肠杆菌科基因组注释在破译由16S RRNA基因扩增子测序获得的胃肠道微生物组数据集中的困难

IF 0.2 Q4 MEDICINE, GENERAL & INTERNAL
E. Klimenko, N. Belkova, A. Pogodina, L. Rychkova, M. Darenskaya
{"title":"肠杆菌科基因组注释在破译由16S RRNA基因扩增子测序获得的胃肠道微生物组数据集中的困难","authors":"E. Klimenko, N. Belkova, A. Pogodina, L. Rychkova, M. Darenskaya","doi":"10.15275/rusomj.2022.0413","DOIUrl":null,"url":null,"abstract":"Sequencing of the 16S rRNA gene amplicon is the cornerstone of the method for studying diverse bacteria in complex microbial communities. However, its use is complicated by an error rate of 10–17% when annotating 16S rRNA gene sequences. In our study, we examined the degree of accuracy of the taxonomic database of Enterobacteriaceae, compiled using the SILVA 132 reference database and a previously obtained dataset, viz. the microbiome of the gastrointestinal tract in adolescents with normal body weight and obesity. Material and Methods — In this study, previously obtained 16S rRNA gene amplicon sequencing data were used, and the deciphering was carried out using the QIIME2 2019.4 platform. Phylogenetic analysis was performed using MEGA X software. Results — Phylogenetic analysis of this family based on the studied V3–V4 fragment was hampered by polyphyly among some genera, and for half of the variants of the amplicon sequences it was not possible to clarify their genus. Statistical analysis did not reveal significant differences between the samples. Conclusion — Although the average values of bacterial genera in the studied groups intuitively differed from each other, statistical analysis did not reveal significant differences between the samples. However, it can be assumed that a more detailed study of taxonomic diversity, taking into account factors, such as enterotype, duration of breastfeeding and family history, may reveal differences in the frequency distribution.","PeriodicalId":21426,"journal":{"name":"Russian Open Medical Journal","volume":null,"pages":null},"PeriodicalIF":0.2000,"publicationDate":"2022-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Difficulties Of Enterobacteriaceae Genome Annotation In Deciphering Gastrointestinal Microbiome Datasets Obtained By 16S RRNA Gene Amplicon Sequencing\",\"authors\":\"E. Klimenko, N. Belkova, A. Pogodina, L. Rychkova, M. Darenskaya\",\"doi\":\"10.15275/rusomj.2022.0413\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Sequencing of the 16S rRNA gene amplicon is the cornerstone of the method for studying diverse bacteria in complex microbial communities. However, its use is complicated by an error rate of 10–17% when annotating 16S rRNA gene sequences. In our study, we examined the degree of accuracy of the taxonomic database of Enterobacteriaceae, compiled using the SILVA 132 reference database and a previously obtained dataset, viz. the microbiome of the gastrointestinal tract in adolescents with normal body weight and obesity. Material and Methods — In this study, previously obtained 16S rRNA gene amplicon sequencing data were used, and the deciphering was carried out using the QIIME2 2019.4 platform. Phylogenetic analysis was performed using MEGA X software. Results — Phylogenetic analysis of this family based on the studied V3–V4 fragment was hampered by polyphyly among some genera, and for half of the variants of the amplicon sequences it was not possible to clarify their genus. Statistical analysis did not reveal significant differences between the samples. Conclusion — Although the average values of bacterial genera in the studied groups intuitively differed from each other, statistical analysis did not reveal significant differences between the samples. However, it can be assumed that a more detailed study of taxonomic diversity, taking into account factors, such as enterotype, duration of breastfeeding and family history, may reveal differences in the frequency distribution.\",\"PeriodicalId\":21426,\"journal\":{\"name\":\"Russian Open Medical Journal\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.2000,\"publicationDate\":\"2022-12-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Russian Open Medical Journal\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.15275/rusomj.2022.0413\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"MEDICINE, GENERAL & INTERNAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Russian Open Medical Journal","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.15275/rusomj.2022.0413","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"MEDICINE, GENERAL & INTERNAL","Score":null,"Total":0}
引用次数: 0

摘要

16S rRNA基因扩增子的测序是研究复杂微生物群落中多种细菌的基础。然而,在注释16S rRNA基因序列时,其误差率为10-17%,使用起来很复杂。在我们的研究中,我们检查了肠杆菌科分类数据库的准确性,该数据库使用SILVA 132参考数据库和先前获得的数据集,即正常体重和肥胖青少年胃肠道微生物组。材料与方法:本研究使用先前获得的16S rRNA基因扩增子测序数据,使用QIIME2 2019.4平台进行解密。使用MEGA X软件进行系统发育分析。结果-基于所研究的V3-V4片段对该家族的系统发育分析受到一些属间多聚现象的阻碍,并且对于扩增子序列的一半变体无法澄清其属。统计分析未发现样本间有显著差异。结论-虽然研究组中细菌属的平均值直观上存在差异,但统计分析并未显示样品之间存在显著差异。然而,可以假设,对分类学多样性进行更详细的研究,考虑到肠道类型、母乳喂养持续时间和家族史等因素,可能会揭示频率分布的差异。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Difficulties Of Enterobacteriaceae Genome Annotation In Deciphering Gastrointestinal Microbiome Datasets Obtained By 16S RRNA Gene Amplicon Sequencing
Sequencing of the 16S rRNA gene amplicon is the cornerstone of the method for studying diverse bacteria in complex microbial communities. However, its use is complicated by an error rate of 10–17% when annotating 16S rRNA gene sequences. In our study, we examined the degree of accuracy of the taxonomic database of Enterobacteriaceae, compiled using the SILVA 132 reference database and a previously obtained dataset, viz. the microbiome of the gastrointestinal tract in adolescents with normal body weight and obesity. Material and Methods — In this study, previously obtained 16S rRNA gene amplicon sequencing data were used, and the deciphering was carried out using the QIIME2 2019.4 platform. Phylogenetic analysis was performed using MEGA X software. Results — Phylogenetic analysis of this family based on the studied V3–V4 fragment was hampered by polyphyly among some genera, and for half of the variants of the amplicon sequences it was not possible to clarify their genus. Statistical analysis did not reveal significant differences between the samples. Conclusion — Although the average values of bacterial genera in the studied groups intuitively differed from each other, statistical analysis did not reveal significant differences between the samples. However, it can be assumed that a more detailed study of taxonomic diversity, taking into account factors, such as enterotype, duration of breastfeeding and family history, may reveal differences in the frequency distribution.
求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
Russian Open Medical Journal
Russian Open Medical Journal MEDICINE, GENERAL & INTERNAL-
CiteScore
0.90
自引率
0.00%
发文量
39
期刊介绍: Russian Open Medical Journal (RusOMJ) (ISSN 2304-3415) is an international peer reviewed open access e-journal. The website is updated quarterly with the RusOMJ’s latest original research, clinical studies, case reports, reviews, news, and comment articles. This Journal devoted to all field of medicine. All the RusOMJ’s articles are published in full on www.romj.org with open access and no limits on word counts. Our mission is to lead the debate on health and to engage, inform, and stimulate doctors, researchers, and other health professionals in ways that will improve outcomes for patients. The RusOMJ team is based mainly in Saratov (Russia), although we also have editors elsewhere in Russian and in other countries.
×
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
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
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 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信