利用定量杂交法检测绵羊瘤胃纤维细菌的研究*

实验利用通用细菌探针和3株纤维分解菌的特异性探针,初步建立起对瘤胃细菌进行检测的16S rRNA定量杂交的方法。试验将提取的总RNA按浓度系列稀释后与通用细菌探针进行杂交,检测结果所做的回归分析表明,杂交信号与尼龙膜上的所点RNA的量具有明显线性关系。同时对几份瘤胃样品进行3种纤维分解菌的初步定量检测,结果显示3种纤维分解菌的相对丰度与前人报道相似,表明该方法能够对瘤胃细菌进行定量分析,可在后续相关研究中使用。     

反向线性探针杂交在检测实验动物沙门菌中的研究

目的建立简便、快速、准确、灵敏、特异的沙门菌检测方法。方法根据沙门菌argT基因序列设计通用引物和3'、5'均加有polyC的特异性探针。上游引物5'标记生物素,将探针线性固定在硝酸纤维素膜上,使沙门菌PCR扩增产物与探针进行杂交,通过优化杂交条件,建立反向线性探针杂交检测方法。利用该方法对重庆地区74只实验动物进行检测,同时与传统分离培养方法比较。结果反向线性探针杂交方法灵敏度高,对沙门菌PCR扩增产物在3ng/μL以上可有效检测。从细菌分离培养及DNA提取到PCR扩增及反向杂交结束仅需27h。该检测方法特异性高,对6种非沙门菌的检测中,其特异性为100%。应用传统分离培养方法和反向线性探针杂交方法分别检测42只KM小鼠和32只SD大鼠,两种方法检测结果一致性为100%。结论反向线性探针杂交检测方法,具有快速、可靠、敏感和特异的特点,可用于沙门菌感染时的检测,适合应用于实验动物沙门菌的监测。     

地高辛标记的Northern blot检测鼠疫菌sRNA

[目的]随着高通量测序方法的应用,越来越多的sRNA (small non-coding RNA,sRNA)需验证.本研究建立用地高辛标记Northern blot检测鼠疫菌sRNA的技术,为细菌sRNA验证提供一种灵敏、特异的方法.[方法]在低铁条件下,提取鼠疫菌总RNA,10％ dPAGE分离后电转到尼龙膜上并用紫外线交联RNA.膜经地高辛标记RyhB1或RyhB2寡核苷酸RNA探针过夜杂交后洗脱、封闭和免疫检测,最后曝光显影.[结果]地高辛标记的Northern blot曝光时间为20 s-3 min,RyhB1或RyhB2检测灵敏度分别为0.005 μg和0.05 μg.RyhB1或RyhB2探针特异性好,相互间无交叉反应.带正电或中性的尼龙膜都适用于杂交反应.RNA探针在42℃-65℃内杂交均可,提高温度可减少非特异性反应;而DNA探针杂交温度需摸索.[结论]本研究成功构建一种地高辛标记Northern blot检测鼠疫菌sRNA技术,具有特异性好、灵敏度高、探针易保存、曝光时间短等优点,为细菌sRNA验证和功能研究提供有利工具.     

多功能悬浮点阵技术快速检测肠道致病菌的初步应用研究

目的建立以多功能悬浮点阵技术为基础的临床常见肠道致病菌的快速检测方法。方法以细菌16S rDNA基因保守区序列设计1对通用引物,采用不对称PCR扩增7种临床常见肠道致病菌标准菌株,多功能悬浮点阵技术对不同菌株的PCR产物进行检测以验证相应菌种探针的特异性,最后对48份粪便标本进行肠道致病菌高通量快速检测。结果 7种临床常见肠道致病标准菌株的不对称PCR得到了大量单链产物,其产物用多功能悬浮点阵技术的检测特异性为100%,48份粪便标本不对称PCR产物可与相应探针发生特异性结合,且在多功能悬浮点阵技术的相应检测信号大于阴性对照3倍以上,5种细菌的多功能悬浮点阵技术检测结果与培养鉴定结果符合率100%,48份标本PCR产物均与志贺菌属探针发生杂交反应(阳性率100%)。结论 16S rDNA可以作为细菌快速鉴定的靶序列,不对称PCR产物可以显著提高与悬浮芯片杂交检测的灵敏度,多功能悬浮点阵技术在鉴定细菌方面具有简单快速、高通量、高检出率等特点,可以作为细菌快速鉴定的一种新方法,但无法鉴别志贺菌属和大肠埃希菌属。     

