title: Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products.
abstract: 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.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Almeida
authors.forename: Agnès
authors.initials: A
authors.lastname: Hébert
authors.forename: Anne-Laure
authors.initials: AL
authors.lastname: Abraham
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.forename: Christophe
authors.initials: C
authors.lastname: Monnet
authors.forename: Nicolas
authors.initials: N
authors.lastname: Pons
authors.forename: Céline
authors.initials: C
authors.lastname: Delbès
authors.forename: Valentin
authors.initials: V
authors.lastname: Loux
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Batto
authors.forename: Pierre
authors.initials: P
authors.lastname: Leonard
authors.forename: Sean
authors.initials: S
authors.lastname: Kennedy
authors.forename: Stanislas Dusko
authors.initials: SD
authors.lastname: Ehrlich
authors.forename: Mihai
authors.initials: M
authors.lastname: Pop
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Montel
authors.forename: Françoise
authors.initials: F
authors.lastname: Irlinger
authors.affiliation: Institut National de la Recherche Agronomique, UMR 1319 MICALIS, 78352 Jouy-en-Josas, France. pierre.renault@jouy.inra.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Renault
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D002611:Cheese / Q000382:microbiology; D003611:Dairy Products / Q000382:microbiology*; D030541:Databases, Genetic; D005285:Fermentation; D016680:Genome, Bacterial / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota; D017421:Sequence Analysis