社群环境下的短尾猴肠道微生物群落结构及适应进化

发布时间：2018-06-01 07:36

本文选题：短尾猴 + 肠道微生物　；参考：《安徽大学》2016年博士论文

【摘要】：动物的起源与进化是生命科学和生态科学共同关注的重要科学问题。微生物与动物间经过长期的相互作用而协同进化,他们对动物的适应与进化具有重要作用,不可忽视。长期以来,受绝大部分肠道微生物难以分离培养的技术限制和定量开展研究困难等因素的影响,肠道微生物在动物适应与进化中的作用机制长期被忽视。近年来,生物信息分析方法与高通量测序技术的结合,为肠道微生物定量研究提供了更加精确和快捷的方法与手段,这一长期被忽视的领域,正在成为科学界关注的焦点。从肠道微生物入手,与早期的栖息地、食性、营养、免疫、行为等领域开展的动物适应与进化研究结果交叉,有望进一步揭示动物健康维持与适应性进化的机制,发展动物生态科学研究的新领域。目前,大家普遍关心的问题是：哪些因素会影响寄主的肠道微生物多样性?大量的研究显示,内部和外部因素都会对寄主的肠道微生物多样性产生影响,例如寄主的遗传结构、饮食习惯、地理分布、环境温度等因子会对肠道微生物结构产生作用。除此以外,社会环境和社会交往也会对肠道微生物群落结构也具有重要影响,暗示肠道微生物对群体演化可能具有重要作用。但是,由于在社群背景下开展野生动物肠道微生物多样性的研究较少,有关社群对寄主肠道微生物群落结构的影响机制尚不清楚。非人灵长类动物(Non-human Primate)拥有复杂多样的社会行为和相对稳定的社会结构,是深入探究社群结构与肠道微生物群落关系的理想对象。本课题组近30年长期跟踪研究的、栖息在安徽黄山的、国家二级保护野生动物—短尾猴(Macaca thibetana)是研究上述问题的理想对象。本研究通过对其肠道微生物多样性和进化适应开展研究,探讨社群背景下,短尾猴肠道微生物群落结构形成的影响因素及其对寄主食物资源动态变化的响应,期望回答以下重要科学问题：(1)短尾猴肠道微生物群落有哪些微生物类群组成?(2)社群结构(性别、年龄、亲缘关系)是否会对短尾猴肠道微生物群落产生重要影响?(3)群体生活对短尾猴肠道微生物群落结构影响的路径是什么?(4)短尾猴肠道微生物对食物资源的动态变化是如何响应的?主要研究结果如下：一、发现短尾猴肠道微生物群落组成具有高度的植食性适应：主要表现为：(1)在门水平上,以分解利用植物的门类为优势种群。短尾猴的肠道微生物的优势门为厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes),两者占总肠道微生物的比例高达78%以上。已有大量的研究结果显示：肠道中的厚壁菌门和拟杆菌门有利于动物消化利用来源于植物的食物资源。(2)在科水平上,短尾猴的肠道微生物也表现出了对植食性的高度适应。短尾猴肠道微生物占优势的科为胃瘤菌科(Ruminococcaceae),普雷沃氏菌科(Prevotellaceae)和琥珀酸弧菌科(Succinivibrionaceae)。这些优势科在其它植食性哺乳动物的肠道中也表现出了较高的相对丰富度,有利于寄主分解利用来源于植物的复杂食物资源。(3)在属水平上,短尾猴肠道微生物群落组成再一次表明其对植食性的高度适应。短尾猴肠道中的优势属为普氏菌属(Prevotella)和琥珀酸弧菌属(Succinivibrio)。已有研究显示,具有胃瘤动物的肠道中琥珀酸弧菌属的物种表现出较高的相对丰富度,他们在可以通过分解代谢来自于植物纤维素中的多糖,帮助寄主生产乙酸和琥珀酸等营养物质、协助寄主代谢长链脂肪酸；而普氏菌属中的物种在分解利用来源于水果、谷类和嫩叶中的半纤维素、果胶、淀粉、碳水化合物和单糖具有重要作用。因此普氏菌属和琥珀酸菌属在短尾猴肠道中的大量分布表明：肠道微生物对短尾猴高效利用包括树叶、树根、树皮、植物果实、种子等食物具有重要作用。二、发现社群结构对短尾猴肠道微生物群落结构的影响较小。(1)短尾猴的肠道微生物组成和结构在性别间差异不显著。在门类水平上,不同性别间并未检测出显著的差异,在属类水平上,虽然检测出少量属在性别间存在显著不同,但这些属相对丰富度较低。除此之外,短尾猴性别间的Alpha多样性和Beta多样性也未产生显著的分化。(2)短尾猴的肠道微生物组成和结构在年龄组间差异不显著。在短尾猴的群体中,不同年龄组个体间的拟杆菌门和厚壁菌门并未表现出显著的差异,这与以往的研究有所不同。除此之外,也未在不同年龄组间产生差异。这些结果都表明,与年龄相关的肠道微生物菌群除了受到消化生理的影响外,可能还受到其他未知因素影响。(3)亲缘关系系数并未对短尾猴肠道微生物群落结构产生显著影响。在一些哺乳动物,不同物种间肠道的系统发育与物种的系统发育高度一致。然而,对于群体生活中的短尾猴个体,不同亲缘关系间并未表现出显著的不同,这与早期在冈贝国家公园黑猩猩群体内的研究结果一致。我们推测,群内个体间微生物的水平传播可能影响了亲缘关系个体间和非亲缘关系个体间肠道微生物群落的变异。三、“粪便-口腔-肠道”是影响短尾猴肠道微生物在群体内传播的潜在重要路径。(1)野生短尾猴的口腔和肠道微生物群落的Alpha多样性和Beta多样性均显著不同。该结果表明短尾猴口腔和肠道内含有两种不同类型的微生态系统；而且,短尾猴不同个体间口腔微生物群落的相似性显著高于不同个体间肠道微生物群落的相似性,暗示微生物栖息地的开放程度影响不同个体间特定栖息地微生物群落的相似性。(2)短尾猴口腔微生物群落与肠道微生物群落仍存在着紧密联系。短尾猴的口腔和肠道核心微生物共享普氏菌属(Prevotella)、密螺旋体属(Treponema)和拟普雷沃菌属(Alloprevotella),表明这三个属都可以在肠道和口腔微生态系统中建立自己稳定的种群,因此,短尾猴口腔中的这三种微生物类群对其在肠道中建立种群并长期维持可能具有重要的作用。另外,口腔和肠道共享的OTUs有413个,这些OTUs所对应的属占了肠道核心微生物的比例高达89%,该结果很好的支持了“粪便-口腔-肠道”传播路径假说。伴随着寄主进食行为的发生,这些存在于口腔中的肠道核心微生物极有可能迁移至肠道微生态系统,对肠道核心微生物的补充具有重要意义。四、短尾猴肠道微生物群落结构与功能对食物资源的动态变化具有积极响应。(1)短尾猴肠道微生物组成和结构对食物资源的季节波动具有明显的响应。短尾猴的肠道微生物多样性(Alpha多样性和Beta多样性)在春季和冬季存在显著差异。冬季样本中琥珀酸弧菌属(Succinivibrio)、梭菌属(Clostridium sensu stricto)显著增加,对提高猴子在冬季消化纤维素和半纤维素的食物资源有利。然而,在春季,普氏菌属(Prevotella)的含量显著增加,普氏菌属对水果、谷物和嫩叶中的果胶、碳水化合物和单糖具有更高的利用效率,有利于短尾猴从嫩叶中获取能量,快速恢复因冬季寒冷产生的能量损失。(2)短尾猴肠道微生物组的功能对食物资源的季节波动具有明显的响应。PICRUSt分析结果表明,在冬季样本中,多糖生物合成和代谢途径有关的功能基因显著增加,表明野生短尾猴冬季的肠道微生物组成模式,对于利用难以消化的食物具有更高的效率。在春季样本中,与碳水化合物代谢和能量代谢通路相关的功能基因显著增加,表明春季肠道微生物群落的变化可能有利于快速恢复在冬季损失的能量和营养。(3)冬季样品间的肠道微生物群落结构差异显著高于春季样品间的差异。相对于春季的样品,冬季样品间肠道群落结构差异表现出显著增高的现象,表明个体间肠道群落结构在冬季差异更大,而在春季相似性更高。对这一发现可能的解释是冬天个体间存在着更紧张的食物竞争关系(食物缺乏时期),导致个体间食物资源获取的差异。而春天可利用食物的增加,个体间的食物竞争减少,具有更相似的食物摄入模式。
