人体鼻咽部微生物群落多样性研究进展

定殖于鼻咽部的微生物与人体始终处于动态生态平衡,对于维持人体健康发挥着重要作用,也与多种上呼吸道疾病的发生发展有密切关系。鼻咽部微生物之间及其与宿主之间的相互作用是引发人体上呼吸道疾病的重要因素。微生物的培养方法与分子生物学技术的结合使人们越来越深入地了解人体鼻咽部微生物群落的组成和结构。定殖于人体鼻咽部的微生物以肺炎链球菌(Streptococcus pneumoniae)和流感嗜血杆菌(Haemophilus influenzae)等潜在致病菌为主。本文将分别从鼻咽部微生物与机体的平衡关系、鼻咽部微生物群落的研究方法以及鼻咽部微生物群落的组成及其相互关系三个方面,综述近年来鼻咽部微生物群落结构的相关研究进展,从而为指导实践提供可靠的理论依据。     

青年咽部菌群分布状况

目的调查健康青年上呼吸道的微生物群分布,寻找优势菌群,为微生态方法治疗呼吸道感染性疾病提供科学依据。方法随机自愿原则选取沈阳医学院学生61名,采集咽后壁标本分离培养并生化鉴定。结果青年咽后壁共检出19个菌属,42个菌种。需氧菌的95％可信区间为（4．7×10^6,6．8×10^6）CFU／mL,厌氧菌的95％可信区间为（5．9×10^6,8．4×10^6）CFU／mL;需氧菌菌群密度为4．8816±1．0251,厌氧菌菌群密度为5．1347±0．9118。需氧菌中链球菌属检出率为100％,其次为奈瑟球菌属（77．4％）、葡萄球菌属（33．9％）。链球菌中缓症链球菌和口腔链球菌、奈瑟球菌属中的灰色奈瑟球菌的检出率与构成比均较高。厌氧菌中检出率与构成比较高是的韦荣球菌属、拟杆菌属、孪生球菌和放线杆菌属。结论青年上呼吸道菌群种类复杂多样;需氧菌中的口腔链球菌、缓症链球菌、灰色奈瑟球菌,厌氧菌中的韦荣球菌属、拟杆菌属、孪生球菌属为优势菌群,对于维护上呼吸道微生态平衡可能起重要的作用。     

Culture enriched molecular profiling of the cystic fibrosis airway microbiome

The microbiome of the respiratory tract, including the nasopharyngeal and oropharyngeal microbiota, is a dynamic community of microorganisms that is highly diverse. The cystic fibrosis (CF) airway microbiome refers to the polymicrobial communities present in the lower airways of CF patients. It is comprised of chronic opportunistic pathogens (such as Pseudomonas aeruginosa) and a variety of organisms derived mostly from the normal microbiota of the upper respiratory tract. The complexity of these communities has been inferred primarily from culture independent molecular profiling. As with most microbial communities it is generally assumed that most of the organisms present are not readily cultured. Our culture collection generated using more extensive cultivation approaches, reveals a more complex microbial community than that obtained by conventional CF culture methods. To directly evaluate the cultivability of the airway microbiome, we examined six samples in depth using culture-enriched molecular profiling which combines culture-based methods with the molecular profiling methods of terminal restriction fragment length polymorphisms and 16S rRNA gene sequencing. We demonstrate that combining culture-dependent and culture-independent approaches enhances the sensitivity of either approach alone. Our techniques were able to cultivate 43 of the 48 families detected by deep sequencing; the five families recovered solely by culture-independent approaches were all present at very low abundance (<0.002% total reads). 46% of the molecular signatures detected by culture from the six patients were only identified in an anaerobic environment, suggesting that a large proportion of the cultured airway community is composed of obligate anaerobes. Most significantly, using 20 growth conditions per specimen, half of which included anaerobic cultivation and extended incubation times we demonstrate that the majority of bacteria present can be cultured.     

The role of microbial interactions in infectious disease

The occurrence of infectious disease is affected by interaction between microorganisms in three ways. The indigenous flora (commensal microorganisms) of some mucous surfaces provide one of the main protective mechanisms against infection by pathogens (disease-producing microbes). The commensal populations interfere with the establishment of pathogens on mucous membranes by evoking anaerobic conditions, by competing for space and nutrients and by producing inhibitors. How, at the beginning of successful infection, pathogens in relatively small numbers overcome this protective activity of the commensal population is unknown. Although not a general phenomenon, some pathogens exacerbate the effects of others. The best examples are the potentiation of bacterial infections by existing viral infections: mucosal adherence and penetration by bacteria are enhanced and phagocytic defences against them weakened. Some microorganisms that are unable to produce significant disease on their own may combine with others to cause serious sickness. The harmful effects of these combinations of microorganisms can be explained by the multifactorial nature of pathogenicity (virulence), i.e. the capacity to produce disease. Although each member of the mixed population cannot alone produce the full complement of factors needed for disease production, the complement can be attained by combining contributions from different members.     

