宏基因组学在胃肠道微生物研究中的应用

动物胃肠道中普遍存在大量共生微生物群,对于它们的研究一直受制于纯培养技术。随着分子生物学的快速发展及其在微生物学及生态学上的应用,针对未培养微生物研究的一门新型学科——宏基因组技术应运而生并迅速发展。通过提取胃肠道粘膜表面以及内容物中微生物DNA,构建总DNA文库的方法,利用基因组学的研究策略,来研究胃肠道中微生物遗传组成及群落功能。宏基因组技术在胃肠道微生物研究中广泛的应用,对于医学、生态学、生物能源利用等领域的研究具有重大的价值。     

Microbiocenosis of parietal mucin in the gastrointestinal tract of rats

The qualitative and quantitative composition of the microbial community in parietal mucin at different areas of the gastrointestinal tract (GIT) of rats was revealed. The pronounced variability in the quantitative and qualitative characteristics of microbiocenosis in parietal mucin of rats at different sections was revealed. The differences were most pronounced in the passage from upper to lower GIT sections, the large intestine found to be the richest biocenosis. The microbial composition of rat feces was faintly associated with the GIT parietal microbiocenosis. The individual areas of GIT mucosa were unique of their microbial characteristics and organization. This makes it possible to regard them as relatively independent biotopes and indicates that it is impossible to evaluate the microbial community by one of the colonic mucosal sifes.     

A simulation of microbial competition in the human colonic ecosystem.

Many investigations of the interactions of microbial competitors in the gastrointestinal tract used continuous-flow anaerobic cultures. The simulation reported here was a deterministic 11-compartment model coded by using the C programming language and based on parameters from published in vitro studies and assumptions were data were unavailable. The resource compartments were glucose, lactose and sucrose, starch, sorbose, and serine. Six microbial competitors included indigenous nonpathogenic colonizers of the human gastrointestinal tract (Escherichia coli, Enterobacter aerogenes, Bacteroids ovatus, Fusobacterium varium, and Enterococcus faecalis) and the potential human enteropathogen Salmonella typhimurium. Flows of carbon from the resources to the microbes were modified by resource and space controls. Partitioning of resources to the competitors that could utilize them was calculated at each iteration on the basis of availability of all resources by feeding preference functions. Resources did not accumulate during iterations of the model. The results of the computer simulation of microbial competition model and for various modifications of the model. The results were based on few measured parameters but may be useful in the design of user-friendly software to aid researchers in defining and manipulating the microbial ecology of colonic ecosystems as relates to food-borne disease.     

Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function

During the past decade it became evident that anaerobic cultivation-based approaches provides an incomplete picture of the microbial diversity in the GI tract, since at present only a minority of microbes can be obtained in culture. The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the gastrointestinal (GI) tract. This critical review summarizes the impact of these culture-independent approaches on our knowledge of the ecology of the GI tract and provides directions for future studies which should emphasize function of specific strains, species and groups of microbes.     

Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases

The human gastrointestinal tract is home to immense and complex populations of microorganisms. Using recent technical innovations, the diversity present in this human body habitat is now being analyzed in detail. This review focuses on the microbial ecology of the gut in inflammatory bowel diseases and on how recent studies provide an impetus for using carefully designed, comparative metagenomic approaches to delve into the structure and activities of the gut microbial community and its interrelationship with the immune system.     

Epithelium-associated bacteria in the gastrointestinal tract of Arctic charr (Salvelinus alpinus L.). An electron microscopical study

AIMS: The primary aim was to use transmission electron microscopy (TEM) and scanning electron microscopy (SEM) to define the location of epithelium-associated bacteria in the digestive tract of the salmonid fish, Arctic charr (Salvelinus alpinus). METHODS AND RESULTS: TEM and SEM examination of the gastrointestinal tract demonstrated substantial numbers of ovoid and rod-shaped bacterial cells associated with the microvillous brush borders of enterocytes. Bacteria were found at the tips of microvilli as well as between adjacent microvilli. Endocytosis of bacteria by epithelial cells was observed in two regions (pyloric caeca and midgut). CONCLUSION: Electron microscope examination of the gut is an important tool for evaluating the microbial ecology of the fish digestive tract ecosystem. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of the current study clearly demonstrate that the intestine is involved in bacterial endocytosis.     

