肠道菌群在中药代谢中的作用

近年来,中药在疾病防治方面所发挥的巨大作用受到了广泛认可。科学合理地解释中药的作用机制将有助于提高其利用价值。越来越多的证据表明肠道菌群在中药治疗中起着至关重要的作用,是打开我国中医药宝库的一把钥匙。肠道菌群在中药成分代谢过程中发挥着复杂的作用：一方面,人类肠道菌群通过编码多种活性酶,促进了中药组分中的非碳水化合物小分子与碳水化合物在肠道中的代谢过程;另一方面,经肠道菌群代谢转化后产生的中药产物具有多种药理作用。因此,在未来中药研究中应更多地考虑肠道微生态因素,这有助于为中药的药理作用机制研究奠定新的科学基础。     

早期灌喂母源粪菌对新生仔猪肠道菌群发育的影响

【目的】粪菌移植(fecal microbiota transplantation,FMT)作为一种治疗手段,已在人类肠道疾病治疗中有较多应用,但在干预新生仔猪肠道菌群上的研究未见报道。本文旨在研究早期母源粪菌移植对新生仔猪肠道菌群发育的影响。【方法】选取一窝12头杜长大新生仔猪,随机分为粪菌处理组(feces treatment,FT)和对照组(control,CO)。FT组仔猪出生后1–5 d每日灌注母源粪菌接种液,CO组灌注等量生理盐水。于1、3、5、7、10、14、18和22日龄采集仔猪粪样,Miseq高通量测序分析仔猪粪便菌群。【结果】灌喂母源粪菌有增加仔猪肠道菌群丰富度的趋势;主坐标分析显示,两组仔猪粪样菌群结构簇并未分开,并在18和22日龄时靠近母猪粪样菌群结构簇;随日龄增加,两组仔猪肠道中的变形菌门丰度均显著降低,而厚壁菌门的丰度显著增加,且从10日龄起拟杆菌门和厚壁菌门之和约为90%;与对照组相比,灌喂母源粪菌增加了10日龄时Escherichia-Shigella的丰度,而降低了18日龄时该菌属的丰富度,18日龄时肠球菌属和普氏菌属的丰度则显著增加。【结论】1–3日龄口服灌喂母源粪菌液并不能影响仔猪肠道菌群的定殖,这一阶段主要受母体微生物结构的影响;灌喂粪菌液对仔猪肠道菌群定殖的影响最多持续10–14 d;而且仔猪在22 d左右,肠道菌群结构逐渐趋同于母猪肠道菌群。     

Establishment and development of intestinal microbiota in preterm neonates

Microbial colonization of the infant gut is essential for the development of the intestine and the immune system. The profile of intestinal microbiota in the full-term, vaginally delivered, breast-fed infant is considered as ideally healthy. However, in preterm infants this process is challenging, mainly because of organ immaturity, antibiotics use, and hospital stay. To assist in a proper microbiota development in these infants, a detailed knowledge of the colonization process, and the differences from that of full-term breast-fed infants, is needed. We assessed the establishment of the gut microbiota and its metabolic activity in preterm neonates (n?=?21) during the first 3?months of life and compared it with that of vaginally delivered, exclusively breast-fed full-term infants (n?=?20) using qualitative and quantitative culture-independent methods. Differences in the gut microbiota composition between both groups were observed. Preterm infants showed higher levels of facultative anaerobic microorganisms and reduced levels of strict anaerobes such as Bifidobacterium, Bacteroides, and Atopobium. Short-chain fatty acids concentrations were lower in preterm infants during the first days of life. Alterations occur in the process of microbiota establishment in preterm infants, indicating the need for intervention strategies to counteract them.     

Biphasic assembly of the murine intestinal microbiota during early development

The birth canal provides mammals with a primary maternal inoculum, which develops into distinctive body site-specific microbial communities post-natally. We characterized the distal gut microbiota from birth to weaning in mice. One-day-old mice had colonic microbiota that resembled maternal vaginal communities, but at days 3 and 9 of age there was a substantial loss of intestinal bacterial diversity and dominance of Lactobacillus. By weaning (21 days), diverse intestinal bacteria had established, including strict anaerobes. Our results are consistent with vertical transmission of maternal microbiota and demonstrate a nonlinear ecological succession involving an early drop in bacterial diversity and shift in dominance from Streptococcus to Lactobacillus, followed by an increase in diversity of anaerobes, after the introduction of solid food. Mammalian newborns are born highly susceptible to colonization, and lactation may control microbiome assembly during early development.     

