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

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dc.contributor.authorAlmeida, Mathieu
dc.contributor.authorHébert, Agnès
dc.contributor.authorAbraham, Anne-Laure
dc.contributor.authorRasmussen, Simon
dc.contributor.authorMonnet, Christophe
dc.contributor.authorPons, Nicolas
dc.contributor.authorDelbès, Céline
dc.contributor.authorLoux, Valentin
dc.contributor.authorBatto, Jean-Michel
dc.contributor.authorLeonard, Pierre
dc.contributor.authorKennedy, Sean
dc.contributor.authorEhrlich, Stanislas Dusko
dc.contributor.authorPop, Mihai
dc.contributor.authorMontel, Marie-Christine
dc.contributor.authorIrlinger, Françoise
dc.contributor.authorRenault, Pierre
dc.date.accessioned2021-08-30T20:43:01Z
dc.date.available2021-08-30T20:43:01Z
dc.date.issued2014-12-13
dc.description.abstractMicrobial 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.en_US
dc.description.urihttps://doi.org/10.1186/1471-2164-15-1101
dc.identifierhttps://doi.org/10.13016/m2ez-o3d0
dc.identifier.citationAlmeida, M., Hébert, A., Abraham, AL. et al. Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products. BMC Genomics 15, 1101 (2014).en_US
dc.identifier.urihttp://hdl.handle.net/1903/27662
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Natural Sciencesen_us
dc.relation.isAvailableAtComputer Scienceen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectGenomic librariesen_US
dc.subjectGenome sequencingen_US
dc.subjectSequence assemblyen_US
dc.subjectNext-generation sequencingen_US
dc.subjectComparative genomicsen_US
dc.subjectMetagenomicsen_US
dc.subjectFood bacteriaen_US
dc.subjectDairy ecosystemsen_US
dc.titleConstruction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented productsen_US
dc.typeArticleen_US

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