Table S5.xlsx from Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerines birds are shaped by diet and flight-associated gut modifications

Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.

动物宿主与微生物共生体（microbial symbionts）之间已演化出复杂的共生关联，二者相互依存以实现特定生理功能。这类共生关联往往会形成系统发育共生（phylosymbiosis）现象：即系统发育关系相近的物种，其微生物组组成相较于远缘物种更为相似。然而，飞行脊椎动物，尤其是鸟类的肠道微生物组中，系统发育共生的证据要么薄弱，要么完全缺失。为进一步阐明这一现象，本研究针对采自新几内亚的37种热带雀形目鸟类（passerine bird）的泄殖腔微生物组（cloacal microbiomes），采用16S rRNA细菌基因测序技术开展对比分析。研究结果表明，此类鸟类既未呈现系统发育共生现象，其微生物组也具有高度变异性。此外，本研究发现肠道细菌群落组成具有物种特异性，且主要受宿主饮食而非采样地点塑造，这一模式可能由各物种所处栖息地的相似性所驱动。研究进一步表明，与飞行相关的肠道结构改造，结合个体间的饮食差异，共同塑造了肠道微生物组的结构与变异程度，这也是系统发育共生现象缺失的原因。上述模式提示，共生关系的稳定性可能取决于微生物的功能多样性，而非其分类学组成。此外，鸟类宿主与微生物共生体之间的宿主-微生物关联更具可变性与动态性，这表明二者协同演化的潜力可能存在显著差异。