Structure of the intestinal flora responsible for development of the gut immune system in a rodent model

The intestinal flora comprising indigenous, autochthonous bacteria is constantly present in the alimentary tract of host animals, including humans. The indigenous bacteria greatly affect the structure and functions of the intestinal mucosa. Studies involving gnotobiotic mice or rats have shown that the presence of limited kinds of intestinal bacteria is responsible for the development of the gut immune system, such as secretory IgA, major histocompatibility complex molecules and intraepithelial lymphocytes. Understanding of the structure of the intestinal flora or the organization of the microbial population in the intestine, based on evaluation of the immunological responses, may clarify its functions in the host animal.     

Antagonistic activity of Lactobacillus bacteria strains against anaerobic gastrointestinal tract pathogens (Helicobacter pylori, Campylobacter coli, Campylobacter jejuni, Clostridium difficile)]

Antagonistic activity of Lactobacillus strains has been known for some time. This property is connected with production of many active substances by lactobacilli e.g., organic acids and bacteriocin-like substances which interfere with other indigenous microorganisms inhabiting the same ecological niche, including also anaerobic gastrointestinal tract pathogens. Growing interest of clinical medicine in finding new approaches to treatment and prevention of common inflammatory infections of the digestive tract resulted in studies on a possible usage of lactic acid bacteria. Last years, several in vitro and in vivo experiments on antagonism of different Lactobacillus strains against Helicobacter pylori and Clostridium difficile were performed. These observations had been done on already established, well known probiotic Lactobacillus strains. We tested antibacterial activities of Lactobacillus strains isolated from human digestive tract. As indicator bacteria, four species known as anaerobic bacterial etiologic agents of gastroenteric infections: Helicobacter pylori, Campylobacter jejuni, C. coli and Clostridium difficile were used. Some of them were obtained from international collections, others were clinical isolates from specimens taken from patients with different defined gastrointestinal infections. We used a slab method of testing inhibitory activity described in details previously. Following conclusions were drawn from our study: All tested human Lactobacillus strains were able to inhibit the growth of all strains of anaerobic human gastrointestinal pathogens used in this study. Inhibitory activities of tested Lactobacillus strains against Helicobacter pylori, Campylobacter spp., and Clostridium difficile as measured by comparing mean diameters of the inhibition zones were similar. Differences in susceptibility of individual indicator strains of Campylobacter spp. and Clostridium difficile to inhibitory activity of Lactobacillus strains were small. A similar mechanism of inhibition of anaerobic bacteria by lactobacilli is postulated.     

模拟油藏条件下内源微生物群落空间分布规律

【背景】油藏内源微生物群落是开展内源微生物驱油技术的物质基础,由于油藏多孔介质取样技术难度大、成本高,实施内源微生物驱油后从注入端到产出端多孔介质中的内源微生物空间分布规律尚不明确。【目的】通过室内长岩心连续驱替实验模拟油藏内源微生物驱油过程,分析实施后不同空间位点油砂上吸附的内源微生物群落结构,揭示从注入端到产出端内源微生物群落的空间分布规律。【方法】借助高通量测序技术及荧光定量PCR技术解析不同空间位点油砂原位微生物群落信息。【结果】注入端到产出端不同空间位点生态环境的差异及菌属间的相互作用造成油藏内源微生物群落空间分布差异,存在明显的好氧、厌氧空间演替变化规律。岩心前端主要存在一些好氧类的产生物表面活性剂类微生物如假单胞菌属,岩心中部主要存在兼性和厌氧类的微生物如地芽孢杆菌、厌氧杆菌属,岩心末端主要分布严格厌氧类细菌和产甲烷古菌,厌氧类微生物代谢产生的H2、CO2和乙酸分子可以为产甲烷古菌提供代谢底物。【结论】通过室内物模油砂研究,首次明确了内源微生物群落在多孔介质中从注入端到产出端的空间分布规律,证实油藏内源微生物的好氧、厌氧空间接替分布规律,深化了对油藏内源微生物的认识。     

