The microbial terroir of goat milk produced in Greece

Goat milk production and processing are key agricultural activities of significant economic importance in Greece. This study employed a metataxonomics approach to investigate the microbiome of goat milk samples collected from geographically diverse farms across Greece during two consecutive lactation periods (2019–2020 and 2020–2021), focusing on indigenous breeds. Complementary chemical and culture-dependent microbiological analyses were performed alongside evaluation of milk fatty acid composition and antioxidant activity. Milk composition analyses showed no significant differences among samples. However, notable variations among samples were observed in several microbial groups enumerated. The farming system primarily influenced the milk content of short-chain fatty acids, with no significant effect on the milk antioxidant capacity. Finally, both classical microbiological and metataxonomic analyses confirmed the presence of indigenous lactic acid bacteria species that are key contributors as starters and/or adjunct cultures in cheese production, and a lower diversity in yeast species compared to bacterial communities.