Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China.
BMC Microbiol. 2021 May 4;21(1):138. doi: 10.1186/s12866-021-02201-6.
Ulcerative colitis (UC) is one of the primary types of inflammatory bowel disease (IBD), the occurrence of which has been increasing worldwide. Although IBD is an intensively studied human microbiome-associated disease, research on Chinese populations remains relatively limited, particularly on the mucosal microbiome. The present study aimed to analyze the changes in the mucosal microbiome associated with UC from the perspectives of medical ecology and complex network analysis.
In total, 56 mucosal microbiome samples were collected from 28 Chinese UC patients and their healthy family partners, followed by amplicon sequencing. Based on sequencing data, we analyzed species diversity, shared species, and inter-species interactions at the whole community, main phyla, and core/periphery species levels. We identified four opportunistic "pathogens" (i.e., Clostridium tertium, Odoribacter splanchnicus, Ruminococcus gnavus, and Flavonifractor plautii) with potential significance for the diagnosis and treatment of UC, which were inhibited in healthy individuals, but unrestricted in the UC patients. In addition, we also discovered in this study: (i) The positive-to-negative links (P/N) ratio, which measures the balance of species interactions or inhibition effects in microbiome networks, was significantly higher in UC patients, indicating loss of inhibition against potentially opportunistic "pathogens" associated with dysbiosis. (ii) Previous studies have reported conflicting evidence regarding species diversity and composition between UC patients and healthy controls. Here, significant differences were found at the major phylum and core/periphery scales, but not at the whole community level. Thus, we argue that the paradoxical results found in existing studies are due to the scale effect.
Our results reveal changes in the ecology and network structure of the gut mucosal microbiome that might be associated with UC, and these changes might provide potential therapeutic mechanisms of UC. The four opportunistic pathogens that were identified in the present study deserve further investigation in future studies.
溃疡性结肠炎（UC）是炎症性肠病（IBD）的主要类型之一，其发病率在全球范围内呈上升趋势。尽管 IBD 是一种深入研究的人类微生物组相关疾病，但针对中国人群的研究仍然相对有限，特别是在黏膜微生物组方面。本研究旨在从医学生态学和复杂网络分析的角度分析与 UC 相关的黏膜微生物组的变化。
共从 28 名中国 UC 患者及其健康的家族成员中采集了 56 个黏膜微生物组样本，随后进行了扩增子测序。基于测序数据，我们分析了整个群落、主要门和核心/边缘物种水平上物种多样性、共享物种和种间相互作用。我们鉴定了四种具有潜在诊断和治疗 UC 意义的机会性病原体（即 Clostridium tertium、Odoribacter splanchnicus、Ruminococcus gnavus 和 Flavonifractor plautii），这些病原体在健康个体中受到抑制，但在 UC 患者中不受限制。此外，我们还在本研究中发现：（i）正-负关系（P/N）比值，用于衡量微生物组网络中物种相互作用或抑制作用的平衡，在 UC 患者中显著升高，表明对与失调相关的潜在机会性病原体的抑制作用丧失。（ii）先前的研究报告了 UC 患者和健康对照者之间在物种多样性和组成方面存在矛盾的证据。在这里，在主要门和核心/边缘尺度上发现了显著差异，但在整个群落水平上没有。因此，我们认为现有研究中出现的矛盾结果是由于规模效应。
我们的研究结果揭示了与 UC 相关的肠道黏膜微生物组的生态和网络结构变化，这些变化可能为 UC 提供潜在的治疗机制。本研究中鉴定的四种机会性病原体值得在未来的研究中进一步研究。
