hamady M;Bushman FD;Knight R
通讯作者：
Knight R
影响因子：
14.9
作者：
Cole JR;Wang Q;Cardenas E;Fish J;Chai B;Farris RJ;Kulam-Syed-Mohideen AS;McGarrell DM;Marsh T;Garrity GM;Tiedje JM
通讯作者：
Tiedje JM
DOI：
10.1073/pnas.1000080107
发表时间：
2011-03-15
影响因子：
11.1
作者：
Caporaso, J. Gregory;Lauber, Christian L.;Knight, Rob
通讯作者：
Knight, Rob