Use of stable isotopes to measure the metabolic activity of the human intestinal microbiota

The human intestinal microbiota is a complex biological system comprising a vast repertoire of microbes with considerable metabolic activity relevant to both bacterial growth and host health. Greater strides have been made in the analysis of microbial diversity than in the measurement of functional activity, particularly in vivo. Stable isotope probing offers a new approach by coupling measurements of metabolic activity with microbial identification. Using a low-enrichment labeling strategy in vitro, this study has identified metabolically active bacterial groups via magnetic-bead capture methodology and stable isotope ratio analysis. Using five probes (EUB338, Bac303, Bif164, EREC482, and Clep866), changes in the activities of key intestinal microbial groups were successfully measured by exploiting tracers of de novo RNA synthesis. Perturbation of the nutrient source with oligofructose generated changes in the activity of bifidobacteria as expected, but also in the Bacteroides-Prevotella group, the Eubacterium rectale-Clostridium coccoides group, and the Clostridium leptum subgroup. Changes in activity were also observed in response to the medium type. This study suggests that changes in the functional activity of the gut microbiota can be assessed using tracers of de novo nucleic acid synthesis combined with measurement of low isotopic enrichment in 16S rRNA. Such tracers potentially limit substrate bias because they are universally available to bacteria. This low-enrichment labeling approach does not depend on the commercial availability of specific labeled substrates and can be easily translated to in vivo probing experiments of the functional activity of the microbiota in the human gut.     

Amino acid supplements and metabolic health: a potential interplay between intestinal microbiota and systems control

Dietary supplementation of essential amino acids (EAAs) has been shown to promote healthspan. EAAs regulate, in fact, glucose and lipid metabolism and energy balance, increase mitochondrial biogenesis, and maintain immune homeostasis. Basic science and epidemiological results indicate that dietary macronutrient composition affects healthspan through multiple and integrated mechanisms, and their effects are closely related to the metabolic status to which they act. In particular, EAA supplementation can trigger different and even opposite effects depending on the catabolic and anabolic states of the organisms. Among others, gut-associated microbial communities (referred to as gut microbiota) emerged as a major regulator of the host metabolism. Diet and host health influence gut microbiota, and composition of gut microbiota, in turn, controls many aspects of host health, including nutrient metabolism, resistance to infection, and immune signals. Altered communication between the innate immune system and the gut microbiota might contribute to complex diseases. Furthermore, gut microbiota and its impact to host health change largely during different life phases such as lactation, weaning, and aging. Here we will review the accumulating body of knowledge on the impact of dietary EAA supplementation on the host metabolic health and healthspan from a holistic perspective. Moreover, we will focus on the current efforts to establish causal relationships among dietary EAAs, gut microbiota, and health during human development.     

Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates

To gain insights into the adaptation of the Escherichia coli species to different environments, we monitored protein abundances using quantitative proteomics and measurements of enzymatic activities of central metabolism in a set of five representative strains grown in four contrasted culture media including human urine. Two hundred and thirty seven proteins representative of the genome‐scale metabolic network were identified and classified into pathway categories. We found that nutrient resources shape the general orientation of metabolism through coordinated changes in the average abundances of proteins and in enzymatic activities that all belong to the same pathway category. For example, each culture medium induces a specific oxidative response whatever the strain. On the contrary, differences between strains concern isolated proteins and enzymes within pathway categories in single environments. Our study confirms the predominance of genotype by environment interactions at the proteomic and enzyme activity levels. The buffering of genetic variation when considering life‐history traits suggests a multiplicity of evolutionary strategies. For instance, the uropathogenic isolate CFT073 shows a deregulation of iron demand and increased oxidative stress response.     

Human intestinal microbiota: Role in development and functioning of the nervous system

Recent results related to investigation of the role of intestinal microbiota (IM) in development and functioning of the human nervous system are discussed. The role of the microbiota in bidirectional communication between the gastrointestinal tract and the central nervous system is considered. Special attention is paid to the primary IM of infants, which is actively involved in formation of immune and other physiological mechanisms, including the nervous system, and is responsible for the subsequent general and psychical health of a human. The results of research on ability of the commensal intestinal microflora to produce neuroactive compounds, including neurotransmitters, short- and long-chain fatty acids, γ-aminobutyric acid, etc., are summarized. These compounds may have a considerable effect on development and functioning of the central nervous system, including the brain. Research on various animal models is discussed, including investigation of IM effect on behavior, learning abilities and memory, anxiety and depression levels, reaction to emotional stimuli, and stress resistance. A special section deals with probiotic bacteria, which are presently considered as psychobiotics with preventive and therapeutic potential for treatment of neurological and neurophysiological disorders. Development of new paradigms and concepts, rejection of some classical concepts of neurobiology is presently the key condition for the future breakthrough in investigation of human nervous activity.     