微生物增产煤层气技术研究进展

微生物增产煤层气技术能够产生新的煤层气,有效缓解能源紧张问题,是煤层气开采、增产的研究热点。微生物增产煤层气技术的核心机理是煤的厌氧生物降解产甲烷。国内外研究学者通过实验室模拟研究了本源和外源微生物的降解煤产甲烷能力及影响因素。部分煤层气公司富集或分离获得了高效产甲烷菌群,并研究了微生物增产煤层气技术的现场实施方法。开发煤的预处理技术、构建新型高效菌群等可进一步提高微生物的增产煤层气能力,促进微生物增产煤层气技术的应用。     

Effect of antimicrobial therapy on bowel flora and bacterial infection in irradiated mice

Mice exposed to 10 Gy cobalt-60 radiation were given intramuscular antimicrobial therapy of gentamicin, or metronidazole, or a combination of the two. Mortality in the mice treated with metronidazole alone or in combination with gentamicin occurred earlier than in the controls (P less than 0.001). Microorganisms were recovered from the blood, spleen, and liver of the metronidazole-treated mice earlier than from other groups. The predominant organisms recovered from these animals were Enterobacteriaceae. Quantitative cultures of the ileal flora showed a decrease in the number of aerobic, facultative anaerobic and strict anaerobic bacteria after irradiation, and a subsequent increase only in the number of strict aerobic bacteria. As compared to untreated mice, a rapid decrease (by 8.8 logs) in the number of anaerobic flora occurred in the mice treated with metronidazole 5 days after irradiation. This was followed by a rapid increase in the number of aerobic organisms which coincided with the earlier mortality in this group. These data suggest that antimicrobial agents that decrease the number of the strict anaerobic component of the gut flora enhance systemic infection by aerobic or facultative anaerobic bacteria, and this facilitates mortality after irradiation.     

Production of anti-Candida antibodies in mice with gut colonization of Candida albicans

BACKGROUND: Production of antibodies that are specific for allergens is an important pathological process in inflammatory allergic diseases. These contain the antibodies against antigens of Candida albicans, one of the normal microbial flora in an intestinal tract. We studied the effects of the prednisolone administration on the production of anti-Candida antibodies in the gastrointestinally C. albicans-colonized mice. METHODS AND MATERIALS: BALB/c mice, treated with antibacterial antibiotics to decontaminate indigenous intestinal bacterial flora, were inoculated intragastrically with C. albicans. The mice, in which C. albicans grows intestinally, were administered prednisolone to induce temporary immunosuppression. The Candida growth in their intestinal tract and their antibody response to Candida were examined. RESULTS: Antibiotic treatment allowed establishment of C. albicans gastrointestinal colonization, but did not cause subsequent systemic dissemination of C. albicans in all the animals. When these animals received an additional treatment with prednisolone, they showed a significantly higher population of C. albicans in their feces than those of animals treated with antibiotics alone, and the organisms were recovered even from their kidney. This systemic dissemination by C. albicans appeared to be temporal, because all the mice survived without any symptoms for more than 2 months. Examination of the serum titers of total immunoglobulin (Ig)E antibodies and specific IgE and IgG antibodies against Candida antigens demonstrated that titers of total IgE increased, partially by day 14 and clearly at day 27, in prednisolone-treated Candida-colonized mice. Without prednisolone treatment, an increment of the serum titer was scarcely observed. By day 27, corresponding to the increase of total IgE, the anti-Candida IgE and IgG titer increased in mice of the prednisolone-treated group. CONCLUSION: Administration of prednisolone to Candida-colonized mice can induce production of the IgG, IgE antibodies against Candida antigens, perhaps through temporal systemic dissemination of Candida from the intestinal tract.     

哈尼梯田稻-渔共作模式下杂交黄颡鱼肠道微生物研究

为了探究哈尼梯田稻-鱼共作综合种养模式(稻渔组, DY组)和传统池塘养殖模式(池塘组, CT组)下杂交黄颡鱼(Tachysurus fulvidraco♀×Pseudobagrus vachellii♂)肠道微生物结构变化,试验采用16S rDNA测序技术对不同养殖模式下黄颡鱼肠道微生物进行分析。测序结果显示, CT组和DY组优势菌门均为变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)和梭杆菌门(Fusobacteria)。和CT组相比,在门水平上DY组厚壁菌门和拟杆菌门相对丰度显著上升,而变形菌门相对丰度显著下降。在属水平上DY组梭状芽孢杆菌属、Romboutsia属、Paludibacter属、Epulopiscium属和拟杆菌属相对丰度显著上升,而邻单胞菌属丰度显著下降。不同的养殖模式没有显著影响黄颡鱼肠道微生物的丰富度(Richness),但DY组拥有更高的微生物均匀度(Evenness)。BugBase表型预测结果如下, CT组革兰氏阴性菌,兼性厌氧菌丰度更高, DY组则革兰氏阳性菌,厌氧菌丰度更高。同时DY组...     

