Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

GigaScience
Alexandre AlmeidaRobert D Finn

Abstract

Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. Quantitative Insights Into Microbial Ecology (QIIME) and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean, and soil environments. We evaluate their accuracy when paired with both different reference databases and variable sub-regions of the 16S rRNA gene. We show that QIIME 2 provided the best recall and F-scores at genus and family levels, together with the lowest distance estimates between the observed and simulated samples. However, MAPseq showed the highest precision, with miscall rates consistently <2%. Notably, QIIME 2 was the most computationally expensive tool, with CPU time and memory usage almost 2 and 30 times higher than MAPseq, respectively. Using the SILVA database generally yielded a higher rec...Continue Reading

References

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Citations

Sep 22, 2020·Omics : a Journal of Integrative Biology·Ibrahim MohamedAmro Hanora
Jul 2, 2019·Parasitology·Alba CortésCinzia Cantacessi
Jun 24, 2020·Scientific Reports·Montree Wutthi-InSiriporn Chattipakorn
Aug 1, 2019·GigaScience·Muhammad Zohaib AnwarCarsten Suhr Jacobsen
Oct 3, 2020·Ecology and Evolution·Devon R O'RourkeJeffrey T Foster
Aug 30, 2020·Microbiome·Jennifer Lu, Steven L Salzberg
Oct 31, 2020·Frontiers in Microbiology·Keith MitchellJordan Moberg Parker
Feb 15, 2020·Forensic Science International. Genetics·Lusine KhachatryanJeroen F J Laros
Mar 10, 2021·Maternal Health, Neonatology and Perinatology·Jacob A F WestawayDonna Rudd
Apr 28, 2021·Molecular Ecology Resources·Jose S HleapMelania E Cristescu
Feb 26, 2021·MSphere·Isabel Abellan-SchneyderKlaus Neuhaus
Jul 6, 2021·Frontiers in Microbiology·Michal ZiemskiBenjamin D Kaehler
Aug 3, 2021·Frontiers in Microbiology·Danielle PetersonVanja Klepac-Ceraj
Nov 9, 2021·PLoS Computational Biology·Michael S RobesonNicholas A Bokulich

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Methods Mentioned

BETA
genotyping
PCR

Key Resources (RRID) Mentioned

SCR_006538
SCR_011947
SCR_008249
SCR_013080
SCR_011950

Software Mentioned

BioPython
R
python script
UCLUST
RColorBrewer
Quantitative Insights Into Microbial Ecology ( QIIME )
EXCELERATE
Greengenes
MiSeq SOP
mothur SOP

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