多组学分析在炎症性肠病中的应用与研究进展

炎症性肠病(IBD)是一种累及回肠、直肠和结肠的特发性慢性肠道炎症性疾病,主要包括溃疡性结肠炎和克罗恩病,在临床表现、病程和治疗反应等方面具有高度异质性。目前,关于IBD的发病机制尚未明确,治疗方法相对有限。由遗传、环境、肠道微生态以及宿主免疫失衡在内的多因素共同导致了过度活跃的炎症反应并最终引发患者的肠道粘膜屏障受损和管腔菌群紊乱。单一组学的分析无法全面揭示IBD发病过程中复杂的相互协同作用机制,更无法挖掘潜在的治疗靶点和开发有效的干预策略。因此需要运用多组学关联分析技术以帮助研究者从多个维度解析IBD的发病机制。回顾和分析了多组学技术在IBD相关研究领域中的应用,并且讨论了使用这些方法在IBD分型、早期诊断和个性化医疗等领域的潜力,以期为进一步研究IBD发病机制奠定良好基础。     

益生菌在炎症性肠病中的治疗作用

炎症性肠病(inflammatory bowel disease,IBD)包括溃疡性结肠炎(ulcerative colitis,UC)和克罗恩病(Crohn’s disease,CD)。随着对肠道微生物群在IBD发病机制中作用的认识不断深入,近年来益生菌广泛应用于IBD治疗。大量临床试验结果表明,益生菌治疗IBD的疗效主要体现在对UC和贮袋炎的治疗,对CD的疗效不明确。益生菌治疗IBD可能通过促进肠道微生物群平衡、改善肠道屏障功能、调节肠道黏膜免疫及营养物质代谢等途径。     

炎症性肠病与肠道微生态的研究进展

炎症性肠病(inflammatoryboweldisease,IBD)是一种肠道慢性炎症性疾病,其发病机制尚不清楚。然而,IBD的发病率不断上升给患者及其家属带来了巨大的经济负担,需要找到积极有效的治疗方法来帮助患者。最新的观点认为,宿主和肠道微生物之间的平衡被打破会触发遗传易感个体的免疫炎症反应。肠道菌群失调在炎症性肠病的发病及发展过程中起着重要的作用。临床研究发现,IBD患者肠道菌群失调程度不同,而联合应用益生菌可以改善这些患者的症状。越来越多的研究者密切关注肠道菌群与IBD的关系,并进行了深入的基础和临床研究。本文从肠道菌群对IBD的生理影响以及益生菌和粪便细菌移植等方面进行综述。     

宿主肠道微生物群落多样性和演替分析技术的演变和发展

人或动物等宿主肠道内定植有大量微生物。但是,宿主肠道内微生物的多样性和演替一直被认为是人和动物营养研究中的黑箱（black box）。经过科学家几个世纪的研究已证实：正常微生物群是一个新的人体生理学系统;肠道微生物菌群参与宿主对营养素的消化、吸收与合成;刺激其免疫机制。近年又发现：微生物群影响宿主基因表达,可进行微生物与宿主之间的“分子对话”,例如：一个人肥胖或者苗条的倾向可能部分是由生活在肠道中的微生物群体的组成所决定的（戈登,2005）。可见,肠道微生物是未来微生态科学极其重要的研究领域。对于肠道微生物群落的分析方法主要有沿用已久的传统培养法和近年来兴起的基于基因序列的微生物分子生态学方法。     

肠上皮与肠道微生物相互作用研究进展

肠道不仅是消化和吸收的主要场所,也是机体重要的免疫器官。人类肠道中存在着超过百万亿的微生物,其在漫长的自然选择及共同进化中与宿主形成了紧密的共生关系。肠上皮是先天免疫的一个组成部分,通过各种黏膜保护屏障将肠腔内容物与机体内环境分隔开。各种肠上皮细胞相互协调维持肠道内稳态,并与肠道微生物、肠黏膜免疫系统共同形成抵御肠腔内有害抗原的第一道防线。肠上皮作为肠道微生物和肠黏膜免疫系统相互作用的枢纽,在黏膜免疫防御体系中具有重要作用,本文就肠上皮与肠道微生物之间的相互作用进行综述,旨在深入理解肠上皮,为探索肠道相关疾病的治疗提供新思路。     