Effects of heat and microbiological pretreatments of wheat straw substrate on the initial phase of solid state fermentation (SSF) by white rot fungi

Summary Quantitative differentiation of microbial activity and saprophytic colonisation in wheat straw substrate during SSF is described. Wheat straw contains an active indigenous microbial flora. In both untreated and heat pretreated substrates a peak of microbial respiratory activities occurs generally after 24 h of fermentation; addition of actidione and streptomycin has no marked inhibitory effect. Quantitative differences between endogenous microbial respiration and respiration byPleurotus during the initial four days of SSF are least in the heat pretreated substrates and greater when microbiological pretreatment is used. In treatments subjected to 48 h anaerobic fermentation at 50°C, saprophytic colonization similar to that observed in sterile substrates is obtained.     

In Vitro Communities Derived from Oral and Gut Microbial Floras Inhibit the Growth of Bacteria of Foreign Origins

The gastrointestinal (GI) tract is home to trillions of microbes. Within the same GI tract, substantial differences in the bacterial species that inhabit the oral cavity and intestinal tract have been noted. While the influence of host environments and nutritional availability in shaping different microbial communities is widely accepted, we hypothesize that the existing microbial flora also plays a role in selecting the bacterial species that are being integrated into the community. In this study, we used cultivable microbial communities isolated from different parts of the GI tract of mice (oral cavity and intestines) as a model system to examine this hypothesis. Microbes from these two areas were harvested and cultured using the same nutritional conditions, which led to two distinct microbial communities, each with about 20 different species as revealed by PCR-based denaturing gradient gel electrophoresis analysis. In vitro community competition assays showed that the two microbial floras exhibited antagonistic interactions toward each other. More interestingly, all the original isolates tested and their closely related species displayed striking community preferences: They persisted when introduced into the bacterial community of the same origin, while their viable count declined more than three orders of magnitude after 4 days of coincubation with the microbial flora of foreign origin. These results suggest that an existing microbial community might impose a selective pressure on incoming foreign bacterial species independent of host selection. The observed inter-flora interactions could contribute to the protective effect of established microbial communities against the integration of foreign bacteria to maintain the stability of the existing communities.     

Bacterial translocation from the gastrointestinal tracts of thymectomized mice

The incidence of translocation of viable indigenous bacteria from the gastrointestinal tract to the mesenteric lymph node, spleen, liver, and kidney was compared in neonatally thymectomized mice and sham-thymectomized specific pathogen-free mice. The immunologic responses of the thymectomized mice to sheep erythrocytes were decreased compared to the responses of sham-thymectomized mice. Strictly anaerobic bacteria were isolated from only 1.8% of the organs from thymectomized mice and from none of the organs of shamthymectomized mice. Aerobic or facultatively anaerobic bacteria were cultured from 27.4% of the organs of thymectomized mice. Of the thymectomized mice, 70.7% contained viable aerobic or facultatively anaerobic bacteria in one or more of their organs tested, compared with only 10% of the sham-thymectomized mice.Escherichia coli was the predominant bacterial species isolated from these organs, althoughStaphylococcus aureus, Streptococcus, andCorynebacterium also were present.Bacteroides were the only strictly anaerobic bacteria cultured. Neonatal thymectomy promotes the translocation of certain indigenous bacteria from the gastrointestinal tract to the mesenteric lymph node, spleen, liver, and kidney.     

Bacterial flora of newly caught Antarctic fish Notothenia neglecta

Summary The heterotrophic bacterial flora of Antarctic fish Notothenia neglecta was studied in Potter Cove (King George Island, South Shetland Islands). Quantitative and qualitative analysis of aerobic bacteria from sea water, skin, stomach and intestine were carried out. In addition, anaerobic flora of stomach and intestine was studied and compared. Pseudomonas was dominant in sea water samples but, neither skin nor digestive tract samples showed to be rich in this genus. Stomach flora showed variable results between samples. The gut flora was composed almost exclusively of Vibrio. Despite extreme environmental conditions this Antarctic fish show an intestinal indigenous microflora very similar to warmer waters fish. Several factors, that we discussed, could be determining the Vibrio dominance in the gut of marine teleosts.     

