ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Food Microbiology
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
- YW
Yating Wu 1
- SW
Shuai Wang 2
- XM
Xianlan Ma 2
- XL
Xiaoxiao Lou 2
- NZ
Nan Zheng 3
- WS
Wei Shao 4
- LM
Lu Meng 3
- HC
He Chen 2
- WC
Wang Cheng 2
- YZ
Yankun Zhao 2
1. Ministry of Agriculture and Rural Affairs-Laboratory of Quality and Safety Risk Assessment for Agro-Products, Agricultural Product Quality and Safety Risk Assessment Laboratory, Institute of Quality Standards & Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Urumqi, China
2. Xinjiang Academy of Agricultural Sciences, Urumqi, China
3. Chinese Academy of Agricultural Sciences, Beijing, China
4. Xinjiang Agricultural University, Ürümqi, China
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Abstract
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.
Summary
Keywords
Microbial Diversity, production environment, Raw camel milk, single-molecule real-time sequencing, source tracking
Received
14 July 2026
Accepted
17 August 2026
Copyright
© 2026 Wu, Wang, Ma, Lou, Zheng, Shao, Meng, Chen, Cheng and Zhao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Wang Cheng; Yankun Zhao
Disclaimer
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