[Abstract]:The origin and evolution of animals are important scientific issues of common concern in life science and ecological science. Microbes and animals have evolved cooperatively through long-term interactions. They have an important role in the adaptation and evolution of animals and can not be ignored. For a long time, the technical limitations and determination of most intestinal microbes are difficult to be separated and cultivated. The role of intestinal microorganism in animal adaptation and evolution has been neglected for a long time. In recent years, the combination of bioinformatics analysis and high throughput sequencing technology has provided a more accurate and quicker method and means for the quantitative study of intestinal microbes. It is the focus of the scientific community. Starting from the intestinal microorganism, the results of animal adaptation and evolution are intersecting with the early habitat, food, nutrition, immunity, behavior and other fields. It is expected to further reveal the mechanism of animal health maintenance and adaptive evolution, and develop new fields of ecological science research of animal and animal. At present, people are concerned about the new field of ecological science. The question is: what factors affect the host's intestinal microbial diversity? A large number of studies have shown that both internal and external factors have an impact on the host's intestinal microbial diversity, such as the host genetic structure, dietary habits, geographical distribution, environmental temperature and other factors that affect the intestinal microbial structure. The environmental and social interaction also has an important influence on the intestinal microbial community structure, suggesting that intestinal microorganism may play an important role in the population evolution. However, there are few studies on the diversity of intestinal microorganism in the wild animals in the community background, and the influence mechanism of community on the community structure of host intestinal microorganism is still available. It is not clear that Non-human Primate has complex and diverse social behavior and relatively stable social structure. It is an ideal object to explore the relationship between community structure and intestinal microbial community. This group has been tracked in the past 30 years, perched in Mount Huangshan, Anhui, and the national two level protected wild animal (Ma CACA thibetana) is an ideal object to study the above problems. By studying the microbial diversity and evolutionary adaptation of the intestinal tract, this study explores the factors affecting the formation of microorganism community structure in the intestinal tract and the response to the dynamic changes of the host food resources under the community background. The following important scientific questions are expected to be answered: (1) short. What are the microbial communities in the intestinal microflora? (2) does the community structure (sex, age, relationship) have an important effect on the intestinal microorganism community of the short tailing monkey? (3) what is the path of the influence of group life on the intestinal microorganism community structure of the short tailing monkey? (4) the dynamic changes in the food resources of the enteric microorganism of the short tailed monkey The main results are as follows: first, it is found that the microbial community composition of the intestinal tract is highly adaptable: (1) at the portal level, the dominant species of the plant are divided into the dominant species. The dominant gate of the intestinal microorganism of the short tailed monkey is Firmicutes and Bacteroid Etes), both of which account for more than 78% of the total intestinal microflora. A large number of studies have shown that the phylum and bacilli in the intestinal tract are beneficial to the animal's digestion and utilization of the food resources from plants. (2) at the level of the family, the intestinal microorganism of the short tailed monkey is