Leptin, Leptin Receptors and ACTH Immunoreactivities are Present in the Gastrointestinal Tract and the Neural Tube of Tadpoles of the Newt Triturus

Leptin, its receptor and ACTH were detected by immunohistochemistry in the gastrointestinal tract and the neural tube of the amphibian urodele, Triturus cristatus carnifex, during development. These molecules were found after hatching of tadpoles, starting from stage 41. In the gastrointestinal tract, cells immunoreactive to leptin and its receptor were first revealed in the stomach, the liver and the gut and then in the pancreas. Both immunoreactives were colocalized in the same cells in some areas. Immunostaining for ACTH appeared at stages 43/45 in the stomach, the gut and the pancreas. In adjacent sections, a few cells immunoreactive to both ACTH and leptin receptor were detected. A few cells were immunoreactive to both insulin and leptin receptor. Immunoreactivities to leptin and its receptor were also found in adjacent sections of the neural tube, often colocalized in the same cell. Moreover, in prosencephalon, mesencephalon, rhomboencephalon and spinal cord, ACTH-immunoreactive cells were detected in the same areas as the leptin receptor immunoreactive cells. These results suggest the existence of a neuroendocrine network in newt tadpoles both at the central level, where it resembles that of mammals, and at the peripheral level, where it may act locally to regulate food intake and metabolism, e.g. yolk digestion.     

胃肠道微生态系统及其功能研究

随着生物技术和生理科学研究的不断深入,人们对胃肠道微生物生态及其功能的研究取得了重大进步。对胃肠道微生物的多样性、不同生理时期微生物菌群的演化和特定微生物种属的研究有新的发现。胃肠道微生物生态系统的生理功能得到不断的揭示,成为许多学者和多个学科关注的焦点。     

Immunocytochemical detection of orexin A in endocrine cells of the developing mouse gut.

Orexins are novel neuropeptides that were originally localized in neurons of the hypothalamus and neuronal fibers of the brain. Recently orexin A and its receptor have also been reported in neurons and endocrine cells of the gastrointestinal tract. Because no studies have been done at the embryonic period, we studied the appearance and distribution of orexin A during the development of mouse gastrointestinal tract using immunocytochemical methods. Immunoreactivity to orexin A was detected in neuroendocrine cells of the pyloric region of the stomach at gestational Day 14 and 1 day after in the small intestine. The numbers of immunoreactive cells progressively increased through development until the adult pattern was reached. Staining of reverse-face sections demonstrated that orexin A and serotonin co-localized in some endocrine cells of the mouse stomach and small intestine. These findings suggest that orexin A may be relevant in the growth and maturation of the gastrointestinal tract during intrauterine life.     

The role of the epidermal growth factor receptor in microbial infections of the gastrointestinal tract

The epidermal growth factor receptor (EGFr) is a transmembrane glycoprotein with an intrinsic tyrosine kinase. Ligand-binding to the EGFr activates cell signaling, phosphorylates protein kinases, and rearranges cytoskeletal proteins - responses that resemble those induced by microbial attachment to cell surfaces, a process known to be mediated by host cell receptors in a number of cases. This article critically reviews the possible role played by the EGFr in microbial colonization, and discusses how modulation of the EGF-EGFr axis may affect infection of the gastrointestinal tract.     

Impact of Fishmeal Replacement in Diets for Gilthead Sea Bream (Sparus aurata) on the Gastrointestinal Microbiota Determined by Pyrosequencing the 16S rRNA Gene

Recent studies have demonstrated the impact of diet on microbiota composition, but the essential need for the optimization of production rates and costs forces farms and aquaculture production to carry out continuous dietary tests. In order to understand the effect of total fishmeal replacement by vegetable-based feed in the sea bream (Sparus aurata), the microbial composition of the stomach, foregut, midgut and hindgut was analysed using high-throughput 16S rDNA sequencing, also considering parameters of growth, survival and nutrient utilisation indices.A total of 91,539 16S rRNA filtered-sequences were analysed, with an average number of 3661.56 taxonomically assigned, high-quality sequences per sample. The dominant phyla throughout the whole gastrointestinal tract were Actinobacteria, Protebacteria and Firmicutes. A lower diversity in the stomach in comparison to the other intestinal sections was observed. The microbial composition of the Recirculating Aquaculture System was totally different to that of the sea bream gastrointestinal tract. Total fishmeal replacement had an important impact on microbial profiles but not on diversity. Streptococcus (p-value: 0.043) and Photobacterium (p-value: 0.025) were highly represented in fish fed with fishmeal and vegetable-meal diets, respectively. In the stomach samples with the vegetable diet, reads of chloroplasts and mitochondria from vegetable dietary ingredients were rather abundant. Principal Coordinate Analysis showed a clear differentiation between diets in the microbiota present in the gut, supporting the presence of specific bacterial consortia associated with the diet.Although differences in growth and nutritive parameters were not observed, a negative effect of the vegetable diet on the survival rate was determined. Further studies are required to shed more light on the relationship between the immune system and sea bream gastrointestinal tract microbiota and should consider the modulation of the microbiota to improve the survival rate and nutritive efficacy when using plant-based diets.     

