Functional and safety profiles of microbial communities in milk of ranched and nomadic goats and their predictive role in mycotoxin reduction.

This study investigates the microbial dynamics, mycotoxin reduction, and biotechnological potentials of bacteria and yeasts in raw goat milk from Nigeria’s ranched and nomadic farming systems. The 16S/26S rRNA gene sequencing identified a rich microbial diversity in goat milk, dominated by bacterial phyla: Firmicutes (also known as Bacillota) (86.5%), Proteobacteria (also known as Pseudomonadota) (13.2%), Actinobacteriota (0.3%), and yeast phylotypes: Ascomycota (55%) and Basidiomycota (44%). Overall, the abundance of the bacteria Enterococcus, Bacillus, Streptococcus, Escherichia-Shigella, and Clostridium sensu stricto 1, and the yeasts Pseudotremella, Saccharomyces, Candida, Kluyveromyces, and Trichosporon accounted for at least 90% of the total genera detected. Significant differences (p < 0.05) in microbial compositions were observed between ranched and nomadic goats, with the latter showing higher richness (Chao1: 59.9 vs. 41.6) and higher abundances of key genera including potential pathogenic groups such as Bacillus, Klebsiella, Neisseria, Pseudomonas, Serratia, Streptococcus, and Cryptococcus. Functional assays highlighted probiotic traits in lactic acid bacteria, e.g., Limosilactobacillus fermentum 30m1 and Weissella cibaria 93m3, and biotechnological abilities in Pediococcus acidilactici 18a. Mycotoxin analysis revealed frequent contamination in critically low levels (<500 ng/L), including aflatoxin M1 (96.2% of samples) and citrinin (61.5%), with nomadic milk exhibiting slightly higher mycotoxin levels than milk from ranched goats. Moderate correlations (0.25 < r2 < 0.49) were found between certain bacterial and yeast genera, such as Streptococcus and Saccharomyces, and concentrations of mycotoxins like aflatoxin B1 and M1, suggesting a potential role for these microbes as mycotoxin decontaminators. Our results indicate that while nomadic practices enhance microbial diversity, they also pose safety risks due to increased pathogen and mycotoxin prevalences. These findings underscore the need for improved farm management to balance microbial benefits (e.g., probiotics, mycotoxin mitigation) with public health risks. This study provides actionable insights for developing safe fermented dairy products and policies to enhance food security in sub-Saharan Africa.