Data from a proteomic comparative analysis highlight differential adaptation of Lactobacillus delbrueckii subsp. bulgaricus to cow milk versus to soy milk environments.

The article presents a proteomic dataset generated by a comparative analysis, using gel-free nanoLC-MS/MS, of the cellular proteome of Lactobacillus delbrueckii subsp. bulgaricus, a yogurt starter, when cultivated in soy milk versus in cow milk. The CIRM-BIA1592 strain was cultivated in the aqueous phase of soy milk, or of cow milk. Whole-cell proteins were extracted, trypsinolyzed and analyzed by nano LC-MS/MS, prior to identification and to classification by function using the X!Tandem pipeline software and the proteomic data from NCBI.nlm.nigh.gov. Quantification of the proteins was moreover performed to evidence changes in their expression, depending on the culture medium. Data are available via ProteomeXchange with the identifier PXD033905 (http://www.proteomexchange.org/). This article is related to the research article entitled "The stressing life of Lactobacillus delbrueckii subsp. bulgaricus in soy milk", by G.Jan et al. in Food Microbiology, 2022. This proteomic differential analysis indeed revealed major modulation of the stress proteome, with many stress proteins upregulated in the soy environment.

The stressing life of Lactobacillus delbrueckii subsp. bulgaricus in soy milk.

Lactobacillus delbrueckii subsp. bulgaricus is a beneficial lactic acid bacterium and constitutes one of the most used, and thus consumed, dairy starters, worldwide. This homofermentative bacterium was the first lactobacillus described and is involved in the fermentation of yogurt and of diverse other fermented products, including cheeses. It has a long history of safe use, as well as documented probiotic lato sensu effects, including alleviation of lactose intolerance. Plant-based fermented products presently experience a considerable development, as a result of evolution of consumers' habits, in a general context of food transition. This requires research and development, and thus scientific knowledge, to allow such transition, including the development of fermented soy milks. These last indeed offer an alternative source of live and active bacteria. The yogurt starters L. delbrueckii subsp. bulgaricus, together with Streptococcus thermophilus, have been implemented to generate yogurt-type fermented soy milks worldwide. While the adaptation of these starters to the dairy environment has been extensively studied, little is known about L. delbrueckii adaptation to the soy environment. We therefore investigated its adaptation to soy milk and compared it to cow's milk. Surprisingly, it did not grow in soy milk, neither alone, nor in co-culture with S. thermophilus. Acidification of soy milk was however faster in the presence of both species. In order to deepen such adaptation, we then compared L. delbrueckii growth and survival in soy milk ultrafiltrate (SUF, the aqueous phase of soy milk) and compared it to cow's milk ultrafiltrate (MUF, the aqueous phase of cow milk). This comparison revealed major differences in terms of cell morphology and proteome composition. Lactobacilli appeared deformed and segmented in soy. Major differences in both the surface and the cellular proteome indicated upregulation of stress proteins, yet downregulation of cell cycle and division machinery. Altogether, these results suggest that soy milk may be a stressing environment for the yogurt starter L. delbrueckii subsp. bulgaricus.

Differential Adaptation of Propionibacterium freudenreichii CIRM-BIA129 to Cow's Milk Versus Soymilk Environments Modulates Its Stress Tolerance and Proteome.

Propionibacterium freudenreichii is a beneficial bacterium that modulates the gut microbiota, motility and inflammation. It is traditionally consumed within various fermented dairy products. Changes to consumer habits in the context of food transition are, however, driving the demand for non-dairy fermented foods, resulting in a considerable development of plant-based fermented products that require greater scientific knowledge. Fermented soymilks, in particular, offer an alternative source of live probiotics. While the adaptation of lactic acid bacteria (LAB) to such vegetable substrates is well documented, little is known about that of propionibacteria. We therefore investigated the adaptation of Propionibacterium freudenreichii to soymilk by comparison to cow's milk. P. freudenreichii grew in cow's milk but not in soymilk, but it did grow in soymilk when co-cultured with the lactic acid bacterium Lactobacillus plantarum. When grown in soymilk ultrafiltrate (SUF, the aqueous phase of soymilk), P. freudenreichii cells appeared thinner and rectangular-shaped, while they were thicker and more rounded in cow's milk utltrafiltrate (MUF, the aqueous phase of cow milk). The amount of extractable surface proteins (SlpA, SlpB, SlpD, SlpE) was furthermore reduced in SUF, when compared to MUF. This included the SlpB protein, previously shown to modulate adhesion and immunomodulation in P. freudenreichii. Tolerance toward an acid and toward a bile salts challenge were enhanced in SUF. By contrast, tolerance toward an oxidative and a thermal challenge were enhanced in MUF. A whole-cell proteomic approach further identified differential expression of 35 proteins involved in amino acid transport and metabolism (including amino acid dehydrogenase, amino acid transporter), 32 proteins involved in carbohydrate transport and metabolism (including glycosyltransferase, PTS), indicating metabolic adaptation to the substrate. The culture medium also modulated the amount of stress proteins involved in stress remediation: GroEL, OpuCA, CysK, DnaJ, GrpE, in line with the modulation of stress tolerance. Changing the fermented substrate may thus significantly affect the fermentative and probiotic properties of dairy propionibacteria. This needs to be considered when developing new fermented functional foods.