Microbiota and associated chemical compounds in South African craft ales

Abstract

Craft beer is typically brewed in smaller batches compared to industrial breweries. Several factors can influence the flavour, quality, and safety throughout the craft beer brewing process, including raw materials, fermentation conditions, and the interactions between the chemical composition and microbial communities. Limited research has been undertaken on the integration of microbial and chemical profiles of craft beers. Therefore, this study aimed to profile the microbial and chemical compositions of South African craft ale beers, to evaluate their safety in relation to the detected microbial and chemical compositions, including the level of mycotoxins, and to explore correlations between the microbiota and the detected compounds. A total of 30 beers (in triplicate) of different styles were purchased from 30 commercial craft breweries and tested for mycotoxin levels using ultra-performance liquid chromatography–electrospray ionisation–tandem mass spectrometry (UPLC-ESI-MS/MS). The most prevalent mycotoxin was deoxynivalenol (DON), which was detected in 10% of the beer samples. The highest concentration of DON (22 μg/L and 41.49 μg/L) was detected in India Pale Ale (IPA) and Stout, while fumonisin FB₁ and FB₂ (0.37 μg/L and 0.16 μg/L) were detected in IPA and Pale Ale, respectively. Nivalenol (NIV) was present in trace amounts (0.13 μg/L) in one IPA sample. The presence of these mycotoxins indicated the need for quality assurance of raw materials used in craft beer production and quality control. Microbial profiling showed total viable microorganisms present up to 1.63 × 10⁵ CFU/mL, yeast was detected in more than 50% of the beer samples, not unexpected since most breweries do not filter or pasteurise their final product. Moulds were present in product from 17% of breweries, and 60% of the breweries presented with lactic acid bacterial (LAB) contamination. Common foodborne pathogens Escherichia coli and Salmonella spp were not detected. Pale Ales from one brewery presented co-occurrence of LAB and Staphylococcus aureus, indicative of post-fermentation contamination. Next-generation sequencing results showed that Acetobacter and Levilactobacillus spp. dominated bacterial communities, while the fungal community was dominated by Saccharomyces cerevisiae, although other non-Saccharomyces genera, including Cladosporium, Vishniacozyma, and Penicillium spp. were also present. Chemical profiling revealed several flavour-active compounds, including isoamyl alcohol (178.9 mg/L), 4-vinylguaiacol (10 mg/L), isoamyl acetate, and vanillic acid (76.7 mg/L), present in concentrations well above sensory thresholds in beer styles in which these compounds are not expected or preferred. The sugar and sugar alcohols varied widely in both type and concentrations. Fructose (107.4 mg/L), xylose (60.6 mg/L), and xylitol (185.4 mg/L) were among the most dominant. A strong positive correlation between higher alcohols, as well as a negative correlation between certain sugars (e.g., maltose, trehalose) and flavour-active compounds was also revealed. This research provides insights into the microbial and chemical profiles of sampled South African craft ales. While these beers may be microbiologically safe and favourably complex, some of the beer samples remain susceptible to post-fermentation contamination and subtle chemical variability. The findings highlight the interconnected role of microorganisms in shaping beer flavour and stability, and they emphasise the importance of maintaining consistent quality in the craft brewery environment. This study establishes valuable baseline data to enhance product safety, sensory consistency, and meet regulatory standards of the rapidly growing craft beer industry.