Shotgun metagenomic analysis reveals taxonomic and functional alterations in the gut microbiome across prodromal and symptomatic Lewy body disease.
The 9 matches
- [1] § Results › Microbial features characterizing the disease continuum of Lewy body disease ↔ 2-microbial_taxa_analysis/2-different_prevalence_analysis_final_version.R, lines 192–281 · score 0.98 · Oscillospiraceae bacterium CLA, Actinomyces oris, GGB3730 SGB5060, GGB9627 SGB15081, GGB9719 SGB15272, Akkermansia muciniphila
- [2] § Materials and methods › Gut microbiome diversity analysis ↔ 1-alpha_beta_diversity/alpha_beta_diversity_final_version.R, lines 86–124 · score 0.73 · PCoA, species richness, arcsine square root, diversity, household ID, lmer
- [3] § Materials and methods › Correlations between clinical characteristics and microbial features ↔ 5-correlation_analysis/partial_correlation_analysis.R, lines 424–489 · score 0.73 · MoCA, CDR SB, partial correlation, clinical measurements, UPDRS, STMS
- [4] § Results › Differentially abundant and prevalent gut microbiome features between LBD patients and their cohabitant controls ↔ 2-microbial_taxa_analysis/2-different_prevalence_analysis_final_version.R, lines 192–281 · score 0.71 · Oscillospiraceae bacterium CLA, Longicatena caecimuris, AA H250, prevalent, taxa, species
- [5] § Materials and methods › Differential abundance and prevalence analysis ↔ 2-microbial_taxa_analysis/1-differential_abundance_analysis_final_version.R, lines 1–66 · score 0.69 · low abundance, noise, preprocessed, zero, microbial species, downstream
- [6] § Materials and methods › Correlations between clinical characteristics and microbial features ↔ 5-correlation_analysis/partial_correlation_analysis.R, lines 81–172 · score 0.65 · pcor.test, partial correlation, clinical measurement, Spearman, age, BMI
- [7] § Results › Correlation between clinical measures and microbial features ↔ 5-correlation_analysis/partial_correlation_analysis.R, lines 424–489 · score 0.63 · MoCA, CDR SB, partial correlation, resampling, UPDRS, STMS
- [8] § Materials and methods › Correlations between clinical characteristics and microbial features ↔ 5-correlation_analysis/partial_correlation_analysis.R, lines 81–172 · score 0.60 · partial correlation, clinical measurement, resampling, validation, Spearman, 80 %
- [9] § Materials and methods › Differential abundance and prevalence analysis ↔ 3-microbial_functional_pathway_analysis/pathway_analysis_final_version.R, lines 539–561 · score 0.59 · arcsine square root, prevalence cutoff, household ID, variables, linear, relative abundance
Paper
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The authors' code
R · 527 lines · 18 KB · no license · 4 matches
partial_correlation_analysis.R at commit f63e83c, no license · at the source
Overview
- Bioinformatics and Computational Biology Program, University of Minnesota, Rochester, MN, United States
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- Department of Neurology, Mayo Clinic, Rochester, MN, United States
- Center for Sleep Medicine, Mayo Clinic, Rochester, MN, United States
- Microbiomics Program, Center of Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Division of Clinical Trials and Biostatistics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, United States
- Department of Radiology, Mayo Clinic, Rochester, MN, United States
- Division of Neonatology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Department of Surgery, School of Medicine, University of Minnesota, Minneapolis, MN, United States
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Department of Food Science and Nutrition, University of Minnesota, St. Paul, MN, United States
Abstract
Background: Lewy body disease (LBD) is a progressive neurodegenerative a-synucleinopathy, whereas isolated REM sleep behavior disorder (iRBD) is recognized as a prodromal stage of LBD. Although growing evidence implicates the gut–brain axis in neurodegeneration, the taxonomic and functional roles of the gut microbiome across the prodromal-to-symptomatic
Methods: Here, we performed shotgun metagenomic sequencing on stool samples from 25 patients with LBD (10 mild cognitive impairment due to LBD [MCI-LB] and 15 dementia with Lewy bodies [DLB]), 10 individuals with iRBD, and their household matched cohabitant controls to characterize disease-associated microbial alterations while minimizing environmental confounding.
