Jingyuan Fu
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View article: Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer
Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer Open
Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 3…
View article: DNA methylation of genes involved in lipid metabolism drives adiponectin levels and metabolic disease
DNA methylation of genes involved in lipid metabolism drives adiponectin levels and metabolic disease Open
Aims/hypothesis Despite playing critical roles in the pathophysiology of type 2 diabetes and other metabolic disorders, the molecular mechanisms underlying circulating adipokine levels remain poorly understood. By identifying genomic regio…
View article: GECSI: Large-scale chromatin state imputation from gene expression
GECSI: Large-scale chromatin state imputation from gene expression Open
Compendiums of chromatin state annotations based on integrating maps of multiple epigenetic marks such as from ChromHMM have become a powerful resource. While these compendiums have coverage of many biological samples, there are many addit…
View article: <i>iMeta</i>: Boosting academic sharing and collaboration via social media
<i>iMeta</i>: Boosting academic sharing and collaboration via social media Open
Social media platforms have revolutionized scientific communication by bridging gaps between researchers, academic journals, and global audiences. This article showcases iMeta, an open-access journal that leverages a diversified soc…
View article: Distinct microbial and metabolic shifts characterize acute coronary syndrome and recovery
Distinct microbial and metabolic shifts characterize acute coronary syndrome and recovery Open
Early identification of patients at risk of acute coronary syndrome (ACS) remains a major unmet need, particularly among those with stable coronary artery disease (sCAD), where timely intervention could markedly improve outcomes. The gut m…
View article: Innovative strategies to enhance MSCs efficacy in acute kidney injury (Review)
Innovative strategies to enhance MSCs efficacy in acute kidney injury (Review) Open
Acute kidney injury (AKI) remains a significant clinical challenge, characterized by rapid kidney dysfunction with potential progression to chronic kidney disease. Mesenchymal stem cells (MSCs) offer promising therapeutic potential due to …
View article: Host and environmental determinants of human milk oligosaccharides and microbiota in the Lifelines NEXT cohort
Host and environmental determinants of human milk oligosaccharides and microbiota in the Lifelines NEXT cohort Open
Human milk is important for infant development, but few large studies have comprehensively investigated milk composition. Here, we characterized human milk oligosaccharides (HMOs) and milk microbiota, their shaping factors, and their links…
View article: Microbial Adaptation in Healthy Ageing: Insights from Age-associated Structural Variation in the Human Gut Microbiome
Microbial Adaptation in Healthy Ageing: Insights from Age-associated Structural Variation in the Human Gut Microbiome Open
In this metagenome-wide association study, we profiled 14,249 structural variants (SVs) in the gut microbiome of 10,215 individuals from five cohorts (four European and one African). This revealed 105 SVs that exhibited replicable associat…
View article: Advanced Dialogues: From Genomes to Microbiomes—A Cross‐Disciplinary Journey
Advanced Dialogues: From Genomes to Microbiomes—A Cross‐Disciplinary Journey Open
View article: Dose-dependent immunotoxic mechanisms of celastrol via modulation of the PI3K-Akt signaling pathway
Dose-dependent immunotoxic mechanisms of celastrol via modulation of the PI3K-Akt signaling pathway Open
Ethnopharmacological relevance Celastrol, a bioactive compound from Tripterygium wilfordii Hook.f. , is known for its anti-inflammatory and immunomodulatory effects, but its immunotoxicity is underexplored. This study investigates the mech…
View article: New insights in amino sugar metabolism by the gut microbiome
New insights in amino sugar metabolism by the gut microbiome Open
Gut microorganisms inhabiting the intestinal tract play key roles in host's health and disease. A properly functioning gut microbiome requires the availability of adequate carbon, nitrogen and energy sources. One of the main sources of ene…
View article: Early-life development of the gut virome and plasmidome: A longitudinal study in cesarean-born infants
Early-life development of the gut virome and plasmidome: A longitudinal study in cesarean-born infants Open
Mobile genetic elements (MGE) are critical yet understudied determinants of gut microbiome composition. In this secondary analysis of a randomized controlled trial (NCT06030713), we characterized the gut virome and plasmidome in 195 sample…
View article: Longitudinal Gut Microbiota Tracking Reveals the Persistent Spread of Mobile Genes and HGT-Driven Community Stabilization
Longitudinal Gut Microbiota Tracking Reveals the Persistent Spread of Mobile Genes and HGT-Driven Community Stabilization Open
Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 3…
View article: High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation
High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation Open
Our study sheds light on the complex interplay between the gut microbiome and CeD, revealing increased interindividual variation and strain-level variation in tCeD patients. These findings expand our understanding of the microbiome's role …
View article: Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis
Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis Open
View article: MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome
MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome Open
View article: Association between gut microbiome profiles and host metabolic health across the life course: a population-based study
Association between gut microbiome profiles and host metabolic health across the life course: a population-based study Open
R.L is supported by European UnionHorizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement No 860898 [FIDELIO].
