To investigate the community structure and diversity characteristics of bacteria and fungi in bulk spices marketed in Yunnan Region.

The 30 samples of bulk spices covering 6 categories, namely,star anise, chili pepper, white pepper, Amomum tsao-ko, Sichuan pepper and cumin, were collected from Yunnan Region. Using whole-genome sequencing, the diversity of bacteria and fungi was analyzed, and the microbial community structures of bacteria and fungi were investigated at the phylum and genus levels.

The dominant bacterial communities of the 6 spices at the phylum level were Proteobacteria, Firmicutes, Bacteroidota,Actinobacteriota, and white pepper samples had high diversity in bacterial community. At the genus level, the dominant bacterial community was Delftia. The dominant groups of fungal communities of 6 spices at the phylum level were Ascomycota and Basidiomycota, and star anise samples had high diversity in fungal community. At the genus level, the dominant community of different spices were different. The main pathogenic bacterial contaminants in the spices were Bacillus cereus and Cronobacter spp., and there was varying degrees of mold contamination.

Spices have high diversity in bacterial and fungal communities, and the dominant communities of bacterial and fungal are more consistent at the phylum level in different spices, while they may be different at the genus level. The bacterial and fungal communities in the spices covered both human pathogenic and plant pathogenic genera.