益生菌在炎症性肠病治疗中的研究进展

益生菌（Probiotics）是一类能够促进肠道微生物菌群平衡,对宿主健康或生理功能产生有益作用的活性微生物。目前广泛应用于生命健康领域、科学研究、生物工程、工农业以及食品安全。大量国内外研究表明益生菌在降血压、降血糖、降血脂、抗过敏、抗炎、调节免疫、维持肠道菌群平衡等方面具有积极作用。炎症性肠病的病因和发病机制尚未完全明确,现多认为与遗传、环境、感染、免疫以及肠道微生物多因素相互作用有关。益生菌通过多种机制介导,在临床治疗炎症性肠病中扮演着重要角色。     

肺微生物组在慢性阻塞性肺疾病中的研究进展CSCD

慢性阻塞性肺疾病（chronic obstructive pulmonary disease,COPD）是一种以持续的呼吸道症状和气流受限为主要特征的异质性疾病。新一代基因测序技术已经证明健康肺部存在庞大的微生物群落。越来越多的研究表明,肺微生物群失调与COPD的发生、急性加重次数及病死率有关。肺微生物可能通过调控炎症或免疫过程参与COPD的发病机制。全面了解肺微生物群在COPD不同阶段的动态变化和微生物与宿主的相互作用,有助于进一步揭示其在COPD发病机制中的作用。本文综述了肺微生物组在COPD中的研究进展,探讨其与COPD进展之间的关系及潜在的机制,以期开发有针对性的治疗方法。     

肠道微生态与炎症性肠病

炎症性肠病(inflammatory bowel disease,IBD)的发病率和患病率近年来在世界范围内呈持续上升趋势,其发病与遗传易感基因、免疫、肠道微生态、环境、饮食等多因素有关。近来的研究显示肠道微生态在其发病中起着关键作用,是目前重要的研究热点。现就IBD患者肠道微生物的变化、肠道微生物在IBD发生中的作用以及基于肠道微生态的治疗方法进行简要叙述。     

肠道共生微生物与健康和疾病

人体是个庞大的动态的微生物群落的天然寄居场所,人体的皮肤、口腔、消化道、呼吸道和生殖道等部位都寄生着大量的微生物.这些微生物与人体互惠互利,形成共生复合体.其中,肠道共生微生物与宿主的相关性及对宿主生理和病理状态的影响已经得到了很好的阐释.肠道共生微生物的主要功能是帮助宿主代谢,使得能量和可吸收的营养物质更好的被利用,为肠道上皮细胞提供营养,增强免疫功能,帮助寄主抵抗外来微生物的入侵.肠道菌群紊乱也是一些疾病的症状或诱发原因,比如肥胖、糖尿病和肠道炎症等.深入研究人类共生微生物与健康和疾病的关系,将为一些疾病的预防和治疗提供新的手段.     

肠道微生物与1型糖尿病的相关性研究

1型糖尿病(type 1 diabetes, T1D)是一种自身免疫性疾病,越来越多的证据支持肠道菌群是T1D发病的重要因素。在T1D发生前,观察到肠道通透性发生改变,使抗原透过肠黏膜进而攻击胰岛β细胞。患有T1D宿主体内的肠道微生物也与健康宿主的微生物有别,其调节性T细胞、Toll样受体(toll-like receptor, TLR)、丁酸、粘蛋白、胰高血糖素样肽-1(glucagon-likepeptide1,GLP-1)等可能与T1D有关。尽管通过细菌定植促进自身免疫的机制在糖尿病动物模型中虽已发现,但有些问题目前尚不清楚。现就肠道黏膜通透性与T1D的关系、宿主体内微生物组成的变化、肠道微生物与T1D的相关性作一阐述。     

Current understanding of microbiota- and dietary-therapies for treating inflammatory bowel disease

