Microbiome Dynamics of Camel Meat During Cold Storage Revealed by 16S rRNA Gene Sequencing

Abstract

Camel meat is an important red meat source, but culture-independent evidence of its bacterial community during refrigerated storage remains limited. No prior study has applied 16S rRNA sequencing to camel meat under aerobic chilled storage. Samples from three butcher shops were evaluated at Day 0 and Day 7 of aerobic storage at 5 °C. Thirty-eight samples were retained for diversity, compositional, and differential abundance analyses using Breakaway, DivNet, Bayesian hierarchical modeling, permutational multivariate analysis of variance (PERMANOVA), and Microbiome Multivariable Associations with Linear Models 2. Richness and Shannon diversity decreased from Day 0 to Day 7, while the Simpson index increased, indicating higher dominance. Storage duration was associated with Bray–Curtis community variation (PERMANOVA: R2 = 0.107, p = 0.001), whereas anatomical cut showed no significant effect; butcher source differed in multivariate dispersion. Differential abundance analysis identified 59 storage-associated amplicon sequence variants, including Pseudomonas enrichment and depletion of Kocuria, Rothia, and Carnobacterium at Day 7. These are relative-abundance findings from 16S rRNA, not culture-based microbial counts. Storage duration was the principal driver of camel meat microbiota composition, providing a compositional baseline that may inform hygiene and storage practices aimed at limiting Pseudomonas-associated spoilage; microbial load and spoilage were not directly assessed.