宏基因组学与动物病原微生物检测

宏基因组学（ metagenome）是直接从土壤、海水、人及动物胃肠道、口腔、呼吸道、皮肤等环境中获取样品DNA,利用载体将其克隆到替代宿主细胞中构建宏基因文库,以高通量检测为主要技术来研究特定环境中全部微生物的基因组及筛选活性物质和基因的新兴学科。利用宏基因组学技术不仅能够有效地检测特定环境的微生物群落结构,扩展了微生物资源的利用空间,发展了新兴的高通量检测技术,丰富了生物信息学内容。基于宏基因组学研究方法在环境微生物研究中的优势,对近年来相关领域、方法及其在人及动物病原微生物研究中的应用进行综述,以期将此方法用于实验动物病原微生物的调查分析及动物疫情、生物安全的监测。     

Current status and prospects on microbial control in Japan

Historically in Japan, studies on the diseases of the silkworm, Bombyx mori, as a factor affecting the well-being of the silk industry, have dominated insect pathology. However, work by Hidaka in 1933 demonstrated the possibility of controlling the pine moth, Dendrolimus spectabilis, with the fungus Beauveria bassiana and since then, various attempts have been made to develop a method to control insect pests using insect pathogens. The cypovirus product, Matsukemin, was the first microbial control product to be registered in 1974, and inactive and live Bacillus thuringiensis products were also registered and put on the market as pesticides in 1981 and 1982, respectively. Currently, there are 25 microbial insecticides on the market that constitute slightly less than 2% of all insecticides used in Japan. Adoption of biopesticides is likely to increase in the near future due to scientific advances and several new government policies that encourage the use of alternative pest control products.     

Fungitoxicity of the essential oil of Citrus sinensis on post-harvest pathogens

Summary The essential oil extracted from the epicarp of Citrus sinensis exhibited absolute fungitoxicity against the 10 post-harvest pathogens. GC–MS studies of the oil revealed the presence of 10 chemical constituents, of which limonene was found to be the major component (84.2%). The activity of the oil was tested by the poisoned food technique (PF) and the volatile activity (VA) assay and the oils showed greater toxicity in the VA assay than in the poisoned food assay. The nature of the toxicity was studied in the VA assay and it was observed that the oil was fungicidal for the 10 pathogens in the 700 ppm (mg/l) to 1000 ppm range. The oil was extremely toxic for spore germination and it was found that at 700 ppm, spore germination was inhibited in the 10 test fungi out of the 12 tested. Treatment at 300 ppm concentration exhibited 70–100% inhibition of spore germination in most of the fungi tested. Scanning electron microscopy (SEM) was done to study the mode of action of the oil in Aspergillus niger and it was observed that treatment with the oil leads to distortion and thinning of the hyphal wall and the reduction in hyphal diameter and absence of conidiophores.     

Antibacterial properties of Apis dorsata honey against some bacterial pathogens

Now-a-days, different bioproducts are being used extensively for the welfare of mankind. However, for proper utility of any bioproduct, the exact biotechnological potential of that product should be explored. Honey is produced in almost every country on the planet. It has long been used as a medicinal agent in addition to its broader use as a popular food throughout the human history. It can be used to treat various diseases without causing any negative side effects. In the present study, the antibacterial potential of honey produced by A. dorsata was investigated at its variable concentrations (25, 50, 75 and 100 %) against four pathogenic bacterial species. The highest antimicrobial action was seen against E. coli at 100 % concentration of the honey while showing zone of inhibition of 37.5 ± 3.5 mm. However, the lowest antibacterial action was observed against E. faecalis. The overall order of growth inhibition by the honey at its 100 % concentration for the implicated bacterial species appeared as: E. coli ˃ P. aeruginosa ˃ S. aureus ˃ E. faecalis. The honey couldn’t show antibacterial action at its 25 % concentration. Our findings of the present study will be helpful for utility of the honey as an alternative medicine for curing different complications caused by microbial pathogens.     

