Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.
Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.
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DOI：
10.1371/journal.pone.0038040
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Weckx S
中科院分区：
文献类型：
--
作者：
Illeghems K;De Vuyst L;Papalexandratou Z;Weckx S
这是第一份报告的社区多样性的一个单一的自发可可豆盒发酵样品通过宏基因组方法，涉及454焦磷酸测序的系统发育分析。使用并评价了几种基于序列和基于组成的分类学分析工具，以避免软件依赖性结果，并通过与先前获得的培养物依赖性和培养物非依赖性数据进行比较来验证其结果。总的来说，这种方法揭示了比以前发现的更广泛的细菌（主要是γ-变形菌）和真菌多样性。此外，以软件独立的方式使用不同分类方法的组合，有助于了解所研究的微生物生态系统的实际组成。细菌多样性部分取决于所使用的方法，因为基于组成的方法预测的多样性比基于序列的方法更广泛，并且与考虑所有读段的方法相比，仅基于系统发育标记基因的分类方法预测的多样性更有限。宏基因组测序分析鉴定出葡萄酒汉逊孢子菌、仙人掌汉逊孢子菌、酿酒酵母、发酵乳杆菌和巴氏醋杆菌为优势种。此外，还发现可可豆发酵过程中偶尔存在的成员（如塔斯马尼亚欧文氏菌、短乳杆菌、干酪乳杆菌、鼠李糖乳杆菌、乳酸乳球菌、肠膜明串珠菌和酒类酒球菌）。此外，与病毒群落相关的序列读段具有有限的多样性，由肌尾病毒科和虹吸病毒科主导，并反映乳杆菌属为优势宿主。总之，揭示了可可豆发酵过程样品的所有成员的准确概述，表明宏基因组测序优于先前使用的技术。
This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.
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