Characterization of bacterial and fungal populations in retail kefirs in Ireland

Kefir is an increasingly popular dairy- or sugar-based fermented food product. The aim of our study was to investigate the bacterial and fungal communities in 28 retail kefirs including 21 milk kefirs, 3 thick kefir yogurts, and 4 water kefir products. Full-length amplicon nanopore sequencing of both 16S rRNA genes (for bacteria) and intergenic spacer genes (for fungi) was undertaken. The diversity within and between groups was analyzed (α- and β-diversity) and linear discriminant analysis effect size analysis was undertaken to identify biomarkers that differentially characterize the microbial communities associated with different kefir types. The pH, lactic acid concentration, total viable counts (TVC), lactic acid bacteria (LAB), total coliform counts (TCC), and yeast counts were also investigated. The main bacterial genera (and species) were Lactococcus (cremoris) and Streptococcus (thermophilus), and other bacteria such as Lactobacillus (delbrueckii) and Lentilactobacillus (kefiri) were also detected. The fungal populations were mainly composed of Brettanomyces (anomalus), Zygotorulaspora (florentina) and Kazachstania (unispora), but with many different fungal genera/species detected. The pH ranged from 3.1 to 4.7 with a mean of 4.2 ± 0.07 and the lactic acid content ranged from 0.1 to 9 g/L with a mean of 5.6 ± 0.53 g/L. In milk kefirs the TVC, LAB, TCC, and yeast counts ranged from 3.1 to 9.1, 3.4 to 9.0, not detected (ND) to 2 and ND to 6.5 log₁₀ cfu/mL or cfu/g, respectively. The corresponding counts in water kefirs were 4.1 to 7.3 (TVC), 4.1 to 7.0 (LAB), ND to 1.1 (TCC), and 3.9 to 7.0 (yeast) log₁₀ cfu/mL or cfu/g, respectively. It was concluded that, although the 28 retail kefirs analyzed had a rich diversity of bacteria and fungi, the bacteriome was dominated by bacteria belonging to the Lactococcus and Streptococcus genera and the main bacterial species were Lactococcus cremoris, Streptococcus thermophiles, Streptococcus suis, Lactobacillus delbrueckii, and Streptococcus sp. HSISS1. The fungal microbiome was dominated by Zygotorulaspora, and the most abundant fungal species included Zygotorulaspora florentina, Brettanomyces anomalus, and Kazachstania unispora. To the best of our knowledge, this is the first study in Ireland to use full-length nanopore sequencing to characterize both bacterial and fungal communities in retail kefirs.