Species,developmental stage and infection with microbial pathogens of engorged ticks removed from dogs and questing ticks

Research into tick‐borne diseases implies vector sampling and the detection and identification of microbial pathogens. Ticks were collected simultaneously from dogs that had been exposed to tick bites and by flagging the ground in the area in which the dogs had been exposed. In total, 200 ticks were sampled, of which 104 came from dogs and 96 were collected by flagging. These ticks were subsequently examined for DNA of Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, Rickettsia spp. and Babesia canis. A mixed sample of adult ticks and nymphs of Ixodes ricinus (Ixodida: Ixodidae) and Haemaphysalis concinna (Ixodida: Ixodidae) was obtained by flagging. Female I. ricinus and adult Dermacentor reticulatus (Ixodida: Ixodidae) ticks dominated the engorged ticks removed from dogs. Rickettsia spp. were detected in 17.0% of the examined ticks, A. phagocytophilum in 3.5%, B. canis in 1.5%, and B. burgdorferi s.l. in 16.0%. Ticks with multiple infections were found only among the flagging sample. The ticks removed from the dogs included 22 infected ticks, whereas the flagging sample included 44 infected ticks. The results showed that the method for collecting ticks influences the species composition of the sample and enables the detection of a different pattern of pathogens. Sampling strategies should be taken into consideration when interpreting studies on tick‐borne pathogens.     

Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens

The gastrointestinal tract is a complex ecosystem that associates a resident microbiota and cells of various phenotypes lining the epithelial wall expressing complex metabolic activities. The resident microbiota in the digestive tract is a heterogeneous microbial ecosystem containing up to 1 x 10(14) colony-forming units (CFUs) of bacteria. The intestinal microbiota plays an important role in normal gut function and maintaining host health. The host is protected from attack by potentially harmful microbial microorganisms by the physical and chemical barriers created by the gastrointestinal epithelium. The cells lining the gastrointestinal epithelium and the resident microbiota are two partners that properly and/or synergistically function to promote an efficient host system of defence. The gastrointestinal cells that make up the epithelium, provide a physical barrier that protects the host against the unwanted intrusion of microorganisms into the gastrointestinal microbiota, and against the penetration of harmful microorganisms which usurp the cellular molecules and signalling pathways of the host to become pathogenic. One of the basic physiological functions of the resident microbiota is that it functions as a microbial barrier against microbial pathogens. The mechanisms by which the species of the microbiota exert this barrier effect remain largely to be determined. There is increasing evidence that lactobacilli and bifidobacteria, which inhabit the gastrointestinal microbiota, develop antimicrobial activities that participate in the host's gastrointestinal system of defence. The objective of this review is to analyze the in vitro and in vivo experimental and clinical studies in which the antimicrobial activities of selected lactobacilli and bifidobacteria strains have been documented.     

Identification of aspirin and diclofenac binding proteins in the red complex pathogens

Red complex organisms are a group of organisms (Porphyromonas gingivalis ATCC 33277, Treponema denticola ATCC 35405, Tannerella forsythia ATCC 43037) that have been identified for the causation of periodontal diseases. Aspirin and diclofenac have been used as regular analgesics. Therefore, it is of interest to document the identification of aspirin and diclofenac binding proteins in the red complex pathogens using the STITCH v.5 pipeline. The virulence properties of these proteins were analyzed using VICMPred and VirulentPred software. Thus, we document 000 number of proteins having optimal binding features with the known analgesics.     

Identification of Microbial Pathogens in Periodontal disease and Diabetic patients of South Indian Population

Periodontitis have been referred to as the sixth complication of diabetes found in high prevalence among diabetic patients than among healthy controls. The aim of the present study was to examine the periodontal disease status among collected dental plaque samples. Chromosomal DNA was isolated and amplified by universal primers. The DNA was sequenced for bacterial confirmation and phylogenetic analysis performed for the evolutionary relationship with other known pathogens. No amplification products were observed in groups labeled non periodontal and non Diabetes (NP&ND) and non Periodontal and Diabetes (NP&D). But in the case of Periodontal and non Diabetes (P&ND) groups 22 amplified products were observed. In case of Periodontal and Diabetes (P&D), 32 amplified products were positive for microbes. Among the four microbial groups, Treponemadenticola, and Tannerella forsythia were found to be prevalent in P&D. The phylogenetic analysis of 16s rRNA of Treponemadenticola showed the relationship with other Treponema oral pathogen species and with the Spirochaetazuelaera. Tannerella forsythia shows its evolutionary relationship only with four oral pathogens (Macellibacteroidesfermentans, Porphyromadaceae bacterium, Parabacteroidesmeredae and Bacillus fosythus). Prevotellaintermedia also showed its evolutionary relationship only with Prevotella Spcs while Fusobacterium revealed close evolutionary relationship only with Porpiromonasgingivalis.     

