微生物组与动物疫病防控

微生物组研究的发展推动了人类不断探索人体微生物群与疾病之间的相关性。然而,微生物组学在动物疫病防控中的研究尚处于起步阶段。本文对动物疫病防控领域中微生物组研究所发挥的6个作用进行了阐述：揭示疾病与菌群的相关性,鉴定新发病原体,确立有益于维持机体健康生长的菌群,筛选疾病防控的新药物和新制剂,开发新疫苗或改进疫苗的使用效果,提出更简单有效的防控措施。     

口腔微生物群和人体健康

口腔微生物群作为人体微生物群的重要组成部分,其与人体健康之间的关系已成为各领域研究的焦点。口腔微生物群种类繁多、组成复杂,涵盖了细菌、真菌、古细菌和病毒等。近年来的研究显示,口腔微生物群的组成和比例与人体健康密切相关,会影响口腔疾病如龋齿、牙周病的发生。同时口腔微生物也是全身系统性疾病如肺炎、肿瘤和糖尿病等发生的危险因素之一。大量研究认为,口腔微生物群组成的改变、口腔微生物群之间的相互作用对疾病的发生有协同促进作用。本文聚焦于口腔微生物群的组成相关研究、口腔微生物组的最新进展,并对其与人体健康之间的关系进行综述。     

基于人体微生物群的特应性皮炎研究进展

皮肤和人体微生物群相互作用,关系复杂。特应性皮炎（atopic dermatitis,AD）是一种常见的慢性和易复发性疾病,与机体的内部和外部环境相关,发病率呈上升趋势。AD的发生往往会改变人体微生物群的组成和数量,微生物群的定植在AD的发生和发展中起着主要作用。本文就人体微生物群与AD的关系、基于皮肤微生物群的AD研究及基于肠道微生物群的AD研究三方面进行综述,主要阐述了皮肤微生物群和肠道微生物群与AD的关系,重点讨论金黄色葡萄球菌在AD发生中的作用以及益生菌等微生物在AD治疗中的重要作用,以期为AD的防治提供新的思路。     

肠道微生物群对肺部免疫微环境稳态影响的研究进展

肠道微生物群是与宿主共生的最大的微生态系统的重要组成部分,它们通过调节宿主的内分泌、代谢、神经和免疫微环境影响人体的多种基本功能。近年来,肠道微生物群对机体局部和远端免疫器官的影响引起了科学家们的广泛关注。肠道微生物和肺之间的相互作用被称为“肠-肺轴”,对肺部免疫微环境稳态的维持至关重要。研究表明,肠道微生物群失调与哮喘、肺炎和囊性纤维化等多种肺部疾病密切相关。本文将对肠道微生物群对肺部免疫微环境稳态的影响及在多种肺部疾病中的作用进行阐述,为临床通过调整肠道微生物群来治疗肺部疾病和维持肺部免疫微环境稳态提供理论依据。     

正畸治疗与口腔微生物群变化的相关性研究

随着口腔微生物群变化的研究不断深入，正畸治疗与口腔微生物群之间的关系逐渐显现。正畸治疗会对口腔微生物群甚至全身微生物群产生重要的影响。一般的正畸治疗主要是让患者佩戴牙齿矫正器，这会导致患者的口腔微生物群被破坏，从而引发一系列如龋齿、牙周炎、牙龈炎等口腔疾病，甚至会威胁到人体的其他器官，有研究表明口腔微生物群比例失衡会导致人体的肝脏等器官感染，从而诱发一系列人体疾病。所以，进行正畸治疗的患者要特别重视口腔健康，做好口腔清洁工作，防止口腔疾病的出现。     

肠道微生物群与药物相互作用的研究进展

药物的代谢是机体对药物处置过程的关键步骤,而肠道作为机体中重要的微生态系统,其在药物代谢方面的作用至关重要。肠道微生物群能够对各种药物等外源化合物进行生物转化、积累,并改变这些物质的活性和毒性,从而影响宿主机体对它们的反应。肠道微生物群与药物之间的相互作用相当复杂,亟待更多更加深入、全面的发掘和研究。近年来,随着人们对肠道微生物群代谢及其与药物互作关系,肠道菌-宿主共代谢认知的不断深化,越来越多的研究表明肠道微生物在药代动力学中扮演重要角色。本文通过调研、整理、归纳和总结国内外相关文献资料,对机体肠道微生物的分类、功能,几种常用药物对肠道微生物的影响以及肠道菌群对药物的代谢作用效果与几个主要的机制进行了梳理和综述,并讨论了微生物和药物之间的双向互作。有利于增进对微生物群影响药物疗效及其代谢途径和机制的了解,提高调控肠道微生物改善治疗的可能性,为指导临床合理用药、精准用药、个体化治疗、药物的评价和新药研发等提供科学参考。     