Preservation by lyophilization of a human intestinal microbiota: influence of the cultivation pH on the drying outcome and re-establishment ability

Faecal microbiota transplantation is an emerging medical concept for the treatment of gastrointestinal diseases. This concept, however, has disadvantages as low storability of stool and intensive donor screening. A solution to overcome these problems would be the preservation of an in vitro microbiota through freeze–drying. However, the influence of the entire preservation process, including cultivation and lyophilization, has not been assessed so far. In this study, the influences of the process steps cultivation, drying and re-cultivation were determined with cell count, production of metabolites, microbial composition and diversity in the system as evaluation criteria. All pH conditions resulted in stable, culturable communities after re-cultivation. Cell count, richness, diversity and microbial composition were affected by freeze–drying, but these effects were reversible and vanished during re-cultivation. Hence, the re-cultivated system did not differ from the system before drying. The metabolism, measured by short-chain fatty acids as indicators, showed slight changes due to natural dynamics. Consequently, the cultivation prior to drying was identified to have more influence than the drying itself on the preservation process and therefore the biggest potential for optimization. Hence, the highest similarity with the initial stool sample was obtained with pH 6.0 - 6.5 during cultivation.     

Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears

The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C.?perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.     

An inhibitor of the stretch-activated cation receptor exerts a potent effect on chondrocyte phenotype

Rat chondrosarcoma (RCS) cells are unusual in that they display a stable chondrocyte phenotype in monolayer culture. This phenotype is reflected by a rounded cellular morphology with few actin-containing stress fibers and production of an extracellular matrix rich in sulfated proteoglycans, with high-level expression of aggrecan, COMP, Sox9, and collagens type II, IX, and XI. Additionally, these cells do not express collagen type I. Here it is shown that in the absence of any mechanical stimulation, treatment of RCS cells with gadolinium chloride (Gd3+), a stretch-activated cation channel blocker, caused the cells to undergo de-differentiation, adopting a flattened fibroblast phenotype with the marked appearance of actin stress fibers and vinculin-containing focal contacts. This change was accompanied by a dramatic reduction in the expression of aggrecan, Sox9, collagen types II, IX, and XI, with a corresponding increase in the expression of collagen type I and fibronectin. These effects were found to be reversible by simple removal of Gd3+ from the medium. Gd3+ also had a similar effect on expression of chondrocyte marker genes in freshly isolated human chondrocytes. These data suggest that mechanoreceptor signaling plays a key role in maintenance of the chondrocyte phenotype, even in the absence of mechanical stimulation. Further, treatment of RCS cells with Gd3+ provides a tractable system for assessing the molecular events underlying the reversible differentiation of chondrocytes.     

肠道菌群在肿瘤发生发展及免疫治疗中作用的研究进展北大核心CSCD

肠道菌群是一个与人体共生的复杂微生物区系,近年来被越来越多的研究者所关注。研究发现,肠道菌群不仅在维持人体正常生理功能中起到重要作用,在肿瘤发生、发展、诊断及治疗中也有不可忽视的作用。本文在对肠道菌群与肿瘤关系进行概述的基础上,重点介绍了肠道菌群促进肿瘤发生、发展的主要机制,以及肠道菌群对抗肿瘤免疫治疗尤其是免疫检查点抑制疗法的影响。此外,文中还总结了目前可行的调节肠道菌群以提高肿瘤治疗疗效的方法,并提出了其中可能存在的困难和挑战。     

饮酒对肠道微生态的影响研究

肠道微生态是肠道菌群和宿主相互作用共同构成的一个整体,与宿主的生长发育、物质代谢和衰老等有密切的关系。已报道的饮酒保健功能,多从药理学的角度评价,具有抗氧化、清除活性氧自由基、抗肿瘤、阻断致癌物的形成和抑制机体内的代谢转化、提高机体的免疫力、抗菌、抗病毒等功能。但缺乏饮酒与肠道微生态关系的研究,本综述主要论述饮酒与肠道微生态之间的关系。     

Characterizing the metabolic phenotype: a phenotype phase plane analysis.

Genome-scale metabolic maps can be reconstructed from annotated genome sequence data, biochemical literature, bioinformatic analysis, and strain-specific information. Flux-balance analysis has been useful for qualitative and quantitative analysis of metabolic reconstructions. In the past, FBA has typically been performed in one growth condition at a time, thus giving a limited view of the metabolic capabilities of a metabolic network. We have broadened the use of FBA to map the optimal metabolic flux distribution onto a single plane, which is defined by the availability of two key substrates. A finite number of qualitatively distinct patterns of metabolic pathway utilization were identified in this plane, dividing it into discrete phases. The characteristics of these distinct phases are interpreted using ratios of shadow prices in the form of isoclines. The isoclines can be used to classify the state of the metabolic network. This methodology gives rise to a "phase plane" analysis of the metabolic genotype-phenotype relation relevant for a range of growth conditions. Phenotype phase planes (PhPPs) were generated for Escherichia coli growth on two carbon sources (acetate and glucose) at all levels of oxygenation, and the resulting optimal metabolic phenotypes were studied. Supplementary information can be downloaded from our website (http://epicurus.che.udel.edu).     

