抗生素和高脂饮食对大鼠肠道乳杆菌多样性的影响

【目的】对正常、高脂、抗生素处理大鼠肠道内乳杆菌进行定性和定量分析,比较不同处理组大鼠肠道乳杆菌的多样性。【方法】应用纯培养和非培养技术(16S r RNA基因序列分析、变性梯度凝胶电泳、实时荧光定量PCR)对大鼠肠道乳杆菌进行分离鉴定和多样性分析。【结果】16S r RNA基因序列同源性分析结果显示,正常组大鼠肠道内分离出的乳杆菌包括约氏乳杆菌(Lactobacillus johnsonii)、鼠乳杆菌(Lactobacillus murinus)、嗜酸乳杆菌(Lactobacillus acidophilus)、罗伊氏乳杆菌(Lactobacillus reuteri)、植物乳杆菌(Lactobacillus plantarum)、肠道乳杆菌(Lactobacillus intestinals)、动物乳杆菌(Lactobacillus animalis)和阴道乳杆菌(Lactobacillus vaginalis);但L.animalis在高脂处理组大鼠肠道内未分离到,L.intestinals和L.vaginalis在抗生素处理组大鼠中未分离到。DGGE结果显示3个组别大鼠肠道中乳杆菌构成差异明显,同一组内样品间相似性较高;相较于正常组和高脂组,抗生素组的丰度较差;且正常组大鼠肠道内乳杆菌的多样性高于高脂组和抗生素组。q-PCR结果显示正常组大鼠肠道乳杆菌的数量明显高于高脂组和抗生素组,高脂组的数量也明显高于抗生素组,且3个组别之间存在显著差异(P0.01)。【结论】高脂饮食及抗生素的使用会减少肠道内乳杆菌多样性。     

哈尔滨城市和乡村青年居民肠道菌群多样性研究

【目的】分析居住于哈尔滨城市和乡村的青年居民肠道菌群多样性的异同。【方法】采用PCR和DGGE技术相结合的方法对生活于哈尔滨城市和乡村的青年志愿者肠道菌群多样性进行研究。基于DGGE指纹图谱,分别使用聚类和PCA分析对志愿者肠道微生物相似性进行分析,使用Shannon-Weine多样性指数(H′)、丰度(S)和均匀度(EH)对志愿者肠道微生物多样性进行分析,对图谱中具有代表性的共性和特异性条带进行胶回收和克隆测序以分析志愿者肠道微生物组成。基于PCR技术在种水平上对城乡志愿者肠道内乳杆菌属和双歧杆菌属多样性进行定性分析。【结果】相似性分析显示,城乡青年居民间肠道微生物群落结构存在分开趋势,相似性小于城市或乡村青年居民内部;多样性分析显示,城乡青年居民肠道微生物多样性差异不显著;测序结果表明,城乡居民肠道微生物组成在门水平上相同,但是在种属水平上存在差异。PCR定性分析显示Lactobacillus plantarum、L.casei和L.salivarius在哈尔滨城乡青年居民肠道内检出率接近100%,Bifidobacterium longum和B.breve的检测率约90%,在哈尔滨城乡青年居民肠道内普遍存在;乳杆菌属和双歧杆菌属各细菌种在城乡居民肠道中的检出频率差异不显著。【结论】哈尔滨城市和乡村青年居民肠道微生物多样性差异不显著。     