结直肠癌与肠道微生物群研究进展

肠道微生物群是人体内环境的重要组成部分,与宿主共进化、共代谢、共发育,并与宿主之间相互调控,影响宿主健康。近年研究显示,肠道微生物群参与了结直肠癌的发生和发展。了解肠道微生物群的特征性变化及其诱发结直肠癌的机制对于结直肠癌的防治有着重要意义。目前以肠道微生物群为靶点的干预性基础研究也取得了一些突破性的研究进展。本文主要对结直肠癌患者肠道微生物群的变化、其可能的致病机制及临床相关研究进展等进行综述。     

肺部真菌微生物组研究进展

人体微生物组在健康维护与疾病发展过程中发挥着重要作用。最新研究发现,曾经被视为无菌部位的肺部,其微生物构成也非常丰富,不过针对肺微生物组方面的研究仍然处于早期阶段。真菌及相关基因产物作为人体微生物组的重要组成部分,其在肺部或其他疾病发生与防治方面所具有的潜在功能和意义尚不清晰。本文主要对肺部真菌微生物组的研究技术方法、群落结构特征与功能作用等进行综述,分析了该研究领域目前存在的主要不足,并提出了相关研究建议。     

人体微生物菌群与疾病关系

人体含有大量的正常微生物群,其组成复杂、种类繁多,在机体内发挥各种生理作用,如参与机体代谢、调节免疫等。当受到某些内外源性因素的影响时,微生物群平衡可能会被打破,从而引起微生物群失调,进而引发一系列疾病。越来越多的研究表明,菌群失调与癌症、代谢性疾病及感染性疾病等疾病的发生与发展具有相关性,且恢复微生态平衡对疾病的预防和治疗至关重要。本文就正常微生物菌群与癌症、代谢性疾病及感染性疾病的关系研究进展进行了综述。     

口腔微生物群与牙周病

口腔微生物群作为人体微生物群的重要组成部分,种类繁多、组成复杂,其组成和比例与各类口腔疾病密切相关。牙周炎是一种多微生物的复合感染,它由口腔内微生物群中潜在的致病微生物丰度增加引起,这些微生物通过介导炎症反应及调节口腔微生物群的基础营养环境而致病。本文综述了近年来口腔微生物群与牙周疾病之间的关系及相关影响因素,并分析了目前牙周病微生物群研究的挑战与瓶颈,为将微生物群作为预防、诊断和治疗牙周相关疾病的生物标记物并进一步应用于临床提供理论基础。     

Human gut microbiota and bifidobacteria: from composition to functionality

The human gut is the home of an estimated 10(18) bacterial cells, many of which are uncharacterized or unculturable. Novel culture-independent approaches have revealed that the majority of the human gut microbiota consists of members of the phyla Bacteroidetes and Firmicutes. Nevertheless the role of bifidobacteria in gut ecology illustrates the importance of Actinomycetes and other Actinobacteria that may be underestimated. The human gut microbiota represents an extremely complex microbial community the collective genome of which, the microbiome, encodes functions that are believed to have a significant impact on human physiology. The microbiome is assumed to significantly enhance the metabolism of amino and glycan acids, the turnover of xenobiotics, methanogenesis and the biosynthesis of vitamins. Co-colonisation of the gut commensals Bifidobacterium longum and Bacteroides thetaiotaomicron in a murine model system revealed that the presence of bifidobacteria induced an expansion in the diversity of polysaccharides targeted for degradation by Bacteroides and also induced host genes involved in innate immunity. In addition, comparative analysis of individual human gut microbiomes has revealed various strategies that the microbiota use to adapt to the intestinal environment while also pointing to the existence of a distinct infant and adult-type microbiota.     

The role of IL-10 in microbiome-associated immune modulation and disease tolerance

Current research on the microbiome of humans and other species is revealing a fundamental role for the interaction between the microbiota and the immune system in determining the health status of the host. In these studies, the cytokine interleukin-10 (IL-10) is emerging as an important player. We present here an overview of the developments in the field emphasizing how the microbiota composition and its interplay with immune cells affect the health of the host through changes in IL-10 production. In addition, we explore the function that IL-10-producing immune cells may have on the qualitative and quantitative changes in the microbiota and thus influence the balance between microbial commensalism and pathogenicity. In the last section of this review, we present a summary of the strategies that target IL-10 for therapeutic purposes using probiotics, purified proteins or biologicals.     

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology

The role of the microbiome in health and disease is attracting the attention of researchers seeking to engineer microorganisms for diagnostic and therapeutic applications. Recent progress in synthetic biology may enable the dissection of host–microbiota interactions. Sophisticated genetic circuits that can sense, compute, memorize, and respond to signals have been developed for the stable commensal bacterium Bacteroides thetaiotaomicron, dominant in the human gut. In this review, we highlight recent advances in expanding the genetic toolkit for B. thetaiotaomicron and foresee several applications of this species for microbiome engineering. We provide our perspective on the challenges and future opportunities for the engineering of human gut-associated bacteria as living therapeutic agents.     

Colliding and interacting microbiomes and microbial communities - consequences for human health

Living ‘things’ coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world – paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.     

