Microbial Diversity of Camel Milk Production Environments in Xinjiang, China

This study employed PacBio Single-Molecule Real-Time(SMRT) full-length 16S rRNA gene 17 sequencing to characterize the microbial community structure of production-associated environments 18 across five key environmental matrices (bedding, feces, teat skin, feed, and soil) in camel breeding farms in the Altay and Hami regions of Xinjiang, China. The dominant phyla in the filtered environmental microbiome (post-removal of chloroplast and mitochondrial sequences) were Firmicutes (43.20%), Proteobacteria (20.12%), and Actinobacteriota (12.02%), calculated from pooled read counts across all samples. Alpha diversity analysis revealed significantly higher richness of fecal and feed microbial communities in Altay compared to Hami (Padj < 0.05), while beta diversity analyses (PCoA, NMDS, PERMANOVA) confirmed distinct taxonomic profiles between the two regions, driven by both regional and sample-type effects. Functional profiling based on the COG database indicated conserved metabolic potentials across regions, with enrichment of pathways related to amino acid transport and energy conversion. This work provides a foundational baseline of camel farm environmental microbiomes, informing targeted hygiene interventions and future studies linking environmental reservoirs to raw milk quality. A core limitation is the absence of raw milk samples, precluding direct inference of microbial transmission routes to milk.