Anode microbial communities produced by changing from microbial fuel cell to microbial electrolysis cell operation using two different wastewaters

Conditions in microbial fuel cells (MFCs) differ from those in microbial electrolysis cells (MECs) due to the intrusion of oxygen through the cathode and the release of H₂ gas into solution. Based on 16S rRNA gene clone libraries, anode communities in reactors fed acetic acid decreased in species richness and diversity, and increased in numbers of Geobacter sulfurreducens, when reactors were shifted from MFCs to MECs. With a complex source of organic matter (potato wastewater), the proportion of Geobacteraceae remained constant when MFCs were converted into MECs, but the percentage of clones belonging to G. sulfurreducens decreased and the percentage of G. metallireducens clones increased. A dairy manure wastewater-fed MFC produced little power, and had more diverse microbial communities, but did not generate current in an MEC. These results show changes in Geobacter species in response to the MEC environment and that higher species diversity is not correlated with current.     

Inhibitory effect of garlic on bacterial pathogens from spices

An unconventional technique for primary screening of bacterial susceptibility to garlic (Allium sativum Linn.), using a slice from its clove, was described. Aqueous extracts of garlic were found to possess a potent bacteriostatic principle against Gram-positive as well as Gram-negative foodborne bacterial pathogens. In agar medium, the minimum inhibitory concentrations (MICs) of garlic were 6–10 mg ml^–1 for Bacillus cereus, 30–40 mg ml^–1 for Staphylococcus aureus (excepting the isolate from garlic, where the MIC was 100 mg ml^–1), 20–30 mg ml^–1 for Clostridium perfringens, 10 mg ml^–1 for Escherichia coli (30 mg ml^–1 for the garlic isolate), 40–100 mg ml^–1 for Salmonella, and 10–40 mg ml^–1 for Shigella. It inhibited the growth of all these strains, which were resistant to some commonly used antibiotics. Most of the tested strains were resistant to penicillins, although sensitive to garlic. While the growth of B. cereus and Cl. perfringens was completely inhibited at 10 and 70 mg garlic, respectively, ml^–1 test broth, their respective enterotoxin production ceased at 10 and 50 mg garlic ml^–1.     

碳源对活性污泥微生物细胞膜特性和群落结构影响

【目的】揭示碳源对活性污泥微生物细胞膜特性(磷脂脂肪酸组成和流动性)以及群落结构的影响规律。【方法】采用原子力显微镜、磷脂脂肪酸(PLFA)、荧光漂白恢复(FRAP)和Mi Seq分析技术,考察以葡萄糖、乙酸钠、蛋白胨、葡萄糖?蛋白胨(1?1)和乙酸钠?蛋白胨(1?1)为基质的序批式活性污泥(SBR)反应器中,活性污泥微生物表面粘附力、细胞膜PLFA组成和流动性及群落结构的差异。【结果】含有蛋白胨为碳源时相比于葡萄糖和乙酸钠为单一碳源,细胞膜磷脂流动性增加,且18?1ω9c、15?0iso和17?0iso的含量提高了53.1%-354.7%、135.6%-407.9%和88.1%-264.3%;同时其微生物表面粘附力和群落多样性均增大。优势菌群对碳源的响应呈现出不一致的规律:葡萄糖和乙酸钠为单一碳源时其优势菌门分别为放线菌门和变形菌门,Nakamurella和Flavobacterium分别为其优势菌属,群落多样性指数分别为3.65和4.25;蛋白胨为碳源时促进了Candidatus Saccharibacteria门的累积,群落多样性指数在4.96-5.09。【结论】主成分分析(PCA)表明,含有蛋白胨为碳源时微生物细胞膜PLFA组成具有相似性;冗余分析(RDA)表明,不同碳源驯化出不同的微生物群落,进而也对细胞膜磷脂组成产生了影响。     