Comparison of cellular fatty acid profiles of the microbiota in different gut regions of BALB/c and C57BL/6J mice

The gastrointestinal tracts of developed animals are colonized by an extremely complex and diverse microbial ecosystem. The host and its microbiota are in close interaction with each other, and the hosts genetic characteristics have been suggested to have an influence on the composition of fecal bacteria. However, different sections of gastrointestinal tract harbor microbes typical of each particular section and knowledge of the effect of the hosts genotype on the microbiota in the different parts of the gastrointestinal tract is limited. In this study, mice from two inbred strains, C57BL/6J and BALB/c, were raised in identical conditions. Bacterial samples were collected from four parts of the gastrointestinal tract and analyzed for bacterial fatty acids using gas-liquid chromatography (GLC). Significant differences between the microbiota in the feces, in the cecum, in the small bowel and in the stomach were observed. Cecal samples produced more diverse bacterial fatty acid profiles than any of the other samples, revealing a higher bacterial density and a higher number of bacterial species. Further, a significant difference between the two strains of mice was observed throughout the gastrointestinal tract. These findings indicate that the hosts genotype has an influence on the gastrointestinal microbiota as a whole, and provide further evidence that the cecum is the most species-rich region of the murine gut.     

宏基因组学在人和动物胃肠道微生物研究中的应用进展

人和动物胃肠道存在大量微生物群落,这些微生物是与宿主长期共同进化的结果,并且同宿主的健康和疾病密切相关,因此胃肠道微生物研究已成为当今的热点研究领域。宏基因组学技术在这一领域的应用,使我们不仅能够对胃肠道微生物群落结构及多样性进行分析,还能进一步深入了解其代谢功能,开发和利用潜在的微生物及其基因资源。文中结合我们的研究工作,综述了宏基因组学在人和动物胃肠道微生物研究中的应用,同时着重介绍宏基因组研究的生物信息学技术。     

Foodborne Salmonella ecology in the avian gastrointestinal tract

Foodborne Salmonella continues to be a major cause of salmonellosis with Salmonella Enteritidis and S. Typhimurium considered to be responsible for most of the infections. Investigation of outbreaks and sporadic cases has indicated that food vehicles such as poultry and poultry by-products including raw and uncooked eggs are among the most common sources of Salmonella infections. The dissemination and infection of the avian intestinal tract remain somewhat unclear. In vitro incubation of Salmonella with mammalian tissue culture cells has shown that invasion into epithelial cells is complex and involves several genetic loci and host factors. Several genes are required for the intestinal phase of Salmonella invasion and are located on Salmonella pathogenicity island 1 (SPI 1). Salmonella pathogenesis in the gastrointestinal (GI) tract and the effects of environmental stimuli on gene expression influence bacterial colonization and invasion. Furthermore, significant parameters of Salmonella including growth physiology, nutrient availability, pH, and energy status are considered contributing factors in the GI tract ecology. Approaches for limiting Salmonella colonization have been primarily based on the microbial ecology of the intestinal tract. In vitro studies have shown that the toxic effects of short chain fatty acids (SCFA) to some Enterobacteriaceae, including Salmonella, have resulted in a reduction in population. In addition, it has been established that native intestinal microorganisms such as Lactobacilli provide protective mechanisms against Salmonella in the ceca. A clear understanding of the key factors involved in Salmonella colonization in the avian GI tract has the potential to lead to better approach for more effective control of this foodborne pathogen.     

Experimental evaluation of the biological safety of gene-engineered bacteria using a model strain Bacillus subtilis interferon-producing strain

The in vitro and in vivo evaluation of the biological and ecological safety of genetically modified bacteria (GMB) was carried out on B. subtilis recombinant strain 2335/105, capable of producing human interferon alpha-2, used as experimental model. As shown in this investigation made with the use of bacteriological analysis and polymerase chain reaction, the oral administration of GMB to calves, chickens and white mice produced no disturbances in the microbial ecology of the gastrointestinal tract of warm-blooded animals and did not lead to the appearance of spontaneous transformants. The present work is the first experimental evaluation of the biological safety of genetically modified microorganisms, used as the component of Subalin, a probiotic preparation intended for use in veterinary practice.     

Diversity of the human gastrointestinal tract microbiota revisited

Since the early days of microbiology, more than a century ago, representatives of over 400 different microbial species have been isolated and fully characterized from human gastrointestinal samples. However, during the past decade molecular ecological studies based on ribosomal RNA (rRNA) sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. The increasing number of deposited rRNA sequences calls for the setting up a curated database that allows handling of the excessive degree of redundancy that threatens the usability of public databases. The integration of data from cultivation-based studies and molecular inventories of small subunit (SSU) rRNA diversity, presented here for the first time, provides a systematic framework of the microbial diversity in the human gastrointestinal tract of more than 1000 different species-level phylogenetic types (phylotypes). Such knowledge is essential for the design of high-throughput approaches such as phylogenetic DNA microarrays for the comprehensive analysis of gastrointestinal tract microbiota at multiple levels of taxonomic resolution. Development of such approaches is likely to be pivotal to generating novel insights in microbiota functionality in health and disease.     