Microbiome engineering: Current applications and its future

Microbiomes exist in all ecosystems and are composed of diverse microbial communities. Perturbation to microbiomes brings about undesirable phenotypes in the hosts, resulting in diseases and disorders, and disturbs the balance of the associated ecosystems. Engineering of microbiomes can be used to modify structures of the microbiota and restore ecological balance. Consequently, microbiome engineering has been employed for improving human health and agricultural productivity. The importance and current applications of microbiome engineering, particularly in humans, animals, plants and soil is reviewed. Furthermore, we explore the challenges in engineering microbiome and the future of this field, thus providing perspectives and outlook of microbiome engineering.     

Tuning constitutive and pathological inflammation in the gut via the interaction of dietary nitrate and polyphenols with host microbiome

Chronic inflammation is currently recognized as a critical process in modern-era epidemics such as diabetes, obesity and neurodegeneration. However, little attention is paid to the constitutive inflammatory pathways that operate in the gut and that are mandatory for local welfare and the prevention of such multi-organic diseases. Hence, the digestive system, while posing as a barrier between the external environment and the host, is crucial for the balance between constitutive and pathological inflammatory events. Gut microbiome, a recently discovered organ, is now known to govern the interaction between exogenous agents and the host with ensued impact on local and systemic homeostasis. Whereas gut microbiota may be modulated by a myriad of factors, diet constitutes one of its major determinants. Thus, dietary compounds that influence microbial flora may thereby impact on inflammatory pathways. One such example is the redox environment in the gut lumen which is highly dependent on the local generation of nitric oxide along the nitrate-nitrite-nitric oxide pathway and that is further enhanced by simultaneous consumption of polyphenols. In this paper, different pathways encompassing the interaction of dietary nitrate and polyphenols with gut microbiota will be presented and discussed in connection with local and systemic inflammatory events. Furthermore, it will be discussed how these interactive cycles (nitrate-polyphenols-microbiome) may pose as novel strategies to tackle inflammatory diseases.     

Protists’ microbiome: A fine-scale,snap-shot field study on the ciliate Euplotes

Host-microbiome relationships play a fundamental role in the evolution and ecology of any living being. As unicellular organisms, protists represent a unique eukaryotic model to investigate selection mechanisms of the prokaryotic microbiome at the cellular level. Field investigations are central to disentangle relative importance of selective drivers in nature. Here we performed an analysis on data from a snap-shot field study reported previously on bacterial microbiomes associated to natural populations of protist ciliates of the genus Euplotes to detect at a fine scale any influence of habitat and/or host identity in microbiome selection. Comparative analyses revealed environment at a relatively large scale (sampling area) as the main driving factor in shaping prokaryotic communities’ structures. No evidence of habitat as key-factor emerged when a smaller spatial scale was considered (pond/channel or site). When only microbiomes of ciliates from the same site were compared, a clear assessment on the influence of host identity at the species level was not achieved, probably due to the small and unbalanced number of individuals for the two considered host species. Starting from this point, wider sampling campaigns will contribute in the future to depict a general view of the drivers influencing the prokaryotic microbiomes of natural protist populations.     

肠道微生态与肥胖

人的肠道是一个丰富的微生态系统,含有100万亿多的微生物,种类多达500-1000个,这些微生物的基因总数是人体基因组所含基因总数的100倍。肠道微生物丛的组成种类和数量与宿主的肥胖有关,无菌小鼠含有的脂肪量比正常饲养小鼠低42％,如果将微生物丛植入到无菌小鼠体内后,导致脂肪总量增加57％。提示肠道微生物丛可以明显的促进小鼠对热能的摄人,促使脂肪的沉积,触动全身性炎症反应。因此,对肥胖的治疗可以采用益生菌和益生元来调节肠道微生物丛的状态以期获得治疗效果。本研究述及肠道微生丛对宿主肥胖及其代谢机制的研究进展。     

Rapidly expanding knowledge on the role of the gut microbiome in health and disease

The human gut is colonized by a wide diversity of micro-organisms, which are now known to play a key role in the human host by regulating metabolic functions and immune homeostasis. Many studies have indicated that the genomes of our gut microbiota, known as the gut microbiome or our “other genome” could play an important role in immune-related, complex diseases, and growing evidence supports a causal role for gut microbiota in regulating predisposition to diseases. A comprehensive analysis of the human gut microbiome is thus important to unravel the exact mechanisms by which the gut microbiota are involved in health and disease. Recent advances in next-generation sequencing technology, along with the development of metagenomics and bioinformatics tools, have provided opportunities to characterize the microbial communities. Furthermore, studies using germ-free animals have shed light on how the gut microbiota are involved in autoimmunity. In this review we describe the different approaches used to characterize the human microbiome, review current knowledge about the gut microbiome, and discuss the role of gut microbiota in immune homeostasis and autoimmunity. Finally, we indicate how this knowledge could be used to improve human health by manipulating the gut microbiota. This article is part of a Special Issue entitled: From Genome to Function.