Abstract
Kefir is a high nutritional fermented dairy beverage associated with a wide range of health benefits. It constitutes a unique symbiotic association, comprising mainly lactic acid bacteria, yeasts, and occasionally acetic acid bacteria, which is strongly influenced by the geographical origin of the grains, the type of milk used, and the manufacture technology applied. Until recently, kefir microbiota has been almost exclusively studied by culture-dependent techniques. However, high-throughput sequencing, alongside omics approaches, has revolutionized the study of food microbial communities. In the present study, the bacterial, and yeast/fungal microbiota of four home-made samples (both grains and drinks), deriving from well spread geographical regions of Greece, and four industrial beverages, was elucidated by culture-dependent and -independent analyses. In all samples, classical microbiological analysis revealed varying populations of LAB and yeasts, ranging from 5.32 to 9.60 log CFU mL–1 or g–1, and 2.49 to 7.80 log CFU mL–1 or g–1, respectively, while in two industrial samples no yeasts were detected. Listeria monocytogenes, Salmonella spp. and Staphylococcus spp. were absent from all the samples analyzed, whereas Enterobacteriaceae were detected in one of them. From a total of 123 isolates, including 91 bacteria and 32 yeasts, Lentilactobacillus kefiri, Leuconostoc mesenteroides, and Lactococcus lactis as well as Kluvyeromyces marxianus and Saccharomyces cerevisiae were the mostly identified bacterial and yeast species, respectively, in the home-made samples. On the contrary, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lacticaseibacillus rhamnosus along with Debaryomyces hansenii and K. marxianus were the main bacterial and yeast species, respectively, isolated from the industrial beverages. In agreement with the identification results obtained from the culture-dependent approaches, amplicon-based metagenomics analysis revealed that the most abundant bacterial genera in almost all home-made samples (both grains and drinks) were Lactobacillus and Lactococcus, while Saccharomyces, Kazachstania, and Kluvyeromyces were the predominant yeasts/fungi. On the other hand, Streptococcus, Lactobacillus, and Lactococcus as well as Kluvyeromyces and Debaryomyces dominated the bacterial and yeast/fungal microbiota, respectively, in the industrial beverages. This is the first report on the microbiota of kefir produced in Greece by a holistic approach combining classical microbiological, molecular, and amplicon-based metagenomics analyses.
Highlights
At both research and industrial level, dairy fermented foods are the protagonists among functional foods, i.e., foods having a positive impact on human health beyond the known nutritional value, such as benefits concerning gastrointestinal health, hypertension, cholesterol reduction, immune system regulation, interaction between gut and brain, etc. (Shiby and Mishra, 2013)
Other fermented milks, such as kefir, koumiss, chigo, viili, nunu, amabere, amaruranu, and suusac (Ishii et al, 1997; Lore et al, 2005; Kahala et al, 2008; Akabanda et al, 2013; Nyambane et al, 2014; Yao et al, 2017) are known as alcoholic milk beverages, since milk is fermented by both lactic acid bacteria (LAB) and yeasts (Wszolek et al, 2006)
The aim of the present study was to elucidate and compare the bacterial and yeast/fungal microbiota of home-made and industrial kefir samples produced in Greece, deriving from well-spread geographical origin and types of milk, using a dual approach that includes both classical microbiological and amplicon-based metagenomics analyses
Summary
At both research and industrial level, dairy fermented foods are the protagonists among functional foods, i.e., foods having a positive impact on human health beyond the known nutritional value, such as benefits concerning gastrointestinal health, hypertension, cholesterol reduction, immune system regulation, interaction between gut and brain, etc. (Shiby and Mishra, 2013). Consumption of kefir has been associated with numerous health benefits including anticarcinogenic and antiinflammatory effects (Rodrigues et al, 2005; de Moreno de Leblanc et al, 2007; Lee et al, 2007; Kim et al, 2016), alleviation of lactose intolerance symptoms and cholesterol reduction (Hertzler and Clancy, 2003; Liu et al, 2006) This viscous, slightly carbonated dairy beverage comprises a complex microbial association of mainly LAB, acetic acid bacteria (AAB) and yeasts. The aim of the present study was to elucidate and compare the bacterial and yeast/fungal microbiota of home-made and industrial kefir samples produced in Greece, deriving from well-spread geographical origin and types of milk, using a dual approach that includes both classical microbiological and amplicon-based metagenomics analyses
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