View article: Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study
Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study Open
View article: Metabolomics profiling of Type D personality traits
Metabolomics profiling of Type D personality traits Open
In this large meta-analysis, SI was associated with omega-3 fatty acids to total fatty acids ratio, which is suggestive of lower omega-3 fatty acid intake. Only some metabolite biomarkers showed tentative links to Type D and NA. In sum, it…
View article: Pregnancy and Early Life Gut Microbiome: Influencing Factors and Health Implications
Pregnancy and Early Life Gut Microbiome: Influencing Factors and Health Implications Open
The gut microbiomes during pregnancy and infancy play a critical role in maternal and infant health, yet our understanding of what determines their temporal dynamics, interactions, and health impacts remains poor. In this study, we profile…
View article: Microbiome-wide PheWAS links gut microbial SNVs to human health and exposures
Microbiome-wide PheWAS links gut microbial SNVs to human health and exposures Open
The importance of the gut microbiome in human health has been widely recognized, with alterations in species abundances now reported for many different diseases. In recent years, observations of within-species genetic diversity and strain-…
View article: Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation
Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation Open
Our findings reveal a potential feedback mechanism in which glycine and serine regulate gene expression through DNA methylation.
View article: Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study
Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study Open
Our findings suggest that microbial balances could be a reproducible method for identifying BD/SSD-specific microbial signatures, with potential diagnostic and prognostic applications. Notably, Lachnoclostridium and Eggerthella emerge as f…
View article: A Study of Fresh Commodities Sales Analysis Based on Time Series Modeling - Taking Vegetable Category Commodities as an Example
A Study of Fresh Commodities Sales Analysis Based on Time Series Modeling - Taking Vegetable Category Commodities as an Example Open
This paper serves as a decision-making aid for pricing and replenishing vegetables in fresh produce supermarkets. Initially, the sales data of various vegetable categories are thoroughly examined for trends and seasonal patterns, utilizing…
View article: Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries
Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries Open
View article: Multiple indicators of gut dysbiosis predict all-cause and cause-specific mortality in solid organ transplant recipients
Multiple indicators of gut dysbiosis predict all-cause and cause-specific mortality in solid organ transplant recipients Open
Objective Gut microbiome composition is associated with multiple diseases, but relatively little is known about its relationship with long-term outcome measures. While gut dysbiosis has been linked to mortality risk in the general populati…
View article: Antibody signatures against viruses and microbiome reflect past and chronic exposures and associate with aging and inflammation
Antibody signatures against viruses and microbiome reflect past and chronic exposures and associate with aging and inflammation Open
View article: Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content
Genome-wide Studies Reveal Genetic Risk Factors for Hepatic Fat Content Open
Genetic susceptibility to metabolic associated fatty liver disease (MAFLD) is complex and poorly characterized. Accurate characterization of the genetic background of hepatic fat content would provide insights into disease etiology and cau…
View article: Unraveling interindividual variation of trimethylamine <i>N</i>‐oxide and its precursors at the population level
Unraveling interindividual variation of trimethylamine <i>N</i>‐oxide and its precursors at the population level Open
Trimethylamine N ‐oxide (TMAO) is a circulating microbiome‐derived metabolite implicated in the development of atherosclerosis and cardiovascular disease (CVD). We investigated whether plasma levels of TMAO, its precursors (betaine, carnit…
View article: High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation
High-resolution analysis of the treated coeliac disease microbiome reveals strain-level variation Open
Background Coeliac disease (CeD) is an immune-mediated disorder primarily affecting the small intestine, characterised by an inflammatory immune reaction to dietary gluten. CeD onset results from a multifaceted interplay of genetic and env…