本文選題：短尾猴 + 腸道微生物�。� 參考：《安徽大學(xué)》2016年博士論文

【摘要】：動(dòng)物的起源與進(jìn)化是生命科學(xué)和生態(tài)科學(xué)共同關(guān)注的重要科學(xué)問(wèn)題。微生物與動(dòng)物間經(jīng)過(guò)長(zhǎng)期的相互作用而協(xié)同進(jìn)化,他們對(duì)動(dòng)物的適應(yīng)與進(jìn)化具有重要作用,不可忽視。長(zhǎng)期以來(lái),受絕大部分腸道微生物難以分離培養(yǎng)的技術(shù)限制和定量開(kāi)展研究困難等因素的影響,腸道微生物在動(dòng)物適應(yīng)與進(jìn)化中的作用機(jī)制長(zhǎng)期被忽視。近年來(lái),生物信息分析方法與高通量測(cè)序技術(shù)的結(jié)合,為腸道微生物定量研究提供了更加精確和快捷的方法與手段,這一長(zhǎng)期被忽視的領(lǐng)域,正在成為科學(xué)界關(guān)注的焦點(diǎn)。從腸道微生物入手,與早期的棲息地、食性、營(yíng)養(yǎng)、免疫、行為等領(lǐng)域開(kāi)展的動(dòng)物適應(yīng)與進(jìn)化研究結(jié)果交叉,有望進(jìn)一步揭示動(dòng)物健康維持與適應(yīng)性進(jìn)化的機(jī)制,發(fā)展動(dòng)物生態(tài)科學(xué)研究的新領(lǐng)域。目前,大家普遍關(guān)心的問(wèn)題是：哪些因素會(huì)影響寄主的腸道微生物多樣性?大量的研究顯示,內(nèi)部和外部因素都會(huì)對(duì)寄主的腸道微生物多樣性產(chǎn)生影響,例如寄主的遺傳結(jié)構(gòu)、飲食習(xí)慣、地理分布、環(huán)境溫度等因子會(huì)對(duì)腸道微生物結(jié)構(gòu)產(chǎn)生作用。除此以外,社會(huì)環(huán)境和社會(huì)交往也會(huì)對(duì)腸道微生物群落結(jié)構(gòu)也具有重要影響,暗示腸道微生物對(duì)群體演化可能具有重要作用。但是,由于在社群背景下開(kāi)展野生動(dòng)物腸道微生物多樣性的研究較少,有關(guān)社群對(duì)寄主腸道微生物群落結(jié)構(gòu)的影響機(jī)制尚不清楚。非人靈長(zhǎng)類動(dòng)物(Non-human Primate)擁有復(fù)雜多樣的社會(huì)行為和相對(duì)穩(wěn)定的社會(huì)結(jié)構(gòu),是深入探究社群結(jié)構(gòu)與腸道微生物群落關(guān)系的理想對(duì)象。本課題組近30年長(zhǎng)期跟蹤研究的、棲息在安徽黃山的、國(guó)家二級(jí)保護(hù)野生動(dòng)物—短尾猴(Macaca thibetana)是研究上述問(wèn)題的理想對(duì)象。本研究通過(guò)對(duì)其腸道微生物多樣性和進(jìn)化適應(yīng)開(kāi)展研究,探討社群背景下,短尾猴腸道微生物群落結(jié)構(gòu)形成的影響因素及其對(duì)寄主食物資源動(dòng)態(tài)變化的響應(yīng),期望回答以下重要科學(xué)問(wèn)題：(1)短尾猴腸道微生物群落有哪些微生物類群組成?(2)社群結(jié)構(gòu)(性別、年齡、親緣關(guān)系)是否會(huì)對(duì)短尾猴腸道微生物群落產(chǎn)生重要影響?(3)群體生活對(duì)短尾猴腸道微生物群落結(jié)構(gòu)影響的路徑是什么?(4)短尾猴腸道微生物對(duì)食物資源的動(dòng)態(tài)變化是如何響應(yīng)的?主要研究結(jié)果如下：一、發(fā)現(xiàn)短尾猴腸道微生物群落組成具有高度的植食性適應(yīng)：主要表現(xiàn)為：(1)在門(mén)水平上,以分解利用植物的門(mén)類為優(yōu)勢(shì)種群。