Inflammatory bowel disease (IBD) is a result of chronic inflammation caused, in some part, by dysbiosis of intestinal microbiota, mainly commensal bacteria. Gut dysbiosis can be caused by multiple factors, including abnormal immune responses which might be related to genetic susceptibility, infection, western dietary habits, and administration of antibiotics. Consequently, the disease itself is characterized as having multiple causes, etiologies, and severities. Recent studies have identified >200 IBD risk loci in the host. It has been postulated that gut microbiota interact with these risk loci resulting in dysbiosis, and this subsequently leads to the development of IBD. Typical gut microbiota in IBD patients are characterized with decrease in species richness and many of the commensal, and beneficial, fecal bacteria such as Firmicutes and Bacteroidetes and an increase or bloom of Proteobacteria. However, at this time, cause and effect relationships have not been rigorously established. While treatments of IBD usually includes medications such as corticosteroids, 5-aminosalicylates, antibiotics, immunomodulators, and anti-TNF agents, restoration of gut dysbiosis seems to be a safer and more sustainable approach. Bacteriotherapies (now called microbiota therapies) and dietary interventions are effective way to modulate gut microbiota. In this review, we summarize factors involved in IBD and studies attempted to treat IBD with probiotics. We also discuss the potential use of microbiota therapies as one promising approach in treating IBD. As therapies based on the modulation of gut microbiota becomes more common, future studies should include individual gut microbiota differences to develop personalized therapy for IBD.     

Microbiota dysbiosis and barrier dysfunction in inflammatory bowel disease and colorectal cancers: exploring a common ground hypothesis

Inflammatory bowel disease (IBD) is a multifactorial disease which arises as a result of the interaction of genetic, environmental, barrier and microbial factors leading to chronic inflammation in the intestine. Patients with IBD had a higher risk of developing colorectal carcinoma (CRC), of which the subset was classified as colitis-associated cancers. Genetic polymorphism of innate immune receptors had long been considered a major risk factor for IBD, and the mutations were also recently observed in CRC. Altered microbial composition (termed microbiota dybiosis) and dysfunctional gut barrier manifested by epithelial hyperpermeability and high amount of mucosa-associated bacteria were observed in IBD and CRC patients. The findings suggested that aberrant immune responses to penetrating commensal microbes may play key roles in fueling disease progression. Accumulative evidence demonstrated that mucosa-associated bacteria harbored colitogenic and protumoral properties in experimental models, supporting an active role of bacteria as pathobionts (commensal-derived opportunistic pathogens). Nevertheless, the host factors involved in bacterial dysbiosis and conversion mechanisms from lumen-dwelling commensals to mucosal pathobionts remain unclear. Based on the observation of gut leakiness in patients and the evidence of epithelial hyperpermeability prior to the onset of mucosal histopathology in colitic animals, it was postulated that the epithelial barrier dysfunction associated with mucosal enrichment of specific bacterial strains may predispose the shift to disease-associated microbiota. The speculation of leaky gut as an initiating factor for microbiota dysbiosis that eventually led to pathological consequences was proposed as the “common ground hypothesis”, which will be highlighted in this review. Overall, the understanding of the core interplay between gut microbiota and epithelial barriers at early subclinical phases will shed light to novel therapeutic strategies to manage chronic inflammatory disorders and colitis-associated cancers.     

Commensal microbial regulation of natural killer T cells at the frontiers of the mucosal immune system

The commensal microbiota co-exists in a mutualistic relationship with its human host. Commensal microbes play critical roles in the regulation of host metabolism and immunity, while microbial colonization, conversely, is under control of host immunity and metabolic pathways. These interactions are of central importance to the maintenance of homeostasis at mucosal surfaces and their perturbation can provide the basis for atopic and chronic inflammatory diseases such as asthma and inflammatory bowel disease (IBD). Recent evidence has revealed that natural killer T (NKT) cells, a subgroup of T cells which recognizes self and microbial lipid antigens presented by CD1d, are key mediators of host-microbial interactions. Mucosal and systemic NKT cell development is under control of the commensal microbiota, while CD1d regulates microbial colonization and influences the composition of the intestinal microbiota. Here, we outline the mechanisms of bidirectional cross-talk between the microbiota and CD1d-restricted NKT cells and discuss how a perturbation of these processes can contribute to the pathogenesis of immune-mediated disorders at mucosal surfaces.     

Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease

The intestinal microbiota is important for induction of inflammatory bowel disease (IBD). IBD is associated with complex shifts in microbiota composition, but it is unclear whether specific bacterial subsets induce IBD and, if so, whether their proportions in the microbiota are altered during disease. Here, we fulfilled Koch's postulates in host-genotype-specific fashion using a mouse model of IBD with human-relevant disease-susceptibility mutations. From screening experiments we isolated common commensal Bacteroides species, introduced them into antibiotic-pretreated mice, and quantitatively reisolated them in culture. The bacteria colonized IBD-susceptible and -nonsusceptible mice equivalently, but induced disease exclusively in susceptible animals. Conversely, commensal Enterobacteriaceae were >100-fold enriched during spontaneous disease, but an Enterobacteriaceae isolate failed to induce disease in antibiotic-pretreated mice despite robust colonization. We thus demonstrate that IBD-associated microbiota alterations do not necessarily reflect underlying disease etiology. These findings establish important experimental criteria and a conceptual framework for understanding microbial contributions to IBD.     

Role of nutrition and microbiota in susceptibility to inflammatory bowel diseases

Inflammatory bowel diseases (IBDs), Crohn's disease (CD), and ulcerative colitis (UC) are chronic inflammatory conditions, which are increasing in incidence, prevalence, and severity, in many countries. While there is genetic susceptibility to IBD, the probability of disease development is modified by diet, lifestyle, and endogenous factors, including the gut microbiota. For example, high intakes of mono- and disaccharides, and total fats consistently increases the risk developing both forms of IBD. High vegetable intake reduces the risk of UC, whereas increased fruit and/or dietary fiber intake appears protective against CD. Low levels of certain micronutrients, especially vitamin D, may increase the risk of both diseases. Dietary patterns may be even more important to disease susceptibility than the levels of individual foods or nutrients. Various dietary regimes may modify disease symptoms, in part through their actions on the host microbiota. Both probiotics and prebiotics may modulate the microflora, and reduce the likelihood of IBD regression. However, other dietary factors affect the microbiota in different ways. Distinguishing cause from effect, and characterizing the relative roles of human and microbial genes, diet, age of onset, gender, life style, smoking history, ethnic background, environmental exposures, and medications, will require innovative and internationally integrated approaches.     

Dysbiosis of Salivary Microbiota in Inflammatory Bowel Disease and Its Association With Oral Immunological Biomarkers

Analysis of microbiota in various biological and environmental samples under a variety of conditions has recently become more practical due to remarkable advances in next-generation sequencing. Changes leading to specific biological states including some of the more complex diseases can now be characterized with relative ease. It is known that gut microbiota is involved in the pathogenesis of inflammatory bowel disease (IBD), mainly Crohn''s disease and ulcerative colitis, exhibiting symptoms in the gastrointestinal tract. Recent studies also showed increased frequency of oral manifestations among IBD patients, indicating aberrations in the oral microbiota. Based on these observations, we analyzed the composition of salivary microbiota of 35 IBD patients by 454 pyrosequencing of the bacterial 16S rRNA gene and compared it with that of 24 healthy controls (HCs). The results showed that Bacteroidetes was significantly increased with a concurrent decrease in Proteobacteria in the salivary microbiota of IBD patients. The dominant genera, Streptococcus, Prevotella, Neisseria, Haemophilus, Veillonella, and Gemella, were found to largely contribute to dysbiosis (dysbacteriosis) observed in the salivary microbiota of IBD patients. Analysis of immunological biomarkers in the saliva of IBD patients showed elevated levels of many inflammatory cytokines and immunoglobulin A, and a lower lysozyme level. A strong correlation was shown between lysozyme and IL-1β levels and the relative abundance of Streptococcus, Prevotella, Haemophilus and Veillonella. Our data demonstrate that dysbiosis of salivary microbiota is associated with inflammatory responses in IBD patients, suggesting that it is possibly linked to dysbiosis of their gut microbiota.     

益生菌与肠黏膜互作的分子机制研究进展

益生菌是一类定植于动物肠道,可辅助动物消化功能,维护肠道菌群平衡并可影响肠道免疫系统,有益于动物健康的重要调节性菌群。该类菌群与动物肠上皮细胞间互作的分子机制包括菌体表面分子如磷脂壁酸（phosphatidicacid,LTA）、表面层蛋白（Slayerprotein）等与宿主的粘附相关蛋白分子结合,通过占位效应抑制有害菌群在肠道内的定植;益生菌还可刺激肠道细胞分泌B防御素2、细菌素和有机酸等可抑制甚至杀灭有害菌群;在益生菌作用下,肠道上皮细胞可增强粘液糖蛋白、紧密连接蛋白occludin和ZO-1等分子的表达,加厚并加固肠道黏膜屏障;益生菌相关抗原可通过与抗原递呈细胞表面模式识别受体（TLRs等）分子结合,激活递呈细胞,启动各免疫细胞的交互作用,调节肠道免疫状态。     