运用基因芯片技术建立检测水产食品中常见病原微生物方法的研究

目的:利用基因芯片技术,以细菌16S rDNA和23S rDNA为靶序列筛选引物和探针,建立快速、准确的检测水产食品中肠道致病菌的方法。方法:将致病菌的16S rDNA和23S rDNA全序列进行软件比对,在可变区和恒定区分别设计特异性寡核苷酸探针和通用性引物,点样于玻片制成基因芯片。致病菌DNA经过通用引物扩增后与芯片上的探针杂交,然后通过扫描图像对结果进行判断。对基因芯片检测的灵敏度进行了评价,并对模拟污染样本进行了实际检测,以验证所建立的方法。结果:设计的4对通用引物在同一条件下能够扩增7种常见肠道致病菌。在均一的杂交条件下能够同时检测单核细胞增生利斯特菌、副溶血性弧菌、霍乱弧菌、金黄色葡萄球菌、弗氏志贺氏菌、鼠伤寒沙门氏菌和肠出血性大肠杆菌O157∶H7;以鼠伤寒沙门氏菌为对象,本方法的检测灵敏度可达到10~3 cfu/mL,实际检测模拟污染的样本的正确率达到100%。结论:建立的基因芯片系统可以准确而稳定地实现对7种水产食品中常见致病菌的通用检测,为食源性感染的诊治与预防提供了有效的技术手段和方法依据。     

定量测定黑鲷生长激素受体mRNA的液相杂交/RNase保护法

目的　建立液相杂交 核糖核酸酶保护测定 (RibonucleaseProtectionAssay,RPA)技术定量检测黑鲷(Sparusmacrocephalus)生长激素受体mRNA水平。方法　将黑鲷生长激素受体cDNA片断亚克隆至pGEM T载体 ,制备特异性的放射性反义RNA探针及正义RNA ,将反义RNA探针与正义RNA及样品总RNA进行液相杂交 ,用RNaseA和RNaseT1 降解杂交产物的单链RNA ,双链杂交体得到保护 ,然后检测杂交体的分子大小及放射强度。结果　检测出了黑鲷生长激素受体反义RNA探针与正义RNA及样品总RNA的特异性杂交片断 ,由此建立了定量测定黑鲷生长激素受体mRNA的液相杂交 RNase保护法 ,并采用该方法在黑鲷的多种组织中检测出了生长激素受体基因的表达 ,表达水平在肝脏中最高。该结果与我们曾采用生长激素放射受体分析法对黑鲷生长激素受体所研究的结果相吻合。结论　为进一步深入研究鱼类生长激素受体分子内分泌的调控理论提供了有力手段。     

基于锁式探针技术快速检测玉米细菌性枯萎病菌和玉米内州萎蔫病菌

目的:建立一种检测玉米细菌性枯萎病菌和玉米内州萎蔫病菌的方法,为同时检测这2种检疫性细菌提供技术手段。方法:基于靶标序列设计2种检疫性细菌的锁式探针,与靶标菌进行连接消化反应,然后采用通用引物进行滚环扩增,其产物与偶联上对应捕获探针的微球进行杂交,最后通过液相悬浮芯片二重检测。结果:该检测方法能够有效地检测2种检疫性细菌,其检测阈值为103CFU/m L,具有良好的可重复性。结论:建立了一种快速、灵敏的玉米细菌性枯萎病菌和玉米内州萎蔫病菌的二重检测方法。     

牙龈卟啉菌特异性克隆探针的筛选

目的 从牙龈卟啉菌47A－1的基因文库中筛选出特异性片段,制备成特异性克隆探针,方法 将牙龈卟啉菌47A－1基因文库中的重组质粒大量扩增和纯化,采用地高辛标记法制备成探针,与口腔中14种常见细菌DNA进行杂交鉴定,检测其特异性,从中筛选出对牙龈叶卟啉菌具有特异性的克隆探针。结果 重组质粒pZJ1与牙龈卟啉菌47A－1杂交,而与其它细菌DNA均不杂交,包括牙龈卟啉菌ATCC33277和W83。结论 重组质粒pZJI可制备成高特异笥克隆探针。     

