Abstract
BackgroundMicrobial 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.ResultsWe 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1101) contains supplementary material, which is available to authorized users.
Highlights
Microbial communities of traditional cheeses are complex and insufficiently characterized
Only 80 (41%) comprise at least one isolate for which a genome sequence isolated from food is available, with almost half of them within Lactobacillus species (NCBI database, May 2014)
Creation of a dairy reference genome catalog After bibliographic investigation for bacterial species occurring in dairy products, we collected 142 dairy bacteria of various origins
Summary
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. Only 80 (41%) comprise at least one isolate for which a genome sequence isolated from food is available, with almost half of them within Lactobacillus species (NCBI database, May 2014) This list cannot be considered as exhaustive of the cheese microbial diversity, since occurrences of species previously undetected in milk and cheese are periodically reported [11,12,13] and isolates affiliated to novel taxa characterized [4]. An increase in the number of genome sequences of dairy bacteria is useful for a better understanding of the genetic determinants involved in the adaptation to the dairy habitat and the generation of functional properties [20,21,22,23]
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