73例中国人血友病甲基因突变的分析

我们用Southern blotting、PCR、变性梯度凝胶电泳(DGGE)和DNA测序等方法对73例血友病甲患者(经上海瑞金医院测定血浆FVⅢ:C和vWF:Ag诊断,其中无亲缘关系患者65例,按FVⅢ:C水平分为轻、中、重三型。FVⅢ:C< 2%为重型,共47例;FVⅢ:C 2%-5%为中型,共9例;FVⅢ:C5%-25%为轻型,共1 7例)进行FVⅢ基因突变检测。共检出内含子22倒位23例,均为重型,约占重型的49%,与国外报道相似。余下50例(其中无亲缘关系者45)用PCR-DGG E分析所有外显子及其侧翼内含子序列,发现异常条带则进行DNA测序。在17例患者中检出突变13种,其中无义突变5种,均为重型;错义突变6种,除1例外都是轻中型;小缺失2例,都是重型;其中,AA466Lys(AAG)-Thr(ACG)、719Tyr(TAC)-Stop(TAG)、AA826 Asp(GAC)-Glu(GAA)、312Ile(ATC)-xxC及AA1551-1552del(AGAA)为新发现的突变。有亲缘关系的患者都有相同的基因突变,而在无亲缘关系患者未发现相同突变。基因突变与临床表现基本相符。 Abstract:We use Southern blotting,PCR,denaturing gradient gel electrophoresis(DGGE)and DNA sequencing to detect gene mutations of haemophilia A in Chinese population.73 cases(47 severe)(FVIII:C<2%),9 moderate(FVIII:C 2%~5%),17 mild(FVIII:C 5%~25%)of haemophilia A were first screened with Southern blotting,23 were found to be the intron 22 inversion type,all being severe cases.The remaining 50 cases without intron 22 in version were examined with PCR-DGGE.Genomic DNA were amplified using GC-clamped primers covering all the exons and all flanking intron regions.Abnormal bands were sequenced.13 different mutations were identified,including 5 nonsense mutations,6 missense mutations and 2 small deletions.5 mutations,AA466Lys(AAG)-Thr(ACG),AA719Tyr(TAC)-Stop(TAG),AA826Asp(GAC)-Glu(GAA),AA312Ile(ATC)-xxC and AA1551-1552del(AGAA)have not been reported before.Generally the genetic defects correspond to the clinical conditions.     

Relationships between biological soil crusts,bacterial diversity and abundance,and ecosystem functioning: Insights from a semi‐arid Mediterranean environment

Questions: To what degree do biological soil crusts (BSCs), which are regulators of the soil surface boundary, influence associated microbial communities? Are these associations important to ecosystem functioning in a Mediterranean semi‐arid environment? Location: Gypsum outcrops near Belmonte del Tajo, Central Spain. Methods: We sampled a total of 45 (50 cm × 50 cm) plots, where we estimated the cover of every lichen and BSC‐forming lichen species. We also collected soil samples to estimate bacterial species richness and abundance, and to assess different surrogates of ecosystem functioning. We used path analysis to evaluate the relationships between the richness/abundance of above‐ and below‐ground species and ecosystem functioning. Results: We found that the greatest direct effect upon the ecosystem function matrix was that of the biological soil crust (BSC) richness matrix. A few bacterial species were sensitive to the lichen community, with a disproportionate effect of Collema crispum and Toninia sedifolia compared to their low abundance and frequency. The lichens Fulgensia subbracteata and Toninia spp. also had negative effects on bacteria, while Diploschistes diacapsis consistently affected sensitive bacteria, sometimes positively. Despite these results, very few of the BSC effects on ecosystem function could be ascribed to changes within the bacterial community. Conclusion: Our results suggest the primary importance of the richness of BSC‐forming lichens as drivers of small‐scale changes in ecosystem functioning. This study provides valuable insights on semi‐arid ecosystems where plant cover is spatially discontinuous and ecosystem function in plant interspaces is regulated largely by BSCs.     

Molecular Characterization of Microbial Population Dynamics during Sildenafil Citrate Degradation

Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to retrieve sildenafil citrate contaminated sites.     

Comparison of Metagenomic DNA Extraction Methods for Soil Sediments of High Elevation Puga Hot Spring in Ladakh,India to Explore Bacterial Diversity

Extraction of good-quality metagenomic DNA from extreme environments is quite challenging, particularly from high elevation hot spring sediments. Low microbial load, high humic acid content and other contaminants complicate the process of extraction of metagenomic DNA from hot spring sediments. In the present study, efficacy of five manual DNA extraction protocols with modifications has been evaluated for metagenomic DNA extraction from boron–sulfur rich high elevation Puga hot spring sediments. Best suited protocol was identified based on the cell lysis efficiency, DNA yield, humic acid content, PCR reproducibility and representation of bacterial diversity. Quantity as well as quality of crude metagenomic DNA differed remarkably between various protocols used and were not pure enough to give PCR amplification using 16S rRNA bacterial and archaeal primers. Crude metagenomic DNA extracted using five different DNA extraction protocols was purified using spin column based purification method. Even after purification, only three protocols C, D and E yielded metagenomic DNA that could be amplified using both archaeal and bacterial primers. To evaluate the degree of microbial diversity represented by protocols C, D and E, phylogenetic genes amplified were subjected to amplified ribosomal DNA restriction analysis (ARDRA) and denaturing gradient gel electrophoresis analysis (DGGE) analysis. ARDRA banding pattern of amplicons generated for all the three extraction protocols, i.e., C, D and E were found to be similar. DGGE of protocol E derived amplicons resulted in the similar number of dominant bands but a greater number of non-dominant bands, i.e., the highest microbial diversity in comparison to protocols C and D, respectively. In the present study, protocol E developed from Yeates et al. protocol has been found to be best in terms of DNA yield, DNA purity and bacterial diversity depiction associated with boron–sulfur rich sediment of high elevation hot springs.     

