Chili powder is the most frequently consumed spice in Mexican diets. Thus, the dissemination of microorganisms associated with chili powder derived from Capsicum annuum L. is significant during microbial quality analysis, with special attention on detection of potential pathogens. The results presented here describe the initial characterization of bacterial community structure in commercial chili powder samples. Our results demonstrate that, within the domain Bacteria, the most abundant family was Bacillaceae, with a relative abundance of 99% in 71.4% of chili powder samples, while 28.6% of samples showed an average relative abundance of 60% for the Enterobacteriaceae family. Bacterial load for aerobic mesophilic bacteria (AMB) ranged from 104 to 106 cfu/g, while for sporulated mesophilic bacteria (SMB), the count ranged from 102 to 105 cfu/g. Bacillus cereus sensu lato (s.l.) was observed at ca. ˂600 cfu/g, while the count for Enterobacteriaceae ranged from 103 to 106 cfu/g, Escherichia coli and Salmonella were not detected. Fungal and yeast counts ranged from 102 to 105 cfu/g. Further analysis of the opportunistic pathogens isolated, such as B. cereus s.l. and Kosakonia cowanii, using antibiotic-resistance profiles and toxinogenic characteristics, revealed the presence of extended-spectrum β-lactamases (ESBLs) and Metallo-β-lactamases (MBLs) in these organisms. These results extend our knowledge of bacterial diversity and the presence of opportunistic pathogens associated with Mexican chili powder and highlight the potential health risks posed by its use through the spread of antibiotic-resistance and the production of various toxins. Our findings may be useful in developing procedures for microbial control during chili powder production.

Kosakonia cowanii strain Ch1 was isolated from Mexican chili powder, and the genome was sequenced. The genome was 4,765,544 bp in length, with an average G + C content of 56.22%, and a plasmid (pCh1) of 128,063 bp with an average G + C content of 52.50%. A phylogenetic analysis revealed a close relation with pathogenic strains; nevertheless, some virulence-related genes were absent, and this genetic characteristic may explain the fact that K. cowanii Ch1 behaved as a non-pathogenic strain when infection assays were performed on the leaves and fruits of Capsicum annuum L. Surprisingly, we observed that this bacterial strain had the ability to spread throughout serrano pepper seeds. Furthermore, K. cowanii Ch1 was evaluated for the production of volatile organic compounds (VOCs) against fungal pathogens, and the results showed that Alternaria alternata and Sclerotium rolfsii were inhibited in a radial mycelial growth assay by a mean rate of 70% and 64%, while Fusarium oxysporum was inhibited by only approximately 10%. Based on the headspace solid-phase microextraction combined with the gas chromatography mass spectrometry (HS-SPME-GC-MS), 67 potential VOCs were identified during the fermentation of K. cowanii Ch1 in TSA medium. From these VOCs, nine main compounds were identified based on relative peak area: dodecanoic acid; 3-hydroxy ethanol; 1-butanol-3-methyl; acetaldehyde; butanoic acid, butyl ester; cyclodecane; 2-butanone, 3-hydroxy; disulfide, dimethyl and pyrazine-2,5-dimethyl. Our findings show the potential of K. cowanii Ch1 for the biocontrol of fungal pathogens through VOCs production and reveal additional abilities and metabolic features as beneficial bacterial specie.