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.
Highlights
The genus Propionibacterium belongs to the class of high GC actinobacteria
Annotation of the P. freudenreichii genome reveals the hardiness of the bacterium, its ability to cope with different stresses, to withstand phage attack, to accumulate glycogen and polyphosphate under favorable conditions, to mobilize these compounds during starvation conditions and, lastly, to synthesize most vitamins and amino acids
Unlike lactic acid bacteria such as L. bulgaricus, Propionibacteria do not seem to be over-adapted to cheese conditions
Summary
The genus Propionibacterium belongs to the class of high GC actinobacteria. All species of this genus produce propionic acid as a major metabolic end-product. Other dairy propionibacteria species such as P. acidipropionici, and P. thoenii have been found in milk and cheese, and sometimes in various biotopes like silage, soil, rumen, and waste water [3] These observations indicate the ability to adapt to various environmental conditions. Propionibacterium freudenreichii is essential as a ripening culture in Swiss-type cheeses and is 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
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