Advanced high-power pulsed light device to decontaminate food from pathogens: effects on Salmonella typhimurium viability in vitro

AIMS: The aim of this study was to construct an advanced high-power pulsed light device for decontamination of food matrix and to evaluate its antibacterial efficiency. Key parameters of constructed device-emitted light spectrum, pulse duration, pulse power density, frequency of pulses, dependence of emitted spectrum on input voltage, irradiation homogenicity, possible thermal effects as well as antimicrobial efficiency were evaluated. METHODS AND RESULTS: Antimicrobial efficiency of high-power pulsed light technique was demonstrated and evaluated by two independent methods - spread plate and Miles-Misra method. Viability of Salmonella typhimurium as function of a given light dose (number of pulses) and pulse frequency was examined. According to the data obtained, viability of Salmonella typhimurium reduced by 7 log order after 100 light pulses with power density 133 W cm(-2). In addition, data indicate, that the pulse frequency did not influence the outcome of pathogen inactivation in the region 1-5 Hz. Moreover, no hyperthermic effect was detected during irradiation even after 500 pulses on all shelves with different distance from light source and subsequently different pulse power density (0-252 W cm(-2)). CONCLUSION: Newly constructed high-power pulsed light technique is effective nonthermal tool for inactivation of Salmonella typhimurium even by 7 log order in vitro. SIGNIFICANCE AND IMPACT OF THE STUDY: Novel advanced high-power pulsed light device can be a useful tool for development of nonthermal food decontamination technologies.     

红树林样品不经分离的微生物群体培养物生物活性研究

从海南、广西与广东三省的红树林区采集了181个样品,不进行微生物分离而直接作发酵剂接种到发酵培养基进行发酵,取发酵上清液进行抗细菌、抗真菌与肿瘤细胞毒活性的测定。同时对样品进行可培养微生物的分离与生物活性测定。结果显示:不同样品类型的生物活性差异较大。在15个具有强抗活性的样品中,有5个样品分离到的单株菌均无任何生物活性,说明这5个样品的生物活性可能是由微生物的群体作用产生的,也可能是某种没有培养出的微生物产生的。初步表明了探索微生物混合培养获得生物活性代谢产物的可能性。     

硝酸银对常见呼吸道病原体的抑制作用

目的证实硝酸银对常见呼吸道病原体具有抑制作用。方法采用血凝试验和鸡胚培养法观察硝酸银对副流感病毒的抑制作用;采用细胞培养法观察硝酸银对腺病毒的抑制作用;采用细菌培养法观察硝酸银对肺炎链球菌和乙型溶血型链球菌的抑制作用。结果硝酸银对副流感病毒和腺病毒有明显的抑制作用,对肺炎链球菌和乙型溶血型链球菌有极强的杀菌作用。结论硝酸银对常见呼吸道病原体有明显的抑制作用。     

Shift of microbial community in gas-phase biofilters with different inocula,inlet loads and nitrogen sources

The research on gaseous VOCs biofilters has often concentrated on process optimization. However, the microbial community change upon operating conditions is not well understood. In this study, three lab-scale biofilters treating gaseous toluene were operated for 66 days with different inocula under changes in inlet loads and nitrogen sources. Three biofilters were inoculated with activated sludge, river sediment or microbial consortia, respectively. The microbial community differed a lot initially but gradually deviated toward similar structures with the same dominant microorganisms, i.e. Proteobacteria, Actinobacteria (phylum level) and Rhodococcus,Pseudomonas(genus level). Among three biofilters, the two biofilters inoculated with activated sludge and river sediment showed higher microbial diversity, better VOCs removal performance and higher metabolic activity. Higher relative abundance of Alcanivorax (3% compared with lower than 0.03%), Pimelobacte (0.05% compared with lower than 0.01%)were detected under low inlet load, and Zoogloea(0.1%), Alkaliphilus(0.2%) were detected when the inlet load was increased. the abundance of Pseudomonasdecreased from 14% to 2% when ammonia was used as nitrogen source instead of nitrate, meanwhile the abundance of Bacillus and Gordoniaincreased from 0.01% to 0.05% and 0.8% to 5.8% respectively. Some special organisms were observed i.e. the intestinal microorganism.     

