Establishing microbial composition measurement standards with reference frames

Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial load, or absolute number of microorganisms, to accurately determine taxonomic shifts. Therefore, most studies rely on relative abundance data. H...

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Podrobná bibliografia
Vydané v:	Nature communications Ročník 10; číslo 1; s. 2719 - 11
Hlavní autori:	Morton, James T., Marotz, Clarisse, Washburne, Alex, Silverman, Justin, Zaramela, Livia S., Edlund, Anna, Zengler, Karsten, Knight, Rob
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London Nature Publishing Group UK 20.06.2019 Nature Publishing Group Nature Portfolio
Predmet:	13/31 45/22 45/23 45/77 631/114 631/326/2565/2134 631/326/41/2142 639/705/1041 Abundance Alliances Atopic dermatitis Bacteria - genetics Bacteria - isolation & purification Bacterial Load - standards Computer Simulation - standards Data Analysis Datasets as Topic Dermatitis Dermatitis, Atopic - microbiology Eczema Feasibility Studies Healthy Volunteers High-Throughput Nucleotide Sequencing - statistics & numerical data Humanities and Social Sciences Humans Metagenome - genetics Microbiomes Microbiota - genetics Microorganisms Models, Biological multidisciplinary Reference Standards Relative abundance RNA, Ribosomal, 16S - isolation & purification Saliva - microbiology Science Science (multidisciplinary) Sequences Soil Microbiology
ISSN:	2041-1723, 2041-1723
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Popis
Shrnutí:	Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial load, or absolute number of microorganisms, to accurately determine taxonomic shifts. Therefore, most studies rely on relative abundance data. Here, we demonstrate common pitfalls in comparing relative abundance across samples and identify two solutions that reveal microbial changes without the need to estimate total microbial load. We define the notion of “reference frames”, which provide deep intuition about the compositional nature of microbiome data. In an oral time series experiment, reference frames alleviate false positives and produce consistent results on both raw and cell-count normalized data. Furthermore, reference frames identify consistent, differentially abundant microbes previously undetected in two independent published datasets from subjects with atopic dermatitis. These methods allow reassessment of published relative abundance data to reveal reproducible microbial changes from standard sequencing output without the need for new assays. Most microbiome studies make conclusions based on changes in relative abundance of taxa, inferred from sequencing data. Here, the authors highlight common pitfalls in comparing relative abundance across samples, and identify solutions that reveal microbial changes without the need to estimate total microbial load.
Bibliografia:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-019-10656-5