Natural-setting evidence of stochastic-to-deterministic gut microbiome assembly and metabolic shifts in regenerating tropical sea cucumber Stichopus monotuberculatus.
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| Main Authors: | , , , , , |
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| Format: | Artículo científico |
| Language: | en |
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Environmental research
2025
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| _version_ | 1868266181675188225 |
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| author | Yang, Xinyuan Huang, Xinxin Zheng, Bojun Gao, Fei He, Linwen Xu, Qiang |
| author_facet | Yang, Xinyuan Huang, Xinxin Zheng, Bojun Gao, Fei He, Linwen Xu, Qiang Yang, Xinyuan Huang, Xinxin Zheng, Bojun Gao, Fei He, Linwen Xu, Qiang |
| collection | PubMed - marine biology |
| contents | Natural-setting evidence of stochastic-to-deterministic gut microbiome assembly and metabolic shifts in regenerating tropical sea cucumber Stichopus monotuberculatus. Yang, Xinyuan Huang, Xinxin Zheng, Bojun Gao, Fei He, Linwen Xu, Qiang Animals Gastrointestinal Microbiome Stichopus Regeneration Metabolome RNA, Ribosomal, 16S Sea Cucumbers Holothurians exhibit a distinctive ability to eviscerate and regenerate internal organs, making them an ideal model for investigating host-microbe interactions. This study examined the dynamics of the gut microbiome and the associated metabolome during intestinal regeneration in the tropical sea cucumber Stichopus monotuberculatus under natural conditions. Through a combination of 16S rDNA sequencing and GC-MS-based metabolomics, we determined stage-specific shifts in gut microbial communities and metabolite profiles. Early regeneration was characterized by a stochastic influx of environmental microbes, low microbial network connectivity, and high metabolite-microbe correlation complexity, which suggested that the host relied on metabolic signals to coordinate the initial colonization of a diverse microbial community sourced from environment. As regeneration advanced, the microbial network grew increasingly cohesive, environmental contribution diminished, and metabolite-microbe correlation decreased. The reestablished gut microbiome exhibited no significant structural differences compared to pre-evisceration communities. This process reflected a transition from stochastic recruitment to host-filtered deterministic assembly, ultimately restoring a stable microbiome. Core microbial taxa such as Roseburia, Faecalibacterium, and Ruegeria were associated with pathways related to nutrient provisioning, energy production, and immune regulation, suggesting their potential contributions to intestinal recovery. Metabolomic analysis revealed significant alterations in amino acid, lipid, and carbohydrate metabolism, highlighting the functional integration between the gut bacteria and regenerated host tissue. Our findings provide novel insight into the interactions among host, microbe, and environment during gut microbiome assembly, as well as highlight the balance between stochastic and deterministic factors in the formation of marine holobiont communities. |
| format | Artículo científico |
| id | pubmed_40614851 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | Environmental research |
| record_format | pubmed |
| spellingShingle | Natural-setting evidence of stochastic-to-deterministic gut microbiome assembly and metabolic shifts in regenerating tropical sea cucumber Stichopus monotuberculatus. Yang, Xinyuan Huang, Xinxin Zheng, Bojun Gao, Fei He, Linwen Xu, Qiang Animals Gastrointestinal Microbiome Stichopus Regeneration Metabolome RNA, Ribosomal, 16S Sea Cucumbers Natural-setting evidence of stochastic-to-deterministic gut microbiome assembly and metabolic shifts in regenerating tropical sea cucumber Stichopus monotuberculatus. Yang, Xinyuan Huang, Xinxin Zheng, Bojun Gao, Fei He, Linwen Xu, Qiang Animals Gastrointestinal Microbiome Stichopus Regeneration Metabolome RNA, Ribosomal, 16S Sea Cucumbers Holothurians exhibit a distinctive ability to eviscerate and regenerate internal organs, making them an ideal model for investigating host-microbe interactions. This study examined the dynamics of the gut microbiome and the associated metabolome during intestinal regeneration in the tropical sea cucumber Stichopus monotuberculatus under natural conditions. Through a combination of 16S rDNA sequencing and GC-MS-based metabolomics, we determined stage-specific shifts in gut microbial communities and metabolite profiles. Early regeneration was characterized by a stochastic influx of environmental microbes, low microbial network connectivity, and high metabolite-microbe correlation complexity, which suggested that the host relied on metabolic signals to coordinate the initial colonization of a diverse microbial community sourced from environment. As regeneration advanced, the microbial network grew increasingly cohesive, environmental contribution diminished, and metabolite-microbe correlation decreased. The reestablished gut microbiome exhibited no significant structural differences compared to pre-evisceration communities. This process reflected a transition from stochastic recruitment to host-filtered deterministic assembly, ultimately restoring a stable microbiome. Core microbial taxa such as Roseburia, Faecalibacterium, and Ruegeria were associated with pathways related to nutrient provisioning, energy production, and immune regulation, suggesting their potential contributions to intestinal recovery. Metabolomic analysis revealed significant alterations in amino acid, lipid, and carbohydrate metabolism, highlighting the functional integration between the gut bacteria and regenerated host tissue. Our findings provide novel insight into the interactions among host, microbe, and environment during gut microbiome assembly, as well as highlight the balance between stochastic and deterministic factors in the formation of marine holobiont communities. |
| title | Natural-setting evidence of stochastic-to-deterministic gut microbiome assembly and metabolic shifts in regenerating tropical sea cucumber Stichopus monotuberculatus. |
| topic | Animals Gastrointestinal Microbiome Stichopus Regeneration Metabolome RNA, Ribosomal, 16S Sea Cucumbers |
| url | https://pubmed.ncbi.nlm.nih.gov/40614851/ |