肠道微生物功能宏基因组学与代谢组学关联分析方法研究进展

近年来基于高通量基因测序的微生物组学研究极大加深了人们对微生物与健康和疾病关系的认识。然而基因测序方法不能直接测定微生物的功能活性,难以鉴定微生物中的关键功能分子,单独使用无法回答肠道微生物何种成员通过何种方式影响宿主等关键科学问题。单一组学研究弊端尽显,多组学联用势在必行。肠道微生物代谢组学以微生物群落所有小分子代谢物为研究对象,可发现肠道微生物随宿主病理生理变化的关键代谢物,为微生物组-宿主互作机制研究提供线索,成为微生物组学研究的重要补充。肠道微生物功能基因组学与代谢组学关联分析在宿主生理、疾病病理、药物药理等方面取得众多进展,展现良好应用前景。然而目前肠道微生物功能基因组学与代谢组学关联分析存在方法滥用、相关性结论与生物学知识相悖等突出问题。为帮助正确应用肠道微生物功能宏基因组学与代谢组学关联分析,本文综述了各种多组学数据整合分析方法的原理、优缺点与适用范围,并给出了应用建议。     

药用杜仲树皮真菌群落的核心真菌组研究

微生物在生态系统中起着重要作用。最近的研究表明,微生物群落具有核心组(分类单元),这些类群对宿主的健康、生长和生产有着重要的影响。基于MetaCoMET与共存网络两种方法对采自湖南、四川和贵州的药用杜仲树皮真菌群落进行了核心真菌组分析。MetaCoMET结果显示,在OTU水平上,核心真菌组共有16个分类单元,优势菌是丛赤壳科一未定真菌,其次为Fusarium pseudensiforme、一种黄丝菌Cephalothecaceae sp.和一种镰刀菌Fusarium sp.等。共存网络分析揭示了11个中枢真菌分类单元。虽然两种方法的分析结果不完全吻合,但在11个中枢真菌上具有较好的一致性。整体而言,特定核心真菌组具有一定的稳定性。研究结果为进一步揭示植物微生物组的功能提供支撑。     

基于高通量测序技术马肠道菌群研究进展

马肠道非常发达,其中定居着丰富又复杂的微生物菌群,这些微生物在宿主的生理、代谢、营养和免疫功能等方面有着重要作用.基于高通量测序的宏基因组学技术和分析手段的改进,对复杂环境中微生物的研究更加方便、透彻.本文就基于高通量测序的宏基因组技术在马肠道核心菌群、不同肠道段菌群结构、不同因素对肠道菌群结构的影响,以及马肠道微生物...     

黑水虻幼虫肠道微生物的功能及组学应用

黑水虻Hemertia illucens幼虫肠道中栖息着许多种类的微生物,这些微生物与宿主之间的相互作用极为复杂,它们可以影响宿主的生长发育、繁殖能力、营养代谢、行为偏好和寿命。此外,它们还可以调节宿主的免疫系统并保护宿主免受病原体的侵害。深入了解微生物与黑水虻的互作机制,有助于优化黑水虻的生长环境,从而实现更高效的人工繁育。相关文章对微生物与黑水虻互作机理进行了总结,但这些研究方法只能提供微生物群落的结构信息,而无法揭示微生物的功能和代谢能力。因此,宏基因组学、宏转录组学、宏蛋白质组学和代谢组学逐渐被应用,这些技术除了提供关于微生物种群的完整分类,还揭示了它们的功能和代谢能力。通过了解肠道菌群的组成和功能,可以有效调整黑水虻的饲料、饲养环境和生长条件,从而提升黑水虻肠道菌群的稳定,提高黑水虻的生产性能和经济效益。     

动物胃肠道微生物元基因组学研究进展

动物胃肠道中寄居着庞大复杂的微生物,它们对宿主营养、健康和生产有着重要的作用.随着分子生物学的发展,未培养微生物的研究越来越被重视,宏基因组学方法研究胃肠道微生物不仅能了解未培养微生物多样性,还能获得微生物的遗传、代谢和生理等方面的信息.探讨了元基因组文库的构建和分析方法,并重点介绍了元基因组学在动物胃肠道尤其是反刍动物瘤胃微生物研究中的应用.     