短尾猴的腸道微生物的優(yōu)勢(shì)門(mén)為厚壁菌門(mén)(Firmicutes)和擬桿菌門(mén)(Bacteroidetes),兩者占總腸道微生物的比例高達(dá)78%以上。已有大量的研究結(jié)果顯示：腸道中的厚壁菌門(mén)和擬桿菌門(mén)有利于動(dòng)物消化利用來(lái)源于植物的食物資源。(2)在科水平上,短尾猴的腸道微生物也表現(xiàn)出了對(duì)植食性的高度適應(yīng)。短尾猴腸道微生物占優(yōu)勢(shì)的科為胃瘤菌科(Ruminococcaceae),普雷沃氏菌科(Prevotellaceae)和琥珀酸弧菌科(Succinivibrionaceae)。這些優(yōu)勢(shì)科在其它植食性哺乳動(dòng)物的腸道中也表現(xiàn)出了較高的相對(duì)豐富度,有利于寄主分解利用來(lái)源于植物的復(fù)雜食物資源。(3)在屬水平上,短尾猴腸道微生物群落組成再一次表明其對(duì)植食性的高度適應(yīng)。短尾猴腸道中的優(yōu)勢(shì)屬為普氏菌屬(Prevotella)和琥珀酸弧菌屬(Succinivibrio)。已有研究顯示,具有胃瘤動(dòng)物的腸道中琥珀酸弧菌屬的物種表現(xiàn)出較高的相對(duì)豐富度,他們?cè)诳梢酝ㄟ^(guò)分解代謝來(lái)自于植物纖維素中的多糖,幫助寄主生產(chǎn)乙酸和琥珀酸等營(yíng)養(yǎng)物質(zhì)、協(xié)助寄主代謝長(zhǎng)鏈脂肪酸；而普氏菌屬中的物種在分解利用來(lái)源于水果、谷類和嫩葉中的半纖維素、果膠、淀粉、碳水化合物和單糖具有重要作用。因此普氏菌屬和琥珀酸菌屬在短尾猴腸道中的大量分布表明：腸道微生物對(duì)短尾猴高效利用包括樹(shù)葉、樹(shù)根、樹(shù)皮、植物果實(shí)、種子等食物具有重要作用。二、發(fā)現(xiàn)社群結(jié)構(gòu)對(duì)短尾猴腸道微生物群落結(jié)構(gòu)的影響較小。(1)短尾猴的腸道微生物組成和結(jié)構(gòu)在性別間差異不顯著。在門(mén)類水平上,不同性別間并未檢測(cè)出顯著的差異,在屬類水平上,雖然檢測(cè)出少量屬在性別間存在顯著不同,但這些屬相對(duì)豐富度較低。除此之外,短尾猴性別間的Alpha多樣性和Beta多樣性也未產(chǎn)生顯著的分化。(2)短尾猴的腸道微生物組成和結(jié)構(gòu)在年齡組間差異不顯著。在短尾猴的群體中,不同年齡組個(gè)體間的擬桿菌門(mén)和厚壁菌門(mén)并未表現(xiàn)出顯著的差異,這與以往的研究有所不同。除此之外,也未在不同年齡組間產(chǎn)生差異。這些結(jié)果都表明,與年齡相關(guān)的腸道微生物菌群除了受到消化生理的影響外,可能還受到其他未知因素影響。(3)親緣關(guān)系系數(shù)并未對(duì)短尾猴腸道微生物群落結(jié)構(gòu)產(chǎn)生顯著影響。在一些哺乳動(dòng)物,不同物種間腸道的系統(tǒng)發(fā)育與物種的系統(tǒng)發(fā)育高度一致。然而,對(duì)于群體生活中的短尾猴個(gè)體,不同親緣關(guān)系間并未表現(xiàn)出顯著的不同,這與早期在岡貝國(guó)家公園黑猩猩群體內(nèi)的研究結(jié)果一致。我們推測(cè),群內(nèi)個(gè)體間微生物的水平傳播可能影響了親緣關(guān)系個(gè)體間和非親緣關(guān)系個(gè)體間腸道微生物群落的變異。三、“糞便-口腔-腸道”是影響短尾猴腸道微生物在群體內(nèi)傳播的潛在重要路徑。(1)野生短尾猴的口腔和腸道微生物群落的Alpha多樣性和Beta多樣性均顯著不同。