Expression, localization and potential physiological significance of alcohol dehydrogenase in the gastrointestinal tract.

ADH1 and ADH4 are the major alcohol dehydrogenases (ADH) in ethanol and retinol oxidation. ADH activity and protein expression were investigated in rat gastrointestinal tissue homogenates by enzymatic and Western blot analyses. In addition, sections of adult rat gastrointestinal tract were examined by in situ hybridization and immunohistochemistry. ADH1 and ADH4 were detected along the whole tract, changing their localization and relative content as a function of the area studied. While ADH4 was more abundant in the upper (esophagus and stomach) and lower (colorectal) regions, ADH1 was predominant in the intestine but also present in stomach. Both enzymes were detected in mucosa but, in general, ADH4 was found in outer cell layers, lining the lumen, while ADH1 was detected in the inner cell layers. Of interest were the sharp discontinuities in the expression found in the pyloric region (ADH1) and the gastroduodenal junction (ADH4), reflecting functional changes. The precise localization of ADH in the gut reveals the cell types where active alcohol oxidation occurs during ethanol ingestion, providing a molecular basis for the gastrointestinal alcohol pathology. Localization of ADH, acting as retinol dehydrogenase/retinal reductase, also indicates sites of active retinoid metabolism in the gut, essential for mucosa function and vitamin A absorption.     

Regional features of sensitization of children to some noninfectious allergens

The results of epidemiological investigations within the frames of the ISAAC program are presented. Out of 2,870 children, 172 children (6.0%) with sensitization to some noninfectious (insect, pollen, medicinal) allergens were detected. The number of allergic children was found to be 10.4 +/- 1.8 to 28.2 +/- 3.0 per 1000 of urban child population. Specific features of the sensitization of urban children to regional insect, pollen and medicinal allergens were established. The clinical course of allergic diseases in children was characterized by polymorphism and a great variety of clinical symptoms with frequent lesions of the gastrointestinal tract and functional disturbances of the central nervous system, which adversely affected the school studies of children and the quality of their life. In the development of allergy in children such factors of risk as hereditary predisposition to allergy, allergic diathesis, focal infections and artificial feeding during the first year of life were also of great importance.     

小鼠胚胎胃肠道细菌基因组DNA提取方法比较

目的:筛选能均衡地提取小鼠胚胎胃肠道微生物区系各种细菌总DNA的方法.方法:分别采用反复冻融法、CTAB -SDS法、柱式基因组DNA提取试剂盒法提取小鼠胚胎胃肠道细菌基因组DNA,对其进行琼脂糖凝胶电泳、紫外分光光度计测定、PCR扩增等质量检测.结果:CTAB -SDS方法提取的基因组DNA纯度较高,OD260/OD280平均值最高,为1.845,电泳条带清晰,能满足下游的PCR扩增等分子操作.结论:确定CTAB -SDS方法为提取小鼠胚胎胃肠道细菌基因组DNA的最佳方法,为研究不同种动物胚胎的肠道菌群的结构和多样性奠定了基础.     

Investigation of the intestinal microbiota in preterm infants using different methods

Modifications in microbial colonization of the human gut are believed to affect intestinal homeostasis and increase the risk of gastrointestinal diseases. The present study examined different methods for investigating the dynamic characterization of the intestinal microbiota in preterm infants. Fecal samples were collected weekly from ten preterm infants during their stay in a neonatal intensive care unit. The infants had a mean gestational age of 29 weeks (range: 28–32 weeks) and a mean birth weight of 1233 g (range: 935–1450 g). Bacterial colonization was assessed using conventional culture techniques and molecular biological methods. More specifically, the recently developed denaturing high performance liquid chromatography (dHPLC) technique was compared to established methods such as temporal temperature gradient gel electrophoresis (TTGE) and rRNA gene library sequencing. Our results indicate that the gastrointestinal tract of preterm infants, born at a gestational age of less than 33 weeks, has a low biodiversity of mainly, culturable bacteria. Finally, dHPLC was evaluated in terms of speed, labor and sensitivity for its use as a tool to analyze microbial colonization in preterm infants. We found that this technique provided major improvements over gel-based fingerprinting methods, such as TTGE, that are commonly used for studying microbial ecology. As such, it may become a common analytical tool for this purpose.