Fu Jiongxing, Yu Danxia, Zheng Wei, Jiang Yu, Wang Lei, Cai Hui, Xia Qinghua, Shu Xiao-Ou, Xu Wanghong
Department of Epidemiology, School of Public Health, Fudan University, 130 Dong An Road, Shanghai, 200032 China.
Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203 USA.
Phenomics. 2025 Feb 21;5(1):91-108. doi: 10.1007/s43657-024-00211-8. eCollection 2025 Feb.
Gut microbiota with co-abundant behaviors is considered belonging to the same guild in micro-ecosystem. In this study, we established co-abundance networks of operational taxonomic units (OTUs) among 2944 Chinese adults from the Shanghai Men's and Women's Health Studies and observed a positive connection-dominated scale-free network using Sparse Correlations for Compositional data (SparCC). The closeness centrality was negatively correlated with other degree-based topological metrics in the network, indicating the isolated modularization of the bacteria. A total of 130 guilds were constructed, with a high modularity of 0.68, and retaining more diversity of OTUs than genus classification. The scores of guild structure similarity for comparisons between all, the healthy and the unhealthy subjects were higher than those derived from randomized permutations, suggesting a robust guild structure. We further used the constructed 130 guilds as the aggregation units to identify gut microbiota that may be associated with type 2 diabetes, and found that the OTUs in 21 significant guilds relevant to diabetes belonged to 19 of 41 (46.3%) previously reported genera (derived from Disbiome database), while only 10 (24.4%) showed different abundances between diabetes patients and healthy subjects in genus-based analysis. Our study reveals modularization of gut microbiota as guilds in Chinese populations, and demonstrates advantages of guild-based analysis in identifying diabetes-related gut bacteria. The analytical method based on microbial networks should be widely used to deepen our understanding of the role of gut microbiota in human health.
The online version contains supplementary material available at 10.1007/s43657-024-00211-8.
具有共丰度行为的肠道微生物群在微生态系统中被认为属于同一功能群。在本研究中，我们建立了来自上海男性和女性健康研究的2944名中国成年人中可操作分类单元（OTU）的共丰度网络，并使用成分数据的稀疏相关性（SparCC）观察到一个以正连接为主的无标度网络。网络中的紧密中心性与其他基于度的拓扑指标呈负相关，表明细菌的孤立模块化。共构建了130个功能群，模块化程度高达0.68，与属分类相比保留了更多的OTU多样性。所有、健康和不健康受试者之间的功能群结构相似性得分高于随机排列得出的得分，表明功能群结构稳健。我们进一步将构建的130个功能群作为聚集单元来识别可能与2型糖尿病相关的肠道微生物群，发现与糖尿病相关的21个显著功能群中的OTU属于先前报道的41个属中的19个（46.3%）（源自Disbiome数据库），而在基于属的分析中，只有10个（24.4%）在糖尿病患者和健康受试者之间显示出不同的丰度。我们的研究揭示了中国人群中肠道微生物群作为功能群的模块化，并证明了基于功能群的分析在识别糖尿病相关肠道细菌方面的优势。基于微生物网络的分析方法应广泛应用，以加深我们对肠道微生物群在人类健康中作用的理解。
在线版本包含可在10.1007/s43657-024-00211-8获取的补充材料。
