ArticleeLife2017
A phylogenetic transform enhances analysis of compositional microbiota data.
Article in eLife, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 174 papers, 2 of them syntheses that pooled it.
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Who cites it
174 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-analysis of caries microbiome studies can improve upon disease prediction outcomes.APMIS : acta pathologica, microbiologica, et immunologica Scandinavica · 2022Pooled it
- Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet.Cell host & microbe · 2019Pooled it
- Disentangling microbiota-dependent and -independent impacts of antibiotics on host physiology.Nature microbiology · 2026Article
- The Adult Aedes aegypti Bacterial Microbiota is Robust to Infection with the Obligate Microsporidian Parasite Edhazardia aedis.Environmental microbiology · 2026Article
- From trees to graphs: rethinking phylogeny in microbiome prediction.Applied and environmental microbiology · 2026Article
- Environmental factors associated with nesting habits and age shape the composition and connection between skin and uropygial gland microbiomes of birds.The Journal of animal ecology · 2026Article
- A robust, sensitive phylogenetic method enables gene-level metagenomic analyses.bioRxiv : the preprint server for biology · 2026Article
- Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources.Environmental microbiology · 2026Article
- Article
- Microbial product translocation and mortality in adults hospitalised with HIV-associated tuberculosis: a prospective observational cohort study.Research square · 2026Article
- A Tree-Based Model for Addressing Sparsity and Taxa Covariance in Microbiome Compositional Count Data.Statistics in medicine · 2026Article
- Article
- Assessing differential cell composition in single-cell studies using voomCLR.Bioinformatics (Oxford, England) · 2026Article
- Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.Computational and structural biotechnology journal · 2026Article
- Shredder identity matters: taxon-specific gut microbiota in aquatic shredders drives bacterial diversity during leaf breakdown in streams.ISME communications · 2026Article
- FAVABEAN and FALAPhyl: Open-source pipelines for scalable 16s rRNA microbiome data processing and visualization.PloS one · 2026Article
- Design, processing, and modeling for longitudinal multiomics microbiome data.Frontiers in cellular and infection microbiology · 2026Review
- Single microorganism RNA sequencing of microbiomes using smRandom-Seq.Nature protocols · 2026Review
- Distinct bacterial communities affiliated with two types of shredder-produced particles in streams.FEMS microbiology ecology · 2025Article
- Gut microbiota composition is related to anxiety and aggression scores in companion dogs.Scientific reports · 2025Article
114 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.