Microbial diversity of camel milk production environments in Xinjiang, China: a full-length 16S rRNA survey of farm environmental matrices across Altay and Hami regions

Introduction Camel milk production in Xinjiang, China is predominantly managed under extensive pastoral systems, yet the taxonomic and functional profiles of key production-associated environmental matrices remain poorly characterized. Methods This study employed PacBio Single-Molecule Real-Time (SMRT) full-length 16S rRNA gene sequencing to characterize microbial communities across five environmental matrices (bedding, feces, teat skin, feed, and soil) from camel breeding farms in the Altay and Hami regions of Xinjiang. Results After removing chloroplast and mitochondrial sequences, the dominant phyla across all samples were Firmicutes (43.20%), Proteobacteria (20.12%), and Actinobacteriota (12.02%). Alpha diversity analysis revealed significantly higher richness in fecal and feed microbial communities in Altay compared to Hami (Padj < 0.05). Beta diversity analyses (PCoA, NMDS, PERMANOVA) confirmed distinct taxonomic profiles between the two regions, driven by both regional and sample-type effects. Functional profiling indicated conserved metabolic potentials across regions, with enrichment of pathways related to amino acid transport and energy conversion. Discussion This study establishes a foundational baseline of the camel farm environmental microbiome in Xinjiang, informing targeted hygiene interventions and future studies investigating environmental contributions to raw camel milk quality. A key limitation is the absence of raw milk samples, precluding direct inference of microbial transmission routes to milk.