汉族与维吾尔族儿童封闭型不同龋敏感中变形链球菌乳酸脱氢酶遗传多态性研究

目的探讨汉族与维吾尔族儿童封闭型不同龋敏感中变形链球菌乳酸脱氢酶活性与ldh基因多态性及龋病发生的关系。方法从前期实验分离的维吾尔族与汉族儿童口腔变形链球菌中筛选出:维吾尔族儿童封闭型口腔变形链球菌高龋组变形链球菌35株[龋失补牙数(dmft)≥5],无龋组变形链球菌37株[龋失补牙数(dmft)=0];27株表现乳酸脱氢酶高活性,24株低活性;汉族儿童口腔中分离的高龋和无龋变形链球菌各35株,高活性和低活性各25株,使用特异引物扩增细菌组DNA,获得结构基因ldh,进行聚合酶链反应-限制性内切酶多态性分析。结果维吾尔族儿童封闭型和汉族儿童MseⅠ酶切ldh-RFLP表现A、B两种基因型;而MnlⅠ、DdeⅠ、NlaⅢ和AluⅠ消化扩增产物未发现多态性。MseⅠ产生的B基因型菌株在维吾尔族儿童封闭型,汉族儿童高龋组的检出均高于无龋组(P0.05),A、B两种基因型在不同酶活性组的分布不同(P0.05),高酶活性组B基因型菌株的比例高于低酶活性组;A、B基因型在维吾尔族儿童封闭型和汉族高龋组、无龋组,高酶活性组和低酶活性组的检出比较差异无统计学意义(P0.05)。结论变形链球菌乳酸脱氢酶基因多态性在维吾尔族与汉族儿童并未表现出差异性,ldh基因多态性与变形链球菌乳酸脱氢酶活性及龋高敏感性相关。ldh基因分布与酶活性及乳牙龋具有正相关性。     

一种快速检测儿童唾液内MS菌的方法——刃天青纸片法

本试验收集202例3～5岁学龄前儿童唾液标本,用微氧培养法及刃天青纸片法检查唾液内致龋的MS菌群(包括:Streptococeus·mutans,S·sobcinus,S·cncetus,S·sattus四个菌种),同时记录每个儿童口腔内患龋情况。通过对试验结果的对照分析发现:儿童的龋齿发生的数量和唾液内MS菌群的数量成正比关系,有龋和无龋之间的菌数有一个明显界线(1.6×10~5)。同时从唾液与刃天青纸片的颜色反应发现:不同的颜色反应(兰、     

维吾尔族与汉族儿童肠道细菌群落分析

【背景】肠道菌群是人体的重要组成部分,在人体的多种生命活动中发挥着重要作用。【目的】探究维吾尔族和汉族儿童肠道细菌群落特征,为儿童营养健康状况监测和营养改善工作提供更有效精准的营养干预策略。【方法】从新疆维吾尔自治区泽普县维吾尔族和河南省民权县汉族人群中分别随机选取10?12岁学龄期儿童各20名,同一时间段收集其新鲜粪便,提取细菌总DNA,通过高通量测序和生物信息学分析,研究两地区健康维吾尔族儿童与汉族儿童肠道细菌群落的差异。【结果】获得测序序列2 007 100条,归类于994个OTU;所有样本共含15个细菌门139属。α多样性和β多样性分析表明,调查地区的2个民族儿童肠道细菌的丰富度和多样性均有统计学意义上的差异,维吾尔族儿童肠道细菌群落丰富度高于汉族儿童,而物种多样性不如汉族儿童。其中,维吾尔族儿童肠道细菌丰度相对占优势的门和属及其丰度值为：拟杆菌门(Bacteroidetes,63%)、厚壁菌门(Firmicutes,22%)、普氏菌属(Prevotella,61%)、琥珀酸弧菌属(Succinivibrio,9%)和粪杆菌属(Faecalibacterium,5%);汉族儿童肠道细菌丰度占优势的门和属及其丰度值为：厚壁菌门(57%)、拟杆菌门(23%)、粪杆菌属(16%)、普氏菌属(11%)和拟杆菌属(Bacteroides,11%)。【结论】调查地区维吾尔族与汉族儿童肠道细菌群落差异较大,这为进一步研究肠道菌群与膳食因素及人体营养健康状况之间的关系提供了依据。     

