ArticlemSystems2022
Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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.
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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
22 citing papers in PubMed.
- Population-based characterisation of child and adolescent oral bacterial microbiomes.Microbiome · 2026Article
- Higher-dimensional ordination analysis teases out impacts ofMicrobiology spectrum · 2026Article
- Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome.bioRxiv : the preprint server for biology · 2026Article
- Unraveling the diagnostic and prognostic signatures of oral microbiota in head and neck cancer.BMC biology · 2026Article
- Transplant of cryopreserved mosquito gut microbiota reveals strain-specific patterns of microbial acquisition and assembly.ISME host microbe · 2026Article
- Cats on dry kibble diet have significantly different microbiome than those on canned wet food.npj veterinary sciences · 2026Article
- Impact of data compositionality on the detection of microbiota responses.Gut microbes · 2025Article
- Oral short-chain fatty acid-producing bacteria may be associated with biological age and cognition among the oldest old.Communications medicine · 2025Article
- Environmental and maternal imprints on infant gut metabolic development.Cell host & microbe · 2025Article
- Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.Microbiology spectrum · 2025Article
- GIMIC: smoothed graph-image representation of microbiome samples induce an optimal distance.Genome biology · 2025Article
- Interaction between haploinsufficiency of PTPN2 and patient microbiome promotes autoimmune arthritis in mice.Journal of autoimmunity · 2025Article
- Effect of interferon on broilers' fecal microbiome composition.Journal of advanced veterinary and animal research · 2025Article
- Article
- PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.Microbiome · 2025Article
- Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat.ISME communications · 2025Article
- DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice.Nature communications · 2024Article
- Association of Subjective and Objective Measures of Sleep With Gut Microbiota Composition and Diversity in Older Men: The Osteoporotic Fractures in Men Study.The journals of gerontology. Series A, Biological sciences and medical sciences · 2023Article
- Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes.Bioinformatics (Oxford, England) · 2023Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Microbiome data have several specific characteristics (sparsity and compositionality) that introduce challenges in data analysis. The integration of prior information regarding the data structure, such as phylogenetic structure and repeated-measure study designs, into analysis, is an effective approach for revealing robust patterns in microbiome data. Past methods have addressed some but not all of these challenges and features: for example, robust principal-component analysis (RPCA) addresses sparsity and compositionality; compositional tensor factorization (CTF) addresses sparsity, compositionality, and repeated measure study designs; and UniFrac incorporates phylogenetic information. Here we introduce a strategy of incorporating phylogenetic information into RPCA and CTF. The resulting methods, phylo-RPCA, and phylo-CTF, provide substantial improvements over state-of-the-art methods in terms of discriminatory power of underlying clustering ranging from the mode of delivery to adult human lifestyle. We demonstrate quantitatively that the addition of phylogenetic information improves effect size and classification accuracy in both data-driven simulated data and real microbiome data.
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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.