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

Abstract

BackgroundMicrobial 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.ResultsWe 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1101) contains supplementary material, which is available to authorized users.

Fermented Foods as Experimentally Tractable Microbial Ecosystems

“…Trait-based approaches attempt to use either directly measured microbial life-history traits, such as growth rate or predicted traits from genomic data (Fierer et al, 2014), to explain distributions or functions of microbial species. Unlike many microbial communities dominated by unculturable taxa, it is fairly straightforward to measure phenotypic and genomic traits of species within MCoFFs (Bayjanov et al, 2013;Almeida et al, 2014;Douillard and de Vos, 2014). MCoFFs that are open to dispersal, widely distributed, and are not heavily inoculated with starter cultures, including naturally fermented wines, unpasteurized rind cheeses, and sourdough breads (Table 1), could be ideal MCoFFs for linking the genetic basis of interspecific trait variation with geographic distributions.…”

SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species

“…comm.) and dairy-related bacteria from the list of bacterial species and subspecies with technological beneficial use in food products (Almeida et al, 2014).…”

Long read-based de novo assembly of low complex metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

“…So far, WMGS studies have mainly relied on short read next-generation sequencing (NGS) technologies, which are not able to span intra-and intergenomic repeats. As a consequence, the assemblies remained highly fragmented [11,12]. Binning methods, both supervised (reference based) [13] and unsupervised (coverage and nucleotide composition based) [14], have advanced the study of metagenomes to a certain extent [15].…”