Table S6.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）之间演化出了复杂的共生关联，二者彼此依赖以完成特定生理功能。在多数情况下，这类共生关系会催生系统发育共生（phylosymbiosis）现象：即系统发育亲缘关系较近的物种，其微生物组的组成相较于亲缘关系较远的物种更为相似。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十分薄弱，要么完全缺失。为进一步阐明该现象，本研究采用16S rRNA细菌基因测序（16S rRNA bacterial gene sequencing）技术，对来自新几内亚的37种热带雀形目鸟类的泄殖腔微生物组进行了对比分析。结果显示，这些鸟类的肠道微生物组并不存在系统发育共生现象，且微生物组具有高度的变异性。此外，研究发现肠道细菌群落组成具有物种特异性，其主要受宿主饮食而非采样地点塑造，这一特征可能源于各物种所利用的栖息环境具有相似性。本研究进一步证实，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模式，这也是导致系统发育共生现象缺失的重要原因。上述结果表明，共生关系的稳定性或许取决于微生物的功能多样性，而非其分类学组成。此外，宿主-微生物共生关联的高变异性与动态性，暗示鸟类宿主与微生物共生体之间的协同进化（coevolution）潜力可能存在显著差异。