Reduction of indicator and pathogenic microorganisms by psychrophilic anaerobic digestion in swine slurries

The objective of this study was to evaluate the efficiency of a low temperature anaerobic treatment to reduce viable populations of indicator microorganisms (total coliforms, Escherichia coli) and the presence of selected pathogens (Salmonella, Yersinia enterocolitica, Cryptosporidium and Giardia) in swine slurries from different sources. Experiments were carried out in 40 l Sequencing Batch Reactors (SBRs). Experimental results indicated that anaerobic digestion of swine manure slurry at 20 degrees C for 20 days in an intermittently fed SBR: (1) reduced indigenous populations of total coliforms by 97.94-100%; (2) reduced indigenous populations of E. coli by 99.67-100%; (3) resulted in undetectable levels of indigenous strains of Salmonella, Cryptosporidium, and Giardia. It can be considered as a promising method for reducing indigenous indicator and pathogenic microorganisms populations in liquid swine manure slurries.     

Colonization of denture plaque by respiratory pathogens in dependent elderly

Objectives: Recently, there has been a resurgence of interest in the interactions between oral conditions and a number of prevalent systemic diseases. The morbidity and mortality of the dependent elderly that result from aspiration pneumonia have been recognized as a major geriatric health problem. The purpose of this study was to gain more information on the microflora of plaque on dentures and to assess the existence of oral infectious pathogens potentially causing the respiratory disease in the dependent elderly. Subjects and Methods: The denture bacterial flora of 50 dependent elderly were examined to identify microorganisms by the culture method. Results: 18 species of microorganisms were detected in denture plaque in this study. A variety of pathogens with the potential to cause respiratory infection pathogens colonized on the dentures of dependent elderly. Conclusion: The results of the present study revealed that bacteria that commonly cause respiratory infection colonized on the dentures of dependent elderly, suggesting that denture plaque may function as a reservoir of potential respiratory pathogens to facilitate colonization on the oropharynx.     

下呼吸道感染患者病原菌分布及耐药性

目的分析下呼吸道感染患者病原菌分布及耐药性,指导临床合理用药。方法收集我院2013年至2015年院内感染患者痰标本进行细菌培养和药物敏感性试验。结果 3年共收集下呼吸道痰液标本21 615份,分离病原菌5 621株,阳性率为26.0%;其中革兰阴性(G~-)菌4 249株,占75.6%,以铜绿假单胞菌居多(20.7%);真菌764株,占13.6%,以白假丝酵母居多(12.6%);革兰阳性(G~+)菌608株,占10.8%,以金黄色葡萄球菌居多(9.9%)。药物敏感试验结果显示:G~-杆菌对亚胺培南、美洛培南耐药率最低,对青霉素类、喹诺酮类和部分三代头孢类等抗菌药耐药率较高(50.0%)。G~+球菌对万古霉素、利奈唑胺耐药率为零,对青霉素类、喹诺酮类和红霉素等抗菌药耐药率较高(40.0%)。结论下呼吸道感染患者病原菌以G~-杆菌为主,耐药性呈增长趋势,临床应加大病原菌分布检测及其耐药性监测力度,及时调整抗菌药物用药。     

Phenolics and antimicrobial activity of traditional stoned table olives 'alcaparra'

In the present work, we report the determination of phenolic compounds in ‘alcaparra’ table olives by reversed-phase HPLC/DAD, and the evaluation of their extract in vitro activity against several microorganisms that may be causal agents of human intestinal and respiratory tract infections, namely Gram positive (Bacillus cereus, Bacillus subtilis, and Staphylococcus aureus), Gram negative bacteria (Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae) and fungi (Candida albicans and Cryptococcus neoformans). Three flavonoidic compounds were identified and quantified: luteolin 7-O-glucoside, apigenin 7-O-glucoside, and luteolin. At low concentrations (0.05 mg/mL) ‘alcaparra’ extract revealed significant inhibition of both Gram positive and Gram negative bacteria growth, with exception of P. aeruginosa. Nevertheless, no antifungal activity was observed at the tested concentrations.     

典型有机固废厌氧消化微生物研究现状与发展方向

经过人工富集和驯化的兼性和严格厌氧微生物是厌氧消化工艺的核心。不同厌氧消化体系中存在的问题大多可以通过改变微生物群落的代谢活性来得到有效改善。得益于微生物组学检测技术的快速发展,对厌氧消化系统中微生物多样性的认识获得了极大的拓展,同时在微生物类群间、微生物与环境的互作关系研究方面也取得了一系列新的进展。然而,有机固废厌氧消化系统中,各种微生物以及微生物和物质的相互作用构成了更为复杂的代谢网络,所以目前对这些互作关系的解析尚不完善。本文重点关注了厌氧消化过程中的典型菌群互作关系,阐述了典型有机固废厌氧消化系统中存在的问题及微生物在其中发挥的作用,最后,立足于现有组学技术推动的微生物组研究进展,对未来有机固废厌氧消化系统微生物组的研究提出展望。