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Article

Influence of Milking Process and Production System on Raw Goat Milk Bacteriome

by
Ezquibel Montesinos Rivera
1,
Estela Garza Brenner
2,
Pascuala Ambriz Morales
1,
Williams Arellano Vera
1,
Rogelio de J. Treviño-Rangel
3 and
Ana María Sifuentes Rincón
1,*
1
Laboratorio de Biotecnología Animal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa 88710, Tamaulipas, Mexico
2
Facultad de Agronomía, Posgrado Conjunto, Universidad Autónoma de Nuevo León, General Escobedo 66050, Nuevo León, Mexico
3
Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Nuevo León, Mexico
*
Author to whom correspondence should be addressed.
Microbiol. Res. 2025, 16(10), 218; https://doi.org/10.3390/microbiolres16100218
Submission received: 16 August 2025 / Revised: 1 October 2025 / Accepted: 2 October 2025 / Published: 4 October 2025
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Abstract

The aim of this study was to compare, during milking, the bacteriomes of goat milk from farms in Mexico representing traditional and semi-intensive production systems. Metagenomic DNA was isolated from pooled milk samples collected at different milking stages, and following 16S rRNA-targeted sequencing, alpha (Shannon H’ and Simpson D) and beta (Bray–Curtis) diversity indices were calculated. Within the semi-intensive system, fore-stripping showed lower diversity (H’ = 1.5 vs. H’ = 4.0) but greater evenness (D = 0.5 vs. D = 0.8) than the milking stage. In contrast, no differences between stages in the traditional system were observed. The Bray–Curtis index revealed that the use of the semi-intensive system explained 99.4% of the variability, while the traditional system accounted for only 0.5%. In the semi-intensive system, fore-stripping was dominated by Mesoplasma (51.9%) and Staphylococcus (42.1%), whereas Enterococcus (27.2%) and Lactococcus (18.5%) prevailed during milking. Meanwhile, in the traditional system, Pseudomonas (46.9% and 22.7) and Lactococcus (22.7% and 29.2%) predominated in both stages. Management practices strongly influence the microbiological profile of milk, leading to changes in not only the diversity and abundance of pathogenic bacteria but also in the presence of beneficial lactic acid bacteria and, hence, the overall expected milk quality.
Keywords: microbiota composition; milking; fore-stripping; goat production system microbiota composition; milking; fore-stripping; goat production system

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MDPI and ACS Style

Montesinos Rivera, E.; Garza Brenner, E.; Ambriz Morales, P.; Arellano Vera, W.; Treviño-Rangel, R.d.J.; Sifuentes Rincón, A.M. Influence of Milking Process and Production System on Raw Goat Milk Bacteriome. Microbiol. Res. 2025, 16, 218. https://doi.org/10.3390/microbiolres16100218

AMA Style

Montesinos Rivera E, Garza Brenner E, Ambriz Morales P, Arellano Vera W, Treviño-Rangel RdJ, Sifuentes Rincón AM. Influence of Milking Process and Production System on Raw Goat Milk Bacteriome. Microbiology Research. 2025; 16(10):218. https://doi.org/10.3390/microbiolres16100218

Chicago/Turabian Style

Montesinos Rivera, Ezquibel, Estela Garza Brenner, Pascuala Ambriz Morales, Williams Arellano Vera, Rogelio de J. Treviño-Rangel, and Ana María Sifuentes Rincón. 2025. "Influence of Milking Process and Production System on Raw Goat Milk Bacteriome" Microbiology Research 16, no. 10: 218. https://doi.org/10.3390/microbiolres16100218

APA Style

Montesinos Rivera, E., Garza Brenner, E., Ambriz Morales, P., Arellano Vera, W., Treviño-Rangel, R. d. J., & Sifuentes Rincón, A. M. (2025). Influence of Milking Process and Production System on Raw Goat Milk Bacteriome. Microbiology Research, 16(10), 218. https://doi.org/10.3390/microbiolres16100218

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