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The fermented milk matsoni is a traditional, national food product of both Georgia and Armenia. Little is known about the effects of biogeography and milk type on the microbial biodiversity of matsoni or the fungal composition of matsoni fermentations. High-throughput marker-gene sequencing was used to survey the bacterial and fungal communities of matsoni from different milk types and regions throughout Armenia and Georgia. Results demonstrate that both production region and milk type influence matsoni microbiota, suggesting that the traditional production methods preserve the transfer of unique regional microbiota from batch to batch. Bacterial profiles were dominated by Lactobacillus and Streptococcus species. Yeast profiles varied dramatically, with Kluyveromyces marxianus, Candida famata, Saccharomyces cerevisiae, Lodderomyces elongisporus, and Kluyveromyces lactis being the most important species distinguishing production regions and milk types. This survey will enable more detailed capture and characterization of specific microbiota detected within these fermentations., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

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