东太湖表层沉积物放线菌群落结构多样性及其空间异质性

采用基于16SrRNA基因变性梯度凝胶电泳(DGGE)方法,考察东太湖表层沉积物放线菌群落结构多样性及其空间分布特征.结果显示:东太湖表层沉积物中放线菌群落结构多样性较高,DGGE指纹图谱样品的平均条带数为21.5±2个,群落结构多样性(如Shannon-Wiener指数)在空间尺度上差异不明显;聚类分析表明放线菌群落结构空间分布特征表现为相邻采样位点群落结构较为相似,这可能与相邻位点沉积物理化性质类似有关.典型对应分析结果表明,东太湖表层沉积物中放线菌群落结构变化的主要影响因子为沉积物pH.     

舌苔细菌PCR-DGGE分析条件的建立与优化

目的针对口腔舌苔细菌16S rDNA序列进行变性梯度凝胶电泳(denaturing gradient gel electrophoresis,DGGE)适用序列的筛选及电泳条件的优化。方法以DGGE图谱的高分辨率为指标,选择舌苔细菌DGGE分离最适的16S rDNA高变区、电泳电压和电泳时间,并采用优化的条件分析健康青年人舌苔细菌群落的分布。结果舌苔细菌16S rDNA V3高变区引物序列能获得更加丰富清晰的DGGE条带;基于该区,当变性剂浓度为30%～60%、电泳温度60℃、电压60 V和电泳时间14 h时能得到分辨率最佳的DGGE图谱。运用此优化条件对12个样本舌苔细菌群落的分析表明,舌苔微生物主要由厚壁菌门、梭杆菌门、拟杆菌门和变形菌门等组成。优化后的DGGE技术对舌苔细菌多样性的分析具有准确性、灵敏性和可重复性。结论 DGGE图谱显示,不同分析条件对图谱类型和细菌多样性指数均有所差异。利用优化的DGGE条件能有效分离舌苔细菌16S rDNA V3区序列,为口腔微生物群落结构分析提供可靠的技术支持,也为其他不同生态细菌的多样性分析提供参考。     

PCR指纹图谱技术分析人体口腔内微生物菌群结构

目的 应用PCR-DGGE指纹图谱技术对人体口腔微生物菌群结构进行系统性研究.方法 对1例健康人唾液周期性采集的样品和8例健康人个体的唾液与牙菌斑采集的样品,进行微生物群落总DNA的抽提.以此为模板扩增16S rRNA V3可变区,产物经DGGE指纹图谱分析其组成结构,并运用UVIBAND/MAP等软件比较所得群落指纹图谱的相似性指数.结果 同一健康人个体不同采样时间的唾液菌群结构相似性系数＞74%,通过对不同健康个体口腔样本的研究,发现同一个体的唾液与牙菌斑菌群结构存在差异（84%～95%）.结论 同一健康个体其唾液微生物菌群在一定时间内基本稳定,仅有微小的变化;唾液与同个体牙菌斑的微生物组成虽然存在差异,但这种差异要明显小于个体间的差异.     

