Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.
Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.
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DOI：
10.1186/1471-2164-15-1101
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发表时间：
2014-12-13
期刊：
影响因子：
4.4
通讯作者：
Renault P
中科院分区：
文献类型：
--
作者：
Almeida M;Hébert A;Abraham AL;Rasmussen S;Monnet C;Pons N;Delbès C;Loux V;Batto JM;Leonard P;Kennedy S;Ehrlich SD;Pop M;Montel MC;Irlinger F;Renault P
传统奶酪的微生物群落复杂且特征不充分。这些微生物群落的起源、安全性和在奶酪制作中的功能作用仍未得到很好的了解。通过高通量霰弹枪测序对这些群落进行宏基因组分析是表征其基因组和功能概况的一种很有前途的方法。然而，这种分析严重依赖于适当的参考基因组数据库的可用性，以便测序读数可以对齐。我们利用低成本测序策略建立了一个适合短读元基因组分析的参考基因组目录。我们从乳制品中分离出142种67属137个不同种的细菌，成功地对其中117种进行了标准或高质量的基因组重建，其中包括公共数据库中缺失的Kluyvera属、Luteococcus属和Marinilactibacillus属。为了证明该目录的潜力，我们分析了两种涂抹奶酪和一种蓝脉奶酪表面的微生物组成，并表明这些传统奶酪的微生物群中有很大一部分是由我们研究中新测序的微生物组成的。我们的研究提供的数据，结合公开可用的基因组参考，代表了迄今为止最广泛的奶酪相关细菌目录。利用这一扩展的乳制品目录，我们发现传统奶酪中存在未经刻意接种的优势微生物，主要是革兰氏阴性属，如盐浮游假异单胞菌或固定化冷杆菌，这可能有助于传统方法生产的奶酪的特性。本文的在线版本（doi:10.1186/1471-2164-15-1101）包含补充材料，可供授权用户使用。
Microbial communities of traditional cheeses are complex and insufficiently characterized. The origin, safety and functional role in cheese making of these microbial communities are still not well understood. Metagenomic analysis of these communities by high throughput shotgun sequencing is a promising approach to characterize their genomic and functional profiles. Such analyses, however, critically depend on the availability of appropriate reference genome databases against which the sequencing reads can be aligned. We built a reference genome catalog suitable for short read metagenomic analysis using a low-cost sequencing strategy. We selected 142 bacteria isolated from dairy products belonging to 137 different species and 67 genera, and succeeded to reconstruct the draft genome of 117 of them at a standard or high quality level, including isolates from the genera Kluyvera, Luteococcus and Marinilactibacillus, still missing from public database. To demonstrate the potential of this catalog, we analysed the microbial composition of the surface of two smear cheeses and one blue-veined cheese, and showed that a significant part of the microbiota of these traditional cheeses was composed of microorganisms newly sequenced in our study. Our study provides data, which combined with publicly available genome references, represents the most expansive catalog to date of cheese-associated bacteria. Using this extended dairy catalog, we revealed the presence in traditional cheese of dominant microorganisms not deliberately inoculated, mainly Gram-negative genera such as Pseudoalteromonas haloplanktis or Psychrobacter immobilis, that may contribute to the characteristics of cheese produced through traditional methods. The online version of this article (doi:10.1186/1471-2164-15-1101) contains supplementary material, which is available to authorized users.
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DOI：
10.1099/00207713-51-6-1969
发表时间：
2001-11-01
影响因子：
2.8
作者：
Brennan, NM;Brown, R;Fox, PF
通讯作者：
Fox, PF
影响因子：
4.4
作者：
Goerges, Stefanie;Mounier, Jerome;Scherer, Siegfried
通讯作者：
Scherer, Siegfried
影响因子：
4
作者：
Feurer, C;Irlinger, F;Vallaeys, T
通讯作者：
Vallaeys, T
影响因子：
4.4
作者：
Ercolini, Danilo;De Filippis, Francesca;Iacono, Michele
通讯作者：
Iacono, Michele
影响因子：
4.4
作者：
Delbes, Celine;Ali-Mandjee, Leila;Montel, Marie-Christine
通讯作者：
Montel, Marie-Christine