Functional genomics provides insights into the role of Propionibacterium freudenreichii ssp. shermanii JS in cheese ripening

Abstract

Propionibacterium freudenreichii is a commercially important bacterium that is essential for the development of the characteristic eyes and flavor of Swiss-type cheeses. These bacteria grow actively and produce large quantities of flavor compounds during cheese ripening at warm temperatures but also appear to contribute to the aroma development during the subsequent cold storage of cheese. Here, we advance our understanding of the role of P. freudenreichii in cheese ripening by presenting the 2.68-Mbp annotated genome sequence of P. freudenreichii ssp. shermanii JS and determining its global transcriptional profiles during industrial cheese-making using transcriptome sequencing. The annotation of the genome identified a total of 2377 protein-coding genes and revealed the presence of enzymes and pathways for formation of several flavor compounds. Based on transcriptome profiling, the expression of 348 protein-coding genes was altered between the warm and cold room ripening of cheese. Several propionate, acetate, and diacetyl/acetoin production related genes had higher expression levels in the warm room, whereas a general slowing down of the metabolism and an activation of mobile genetic elements was seen in the cold room. A few ripening-related and amino acid catabolism involved genes were induced or remained active in cold room, indicating that strain JS contributes to the aroma development also during cold room ripening. In addition, we performed a comparative genomic analysis of strain JS and 29 other Propionibacterium strains of 10 different species, including an isolate of both P. freudenreichii subspecies freudenreichii and shermanii. Ortholog grouping of the predicted protein sequences revealed that close to 86% of the ortholog groups of strain JS, including a variety of ripening-related ortholog groups, were conserved across the P. freudenreichii isolates. Taken together, this study contributes to the understanding of the genomic basis of P. freudenreichii and sheds light on its activities during cheese ripening.

De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

“…Eighteen of the strains were sequenced with a PacBio RSII instrument, followed by assembly using Hierarchical Genome Assembly Process (HGAP3) in SMRT Analysis software (Table 2 ). The two remaining strains: the type strain JS16 (DSM 20271, CP010341) and JS (LN997841) were published before [ 25 , 26 ]. The other type strain, JS15 (DSM 4902), has been sequenced previously [ 21 ], but it was re-sequenced with PacBio for this study.…”

“…Summary of the genome sequences Strain Sequence name Accession number Genome size (bp) Genome coverage GC% No. of predicted genes Note JS PFREUDJS001 LN997841 2,675,045 691 67% 2382 Sequenced previously [ 26 ]; 261 a JS2 PFRJS2 LT576032 2,655,351 317 67% 2310 257 a JS4 PFRJS4 LT576033 2,654,663 158 67% 2366 259 a JS7 PFRJS7–1 LT618776 2,738,418 300 67% 2412 Genome with prophage; 263 a PFRJS7–2 LT618777 2,700,482 50 67% 2355 Genome without phage PFRJS7-ph LT618778 37,936 60 65% 59 Circular phage JS8 PFRJS8 LT576042 2,655,373 392 67% 2324 264 a JS9 PFRJS9–1 LT618785 2,720,049 219 67% 2405 Additional transposase gene; 265 a PFRJS9–2 LT618786 2,718,592 219 67% 2401 JS10 PFRJS10 LT576035 2,626,110 208 67% 2329 266 a JS11 PFRJS11 LT576038 2,537,402 ...…”

“…This led to questioning the validity of the subdivision [ 21 ], which was proven not warranted [ 22 ]. Sequencing projects resulted in 22 draft genomes [ 23 , 24 ] and two additional complete genomes [ 25 , 26 ] available for the species. Although the draft genomes proved valuable and were used in a number of comparative and functional studies [ 24 , 27 – 29 ], they do not permit studies of genome organization or mobile elements absent from the reference genome [ 30 ].…”

Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains

“…Previous in vivo studies have confirmed that P. freudenreichii can adapt to the porcine colon by altering protein expression and energy substrate utilization (Saraoui et al, 2013). Evolutionary adaptation and probiotic potentials of P. freudenreichii strains have previously been assessed by defining the genome sequences of three dairy-associated strains DSM 20271 T , CIRM BIA 1T and JS (Falentin et al, 2010;Koskinen et al, 2015;Ojala et al, 2017). Compared with the genome of the Acidipropionibacterium strain ATCC4875 (Parizzi et al, 2012), the P. freudenreichii strains have smaller genomes (roughly 3.6 Mbp versus 2.6 Mbp), and although many common genes could be identified, the genomes of the two species vary significantly (Parizzi et al, 2012;Koskinen et al, 2015).…”

Antibacterial Activity of Enterococcus faecium and Propionibacterium sp. against Food-borne and Pathogenic Bacteria

“…acid and vitamin B12 (De Freitas et al, 2015), and synthesize several different bio-protective compounds such as bacteriocins or antifungal compounds (Ojala et al, 2017). Moreover, many members of the dairy industry have a long history of safe use in food manufacturing.…”