宏基因组技术在鸡肠道微生物中应用的研究进展

鸡肠道中生存着丰富的微生物,这些微生物在宿主的营养代谢与免疫方面有重要作用。高通量测序技术的发展为肠道微生物的研究提供了新的思路,文章简要介绍了宏基因组学,阐述肠道微生物结构变化对宿主的影响及不同饲养条件、宿主生理特征改变对肠道微生的影响,并重点从宏基因组的层面透析鸡肠道微生物菌落结构、营养代谢特征、免疫功能与鸡的健康生长之间的关联性,以期为鸡肠道微生物的研究提供思路。     

基于宏基因组学的野生动物肠道微生物研究进展

动物肠道中寄生着数以亿计的微生物,参与到动物机体中如代谢和免疫等重要的生理过程中。然而,在粪便等复杂样本中包含着大量微生物,无法通过纯培养技术进行研究,无法评估样本中的微生物多样性。通过宏基因组学技术可以对微生物群总DNA进行分析,使其成为目前研究复杂样本微生物结构和功能的重要工具。并且伴随高通量测序技术和生物信息学的进步,对微生物的分析流程也在不断地被改进。本文比较了在宏基因组学中普遍应用的标志基因扩增子分析和全宏基因组分析,对宏基因组技术在几类野生脊椎动物肠道微生物领域中的应用进行综述,以期使宏基因组技术在野生动物领域研究中拥有更加广泛的应用。     

宏基因组学在哺乳动物肠道微生物中的应用

哺乳动物的肠道内栖息着庞大复杂的微生物群体，其微生物群体与宿主的消化吸收、物质的营养代谢和免疫功能密切相关，是影响机体健康的重要因素之一。随着分子生物学技术在肠道微生物领域的应用，特别是新一代测序技术的快速发展，使得人们对复杂的肠道微生物的研究更加深入。基于宏基因组学技术不仅能够研究肠道微生物组的多样性、揭示消化道微生物对宿主生理代谢的影响，还能进一步深入挖掘新的功能基因，并揭示宿主基因与微生物组间的互作关系和共同进化。作者综述了宏基因组学技术在哺乳动物肠道微生物中的主要应用和存在的不足，并展望了其在肠道微生物研究中的广阔应用前景，从而加深人们对肠道微生物影响宿主肠道健康作用的认识。     

宏基因组学揭示瘤胃微生物多样性及功能

反刍动物瘤胃内栖息着庞大和复杂的微生物群体,这些微生物与宿主的消化吸收、营养代谢和免疫功能息息相关,宿主及其微生物共同组成了一个"超级生物体"。由于绝大部分瘤胃微生物不可培养,因此以厌氧培养为基础的传统研究方法存在明显的弊端。宏基因组学通过高通量的测序方法,能够全面展示微生物多样性,准确发现新的功能基因。此外,宏基因组学揭示了宿主基因和微生物组之间的互作关系。随着组学技术的不断发展,宏基因组学在瘤胃微生物组研究方面具有广阔的应用前景。     

宏基因组学及其应用前景

Metagenomics is the study of communities of microbial organisms directly in their natural environments, bypassing the need for isolation and laboratory cultivation of individual species and showing strong vitality in research of the metabolic pathway and exploring the resource of rumen microbiota. There are abundance of symbiotic microbiota in the gastrointestinal tract of animals, and they are deeply associated with the well-being of the host because of affecting normal physiology, metabolism and health, as well as the development of diseases. The application of metagenomics may solve many hot and difficult issues in the research of ruminant metabolism, especially camel metabolism. Therefore, this paper reviews the construction and selection procedures, especially introduced the Roche454 and Illumina high-throughput sequencing methods. Meanwhile, the application prospects of metagenomic in communities of microbial organisms are explored.     

