# Girgentana’s Goat Milk Microbiota Investigated in an Organic Farm During Dry Season

## TL;DR

This study explores the milk microbiota of Girgentana goats in Sicily, revealing key microbial communities that could impact milk quality and traditional dairy practices.

## Contribution

The first characterization of the milk microbiota in the Girgentana goat breed using 16S rRNA sequencing.

## Key findings

- Firmicutes and Proteobacteria were the most abundant phyla in Girgentana goat milk.
- Bulk milk samples showed microbial profiles similar to individual samples.
- The study provides a baseline for future comparisons of milk microbiota across goat breeds.

## Abstract

Milk microbiota is a complex microbial ecosystem harboring a diverse community of microorganisms which can influence milk quality, safety, and flavor, and may also play a role in animal health and udder physiology. The Girgentana goat is an ancient dairy breed native to Sicily, known for its good production of high-quality milk intended for direct consumption or processing into ricotta or cheese. Girgentana’s milk microbiota has been investigated for the first time in an organic farm located in Agrigento area. Illumina NovaSeq technology was used to sequence the V3–V4 regions of 16S rRNA from 44 individual and 3 bulk milk samples. Alpha diversity metrics were estimated to assess richness, evenness, and overall milk microbiota diversity, while taxa composition was analyzed to characterize microbial structure. This study is the first to unravel the milk microbiota composition of the Girgentana breed, providing detailed microbial profiling. Moreover, this can represent a baseline for microbial diversity, which can be used for future comparisons with other breeds raised in traditional dairy systems.

Milk microbiota is a complex microbial ecosystem with implications for product quality, safety, and animal health. However, limited data exist on goat milk microbiota, particularly in local breeds. This study provides the first detailed characterization of the milk microbiota of Girgentana goats, a resilient Sicilian breed valued for high-quality dairy products. Illumina NovaSeq sequencing was used to analyze the 16S rRNA V3–V4 regions of 44 individual and 3 bulk milk samples. Briefly, 16S rRNA-gene sequencing produced a total of 8,135,944 high-quality reads, identifying 1134 operational taxonomic units (OTUs) across all individual samples. On average, each sample showed 864 OTUs with counts > 0. Alpha diversity metrics, based on richness estimators (Chao1: 948.1; ACE: 936.3) and diversity indices (Shannon: 4.06; Simpson: 0.95; Fisher: 118.5), indicated a heterogeneous community with both common and low-abundance taxa. Firmicutes (51%) and Proteobacteria (27%) were the predominant phyla, with Lactobacillaceae (54%) and Bifidobacteriaceae (22%) dominating at the family level. Notably, farm bulk milk profiles closely mirrored individual samples. These results establish a milk microbiota baseline for the Girgentana breed and offer valuable insights into microbial ecology in traditional dairy systems, supporting future comparisons across breeds and farming practices.