在组织共生微生物群系的研究中,组织样本中微生物细胞比例远低于宿主细胞,导致高通量测序数据中属于微生物的序列比例很低,不足以准确反映菌群多样性和结构组成.本文比较了HostZEROTM Microbial DNA Kit(ZYM)和NEBNext mircobiome DNA e...在组织共生微生物群系的研究中,组织样本中微生物细胞比例远低于宿主细胞,导致高通量测序数据中属于微生物的序列比例很低,不足以准确反映菌群多样性和结构组成.本文比较了HostZEROTM Microbial DNA Kit(ZYM)和NEBNext mircobiome DNA enrichment kit(NEB)两款商用DNA提取试剂盒、16S r RNA基因V3-V4高变区测序文库构建过程中的巢式PCR(NES)和扩增产物切胶回收(GEL)四种方法.与未经去除宿主DNA的方法相比,四种方法都使胃组织样本测序结果中细菌序列占比显著增加.NES和ZYM明显改变了纯菌菌株混合样本和胃组织样本菌群的组成;NEB未对菌株混合样本菌群组成造成明显影响,但对胃组织样本菌群结构影响大;只有GEL方法对样本菌群结构影响较小.综上所述,GEL方法能够去除大部分宿主DNA又对菌群组成影响最小,这为研究组织微生物群系时减少测序数据中宿主DNA的方法选择提供了参考.展开更多
This is an editorial comment on a recent publication reporting an increased rate of pyogenic liver abscesses(PLAs) after upper gastrointestinal panendoscopy. Its aim is to critically highlight the findings, limitation...This is an editorial comment on a recent publication reporting an increased rate of pyogenic liver abscesses(PLAs) after upper gastrointestinal panendoscopy. Its aim is to critically highlight the findings, limitations and potential clinical implications of this study. Issues of the mucosal barrier, the microbial flora, administration of antibiotics and underlying diseases are discussed. The probability of PLAs after endoscopies is not exactly known and the length of the "incubation period" remains unclear, but a possible causality should already suffice to make us think how to avoid them. Especially in patients with risk factors such as diabetes mellitus, end-stage renal disease, liver cirrhosis, biliary tract infection, and malignancies, the potential risk for PLAs should be considered. Unnecessary insufflation during endoscopy(causing mucosal stretching and microscopic tears) as well as mucosal damage(by direct abrasion with the scope) should be avoided in order to limit the invasiveness of the procedure as much as possible. And, in everyday routine, it should be kept in mind that in patients after endoscopy, especially in those with a breach of the mucosal barrier and significant comorbidities, PLAs can potentially develop and require timely administration of antibiotics as well as further diagnostic and therapeutic steps.展开更多
文摘目的 通过多重置换扩增技术(multiple displacement amplification,MDA)与宏基因组鸟枪法测序相结合的方法研究胃癌患者和健康受试者胃内微生物的组成特征。方法 纳入2017年9月—2017年12月在医院就诊的胃腺癌患者4例,健康受试者4例,收集受试者胃液标本,经过标本预处理、DNA提取、MDA扩增提取的DNA、构建测序文库、高通量测序和生物信息学分析,研究2组受试者胃内微生物的组成特征,寻找与胃癌显著相关的菌种,并评估该方法用于胃内微生物宏基因组学研究的可行性。结果 MDA能显著扩增从胃液样本中提取的微量微生物DNA(207.27±33.17)倍,扩增后的DNA量能满足构建高质量测序文库的要求;总体上看,所有样本共鉴定出131个菌种,胃癌患者胃内菌群多样性显著低于健康受试者( P <0.01, t =4.189);在细菌门水平,受试者胃液菌群主要由变形菌门、拟杆菌门、厚壁菌门、梭杆菌门组成;优势物种的组间差异分析表明,与健康受试者相比,牙髓卟啉单胞菌、口腔链球菌、干燥奈瑟菌在胃癌患者胃液中富集( P <0.05)。结论 MDA能有效用于扩增胃内微量微生物DNA;胃癌患者的胃液菌群构成与健康人存在显著差异;部分口腔及上呼吸道条件致病菌与胃癌显著相关,是潜在的胃癌生物学标志物;通过全基因组扩增和高通量测序相结合的方法可以从菌种甚至菌株的水平上寻找与胃癌发生、发展相关的微生物。
文摘在组织共生微生物群系的研究中,组织样本中微生物细胞比例远低于宿主细胞,导致高通量测序数据中属于微生物的序列比例很低,不足以准确反映菌群多样性和结构组成.本文比较了HostZEROTM Microbial DNA Kit(ZYM)和NEBNext mircobiome DNA enrichment kit(NEB)两款商用DNA提取试剂盒、16S r RNA基因V3-V4高变区测序文库构建过程中的巢式PCR(NES)和扩增产物切胶回收(GEL)四种方法.与未经去除宿主DNA的方法相比,四种方法都使胃组织样本测序结果中细菌序列占比显著增加.NES和ZYM明显改变了纯菌菌株混合样本和胃组织样本菌群的组成;NEB未对菌株混合样本菌群组成造成明显影响,但对胃组织样本菌群结构影响大;只有GEL方法对样本菌群结构影响较小.综上所述,GEL方法能够去除大部分宿主DNA又对菌群组成影响最小,这为研究组织微生物群系时减少测序数据中宿主DNA的方法选择提供了参考.
文摘This is an editorial comment on a recent publication reporting an increased rate of pyogenic liver abscesses(PLAs) after upper gastrointestinal panendoscopy. Its aim is to critically highlight the findings, limitations and potential clinical implications of this study. Issues of the mucosal barrier, the microbial flora, administration of antibiotics and underlying diseases are discussed. The probability of PLAs after endoscopies is not exactly known and the length of the "incubation period" remains unclear, but a possible causality should already suffice to make us think how to avoid them. Especially in patients with risk factors such as diabetes mellitus, end-stage renal disease, liver cirrhosis, biliary tract infection, and malignancies, the potential risk for PLAs should be considered. Unnecessary insufflation during endoscopy(causing mucosal stretching and microscopic tears) as well as mucosal damage(by direct abrasion with the scope) should be avoided in order to limit the invasiveness of the procedure as much as possible. And, in everyday routine, it should be kept in mind that in patients after endoscopy, especially in those with a breach of the mucosal barrier and significant comorbidities, PLAs can potentially develop and require timely administration of antibiotics as well as further diagnostic and therapeutic steps.
