Data Sheet 1_Gut microbiota dynamics and their impact on body condition in nestlings of the yellow-rumped flycatchers, Ficedula zanthopygia.docx

Investigating the gut microbiome during host development is essential for understanding its influence on host health and fitness. While host body condition is a crucial fitness-related trait and a strong predictor of viability in numerous animal species, its relationship with gut bacteria remains underexplored, particularly in non-model organisms. This study examines the gut microbiome of the altricial wild bird species, yellow-rumped flycatchers (Ficedula zanthopygia), by analyzing nestling feces through 16S rRNA sequencing at four developmental stages: Day 3, Day 6, Day 9 and Day 12 post-hatching. We explored the temporal dynamics of the gut microbiome and its correlation with body condition, a key indicator of fitness. Our results demonstrate signinficant shifts in microbial community composition and diversity throughout development. Notably, Day 3 nestlings displayed lower alpha diversity compared to later stages, while microbial diversity stabilized from Days 6 to 12. Both the age of the nestlings and the environmental conditions of the nest box significantly shaped the gut microbial community structure. A contemporaneous relationship was observed, where the scaled-mass index (SMI) at Day 6 positively correlating with microbial diversity at that time. Additionally, a time-lagged effect emerged, linking SMI at Day 9 to microbial diversity at Day 6. These findings highlight the vital role of the gut microbiome in the development of nestlings, particularly emphasizing Day 6 as a critical period due to its stable microbial diversity and association with SMI. This study underscores the influence of gut bacteria on host fitness in developing birds.

探究宿主发育过程中的肠道微生物组（gut microbiome），对于理解其对宿主健康与适合度（fitness）的影响至关重要。尽管宿主身体状况（body condition）是与适合度相关的关键性状，且在众多动物类群中是存活力（viability）的强力预测因子，但其与肠道菌群（gut bacteria）的关联仍未得到充分探索，在非模式生物（non-model organisms）中尤甚。本研究以晚成雏（altricial）野生鸟类黄眉姬鹟（*Ficedula zanthopygia*）为研究对象，通过对其雏鸟粪便进行16S rRNA测序，分析了孵化后第3、6、9、12天四个发育阶段的肠道微生物组。本研究探究了肠道微生物组的时间动态变化及其与适合度关键指标——身体状况的关联。研究结果显示，在整个发育过程中，微生物群落组成与多样性均发生了显著变化。值得注意的是，孵化第3天的雏鸟肠道微生物α多样性（alpha diversity）低于后续发育阶段，而第6至12天的微生物多样性趋于稳定。雏鸟日龄与巢箱环境条件均显著影响肠道微生物群落结构。研究观察到同期关联：孵化第6天的体型质量指数（scaled-mass index, SMI）与当日的微生物多样性呈显著正相关。此外还存在时滞效应：孵化第9天的体型质量指数与第6天的微生物多样性存在关联。本研究结果凸显了肠道微生物组在雏鸟发育过程中的重要作用，尤其强调第6天为关键时期——该阶段微生物多样性趋于稳定，且与体型质量指数存在显著关联。本研究进一步证实了肠道菌群对发育中鸟类宿主适合度的影响。