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Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

ABSTRACT: 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.

SUBMITTER: Almeida M

PROVIDER: S-EPMC4320590 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

Almeida Mathieu M Hébert Agnès A Abraham Anne-Laure AL Rasmussen Simon S Monnet Christophe C Pons Nicolas N Delbès Céline C Loux Valentin V Batto Jean-Michel JM Leonard Pierre P Kennedy Sean S Ehrlich Stanislas Dusko SD Pop Mihai M Montel Marie-Christine MC Irlinger Françoise F Renault Pierre P

BMC genomics 20141213

<h4>Background</h4>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 w ...[more]

PMID: 25496341

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Dataset Information

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

Publications

Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.

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