肠道微生物组与宿主的表观遗传修饰

高通量测序技术已经增加了人们对肠道微生物组和表观遗传学修饰的理解,将肠道微生物组和宿主表观遗传学修饰紧密联系起来,阐明了很多疾病的发生过程如免疫、代谢、心血管疾病甚至是癌症。肠道微生物组与宿主具有相互作用,与人体密不可分,相辅相成。肠道微生物组的生态失调可能诱导疾病的发生并能调控宿主表观遗传学修饰。宿主表观遗传学调控和肠道微生物组(或其代谢产物)变化的相互关系在很多疾病中都有报道。因此,肠道微生物组可作为某些疾病的诊断标记,健康肠道微生物组的移植会逆转这种微生态失调,可作为一种有效的治疗策略。本文主要探讨了肠道微生物组直接调控宿主表观修饰和通过小分子生物活性物质和其他酶辅因子间接影响表观修饰,以及基于肠道微生物组调控宿主表观修饰的诊断和治疗应用等。     

Transfer of dysbiotic gut microbiota has beneficial effects on host liver metabolism

Gut microbiota dysbiosis has been implicated in a variety of systemic disorders, notably metabolic diseases including obesity and impaired liver function, but the underlying mechanisms are uncertain. To investigate this question, we transferred caecal microbiota from either obese or lean mice to antibiotic‐free, conventional wild‐type mice. We found that transferring obese‐mouse gut microbiota to mice on normal chow (NC) acutely reduces markers of hepatic gluconeogenesis with decreased hepatic PEPCK activity, compared to non‐inoculated mice, a phenotypic trait blunted in conventional NOD2 KO mice. Furthermore, transferring of obese‐mouse microbiota changes both the gut microbiota and the microbiome of recipient mice. We also found that transferring obese gut microbiota to NC‐fed mice then fed with a high‐fat diet (HFD) acutely impacts hepatic metabolism and prevents HFD‐increased hepatic gluconeogenesis compared to non‐inoculated mice. Moreover, the recipient mice exhibit reduced hepatic PEPCK and G6Pase activity, fed glycaemia and adiposity. Conversely, transfer of lean‐mouse microbiota does not affect markers of hepatic gluconeogenesis. Our findings provide a new perspective on gut microbiota dysbiosis, potentially useful to better understand the aetiology of metabolic diseases.     

Pharmacomicrobiomics: a novel route towards personalized medicine?

Inter-individual heterogeneity in drug response is a serious problem that affects the patient’s wellbeing and poses enormous clinical and financial burdens on a societal level. Pharmacogenomics has been at the forefront of research into the impact of individual genetic background on drug response variability or drug toxicity, and recently the gut microbiome, which has also been called the second genome, has been recognized as an important player in this respect. Moreover, the microbiome is a very attractive target for improving drug efficacy and safety due to the opportunities to manipulate its composition. Pharmacomicrobiomics is an emerging field that investigates the interplay of microbiome variation and drugs response and disposition (absorption, distribution, metabolism and excretion). In this review, we provide a historical overview and examine current state-of-the-art knowledge on the complex interactions between gut microbiome, host and drugs. We argue that combining pharmacogenomics and pharmacomicrobiomics will provide an important foundation for making major advances in personalized medicine.     

膳食脂肪、肠道微生物与宿主健康的研究进展

作为三大主要营养物质之一,膳食脂肪为人体提供能量和营养。膳食脂肪摄入不当会破坏肠道微生物的稳态,影响宿主的代谢状况,增加慢性疾病发生的风险。建立疾病动物模型是研究肠道微生物与宿主健康的重要手段。文中综述了膳食脂质的数量和种类、肠道微生物和宿主代谢之间的相互作用及其可能的作用机制,阐述了基于不同的疾病动物模型,膳食脂质影响肠道微生物的结构和功能,以及对宿主代谢的调节,为深入了解膳食脂质、肠道微生态和宿主健康三者之间的关系提供了依据。     

