IHB OpenIR  > 淡水生态学研究中心  > 期刊论文
Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota
Xiao, Fanshu1,2; Yu, Yuhe3; Li, Jinjin4; Juneau, Philippe5; Yan, Qingyun1,2
2018-09-01
Source PublicationCURRENT MICROBIOLOGY
ISSN0343-8651
Volume75Issue:9Pages:1240-1246
Abstract

The 16S rRNA gene is one of the most commonly used molecular markers for estimating bacterial diversity during the past decades. However, there is no consistency about the sequencing depth (from thousand to millions of sequences per sample), and the clustering methods used to generate OTUs may also be different among studies. These inconsistent premises make effective comparisons among studies difficult or unreliable. This study aims to examine the necessary sequencing depth and clustering method that would be needed to ensure a stable diversity patterns for studying fish gut microbiota. A total number of 42 samples dataset of Siniperca chuatsi (carnivorous fish) gut microbiota were used to test how the sequencing depth and clustering may affect the alpha and beta diversity patterns of fish intestinal microbiota. Interestingly, we found that the sequencing depth (resampling 1000-11,000 per sample) and the clustering methods (UPARSE and UCLUST) did not bias the estimates of the diversity patterns during the fish development from larva to adult. Although we should acknowledge that a suitable sequencing depth may differ case by case, our finding indicates that a shallow sequencing such as 1000 sequences per sample may be also enough to reflect the general diversity patterns of fish gut microbiota. However, we have shown in the present study that strict pre-processing of the original sequences is required to ensure reliable results. This study provides evidences to help making a strong scientific choice of the sequencing depth and clustering method for future studies on fish gut microbiota patterns, but at the same time reducing as much as possible the costs related to the analysis.

DOI10.1007/s00284-018-1516-y
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada
Indexed BySCI
Language英语
Funding ProjectNational Natural Science Foundation of China[31672262] ; Sun Yat-sen University[38000-18821107] ; Natural Sciences and Engineering Research Council of Canada[RGPIN-2017-06210]
WOS Research AreaMicrobiology
WOS SubjectMicrobiology
WOS IDWOS:000440407200017
WOS KeywordCOMMUNITIES ; SAMPLE ; CLONING
PublisherSPRINGER
Funding OrganizationNational Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Sun Yat-sen University ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada ; Natural Sciences and Engineering Research Council of Canada
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/30559
Collection淡水生态学研究中心_期刊论文
Corresponding AuthorYan, Qingyun
Affiliation1.Sun Yat Sen Univ, Environm Microbi Res Ctr, Guangdong Prov Key Lab Environm Pollut Control &, Guangzhou 510006, Guangdong, Peoples R China
2.Sun Yat Sen Univ, Sch Environm Sci & Engn, Guangzhou 510006, Guangdong, Peoples R China
3.Chinese Acad Sci, Key Lab Aquat Biodivers & Conservat, Inst Hydrobiol, Wuhan 430072, Hubei, Peoples R China
4.Qilu Normal Univ, Jinan 250013, Shandong, Peoples R China
5.Univ Quebec, Lab Aquat Microorganism Ecotoxicol, Dept Sci Biol, GRIL,TOXEN, Succ Ctr Ville,CP 8888, Montreal, PQ H3C 3P8, Canada
Recommended Citation
GB/T 7714
Xiao, Fanshu,Yu, Yuhe,Li, Jinjin,et al. Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota[J]. CURRENT MICROBIOLOGY,2018,75(9):1240-1246.
APA Xiao, Fanshu,Yu, Yuhe,Li, Jinjin,Juneau, Philippe,&Yan, Qingyun.(2018).Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota.CURRENT MICROBIOLOGY,75(9),1240-1246.
MLA Xiao, Fanshu,et al."Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota".CURRENT MICROBIOLOGY 75.9(2018):1240-1246.
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