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Antibacterial Property and Metagenomic Analysis of Milk Kefir

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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 Lentilactobacillus kefiri 25–2 by 16S genomic PCR with confirmed antibacterial activities of fermentation filtrate after growing under both aerobic and anaerobic conditions.

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All data generated and analyzed during this study are included in this published article.

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Acknowledgements

We thank Eric Hoecker and Amber Anderson for their excellent technical assistance.

Funding

USDA is an equal opportunity provider and employer. This work was supported in part by the US Department of Agriculture, Agricultural Research Service. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture.

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Authors and Affiliations

  1. Agricultural Research Service, Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, 1815 N University St, Peoria, IL, 61604, USA

    Siqing Liu, Shao-Yeh Lu & Chris D. Skory

  2. Bioenergy Research Unit, Agricultural Research Service, National Center for Agricultural Utilization Research, USDA, 1815 N University St, Peoria, IL, 61604, USA

    Nasib Qureshi

  3. Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia

    Hesham A. El Enshasy

  4. City of Scientific Research and Technology Applications (SRTA), New Burge Al Arab, Alexandria, 21934, Egypt

    Hesham A. El Enshasy

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  1. Siqing Liu
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  2. Shao-Yeh Lu
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Correspondence to Siqing Liu.

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Liu, S., Lu, SY., Qureshi, N. et al. Antibacterial Property and Metagenomic Analysis of Milk Kefir. Probiotics & Antimicro. Prot. 14, 1170–1183 (2022). https://doi.org/10.1007/s12602-022-09976-8

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  • DOI: https://doi.org/10.1007/s12602-022-09976-8

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