烟草花叶病毒辽宁分离物Northern杂交检测体系的建立

为了建立烟草花叶病毒辽宁分离物(TMV-LN)的高特异性、高灵敏度的分子杂交检测体系,从粗提纯的TMV-LN粒子中提取RNA,设计特异性引物通过RT-PCR扩增TMV-LN的CP和3'端非翻译区域,将片段连至p UC119载体获得重组质粒p UCTMV-PP,体外转录获得地高辛(DIG)标记的TMV-LN正义链RNA杂交检测探针,同时构建DNA检测探针作为对照。采用点印迹(Dot-blot)杂交和Northern杂交对比RNA探针和DNA探针对TMV-LN的检测特异性和灵敏性。检测结果表明,RNA探针和DNA探针在点印记杂交和Northern杂交中均表现出良好的检测特异性,RNA探针在检测灵敏度方面要略好于DNA探针,且点印迹杂交体系在病毒定性方面较为快捷,Northern杂交体系在病毒基因组RNA的定量方面具有明显优势。     

基因芯片技术检测3种肠道病原微生物方法的建立

目的:建立一种运用多重PCR和基因芯片技术检测和鉴定伤寒沙门氏菌、痢疾杆菌和单核细胞增生利斯特菌的方法。方法:分别选取伤寒沙门氏菌染色体ViaB区域中编码调控Vi抗原表达的基因(vipR)、痢疾杆菌编码侵袭质粒抗原H基因(ipaH)和单核细胞增生利斯特菌溶血素基因(hlyA)设计引物和探针,探针3'端进行氨基修饰,下游引物标记荧光素Cy3。在优化的PCR和杂交反应条件下,进行三重PCR扩增,产物与包括3种致病菌特异性探针的基因芯片杂交。在评价基因芯片的特异性和灵敏度之后,对临床样本进行检测。结果:只有3种目的致病菌的PCR产物在相应探针位置出现特异性信号,其他阴性细菌均无信号出现;3种致病菌的检测灵敏度均可达到103CFU/mL;检测30例临床样本的结果与常规细菌学培养结果一致。结论:所建立的可同时检测伤寒沙门氏菌、痢疾杆菌和单核细胞增生利斯特菌的基因芯片方法快速、准确,特异性高,重复性好,为3种肠道致病菌的快速检测和鉴定提供了新方法和新思路。     

In situ identification of carboxymethyl cellulose-digesting bacteria in the rumen of cattle fed alfalfa or triticale

A method was developed and used to arrest and stain reducing sugars (glucose) produced by bacteria with cell-surface-associated carboxymethyl cellulase (CMCase) and endoglucanase activities (CMC bacteria) in the rumen of cows fed alfalfa or triticale. Precipitation of silver oxide on the surface of individual cells was observed using cellulolytic bacterial pure cultures with known CMCase activity and rumen mixed cultures. The CMC bacteria in the liquid and solid fractions of the rumen digesta were identified using fluorescence in situ hybridization (FISH) with currently available and newly designed oligonucleotide probes. The CMC bacteria contributed between 8.2% and 10.1% to the total bacterial cell numbers. Most of the CMC bacteria (75.2-78.5%) could be identified by FISH probing. The known cellulolytic populations Ruminococcus flavefaciens, R.?albus, and Fibrobacter succinogenes constituted 44.5-53.1% of the total. Other CMC bacteria identified hybridized with the probe Clo549 (11.2-23.0%) targeting members of an uncharacterized genus in Clostridia, the probe Inc852 (8.9-10.7%) targeting members of the family Incertae Sedis III and unclassified Clostridiales, and the probe But1243 (相似文献   

An investigation of the relationship between fecal and rumen bacterial concentrations in sheep

With no acceptable method for collecting fresh rumen fluid from zoo ruminants, it was proposed that fecal bacterial concentrations may be correlated with rumen bacteria. If so, fecal bacterial concentrations could be used to study both the effects of diet on rumen bacteria as well as rumen abnormalities. Total and cellulolytic bacterial concentrations were determined in whole rumen contents and feces of sheep using a most‐probable‐number (MPN) assay. In a Latin square design, four crossbred ewes were fed diets of 100% long or chopped orchardgrass hay (OH) and 60% ground or whole shelled corn plus 40% chopped OH. In a second trial, the sheep were fed a pelleted complete feed at varying levels of intake i.e., control at 2.0% of body weight and at 1.8, 1.6, and 1.2% of body weight. Higher total rumen bacterial concentrations (P<0.01) were found on the high concentrate diets as compared with the high forage diets. Grinding the corn also increased total bacterial concentrations (P<0.05). Fecal concentrations of total bacteria were higher (P<0.01) with the high concentrate diets. Chopping the forage decreased the concentration of fecal cellulolytic bacteria (P<0.05) but had no effect on their concentration in the rumen. An inverse linear relationship (P<0.01) was observed between total bacterial concentrations in the feces and diet intake. Although relationships were observed between the rumen and feces for total and cellulolytic bacterial concentrations, they were dependent on diet, particle size, and level of intake. Thus, fecal bacterial concentrations cannot be used to reliably predict rumen bacterial concentrations. Zoo Biol 27:100–108, 2008. © 2008 Wiley‐Liss, Inc.     

