ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microorganisms in Vertebrate Digestive Systems
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1617701
Shotgun Metagenomics Analysis of Gut Microbiota of Three Indigenous Fish Species from the Kizil River, Xinjiang
Provisionally accepted
- College of Animal Science, Tarim University, Alar Xinjiang, China
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Shotgun metagenomics revealed distinct gut microbiota profiles and functional adaptations in three indigenous Xinjiang Kizil River fishes: Schizothorax biddulphi (SB), Diptychus maculatus (DM), and Triplophysa yarkandensis (TY). Dominant taxa included Proteobacteria, Acinetobacter, and Pseudomonas, with species-specific biomarkers: Micromonospora (DM); Proteobacteria, Firmicutes, Aeromonas, and Bacillus (SB); and Mucoromycota, Vibrio, and Alcanivorax (TY). DM and SB exhibited higher Firmicutes/Bacteroidetes ratios and enhanced nutrient utilization capabilities compared to TY. KEGG analysis highlighted fructose/mannose metabolism (SB) and oxidative phosphorylation (DM) as key pathways, while CAZy annotations showed CE3 abundance across species, with GT6/GT10 (SB) and PL22 (TY) as unique biomarkers. Dietary shifts occurred during overwintering: DM and TY transitioned toward herbivory, while SB retained carnivorous tendencies despite increased plant consumption. All species showed reduced immunity, with DM and SB particularly vulnerable to Acinetobacter-related infections. Environmental analysis detected crude oil pollution, elevated nitrogen, and A. baumannii contamination, necessitating preventive measures. TY demonstrated salinity adaptability but heightened pollution sensitivity. Host phylogeny strongly influenced microbiota composition and metabolic functions, emphasizing host-specific microbial adaptation. This study provides critical insights for conservation and sustainable aquaculture strategies of these species in their natural habitat.
Keywords: Metagenomics, Schizothorax biddulphi, Diptychus maculatus, Triplophysa yarkandensis, Gut microbiota . Fish
Received: 24 Apr 2025; Accepted: 02 Jun 2025.
Copyright: © 2025 Yang, Qiang, Zhang, Hao, Wei, Hamid, Wang and Nie. 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: Zhulan Nie, College of Animal Science, Tarim University, Alar Xinjiang, China
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