Education as Risk Factor of Mild Cognitive Impairment: The Link to the Gut Microbiome

The Journal of Prevention of Alzheimer s Disease, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Language: Английский

---

Elevated fecal calprotectin is associated with gut microbial dysbiosis, altered serum markers and clinical outcomes in older individuals

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: June 12, 2024

Abstract Fecal calprotectin is an established marker of gut inflammation in inflammatory bowel disease (IBD). Elevated levels fecal as well microbial dysbiosis have also been observed other clinical conditions. However, systemic and multi-omics alterations linked to elevated older individuals remain unclear. This study comprehensively investigated the relationship between levels, microbiome composition, serum targeted metabolomics markers, relevant lifestyle medical data a large sample (n = 735; mean age ± SD: 68.7 6.3) from TREND cohort study. Low (0–50 μg/g; n 602), moderate (> 50–100 64) high 100 62) groups were stratified. Several pro-inflammatory genera significantly increased short-chain fatty acid producing decreased vs. low groups. In serum, IL-17C, CCL19 toxic metabolite indoxyl sulfate These changes partially mediated by microbiota. Moreover, group showed BMI higher prevalence heart attack obesity. Our findings contribute understanding its broader implications individuals.

Language: Английский

---

Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans

ISME Communications, Journal Year: 2025, Volume and Issue: 5(1)

Published: Jan. 1, 2025

Abstract Microbial communities in marine sediments contribute significantly to the overall health and resiliency of ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by sediments. Here, through a deep shotgun metagenomics sequencing sediment microbiome COI metabarcoding benthic metazoans, we demonstrate that >50% microorganisms’ metazoan’s taxonomic variation can be explained specific chemical pollution indices. Interestingly, there was significant correlation between similarity communities’ taxonomical functional attributes metazoans community composition. Furthermore, mediation analysis conducted evaluate microbiome-mediated indirect effect, suggesting microbial species functions accounted for 36% 26%, respectively, total effect on metazoans. Our study introduces multi-level perspective future studies urbanized coastal areas explore ecosystems, revealing impact stress their critical biogeochemical functions, which turn may influence macrofaunal

Language: Английский

---

Gender affirming hormone therapy preserves skeletal maturation in young mice via the gut microbiome

Journal of Clinical Investigation, Journal Year: 2024, Volume and Issue: 134(10)

Published: March 26, 2024

Gender affirming hormone therapy (GAHT) is often prescribed to transgender (TG) adolescents alleviate gender dysphoria, but the impact of GAHT on growing skeleton unclear. We found improve trabecular bone structure via increased formation in young male mice and not affect female mice. modified gut microbiome composition both However, fecal microbiota transfers (FMT) revealed that GAHT-shaped was a communicable regulator turnover male, Mediation analysis identified two species Bacteroides as significant contributors skeletal effects mice, with supplementation phenocopying bone. have capacity expand Treg populations gut. Accordingly, expanded intestinal regulatory T cells (Tregs) stimulated their homing marrow (BM) Attesting functional relevance Tregs, pharmacological blockade expansion prevented GAHT-induced anabolism. In summary, improved by promoting microbiome-mediated effect. neither nor impaired structure.

Language: Английский

---

PhyloMed: a phylogeny-based test of mediation effect in microbiome

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: April 11, 2023

Abstract Microbiome data from sequencing experiments contain the relative abundance of a large number microbial taxa with their evolutionary relationships represented by phylogenetic tree. The compositional and high-dimensional nature microbiome mediator challenges validity standard mediation analyses. We propose phylogeny-based analysis method called PhyloMed to address this challenge. Unlike existing methods that directly identify individual mediating taxa, discovers signals analyzing subcompositions defined on phylogenic produces well-calibrated test p -values yields substantially higher discovery power than methods.

Language: Английский

---

Statistical and computational methods for integrating microbiome, host genomics, and metabolomics data

eLife, Journal Year: 2024, Volume and Issue: 13

Published: June 4, 2024

Large-scale microbiome studies are progressively utilizing multiomics designs, which include the collection of samples together with host genomics and metabolomics data. Despite increasing number data sources, there remains a bottleneck in understanding relationships between different modalities due to limited statistical computational methods for analyzing such Furthermore, little is known about portability general metagenomic setting few specialized techniques have been developed. In this review, we summarize implement some commonly used methods. We apply these real sets where shotgun sequencing available integration analysis. compare results across methods, highlight strengths limitations each, discuss areas innovation needed.

