无菌动物在肠-肝轴研究中的应用前景

肠道和肝之间通过肠-肝轴紧密相连,肠道疾病可以影响肝功能,肝疾病也可以诱发肠道菌群和功能的改变。无菌动物是一种身体所有部位都没有任何活的细菌、真菌、病毒及寄生虫的动物,无菌动物的出现为研究微生物与宿主之间的相互作用提供了有力的实验工具。同时,由于无菌动物缺乏正常肠道菌群的特点,它在肠-肝轴的研究中也起到了极大的推进作用。本文将对无菌动物在肠-肝轴中的应用前景做简要综述。     

基于无菌动物研究肠道微生物与类风湿关节炎发病相关性

肠道微生物与宿主的生长发育、免疫、代谢等方面均密切相关,但肠道菌群与宿主之间复杂的相互作用在很大程度上仍然是未知的。目前无菌动物已成为探索肠道微生物与宿主相互作用的重要工具,多项研究使用无菌动物模型探讨肠道菌群在宿主代谢、机体免疫系统的发育和成熟等方面的作用,其中包括肠道菌群在自身免疫性疾病发病及预后中的作用。研究发现,肠道菌群作为环境因素之一可能参与类风湿关节炎(rheumatoid arthritis,RA)发病,然而其因果关系未明。本文将对使用无菌动物探讨肠道微生物参与类风湿关节炎发病的相关性研究作一综述,为进一步深入研究肠道菌群在RA发病中的作用及机制研究提供理论依据。     

肠道微生物与认知功能

近年来大量研究表明肠道微生物的改变与认知行为之间存在明显的相关性。通过无菌动物、细菌感染以及益生菌或抗生素干预等方式改变宿主的肠道菌群,可以调节宿主的认知行为,包括学习和记忆能力。应激和饮食结构的变化也会改变宿主的肠道微生物,进而影响宿主行为。同时在胃肠道疾病和某些非肠道疾病状态下也会伴随着宿主认知行为的改变。本研究将重点讨论在人类和动物研究中发现的肠道微生物多样性的改变如何影响大脑功能和认知行为。     

无菌动物在饮食干涉肠道菌群研究中的应用

膳食干涉对肠道菌群与健康的影响已成为医学健康领域的研究热点,从发展来看,肠道菌群有可能会成为研究饮食方式、保健食品、中药制剂等对人体健康影响的重要靶标。然而,肠道菌群由于其复杂性,研究它和饮食干涉的关系对动物模型有高标准的要求,无菌动物体内外不携带任何活的微生物和寄生虫,在生物医学及人体疾病和健康等方面均有一定的应用和研究,是当前肠道菌群研究中应用最多的基础动物模型。采用无菌动物构建人源菌群动物是研究饮食、菌群与健康关系的常用方式。本文主要综述无菌动物构建人源菌群动物的研究应用及饮食干涉对肠道菌群的影响。     

肠道微生物菌群对脑及行为的影响

肠道微生物菌群组成的变化对正常生理的影响及其在疾病中的作用逐渐成为研究热点。肠道微生物菌群通过脑肠轴影响宿主生理学的各个方面,包括脑-肠交流、脑功能甚至行为。对无菌动物、被致病细菌感染的、使用益生菌或用抗生素药物的动物研究表明,肠道微生物菌群可以调节宿主焦虑样症状及行为。研究表明对肠道微生物菌群的调节可能是治疗复杂中枢神经系统失调症的新策略。     

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。     

病毒与细胞的微生态学研究进展

微生态学（microecology）是细胞水平或分子水平的生态学,它是研究微生物群的结构和功能,以及微生物与其宿主相互依赖、相互制约关系的科学。病毒（virus）是一种比细菌还要微小和简单的非细胞形态微生物（acellular microorganism）,不仅可寄生于动植物体的组织细胞表面或内部,还可寄生于细菌、真菌等微生物内部。作为宿主以及细胞内的寄生体,病毒除引起宿主多种类型的感染外,还可参与宿主组织细胞的微生态系的组成,赋予细胞干扰相关病毒增殖与复制、抵抗特定病毒感染感染的作用,并能引起宿主细胞产生特定毒素、获得新抗原性等改变。本研究通过微生态学角度,对病毒与细胞的相互关系及病毒与细胞微生态学在医学上的作用作一综述。     

无菌猪的制备与微生物质量控制

菌群与宿主相互关系等热点研究促进了对无菌动物需求的迅猛发展。无菌猪作为一种特殊的模式动物,其在科学研究中不仅排除了背景微生物因素的影响,而且与常用的无菌小鼠相比,其在解剖、生理、代谢等方面与人更为相似,因此在生命科学研究领域具有重要的应用价值。本文结合现有国外无菌猪研究进展和本实验室在无菌猪研究积累,就无菌猪的制备与微生物质量控制进行简要探讨。     