Results: Despite no significant differences in global microbial diversity, we identified convergent shifts in microbial taxa, metabolic pathways, and gene families across disease stages. Both LBD and iRBD showed increased abundance of microbial taxa potentially associated with gut barrier disruption, as well as higher abundance of functional pathways related to lipopolysaccharide biosynthesis. LBD showed lower abundance of pathways related to complex carbohydrate fermentation, and both groups showed lower abundance of pathways associated with neurotransmitter-related
Discussion: These exploratory findings represent the first high-resolution, shotgun metagenomic characterization of gut microbiome alterations across the LBD continuum, highlighting functional patterns that may serve as candidate markers of disease progression in future longitudinal and mechanistic studies.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
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xiaowei-zhao-1111/LBD_Gut_Microbiome_2026
f63e83c4ee0af68f46830b2546beec93dcff8182, 16 July 2026Availability: 1 check, the latest on 27 September 2026: the link answers
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- 1-alpha_beta_diversity/
alpha_beta_diversity_fin — R, 583 lines, 1 match, shown from its sourceal_version.R - 2-microbial_taxa_analysi
s/ — R, 508 lines, 1 match, shown from its source1-differential_abundance _analysis_final_version. R - 2-microbial_taxa_analysi
s/ — R, 281 lines, 2 matches, shown from its source2-different_prevalence_a nalysis_final_version.R - 3-microbial_functional_p
athway_analysis/ — R, 1,084 lines, 1 match, shown from its sourcepathway_analysis_final_v ersion.R - 3-microbial_functional_p
athway_analysis/ — R, 173 lines, shown from its sourcepathway_taxonomy_analysi s_final_version.R - 3-microbial_functional_p
athway_analysis/ — R, 462 lines, shown from its sourcepathways_contributed_by_ bacterial_species_final_ version.R - 4-gene_families_analysis
/ — R, 437 lines, shown from its sourcegene_families_analysis_f inal_version.R - 5-correlation_analysis/
partial_correlation_anal — R, 527 lines, 4 matches, shown from its sourceysis.R - README.md — Text, 164 lines, shown from its source
The paper's code and data availability statement is in the Data section.
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Data
Datasets cited
- bioproject:PRJNA1393457 — at NCBI BioProject; found in “Data availability statement”
Data availability statement
Sequencing data for stool metagenomes used in this study have been deposited at NCBI’s SRA data repository (PRJNA1393457) and can be downloaded without any restrictions at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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Recorded: type, language, journal, volume, pages, dates, 14 authors, 8 keywords, 2 funders, 89 references.
Cite
This paper
Zhao, X., McCarter, S. J., Gupta, V. K., Grant, K. M., St. Louis, E. K., Kantarci, K., Savica, R., Hill, M., Vuong, H. E., Staley, C., Boeve, B. F., Ross, O. A., Teigen, L. M., & Sung, J. (2026). Shotgun metagenomic analysis reveals taxonomic and functional alterations in the gut microbiome across prodromal and symptomatic Lewy body disease. Frontiers in microbiomes, 5, 1834726. https://
BibTeX
@article{zhao2026shotgun
author = {Zhao, Xiaowei and McCarter, Stuart J. and Gupta, Vinod K. and Grant, Kiera M. and St. Louis, Erik K. and Kantarci, Kejal and Savica, Rodolfo and Hill, Max and Vuong, Helen E. and Staley, Christopher and Boeve, Bradley F. and Ross, Owen A. and Teigen, Levi M. and Sung, Jaeyun},
title = {{Shotgun metagenomic analysis reveals taxonomic and functional alterations in the gut microbiome across prodromal and symptomatic Lewy body disease}},
journal = {Frontiers in microbiomes},
year = {2026},
month = jul,
volume = {5},
pages = {1834726},
publisher = {Frontiers Media SA},
issn = {2813-4338},
doi = {10.3389/
url = {https://
pmid = {42529077},
pmcid = {PMC13416100}
}
RIS
TY - JOUR
AU - Zhao, Xiaowei
AU - McCarter, Stuart J.
AU - Gupta, Vinod K.
AU - Grant, Kiera M.
AU - St. Louis, Erik K.
AU - Kantarci, Kejal
AU - Savica, Rodolfo
AU - Hill, Max
AU - Vuong, Helen E.
AU - Staley, Christopher
AU - Boeve, Bradley F.
AU - Ross, Owen A.
AU - Teigen, Levi M.
AU - Sung, Jaeyun
TI - Shotgun metagenomic analysis reveals taxonomic and functional alterations in the gut microbiome across prodromal and symptomatic Lewy body disease
T2 - Frontiers in microbiomes
J2 - Front Microbiomes
PY - 2026
DA - 2026/
VL - 5
SP - 1834726
SN - 2813-4338
PB - Frontiers Media SA
DO - 10.3389/
UR - https://
LA - en
ER -
CSL-JSON
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