Objective   Changes incurred to the fungal community during the natural fermentation of tomatoes were studied to pave the way for product and process development.

  Methods   Composition and diversity of fungi presented at various stages of the naturally occurring fermentation on tomatoes were analyzed by high-throughput sequencing technique. Physical and chemical parameters for indexing the process were determined.

  Results   A total of 705 309 effective sequences, including 11 phyla and 31 genera, were found in the fermentation broth during the entire process. The richly diverse fungal community was dominated by the families of Ascomycota and Basidiomycota. At the genus level, Penicillium predominated in the early stage of the fermentation which was followed by Verticillium in the middle stage and Hanseniaspora in the final stage. It indicated continual differentiations on fungal growth happened as the fermentation progressed. Along with the changing microbial community, the pH and soluble solids declined with fluctuations on the contents of alcohol and lycopene in the fermentation broth.

  Conclusion   During the fermentation, gradually in the broth, Saccharomyces cerevisiae dominated the fungal community, while soluble solids broke down and pH lowered by the organic acids produced by the microbial metabolism, and alcohol and lycopene contents fluctuated. The revealed regulation roles of fungal flora played on the natural fermentation provided a guideline for future development of technology for an industrial utilization of tomatoes.