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Background  Plant-based milk alternatives are more popular than ever, and chickpea-based milks are among the most commercially relevant products. Unfortunately, limited nutritional value because of low levels of the essential amino acid  l -lysine, low digestibility and unpleasant taste are challenges that must be addressed to improve product quality and meet consumer expectations.    Results  Using  in-silico  screening and food safety classifications, 31 strains were selected as potential  l -lysine producers from approximately 2,500 potential candidates. Beneficially, 30% of the isolates significantly accumulated amino acids (up to 1.4 mM) during chickpea milk fermentation, increasing the natural level by up to 43%. The best-performing strains,  B. amyloliquefaciens  NCC 156 and  L. paracasei  subsp . paracasei  NCC 2511, were tested further. De novo lysine biosynthesis was demonstrated in both strains by  13 C metabolic pathway analysis. Spiking small amounts of citrate into the fermentation significantly activated  l -lysine biosynthesis in NCC 156 and stimulated growth. Both microbes revealed additional benefits in eliminating indigestible sugars such as stachyose and raffinose and converting off-flavour aldehydes into the corresponding alcohols and acids with fruity and sweet notes.    Conclusions   B. amyloliquefaciens  NCC 156 and  L. paracasei  subsp . paracasei  NCC 2511 emerged as multi-benefit microbes for chickpea milk fermentation with strong potential for industrial processing of the plant material. Given the high number of  l -lysine-producing isolates identified in silico, this concept appears promising to support strain selection for food fermentation.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12934-021-01595-2.

microbial cell factories

Genome-based selection and application of food-grade microbes for chickpea milk fermentation towards increased l-lysine content, elimination of indigestible sugars, and improved flavour