Nonparametric richness estimators Chao1 and ACE must not be used with amplicon sequence variant data.

IF 10.8 1区 环境科学与生态学 Q1 ECOLOGY ISME Journal Pub Date : 2024-01-08 DOI:10.1093/ismejo/wrae106
Yongcui Deng, Alexander K Umbach, Josh D Neufeld
{"title":"Nonparametric richness estimators Chao1 and ACE must not be used with amplicon sequence variant data.","authors":"Yongcui Deng, Alexander K Umbach, Josh D Neufeld","doi":"10.1093/ismejo/wrae106","DOIUrl":null,"url":null,"abstract":"","PeriodicalId":50271,"journal":{"name":"ISME Journal","volume":" ","pages":""},"PeriodicalIF":10.8000,"publicationDate":"2024-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11208923/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"ISME Journal","FirstCategoryId":"93","ListUrlMain":"https://doi.org/10.1093/ismejo/wrae106","RegionNum":1,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"ECOLOGY","Score":null,"Total":0}
引用次数: 0
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
非参数丰富度估计器 Chao1 和 ACE 不得用于扩增子序列变异数据。
微生物生态学家使用阿尔法多样性指标来估算小亚基核糖体 RNA 基因高通量测序数据中的物种丰富度和均匀度。这一观点认为,非参数富集度估算器 Chao1 和 ACE 不应与 ASV 数据一起使用,因为生成扩增子序列变体(ASV)的默认过程会去除单子,而单子是这些估算计算所特别需要的。此外,在可能的情况下保留单子,也会给这一丰度类别带来很大比例的假象,导致丰富度被极度高估。我们建议使用其他序列聚类策略和/或多样性指标,以避免 ASV 数据产生毫无意义的丰富度估计值。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
ISME Journal
ISME Journal 环境科学-生态学
CiteScore
22.10
自引率
2.70%
发文量
171
审稿时长
2.6 months
期刊介绍: The ISME Journal covers the diverse and integrated areas of microbial ecology. We encourage contributions that represent major advances for the study of microbial ecosystems, communities, and interactions of microorganisms in the environment. Articles in The ISME Journal describe pioneering discoveries of wide appeal that enhance our understanding of functional and mechanistic relationships among microorganisms, their communities, and their habitats.
期刊最新文献
Spatial sensing as a strategy for public goods regulation by gut microbes. Biotics and bacterial function: impact on gut and host health. Saccharomyces boulardii enhances anti-inflammatory effectors and AhR activation via metabolic interactions in probiotic communities. Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake. Characterizing core microbiota and regulatory functions of the pig gut microbiome.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1