Exosome‐mediated effects and applications in inflammatory bowel disease

Gut mucosal barriers, including chemical and physical barriers, spatially separate the gut microbiota from the host immune system to prevent unwanted immune responses that could lead to intestinal inflammation. In inflammatory bowel disease (IBD), there is mucosal barrier dysfunction coupled with immune dysregulation and dysbiosis. The discovery of exosomes as regulators of vital functions in both physiological and pathological processes has generated much research interest. Interestingly, exosomes not only serve as natural nanocarriers for the delivery of functional RNAs, proteins, and synthetic drugs or molecules, but also show potential for clinical applications in tissue repair and regeneration as well as disease diagnosis and prognosis. Biological or chemical modification of exosomes can broaden, change and enhance their therapeutic capability. We review the modulatory effects of exosomal proteins, RNAs and lipids on IBD components such as immune cells, the gut microbiota and the intestinal mucosal barrier. Mechanisms involved in regulating these factors towards attenuating IBD have been explored in several studies employing exosomes derived from different sources. We discuss the potential utility of exosomes as diagnostic markers and drug delivery systems, as well as the application of modified exosomes in IBD.     

白细胞介素23受体、白细胞介素17A在炎症性肠病患者中的表达及临床意义

目的：通过检测白细胞介素23受体（1L-23R）及白细胞介素17A（IL-17A）在炎症性肠病（IBD）患者肠黏膜及血清中的表达水平,探讨其在IBD发病过程中的作用及意义。方法：收集32例克罗恩病（CD）患者、29例溃疡性结肠炎（UC）患者及27例对照者的内镜肠黏膜活检标本,采用荧光定量PCR技术检测肠黏膜内IL-23R、IL-17AmRNA的表达情况,免疫组化技术分析IL-23R、IL-17A在肠黏膜中的原位表达。结果：与健康对照组相比,CD及UC患者肠黏膜组织内IL-23RmRNA表达显著增高（P〈0．05）,CD及UC组间的表达量差异无统计学意义（P〉0．05）。CD及UC患者肠黏膜组织内IL-17AmRNA表达显著增高（P〈0．05）,CD组肠黏膜组织内IL．17AmRNA表达显著高于uc组（P〈0．05）。免疫组化分析显示IL-23R阳性细胞在CD与uc肠黏膜固有层内有较多表达,较正常黏膜内的肠上皮细胞相比,CD及UC患者肠黏膜IL-23R蛋白表达量最著增高（P〈0．05）,UC及CD组间的表达量差异无统计学意义（P〉0．05）。IL-17A阳性细胞在CD与UC肠黏膜固有层内有较多表达,较正常黏膜内的肠上皮细胞相比,CD及UC患者肠黏膜IL-17A蛋白表达量最著增高（P〈0．05）。结论：IL．23R及IL-17A在IBD患者肠黏膜中表达显著增高,提示IL-23R及IL-17A表达异常与IBD的发生发展密切相关,有可能成为IBD治疗的新靶点。     

SP和CGRP在炎症性肠病大鼠结肠中的表达规律

目的通过研究P物质（SP）和降钙素基因相关肽（CGRP）在炎症性肠病（IBD）大鼠结肠中的表达规律来探讨二者在IBD发生发展过程中发挥的作用。方法采用三硝基苯磺酸（TNBS）化学诱导建立IBD大鼠动物模型,应用real-time RT-PCR方法来检测SP和CGRP mRNA在模型不同时期结肠中的表达变化。结果随着炎症性肠病病理变化的加剧（第3、7天）,sP和CGRP在结肠组织中的表达水平显著升高;随着疾病的恢复（第21、28天）,其表达水平逐渐降低并趋向于正常水平。从总体来看,在IBD大鼠结肠组织中,SP和CGRP mRNA水平的变化与IBD的发生、发展呈正相关。结论神经递质SP和CGRP在IBD炎症和修复中起重要的神经免疫信号传导作用。