Year: 2021
Type: article
Abstract: Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classifying metagenomic data and estimating taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Yet, benchmarking metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while others report relative taxonomic abundance. Here, we show how misleading conclusions can be drawn by neglecting this distinction between relative abundance types when benchmarking metagenomic profilers. Moreover, we show compelling evidence that interchanging sequence abundance and taxonomic abundance will influence both per-sample summary statistics and cross-sample comparisons. We suggest that the microbiome research community should pay attention to potentially misleading biological conclusions arising from this issue when benchmarking metagenomic profilers, by carefully considering the type of abundance data that was analyzed and interpreted, and clearly stating the strategy used for metagenomic profiling.
Source: Nature Methods
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: U.S. Department of Health and Human Services, National Institutes of Health, University of California, San Diego, National Institute on Aging, National Heart, Lung, and Blood Institute, National Institute of Allergy and Infectious Diseases, Eunice Kennedy Shriver National Institute of Child Health and Human Development
Awards: Multi-omic approaches to mechanisms of vitamin D, environmental influences, and the microbiome on asthma, G1357281155, Long-term health consequences of birth by cesarean section, G1681861429, G2094919514, G4404169877, Functional Redundancy of Human Microbiome and its Implication in Fecal Microbiota Transplantation, Prospective Study of the Gut Microbiome in Aging, (2 of 2) Genetic Epidemiology of COPD, G6169845905, G692714771, Pathophysiologic and Therapeutic Mechanisms of Aspirin Exacerbated Respiratory Disease, Prospective Study of the Gut Microbiome in Aging, Immunologic Basis of Resistance and Hypersensitivity
OpenAlex ID: W3162300015