喀什市3～5岁维吾尔族、汉族儿童患龋情况及风险性评估

目的调查喀什市维吾尔族、汉族3~5岁儿童患龋情况及患龋风险因素的相关资料,建立儿童个体龋风险评估(caries risk assessment,CRA)模型,为当地儿童龋病风险性评估和制定综合防控计划提供样本及参考数据。方法采用分层、整群抽样的方式随机抽取喀什市3所幼儿园397名3~5岁健康儿童作为研究对象,进行口腔检查和龋风险评估。分别应用卡方检验、方差分析及Logistic回归分析方法对龋风险评估相关因素进行统计分析。结果 (1)喀什市3~5岁汉族与维吾尔族儿童分布在CAR低度组、中度组和高度组三组比较差异均有统计学意义(χ~2=8.055,P=0.018)。(2)汉族与维吾尔族儿童的龋在不同CAR分度组的差异均具有统计学意义(F1=47.46,P=0.000;F2=74.5,P=0.000)。(3)汉族和维吾尔族在龋风险评估各组之间的患龋率差异有统计学意义(χ~2_1=98.21,P=0.000;χ~2_2=154.89,P=0.000)。(4)多因素Logistic回归分析风险评估相关因素结果显示:年龄更大[OR=1.769,P=0.001]、母亲患有龋齿[OR=2.274,P=0.004]、经常用奶瓶和牛奶或果汁[OR=0.705,P=0.000]、经常吃零食[OR=4.825,P=0.000]是婴幼儿龋的危险因素;刷牙[OR=0.319,P=0.019]、辅助儿童刷牙[OR=0.305,P=0.002]是婴幼儿龋的保护因素。结论喀什市3~5岁儿童患龋情况严重,龋风险评估高的儿童占大多数,应加强口腔健康教育,开展多种防龋措施。     

固定矫治器对口腔菌群的影响

目的利用PCR-DGGE方法探讨戴用牙齿固定矫治器对口腔菌群的影响。方法从20例健康的牙齿正常个体和30例戴用固定矫治器的正畸患者的唾液中提取细菌基因组总DNA,利用聚合酶链式反应—变形梯度凝胶电泳(PCR-DGGE)方法获取口腔菌群的分子指纹图谱,对其进行相似性和多样性的分析以及优势条带的序列分析。结果 PCR-DGGE可明确将正常个体和正畸患者分成2个簇,且正畸患者口腔菌群的多样性明显增加,优势菌群发生转变,序列分析表明口腔链球菌数量明显减少,假单胞菌成为优势菌型。结论戴用固定矫治器能改变口腔菌群分布,引起口腔中有益菌的减少,促使致病菌增长,导致口腔菌群失调。     

应用PCR-DGGE技术分析BKS-2型糖尿病模型小鼠盲肠内容物微生物菌群结构

通过对BKS-DB 2型糖尿病小鼠盲肠内容物微生物群落结构的分析,探讨基因突变模型鼠肠道微生物群落与糖尿病发生的相关性。提取BKS-DB 2型糖尿病小鼠与同窝对照小鼠盲肠内容物细菌总DNA,PCR扩增16S rRNA基因V3区,DGGE方法检测扩增产物,并挑选特异条带测序,对图谱作UPGAMA聚类分析,运用SPSS软件分析多样性。结果显示,UPGAMA聚类分析表明,对照组样本之间相似度0.66-0.91,糖尿病组样本之间相似度0.61-0.88,两组之间最高相似度为0.51。特异性条带测序后经比对与Parabacteroides菌属亲缘关系最近。SPSS统计分析糖尿病组和健康对照组小鼠的DGGE条带数、多样性指数(H’)、丰富度(R)和优势度(D)的差异性显著,具有统计学意义(P<0.05)。糖尿病组小鼠与对照组小鼠的盲肠内容物微生物群落多样性存在差异,糖尿病对肠道微生物的多样性有影响。     

肝硬化患者与健康人群唾液菌群的对比分析

目的 分析肝硬化患者（LC组）与健康人群（N组）唾液菌群丰度及多样性的差异，为后续研究提供参考。方法 收集45例肝硬化患者和44例健康人群唾液样本，应用高通量测序技术进行测序分析，对有效序列进行物种注释及多样性分析。结果 共获得7 729 352条有效序列，平均每个样本获得有效序列86 847条。两组人群唾液样本内菌群丰度及多样性差异无统计学意义（均P>0.05）；而唾液菌群结构差异有统计学意义（F=20.13,P<0.01）。肝硬化患者口腔中厚壁菌门（Firmicutes）、拟杆菌门（Bacteroidota）、梭杆菌门（Fusobacteriota）相对丰度较高，而在健康人群口腔中变形菌门（Proteobacteria）相对丰度较高（均P<0.05）。结论 肝硬化患者与健康人群唾液菌群结构有差异，肝硬化患者相较于健康人群可能更易患龋病、牙周炎。重视口腔健康，防治口腔菌群失调对肝硬化的治疗具有重要意义。     

Comparison of Oral Microbial Profiles between Children with Severe Early Childhood Caries and Caries-Free Children Using the Human Oral Microbe Identification Microarray

Objective

Early childhood caries (ECC) has become a prevalent public health problem among Chinese preschool children. The bacterial microflora is considered to be an important factor in the formation and progress of dental caries. However, high-throughput and large-scale studies of the primary dentition are lacking. The present study aimed to compare oral microbial profiles between children with severe ECC (SECC) and caries-free children.