雌性罗氏鼢鼠肠道微生物群落与功能预测的初步分析

罗氏鼢鼠(Myospalax rothschildi)是陕西南部农区主要害鼠,研究其与当地环境的相互作用对鼠害防控有重要意义。肠道微生物对宿主行为及生理的调控机制是近年来啮齿类动物防控研究新方向。本研究通过Illumina高通量测序技术,对雌性罗氏鼢鼠的盲肠样品进行16S rRNA V3-V4区的高通量测序,分析性别及食物因素对罗氏鼢鼠肠道细菌多样性的影响。结果显示,雌性罗氏鼢鼠的肠道内容物中的细菌隶属10门9纲11目13属。肠道革兰氏阳性厚壁菌门(Firmicutes)和革兰氏阴性菌类的变形菌门(Proteobacteria)的菌种含量较多;埃希氏杆菌属(Escherichia)、瘤胃球菌属(Ruminococcus)、梭杆菌属(Clostridium)和颤螺旋菌属(Oscillospira)为优势菌群属。PICRUSt预测发现,罗氏鼢鼠的肠道微生物参与草本中药材食物在宿主体内的代谢。本研究首次借助生物信息学技术初步分析了罗氏鼢鼠肠道细菌的多样性及其与环境和遗传因素的相互作用,对当地鼠害防控具有一定的理论指导意义。     

益生菌对水产动物的作用研究进展

当宿主动物摄入适量活的微生物时,自身的免疫力得到提高,这类活的微生物即为益生菌.研究表明,益生菌能够改变宿主肠道内的微生物群体,进而大大降低病原菌占据肠道的机会;在动物体内产生消化酶,有助于加强宿主体内的营养代谢;刺激宿主自身免疫系统,改善水体环境,增强宿主的抗病性.益生菌的研究为水产养殖业朝着绿色健康养殖的方向发展提供了理论依据,是水产养殖病害防治的一个的新的方向,具有较好的发展前景.论文就益生菌的概念、免疫作用、定植机制等方面做一简述.     

Mutual interaction between gut microbiota and protein/amino acid metabolism for host mucosal immunity and health

In recent years, many studies have shown that the intestinal microflora has various effects that are linked to the critical physiological functions and pathological systems of the host. The intestinal microbial community is widely involved in the metabolism of food components such as protein, which is one of the essential nutrients in diets. Additionally, dietary protein/amino acids have been shown to have had a profound impact on profile and operation of gut microbiota. This review summarizes the current literature on the mutual interaction between intestinal microbiota and protein/amino acid metabolism for host mucosal immunity and health.     

水禽肠道微生物及其研究进展

动物的肠道内有复杂而动态的微生物生态系统,这些微生物通过促进营养摄取、宿主防御、免疫调节等,在维持机体健康方面起着至关重要的作用。菌落的结构组成因母体、饲粮、环境、生理状态变化及自身菌种间互作等因素而不同。水禽(鸭和鹅)属于卵生动物,与哺乳动物相比,其肠道的微生物系统具有特殊性。作者介绍了水禽肠道微生物的建立、肠段不同部位的微生物群结构组成特征及发育性变化,从肠道微生物对水禽生长性能、养分消化吸收的影响,以及与免疫系统的关系3个方面阐述了水禽肠道微生物的主要功能,同时通过饲粮组成、动物体生理状态、外界环境因素、微生物自身因素及互作等4个方面分析了影响水禽肠道微生物的多重因素,并对水禽肠道微生物今后的研究思路及发展方向进行了展望,以期为养殖中饲料配方设计、改善肠道健康、提高生产效益等提供理论依据,从而为从肠道微生物这一崭新靶点精准调控水禽的营养、免疫和生长过程,以及水禽肠道微生物的进一步深入研究提供借鉴。     

短链脂肪酸介导的肠上皮和抗炎调节研究进展

哺乳动物体中的肠道菌群是细菌生态系统的组成部分,从动物出生时起,这些微生物就对免疫系统的发育、功能和调节起着非常重要的作用。当前,越来越多的研究集中在微生物对宿主细胞代谢的影响上。短链脂肪酸(SCFA)作为肠道菌群的一种代谢产物,对肠道稳态的维持具有重要作用。SCFA是肠道上皮细胞的重要燃料,能增强肠屏障功能。作为信号分子,SCFA可以通过细胞表面G蛋白偶联受体(GPCR)发出信号,从而激活控制免疫功能的信号级联反应;还可以通过底物转运蛋白进入细胞,抑制组蛋白脱乙酰化酶(HDAC),最终达到降低肠道炎症反应。本文综述了微生物SCFA的产生及其对肠道黏膜的影响,并通过激活细胞表面GPCR以及抑制组蛋白去乙酰化酶(HDACs)来调节免疫反应的作用。     

