BugBase predicts organism-level microbiome phenotypes

By Tonya L. Ward, J. Larson, Jeremy Meulemans, Benjamin M Hillmann, Joshua Lynch, Dimitri N Sidiropoulos, J. Spear, G. Caporaso, R. Blekhman, Rob Knight and 2 more. bioRxiv, 2017

396 citations recorded by the source corpus.

Shotgun metagenomics and marker gene amplicon sequencing can be used to directly measure or predict the functional repertoire of the microbiota en masse, but current methods do not readily estimate the functional capability of individual microorganisms. Here we present BugBase, an algorithm that predicts organism-level coverage of functional pathways as well as biologically interpretable phenotypes such as oxygen tolerance, Gram staining and pathogenic potential, within complex microbiomes using either whole-genome shotgun or marker gene sequencing data. We find BugBase’s organism-level pathway coverage predictions to be statistically higher powered than current ‘bag-of-genes’ approaches for discerning functional changes in both host-associated and environmental microbiomes.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2a3a42b9c0191b5ad4c2780cf7094bb8136a8079

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In Ecology

1. Tong Chen
2. Meiping Lu
3. Xubo Qian
4. Yuan Qin
5. Yang Bai
6. Yong-xin Liu
7. Xiaoxuan Guo

In Molecular Biology

1. Tong Chen
2. Meiping Lu
3. Xubo Qian
4. Yuan Qin
5. Yang Bai
6. Yong-xin Liu
7. Xiaoxuan Guo

Citations in the corpus

• A practical guide to amplicon and metagenomic analysis of microbiome data (2020, background): “P r o t e i n & C e l l and pathogenic potential (Ward et al., 2017); this database is mainly used in medical research (Mahnert et al., 2019).”