蝗虫肠道微生物总DNA提取方法的比较

采用Bead beating法和QIAamp DNA stool mini kit法提取蝗虫肠道微生物总DNA,并对2种方法提取DNA的得率、完整性以及16SrRNA基因扩增产物的变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)图谱等进行综合比较。结果表明,Bead beating法提取DNA的得率显著高于QIAamp DNA stool mini kit法(P=0.042),而QIAamp DNA stool mini kit法提取DNA片段更完整。PCR-DGGE检测微生物多样性结果显示,QIAamp DNA stool mini kit法提取DNA所代表的微生物群落多样性略高于Bead beating法,但Mann-Whitley统计学检验表明用2种方法检测蝗虫肠道微生物多样性无显著差异(P=0.17)。因此在蝗虫肠道微生物群落多样性的检测中QIAamp DNA stool mini kit法具一定的优势,而Bead beating法同样适用。     

常见疾病、抗生素及农药对意大利蜜蜂(Apis mellifera ligustica)肠道微生物多样性的影响研究进展

蜜蜂是对农业生产十分重要的授粉昆虫。蜜蜂肠道微生物与蜜蜂健康有密切关系,但肠道微生物也会受多种外界因素的影响。本文就蜜蜂疾病、抗生素等蜂病治疗药物、农药,以及益生菌的应用等对意大利蜜蜂工蜂肠道微生物影响的研究进行了归纳总结,并对蜜蜂与其肠道菌关系研究进行了展望。     

昆虫肠道的宏基因组学:微生物大数据的新疆界

微生物作为自然界中普遍存在的生命体,通常以"微生物群落"的形式共存。这些物种相互协作适应环境变化的同时,也对环境产生了长期而深刻的影响。随着人类对于微生物了解的深入,微生物群落基础研究及其在健康和环境等领域的应用研究日益重要。昆虫肠道内存在种类繁多、数量庞大的微生物,一方面,这些肠道微生物种群结构的多样性与昆虫种类、龄期、消化道形式、食物的来源、环境等都息息相关。另一方面,这些菌群也对宿主的一些生理活动有着一定的影响。随着高通量测序技术、组学技术的发展,昆虫肠道宏基因组大数据挖掘和应用已经成为研究热点,极大地推动人类微生物资源利用的能力。本文概述了昆虫肠道微生物宏基因组学的发展现状和发展趋势,特别是肠道宏基因组学大数据的挖掘工具和应用,以及现阶段昆虫肠道宏基因组学的研究进展、应用、优势和瓶颈,并对今后昆虫肠道微生物组大数据研究方向进行展望。     

肠道微生物对肥胖影响

肠道微生物是哺乳动物最密集的微生物群落,也是最多样化的微生物群落之一。随着宏基因组学的不断发展,肠道微生物成为热门的研究领域。肠道微生物具有保护和代谢等功能,在胰岛素抵抗和肥胖等疾病中发挥重要作用。本文介绍了肠道微生物及其代谢物通过调节食欲、神经递质合成分泌、炎性反应进而调节肥胖,探讨了肠道微生物的影响因素,展望了肠道微生物对治疗人类肥胖的应用前景。     

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。     

肠道微生物与肝硬化及其并发症的研究进展

人体肠道中数量可观、种类丰富的微生物对于维持人体健康起到重要作用。大量研究表明肠道微生物对肝硬化及其并发症有重要影响。当机体内外环境改变时会引起肠道微生物的变化,影响肝硬化及其并发症的发生和发展,而肝硬化及其并发症的发生发展也会引起肠道微生物的紊乱,二者相互联系,相互影响。通过对肠道微生物的检测和调节有助于肝硬化及其并发症的诊断与治疗。本文就肠道微生物与肝硬化及其并发症关系的研究现状,以肠道微生物为靶标的诊断治疗肝硬化及其并发症的策略以及现存在的问题进行综述。     