Effects on microbial activity by extraction of indigenous cells from soil slurries

Abstract: Possible effects on the physiological activity and culturability of soil microorganisms by different soil dispersion procedures, and effects on activity caused by extracting bacteria from soil, were investigated. There was no apparent difference in cfu's with dispersion of a silty loam soil and a loamy sand soil with pyrophosphate as compared to dispersion in NaCl. Substrate-induced respiration was reduced in the silty loam soil, and methanol oxidation was reduced in the loamy sand soil with dispersion in pyrophosphate, and the soil pH was irreversibly increased by the treatment. Extracted bacterial fractions had lower numbers of culturable cells as percentage of the total number of bacteria in each fraction, lower respiration rates and no methanol oxidation activity as compared to the soil slurry both before and after extraction. The physiological activity was apparently not affected by the number of cells extracted. This indicates that the increased extraction rate of indigenous soil bacteria obtained by effective disruption of aggregates and detachment of cells from surfaces, only results in increased extraction of cells that have been physiologically changed as a result of the extraction process.     

Antimicrobial activity of polyphenolic compounds from Spirulina against food-borne bacterial pathogens

Food-borne drug-resistant bacteria have adverse impacts on both food manufacturers and consumers. Disillusionment with the efficacy of current preservatives and antibiotics for controlling food-borne pathogens, especially drug-resistant bacteria, has led to a search for safer alternatives from natural sources. Spirulina have been recognized as a food supplement, natural colorant, and enriched source of bioactive secondary metabolites. The main objectives of this study were to isolate polyphenolic compounds from Spirulina and analyze their antibacterial potential against drug-resistant food-borne bacterial pathogens. We found that fraction B of methanol extract contained a high quantity of polyphenols exhibiting broad spectrum antimicrobial effects against drug-resistant food-borne bacterial pathogens. Potential secondary metabolites, such as benzophenone, dihydro-methyl-phenylacridine, carbanilic acid, dinitrobenzoate, propanediamine, isoquinoline, piperidin, oxazolidin, and pyrrolidine, were identified by gas chromatography and mass spectrophotometry (GCMS). These metabolites are active against both gram-positive and gram-negative pathogens. Our work suggests that phenolic compounds from Spirulina provide a natural and sustainable source of food preservatives for future use.     

Adaptive response of microbial communities to soluble microbial products

We carried out two experiments to study the influence of soluble microbial products (SMP) on biomass concentration [defined as mixed liquor suspended solids (MLSS)] and removal of soluble biological and chemical oxygen demands (sBOD₅ and sCOD): (1) SMP were allowed to accumulate, and (2) SMP content was artificially reduced by washing the biomass. The daily initial sCOD in both experiments was kept constant at 859±6 mg/l for 16 days. In experiment 1, the highest sCOD removal (80%) occurred during the first day. Thereafter, it decreased successively to 40% [sludge retention time (SRT), 12 days], after which it increased steadily to 50±4%. Variations in residual sCOD were accompanied by variations in sBOD₅, showing that the biodegradability of the accumulated SMP components was changing. MLSS fluctuated within the range 1,200±25–1,993±58 mg/l. We attributed the irregular accumulation of the biomass to variations in the biodegradability of SMP components. The initial sBOD₅/MLSS ratio varied according to variations in initial sBOD₅ and MLSS, whereas the residual ratio was constant at 0.025±0.008. This indicated a direct relationship between the concentrations of biomass and SMP produced. In experiment 2, MLSS increased from 1,200±25 to a constant value (2,810±16 mg/l; SRT, 12 days). After this time, no decrease or increase in MLSS was observed. Correspondingly, sCOD and sBOD₅ removal increased from 80–97 to 84–99%. A stable microbial community that could consume organic matter efficiently was developed under these conditions.