also highly adaptable to the phytophagous. The dominant species of biology are Ruminococcaceae, Prevotellaceae and Succinivibrionaceae. These dominant families also exhibit high relative richness in the intestines of other herbivorous mammals, and are beneficial to host decomposition and utilization of complex food resources from plants. (3) At the level of the genus, the microbial community composition of the intestinal tract of the short tailed monkeys is once again shown to be highly adaptable to the phytum. The dominant genus in the intestinal tract of the short tailed monkey is Prevotella and Succinivibrio. They can help the host to produce acetic acid and succinic acid and other nutrients by catabolizing the polysaccharides from plant cellulose, helping the host to metabolize long chain fatty acids, while the species in the genus prantella are decomposed and used in fruit, cereal, and young leaves, with heavy weight, pectin, starch, carbohydrates, and monosaccharides. The large distribution of the genus pransella and succinic bacteria in the intestines of the short tailed monkeys shows that intestinal microbes have an important role in the efficient use of leaves, roots, bark, plant fruit and seeds. Two, it is found that the community structure has little effect on the intestinal microorganism community structure of the short tailed monkey. (1) the intestines of the short tailed monkey There were no significant differences in gender differences in the composition and structure of microbes. There was no significant difference between the sexes at the level of the class. At the level of the genus, there were significant differences in the sex between the sexes, but the Alpha diversity and Beta diversity among the sexes were also not. Significant differentiation was produced. (2) there was no significant difference in the composition and structure of intestinal microbes in the intestinal tract of the short tailed monkeys. In the group of short tailed monkeys, there was no significant difference between the phylum phylum and the thick wall bacteria in different age groups, which was different from the previous studies. The results show that the age related intestinal microflora may be affected by other unknown factors besides the effects of digestive physiology. (3) the relationship coefficient does not have a significant influence on the intestinal microbial community structure of the short tailed monkey. In some mammals, the phylogenetic development of the intestinal tract between different species and the systematic development of species in some mammals. However, there is no significant difference between different relationships in the group life of the short tailed monkeys, which is consistent with the early research results within the chimpanzee group of the genre National Park. We speculate that the horizontal transmission of microbes in the group may affect the relationship between individuals and unrelated relationships. The variation of intestinal microorganism community in interbody. Three, "stool oral gut" is a potential important path to affect the transmission of microorganism in the intestinal tract of the short tailed monkey. (1) the Alpha diversity and the Beta diversity of the oral and intestinal microbes of the wild short tailed monkeys are significantly different. The results show that there are two kinds of different species in the mouth and intestines of the short tailed monkey. The same type of microecological system; moreover, the similarity of oral microorganism community among the different individuals of the short tailed monkeys was significantly higher than that of the intestinal