基于DNA复合条形码技术的蝗虫肠道共生真菌多样性研究

利用DNA复合条形码技术,研究了11个样本的蝗虫肠道共生真菌的多样性。结果显示:ITS在所研究的物种中鉴定了5门16纲29目40属2786 OTU真菌。肠道真菌群落组成分析结果显示:所有物种肠道真菌类群中含量最高的是木耳菌目和银耳目,其中斑翅蝗科的真菌类群多样性相对最高,斑腿蝗科的真菌类群多样性相对最低,表明各蝗虫肠道之间存在着明显的菌群多样性变化。α多样性分析结果显示:斑翅蝗科的共生真菌群落丰富度和多样性最高,斑腿蝗科的则最低。β多样性分析结果显示:(1)同科的各个种的肠道真菌群落结构差异性较小,不同科的种的肠道真菌群落结构差异性较大;(2)剑角蝗科的肠道真菌群落结构与其他物种的相似性均相对较低,而且在两个不同取样地得到的中华剑角蝗的真菌群落结构相似性也相对较低。聚类分析结果显示:(1)同科的蝗虫肠道真菌首先聚到一起,且群落相似性也相对较高;(2)布勒掷孢酵母属、内疣衣属和外瓶霉属3个属在蝗虫肠道真菌中是优势菌属。     

肠道上皮与肠道微生物相互作用的研究现状

肠道上皮是肠上皮细胞及其分泌物有机构成的黏膜界面。随着技术的进步和对肠道菌群作用的逐渐重视,研究者对肠道上皮与肠道微生物相互作用的认识也不断深入。研究表明,肠道上皮调节并维持肠道微生物的定殖与分布,肠道微生物也影响肠道上皮的多种屏障功能,二者通过一系列细胞分子机制紧密联系,共同维持肠道稳态。此外,其过程中产生的宿主-肠道菌群共代谢物被发现可以反映宿主的生理病理状态,作为指标被应用于临床疾病诊断、治疗效果评估和预后推测。本文基于近年的研究,综述了肠道上皮与肠道微生物的相互作用及其细胞分子机制,为进一步研究和临床应用总结了理论基础,并探讨了未来可能的研究方向。     

昆虫肠道微生物稳态的调控机制

稳定的肠道微生物内环境是肠道微生物与肠道免疫反应相互作用的结果。在不断的进食过程中,昆虫肠道微生物种类和数量不断发生变化,肠道微生物与肠道上皮细胞之间形成了复杂的、动态的平衡机制。昆虫肠道上皮细胞可以感知有益和有害条件并利用免疫调控通路来实现微生物种群稳态的动态调节,例如双重氧化酶-活性氧(dual oxidase-reactive oxygen species, Duox-ROS)系统和免疫缺陷(immunodeficiency, Imd)信号通路可以感知肠道微生物数量变化并参与到肠道微生物稳态调节过程。除此之外,肠道微生物群也会通过群体感应(quorum sensing, QS)释放相应的效应因子来调节菌群行为,间接性起到稳态调节的作用。因此,本文综述了昆虫肠道中物理防御、免疫信号通路以及肠道微生物通过QS在昆虫肠道微生物稳态维持中的作用,加深对肠道组织与肠道微生物互作关系的认识。未来将继续对更多种类昆虫体内微生物的稳态调控机制及调控机制间的作用关系进行研究,并基于调控机制设计开发改变肠道微生物稳态的新型农药,为实现有效害虫防治提供新的靶标和思路。     

白蚁肠道微生物研究方法概述

白蚁是木质纤维素的主要降解者,在森林生态系统碳氮循环过程中发挥着重要作用。白蚁肠道共生微生物主要包括原生生物、细菌、古菌和真菌。在白蚁对木质纤维素进行降解、发酵,从而产生乙酸、氢气和甲烷以及对氮的固定过程中,白蚁肠道共生微生物起着重要的作用。本文对白蚁肠道微生物的研究方法进行总结,概述了各种方法的优缺点,同时对肠道微生物的研究进展进行了总结,以期为白蚁肠道微生物的进一步研究和利用提供参考。     

