Probiotic Lactic Acid Bacteria Associated with Fermented Millet Based Milk Beverage ‘Brukina’ and Effects on the Gut Microbiome

Abstract

Our diet significantly influences our gut microbiome. Fermented foods offer various nutritional advantages and may contain beneficial microorganisms known as probiotics. Brukina, a fermented beverage originating from Burkina Faso, but widely consumed in Ghana is produced from cooked millet and fermented cow milk. For probiotics to be effective, they must survive the acidity levels and bile salt concentration in the gastrointestinal tract. Their adhesion to gastrointestinal epithelial cells is also crucial for colonization and persistence in the gut. Probiotic strains should have limited resistance to antibiotics. This study sought to determine the lactic acid bacteria (LAB) present in Brukina and their impact on the gut microbiome of consumers. FDA approved Brukina sample was obtained from supermarkets in Accra, Ghana. LAB load was determined. 16S rRNA amplicons from cultured LAB strains and DNA extracts from Brukina was sequenced. Acid and bile tolerance, adhesion capacity, antimicrobial activity and antibiotic susceptibility profile of the isolated lactic acid bacteria were determined. Human participants and animal models were given Brukina samples for two weeks. Fecal samples were collected at different time points, DNA was extracted and subjected to 16S PCR amplification. Next generation sequencing was carried out and the sequence data was analyzed using Shannon indices and metagenomics parameters. LAB load ranged from 104 CFU/ml to 106 CFU/ml. 16S rRNA sequencing of genomic DNA identified the cultured LAB strains as Limosilactobacillus fermentum, Enterobacter hormaechei, Alishewanella agri, Neobacillus fumarioli, Bacillus safensis and Faecalibaculum rodentia. The direct extraction from Brukina showed the presence of Lactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus johnsonii, Lactobacillus prophage, and Lactobacillus taiwanensis. The strains exhibited antimicrobial activity against four pathogens (Escherichia coli NCTC 11954 TEM 1, K. pneumoniae NTC 13368, Salmonella typhi ACT 1, and Staphylococcus aureus). There was a notable increase in the abundance of LAB particularly, Lactobacillus delbrueckii and Lactobacillus fermentum in the gastrointestinal tracts of human participants and rat models after two weeks of consistent consumption of Brukina. Most strains that adhered very well to Intestinal Epithelial Cells (IECs) also exhibited a higher tolerance to acid and bile coupled with low resistance to orally administered antibiotics. The abundance of lactic acid bacteria in the GIT after regular consumption of Brukina, helps in the competitive elimination of enteric pathogens. The presence of a diverse range of microbes in the sample underscores the complexity of the microbial community in fermented millet-based milk beverage (Brukina). Brukina is therefore, a potential functional food with a significant LAB load. It also impacts the gut microbiome in a matter of three days of consistent consumption. The LAB strains have good probiotic potential and can be used to formulate a cocktail of starter cultures that would be used in the preparation of yoghurts, fermented foods and other probiotic products.