Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors

Ibacache-Quiroga, Claudia; González-Pizarro, Karoll; Charifeh, Mariam; Canales, Christian; Díaz-Viciedo, Rodrigo; Schmachtenberg, Oliver; Dinamarca, M. Alejandro

doi:10.3390/foods11070900

Open AccessArticle

Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors

by

Claudia Ibacache-Quiroga

^1,2,*

,

Karoll González-Pizarro

²,

Mariam Charifeh

²,

Christian Canales

³,

Rodrigo Díaz-Viciedo

^2,4,

Oliver Schmachtenberg

^5,6 and

M. Alejandro Dinamarca

^1,2,*

¹

Escuela de Nutrición y Dietética, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile

²

Centro de Micro-Bioinnovación, Universidad de Valparaíso, Valparaíso 2360102, Chile

³

Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Concepción 4080871, Chile

⁴

Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso 2360102, Chile

⁵

Instituto de Biología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2360102, Chile

⁶

Centro Interdisciplinario de Neurociencias (CINV), Universidad de Valparaíso, Valparaíso 2381850, Chile

^*

Authors to whom correspondence should be addressed.

Foods 2022, 11(7), 900; https://doi.org/10.3390/foods11070900

Submission received: 18 February 2022 / Revised: 16 March 2022 / Accepted: 17 March 2022 / Published: 22 March 2022

(This article belongs to the Section Nutraceuticals, Functional Foods, and Novel Foods)

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Abstract

Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages’ microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial β-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.

Keywords: kefir; probiotic; curli; β-amyloids; biofilm inhibitor; short-chain fatty acids

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MDPI and ACS Style

Ibacache-Quiroga, C.; González-Pizarro, K.; Charifeh, M.; Canales, C.; Díaz-Viciedo, R.; Schmachtenberg, O.; Dinamarca, M.A. Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. Foods 2022, 11, 900. https://doi.org/10.3390/foods11070900

AMA Style

Ibacache-Quiroga C, González-Pizarro K, Charifeh M, Canales C, Díaz-Viciedo R, Schmachtenberg O, Dinamarca MA. Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. Foods. 2022; 11(7):900. https://doi.org/10.3390/foods11070900

Chicago/Turabian Style

Ibacache-Quiroga, Claudia, Karoll González-Pizarro, Mariam Charifeh, Christian Canales, Rodrigo Díaz-Viciedo, Oliver Schmachtenberg, and M. Alejandro Dinamarca. 2022. "Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors" Foods 11, no. 7: 900. https://doi.org/10.3390/foods11070900

APA Style

Ibacache-Quiroga, C., González-Pizarro, K., Charifeh, M., Canales, C., Díaz-Viciedo, R., Schmachtenberg, O., & Dinamarca, M. A. (2022). Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors. Foods, 11(7), 900. https://doi.org/10.3390/foods11070900

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Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors

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