ArticlemSystems
A Novel Sparse Compositional Technique Reveals Microbial Perturbations.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 328 papers.
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Who cites it
328 citing papers in PubMed.
- Impact of dietary protein quantity on the non-dysbiotic human microbiome: a controlled feeding study.Scientific reports · 2026Trial
- Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.The Journal of physiology · 2025Trial
- Pilot study evaluating tolerability and changes in fecal microbiota associated with novel probiotic administration to dogs with diarrhea.Frontiers in veterinary science · 2025Trial
- Ketogenic diet but not free-sugar restriction alters glucose tolerance, lipid metabolism, peripheral tissue phenotype, and gut microbiome: RCT.Cell reports. Medicine · 2024Trial
- Modifications of lung microbiota structure in traumatic brain injury ventilated patients according to time and enteral feeding formulas: a prospective randomized study.Critical care (London, England) · 2023Trial
- Perinatal ampicillin exposure alters murine maternal fecal bile acid and acylcarnitine profiles.Gut microbes · 2026Article
- Region-associated microbial signatures persist during inoculated fermentation of Nebbiolo grapes.Applied and environmental microbiology · 2026Article
- Associations of Urinary Triclosan Concentrations Across Gestation and Childhood with the Adolescent Gut Microbiome.Environmental health perspectives · 2026Article
- Disturbance History Shapes Microbial Community Assembly and Predictability in a Continuous Culture System.Environmental microbiology · 2026Article
- Microbes on the Mind: Multi-modal Neuroimaging Reveals Gut-Brain Axes in Infants.bioRxiv : the preprint server for biology · 2026Article
- Integrated multi-omics analysis identifies microbial and metabolic signatures and drivers of CNS autoimmunity.mSystems · 2026Article
- Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation.Nature communications · 2026Article
- Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.Cell reports. Medicine · 2026Article
- Age, strain, and gut section shape the microbiome of commercial laying hens.Poultry science · 2026Article
- From onset to healing: temporal dynamics of microbial communities pinpoint Midichloria-like organism's key role in the development of the fish skin disease red mark syndrome.Animal microbiome · 2026Article
- Does permanent tooth eruption introduce periodontal pathogens? A preliminary study.Odontology · 2026Article
- Longitudinal dynamics of the maternal gut virome associate with metabolic features of preterm birth.Nature communications · 2026Article
- Multi-omics links microbial dysbiosis, systemic inflammation, and metabolomic disruptions to SNAE risk in treated HIV.JCI insight · 2026Article
- Bacterial and Green Algal Communities of Norwegian Birch Tree Bark.Microbial ecology · 2026Article
- Metabarcoding Characterization of Fungal Communities in Spanish Cereals with a Special Focus on Fusarium Species.Microbial ecology · 2026Article
268 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The central aims of many host or environmental microbiome studies are to elucidate factors associated with microbial community compositions and to relate microbial features to outcomes. However, these aims are often complicated by difficulties stemming from high-dimensionality, non-normality, sparsity, and the compositional nature of microbiome data sets. A key tool in microbiome analysis is beta diversity, defined by the distances between microbial samples. Many different distance metrics have been proposed, all with varying discriminatory power on data with differing characteristics. Here, we propose a compositional beta diversity metric rooted in a centered log-ratio transformation and matrix completion called robust Aitchison PCA. We demonstrate the benefits of compositional transformations upstream of beta diversity calculations through simulations. Additionally, we demonstrate improved effect size, classification accuracy, and robustness to sequencing depth over the current methods on several decreased sample subsets of real microbiome data sets. Finally, we highlight the ability of this new beta diversity metric to retain the feature loadings linked to sample ordinations revealing salient intercommunity niche feature importance.
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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.