Methods

Both saliva and supragingival plaque samples were obtained from children with SECC (n = 20) and caries-free children (n = 20) aged 3 to 4 years. The samples were assayed using the Human Oral Microbe Identification Microarray (HOMIM).

Results

A total of 379 bacterial species were detected in both the saliva and supragingival plaque samples from all children. Thirteen (including Streptococcus) and two (Streptococcus and Actinomyces) bacterial species in supragingival plaque and saliva, respectively, showed significant differences in prevalence between the two groups. Of these, the frequency of Streptococcus mutans detection was significantly higher in both saliva (p = 0.026) and plaque (p = 0.006) samples from the SECC group than in those from the caries-free group.

Conclusions

The findings of our study revealed differences in the oral microbiota between the SECC and caries-free groups Several genera, including Streptococcus, Porphyromonas, and Actinomyces, are strongly associated with SECC and can be potential biomarkers of dental caries in the primary dentition.     

Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing

Oral microbiota plays a vital role in maintaining the homeostasis of oral cavity. Dental caries are among the most common oral diseases in children and pathogenic bacteria contribute to the development of the disease. However, the overall structure of bacterial communities in the oral cavity from children with dental caries has not been explored deeply heretofore. We used high-throughput barcoded pyrosequencing and PCR-denaturing gradient gel electrophoresis (DGGE) to examine bacterial diversity of oral microbiota in saliva and supragingival plaques from 60 children aged 3 to 6 years old with and without dental caries from China. The multiplex barcoded pyrosequencing was performed in a single run, with multiple samples tagged uniquely by multiplex identifiers. As PCR-DGGE analysis is a conventional molecular ecological approach, this analysis was also performed on the same samples and the results of both approaches were compared. A total of 186,787 high-quality sequences were obtained for evaluating bacterial diversity and 41,905 unique sequences represented all phylotypes. We found that the oral microbiota in children was far more diverse than previous studies reported, and more than 200 genera belonging to ten phyla were found in the oral cavity. The phylotypes in saliva and supragingival plaques were significantly different and could be divided into two distinct clusters (p < 0.05). The bacterial diversity in oral microbiome analyzed by PCR-DGGE and barcoded pyrosequencing was employed to cross validate the data sets. The genera of Streptococcus, Veillonella, Actinomyces, Granulicatella, Leptotrichia, and Thiomonas in plaques were significantly associated with dental caries (p < 0.05). The results showed that there was no one specific pathogen but rather pathogenic populations in plaque that significantly correlated with dental caries. The enormous diversity of oral microbiota allowed for a better understanding of oral microecosystem, and these pathogenic populations in plaque provide new insights into the etiology of dental caries and suggest new targets for interventions of the disease.     

A New Framework to Accurately Quantify Soil Bacterial Community Diversity from DGGE

Denaturing gradient gel electrophoresis (DGGE) has been and remains extensively used to assess and monitor the effects of various treatments on soil bacterial communities. Considering only abundant phylotypes, the diversity estimates produced by this technique have been proven to be uncorrelated to true community diversity. The aim of this paper was to develop a framework to estimate a community’s true diversity from DGGE. Developed using in silico DGGE profiles generated from published pyrosequencing datasets, this framework elongates the rank-abundance distributions (RADs) drawn by band quantification using the peak-to-signal ratio (PSR) parameter, which was proven to be related to bacterial richness. The ability to compare DGGE-based diversity estimates to the true diversity of communities led to a unique opportunity to identify potential pitfalls when analyzing DGGE gels with commercial analysis software programs and gain insight into the process of DNA band clustering in the profiles. Bacterial diversity was compared through richness, Shannon, and Simpson’s 1/D indices. Intermediate results demonstrated that, even though commercial gel analysis software programs were unable to produce consistent results throughout all samples, a newly developed Matlab-based framework unraveled the dominance profiles of communities from band quantification. Elongating these partial RADs using the PSRs extracted from the DGGE profiles chiefly made it possible to accurately estimate the true diversity of communities. For all the samples analyzed, the estimated Shannon and Simpson’s 1/D were accurate at ±10 %. Richness estimations were less accurate, ranging from ?11 to 31 % of the expected values. The framework showed great potential to study the structure and diversity of soil bacterial communities.     