該結(jié)果表明短尾猴口腔和腸道內(nèi)含有兩種不同類型的微生態(tài)系統(tǒng)；而且,短尾猴不同個(gè)體間口腔微生物群落的相似性顯著高于不同個(gè)體間腸道微生物群落的相似性,暗示微生物棲息地的開(kāi)放程度影響不同個(gè)體間特定棲息地微生物群落的相似性。(2)短尾猴口腔微生物群落與腸道微生物群落仍存在著緊密聯(lián)系。短尾猴的口腔和腸道核心微生物共享普氏菌屬(Prevotella)、密螺旋體屬(Treponema)和擬普雷沃菌屬(Alloprevotella),表明這三個(gè)屬都可以在腸道和口腔微生態(tài)系統(tǒng)中建立自己穩(wěn)定的種群,因此,短尾猴口腔中的這三種微生物類群對(duì)其在腸道中建立種群并長(zhǎng)期維持可能具有重要的作用。另外,口腔和腸道共享的OTUs有413個(gè),這些OTUs所對(duì)應(yīng)的屬占了腸道核心微生物的比例高達(dá)89%,該結(jié)果很好的支持了“糞便-口腔-腸道”傳播路徑假說(shuō)。伴隨著寄主進(jìn)食行為的發(fā)生,這些存在于口腔中的腸道核心微生物極有可能遷移至腸道微生態(tài)系統(tǒng),對(duì)腸道核心微生物的補(bǔ)充具有重要意義。四、短尾猴腸道微生物群落結(jié)構(gòu)與功能對(duì)食物資源的動(dòng)態(tài)變化具有積極響應(yīng)。(1)短尾猴腸道微生物組成和結(jié)構(gòu)對(duì)食物資源的季節(jié)波動(dòng)具有明顯的響應(yīng)。短尾猴的腸道微生物多樣性(Alpha多樣性和Beta多樣性)在春季和冬季存在顯著差異。冬季樣本中琥珀酸弧菌屬(Succinivibrio)、梭菌屬(Clostridium sensu stricto)顯著增加,對(duì)提高猴子在冬季消化纖維素和半纖維素的食物資源有利。然而,在春季,普氏菌屬(Prevotella)的含量顯著增加,普氏菌屬對(duì)水果、谷物和嫩葉中的果膠、碳水化合物和單糖具有更高的利用效率,有利于短尾猴從嫩葉中獲取能量,快速恢復(fù)因冬季寒冷產(chǎn)生的能量損失。(2)短尾猴腸道微生物組的功能對(duì)食物資源的季節(jié)波動(dòng)具有明顯的響應(yīng)。PICRUSt分析結(jié)果表明,在冬季樣本中,多糖生物合成和代謝途徑有關(guān)的功能基因顯著增加,表明野生短尾猴冬季的腸道微生物組成模式,對(duì)于利用難以消化的食物具有更高的效率。在春季樣本中,與碳水化合物代謝和能量代謝通路相關(guān)的功能基因顯著增加,表明春季腸道微生物群落的變化可能有利于快速恢復(fù)在冬季損失的能量和營(yíng)養(yǎng)。(3)冬季樣品間的腸道微生物群落結(jié)構(gòu)差異顯著高于春季樣品間的差異。相對(duì)于春季的樣品,冬季樣品間腸道群落結(jié)構(gòu)差異表現(xiàn)出顯著增高的現(xiàn)象,表明個(gè)體間腸道群落結(jié)構(gòu)在冬季差異更大,而在春季相似性更高。對(duì)這一發(fā)現(xiàn)可能的解釋是冬天個(gè)體間存在著更緊張的食物競(jìng)爭(zhēng)關(guān)系(食物缺乏時(shí)期),導(dǎo)致個(gè)體間食物資源獲取的差異。而春天可利用食物的增加,個(gè)體間的食物競(jìng)爭(zhēng)減少,具有更相似的食物攝入模式。
[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.
【學(xué)位授予單位】：安徽大學(xué)
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2016
【分類號(hào)】：Q48;Q93

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