Which sequencing depth is sufficient to describe patterns in bacterial alpha- and beta-diversity?

Lundin, Daniel (author): KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,KTH Royal Institute of Technology ; Vetenskapsrådet,Jarone Pinhassi

Logue, Jürg Brendan (author): Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Uppsala universitet,Limnologi,Bibliotek,Library,Uppsala University

Östman, Örjan (author): Uppsala universitet,Populationsbiologi och naturvårdsbiologi,Uppsala University

Andersson, Anders F. (author): KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,KTH Royal Institute of Technology

(creator_code:org_t)

2012-04-23
2012
English.
In: Environmental Microbiology Reports. - : Wiley. - 1758-2229 .- 1758-2229. ; 4:3, s. 367-372

Related links:: https://urn.kb.se/re...; show more...; https://doi.org/10.1...; https://urn.kb.se/re...; https://res.slu.se/i...; https://urn.kb.se/re...; show less...

Abstract Subject headings

The vastness of microbial diversity implies that an almost infinite number of individuals needs to be identified to accurately describe such communities. Practical and economical constraints may therefore prevent appropriate study designs. However, for many questions in ecology it is not essential to know the actual diversity but rather the trends among samples thereof. It is, hence, important to know to what depth microbial communities need to be sampled to accurately measure trends in diversity. We used three data sets of freshwater and sediment bacteria, where diversity was explored using 454 pyrosequencing. Each data set contained 615 communities from which 15 00020 000 16S rRNA gene sequences each were obtained. These data sets were subsampled repeatedly to 10 different depths down to 200 sequences per community. Diversity estimates varied with sequencing depth, yet, trends in diversity among samples were less sensitive. We found that 1000 denoised sequences per sample explained to 90% the trends in beta-diversity (Bray-Curtis index) among samples observed for 15 00020 000 sequences. Similarly, 5000 denoised sequences were sufficient to describe trends in a-diversity (Shannon index) with the same accuracy. Further, 5000 denoised sequences captured to more than 80% the trends in Chao1 richness and Pielou's evenness.

By the author/editor: Lundin, Daniel; Severin, Ina; Logue, Jürg Bren ...; Östman, Örjan; Andersson, Ander ...; Lindström, Eva S

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Biological Scien ...; and Microbiology

By the university: Royal Institute of Technology; Uppsala University; Swedish University of Agricultural Sciences; Linnaeus University

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