Analysis of oral microbial community and Th17‐associated cytokines in saliva of patients with oral lichen planus

Oral lichen planus (OLP) is a chronic inflammatory disorder of oral mucosa of unknown cause. Microbial infection and dysimmunity appear to play important roles in its pathogenesis. In this study, differences in genetic profiling of salivary microbial communities in two subtypes of OLP and healthy controls were evaluated by means of PCR‐denaturing gradient gel electrophoresis (DGGE). Additionally, ELISA was used to investigate the possible role of Th17 in lesion formation by detecting two related cytokines IL‐17 and IL‐23 in the saliva of OLP patients. When the DGGE profiles were analyzed, the bacterial populations were found to be significantly less rich in subjects with reticular and erosive OLP than in healthy controls. There was significantly less microbial diversity, as denoted by the Shannon index, in saliva samples from subjects with erosive OLP than in those from healthy controls. Cluster analysis and principal component analysis showed that the DGGE profiles formed distinctly group‐specific clusters. Salivary concentrations of IL‐17 in subjects with erosive OLP group were significantly higher than in those with reticular OLP and healthy controls. What's more, significantly positive correlations were observed between salivary IL‐17 concentrations and disease clinical scores. Microbial richness and diversity was negatively correlated with salivary IL‐17 concentrations. These results suggest there is significantly less salivary bacterial diversity and complexity in subjects with OLP han in healthy controls and that the shifted community composition is closely related to an immune cytokine, IL‐17.     

Comparison of automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) techniques for analysing the influence of diet on ruminal bacterial diversity

The objective of this study was to compare the automated ribosomal intergenic spacer analysis (ARISA) and the denaturing gradient gel electrophoresis (DGGE) techniques for analysing the effects of diet on diversity in bacterial pellets isolated from the liquid (liquid-associated bacteria (LAB)) and solid (solid-associated bacteria (SAB)) phase of the rumen. The four experimental diets contained forage to concentrate ratios of 70:30 or 30:70 and had either alfalfa hay or grass hay as forage. Four rumen-fistulated animals (two sheep and two goats) received the diets in a Latin square design. Bacterial pellets (LAB and SAB) were isolated at 2 h post-feeding for DNA extraction and analysed by ARISA and DGGE. The number of peaks in individual samples ranged from 48 to 99 for LAB and from 41 to 95 for SAB with ARISA, and values of DGGE-bands ranged from 27 to 50 for LAB and from 18 to 45 for SAB. The LAB samples from high concentrate-fed animals tended (p < 0.10) to show greater peak numbers and Shannon index values than those isolated from high forage-fed animals with ARISA, but no differences were identified with DGGE. The SAB samples from high concentrate-fed animals had lower (p < 0.05) peak numbers and Shannon index values than those from animals fed high-forage diets with ARISA, but only a trend was noticed for these parameters with DGGE (p < 0.10). The ARISA detected that animals fed alfalfa hay diets showed lower (p < 0.05) SAB diversity than those fed grass hay diets, but no differences were observed with DGGE. No effect of forage type on LAB diversity was detected by any technique. In this study, ARISA detected some changes in ruminal bacterial communities that were not detected by DGGE, and therefore ARISA was considered more appropriate for assessing bacterial diversity of ruminal bacterial pellets. The results highlight the impact of the fingerprinting technique used to draw conclusions on dietary factors affecting bacterial diversity in ruminal bacterial pellets.     

