Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute > 98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of > 22,000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database (Mitchell et al. in Nucleic Acids Res 46:D726–D735, 2018). By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD.

中文翻译：

---

不同分类水平炎症性肠病患者的微生物失衡

炎症性肠病 (IBD) 是一组使人衰弱的慢性疾病，包括克罗恩病 (CD) 和溃疡性结肠炎 (UC)，可导致肠道炎症并影响全球数百万人。在不同的分类水平上，与健康个体相比，IBD 患者的肠道菌群结构发生了显着变化。然而，目前尚不清楚这些受 IBD 影响的细菌群如何与肠道中的其他常见细菌相关，以及它们如何在全球范围内与不同疾病状况相关联。在这项研究中，我们使用来自 IBD 患者的粪便样本，通过基于 16S rRNA 基因的微生物群落结构的多样性分析表明，与健康个体相比，IBD 患者的肠道微生物群落的多样性较少。此外，我们已经确定了与健康对照相比，CD 和 UC 中哪些细菌群的丰度发生了变化。在包括厚壁菌门、拟杆菌门、变形菌门和放线菌门在内的四种主要细菌门中观察到了显着的不平衡，它们共同构成了 > 98% 的肠道微生物群。接下来，我们根据从患病和健康个体采集的 > 22,000 个粪便和肠道活检样本的公共肠道微生物组数据中获得的丰度分布的相关性，重建了一个细菌家族共丰度网络。数据是使用 EBI 宏基因组数据库（Mitchell 等人在 Nucleic Acids Res 46:D726–D735, 2018）编译的。通过将 IBD 改变的细菌家族映射到网络，我们表明，在 IBD 条件下表现出丰度增加的细菌家族与其他群体没有很好的联系，这意味着这些家族通常不会与常见的肠道生物共存。然而，与健康状况相比，IBD 状况中丰度减少或未发生变化的细菌家族与其他细菌群有很好的联系，这表明它们是肠道中非常重要的细菌群，可以在一系列范围内与其他细菌共存条件。与健康个体相比，IBD 患者的肠道微生物群多样性较低。在 IBD 患者中发生变化的细菌群被发现是与常见的肠道共生细菌不能很好共存的群，而在 IBD 患者中未发生变化的细菌群被发现通常与共生肠道微生物群共存。这为了解 IBD 患者肠道微生物群的动态提供了潜在的洞察力。