Table_1_Adapting to Novel Environments Together: Evolutionary and Ecological Correlates of the Bacterial Microbiome of the World’s Largest Cavefish Diversification (Cyprinidae, Sinocyclocheilus).XLSX

The symbiosis between a host and its microbiome is essential for host fitness, and this association is a consequence of the host’s physiology and habitat. Sinocyclocheilus, the largest cavefish diversification of the world, an emerging multi-species model system for evolutionary novelty, provides an excellent opportunity for examining correlates of host evolutionary history, habitat, and gut-microbial community diversity. From the diversification-scale patterns of habitat occupation, major phylogenetic clades (A–D), geographic distribution, and knowledge from captive-maintained Sinocyclocheilus populations, we hypothesize habitat to be the major determinant of microbiome diversity, with phylogeny playing a lesser role. For this, we subject environmental water samples and fecal samples (representative of gut-microbiome) from 24 Sinocyclocheilus species, both from the wild and after being in captivity for 6 months, to bacterial 16S rRNA gene profiling using Illumina sequencing. We see significant differences in the gut microbiota structure of Sinocyclocheilus, reflective of the three habitat types; gut microbiomes too, were influenced by host-related factors. There is no significant association between the gut microbiomes and host phylogeny. However, there is some microbiome related structure at the clade level, with the most geographically distant clades (A and D) being the most distinct, and the two overlapping clades (B and C) showing similarities. Microbes inhabiting water were not a cause for significant differences in fish-gut microbiota, but water quality parameters were. Transferring from wild to captivity, the fish microbiomes changed significantly and became homogenized, signifying plastic changes and highlighting the importance of environmental factors (habitat) in microbiome community assembly. The core microbiome of this group, at higher taxonomic scale, resembled that of other teleost fishes. Our results suggest that divergent natural environments giving rise to evolutionary novelties underlying host adaptations, also includes the microbiome of these fishes.

宿主与其微生物组（microbiome）之间的共生关系对宿主适合度至关重要，而这种关联是宿主生理特征与栖息环境共同作用的结果。作为全球物种多样性最丰富的洞穴鱼类类群，金线鲃属（Sinocyclocheilus）同时也是新兴的多物种进化创新研究模型体系，为探究宿主进化历史、栖息环境与肠道微生物组群落多样性之间的关联提供了绝佳契机。基于栖息地占领的演化尺度格局、主要系统发育支系（A-D）、地理分布特征，以及人工饲养金线鲃种群的相关研究基础，我们提出假说：栖息环境是微生物组多样性的主要决定因素，而宿主系统发育的影响相对较弱。为此，我们针对24种野生及人工饲养6个月的金线鲃，采集其环境水样与粪便样本（粪便样本可作为肠道微生物组的代表样本），采用Illumina测序技术进行细菌16S核糖体RNA（16S rRNA）基因扩增子测序分析。研究结果显示，金线鲃的肠道微生物组结构存在显著差异，且该差异与三类栖息环境类型相契合；同时肠道微生物组也受到宿主相关因素的影响。不过肠道微生物组与宿主系统发育之间并未呈现显著关联。但在支系层面仍存在一定的微生物组结构特征：地理分布差异最大的支系A与支系D的微生物组差异最为显著，而地理分布重叠的支系B与支系C则表现出相似的微生物组组成。栖息于水环境的微生物并非鱼类肠道微生物组产生显著差异的原因，而水环境的水质参数才是相关影响因素。将野生金线鲃转入人工饲养环境后，其肠道微生物组发生了显著变化并趋于同质化，这表明微生物组存在可塑性变化，同时也凸显了环境因素（栖息环境）在微生物组群落构建中的重要作用。该类群在更高分类层级上的核心微生物组，与其他硬骨鱼类（teleost fishes）的核心微生物组具有相似性。本研究结果表明，催生宿主适应性进化创新的多样自然环境，同样也塑造了这些鱼类的微生物组。