The species accumulation curve, or collector＇s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers ...The species accumulation curve, or collector＇s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non- parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45~63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and R-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.展开更多
目的从微生物角度探究重度低龄儿童龋(severe early childhood caries,S⁃ECC)患儿一次完成龋病治疗前、治疗后3个月内菌斑微生物群落构成和多样性的变化及治疗对于远期无龋状态维持的作用。方法S⁃ECC患儿在全身麻醉下一次完成龋病治疗,...目的从微生物角度探究重度低龄儿童龋(severe early childhood caries,S⁃ECC)患儿一次完成龋病治疗前、治疗后3个月内菌斑微生物群落构成和多样性的变化及治疗对于远期无龋状态维持的作用。方法S⁃ECC患儿在全身麻醉下一次完成龋病治疗,采集治疗前(C)、术后7 d(C⁃7D)、1个月(C⁃1M)、3个月(C⁃3M)无龋牙面集合菌斑,并纳入无龋儿童(CF)为对照组,分析治疗前后菌斑微生物群落短期内的动态改建过程。结果S⁃ECC组和CF组菌斑群落组成高度相似;组间α多样性指数差异无统计学意义(P>0.05);从相对丰度值分析,纤毛菌属、聚集杆菌属等在治疗后较术前下降(P<0.05),C⁃7D组血链球菌较C组上升并在3个月内逐渐下降;治疗前韦荣菌属、放线菌属、拟普雷沃菌属、二氧化碳嗜纤维菌属、变异链球菌在C组和CF组间存在显著差异(P<0.05),其中变异链球菌经治疗后的C⁃7D、C⁃1M组与CF组未存在显著差异,而C⁃3M组较CF组出现上升(P<0.01)。结论S⁃ECC患儿在接受治疗后菌群结构的迅速改变,并在治疗后1~3个月逐渐开始建立新的无龋状态下的平衡。核心微生物群的存在使得菌斑群落保持稳定,韦荣菌属、拟普雷沃菌属、变异链球菌等具备作为龋病菌斑微生物标记物潜能。展开更多
文摘The species accumulation curve, or collector＇s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling. Traditional applications have focused on ecological populations but emerging large-scale applications, for example in DNA sequencing, are orders of magnitude larger and present new challenges. We developed a method to estimate accumulation curves for predicting the complexity of DNA sequencing libraries. This method uses rational function approximations to a classical non- parametric empirical Bayes estimator due to Good and Toulmin [Biometrika, 1956, 43, 45~63]. Here we demonstrate how the same approach can be highly effective in other large-scale applications involving biological data sets. These include estimating microbial species richness, immune repertoire size, and R-mer diversity for genome assembly applications. We show how the method can be modified to address populations containing an effectively infinite number of species where saturation cannot practically be attained. We also introduce a flexible suite of tools implemented as an R package that make these methods broadly accessible.
文摘目的从微生物角度探究重度低龄儿童龋(severe early childhood caries,S⁃ECC)患儿一次完成龋病治疗前、治疗后3个月内菌斑微生物群落构成和多样性的变化及治疗对于远期无龋状态维持的作用。方法S⁃ECC患儿在全身麻醉下一次完成龋病治疗,采集治疗前(C)、术后7 d(C⁃7D)、1个月(C⁃1M)、3个月(C⁃3M)无龋牙面集合菌斑,并纳入无龋儿童(CF)为对照组,分析治疗前后菌斑微生物群落短期内的动态改建过程。结果S⁃ECC组和CF组菌斑群落组成高度相似;组间α多样性指数差异无统计学意义(P>0.05);从相对丰度值分析,纤毛菌属、聚集杆菌属等在治疗后较术前下降(P<0.05),C⁃7D组血链球菌较C组上升并在3个月内逐渐下降;治疗前韦荣菌属、放线菌属、拟普雷沃菌属、二氧化碳嗜纤维菌属、变异链球菌在C组和CF组间存在显著差异(P<0.05),其中变异链球菌经治疗后的C⁃7D、C⁃1M组与CF组未存在显著差异,而C⁃3M组较CF组出现上升(P<0.01)。结论S⁃ECC患儿在接受治疗后菌群结构的迅速改变,并在治疗后1~3个月逐渐开始建立新的无龋状态下的平衡。核心微生物群的存在使得菌斑群落保持稳定,韦荣菌属、拟普雷沃菌属、变异链球菌等具备作为龋病菌斑微生物标记物潜能。