单胃动物肠道微生物菌群与肠道免疫功能的相互作用

动物胃肠道栖息着大量的微生物,这些微生物及其代谢产物在营养、免疫等方面对宿主的健康有重要的意义。近年来研究发现肠道微生物与免疫系统间存在密切的交流和互作机制,尽管肠道共生菌具有定植抑制效应,但肠道微生物也可通过其特定组分刺激免疫细胞如Tregs细胞、Th17细胞的分化,肠道菌群的紊乱可能导致细菌移位、肠道屏障功能损伤,影响机体健康。宿主免疫系统可通过分泌多种免疫效应因子如MUC、sIgA、ITF、RegIIIγ、α-防御素等调节肠道微生物的分布和组成,调节肠道菌群的稳态。本文综述了单胃动物肠道微生物菌群的组成,深入探讨了肠道微生物菌群与动物肠道免疫功能之间的相互作用。     

EB病毒致病机制研究进展

EB病毒(Epstein-Barr virus,EBV)是一种常见的人类4型疱疹病毒,原发感染后可终身携带病毒。EBV感染无法从宿主中清除,呈现潜伏状态,一旦激活即可成为很多疾病的相关病因,与人类多种疾病特别是恶性肿瘤相关,包括Burkitt淋巴瘤、鼻咽癌、胃癌等。EBV致病机制复杂多样,目前致病机制的具体分子遗传机制尚未明确。本文主要从EBV与宿主细胞相互作用、免疫逃逸、EBV感染周期表达的相关产物与宿主的相互作用等几个方面,综述目前EBV致病机制的研究进展。     

环境微生物研究中机器学习算法及应用

微生物在环境中无处不在，它们不仅是生物地球化学循环和环境演化的关键参与者，也在环境监测、生态治理和保护中发挥着重要作用。随着高通量技术的发展，大量微生物数据产生，运用机器学习对环境微生物大数据进行建模和分析，在微生物标志物识别、污染物预测和环境质量预测等领域的科学研究和社会应用方面均具有重要意义。机器学习可分为监督学习和无监督学习2大类。在微生物组学研究当中，无监督学习通过聚类、降维等方法高效地学习输入数据的特征，进而对微生物数据进行整合和归类。监督学习运用有特征和标记的微生物数据集训练模型，在面对只有特征没有标记的数据时可以判断出标记，从而实现对新数据的分类、识别和预测。然而，复杂的机器学习算法通常以牺牲可解释性为代价来重点关注模型预测的准确性。机器学习模型通常可以看作预测特定结果的“黑匣子”，即对模型如何得出预测所知甚少。为了将机器学习更多地运用于微生物组学研究、提高我们提取有价值的微生物信息的能力，深入了解机器学习算法、提高模型的可解释性尤为重要。本文主要介绍在环境微生物领域常用的机器学习算法和基于微生物组数据的机器学习模型的构建步骤，包括特征选择、算法选择、模型构建和评估等，并对各种机器学习模型在环境微生物领域的应用进行综述，深入探究微生物组与周围环境之间的关联，探讨提高模型可解释性的方法，并为未来环境监测、环境健康预测提供科学参考。     

Manipulation of the seagrass-associated microbiome reduces disease severity

Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host–microbe–pathogen relationships may continue to show new relationships between plant microbiomes and diseases.     

核心微生物组的研究及利用现状

随着分子生物学和生物信息学的飞速发展,新一代测序技术可以轻松地检测不同样本中复杂的微生物分类单元。面对这些复杂而大量的微生物组数据带来的分析挑战,利用核心微生物组的方法来描述和分析样本中的核心微生物组和关键种是近年来新的研究热点,这些结果将揭示与宿主健康、生长和生产等密切相关的微生物种类,有助于深入认识微生物与宿主间的相互关系,深刻理解微生物对宿主的影响作用,更好地理解微生物组在自然生态系统中的功能。本文阐述了核心微生物组的定义、研究方法、与动植物的关系等方面的研究及利用现状,为更好地利用核心微生物组解决环境、人类健康和农业生产问题提供思路。     

Context-dependent effects of glucocorticoids on the lizard gut microbiome

The vertebrate gut microbiota (bacterial, archaeal and fungal communities of the gastrointestinal tract) can have profound effects on the physiological processes of their hosts. Although relatively stable, changes in microbiome structure and composition occur due to changes in the environment, including exposure to stressors and associated increases in glucocorticoid hormones. Although a growing number of studies have linked stressor exposure to microbiome changes, few studies have experimentally explored the specific influence of glucocorticoids on the microbiome in wild animals, or across ecologically important processes (e.g., reproductive stages). Here we tested the response of the gut microbiota of adult female Sceloporus undulatus across gestation to ecologically relevant elevations of a stress-relevant glucocorticoid hormone (CORT) in order to determine (i) how experimentally elevated CORT influenced microbiome characteristics, and (ii) whether this relationship was dependent on reproductive context (i.e., whether females were gravid or not, and, in those that were gravid, gestational stage). We show that the effects of CORT on gut microbiota are complex and depend on both gestational state and stage. CORT treatment altered microbial community membership and resulted in an increase in microbiome diversity in late-gestation females, and microbial community membership varied according to treatment. In nongravid females, CORT treatment decreased interindividual variation in microbial communities, but this effect was not observed in late-gestation females. Our results highlight the need for a more holistic understanding of the downstream physiological effects of glucocorticoids, as well as the importance of context (here, gestational state and stage) in interpreting stress effects in ecology.     

