Hernandez Jordan B, Hayer Shivdeep S, Alvarez Sophie, Fischer Anne, Hassenstab Haley R, Cooper Katherine, Alsafwani Zahraa W, Benson Andrew K, Suhr Van Haute Mallory J, Izard Jacques, Song Hyun-Seob, Clayton Jonathan B
Department of Biology, University of Nebraska Omaha, Omaha, Nebraska, USA.
Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
mSystems. 2025 Jul 7:e0021425. doi: 10.1128/msystems.00214-25.
The common marmoset (), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest modifies bile acids to exert its influence. and several members had the most bacterial associations and were negatively associated with , indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified and as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.
普通狨猴是一种非人类灵长类动物，由于其在包括微生物组学领域在内的各种研究环境中的转化价值，它是一种备受关注的模式生物。虽然圈养条件下狨猴肠道微生物组的组成已得到一定程度的描述，但对于肠道微生物群如何随时间相互作用以及它们与代谢产物产生之间的关系却知之甚少。为了帮助回答这个问题，我们通过计算从10只圈养狨猴纵向收集的16S rDNA衍生的相对属丰度数据与靶向代谢组学数据之间的斯皮尔曼相关系数，对普通狨猴肠道微生物组中的相互作用进行了表征。关联网络图用于可视化显著相关性，并识别具有高度中心性的属和代谢产物，将它们标记为在微生物组中更具影响力的成分。[具体属名]参与了最多的代谢组学关联，表明它可能对参与微生物生长和信号传导的代谢产物起着守门作用。它与下调的牛磺酸和胆汁酸的关联进一步表明[具体属名]通过修饰胆汁酸来发挥其影响。[具体属名]和几个[具体属名]成员具有最多的细菌关联，并且与[具体属名]呈负相关，表明存在潜在的竞争关系。为了进一步表征微生物组相互作用，我们对数据集中显著的内部关联进行了层次聚类，并开发了一种新的“关键候选评分”指标，该指标将[具体属名]和[具体属名]确定为狨猴肠道微生物组中最具影响力的细菌（即所谓的候选关键属）。
重要性
先前的研究已经确定普通狨猴的肠道微生物组内存在显著的个体差异。由于缺乏关于特定微生物群之间动态相互作用的知识，这种个体间变异性的原因及其与圈养健康状况的关系尚不清楚。为此，本研究对健康圈养狨猴的肠道微生物组和代谢组之间的显著时间关联进行了表征。我们的研究结果表明，某些微生物分类群在肠道内比其他分类群具有更强的影响力。具体而言，[具体属名]是最丰富的属，也是个体特异性微生物组差异背后的主要驱动力，而严格意义上的梭菌属1和拟杆菌目的细菌分别是显著的细菌 - 代谢产物和细菌 - 细菌关联的主要来源。总之，这表明[具体属名]可能与其他分类群在狨猴微生物组中竞争资源和代谢生态位。