Individual microflora beget unique oral microcosms

AIMS: To examine the efficacy of the multiple Sorbarod device (MSD) for the reproduction of inter-individual variations in oral microbiotas. The MSD supports sessile growth on parallel cellulose filters, perfused with artificial saliva. This enables biofilms (BF) to be grown and sampled, together with released cells in eluted medium (perfusates, PAs). METHODS AND RESULTS: Two sets of triplicate MSDs were established. One set was inoculated using fresh saliva from three separate volunteers; the second set was inoculated from one saliva donor. Both were incubated in an anaerobic cabinet. BF and PA were analysed at 24-h intervals by PCR-denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Hierarchical dendrograms were constructed in order to sort community fingerprints over time, based on community relatedness. The MSD supported complex oral communities, as evidenced by DGGE (>20 distinct DGGE bands) and confocal scanning laser microscopy. DGGE band sequencing revealed bacteriological diversity and a high incidence of anaerobic species, including Prevotella sp. Dendrograms demonstrated marked inter-individual variation in the relative species abundance within salivary inocula from different volunteers (DV) and each associated MSD (all >45%, majority c. 85% concordance). Less variation was shown between triplicate models established using saliva from a single volunteer (SV) (all >58%; majority c. 95% concordance). PAs clustered together with the associated biofilms and inocula in the majority of cases for the DV MSDs whilst SV MSD community profiles clustered between replicate MSDs. CONCLUSIONS: Data indicate that marked inter-individual variations in human salivary composition can be partially replicated in individualized MSD microcosms. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrates the in vitro reproduction of individual oral microbiotas and suggests that taking inter-individual variability into account will increase the relevance of microcosm studies.     

Effect of monoculture soybean on soil microbial community in the Northeast China

Monoculture (MC) soybean, a common practice in the Northeast China, causes significant declines in soybean yield and quality. The objective of this study was to evaluate the responses of the soil microbial community and soybean yield to different soybean cropping systems. Three cropping systems were compared, (1) corn-soybean rotation (corn-corn-soybean, CS), (2) MC soybean for 3 years (S3), (3) MC soybean for 9 years (S9). Both bulk and rhizosphere soil samples were collected at three growth stages: two trifoliate (V2), full bloom (R2), and full seed (R6), respectively. Soil microbial DNA was analyzed using polymerase chain reaction (PCR)—denaturing gradient gel electrophoresis (DGGE) to assess changes in composition of bacterial and fungal communities. Prominent DGGE bands were excised and sequenced to gain insight into the identities of the predominant microbial populations. Some prominent differences were observed in bacterial DGGE patterns of amplified 16S rDNA (V3 region) among rhizosphere soils. These major differences included one DGGE band (showing 100% similarity to Arthrobacter sp.) that was enriched at R2 stages in CS and S9, and another band with 97% sequence similarity to an uncultured actinobacterium was detected at R6 stage in CS, and at R2 and R6 stages in S9. The bacterial community from bulk soil showed no significant band change in DGGE patterns among different cropping systems. In fungal DGGE patterns of the amplified 18S rDNA partial fragment, one specific band (showing 98% similarity to Trichoderma viride) occurred in rhizosphere soil of treatment CS at V2 and R6 stages and treatment S9 at R6 stage. None of the above bands were detected in treatment S3. The soybean yields and plant heights from CS and S9 were greater than those from S3. Moreover, catalase activities from CS and S9 at V2 and R2 stages were higher than those tested from S3 at the corresponding times in rhizosphere soil. The present results showed that DGGE patterns were not able to detect significant differences in diversity or evenness among microbial communities, but significant differences were found in the composition of bacterial and fungal community structures. Some distinguished bands from bacterial and fungal DGGE patterns were only enriched in CS and S9 soil, which could potentially play an important role in soybean growth development.     