Microbiome-related aspects of locust density-dependent phase transition

Locust plagues are a notorious, ancient phenomenon. These swarming pests tend to aggregate and perform long migrations, decimating cultivated fields along their path. When population density is low, however, the locusts will express a cryptic, solitary, non-aggregating phenotype that is not considered a pest. Although the transition from the solitary to the gregarious phase has been well studied, associated shifts in the locust's microbiome have yet to be addressed. Here, using 16S rRNA amplicon sequencing, we compared the bacterial composition of solitary desert locusts before and after a phase transition. Our findings revealed that the microbiome is altered during the phase transition, and that a major aspect of this change is the acquisition of Weissella (Firmicutes). Our findings led us to hypothesize that the locust microbiome plays a role in inducing aggregation behaviour, contributing to the formation and maintenance of a swarm. Employing a mathematical model, we demonstrate the potential evolutionary advantage of inducing aggregation under different conditions; specifically, when the aggregation-inducing microbe exhibits a relatively high horizontal transmission rate. This is the first report of a previously unknown and important aspect of locust phase transition, demonstrating that the phase shift includes a shift in the gut and integument bacterial composition.     

Characterization of the gut microbiome in the beet armyworm Spodoptera exigua in response to the short-term thermal stress

The gut microbiota is critical for energy and nutrient utilization and plays a role in host immunity in response to environmental changes. The beet armyworm Spodoptera exigua is a worldwide polyphagous agricultural pest and has frequently experienced potentially stressful temperature fluctuations under natural environmental conditions. However, little is known about the effects of thermal stress on the gut microbiome of this moth pest. Therefore, we investigated the gut microbiome variations, composition and community structure of S. exigua among low-temperature (10 °C), control (26 °C) and high temperature (35 °C) treatments using 16S amplicon sequencing. Overall, 1,192,707 high-quality reads and 762 operational taxonomic units (OTUs) were detected from 15 samples. A total of 289 genera belonging to 19 bacterial phyla were captured, with Firmicutes and Proteobacteria being the most prominent phyla. Alpha diversity metrics indicated no significant differences in the gut bacterial diversity of S. exigua among the three temperature treatments. Principal coordinates and hierarchical cluster analysis revealed significant differences in the structure of gut microbiota between the low-temperature treatment and the other two temperature treatments. In addition, PICRUSt2 analysis demonstrated that the predicted metagenomes associated with the gut microbiome were amino carbohydrate transport and metabolism, acid transport and metabolism, inorganic ion transport and metabolism and cellular processes. Our study showed that thermal stress induced changes in the gut microbiome of the beet armyworm, which may contribute to better understanding the ecological adaptation of S. exigua under changing temperature trends and to evaluating the use of gut microorganisms as biocontrol agents for this pest.     

The maternal foam plug constitutes a reservoir for the desert locust's bacterial symbionts

A hallmark of the desert locust's ancient and deserved reputation as a devastating agricultural pest is that of the long-distance, multi-generational migration of locust swarms to new habitats. The bacterial symbionts that reside within the locust gut comprise a key aspect of its biology, augmenting its immunity and having also been reported to be involved in the swarming phenomenon through the emission of attractant volatiles. However, it is still unclear whether and how these beneficial symbionts are transmitted vertically from parent to offspring. Using comparative 16S rRNA amplicon sequencing and direct experiments with engineered bacteria, we provide evidence for vertical transmission of locust gut bacteria. The females may perform this activity by way of inoculation of the egg-pod's foam plug, through which the larvae pass upon hatching. Furthermore, analysis of the composition of the foam revealed chitin to be its major component, along with immunity-related proteins such as lysozyme, which could be responsible for the inhibition of some bacteria in the foam while allowing other, more beneficial, strains to proliferate. Our findings reveal a potential vector for the transgenerational transmission of symbionts in locusts, which contributes to the locust swarm's ability to invade and survive in new territories.     

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.     

