ArticlePeerJ2017
Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
60 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Paramyxoviruses in Old World fruit bats (Pteropodidae): An open database and synthesis of sampling effort, viral positivity, and coevolution.PLoS neglected tropical diseases · 2025Pooled it
- Adaptive graph learning of microbial phylogeny enables accurate and interpretable microbiome-based host phenotype prediction.Applied and environmental microbiology · 2026Article
- Article
- A test for microbiome-mediated rescue via host phenotypic plasticity inProceedings. Biological sciences · 2025Article
- Soil properties in agricultural systems affect microbial genomic traits.FEMS microbes · 2025Article
- A benchmark analysis of feature selection and machine learning methods for environmental metabarcoding datasets.Computational and structural biotechnology journal · 2025Article
- Constructing phylogenetic trees for microbiome data analysis: A mini-review.Computational and structural biotechnology journal · 2024Review
- A test for microbiome-mediated rescue via host phenotypic plasticity inbioRxiv : the preprint server for biology · 2024Article
- A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice.Microorganisms · 2023Article
- Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.Genome biology · 2023Article
- Impact of HIV on the Oral Microbiome of Children Living in Sub-Saharan Africa, Determined by Using anMicrobiology spectrum · 2023Article
- Homogeneous Environmental Selection Structures the Bacterial Communities of Benthic Biofilms in Proglacial Floodplain Streams.Applied and environmental microbiology · 2023Article
- Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations.Frontiers in microbiology · 2023Review
- Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere.International journal of molecular sciences · 2022Article
- Glacier shrinkage will accelerate downstream decomposition of organic matter and alters microbiome structure and function.Global change biology · 2022Article
- CBEA: Competitive balances for taxonomic enrichment analysis.PLoS computational biology · 2022Article
- Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy.mSystems · 2022Article
- Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome.The ISME journal · 2022Article
- Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.Frontiers in bioinformatics · 2022Review
- Learning sparse log-ratios for high-throughput sequencing data.Bioinformatics (Oxford, England) · 2021Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, "phylofactorization," to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.
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Registered trials
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.