微生物组学研究的“淘金时代”

人体及动物肠道中生存着数量庞大的共生微生物;这些微生物无时无刻不参与着宿主的生命活动。揭示这些共生微生物在宿主体内的变化规律、与宿主之间的依存和博弈关系等,将使人类更加全面的认知高等生物体的生命本质。本专刊从肠道微生物与疾病、肠道微生物群落结构、肠道微生物与宿主互作、肠道微生物资源和肠道微生物研究方法 5个层面展示了我国科研工作者在肠道微生物研究领域的新进展及新观点。     

肠道菌群与免疫的相关性研究

由大量微生物构成的复杂微生物群落栖息在人体的肠道内,这些微生物统称作肠道菌群。肠道菌群在人体的消化吸收、免疫、生物拮抗、抗肿瘤等各项生命活动中发挥着重要的作用。近年来的许多研究提示,肠道内复杂的微生物群落和人体的免疫系统间存在着极为密切的关系。免疫系统发挥正常的功能及建立免疫的稳态与肠道菌群的作用密不可分。研究表明肠道菌群能阻止致病微生物入侵从而影响肠道免疫系统,同时还能影响全身免疫系统,在人体的自身免疫性疾病中有较为重要的作用。     

人类肠道微生物组与相关疾病研究进展

人体肠道共生着数以万亿计的微生物,肠道微生物在维持宿主正常生理功能中发挥重要作用,其成分和功能变化可导致严重的肠道和全身性疾病。以新一代测序技术和生物信息学分析为基础的元基因组学研究不仅极大地推动了对人类肠道微生物的整体认识,还加深了对肠道微生物代谢产物促进人类健康机理的理解,为肠道炎症、代谢性疾病和癌症等人类疾病的诊断与治疗提供了新思路。就肠道微生物元基因组学与肠道相关疾病的研究进展作一综述。     

从粪菌移植到下一代益生菌:挑战与进展CSCD

细菌、真菌、病毒和原生动物等微生物生活在肠道中,共同组成肠道微生物群。其中,细菌在肠道微生物群中占主导地位。肠道菌群对于维持肠道及全身健康至关重要,肠道微生态失调与人类多种疾病相关。调节失衡的肠道菌群有助于这些疾病的治疗,粪菌移植因在治疗艰难梭菌感染方面取得成功而备受关注。许多临床试验证实了粪菌移植在治疗其他肠道疾病及全身疾病方面具有潜力,但疗效却因人而异,具体机制不明。研究者们致力于从健康供体肠道菌群中寻找真正具有“益生”作用的新型细菌,这些细菌被称为下一代益生菌。     

"肠道微生物-肠道-脑轴"机制--肠道微生物干预神经退行性病变研究进展

肠道微生物是人体中最为庞大和复杂的微生物群落,其对机体的健康,尤其是中枢神经退行性病变具有重要调节作用。其中,"肠道微生物-肠道-脑轴"机制是肠道微生物干预中枢神经退行性病变的重要途径。该机制主要通过以下三种方式来调节大脑功能:一是肠道微生物直接产生神经递质通过肠神经细胞上行至中枢神经系统;二是肠道微生物代谢产物刺激肠内分泌细胞产生神经肽类和胃肠激素类物质,影响大脑功能;三是肠道微生物或其代谢产物直接刺激肠道免疫系统,产生干扰素类物质干扰大脑免疫反应。本文对"肠道微生物-肠道-脑轴"机制的概念及研究进展进行了详细的介绍,同时总结了有关肠道微生物与阿尔兹海默症、帕金森症和多发性硬化症等神经退行性疾病相互作用的相关文献。依据"肠道微生物-肠道-脑轴"机制,利用肠道微生物预防和治疗神经退行性病变,或将成为解决中枢神经系统疾病的新措施。     

早期饮食如何影响婴儿肠道微生态

母乳是一种多功能的生物液体,为婴儿提供一系列营养及多样化的非营养活性成分,如抗体、细菌和免疫调节蛋白。过去十年的研究已证实母乳中具有生物活性的成分在建立婴儿健康的肠道菌群结构过程中起重要作用。完全母乳喂养的婴儿其肠道菌群以若干种双歧杆菌为主,起决定性作用,被称为母乳源型微生物(MOM)。MOM不但可以降低婴儿的感染风险,而且还能减少成年期某些慢性疾病患病风险。MOM的形成依赖于母乳中复杂的可以帮助婴儿消化的糖结构。本文主要阐述母乳中的多糖、糖基化蛋白以及母体表型对于肠道菌群形成的影响,从而来了解早期饮食中的各种因素是如何形影响婴儿肠道微生物的。     