鳞翅目昆虫肠道微生物的多样性及其与宿主的相互作用

作为地球上数量最多的动物群体,昆虫种类繁多、形态各异,其肠道内也栖息着大量的微生物,这些微生物直接或间接对宿主发挥着重要的作用,如参与消化、吸收利用营养物质、合成信息素,同时在抵御外来病原的侵入与定殖、提高宿主免疫活性的过程中也起着关键作用。鳞翅目是昆虫纲中仅次于鞘翅目的第二大目,其中既有严重危害农作物的害虫,又有能够授粉和产生经济效益的益虫,对生态系统和人类影响深远。近年来,随着新方法、新技术在肠道微生态学上的应用,国内外鳞翅目昆虫肠道微生物的研究也日趋热烈。本文将围绕家蚕Bombyx mori、海灰翅夜蛾Spodoptera littoralis、小菜蛾Plutella xylostella等几种代表性鳞翅目昆虫,介绍目前为止针对鳞翅目昆虫肠道微生物组的研究,包括肠道的内环境、微生物的多样性及其研究方法,随后对已明确的鳞翅目昆虫肠道微生物的组成,以及共生菌具体对宿主代谢解毒、免疫健康等方面做出的贡献进行分析,以期为进一步深入探究鳞翅目昆虫肠道微生物打下基础,以及转化这些知识来控制害虫(海灰翅夜蛾、小菜蛾等),促进益虫(家蚕等)生长,确保农业和经济更好地发展。     

宏基因组学在人和动物胃肠道微生物研究中的应用进展

人和动物胃肠道存在大量微生物群落,这些微生物是与宿主长期共同进化的结果,并且同宿主的健康和疾病密切相关,因此胃肠道微生物研究已成为当今的热点研究领域。宏基因组学技术在这一领域的应用,使我们不仅能够对胃肠道微生物群落结构及多样性进行分析,还能进一步深入了解其代谢功能,开发和利用潜在的微生物及其基因资源。文中结合我们的研究工作,综述了宏基因组学在人和动物胃肠道微生物研究中的应用,同时着重介绍宏基因组研究的生物信息学技术。     

肠道中多不饱和脂肪酸及其衍生物研究进展

肠道菌群是人体微生态学的重要组成部分,也是最大、最复杂的微生态系统,在宿主的营养吸收、肠道与免疫系统发育等重要生理过程中发挥作用,与人类健康和疾病密切相关。这些共生微生物排除肠道病原体的功能主要依赖于其产生的生物活性物质,如多不饱和脂肪酸等。同时这些脂肪酸在肠道微生物的作用下能够进一步转化为具有特殊结构和功能的多不饱和脂肪酸衍生物。这些多不饱和脂肪酸衍生物对维持健康稳定的肠道菌群至关重要。此外,多不饱和脂肪酸在宿主防御和免疫中发挥了多重关键作用,包括抗癌、抗炎、抗氧化活性,以及降低肠道致病菌的竞争能力等。主要对肠道中多不饱和脂肪酸的来源及其重要的生理功能,以及肠道微生物对多不饱和脂肪酸的转化衍生机制进行了综述,并提出肠道微生物是特殊多不饱和脂肪酸及衍生物生产菌株潜在的种子及基因库,以扩展功能油脂生产菌株的来源。     

基于宏基因组数据的菌株分析方法及其应用

菌株是微生物研究中最基础的生命实体,其功能多样性对宿主表型有着重要影响。随着微生物组研究的深入,对复杂微生物群落进行菌株水平的构成分析和功能分析,在基础科研、临床应用等方面都有重要的价值。文中介绍了基于宏基因组数据的菌株分析的主流算法,以及菌株分析在微生物组研究中的潜在应用和未来的发展方向。     

2020微生物组测序与分析专题序言

微生物是人体、动植物、土壤、沉积物、水体、空气等生境中最重要的生命体。对这些生境中微生物的分析已经成为一项基础的研究技术。微生物组测序与分析作为近年来快速发展的技术,已经在人类健康、环境污染治理、食品工业以及农牧业等领域得到了广泛应用。为了梳理和总结微生物组测序与分析技术的现状、发展状况和应用前景,本专题收录了16篇本领域的论文,分别从样本保存和处理、单菌基因组测序与分析、特殊生境中的微生物组特征分析、微生物组相关数据库和算法以及微生物组测序与分析专家共识等方面,详细介绍了微生物组测序与分析领域的发展态势,为推动我国微生物组测序与分析产业和科研的快速发展、促进微生物组相关产业的良性发展提供必要的参考。     

