Determination of bacterial community structure of Turkish kefir beverages via metagenomic approach

Yegin, Zeynep; Yurt, Mediha Nur Zafer; Taşbaşi, Behiye Büşra; Acar, Elif Esma; Altunbaş, Osman; Uçak, Samet; Özalp, Veli Cengiz; Sudağıdan, Mert

doi:10.1016/j.idairyj.2022.105337

Cited by 13 publications

(13 citation statements)

References 32 publications

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“…With less than 20%, LAB species represented a minor component of these Chilean kefir beverages, which differs from previous studies where LAB from the phylum Firmicutes were the most abundant microorganisms in kefir beverages [ 9 , 21 , 33 , 34 , 35 , 45 , 70 ]. Among lactic acid bacteria, the only genus identified in K02 and K03 was Lactobacillus.…”

Section: Discussioncontrasting

confidence: 89%

“…The beneficial effects of kefir beverages are tightly related to their microbial composition and productive conditions. In this context, during the past decade, the development and massification of new generation sequencing (NGS) have allowed the identification of the microbial structure in kefir beverages and other fermented foods and the metabolic genetic networks of the microbial community through amplicon-based [ 32 , 33 , 34 , 35 , 36 , 37 ] and shotgun metagenomic sequencing [ 38 , 39 , 40 , 41 , 42 ], respectively. Even though most metagenomic studies have focused on the kefir grain microbiota [ 32 , 33 , 36 , 37 , 38 , 41 , 43 ], during the past years the analysis of the kefir beverages has gained relevance [ 35 , 39 , 42 , 44 , 45 ].…”

Section: Introductionmentioning

confidence: 99%

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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

Ibacache-Quiroga

González-Pizarro

Charifeh

et al. 2022

Foods

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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.

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Section: Discussioncontrasting

confidence: 89%

Section: Introductionmentioning

confidence: 99%

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

González-Pizarro

Charifeh

et al. 2022

Foods

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“…(2021) and Yegin et al. (2022) using a metagenomic approach found that the most abundant genera were Streptococcus and Lactococcus , followed by Lactobacillus . This composition differs greatly from kefir produced from grains, where Lactobacillus is the most abundant genus across studies.…”

Section: Resultsmentioning

confidence: 99%

Metagenomic analysis and antibacterial activity of kefir microorganisms

González‐Orozco

García‐Cano

Escobar‐Zepeda

et al. 2023

Journal of Food Science

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The microbiota composition of kefir grain and milk kefir was assessed via a metagenomic approach. Significant microorganisms were isolated and identified using molecular methods. A safety assessment was conducted based on antibiotic susceptibility and blood hemolysis. Probiotic traits such as resistance to gastric tract conditions, surface characteristics, adhesion to intestinal cells, and antibacterial activity were also assessed. Metagenomic analysis revealed that kefir grains are a more stable community with clear dominant species as compared to milk kefir. Lactobacillus kefiranofaciens BDGO‐A1, Lactobacillus helveticus BDGO‐AK2, and Lactobacillu kefiri strains showed tolerance to acidic pH and the presence of bile salts, adhesion capability to Caco‐2 cells, in vitro antibacterial activity, and the production of antibacterial proteins. In the metagenomic analysis, contigs associated with these species showed the presence of genes involved in exporting polyketide antibiotics and bacteriocin production. To fully exploit the potential probiotic properties of these microorganisms to help human health, further investigation is necessary to elucidate the mechanisms behind the biological activity and the genotypic characteristics of the isolated strains.

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“…NGS is a culture-independent method and it is successfully applied to identify the microbiota of fermented foods (Demirci et al, 2022;Ucak et al, 2022;Soyuçok et al, 2021;Yegin et al, 2022). In this study, a total of 459,430 high-quality reads were obtained by NGS.…”

Section: Metagenomic Analysis Of Tarhana Microbiotamentioning

confidence: 98%

Bacterial Microbiota and Chemical Properties of Turkish Tarhana

Omeroglu

Can

Temiz³

et al. 2022

J microb biotech food sci

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Tarhana is one of the traditional Turkish fermented food and it is served as a soup. In this study, bacterial microbiota and chemical properties (acidity, salt, and moisture content) of tarhana samples (n=96) were examined. The metagenomic analysis revealed that Firmicutes were the dominant phylum and Bacillaceae, Enterococcaceae, Paenibacillaceae, Enterobacteriaceae, and Clostridiaceae were the dominant bacterial families. In the samples, Bacillus, Enterococcus, and Paenibacillus were mostly identified at the genus level. Alpha diversity and evenness showed that sample 30 had the highest diversity collected from İzmir. Principal Coordinate Analysis was used to identify relationships of samples at different taxonomic levels and it was found that most of the samples were closely related at the phylum level. Chemical analysis indicated that the acidity of tarhana samples varied between 5.00% and 42.5%, moisture contents were 4.39–18.66% and salt values were from 0.32% to 6.64%. The results of this study extensively demonstrated the chemical properties and the dominant bacterial communities present in tarhana samples collected from different parts of Türkiye.

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Determination of bacterial community structure of Turkish kefir beverages via metagenomic approach

Cited by 13 publications

References 32 publications

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

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

Metagenomic analysis and antibacterial activity of kefir microorganisms

Bacterial Microbiota and Chemical Properties of Turkish Tarhana

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