Antibacterial property and metagenomic analysis of milk kefir

Authors: Liu, Siqing; Lu, Shao; Qureshi, Nasib; EL ENSHASY, HESHAM - Universiti Teknologi Mara (UITM); Skory, Christopher - Chris

Submitted to: Probiotics and Antimicrobial Proteins
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/12/2022
Publication Date: 8/22/2022
Citation: Liu, S., Lu, S.Y., Qureshi, N., El Enshasy, H.A., Skory, C.D. 2022. Antibacterial property and metagenomic analysis of milk kefir. Probiotics and Antimicrobial Proteins. 14:1170-1183. https://doi.org/10.1007/s12602-022-09976-8.
DOI: https://doi.org/10.1007/s12602-022-09976-8

Interpretive Summary: Milk kefir fermentation refers to the process of creating carbonated, acidic, and lightly alcoholic milk beverages from dairy milk by using kefir grains as starter cultures. Consumption of kefir milk has been associated with various health benefits, presumably from the probiotics of yeast and bacteria that make up the kefir grains. In addition, many of the microbes are known to produce novel antimicrobial compounds that can be used for other applications. The microbes living inside kefir grains differ significantly depending on geographical location and production methods. In this study, three kefir grain sources were analyzed for microbial compositions using genomic sequencing technologies and tested for antimicrobial properties. One of the kefir samples was found to have a unique microbial population and exhibited high antibacterial properties. Subsequentially two lactic acid bacterial strains with antibacterial activities were purified from this sample. This research could be valuable in the production of new probiotics for improved health and the discovery of new antimicrobial compounds.

Technical Abstract: Milk kefir fermentation has been used in households for generations. Consumption of milk kefir has been associated with various health benefits, presumably from the probiotics of yeast and bacteria that make up the kefir grains. In addition, many of the microbes are known to produce novel antimicrobial compounds that can be used for other applications. The microbes living inside kefir grains differ significantly depending on geographical location and production methods. In this study, we aimed to use metagenomic analysis of fermented milk by using three different kefir grains (Kefir 1, Kefir 2 and Kefir 3) from different US sources. We analyzed the microbial compositions of the three milk fermentation samples. This study revealed that each sample contains unique and distinct groups of microbes, Kefir 1 showed the least diversity and Kefir 3 showed the highest diversity. Kefir 3 is rich in Proteobacteria while Kefir 2 is dominated by the Firmicutes. Using bacterial indicator growth analyses carried out by continuous readings from microplate-based bioreactor assays suggested that Kefir 2 fermentation filtrate has higher antibacterial property. We have screened 30 purified cultures of Kefir 2 sample and isolated two lactic acid bacteria strains with higher antibacterial activities, the two strains were identified as Leuconostoc mesenteroides 28-1 and Lactobacillus kefiri 25-2 by 16S genomic PCR with confirmed antibacterial activities of fermentation filtrate after growing under both aerobia and anaerobic conditions.