The carbohydrate metabolism signature of lactococcus lactis strain A12 reveals its sourdough ecosystem origin

Abstract

Lactococcus lactis subsp. lactis strain A12 was isolated from sourdough. Combined genomic, transcriptomic, and phenotypic analyses were performed to understand its survival capacity in the complex sourdough ecosystem and its role in the microbial community. The genome sequence comparison of strain A12 with strain IL1403 (a derivative of an industrial dairy strain) revealed 78 strain-specific regions representing 23% of the total genome size. Most of the strain-specific genes were involved in carbohydrate metabolism and are potentially required for its persistence in sourdough. Phenotype microarray, growth tests, and analysis of glycoside hydrolase content showed that strain A12 fermented plant-derived carbohydrates, such as arabinose and α-galactosides. Strain A12 exhibited specific growth rates on raffinose that were as high as they were on glucose and was able to release sucrose and galactose outside the cell, providing soluble carbohydrates for sourdough microflora. Transcriptomic analysis identified genes specifically induced during growth on raffinose and arabinose and reveals an alternative pathway for raffinose assimilation to that used by other lactococci.

Fig 1

Raffinose metabolism by L. lactis subsp. lactis strain A12. (A) Kinetics of carbohydrates quantified in supernatant culture; (B) sucrose and galactose excreted, as a function of the raffinose metabolized. The line y = x represents the theoretical maximum of excreted sugar without any consumption of sugar. Data for raffinose (△), galactose (○), and sucrose (□) are shown. No melibiose, fructose, or glucose was detected.

Fig 2

Venn diagrams representing the number of strain A12 genes with variable expression in different sugar substrates: combined comparison of raffinose (raff) (A) or arabinose (ara) (B) with the three simple sugars (glucose [glu], fructose [fru], and galactose [gal]), highlighting raffinose- and arabinose-specific genes. The variation of gene expression was considered significant when the false discovery rate was <10%.

Fig 3

Arabinose metabolism by L. lactis subsp. lactis. (A) Localization and genetic organization of the arabinose operon in sequenced genomes; (B) diagram of the related metabolic pathway. The numbers in brackets correspond to the average ratio values obtained by transcriptomic analysis for arabinose versus that of simple sugars. xylX, acetyltransférase; xylT, d-xylose proton-symporter; araA, l-arabinose isomerase; araD, l-ribulose-5-phosphate 4-epimerase; araB, l-ribulokinase; araT, arabinose-proton symporter; araF, α-N-arabinofuranosidase; araP, disaccharide permease; araR, GntR family arabinose operon repressor; ptk, phosphoketolase.

Fig 4

Comparison of the organization of genes involved in raffinose metabolism in Lactococcus raffinolactis ATCC 43920, Lactococcus lactis subsp. lactis KF147, and Lactococcus lactis subsp. lactis A12. Arrows correspond to the different genes: sugar catabolism genes are indicated by hatched arrows, sugar transporter genes are represented in gray, regulatory genes are represented in black, and strain-specific or unknown genes are represented in white. Numbers indicate the percent identities of nucleotide sequences of common CDS identified.