肠道硫酸盐还原菌DGGE分析技术的建立

目的 建立分析肠道内硫酸盐还原菌(Sulfate-reducing bacteria,SRB)组成的变性梯度凝胶电泳(Denaturing gradient gel electrophoresis,DGGE)技术,并用于分析10例健康人粪便样品中的SRB组成.方法 从GenBank中下载13株脱硫弧菌科细菌的腺苷酰硫酸还原酶α亚基基因(aprA)的序列,利用Clustal X、Simulated PCR (SPCR)软件比较、评估了2对针对aprA 基因的引物(AprA-3-FW/APS-RV和AprA-1-FW/AprA-5-RV)用于扩增粪便样品中的SRB的特异性.确定PCR引物和条件,进一步摸索并建立DGGE分析体系.结果 Clustal X和SPCR软件分析的结果均表明引物AprA-3-FW/APS-RV优于AprA-1-FW/AprA-5-RV.实际PCR的结果也显示AprA-1-FW/AprA-5-RV扩增效率低并有非特异扩增.建立DGGE体系,对10例健康人肠道中SRB的分析显示,每个个体肠道中SRB的种类有l到5种不等.结论 基于aprA序列的DGGE技术是分析肠道SRB组成的有效方法.     

橘小实蝇成虫肠道可培养细菌群落结构分析

【目的】研究橘小实蝇(Bactrocera dorsalis) 3个种群(实验室正常喂养种群、实验室无菌糖水喂养种群和野生种群)成虫肠道可培养细菌的群落结构组成。【方法】利用16S rRNA基因的聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)分析技术,结合菌落形态观察和生理生化特征鉴定细菌种类。【结果】从橘小实蝇3个种群成虫肠道600株可培养细菌得到53种不同细菌遗传型,分属于肠杆菌科(Enterobacteriaceae)、肠球菌科(Enterococcaceae)和芽孢杆菌科(Bacillaceae)等3个科。其中肠杆菌科是肠道可培养细菌最优势的细菌种类。同样以序列相似性大于97%的菌株归为相同的细菌种类为标准,找到了橘小实蝇3个种群可培养细菌的共有菌种,结合菌落形态观察和生理生化特征鉴定,确定共有菌种为肠杆菌属5株,克雷伯氏菌属2株,柠檬酸杆菌属1株,泛菌属1株,肠球菌属2株,以及芽孢杆菌属4株。【结论】通过研究橘小实蝇成虫肠道可培养细菌群落结构组成,可为探讨肠道菌群对寄主的生理功能和生态学意义奠定基础,最终为利用微生物防治此类害虫提供新思路。     

SELECTIVE CULTURES FOR THE ISOLATION OF BIOSURFACTANT PRODUCING BACTERIA: COMPARISON OF DIFFERENT COMBINATIONS OF ENVIRONMENTAL INOCULA AND HYDROPHOBIC CARBON SOURCES

The potential of estuarine microniches as reservoirs of biosurfactant-producing bacteria was evaluated by testing different combinations of inocula and hydrophobic carbon sources. Selective cultures using diesel, petroleum, or paraffin as hydrophobic carbon sources were prepared and inoculated with water from the surface microlayer, bulk sediments, and sediment of the rhizosphere of Halimione portulacoides. These inocula were compared regarding the frequency of biosurfactant-producing strains among selected isolates. The community structure of the selective cultures was profiled using denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene fragments at the end of the incubation. The DGGE profiles corresponding to the communities established in selective cultures at the end of the incubation revealed that communities were different in terms of structural diversity. The highest diversity was observed in the selective cultures containing paraffin (H ^' = 2.5). Isolates were obtained from the selective cultures (66) and tested for biosurfactant production by the atomized oil assay. Biosurfactant production was detected in 17 isolates identified as Microbacterium, Pseudomonas, Rhodococcus, and Serratia. The combination of estuarine surface microlayer (SML) water as inoculum and diesel as carbon source seems promising for the isolation of surfactant-producing bacteria. Supplemental materials are available for this article. Go to the publisher's online edition of Preparative Biochemistry and Biotechnology to view the supplemental file.