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Ye C, Geng S, Zhang Y, Qiu H, Zhou J, Zeng Q, Zhao Y, Wu D, Yu G, Gong H, Hu B, Hong Y. The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis). Anim Microbiome 2023; 5:20. [PMID: 37005679 PMCID: PMC10067185 DOI: 10.1186/s42523-023-00239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/08/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND The gut microbiota of fish confers various effects on the host, including health, nutrition, metabolism, feeding behaviour, and immune response. Environment significantly impacts the community structure of fish gut microbiota. However, there is a lack of comprehensive research on the gut microbiota of bighead carp in culture systems. To demonstrate the impact of culture systems on the gut microbiome and metabolome in bighead carp and investigate a potential relationship between fish muscle quality and gut microbiota, we conducted a study using 16S ribosomal ribonucleic acid sequencing, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry techniques on bighead carp in three culture systems. RESULTS Our study revealed significant differences in gut microbial communities and metabolic profiles among the three culture systems. We also observed conspicuous changes in muscle structure. The reservoir had higher gut microbiota diversity indices than the pond and lake. We detected significant differences in phyla and genera, such as Fusobacteria, Firmicutes, and Cyanobacteria at the phylum level, Clostridium sensu stricto 1, Macellibacteroides, Blvii28 wastewater sludge group at the genus level. Multivariate statistical models, including principal component analysis and orthogonal projections to latent structures-discriminant analysis, indicated significant differences in the metabolic profiles. Key metabolites were significantly enriched in metabolic pathways involved in "arginine biosynthesis" and "glycine, serine, and threonine metabolism". Variation partitioning analysis revealed that environmental factors, such as pH, ammonium nitrogen, and dissolved oxygen, were the primary drivers of differences in microbial communities. CONCLUSIONS Our findings demonstrate that the culture system significantly impacted the gut microbiota of bighead carp, resulting in differences in community structure, abundance, and potential metabolic functions, and altered the host's gut metabolism, especially in pathways related to amino acid metabolism. These differences were influenced substantially by environmental factors. Based on our study, we discussed the potential mechanisms by which gut microbes affect muscle quality. Overall, our study contributes to our understanding of the gut microbiota of bighead carp under different culture systems.
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Affiliation(s)
- Chen Ye
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Shiyu Geng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yingyu Zhang
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Huimin Qiu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Jie Zhou
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Qi Zeng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yafei Zhao
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Di Wu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Guilan Yu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Haibo Gong
- Jiangxi Provincial Aquatic Biology Protection and Rescue Center, Nanchang, 330000, China
| | - Beijuan Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
| | - Yijiang Hong
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
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Zhao R, Symonds JE, Walker SP, Steiner K, Carter CG, Bowman JP, Nowak BF. Relationship between gut microbiota and Chinook salmon ( Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems. Front Microbiol 2023; 14:1065823. [PMID: 36825086 PMCID: PMC9941681 DOI: 10.3389/fmicb.2023.1065823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/06/2023] [Indexed: 02/10/2023] Open
Abstract
Gut microbiota play important roles in fish health and growth performance and the microbiome in fish has been shown to be a biomarker for stress. In this study, we surveyed the change of Chinook salmon (Oncorhynchus tshawytscha) gut and water microbiota in freshwater recirculating aquaculture systems (RAS) for 7 months and evaluated how gut microbial communities were influenced by fish health and growth performance. The gut microbial diversity significantly increased in parallel with the growth of the fish. The dominant gut microbiota shifted from a predominance of Firmicutes to Proteobacteria, while Proteobacteria constantly dominated the water microbiota. Photobacterium sp. was persistently the major gut microbial community member during the whole experiment and was identified as the core gut microbiota for freshwater farmed Chinook salmon. No significant variation in gut microbial diversity and composition was observed among fish with different growth performance. At the end of the trial, 36 out of 78 fish had fluid in their swim bladders. These fish had gut microbiomes containing elevated proportions of Enterococcus, Stenotrophomonas, Aeromonas, and Raoultella. Our study supports the growing body of knowledge about the beneficial microbiota associated with modern salmon aquaculture systems and provides additional information on possible links between dysbiosis and gut microbiota for Chinook salmon.
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Affiliation(s)
- Ruixiang Zhao
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia,*Correspondence: Ruixiang Zhao, ✉
| | - Jane E. Symonds
- Cawthron Institute, Nelson, New Zealand,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | | | | | - Chris G. Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - John P. Bowman
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, Hobart, TAS, Australia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Newnham, TAS, Australia,Barbara F. Nowak, ✉
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