Evaluation of Marine Bacteroidetes-Specific Primers for Microbial Diversity and Dynamics Studies

Assumptions on the matching specificity of group-specific bacterial primers may bias the interpretation of environmental microbial studies. As available sequence data continue growing, the performance of primers and probes needs to be reevaluated. Here, we present an evaluation of several commonly used and one newly designed Bacteroidetes-specific primer (CF418). First, we revised the in silico primer coverage and specificity with the current SILVA and RDP databases. We found minor differences with previous studies, which could be explained by the chosen databases, taxonomies, and matching criteria. We selected eight commonly used Bacteroidetes primers and tested them with a collection of assorted marine bacterial isolates. We also used the denaturing gradient gel electrophoresis (DGGE) approach in environmental samples to evaluate their ability to yield clear and diverse band patterns corresponding to Bacteroidetes phylotypes. Among the primers tested, CF968R did not provide satisfactory results in DGGE, although it exhibited the highest in silico coverage for Flavobacteria. Primers CFB560 and CFB555 presented undesirable features, such as requiring nested protocols or presence of degeneracies. Finally, the new primer CF418 and primer CF319a were used to explore the Bacteroidetes dynamics throughout a 1-year cycle in Mediterranean coastal waters (Blanes Bay Microbial Observatory). Both primers provided clear and diverse banding patterns, but the low specificity of CF319a was evidenced by 83.3?% of the bands sequenced corresponding to nontarget taxa. The satisfactory DGGE banding patterns and the wide diversity of sequences retrieved from DGGE bands with primer CF418 prove it to be a valuable alternative for the study of Bacteroidetes communities, recovering a wide range of phylotypes within the group.     

氧化钠胁迫下苯丙烯酸对黄瓜根际细菌DNA分子水平多态性的影响

采用PCR-DGGE技术,研究了NaCl（0、292.5、585 mg·kg^-1土）胁迫下,不同浓度苯丙烯酸（0、25、50、100、200 mg·kg^-1土）对黄瓜根际细菌DNA分子水平多态性的影响.结果表明：在黄瓜幼苗的不同时期,低浓度苯丙烯酸（50 mg·kg^-1土）处理使DGGE图谱中的条带数和条带灰度与对照（CK,0 mg·kg^-1土）相近,多样性指数、均匀度指数和丰富度指数最高;高浓度苯丙烯酸（100、200 mg·kg^-1土）处理使土壤DGGE图谱中的条带数减少,条带灰度变暗,多样性指数、均匀度指数和丰富度指数较低.表明NaCl胁迫下,低浓度苯丙烯酸缓解而高浓度苯丙烯酸加重了盐分对土壤微生物的胁迫.对目的条带的克隆测序结果表明,受影响的主要细菌类群多数为不可培养细菌及α-、γ-和β-变形菌门,有少部分属于厚壁菌门、酸杆菌门和放线菌门.     

Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma

ABSTRACT: BACKGROUND: Bacterial infections have been linked to malignancies due to their ability to induce chronicinflammation. We investigated the association of oral bacteria in oral squamous cellcarcinoma (OSCC/tumor) tissues and compared with adjacent non-tumor mucosa sampled 5cm distant from the same patient (n = 10). By using culture-independent 16S rRNAapproaches, denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing, weassessed the total bacterial diversity in these clinical samples. RESULTS: DGGE fingerprints showed variations in the band intensity profiles within non-tumor andtumor tissues of the same patient and among the two groups. The clonal analysis indicatedthat from a total of 1200 sequences characterized, 80 bacterial species/phylotypes weredetected representing six phyla, Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria,Actinobacteria and uncultivated TM7 in non-tumor and tumor libraries. In combined library,12 classes, 16 order, 26 families and 40 genera were observed. Bacterial species,Streptococcus sp. oral taxon 058, Peptostreptococcus stomatis, Streptococcus salivarius,Streptococcus gordonii, Gemella haemolysans, Gemella morbillorum, Johnsonella ignavaand Streptococcus parasanguinis I were highly associated with tumor site where asGranulicatella adiacens was prevalent at non-tumor site. Streptococcus intermedius waspresent in 70% of both non-tumor and tumor sites. CONCLUSIONS: The underlying changes in the bacterial diversity in the oral mucosal tissues from non-tumorand tumor sites of OSCC subjects indicated a shift in bacterial colonization. These mostprevalent or unique bacterial species/phylotypes present in tumor tissues may be associatedwith OSCC and needs to be further investigated with a larger sample size.