The Complete Genome of Propionibacterium freudenreichii CIRM-BIA1T, a Hardy Actinobacterium with Food and Probiotic Applications

Abstract

Background Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is also considered for its probiotic use [1]. This species exhibits slow growth, low nutritional requirements, and hardiness in many habitats. It belongs to the taxonomic group of dairy propionibacteria, in contrast to the cutaneous species P. acnes. The genome of the type strain, P. freudenreichii subsp. shermanii CIRM-BIA1 (CIP 103027T), was sequenced with an 11-fold coverage.Methodology/Principal FindingsThe circular chromosome of 2.7 Mb of the CIRM-BIA1 strain has a GC-content of 67% and contains 22 different insertion sequences (3.5% of the genome in base pairs). Using a proteomic approach, 490 of the 2439 predicted proteins were confirmed. The annotation revealed the genetic basis for the hardiness of P. freudenreichii, as the bacterium possesses a complete enzymatic arsenal for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) as well as sequences involved in metabolism of various carbon sources, immunity against phages, duplicated chaperone genes and, interestingly, genes involved in the management of polyphosphate, glycogen and trehalose storage. The complete biosynthesis pathway for a bifidogenic compound is described, as well as a high number of surface proteins involved in interactions with the host and present in other probiotic bacteria. By comparative genomics, no pathogenicity factors found in P. acnes or in other pathogenic microbial species were identified in P. freudenreichii, which is consistent with the Generally Recognized As Safe and Qualified Presumption of Safety status of P. freudenreichii. Various pathways for formation of cheese flavor compounds were identified: the Wood-Werkman cycle for propionic acid formation, amino acid degradation pathways resulting in the formation of volatile branched chain fatty acids, and esterases involved in the formation of free fatty acids and esters.Conclusions/SignificanceWith the exception of its ability to degrade lactose, P. freudenreichii seems poorly adapted to dairy niches. This genome annotation opens up new prospects for the understanding of the P. freudenreichii probiotic activity.

Dairy Propionibacteria: Less Conventional Probiotics to Improve the Human and Animal Health

“…Interestingly, the cell machinery involved in general stress adaptation in P. freudenreichii was shown to be encoded by multicopy stress-induced genes [40]. The redundancy and inducibility of this chaperone and protease machinery is in agreement with the ability of P.…”

“…shermanii strain CIRM-BIAlT, was sequenced with an 11-fold coverage [40]. It consists of a circular chromosome of 2,616,384 base pairs (bp) with 67% GC content, 2 rRNA operons and 45 tRNAs.…”

“…The chromosome is predicted to contain 2439 protein-coding genes and also contains 22 different insertion sequences that represent 3.47% (in base pairs) of the genome. Insertion sequences and transposable elements may promote genome plasticity and induce phenotypic changes that contribute to bacterial adaptation to different environments; being particular for propionibacteria the synthesis of capsular EPS and the ability to ferment lactose [40].…”

“…The genome sequence also showed that P. freudenreichii possesses a complete enzymatic machinery for de novo biosynthesis of aminoacids and vitamins (except panthotenate and biotin) and genes involved in the metabolism of carbon sources, immunity against phages, chaperones for stress resistance, and storage of inorganic polyphosphate, glycogen and compatible solutes such as trehalose that confer these bacteria a long survival in stationary phase [40]. Although propionibacteria are usually described as anaerobes, all the genes encoding enzymes required for aerobic respiration such as NADH dehydrogenase, succinate dehydrogenase, cytochrome bd complex, ATPase and the complete pathway for heme synthesis have been identified in the genome of P.…”

“…Their nutritional requirements are low and almost the same for all the species. Dairy propionibacteria like P. freudenreichii are able to synthesize all amino acids [40]. They can grow in a minimal medium containing ammonium as the sole nitrogen source, but a higher growth is observed in media containing amino acids [45].…”