Table_6_Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis.xlsx

The collection of whole microbial communities (bacteria, archaea, fungi, and viruses) together constitutes the gut microbiome. Diet, age, stress, host genetics, and diseases cause increases or decreases in the relative abundance and diversity of bacterial species (dysbiosis). We aimed to investigate the gut microbial composition at different taxonomic levels of healthy controls (HCs) with active Crohn’s disease (CD), ulcerative colitis (UC), and ischemic colitis (IC) using culture- and non-culture-based approaches and identify biomarkers to discriminate CD, UC, or IC. We determined the specific changes in the gut microbial profile using culture-independent (16S rRNA gene amplicon sequencing) as well as culture-based (culturomic) approaches. Biomarkers were validated using quantitative Real-Time PCR (qPCR). In both methods, bacterial diversity and species richness decreased in disease-associated conditions compared with that in HCs. Highly reduced abundance of Faecalibacterium prausnitzii and Prevotella sp. and an increased abundance of potentially pathogenic bacteria such as Enterococcus faecium, Enterococcus faecalis, and Escherichia coli in all CD, UC, or IC conditions were observed. We noted a high abundance of Latilactobacillus sakei in CD patients; Ligilactobacillus ruminis in UC patients; and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC patients. Highly reduced abundance of Faecalibacterium prausnitzii in all cases, and increased abundance of Latilactobacillus sakei and Enterococcus faecium in CD, Ligilactobacillus ruminis and Enterococcus faecium in UC, and Enterococcus faecium, Escherichia coli, and Enterococcus faecalis in IC could be biomarkers for CD, UC, and IC, respectively. These biomarkers may help in IBD (CD or UC) and IC diagnosis.

包含细菌、古菌、真菌与病毒的完整微生物群落集合，共同构成肠道微生物组（gut microbiome）。饮食、年龄、应激、宿主遗传及疾病等因素，可引发细菌物种相对丰度与多样性的增减变化，即菌群失调（dysbiosis）。本研究旨在借助培养法与非培养法，探究健康对照（healthy controls, HCs）、活动性克罗恩病（active Crohn’s disease, CD）、溃疡性结肠炎（ulcerative colitis, UC）及缺血性结肠炎（ischemic colitis, IC）患者不同分类学层级的肠道微生物组成，并筛选可区分CD、UC与IC的生物标志物。本研究通过非培养法（16S rRNA基因扩增子测序）与培养法（培养组学，culturomic）两种手段，明确了肠道微生物组特征的特异性变化。生物标志物通过实时荧光定量PCR（quantitative Real-Time PCR, qPCR）进行验证。两种方法均显示，与健康对照相比，疾病状态下的细菌多样性与物种丰富度均有所降低。研究观察到，在CD、UC及IC患者中，普拉梭菌（Faecalibacterium prausnitzii）与普雷沃菌属（Prevotella sp.）的丰度显著降低，而粪肠球菌（Enterococcus faecalis）、屎肠球菌（Enterococcus faecium）与大肠杆菌（Escherichia coli）等潜在致病菌的丰度则显著升高。本研究还发现，CD患者体内清酒乳杆菌（Latilactobacillus sakei）丰度较高；UC患者体内瘤胃乳杆菌（Ligilactobacillus ruminis）丰度较高；而IC患者体内则以屎肠球菌、大肠杆菌与粪肠球菌的丰度升高为特征。综上，所有患者均存在普拉梭菌丰度显著降低的特征；其中，CD患者可选用清酒乳杆菌与屎肠球菌丰度升高作为生物标志物，UC患者可选用瘤胃乳杆菌与屎肠球菌丰度升高作为生物标志物，而IC患者则可选用屎肠球菌、大肠杆菌与粪肠球菌丰度升高作为各自对应的生物标志物。上述生物标志物可辅助炎症性肠病（inflammatory bowel disease, IBD，即CD或UC）与缺血性结肠炎的临床诊断。