肠道菌群与结核病之间相关性的研究进展

随着新一代测序技术的发展,肠道菌群成为生物学研究领域的一大热点,特别是肠道菌群与人体各种疾病之间的关系受到广泛关注。目前已有研究发现结核分枝杆菌感染会引起肠道菌群改变,而肠道菌群失调也会增加机体对结核分枝杆菌的易感性,两者通过机体免疫反应、菌群代谢产物等因素相互影响。本文就肠道菌群与结核病的关系、肠道菌群与结核病相互影响的可能机制、抗结核治疗对肠道菌群的影响等方面的相关研究进行综述。     

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.     

Microbial community in human gut: a therapeutic prospect and implication in health and diseases

The interest in the working and functionality of the human gut microbiome has increased drastically over the years. Though the existence of gut microbes has long been speculated for long over the last few decades, a lot of research has sprung up in studying and understanding the role of gut microbes in the human digestive tract. The microbes present in the gut are highly instrumental in maintaining the metabolism in the body. Further research is going on in this field to understand how gut microbes can be employed as potential sources of novel therapeutics; moreover, probiotics have also elucidated their significant place in this direction. As regards the clinical perspective, microbes can be engineered to afford defence mechanisms while interacting with foreign pathogenic bodies. More investigations in this field may assist us to evaluate and understand how these cells communicate with human cells and promote immune interactions. Here we elaborate on the possible implication of human gut microbiota into the immune system as well as explore the probiotics in the various human ailments. Comprehensive information on the human gut microbiome at the same platform may contribute effectively to our understanding of the human microbiome and possible mechanisms of associated human diseases.     

Progress of analytical tools and techniques for human gut microbiome research

Massive DNA sequencing studies have expanded our insights and understanding of the ecological and functional characteristics of the gut microbiome. Advanced sequencing technologies allow us to understand the close association of the gut microbiome with human health and critical illnesses. In the future, analyses of the gut microbiome will provide key information associating with human individual health, which will help provide personalized health care for diseases. Numerous molecular biological analysis tools have been rapidly developed and employed for the gut microbiome researches; however, methodological differences among researchers lead to inconsistent data, limiting extensive share of data. It is therefore very essential to standardize the current methodologies and establish appropriate pipelines for human gut microbiome research. Herein, we review the methods and procedures currently available for studying the human gut microbiome, including fecal sample collection, metagenomic DNA extraction, massive DNA sequencing, and data analyses with bioinformatics. We believe that this review will contribute to the progress of gut microbiome research in the clinical and practical aspects of human health.     

Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research

To date, most insights into the processes shaping vertebrate gut microbiomes have emerged from studies with cross‐sectional designs. While this approach has been valuable, emerging time series analyses on vertebrate gut microbiomes show that gut microbial composition can change rapidly from 1 day to the next, with consequences for host physical functioning, health, and fitness. Hence, the next frontier of microbiome research will require longitudinal perspectives. Here we argue that primatologists, with their traditional focus on tracking the lives of individual animals and familiarity with longitudinal fecal sampling, are well positioned to conduct research at the forefront of gut microbiome dynamics. We begin by reviewing some of the most important ecological processes governing microbiome change over time, and briefly summarizing statistical challenges and approaches to microbiome time series analysis. We then introduce five questions of general interest to microbiome science where we think field‐based primate studies are especially well positioned to fill major gaps: (a) Do early life events shape gut microbiome composition in adulthood? (b) Do shifting social landscapes cause gut microbial change? (c) Are gut microbiome phenotypes heritable across variable environments? (d) Does the gut microbiome show signs of host aging? And (e) do gut microbiome composition and dynamics predict host health and fitness? For all of these questions, we highlight areas where primatologists are uniquely positioned to make substantial contributions. We review preliminary evidence, discuss possible study designs, and suggest future directions.     

Are you what you eat? A highly transient and prey‐influenced gut microbiome in the grey house spider Badumna longinqua

Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet‐driven. This assumption is supported by a feeding experiment, in which two types of prey—crickets and fruit flies—both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket‐derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey‐associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.