Métagénomique : Ce que nous apprennent les nouveaux outils d’exploration du vivant

International audienc

DAIRYdb: Une base de données de références pour une meilleure assignation taxonomique des ARNr 16S issus des produits laitiers

International audienc

Stability of microbial communities in goat milk during a lactation year: molecular approaches

The microbial communities in milks from one herd were evaluated during 1-year of lactation, using molecular methods to evaluate their stability and the effect of breeding conditions on their composition. The diversity of microbial communities was measured using two approaches: molecular identification by 16S and 18S rDNA sequencing of isolates from counting media (two milks), and direct identification using 16S rDNA from clone libraries (six milks). The stability of these communities was evaluated by counting on selective media and by Single Strand Conformation Polymorphism (SSCP) analysis of variable region V3 of the 16S rRNA gene and variable region V4 of the 18S rRNA gene. One hundred and eighteen milk samples taken throughout the year were analyzed. Wide diversity among bacteria and yeasts in the milk was revealed. In addition to species commonly encountered in milk, such as Lactococcus lactis, Lactococcus garvieae, Enterococcus faecalis, Lactobacillus casei, Leuconostoc mesenteroides, Staphylococcus epidermidis, Staphylococcus simulans, Staphylococcus caprae, Staphylococcus equorum, Micrococcus sp., Kocuria sp., Pantoea agglomerans and Pseudomonas putida, sequences were affiliated to other species only described in cheeses, such as Corynebacterium variabile, Arthrobacter sp., Brachybacterium paraconglonleratum, Clostridium sp. and Rothia sp. Several halophilic species atypical in milk were found, belonging to Jeotgalicoccus psychrophilus, Salinicoccus sp., Dietza maris, Exiguobacterium, Ornithinicoccus sp. and Hahella chjuensis. The yeast community was composed of Debaryomyces hansenii, Kluyveromyces lactis, Trichosporon beigelii, Rhodolorula glutinis, Rhodotorula minuta, Candida pararugosa, Candida intermedia, Candida inconspicua, Cryptococcus curvatus and Cryptococcus magnus. The analyses of microbial counts and microbial SSCP profiles both distinguished four groups of milks corresponding to four periods defined by season and feeding regime. The microbial community was stable within each period. Milks from winter were characterized by Lactococcus and Pseudomonas, those from summer by P. agglomerans and Klebsiella and those from autumn by Chryseobacterium indologenes, Acinetobacter baumanii, Staphylococcus, Corynebacteria and yeasts. However, the composition of the communit

Comment approcher les systèmes microbiens complexes ?

National audienc

Application of SSCP-PCR fingerprinting to profile the yeast community in raw milk Salers cheeses

International audienceBacteria and yeasts are important sensory factors of raw-milk cheeses as they contribute to the sensory richness and diversity of these products. The diversity and succession of yeast populations in three traditional Registered Designation of Origin (R.D.O.) Salers cheeses have been determined by using phenotypic diagnoses and Single-Strand Conformation Polymorphism (SSCP) analysis. Isolates were identified by phenotypic tests and the sequencing of the D1-D2 domains of the 26S rRNA gene. Ninety-two percent of the isolates were identified as the same species in both tests. Yeast-specific primers were designed to amplify the V4 region of the 18S rRNA gene for SSCP analysis. The yeast species most frequently encountered in the three cheeses were Kluyveromyces lactis, Kluyveromyces marxianus. Saccharmoyces cerevisiae, Candida zeylanoides and Debaryomyces hansenii. Detection of less common species, including Candida parapsilosis, Candida siivae, Candida intermedia, Candida rugosa, Saccharomyces unisporus, and Pichia guilliermondii was more efficient with the conventional method. SSCP analysis was accurate and could be used to rapidly assess the proportions and dynamics of the various species during cheese ripening. Each cheese was clearly distinguished by its own microbial community dynamics

Characterization of inhibition mechanisms of Staphylococcus aureus by Lactococcus garvieae

International audienc

Staphylococcus aureus growth and enterotoxin production during the manufacture of uncooked, semihard cheese from cows' raw milk

International audienceStaphylococcus aureus growth and enterotoxin production during the manufacture of model Saint-Nectaire, Registered Designation of Origin Saint-Nectaire, and Registered Designation of Origin Salers cheeses, three types of uncooked, semihard, raw milk cheese, were investigated. Coagulase-positive staphylococci (SC+) grew rapidly during the first 6 h. Between 6 and 24 h, counts increased by less than 0.5 log CFU/ml. Raw milk counts ranged from undetectable ( 0.80) but pH at 6 h influenced the SC+ growth observed between 6 and 24 h (r > 0.70). Thus, the initial level of SC+ in raw milk should be maintained below 100 CFU/ml and best below 40 CFU/ml. To limit growth, acidification should be managed to obtain pH values around or below 5.8 at 6 h in Saint-Nectaire cheeses and around or below 6.3 at 6 h in Salers cheeses. Enterotoxins were only detected in two Salers cheeses whose SC+ counts on day 1 were 5.55 log CFU/g and 5.06 log CFU/g, respectively, and whose pH values at 6 h were high (approximately 6.6 and 6.5, respectively)

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation

Effect of fat composition on the development of bacterial communities in Cantal-type cheeses

Effect of fat composition on the development of bacterial communities in Cantal-type cheeses. IDF Cheese Science and Technology 201