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<p>To address the challenge of fishmeal shortage and improve the utilization of fishmeal-free (FMF) diets in large yellow croaker (<i>Larimichthys crocea</i>), we conducted an integrative analysis combining host genetics and gut microbiota. A 28-day indoor feeding trial was performed with 185 fish using an FMF-based diet, during which single nucleotide polymorphism (SNP) genotyping and feed efficiency evaluations were conducted. The V3-V4 regions of the 16S rRNA gene were sequenced from both distal (DI) and proximal (PI) intestinal segments. Significant microbial contributions (microbiability) were only observed for daily feed intake (DFI) and residual feed intake (RFI). Microbiability estimates reached 0.25 (DI) and 0.17 (PI) for DFI, while RFI in DI exhibited higher microbiability (<i>m</i><sup>2</sup>&#xa0;= 0.11) than heritability (<i>h</i><sup>2</sup>&#xa0;= 0.08). In contrast, correlations between host genetic variation and microbial community distances were extremely weak. We further identified heritable microbial taxa, including <i>Lactococcus</i>, <i>Alicyclobacillus acidoterrestris</i>, and <i>Bacillus,</i> as well as microbial biomarkers such as <i>Lactococcus</i>, <i>Listeria</i>, <i>Methylobacterium</i>, and <i>Alicyclobacillus acidoterrestris</i>, which were significantly associated with FMF feed adaptation. These findings highlight the complementary roles of host genetics and gut microbiota in shaping FMF feed utilization in marine fish, and provide valuable targets for selective breeding of strains with enhanced adaptability to plant-based diets.</p>

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Integrative Microbiome-Genetic Analysis Reveals Mechanisms of Fishmeal-Free Feed Adaptability in Large Yellow Croaker (Larimichthys crocea)

  • 期刊论文

  • 发表日期：

    2025年12月29日

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  • Gongsi Wang,
  • Xiaotong Li,
  • Peng Ren,
  • Qinghui Ai,
  • Zhiyong Wang

摘要

To address the challenge of fishmeal shortage and improve the utilization of fishmeal-free (FMF) diets in large yellow croaker (Larimichthys crocea), we conducted an integrative analysis combining host genetics and gut microbiota. A 28-day indoor feeding trial was performed with 185 fish using an FMF-based diet, during which single nucleotide polymorphism (SNP) genotyping and feed efficiency evaluations were conducted. The V3-V4 regions of the 16S rRNA gene were sequenced from both distal (DI) and proximal (PI) intestinal segments. Significant microbial contributions (microbiability) were only observed for daily feed intake (DFI) and residual feed intake (RFI). Microbiability estimates reached 0.25 (DI) and 0.17 (PI) for DFI, while RFI in DI exhibited higher microbiability (m2 = 0.11) than heritability (h2 = 0.08). In contrast, correlations between host genetic variation and microbial community distances were extremely weak. We further identified heritable microbial taxa, including Lactococcus, Alicyclobacillus acidoterrestris, and Bacillus, as well as microbial biomarkers such as Lactococcus, Listeria, Methylobacterium, and Alicyclobacillus acidoterrestris, which were significantly associated with FMF feed adaptation. These findings highlight the complementary roles of host genetics and gut microbiota in shaping FMF feed utilization in marine fish, and provide valuable targets for selective breeding of strains with enhanced adaptability to plant-based diets.