ArticleBioinformatics (Oxford, England)2019
pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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
13 citing papers in PubMed.
- The Gut Microbiota during a Behavioral Weight Loss Intervention.Nutrients · 2021Trial
- Association between postmenopausal vulvovaginal discomfort, vaginal microbiota, and mucosal inflammation.American journal of obstetrics and gynecology · 2021Trial
- A Comprehensive Self-Management Program With Diet Education Does Not Alter Microbiome Characteristics in Women With Irritable Bowel Syndrome.Biological research for nursing · 2021Trial
- PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data.Briefings in bioinformatics · 2024Article
- Prospective, longitudinal analysis of the gut microbiome in patients with locally advanced rectal cancer predicts response to neoadjuvant concurrent chemoradiotherapy.Journal of translational medicine · 2023Article
- Article
- A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome.Bioinformatics (Oxford, England) · 2022Article
- Phylogeny-guided microbiome OTU-specific association test (POST).Microbiome · 2022Article
- Intestinal butyrate-metabolizing species contribute to autoantibody production and bone erosion in rheumatoid arthritis.Science advances · 2022Article
- Beyond samples: A metric revealing more connections of gut microbiota between individuals.Computational and structural biotechnology journal · 2021Article
- Respiratory microbiome profiles differ by recent hospitalization and nursing home residence in patients on mechanical ventilation.Journal of translational medicine · 2020Article
- A quasi-paired cohort strategy reveals the impaired detoxifying function of microbes in the gut of autistic children.Science advances · 2020Article
- Precision medicine in perinatal depression in light of the human microbiome.Psychopharmacology · 2020Review
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Authors and funding
4 authors.
Funding
Abstract
motivationThe human microbiome is notoriously variable across individuals, with a wide range of 'healthy' microbiomes. Paired and longitudinal studies of the microbiome have become increasingly popular as a way to reduce unmeasured confounding and to increase statistical power by reducing large inter-subject variability. Statistical methods for analyzing such datasets are scarce.
resultsWe introduce a paired UniFrac dissimilarity that summarizes within-individual (or within-pair) shifts in microbiome composition and then compares these compositional shifts across individuals (or pairs). This dissimilarity depends on a novel transformation of relative abundances, which we then extend to more than two time points and incorporate into several phylogenetic and non-phylogenetic dissimilarities. The data transformation and resulting dissimilarities may be used in a wide variety of downstream analyses, including ordination analysis and distance-based hypothesis testing. Simulations demonstrate that tests based on these dissimilarities retain appropriate type 1 error and high power. We apply the method in two real datasets. AVAILABILITY AND IMPLEMENTATION: The R package pldist is available on GitHub at https://github.com/aplantin/pldist. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.