肠道微生物与慢性疾病研究进展

慢性疾病是影响人类健康和生活质量的主要疾病,肠道微生物被发现与慢性疾病的发病、发展有潜在的联系。综述了肠道微生物的认识、肠道微生物与慢性疾病的发病和发展,通过修复肠道微生物来改善慢性疾病的研究进展。     

肠道微生物与人体健康研究进展

人类肠道中定居着许多对宿主有益的微生物,包括细菌、病毒、真核生物等,它们在肠道内能与其他微生物及免疫系统相互作用,对人体健康具有重要影响,被称为"被遗忘的器官",它们的基因组也被誉为人类的"第二基因组",与人体的能量代谢及物质代谢有关。本文总结了人体肠道中病毒、真核生物、细菌和宿主免疫系统的相互作用,微生物群的失衡可能导致的疾病如肥胖和克罗恩病等,以及微生物环境在人体内的成熟过程,期望有助于诊断和治疗与肠道微生物失衡相关的疾病。     

人体微生物与人类健康及生理机制

近年来,肠道微生物与机体健康之间关系的研究越来越受关注。研究发现,肠道微生物对身体免疫系统的调节、食物的消化、药物的代谢,以及很多疾病的发生与治疗都密切相关。事实上,微生物不仅仅在肠道中大量存在,而且在皮肤、眼睛、口腔、子宫等身体其他部位也存在,且具备丰富的多样性;不同部位微生物与疾病的发生及其生理机制也不同。目前对于这些人体微生物的生物学功能以及紊乱导致的疾病尚未有系统的总结。文章对肠道、皮肤、眼睛、口腔、子宫在宿主健康和生理代谢活动方面进行综述,为相关疾病的预防和治疗提供参考。     

动物肠道菌群与宿主肠道免疫系统相互作用的研究进展

作为动物机体中最大的免疫器官之一,动物肠道是机体阻止外源病原体入侵的重要防线。动物肠道中定殖的微生物与宿主的营养物代谢,疾病和免疫系统发育等密切相关。该文主要综述了肠道微生物对于维持肠道屏障完整性的作用、诱导机体T、B淋巴细胞的发育和分化的分子机制及与一些代谢类疾病发生的关系等内容。尽管如此,肠道微生物与宿主免疫系统相互作用的机制还有待深入研究。随着免疫学、微生物学及分子生物学等学科的发展,对动物肠道菌群与宿主免疫系统互作机制的研究也得到快速发展,并为临床上预防和治疗人类疾病提供理论支撑。     

The role of gut microbiota in the gut-brain axis: current challenges and perspectives

Brain and the gastrointestinal (GI) tract are intimately connected to form a bidirectional neurohumoral communication system. The communication between gut and brain, knows as the gut-brain axis, is so well established that the functional status of gut is always related to the condition of brain. The researches on the gut-brain axis were traditionally focused on the psychological status affecting the function of the GI tract. However, recent evidences showed that gut microbiota communicates with the brain via the gut-brain axis to modulate brain development and behavioral phenotypes. These recent fi ndings on the new role of gut microbiota in the gut-brain axis implicate that gut microbiota could associate with brain functions as well as neurological diseases via the gut-brain axis. To elucidate the role of gut microbiota in the gut-brain axis, precise identification of the composition of microbes constituting gut microbiota is an essential step. However, identifi cation of microbes constituting gut microbiota has been the main technological challenge currently due to massive amount of intestinal microbes and the diffi culties in culture of gut microbes. Current methods for identifi cation of microbes constituting gut microbiota are dependent on omics analysis methods by using advanced high tech equipment. Here, we review the association of gut microbiota with the gut-brain axis, including the pros and cons of the current high throughput methods for identifi cation of microbes constituting gut microbiota to elucidate the role of gut microbiota in the gut-brain axis.     

A Drosophila salivary gland mucin is also expressed in immune tissues: evidence for a function in coagulation and the entrapment of bacteria

Our studies on the developmental regulation of glycosylation in Drosophila melanogaster led us to identify and characterize gp150, an ecdysone-regulated mucin that is found in hemocytes, the gut (peritrophic membrane) and in the salivary glands. We are particularly interested in mucin immune functions and found that gp150 is released from larval hemocytes, becomes part of the clot and participates in the entrapment of bacteria. By RT-PCR and RNAi experiments, we identified gp150 as the previously described I71-7, an ecdysone-induced salivary glue protein. We discuss the evolutionary and biochemical implications of the dual use of salivary proteins for immune functions in insects. Further molecular characterization of such shared proteins may enable a better understanding of the properties of proteins involved in containment and elimination of microbes, as well as hemostasis and wound repair.     