microflora of different individuals, suggesting that the degree of opening of the microbial habitat affects the similarity of the microbial community in the specific habitats of different individuals. (2) the oral microorganism community and the intestine of the short tailed monkey There are still close links in the microorganism community. The oral and intestinal core microbes of the short tailed monkeys share Prevotella, Treponema and Alloprevotella, indicating that these three genera can establish their own stable population in the intestinal and oral microecosystem and therefore, in the oral cavity of the monkeys. The three kinds of microbial groups may play an important role in the establishment of a population in the intestinal tract and long-term maintenance. In addition, there are 413 OTUs shared by the oral and intestinal tract, and the proportion of these OTUs's corresponding genera accounts for up to 89% of the core intestinal microbes. This result is a good support for the hypothesis of the "fecal oral gut" transmission path hypothesis. The occurrence of main eating behavior, these core microbes, which exist in the oral cavity, are very likely to migrate to the intestinal microecosystem, which is of great significance to the supplement of the intestinal microbes. Four, the microbial community structure and function of the intestinal tract of the short tailed monkey have a positive response to the dynamic changes of the food resources. (1) the microbial composition of the intestinal tract of the short tailed monkey The diversity of intestinal microflora (Alpha diversity and Beta diversity) was significantly different in spring and winter. In winter samples, the genus Vibrio succinate (Succinivibrio) and Clostridium (Clostridium sensu stricto) increased significantly to improve the monkey's digestive fiber in winter. Vitamin and hemicelluloses are favorable for food resources. However, in spring, the content of Prevotella is significantly increased. The genus pricellus has higher utilization efficiency for pectin, carbohydrates and monosaccharides in fruit, cereal and tender leaves, and is beneficial to the acquisition of energy from the young leaves and the rapid recovery of energy loss caused by cold winter. (2) the function of the intestinal microorganism group of the short tailed monkey intestinal microflora has an obvious response to the seasonal fluctuation of food resources. The results of.PICRUSt analysis show that in winter samples, the functional genes related to polysaccharide biosynthesis and metabolic pathways are significantly increased, indicating the intestinal microflora pattern of wild short tailed monkeys in winter, for the use of undigested food. In spring samples, the functional genes associated with carbohydrate metabolism and energy metabolism pathway increased significantly, indicating that the changes in the intestinal microbial community in the spring may be beneficial to the rapid recovery of energy and nutrition in winter loss. (3) the intestinal microbial community structure in winter samples was significantly higher than that in spring samples. The differences in the intestinal community structure in winter samples showed a significant increase compared to the spring samples, indicating that the inter individual intestinal community structure was more different in winter and more similar in spring. The difference in food resources among individuals is caused by the increase of food availability in spring, and the reduction of food competition among individuals, with a similar pattern of food intake.
【学位授予单位】：安徽大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q48;Q93

【参考文献】