Microbiome of indigenous dried plant foods from South African informal markets

Indigenous plant-based products offer significant advantages for human nutrition and health. However, the indigenous foods consumed are often preserved before being sold at urban informal markets, where food safety can be inconsistent. Here, we investigated the bacterial communities of five indigenous dried plant products (the fruits baobab, masau and nyii, and the leafy greens dinawa and lude) sourced from urban informal markets in South Africa. Bacterial abundance, diversity and community composition varied significantly across products. Baobab fruit exhibited low bacterial abundance (106 gene copy numbers) but the highest bacterial richness (up to 1,460 ASVs), and was associated with beneficial taxa such as Bifidobacterium and Prevotella. In contrast, dried leafy greens showed higher overall bacterial loads (109 gene copy numbers) and a greater prevalence of potential pathogens, including Salmonella, Vibrio, and Acinetobacter baumannii. Moreover, the opportunistic pathogens Stenotrophomonas maltophilia and A. baumannii were abundant members of the core microbiome. Cultivation-dependent assays identified bacterial isolates with beneficial traits, such as protease activity, bile salt tolerance, and antagonism to human pathogens, though a diverse array of antimicrobial resistance, mainly against sulfadiazine and ampicillin, raises potential health concerns. Multi-resistant strains belonging to Acinetobacter radioresistens, Enterobacter faecium, E. durans, Mixta gaviniae or Pantoaea agglomerans were isolated from all products. These findings emphasize the dual nature of indigenous dried foods at their point of sale, serving as a reservoir for both beneficial and potentially harmful bacteria. Improved food handling and processing are therefore key to ensuring the preservation of their health benefits, particularly in informal markets.