Directed Evolution of Microbial Communities in Fermented Foods: Strategies, Mechanisms, and Challenges

Directed Evolution of Microbial Communities (DEMC) offers a promising approach to enhance the functional attributes of microbial consortia in fermented foods by mimicking natural selection processes. This review details the application of DEMC in fermented foods, focusing on optimizing community traits to improve both fermentation efficiency and the sensory quality of the final products. We outline the core techniques used in DEMC, including the strategic construction of initial microbial communities, the systematic introduction of stress factors to induce desirable traits, and the use of artificial selection to cultivate superior communities. Additionally, we explore the integration of genomic tools and dynamic community analysis to understand and guide the evolutionary trajectories of these communities. While DEMC shows substantial potential for refining fermented food products, it faces challenges such as maintaining genetic diversity and functional stability of the communities. Looking ahead, the integration of advanced omics technologies and computational modeling is anticipated to significantly enhance the predictability and control of microbial community evolution in food fermentation processes. By systematically improving the selection and management of microbial traits, DEMC serves as a crucial tool for enhancing the quality and consistency of fermented foods, directly contributing to more robust and efficient food production systems.

High throughput screening of technological and biopreservation traits of a large set of wild lactic acid bacteria from Brazilian artisanal cheeses

This study aimed to evaluate technological (acidification, proteolysis, lipolysis, resistance to low pH, NaCl, and bile salts) and biopreservation (antimicrobial activity against foodborne pathogens) features of 1002 LAB by high throughput screening (HTS) methods. The LAB was isolated from 11 types of Brazilian artisanal cheeses (BAC) marketed in the main 5 producing regions. Remarkable intra-species variability in acidification rates have been found, which was most pronounced between isolates from Mina's artisanal cheeses, Caipira and Coalho cheeses. Lacticaseibacillus paracasei and Levilactobacillus brevis showed the fastest acidification rate; however, all isolates showed slower acidification rates than a lactococcal control strain (4.3 × lower). When testing inhibitory effects, > 75% of LAB isolates could inhibit the growth of Staphylococcus aureus ATCC 19095 and Listeria monocytogenes ATCC 7644. Two of these isolates, identified as Lactiplantibacillus plantarum and Lentilactobacillus buchneri, the sterile and neutral supernatants alone, were sufficient to inhibit L. monocytogenes growth. Principal component analysis (PCA) allowed the identification of functional groups based on proteolytic and lipolytic activity, osmotic stress resistance, and inhibition of L. monocytogenes. The type of cheese the isolates were recovered from influenced properties such as anti-listerial compounds and lipolytic enzyme production. The use of HTS and multivariate statistics allowed insights into a diverse set of LAB technological and biopreservation properties. These findings allow a profound knowledge of the heterogeneity of a large set of isolates, which can be further used to design starter cultures with varied and combined properties, such as biopreservation and technological features. Besides that, HTS makes it possible to analyze a vast panel of LAB strains, reducing costs and time within laboratory analysis, while avoiding the loss of information once all LAB are tested at the same time (differently from the traditional labor-intensive approach, in which a few numbers of strains is tested per time).

Whole-genome sequencing and genomic-based acid tolerance mechanisms of Lactobacillus delbrueckii subsp. bulgaricus LJJ

The probiotic efficacy and fermentative ability of Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus), a widely used probiotic, is majorly affected by its acid tolerance. Here, we conducted whole-genome sequencing of the high acid-tolerant L. bulgaricus LJJ stored in the laboratory. Compared with the whole genome of low acid-tolerant strain L. bulgaricus ATCC11842, the results show that 16 candidate acid-tolerant genes may be involved in the regulation of the acid tolerance of L. bulgaricus LJJ. Association analysis of candidate acid-tolerant genes and acid-tolerant traits of different L. bulgaricus strains revealed that the three genes dapA, dapH, and lysC are the main reasons for the strong acid tolerance of L. bulgaricus LJJ. The results of real-time quantitative PCR (RT-qPCR) supported this conclusion. KEGG pathway analysis showed that these three acid-tolerant genes are involved in the synthesis of lysine; the synthesis of lysine may confer L. bulgaricus LJJ strong acid tolerance. This study successfully revealed the acid tolerance mechanism of L. bulgaricus LJJ and provides a theoretical basis for the subsequent selection of strains with high acid tolerance for improved probiotic functions. KEY POINTS: • Three genes are identified as acid-tolerant genes, respectively, lysC, dapA, and dapH. • LysC and dapA are the major key genes in the synthesis of lysine. • The synthesis of lysine may confer L. bulgaricus LJJ strong acid tolerance.

Enhanced Acid Tolerance in Lactobacillus acidophilus by Atmospheric and Room Temperature Plasma (ARTP) Coupled with Adaptive Laboratory Evolution (ALE)

The aim of this study was to improve the acid tolerance of Lactobacillus acidophilus by combining atmospheric and room temperature plasma (ARTP) mutation with adaptive laboratory evolution (ALE). To achieve a high mutation efficiency, 60 s was determined as the ideal exposure time for ARTP mutation of L. acidophilus with a survival rate of 5.91%. The ARTP-ALE mutant strain LAartp-ale2 displayed increased lactic acid stress tolerance with survival rates of 75.67% and 25.78% when cultured in pH 3.0 and 2.5, respectively, for 3 h. Physiological analysis revealed that the ARTP-ALE mutant exhibited a lower inner membrane permeability than that of the parental strain during acid stress. Furthermore, the mutant LAartp-ale2 produced more biofilm in response to lactic acid-induced acid stress and showed an increased hydrophobicity (87.2%) when compared to the parent strain (76.2%) at pH 2.5. LAartp-ale2 exhibited a higher unsaturated fatty acid (UFA) to saturated fatty acid (SFA) ratio that affected the physical state of the cell membrane for increased survival in pH 3.0 and 2.5. The mutation with ARTP coupled with ALE in the present study proved to be effective in enhancing the acid tolerance of L. acidophilus for potential industrial use.