Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese

Salt reduction in film‐ripened, semihard Edam cheese

“…Both the sub4salt ® and the low NaCl as well as the regular NaCl cheeses showed similar bacterial growth in cheese. The progression of microbial growth of the starter and adjunct cultures during fermentation and ripening in Na‐reduced Edam followed a typical development for Edam as documented in previous studies (Wachowska ; Ruyssen et al ; Porcellato and Skeie ). As Edam cheese is mainly manufactured from pasteurised milk, nonstarter lactic acid bacteria (NSLAB) originating from the raw milk are of little significance.…”

Insect frass in stored cereal products as a potential source ofLactobacillus sanfranciscensisfor sourdough ecosystem

“…Bacterial and fungal compositions of the insect frass were studied by sequencing the 16S rRNA gene and the internal transcribed spacer (ITS) region respectively. The libraries were constructed according to the method described by Porcellato and Skeie () with minor changes. In brief, the variable regions V3 and V4 of the bacterial 16S rRNA gene were amplified using the universal primer Uni340F (5′‐CCTACGGGRBGCASCAG‐3′) and Bac806R (5′‐GGACTACYVGGGTATCTAAT‐3′) (Takai and Horikoshi ) while ITS region of fungal operon was amplified with primer BITS (5′ACCTGCGGARGGATCA–3′) and B58S3 (5′–GAGATCCRTTGYTRAAAGTT–3′) (Bokulich and Mills ).…”

“…Chimeras were removed during the OTU clustering step. Taxonomy was assigned to each OTUs as previously described by Porcellato and Skeie () using the Silva 16S rRNA database or the UNITE fungal ITS database. Unannotated OTUs or OTUs with matches lower than 97% against the sequence database were removed from the final OTU table.…”

“…In order to evaluate the Lactobacillus species diversity and to identify L. sanfranciscensis within the insect frass reads, a previously created Lactobacillus database (Porcellato and Skeie ) was used as reference. The database consisted of in silico made PCR products obtained from Lactobacillus sequences found in different databases.…”

Analysis of the Bacterial Diversity of Paipa Cheese (a Traditional Raw Cow’s Milk Cheese from Colombia) by High-Throughput Sequencing

“…High-throughput sequencing (HTS) has become a powerful culture-independent approach that can be used to obtain snapshots of microbial communities from food systems. In the milk and dairy industry, numerous studies based on HTS technologies have been carried out [3] with different purposes, e.g., to decipher the microbiota from farm environments and animals [4], raw and pasteurized milk [5], transportation tanks, vats, utensils and cheese production facilities [6][7][8] and the variations associated with season [6] or animal feeding [9], to establish relationships between microbial communities in the raw materials, the environment and the finished product [8][9][10], to study the changes in the bacterial communities associated with cheese-making [9,11] and cheese ripening processes [9,[12][13][14][15], or to determine the microbial composition of cheeses and cheese varieties [16][17][18][19]. Furthermore, HTS studies can also provide information on adventitious or previously overlooked microbiota or the presence of pathogenic or spoilage bacteria in the cheese and dairy environment [2,3,11,14,20,21].…”