Lu Zhibin, Hao Jingwen, Meng Jilun, Liu Cui, Ye Tiantian, Yan Junjun, Li Guo, Zheng Yutong, Xu Pao, Gu Zhimin
Xianghu Laboratory, Hangzhou 311231, China.
Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China.
Microorganisms. 2025 Aug 12;13(8):1881. doi: 10.3390/microorganisms13081881.
This study aimed to elucidate stage-specific dynamics, assembly mechanisms, and functional roles of bacterial communities during larval development through high-resolution microbiota profiling. A high-frequency sampling strategy (126 samples across 11 zoeal stages and 1 post-larval stage within 21 days) and 16S rRNA absolute quantification sequencing were employed. Bacterial succession, persistent taxa, and ecological processes were analyzed using abundance-occupancy modeling, neutral community modeling, and PICRUSt2-based functional prediction. Absolute bacterial abundance exhibited a triphasic abundance trajectory. Initial accumulation: Linear increase (Dph 1-5, peak Δlog10 = +1.7). Mid-stage expansion: Peak abundance (log10 = 7.5 copies/g, Dph 7-8). Late-stage remodeling: Secondary peak (log10 = 7.1 copies/g, Dph 19). Eighty dominant amplicon sequence variants (ASVs) (dominant taxa: , , and Enterobacteriaceae) comprised > 95% of the total abundance and coexisted via niche partitioning. Community construction was dominated by ecological drift/dispersal limitation (neutral model R = 0.16, < 0.01). Metabolic pathways (e.g., nutrient metabolism) shifted with dietary transition. "Phylogenetic replacement" underpinned microbiota resilience against environmental perturbations. Optimizing aquaculture environments offers a viable antibiotic-free strategy for microbial management, advancing our understanding of host microbe interactions and ecological niche differentiation in aquatic animals.
本研究旨在通过高分辨率微生物群分析阐明幼虫发育过程中细菌群落的阶段特异性动态、组装机制和功能作用。采用了高频采样策略（在21天内对11个蚤状幼体阶段和1个幼体后阶段的126个样本）和16S rRNA绝对定量测序。使用丰度-占有率建模、中性群落建模和基于PICRUSt2的功能预测分析细菌演替、持久性分类群和生态过程。细菌绝对丰度呈现出三相丰度轨迹。初始积累：线性增加（发育天数1-5天，峰值Δlog10 = +1.7）。中期扩张：丰度峰值（log10 = 7.5拷贝/克，发育天数7-8天）。后期重塑：二次峰值（log10 = 7.1拷贝/克，发育天数19天）。80个优势扩增子序列变体（ASVs）（优势分类群： 、 和肠杆菌科）占总丰度的>95%，并通过生态位划分共存。群落构建主要受生态漂变/扩散限制（中性模型R = 0.16，P < 0.01）。代谢途径（如营养代谢）随着饮食转变而变化。“系统发育替代”支撑了微生物群对环境扰动的恢复力。优化水产养殖环境为微生物管理提供了一种可行的无抗生素策略，增进了我们对水生动物宿主-微生物相互作用和生态位分化的理解。