Cellulolytic bacteria in buffalo rumen

The influence of three different feeds, wheat straw, sorghum and berseem, on total and cellulolytic bacterial counts in the buffalo rumen at different time intervals from 0 to 8 h after feeding was studied. Berseem feeding supported maximum growth of rumen bacteria in general and cellulolytic bacteria in particular. Wheat straw supported the poorest growth.
The types of cellulolytic bacteria recovered from the rumen of adult buffaloes were Ruminococcus albus, R. flavefaciens, Bacteroides succinogenes, Butyrivibrio fibrisolvens, Clostridium lochheadii, Cl. longisporum and other Clostridium spp. Cellulolytic cocci were present in smaller numbers than rod forms in the rumen of wheat-straw-fed buffaloes, whereas the cocci outnumbered rod forms in sorghum-and berseem-fed buffaloes.     

Fibrolytic activities and cellulolytic bacterial community structure in the solid and liquid phases of rumen contents.

Four sheep were fed an alfalfa hay diet. Rumen content samples were collected three hours after feeding in order to total microorganism population (TP), solid attached population (SAP) and solid attached firmly population (SAFP). Fibrolytic specific activities (xylanase, CMCase and beta-glycosidases) were estimated by the amount of reducing sugars or p-nitrophenol released from the appropriate substrate. The distribution of the three main cellulolytic bacterial species (Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens) was quantified by dot-blot hybridisation using specific 16S-rRNA-targeting probes. Specific activities of polysaccharidase enzymes were higher in SAP than in TP, and in SAFP than in SAP. The sum of RNA of the three cellulolytic bacterial species represented on average 9% of the total bacterial RNA, and increased after filtration. In all samples, the relative population size of F. succinogenes was higher than that of R. albus and of R. flavefaciens. These results demonstrate that the most active enzymes are secreted by the particle-associated microorganisms. The differences in composition of the microflora between the solid and liquid phase suggest that bacteria are not equally distributed throughout the rumen content: the cellulolytic species are present in a higher proportion in the solid phase of rumen contents.     

Antimicrobial activity of 2-aminophenoxazin-3-one under anaerobic conditions.

Potential toxicity of 2-aminophenoxazin-3-one to 20 bacterial species and two fungi and its inactivation under anaerobic conditions were investigated. Minimum inhibitory concentration for cellulolytic bacteria was in the range of 50-100 micrograms.mL-1, but at 100 micrograms.mL-1 of 2-aminophenoxazin-3-one, there was no effect on the growth of any of the noncellulolytic bacteria. Four noncellulolytic bacterial strains showed no inhibition of growth, even at 200 micrograms.mL-1 of this compound. Under anaerobic conditions and in the presence of cysteine, the long wavelength absorption band of this compound slowly shifted from about 434 to 320 nm, and its inhibitory effect on RNA synthesis was relieved after one-half of a generation time in cultures of cellulolytic ruminal bacteria. A similar shift of absorption band was observed in rumen fluid filtered through a 0.22-microns Millipore filter. It was concluded that protonation of 2-aminophenoxazin-3-one under anaerobic conditions present in the rumen would considerably reduce its potential toxicity to cellulolytic bacteria.     

Ecological factors determining establishment of cellulolytic bacteria and protozoa in the rumens of meroxenic lambs

Ecological factors that control the establishment of cellulolytic bacteria and ciliate protozoa in the lamb rumen were studied in meroxenic animals. Axenic lambs received dilutions of rumen liquor from either conventional lambs and sheep (pool A) or meroxenic lambs (pool B). The total number of bacteria established in the rumen was between 10(9) and 5 x 10(10) g-1. In lambs inoculated with dilutions (10(-6), 10(-7), 10(-8)) of pool A, cellulolytic bacteria did not become established. However, subsequent inoculation with Bacteroides succinogenes, resulted in colonization in lambs that had received 10(-6) and 10(-7) dilutions of pool A. However, B. succinogenes became established in only one of three lambs that received the 10(-8) dilution. Similar results were obtained for the protozoan Entodinium sp. With pool B, lambs were inoculated earlier and cellulolytic bacteria were established directly from the 10(-6) and 10(-7) inocula. Polyplastron multivesiculatum establishment occurred readily when inoculated into the lambs which had received the 10(-6) dilution of pool B. Results obtained in this study suggest that establishment of cellulolytic bacteria and protozoa requires an abundant and complex flora and is favoured by early animal inoculation.     