Mitochondria,the gut microbiome and ROS

In this review, we discuss the connections between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). We examine the mitochondrion as an endosymbiotic organelle that is a hub for energy production, signaling, and cell homeostasis. Maintaining a diverse gut microbiome is generally associated with organismal fitness, intestinal health and resistance to environmental stress. In contrast, gut microbiome imbalance, termed dysbiosis, is linked to a reduction in organismal well-being. ROS are essential signaling molecules but can be damaging when present in excess. Increasing ROS levels have been shown to influence human health, homeostasis of gut cells, and the gastrointestinal microbial community's biodiversity. Reciprocally, gut microbes can affect ROS levels, mitochondrial homeostasis, and host health. We propose that mechanistic understanding of the suite of bi-directional interactions between mitochondria and the gut microbiome will facilitate innovative interdisciplinary studies examining evolutionary divergence and provide novel treatments and therapeutics for disease.GlossIn this review, we focus on the nexus between mitochondria and the gut microbiome provided by reactive oxygen species (ROS). Mitochondria are a cell organelle that is derived from an ancestral alpha-proteobacteria. They generate around 80% of the adenosine triphosphate that an organism needs to function and release a range of signaling molecules essential for cellular homeostasis. The gut microbiome is a suite of microorganisms that are commensal, symbiotic and pathogenic to their host. ROS are one predominant group of essential signaling molecules that can be harmful in excess. We suggest that the mitochondria- microbiome nexus is a frontier of research that has cross-disciplinary benefits in understanding genetic divergence and human well-being.     

Review: The development of the gastrointestinal tract microbiota and intervention in neonatal ruminants

The complex microbiome colonizing the gastrointestinal tract (GIT) of ruminants plays an important role in the development of the immune system, nutrient absorption and metabolism. Hence, understanding GIT microbiota colonization in neonatal ruminants has positive impacts on host health and productivity. Microbes rapidly colonize the GIT after birth and gradually develop into a complex microbial community, which allows the possibility of GIT microbiome manipulation to enhance newborn health and growth and perhaps induce lasting effects in adult ruminants. This paper reviews recent advances in understanding how host-microbiome interactions affect the GIT development and health of neonatal ruminants. Following initial GIT microbiome colonization, continuous exposure to host-specific microorganisms is necessary for GIT development and immune system maturation. Furthermore, the early GIT microbial community structure is significantly affected by early life events, such as maternal microbiota exposure, dietary changes, age and the addition of prebiotics, probiotics and synbiotics, supporting the idea of microbial programming in early life. However, the time window in which interventions can optimally improve production and reduce gastrointestinal disease as well as the role of key host-specific microbiota constituents and host immune regulation requires further study.     

微生物组学的技术和方法及其应用

微生物组是指一个特定环境或生态系统中全部微生物及其遗传信息的集合, 其蕴藏着极为丰富的微生物资源。全面系统地解析微生物组的结构和功能, 将为解决人类面临的能源、生态环境、工农业生产和人体健康等重大问题带来新思路。然而, 微生物组学研究在很大程度上取决于其技术与方法的发展。在高通量测序技术出现以前, 微生物研究主要基于分离培养和指纹图谱等技术, 然而, 由于这些技术存在的缺陷, 人们对于微生物的认识十分有限。自21世纪初以来, 尽管高通量测序和质谱技术的革命性突破极大地促进了人们对于微生物的认识, 微生物组学技术在微生物组研究中的应用仍面临着诸多挑战。此外, 目前微生物组的结构和多样性等描述性研究已臻成熟, 微生物组学研究正处于从数量到质量、从结构到功能的关键转变时期。因此, 该文首先介绍了微生物组学的基本概念及其发展简史, 其次简述了微生物组学研究的相关技术和方法及其发展历程, 并进一步阐述了微生物组学的技术和方法在生态学研究中的应用及存在的主要问题, 最后从技术、理论和应用层面阐述了未来微生物组学技术和方法发展的前沿方向, 并提出了今后微生物组学研究的优先发展领域。     

The rhizosphere microbiome and plant health

The diversity of microbes associated with plant roots is enormous, in the order of tens of thousands of species. This complex plant-associated microbial community, also referred to as the second genome of the plant, is crucial for plant health. Recent advances in plant-microbe interactions research revealed that plants are able to shape their rhizosphere microbiome, as evidenced by the fact that different plant species host specific microbial communities when grown on the same soil. In this review, we discuss evidence that upon pathogen or insect attack, plants are able to recruit protective microorganisms, and enhance microbial activity to suppress pathogens in the rhizosphere. A comprehensive understanding of the mechanisms that govern selection and activity of microbial communities by plant roots will provide new opportunities to increase crop production.     

