Interactions and Stability of Gut Microbiota in Zebrafish Increase with Host Development

Xiao, Fanshu; Zhu, Wengen; Yu, Yuhe; Huang, Jie; Li, Juan; He, Zhili; Wang, Jianjun; Yin, Huaqun; Huang, Yu; Liu, Shengwei; Chen, Pubo; Huang, Zhijian; He, Jianguo; Wang, Cheng; Shu, Longfei; Yan, Qingyun

doi:10.1128/spectrum.01696-21

Cited by 14 publications

(14 citation statements)

References 62 publications

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“…It has been demonstrated that human gut microbiota changes can be deliberately modified across time, which differs from the human genome that is encoded at birth and cannot be altered during life (at least with current technology) ( Martino et al, 2022 ). A recent study on gut microbiota interactions in zebrafish indicates that the increasing gut microbial stability is determined by the development of the immune system and the greater stability of nutrient absorption ( Xiao et al, 2022 ). Furthermore, the change of feeding habit, including the use of probiotics, is also shown to affect the fish gut microbiota, especially at the early life stages ( Deng et al, 2021 ; Vargas-Albores et al, 2021 ).…”

Section: Discussionmentioning

confidence: 99%

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems

et al. 2023

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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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Section: Discussionmentioning

confidence: 99%

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems

et al. 2023

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“…We found that diet had a substantial impact on the structure of the gut microbiome in adult zebra sh. Previous research has found that diets with varying compositions of key macronutrients (e.g., protein, lipids and ber content) impacts zebra sh physiology and the gut microbiome [5,[16][17][18][29][30][31][32]. Moreover, diet's effect on restructuring the host's gut microbiome has been observed across an evolutionarily diverse array of vertebrate and invertebrate animal hosts[8, 9,11,12,33].…”

Section: Discussionmentioning

confidence: 99%

“…For instance, Stephens et al used a variety of live and dry food diets and found that juvenile zebra sh gut microbiomes were highly diverse but declined with age [30], while Wong et al found opposite results for juvenile zebra sh that were fed de ned diets [18]. Furthermore, Burns et al and Xiao et al noted that the observed early life variability of the gut microbiome could be a result of husbandry choices involving diet [29,31,32]. While our study differed in exact length and sampling time points as compared to these prior studies, we do nd congruent trends in gut microbiome diversity to other zebra sh studies that sampled within similar developmental periods as those interrogated in our investigation.…”

Section: Discussionmentioning

confidence: 99%

Common laboratory diets differentially influence zebrafish gut microbiome’s successional development and sensitivity to pathogen exposure

Sieler

Kasschau

Varga³

et al. 2023

Preprint

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Background: Despite the long-established importance of zebrafish (Danio rerio) as a model organism and their increasing use in microbiome-targeted studies, relatively little is known about how husbandry practices involving diet impact the zebrafish gut microbiome. Given the microbiome’s important role in mediating host physiology and the potential for diet to drive variation in microbiome composition, we sought to clarify how three different dietary formulations that are commonly used in zebrafish facilities impact the gut microbiome. We compared the composition of gut microbiomes in approximately 60 AB line adult (4- and 7-month-old) zebrafish fed each diet throughout their lifespan. Results: Our analysis finds that diet has a substantial impact on the composition of the gut microbiome in adult fish, and that diet also impacts the developmental variation in the gut microbiome. We further evaluated whether the 7-month-old fish microbiome compositions that result from dietary variation are differentially sensitive to infection by a common laboratory pathogen, Mycobacterium chelonae. Our analysis finds that the gut microbiome’s sensitivity to M. chelonae infection varies as a function of diet, especially for moderate and low abundance taxa. Conclusions: Overall, our results indicate that diet drives the successional development of the gut microbiome as well as its sensitivity to exogenous exposure. Consequently, investigators should carefully consider the role of diet in their microbiome zebrafish investigations, especially when integrating results across studies that vary by diet.

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“…Although gut microbes play a crucial role in fish nutrition and metabolism, their composition and abundance are strongly influenced by many direct and indirect factors. Many studies have shown that gut microbial communities vary according to host individual development [21], diet [12,22], environment [19,23], and host genetics and phylogeny, which refer to fish populations from different geographic clusters having different gut microbiomes and fish genotypes correlating with gut microbiomes, with the more genetically distinct populations exhibiting greater differences in gut microbiomes [24,25]. However, previous studies have focused on single species in limited environments, such as fish in farmed ponds or under laboratory conditions and fed specific foods [12,15,18,26].…”

Section: Introductionmentioning

confidence: 99%

Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season

Liang,

Wang,

Gao

et al. 2024

Microorganisms

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The gut microbiota of fish is crucial for their growth, development, nutrient uptake, physiological balance, and disease resistance. Yet our knowledge of these microbial communities in wild fish populations in their natural ecosystems is insufficient. This study systematically examined the gut microbial communities of seven wild fish species in Chaohu Lake, a fishing-restricted area with minimal water turnover, across four seasons. We found significant variations in gut microbial community structures among species. Additionally, we observed significant seasonal and regional variations in the gut microbial communities. The Chaohu Lake fish gut microbial communities were predominantly composed of the phyla Firmicutes, Proteobacteria(Gamma), Proteobacteria(Alpha), Actinobacteriota, and Cyanobacteria. At the genus level, Aeromonas, Cetobacterium, Clostridium sensu stricto 1, Romboutsia, and Pseudomonas emerged as the most prevalent. A co-occurrence network analysis revealed that C. auratus, C. carpio, and C. brachygnathus possessed more complex and robust gut microbial networks than H. molitrix, C. alburnus, C. ectenes taihuensis, and A. nobilis. Certain microbial groups, such as Clostridium sensu stricto 1, Romboutsia, and Pseudomonas, were both dominant and keystone in the fish gut microbial network. Our study offers a new approach for studying the wild fish gut microbiota in natural, controlled environments. It offers an in-depth understanding of gut microbial communities in wild fish living in stable, limited water exchange natural environments.

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Interactions and Stability of Gut Microbiota in Zebrafish Increase with Host Development

Cited by 14 publications

References 62 publications

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems

Common laboratory diets differentially influence zebrafish gut microbiome’s successional development and sensitivity to pathogen exposure

Variations and Interseasonal Changes in the Gut Microbial Communities of Seven Wild Fish Species in a Natural Lake with Limited Water Exchange during the Closed Fishing Season

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