Use of a unique gene sequence as a probe to enumerate a strain of Bacteroides ruminicola introduced into the rumen

Cloned fragments of genomic DNA from the ruminal anaerobe Bacteroides ruminicola subsp. brevis B14 were isolated and used as hybridization probes to identify closely related bacterial species. One DNA fragment unique to strain B14 was tested to determine its sensitivity in detecting homologous sequences among total ruminal microbial DNA. In a DNA titration experiment, the probe was capable of detecting strain B14 sequences in vitro down to 0.1% of the total bacterial DNA present in a hybridization assay. There was no detectable signal for total ruminal bacterial DNA. The specificity of this DNA fragment was exploited to enumerate strain B14 in a fresh mixed suspension of ruminal bacteria in vitro and after inoculation of the strain into the rumen. In vitro strain B14 had a half-life of 9 h. However, following inoculation into the rumen there was a very rapid loss of the strain to below the detectable limit within 3 h. The half-life was less than 30 min. This loss was not due to ruminal dilution or to bacteriophage attack but was possibly the result of a specific bacteriocinlike activity present in the rumen and detectable in fresh ruminal fluid.     

Use of a unique gene sequence as a probe to enumerate a strain of Bacteroides ruminicola introduced into the rumen.

Cloned fragments of genomic DNA from the ruminal anaerobe Bacteroides ruminicola subsp. brevis B14 were isolated and used as hybridization probes to identify closely related bacterial species. One DNA fragment unique to strain B14 was tested to determine its sensitivity in detecting homologous sequences among total ruminal microbial DNA. In a DNA titration experiment, the probe was capable of detecting strain B14 sequences in vitro down to 0.1% of the total bacterial DNA present in a hybridization assay. There was no detectable signal for total ruminal bacterial DNA. The specificity of this DNA fragment was exploited to enumerate strain B14 in a fresh mixed suspension of ruminal bacteria in vitro and after inoculation of the strain into the rumen. In vitro strain B14 had a half-life of 9 h. However, following inoculation into the rumen there was a very rapid loss of the strain to below the detectable limit within 3 h. The half-life was less than 30 min. This loss was not due to ruminal dilution or to bacteriophage attack but was possibly the result of a specific bacteriocinlike activity present in the rumen and detectable in fresh ruminal fluid.     

Growth Factor Requirements of Ruminococcus flavefaciens Isolated from the Rumen of Cattle Fed Purified Diets

Eight strains of cellulolytic cocci were isolated from a 10^-8 dilution of rumen ingesta and were presumptively identified as Ruminococcus flavefaciens. Four strains were isolated from a steer fed a purified diet which contained isolated soy protein, and four strains were isolated from a steer fed a purified diet which contained urea. Certain growth factor requirements of these bacteria were determined. All strains grew with clarified rumen fluid added to the medium. However, fatty acids could substitute for rumen fluid in four strains. Two strains isolated from each steer either required or their growth was stimulated by isobutyric and/or isovaleric and/or 2-methyl-butyric acid. These results indicate that, even when a diet was fed which contained no branched-chain amino acids, the carbon skeleton precursors of branched-chain fatty acids, the cattle were still able to maintain a large population of cellulolytic bacteria that require fatty acids for growth. Therefore, the fatty acids appear to be provided by other bacteria, by protozoa, or by the host animal.     

Development of an oligonucleotide probe targeting 16S rRNA and its application for detection and quantitation of the ruminal bacterium Synergistes jonesii in a mixed-population chemostat.

Radiolabelled and fluorescent-dye-conjugated oligonucleotide probes which targeted rRNA sequences were developed for the enumeration of the ruminal bacterium Synergistes jonesii 78-1 in mixed culture. Two probes were tested, and both were highly specific for the respective complementary sequences of the target organism. Individual cells of S. jonesii in pure and mixed cultures were clearly visualized in situ by hybridization with the fluorescent-dye-conjugated probe but could not be detected in natural samples. Therefore the radiolabelled probe was used to monitor the population of S. jonesii introduced into a chemostat which simulated the rumen ecosystem. The S. jonesii probe did not hybridize to RNA extracted from the culture prior to inoculation with the target organism. After inoculation, S. jonesii rRNA represented 4.5% of the total bacterial rRNA and then rapidly declined to < 0.2% before increasing to about 1% of the total bacterial rRNA during the following 3 weeks. This study demonstrates that rRNA-targeted probes could be used for tracking organisms introduced into the rumen ecosystem.