Language: Английский

---

Specialty grand challenge: how can we use integrative approaches to understand microbial community dynamics?

Frontiers in Systems Biology, Journal Year: 2024, Volume and Issue: 4

Published: June 17, 2024

SPECIALTY GRAND CHALLENGE article Front. Syst. Biol., 17 June 2024Sec. Integrative Systems Microbiology Volume 4 - 2024 | https://doi.org/10.3389/fsysb.2024.1432791

Language: Английский

---

Comprehensive microbiome causal mediation analysis using MiMed on user-friendly web interfaces

Biology Methods and Protocols, Journal Year: 2023, Volume and Issue: 8(1)

Published: Jan. 1, 2023

Abstract It is a central goal of human microbiome studies to see the roles as mediator that transmits environmental, behavioral, or medical exposures health disease outcomes. Yet, mediation analysis not used much it should be. One reason because lack carefully planned routines, compilers, and automated computing systems for (MiMed) perform series data processing, diversity calculation, normalization, downstream analysis, visualizations. Many researchers in various disciplines (e.g. clinicians, public practitioners, biologists) are also familiar with related statistical methods programming languages on command-line interfaces. Thus, this article, we introduce web cloud platform, named MiMed, enables comprehensive MiMed user-friendly The main features follows. First, can survey spheres (i) whole microbial ecosystem using different ecological measures alpha- beta-diversity indices) (ii) individual taxa phyla, classes, orders, families, genera, species) normalization methods. Second, covariate-adjusted control potential confounding factors age gender), which essential enhance causality results, especially observational studies. Third, breadth inferences both effect estimation significance testing. Fourth, provides flexible easy-to-use processing analytic modules creates nice graphical representations. Finally, employs ChatGPT search what has been known about found significantly mediators artificial intelligence technologies. For demonstration purposes, applied study mediating oral subgingival niches between e-cigarette smoking gingival inflammation. freely available our server (http://mimed.micloud.kr).

Language: Английский

---

Extension of PERMANOVA to Testing the Mediation Effect of the Microbiome

Genes, Journal Year: 2022, Volume and Issue: 13(6), P. 940 - 940

Published: May 25, 2022

Recently, we have seen a growing volume of evidence linking the microbiome and human diseases or clinical outcomes, as well environmental exposures. Now comes time to assess whether mediates effects exposures on which will enable researchers develop interventions modulate outcomes by modifying compositions. Use distance matrices is popular approach analyzing complex data that are high-dimensional, sparse, compositional. However, existing distance-based methods for mediation analysis data, MedTest MODIMA, only work in limited scenarios. PERMANOVA currently most commonly used method testing associations. Using idea inverse regression, here extend test microbiome-mediation including both exposure outcome covariates basing product their F statistics. This extension PERMANOVA, call PERMANOVA-med, naturally inherits all flexible features e.g., allowing adjustment confounders, accommodating continuous, binary, multivariate variables survival providing an omnibus combines results from multiple matrices. Our extensive simulations indicated PERMANOVA-med always controlled type I error had compelling power over MODIMA. Frequently, diminished MODIMA inflated error. real melanoma immunotherapy response, demonstrated wide applicability through 16 different analyses, 6 could be performed 4

Language: Английский

---

Compositional analysis of microbiome data using the linear decomposition model (LDM)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 29, 2023

There are compelling reasons to test compositional hypotheses about microbiome data. We present here LDM-clr, an extension of our linear decomposition model (LDM) approach allow fitting models centered-log-ratio-transformed taxa count As LDM-clr is implemented within the existing LDM program, it enjoys all features supported by LDM, including a analysis differential abundance at both taxon and community levels, while allowing for wide range covariates study designs either association or mediation analysis.LDM-clr has been added R package which available on GitHub https://github.com/yijuanhu/LDM [email protected] data Bioinformatics online.

Language: Английский

---