TY - JOUR
T1 - Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products
AU - Almeida, Mathieu
AU - Hebert, Agnes
AU - Abraham, Anne-Laure
AU - Rasmussen, Simon
AU - Monnet, Christophe
AU - Pons, Nicolas
AU - Delbes, Celine
AU - Loux, Valentin
AU - Batto, Jean-Michel
AU - Leonard, Pierre
AU - Kennedy, Sean
AU - Ehrlich, Stanislas Dusko
AU - Pop, Mihai
AU - Montel, Marie-Christine
AU - Irlinger, Francoise
AU - Renault, Pierre
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
KW - Genomic libraries
KW - Genome sequencing
KW - Sequence assembly
KW - Next-generation sequencing
KW - Comparative genomics
KW - Metagenomics
KW - Food bacteria
KW - Dairy ecosystems
U2 - 10.1186/1471-2164-15-1101
DO - 10.1186/1471-2164-15-1101
M3 - Journal article
C2 - 25496341
SN - 1471-2164
VL - 15
JO - B M C Genomics
JF - B M C Genomics
IS - 1101
ER -