Journal Article

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

Loux, Valentin, Kennedy, Sean, Pons, Nicolas, Abraham, Anne-Laure, Montel, Marie-Christine, Monnet, Christophe, Delbès, Céline, Irlinger, Françoise, Rasmussen, Simon, Pop, Mihai, Batto, Jean-Michel, Ehrlich, Stanislas Dusko, Almeida, Mathieu, Renault, Pierre, Hébert, Agnès, Leonard, Pierre

2014

Overview

Background 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. Results 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. Conclusions 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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Animal Genetics and Genomics / Bacteria / Bacteria - genetics / Bacteria - metabolism / Bioinformatics / Biomedical and Life Sciences / Cheese - microbiology / Colleges & universities / Dairy products / Dairy Products - microbiology / Databases, Genetic / Deoxyribonucleic acid / DNA / DNA sequencing / Fermentation / Food / Genetic aspects / Genetic diversity / Genome, Bacterial - genetics / Genomes / Genomics / Kluyvera / Life Sciences / Metagenomics - methods / Methods / Microarrays / Microbial activity / Microbial Genetics and Genomics / Microbiota / Microorganisms / Nucleotide sequencing / Phylogenetics / Plant Genetics and Genomics / Prokaryote microbial genomics / Proteomics / Pseudoalteromonas haloplanktis / Psychrobacter immobilis / Research Article / Sequence Analysis / Taxonomy