日粮纤维对猪肠道微生物影响的研究进展

肠道微生物不仅为宿主提供营养物质,也有利于维持肠道微生态的平衡,对保证肠道的健康发育至关重要。日粮纤维是肠道微生物发酵的底物之一,能够改善肠道微生物菌群结构。本文从日粮纤维对猪肠道微生物的功效及影响猪肠道微生物利用日粮纤维的因素展开综述,为日粮纤维在生猪生产实践及研究提供一定理论依据。     

培养组学在动物肠道微生物应用的研究进展

肠道微生物被称为动物的“隐藏免疫器官”,不仅能参与宿主代谢还能影响宿主的免疫系统,对维持机体健康至关重要。作者主要介绍了培养组学的发展历程及其对动物肠道微生物研究的重要意义、传统微生物培养方法和分子生物学方法在研究微生物时各自的优、缺点。培养组学是基于传统微生物培养方法同时采用多种培养条件进行微生物培养,再辅以基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)和16S rRNA基因测序技术建立的一种新型微生物分离、鉴定方法,该方法将传统微生物培养技术与分子生物学技术的优点融为一体。该方法在挖掘“新微生物”的研究中,具有发现、找到并获得的优势;在微生物的研究中可定制分离目标菌株进行验证,并能通过丰富注释清楚地了解肠道微生物组。此外,分析了培养组学分别在家禽肠道、猪肠道、反刍动物肠道等动物肠道的研究应用现状,提出了环境条件对肠道微生物的影响,如人类接触对肠道菌群的影响、同物种不同性别肠道菌群的差异,以期为培养组学在动物肠道微生物的研究运用中提供参考。     

Coccidia-induced mucogenesis promotes the onset of necrotic enteritis by supporting Clostridium perfringens growth

This study tested the hypothesis that a host mucogenic response to an intestinal coccidial infection promotes the onset of necrotic enteritis (NE). A chick NE model was used in which birds were inoculated with Eimeria acervulina and E. maxima and subsequently with Clostridium perfringens (EAM/CP). A second group of EAM/CP-infected birds was treated with the ionophore narasin (NAR/EAM/CP). These groups were compared to birds that were either non-infected (NIF), or infected only with E. acervulina and E. maxima (EAM), or C. perfringens (CP). The impact of intestinal coccidial infection and anti-coccidial treatment on host immune responses and microbial community structure were evaluated with histochemical-, cultivation- and molecular-based techniques. Barrier function was compromised in EAM/CP-infected birds as indicated by elevated CFUs for anaerobic bacteria and C. perfringens in the spleen when compared to NIF controls at day 20, with a subsequent increase in intestinal NE lesions and mortality at day 22. These results correlate positively with a host inflammatory response as evidenced by increased ileal interleukin (IL)-4, IL-10 and IFN-gamma RNA expression. Concurrent increases in chicken intestinal mucin RNA expression, and goblet cell number and theca size indicate that EAM/CP induced an intestinal mucogenic response. Correspondingly, the growth of mucolytic bacteria and C. perfringens as well as alpha toxin production was greatest in EAM/CP-infected birds. The ionophore narasin, which directly eliminates coccidia, reduced goblet cell theca size, IL-10 and IFN-gamma expression, the growth of mucolytic bacteria including C. perfringens, coccidial and NE lesions and mortality in birds that were co-infected with coccidia and C. perfringens. Collectively the data support the hypothesis that coccidial infection induces a host mucogenic response providing a growth advantage to C. perfringens, the causative agent of NE.     