肥胖相关的肠道微生物群落结构动力学与功能解析研究

肥胖及相关的慢性代谢性疾病近年来已经成为威胁全球的公共健康问题。越来越多的证据表明,在宿主的营养、免疫和代谢中有不可替代的作用的肠道菌群不仅可以通过调节宿主脂肪吸收存储相关的基因,影响后者的能量平衡,更重要的是其结构失调导致宿主循环系统中内毒素增加,诱发慢性、低水平炎症,导致肥胖和胰岛素抵抗。运用微生物分子生态学、元基因组学和代谢组学的方法,揭示与代谢性疾病相关的菌群结构失调,并鉴定出相关的特定细菌类群及其功能,使得通过以菌群为靶点的营养干预手段防止慢性代谢性疾病成为可能,将带来代谢性疾病预防和控制策略的革命性的变化。     

The chemical interactome space between the human host and the genetically defined gut metabotypes

The bacteria that colonize the gastrointestinal tracts of mammals represent a highly selected microbiome that has a profound influence on human physiology by shaping the host''s metabolic and immune system activity. Despite the recent advances on the biological principles that underlie microbial symbiosis in the gut of mammals, mechanistic understanding of the contributions of the gut microbiome and how variations in the metabotypes are linked to the host health are obscure. Here, we mapped the entire metabolic potential of the gut microbiome based solely on metagenomics sequencing data derived from fecal samples of 124 Europeans (healthy, obese and with inflammatory bowel disease). Interestingly, three distinct clusters of individuals with high, medium and low metabolic potential were observed. By illustrating these results in the context of bacterial population, we concluded that the abundance of the Prevotella genera is a key factor indicating a low metabolic potential. These metagenome-based metabolic signatures were used to study the interaction networks between bacteria-specific metabolites and human proteins. We found that thirty-three such metabolites interact with disease-relevant protein complexes several of which are highly expressed in cells and tissues involved in the signaling and shaping of the adaptive immune system and associated with squamous cell carcinoma and bladder cancer. From this set of metabolites, eighteen are present in DrugBank providing evidence that we carry a natural pharmacy in our guts. Furthermore, we established connections between the systemic effects of non-antibiotic drugs and the gut microbiome of relevance to drug side effects and health-care solutions.     

念珠菌适应宿主环境压力的共生机制研究进展

作为人体微生物菌群中真菌菌群的一个重要组成部分,念珠菌通常定植于人体的众多生态位,在免疫系统功能正常的健康人群中与宿主保持共生状态。为适应宿主体内复杂多变的环境,拮抗宿主免疫系统的攻击,以及应对其他微生物菌群的竞争等诸多生存压力,念珠菌进化出一系列极为有效的应对机制以维持其在宿主体内的共生。本文总结了念珠菌通过形态转换、环境适应、免疫调节以及与其他微生物菌群相互作用等策略应对宿主环境生存压力的分子机制,重点阐述了念珠菌、宿主免疫系统以及微生物菌群三者之间的相互作用和相互平衡对于念珠菌实现成功定植和共生的重要意义。     

Effect of β-1/3,1/6-glucan upon immune responses and bacteria in the gut of healthy common carp (Cyprinus carpio)

β-glucans are frequently included in the diet of healthy common carp Cyprinus carpio as a pre-emptive measure for combatting disease. In order to study the effect this has on the relationship between the gut bacteria and host immune response, carp were maintained on either a β-glucan free diet or feed containing 0.1% MacroGard®, a β-1/3, 1/6-glucan, for up to 7 weeks and analysis of innate immune gene expression and molecular analysis of the gut bacteria was performed. The data reveals feeding of MacroGard® to healthy carp does not induce bactericidal innate immune gene expression in the gut but does appear to alter bacterial species richness that did not have a negative effect on overall health. Analysis of innate immune gene expression within the upper midgut revealed that there were significant changes over time in the expression of Interleukin (il)-1β, inducible nitric oxide synthase (inos), mucin (muc2) and C-reactive protein (crp2). Diet did not affect the number of copies of the bacterial 16s rDNA gene in the gut, used as a as a measure of total bacteria population size. However, PCR-denaturing gradient gel electrophoresis (DGGE) analysis revealed a shift in bacterial species richness with MacroGard feeding. Bactericidal immune gene expression of crp2, muc2 and il-1β was weakly correlated with gut bacteria population size indicating a potentially limited role of these genes in interacting with the gut bacteria in healthy carp in order to maintain gut homeostatic conditions. These findings highlight the importance of considering both host immunity and the microbiome together in order to fully elucidate the effeect of immunomodulants, such as β-glucans, upon gut health.