Analyzing the Secretome of Gut Microbiota as the Next Strategy For Early Detection of Colorectal Cancer

Dysbiosis of gut microbiome can contribute to inflammation, and subsequently initiation and progression of colorectal cancer (CRC). Throughout these stages, various proteins and metabolites are secreted to the external environment by microorganisms or the hosts themselves. Studying these proteins may help enhance our understanding of the host–microorganism relationship or they may even serve as useful biomarkers for CRC. However, secretomic studies of gut microbiome of CRC patients, until now, are scarcely performed. In this review article, the focus is on the roles of gut microbiome in CRC, the current findings on CRC secretome are highlighted, and the emerging challenges and strategies to drive forward this area of research are addressed.     

Microbiome evolution along divergent branches of the vertebrate tree of life: what is known and unknown

Vertebrates harbour microbes both internally and externally, and collectively, these microorganisms (the ‘microbiome’) contain genes that outnumber the host's genetic information 10‐fold. The majority of the microorganisms associated with vertebrates are found within the gut, where they influence host physiology, immunity and development. The development of next‐generation sequencing has led to a surge in effort to characterize the microbiomes of various vertebrate hosts, a necessary first step to determine the functional role these communities play in host evolution or ecology. This shift away from a culture‐based microbiological approach, limited in taxonomic breadth, has resulted in the emergence of patterns suggesting a core vertebrate microbiome dominated by members of the bacterial phyla Bacteroidetes, Proteobacteria and Firmicutes. Still, there is a substantial variation in the methodology used to characterize the microbiome, from differences in sample type to issues of sampling captive or wild hosts, and the majority (>90%) of studies have characterized the microbiome of mammals, which represent just 8% of described vertebrate species. Here, we review the state of microbiome studies of nonmammalian vertebrates and provide a synthesis of emerging patterns in the microbiome of those organisms. We highlight the importance of collection methods, and the need for greater taxonomic sampling of natural rather than captive hosts, a shift in approach that is needed to draw ecologically and evolutionarily relevant inferences. Finally, we recommend future directions for vertebrate microbiome research, so that attempts can be made to determine the role that microbial communities play in vertebrate biology and evolution.     

肠道微生物对寿命的影响及其机制*

延长健康寿命的跨度对每个人都有重要意义,百岁老人存在独特的肠道菌群特征,肠道微生物群是许多年龄相关变化的核心,菌群特征以及菌群基因组成改变都能影响机体寿命。一些饮食和药物要发挥延寿效果也离不开微生物的参与,微生物具有重要的介导和转化作用,益生菌和粪便移植等措施在动物模型中已被明确可以影响机体寿命。越来越多的研究表明微生物不仅能产生小分子化合物促进健康寿命跨度的增加乃至延长个体寿命如γ-氨基丁酸、荚膜异多糖酸,还能影响宿主的生物合成代谢如5-羟色胺,甚至间接参与宿主信号通路的调控。目前对于这些微生物的生物学功能以及对宿主寿命的影响还没有系统的总结,对肠道微生物影响寿命的证据以及生理机制进行综述,为改善老年期健康状况的干预措施提供参考。     

Beyond the Venn diagram: the hunt for a core microbiome

Discovering a core microbiome is important for understanding the stable, consistent components across complex microbial assemblages. A core is typically defined as the suite of members shared among microbial consortia from similar habitats, and is represented by the overlapping areas of circles in Venn diagrams, in which each circle contains the membership of the sample or habitats being compared. Ecological insight into core microbiomes can be enriched by 'omics approaches that assess gene expression, thereby extending the concept of the core beyond taxonomically defined membership to community function and behaviour. Parameters defined by traditional ecology theory, such as composition, phylogeny, persistence and connectivity, will also create a more complex portrait of the core microbiome and advance understanding of the role of key microorganisms and functions within and across ecosystems.     

Integrating '-omics' and natural product discovery platforms to investigate metabolic exchange in microbiomes

The microbiome is an abundance of microorganisms within a host (e.g. human microbiome). These microorganisms produce small molecules and metabolites that have been shown to affect and dictate the physiology of an individual. Functional knowledge of these molecules, often produced for communication or defense, will reveal the interplay between microbes and host in health and disease. The vast diversity in structure and function of microbiome-associated small molecules necessitate tools that will utilize multiple '-omics' strategies to understand the interactions within the human microbiome. This review discusses the importance of these investigations and the integration of current '-omics' technologies with tools established in natural product discovery in order to identify and characterize uncharacterized small molecules in the effort towards diagnostic modeling of the human microbiome.