Microbial-host interactions specifically control the glycosylation pattern in intestinal mouse mucosa

The glycosylation of the intestinal cell layer is thought to control several key functions of the gut such as vectorial transports, defence against microbial agents or immunological processes. It has been assumed that the gut microflora may modulate the glycosylation pattern of the intestinal cell layer. However, there is no direct evidence for this regulatory process. The first goal of this work was to establish the germ-free mice intestinal glycosylation baseline using a histochemical approach and a panel of ten lectins with defined glycan specificities to tissue sections prepared from various cellular compartments of the small and large intestine. Using this baseline, we have studied the contribution of the gut microflora on the carbohydrate composition of glycoconjugates of intestinal cells by comparing the germ-free and conventional mice glycosylation patterns. Analysis of the germ-free mice intestinal glycosylation baseline revealed that the expression of glycans depends on the proximodistal gradient (small to large intestine) and on the cell lineage (absorptive, goblet, crypt, and Paneth cells), indicating that mice are able to create and maintain a strict topological and cell lineage-specific regulation of glycosyltransferase expression. By comparing germ-free and conventional mice, we find that the gut microflora specifically modulates the gut glycosylation pattern, quantitatively as well as qualitatively by changing the cellular and subcellular distribution of glycans. This is the first report in mice to directly demonstrate the critical contribution of microflora to intestinal glycosylation, a key characteristic of the gut.     

动物宿主——肠道微生物代谢轴研究进展

肠道中栖息着数量庞大且复杂多样的微生物菌群,在维持宿主肠道微环境稳态中发挥重要作用。微生物菌群可以利用宿主肠道的营养素,发酵产生代谢产物,与宿主机体形成宿主—微生物代谢轴(host-microbe metabolic axis)。该代谢轴既能影响营养素吸收和能量代谢,又可调控宿主各项生理过程。本文主要阐述宿主-肠道微生物代谢轴的概念、肠-肝轴、肠-脑轴、肠道微生物与宿主肠道代谢轴的互作以及对机体健康的影响。     

Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings

The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.     

Molecular Paths Linking Metabolic Diseases,Gut Microbiota Dysbiosis and Enterobacteria Infections

Alterations of both ecology and functions of gut microbiota are conspicuous traits of several inflammatory pathologies, notably metabolic diseases such as obesity and type 2 diabetes. Moreover, the proliferation of enterobacteria, subdominant members of the intestinal microbial ecosystem, has been shown to be favored by Western diet, the strongest inducer of both metabolic diseases and gut microbiota dysbiosis. The inner interdependence between the host and the gut microbiota is based on a plethora of molecular mechanisms by which host and intestinal microbes modify each other. Among these mechanisms are as follows: (i) the well-known metabolic impact of short chain fatty acids, produced by microbial fermentation of complex carbohydrates from plants; (ii) a mutual modulation of miRNAs expression, both on the eukaryotic (host) and prokaryotic (gut microbes) side; (iii) the production by enterobacteria of virulence factors such as the genotoxin colibactin, shown to alter the integrity of host genome and induce a senescence-like phenotype in vitro; (iv) the microbial excretion of outer-membrane vesicles, which, in addition to other functions, may act as a carrier for multiple molecules such as toxins to be delivered to target cells. In this review, I describe the major molecular mechanisms by which gut microbes exert their metabolic impact at a multi-organ level (the gut barrier being in the front line) and support the emerging triad of metabolic diseases, gut microbiota dysbiosis and enterobacteria infections.     

Kin recognition in Drosophila: the importance of ecology and gut microbiota

The animal gut commonly contains a large reservoir of symbiotic microbes. Although these microbes have obvious functions in digestion and immune defence, gut microbes can also affect behaviour. Here, we explore whether gut microbiota has a role in kin recognition. We assessed whether relatedness, familiarity and food eaten during development altered copulation investment in three species of Drosophila with diverse ecologies. We found that a monandrous species exhibited true kin recognition, whereas familiarity determined kin recognition in a species living in dense aggregations. Finally, in a food generalist species, food eaten during development masked kin recognition. The effect of food type on copulation duration, in addition to the removal of this effect via antibiotic treatment, suggests the influence of bacteria associated with the gut. Our results provide the first evidence that varied ecologically determined mechanisms of kin recognition occur in Drosophila, and that gut bacteria are likely to have a key role in these mechanisms.     

Termite-Microbe Symbiotic System and Its Efficient Degradation of Lignocellulose

Termites thrive in the tropics and play an important role in lignocellulose degradation. This ability depends mainly on intestine microbes in the gut, but most of them are so-called unculturable microbes, which can not be cultivated by traditional culture methods. The recent development of molecular approaches such as the PCR method has made it possible to access the enormous numbers of unculturable microbes in the gut of termites.

This review explains our research on the ecological role of the termite, the termite-microbe symbiotic system, and the functions of lignocellulose degradation using various molecular methods. In the future, new technologies such as genomics should make it possible to analyze and utilize unculturable microbial resources in natural environments.