Assembly of the human intestinal microbiota

Complex microbial ecosystems occupy the skin, mucosa and alimentary tract of all mammals, including humans. Recent advances have highlighted the tremendous diversity of these microbial communities and their importance to host physiology, but questions remain about the ecological processes that establish and maintain the microbiota throughout life. The prevailing view, that the gastrointestinal microbiota of adult humans is a climax community comprised of the superior competitors for a stable set of niches, does not account for all of the experimental data. We argue here that the unique history of each community and intrinsic temporal dynamics also influence the structure of human intestinal communities.     

Assessment of metabolic diversity within the intestinal microbiota from healthy humans using combined molecular and cultural approaches

The human gut harbours a wide range of bacterial communities that play key roles in supplying nutrients and energy to the host through anaerobic fermentation of dietary components and host secretions. This fermentative process involves different functional groups of microorganisms linked in a trophic chain. Although the diversity of the intestinal microbiota has been studied extensively using molecular techniques, the functional aspects of this biodiversity remain mostly unexplored. The aim of the present work was to enumerate the principal metabolic groups of microorganisms involved in the fermentative process in the gut of healthy humans. These functional groups of microorganisms were quantified by a cultural approach, while the taxonomic composition of the microbiota was assessed by in situ hybridization on the same faecal samples. The functional groups of microorganisms that predominated in the gut were the polysaccharide-degrading populations involved in the breakdown of the most readily available exogenous and endogenous substrates and the predominant butyrate-producing species. Most of the functional groups of microorganisms studied appeared to be present at rather similar levels in all healthy volunteers, suggesting that optimal numbers of these various bacterial groups are crucial for efficient gut fermentation, as well as for host nutrition and health. Significant interindividual differences were, however, confirmed with respect to the numbers of methanogenic archaea, filter paper-degrading and acetogenic bacteria and the products formed by lactate-utilizing bacteria.     

Indigestible carbohydrates alter the intestinal microbiota but do not influence the performance of broiler chickens

Aims:  Prebiotics are a potential alternative to in-feed antimicrobials to improve performance of chickens. We investigated the effects of mannanoligosaccharide (MOS) and fructooligosaccharide (FOS) on growth, performance and the intestinal microbiota.
Methods and Results:  Cobb 500 birds were fed either: Control, starter diet without antimicrobials; ZnB, Control + 50 ppm zinc bacitracin; MOS, Control + 5 g kg⁻¹ MOS; or FOS, Control + 5 g kg⁻¹ FOS. An energy metabolism study was conducted and intestinal microbial communities assessed by T-RFLP and Lac PCR-DGGE. Diet did not influence performance. Ileal microbial communities were significantly different in ZnB-fed birds compared to all diets, and FOS-fed chickens compared to Control. MOS-fed chickens had a different caecal profile to ZnB and FOS-fed birds. Consensus Lac PCR-DGGE profiles indicated Lactobacillus communities clustered according to diet with Lactobacillus johnsonii characteristic of ZnB diet. Control and MOS-fed chickens displayed significantly different jejunal Lactobacillus profiles to each other whilst ileal profiles were different between MOS and FOS-fed birds.
Conclusion:  Prebiotics influenced the intestinal microbiota, but did not affect performance.
Significance and Impact of the Study:  In light of pressure for in-feed antimicrobial withdrawal, the impact of alternative compounds on the intestinal microbiota and bird performance is critical to the poultry industry.     

消化道微生物区系与肥胖关系的研究进展

肥胖以及与肥胖相关的一些疾病威胁着发达国家和发展中国家,这些疾病包括Ⅱ型糖尿病、高血压、心血管疾病、非酒精型脂肪肝。最新研究表明消化道微生物区系(microbiota,指一个特定区域中所有活的微生物群落的统称。)可能与宿主肥胖相关。目前此类研究尚处于起步阶段,作者总结了以往研究结果,对消化道微生物区系的组成和作用、与宿主能量代谢相关的消化道微生物种类和作用、消化道微生物区系影响宿主能量储存的途径作了较为详细的介绍。并探讨了目前研究中存在的问题,总结了本实验室已有研究成果,以及今后可能的研究方向。