Matrotrophic viviparity constrains microbiome acquisition during gestation in a live‐bearing cockroach,Diploptera punctata

The vertical transmission of microbes from mother to offspring is critical to the survival, development, and health of animals. Invertebrate systems offer unique opportunities to conduct studies on microbiome‐development‐reproduction dynamics since reproductive modes ranging from oviparity to multiple types of viviparity are found in these animals. One such invertebrate is the live‐bearing cockroach, Diploptera punctata. Females carry embryos in their brood sac, which acts as the functional equivalent of the uterus and placenta. In our study, 16S rRNA sequencing was used to characterize maternal and embryonic microbiomes as well as the development of the whole‐body microbiome across nymphal development. We identified 50 phyla and 121 classes overall and found that mothers and their developing embryos had significantly different microbial communities. Of particular interest is the notable lack of diversity in the embryonic microbiome, which is comprised exclusively of Blattabacteria, indicating microbial transmission of only this symbiont during gestation. Our analysis of postnatal development reveals that significant amounts of non‐Blattabacteria species are not able to colonize newborn D. punctata until melanization, after which the microbial community rapidly and dynamically diversifies. While the role of these microbes during development has not been characterized, Blattabacteria must serve a critical role providing specific micronutrients lacking in milk secretions to the embryos during gestation. This research provides insight into the microbiome development, specifically with relation to viviparity, provisioning of milk‐like secretions, and mother–offspring interactions during pregnancy.     

Successional dynamics of the cultivated kelp microbiome

Kelp are important primary producers that are colonized by diverse microbes that can have both positive and negative effects on their hosts. The kelp microbiome could support the burgeoning kelp cultivation sector by improving host growth, stress tolerance, and resistance to disease. Fundamental questions about the cultivated kelp microbiome still need to be addressed before microbiome-based approaches can be developed. A critical knowledge gap is how cultivated kelp microbiomes change as hosts grow, particularly following outplanting to sites that vary in abiotic conditions and microbial source pools. In this study we assessed if microbes that colonize kelp in the nursery stage persist after outplanting. We characterized microbiome succession over time on two species of kelp, Alaria marginata and Saccharina latissima, outplanted to open ocean cultivation sites in multiple geographic locations. We tested for host-species specificity of the microbiome and the effect of different abiotic conditions and microbial source pools on kelp microbiome stability during the cultivation process. We found the microbiome of kelp in the nursery is distinct from that of outplanted kelp. Few bacteria persisted on kelp following outplanting. Instead, we identified significant microbiome differences correlated with host species and microbial source pools at each cultivation site. Microbiome variation related to sampling month also indicates that seasonality in host and/or abiotic factors may influence temporal succession and microbiome turnover in cultivated kelps. This study provides a baseline understanding of microbiome dynamics during kelp cultivation and highlights research needs for applying microbiome manipulation to kelp cultivation.     

City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii)

Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large‐scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild non‐model species remains sparse. Using an empirical replicated study system, we show that city life alters the gut microbiome and stable isotope profiling of a wild native non‐model species – the eastern water dragon (Intellagama lesueurii) in Queensland, Australia. City dragons exhibit a more diverse gut microbiome than their native habitat counterparts and show gut microbial signatures of a high fat and plant rich diet. Additionally, we also show that city dragons have elevated levels of the Nitrogen‐15 isotope in their blood suggesting that a city diet, which incorporates novel anthropogenic food sources, may also be richer in protein. These results highlight the role that gut microbial plasticity plays in an animals' response to human‐altered landscapes.     

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.     

Drivers and patterns of microbial community assembly in a Lyme disease vector

Vector‐borne diseases constitute a major global health burden and are increasing in geographic range and prevalence. Mounting evidence has demonstrated that the vector microbiome can impact pathogen dynamics, making the microbiome a focal point in vector‐borne disease ecology. However, efforts to generalize preliminary findings across studies and systems and translate these findings into disease control strategies are hindered by a lack of fundamental understanding of the processes shaping the vector microbiome and the interactions therein. Here, we use 16S rRNA sequencing and apply a community ecology framework to analyze microbiome community assembly and interactions in Ixodes pacificus, the Lyme disease vector in the western United States. We find that vertical transmission routes drive population‐level patterns in I. pacificus microbial diversity and composition, but that microbial function and overall abundance do not vary over time or between clutches. Further, we find that the I. pacificus microbiome is not strongly structured based on competition but assembles nonrandomly, potentially due to vector‐specific filtering processes which largely eliminate all but the dominant endosymbiont, Rickettsia. At the scale of the individual I. pacificus, we find support for a highly limited internal microbial community, and hypothesize that the tick endosymbiont may be the most important component of the vector microbiome in influencing pathogen dynamics.     

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。