胃肠道褪黑素的合成及其对消化道微生物群体影响的研究进展

胃肠道褪黑素主要是由肠嗜铬细胞分泌,具有一定昼夜节律性。褪黑素通过调控细胞因子或NF-κB等调控肠道微生物及其代谢,进而影响动物肠道微生物群体结构以及某些细菌的昼夜节律。本文主要对近几年胃肠道褪黑素的合成分泌及其生理功能、肠道微生物节律性以及褪黑素对肠道微生物的调控作用等研究进行综述,以期为胃肠道褪黑素与菌群之间调控关系的研究提供一定参考。     

产丁酸菌的产酸机制及其在调控肠道健康中的作用研究进展

复杂和多样化的肠道微生物群落对宿主健康发挥着重要作用。产丁酸菌代表了宿主肠道微生态一个重要的功能性群体,多数为革兰阳性厌氧菌。人们发现,该类菌和微生物失调引发的消化道炎症等现象息息相关,因此产丁酸菌成为行业研究热点。产丁酸菌能够利用食物(饲料)中不易消化的碳水化合物合成丁酸,通过调控肠道菌群结构、为肠道上皮细胞供能、增强肠黏膜屏障功能等维护肠道健康,发挥对宿主健康的有益作用。本文从产丁酸菌的生物学分类、消化道产酸机制、肠道炎症调控作用及应用进展等方面做了系统综述,旨在阐明产丁酸菌与宿主健康的互作机制,并提出产丁酸菌的未来发展方向。     

营养因素对肉鸡肠道黏膜免疫的影响

根据肠道黏膜免疫的重要性,结合肉鸡肠道结构特点,阐述日粮中的主要营养因素对肉鸡肠道黏膜免疫的影响,并展开讨论。     

Insights into host-microbe interaction:What can we do for the swine industry?

Recent discoveries have underscored the cross-talk between intestinal microbes and their hosts. Notably, intestinal microbiota impacts the development, physiological function and social behavior of hosts. This influence usually revolves around the microbiota-gut-brain axis (MGBA). In this review, we firstly outline the impacts of the host on colonization of intestinal microorganisms, and then highlight the influence of intestinal microbiota on hosts focusing on short-chain fatty acid (SCFA) and tryptophan metabolite-mediated MGBA. We also discuss the intervention of intestinal microbial metabolism by dietary supplements, which may provide new strategies for improving the welfare and production of pigs. Overall, we summarize a state-of-the-art theory that gut microbiome affects brain functions via metabolites from dietary macronutrients.     

哺乳仔猪断奶前后肠道微生物培养组学研究

近年来国内外研究人员通过下一代测序和分离培养技术,结合宏基因组学相关的生物信息学手段证实了猪肠道微生物的组成及其代谢物活性对宿主的健康具有重要作用.受限于传统培养方法,猪肠道中大多数细菌仍无法培养,因此,为了突破研究人员研究宿主-菌株相互关系及益生菌株开发应用的限制,本研究对仔猪断奶前后回肠和结肠内容物微生物进行高通量...     

以16S rRNA为基础的检测技术在肠道菌群研究中的应用

肠道微生态菌群是一个非常复杂的微生态系统。胃肠菌群对于宿主的健康和生产成绩非常重要。依赖于以细菌分离培养为主的传统分析方法已经远远不能适应深入研究的需要。近些年围绕16S rRNA发展起来的分子方法在肠道微生态菌群研究中的应用越来越广,本文将就这些方法的应用情况作一简述。     

Mechanistic insight into the gut microbiome and its interaction with host immunity and inflammation

The intestinal tract is a host to 100 trillion of microbes that have co-evolved with mammals over the millennia. These commensal organisms are critical to the host survival. The roles that symbiotic microorganisms play in the digestion, absorption, and metabolism of nutrients have been clearly demonstrated. Additionally, commensals are indispensable in regulating host immunity. This is evidenced by the poorly developed gut immune system of germ-free mice, which can be corrected by transplantation of specific commensal bacteria. Recent advances in our understanding of the mechanism of host–microbial interaction have provided the basis for this interaction. This paper reviews some of these key studies, with a specific focus on the effect of the microbiome on the immune organ development, nonspecific immunity, specific immunity, and inflammation.