Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands.
Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands.
BMC Microbiol. 2023 Feb 11;23(1):40. doi: 10.1186/s12866-023-02768-2.
In contrast with macroorganisms, that show well-documented biogeographical patterns in distribution associated with local adaptation of physiology, behavior and life history, strong biogeographical patterns have not been found for microorganisms, raising questions about what determines their biogeography. Thus far, large-scale biogeographical studies have focused on free-living microbes, paying little attention to host-associated microbes, which play essential roles in physiology, behavior and life history of their hosts. Investigating cloacal gut microbiota of closely-related, ecologically similar free-living songbird species (Alaudidae, larks) inhabiting desert, temperate and tropical regions, we explored influences of geographical location and host species on α-diversity, co-occurrence of amplicon sequence variants (ASVs) and genera, differentially abundant and dominant bacterial taxa, and community composition. We also investigated how geographical distance explained differences in gut microbial community composition among larks.
Geographic location did not explain variation in richness and Shannon diversity of cloacal microbiota in larks. Out of 3798 ASVs and 799 bacterial genera identified, 17 ASVs (< 0.5%) and 43 genera (5%) were shared by larks from all locations. Desert larks held fewer unique ASVs (25%) than temperate zone (31%) and tropical larks (34%). Five out of 33 detected bacterial phyla dominated lark cloacal gut microbiomes. In tropical larks three bacterial classes were overrepresented. Highlighting the distinctiveness of desert lark microbiota, the relative abundances of 52 ASVs differed among locations, which classified within three dominant and 11 low-abundance phyla. Clear and significant phylogenetic clustering in cloacal microbiota community composition (unweighted UniFrac) showed segregation with geography and host species, where microbiota of desert larks were distinct from those of tropical and temperate regions. Geographic distance was nonlinearly associated with pairwise unweighted UniFrac distances.
We conclude that host-associated microbiota are geographically structured in a group of widespread but closely-related bird species, following large-scale macro-ecological patterns and contrasting with previous findings for free-living microbes. Future work should further explore if and to what extent geographic variation in host-associated microbiota can be explained as result of co-evolution between gut microbes and host adaptive traits, and if and how acquisition from the environmental pool of bacteria contributes to explaining host-associated communities.
与表现出与生理、行为和生活史的局部适应密切相关的有充分记录的生物地理分布模式的大型生物相反，尚未发现微生物具有强烈的生物地理分布模式，这引发了关于什么决定其生物地理学的问题。到目前为止，大规模的生物地理研究主要集中在自由生活的微生物上，很少关注宿主相关的微生物，而宿主相关的微生物在宿主的生理、行为和生活史中起着至关重要的作用。我们调查了生活在沙漠、温带和热带地区的密切相关、生态相似的自由生活鸣禽（百灵科，云雀）的泄殖腔肠道微生物群，以探索地理位置和宿主物种对 α-多样性、扩增子序列变体 (ASV) 和属的共现、差异丰度和优势细菌分类群以及群落组成的影响。我们还研究了地理距离如何解释云雀肠道微生物群落组成在不同地区的差异。
地理位置不能解释云雀泄殖腔微生物群的丰富度和 Shannon 多样性的变化。在所鉴定的 3798 个 ASV 和 799 个细菌属中，有 17 个 ASV（<0.5%）和 43 个属（5%）被来自所有地点的云雀共享。沙漠云雀拥有的独特 ASV（25%）少于温带（31%）和热带云雀（34%）。33 个检测到的细菌门中的 5 个门主导着云雀的泄殖腔肠道微生物组。在热带云雀中，有三个细菌纲过度代表。突出显示沙漠云雀微生物组的独特性，52 个 ASV 的相对丰度在不同地点存在差异，这些 ASV 分类在三个主要和 11 个低丰度门内。在泄殖腔微生物群落组成（非加权 UniFrac）中清晰而显著的系统发育聚类表明，地理位置和宿主物种的聚类，沙漠云雀的微生物组与热带和温带地区的微生物组明显不同。地理距离与成对非加权 UniFrac 距离呈非线性相关。
我们的结论是，宿主相关的微生物群在一组广泛但密切相关的鸟类物种中具有地理结构，遵循大规模的宏观生态模式，与先前对自由生活微生物的研究结果形成对比。未来的工作应该进一步探索宿主相关微生物群的地理变异是否以及在多大程度上可以解释为肠道微生物与宿主适应性特征的共同进化结果，以及从细菌环境库中获得的微生物群是否以及如何有助于解释宿主相关的群落。
