A5066209659- Gut microbiota and health
- Diet and metabolism studies
- Metabolomics and Mass Spectrometry Studies
- Tryptophan and brain disorders
- Nutritional Studies and Diet
- Clostridium difficile and Clostridium perfringens research
- Adipose Tissue and Metabolism
- Cancer Genomics and Diagnostics
- Epigenetics and DNA Methylation
- Medicinal Plants and Bioactive Compounds
- Meta-analysis and systematic reviews
- HIV/AIDS drug development and treatment
- Diet, Metabolism, and Disease
- Malaria Research and Control
- Oral microbiology and periodontitis research
- Urinary Tract Infections Management
- Mitochondrial Function and Pathology
- Treatment of Major Depression
- Child Nutrition and Feeding Issues
- Schizophrenia research and treatment
- Cholinesterase and Neurodegenerative Diseases
- Health disparities and outcomes
- Pediatric health and respiratory diseases
- Bioinformatics and Genomic Networks
- Probiotics and Fermented Foods
University of California, San Diego
2021-2025
UC San Diego Health System
2024
California Institute of Technology
2022-2023
Alzheimer’s Disease Neuroimaging Initiative
2023
Union Bank of Switzerland
2023
Institute on Aging
2022
The ketogenic diet (KD) is an intriguing therapeutic candidate for Alzheimer's disease (AD) given its protective effects against metabolic dysregulation and seizures. Gut microbiota are essential KD-mediated neuroprotection seizures as well modulation of bile acids, which play a major role in cholesterol metabolism. These relationships motivated our analysis gut metabolites related to cognitive status following controlled KD intervention compared with low-fat-diet intervention.
We identify the Plasmodium falciparum acetyl-coenzyme A synthetase (PfAcAS) as a druggable target, using genetic and chemical validation. In vitro evolution of resistance with two antiplasmodial drug-like compounds (MMV019721 MMV084978) selects for mutations in PfAcAS. Metabolic profiling compound-treated parasites reveals changes acetyl-CoA levels both compounds. Genome editing confirms that PfAcAS are sufficient to confer resistance. Knockdown studies demonstrate is essential asexual...
Alzheimer's disease (AD) is a major neurodegenerative disorder with significant environmental factors, including diet and lifestyle, influencing its onset progression. Although previous studies have suggested that certain diets may reduce the incidence of AD, underlying mechanisms remain unclear. In this post-hoc analysis randomized crossover study 20 elderly adults, we investigated effects modified Mediterranean ketogenic (MMKD) on plasma lipidome in context AD biomarkers, analyzing 784...
Abstract This study investigated the relationship between gut microbiota and neuropsychiatric disorders (NPDs), specifically anxiety disorder (ANXD) and/or major depressive (MDD), as defined by Diagnostic Statistical Manual of Mental Disorders (DSM)-IV or V criteria. The also examined influence medication use, particularly antidepressants anxiolytics, classified through Anatomical Therapeutic Chemical (ATC) Classification System, on microbiota. Both 16S rRNA gene amplicon sequencing (16S)...
Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only few studies have explored KD's impact, especially on blood cerebrospinal fluid (CSF). Our study involved participants at for AD, either cognitively normal or with mild cognitive impairment. The consumed both modified Mediterranean Ketogenic Diet (MMKD) American...
Abstract As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient filtration using prior human references can introduce false sex biases and inadvertently permit flow-through of host-specific during bioinformatic analyses, which could be exploited individual identification. To address these issues, we benchmark three methods varying throughput,...
Herein, we present a tool called Evident that can be used for deriving effect sizes broad spectrum of metadata variables, such as mode birth, antibiotics, socioeconomics, etc., to provide power calculations new study. mine existing databases large microbiome studies (such the American Gut Project, FINRISK, and TEDDY) analyze planning future via analysis. For each metavariable, software is flexible compute many commonly measures analyses, including α diversity, β log-ratio In this work,...
Microbiome data analysis can be difficult because of particular features, some unavoidable and due to technical limitations DNA sequencing instruments. The first step in many analyses that ultimately reveals patterns similarities differences among sets samples (e.g., separating from sick healthy people or seawater versus soil) is calculating the difference between each pair samples.
Alterations to the gut microbiome have been reported between children with autism spectrum disorders (ASDs) and typically developing (TD) children. Characterizing these differences has led proposal of new treatments for ASD, such as probiotic interventions fecal matter transplants. However, no study date characterized or metabolome in Pitt Hopkins syndrome (PTHS), a severe ASD high incidence gastrointestinal (GI) disturbances constipation. Here, we surveyed cohort PTHS individuals their...
Abstract Alzheimer’s disease (AD) is influenced by a variety of modifiable risk factors, including person’s dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only few studies have explored KD’s impact, especially on blood cerebrospinal fluid (CSF). Our study involved participants at for AD, either cognitively normal or with mild cognitive impairment. The consumed both modified Mediterranean-ketogenic (MMKD)...
Abstract Differentiating microbial communities among samples is a major objective in biomedicine. Quantifying the effect size of these differences allows researchers to understand factors most associated with and optimize design clinical resources required address particular research questions. Here, we present Evident, package for calculations power analysis on microbiome data show that Evident scales large datasets numerous metadata covariates.
ABSTRACT Alzheimer’s disease (AD) is a major neurodegenerative disorder with significant environmental factors, including diet and lifestyle, influencing its onset progression. Although previous studies have suggested that certain diets may reduce the incidence of AD, underlying mechanisms remain unclear. In this randomized crossover study 20 elderly adults, we investigated effects modified Mediterranean ketogenic (MMKD) on plasma lipidome, analyzing 784 lipid species across 47 classes. We...
The goal of this study was to examine if mental health and psychosocial well-being differed between middle-aged (MA; 40-59 years), younger-old (YO; 60-79 older-old (OO; 80+ years) adults with respect their trends, heterogeneity, correlates.Eighteen instruments were administered 590 over age 40. Cross-sectional data also included self-report-based measures sociodemographics, cognitive functioning, physical activity, body mass index.Age trends across varied in magnitude shape, but generally...
Abstract Background Gut microbiome features have been linked with many diseases including Alzheimer’s disease (AD). Evidence suggests that the gut microbiota may impact cognition of AD patients. We explored association and three PACC3 cognitive scores in individuals at risk for AD. Method Participants from Microbiome Risk Study clinical diagnosis (N=239) amyloid status (N=93) underwent testing collection samples. Three different types (Animal‐Naming Test (AN), Category Fluency (CFL),...
Abstract This study investigated the relationship between gut microbiota and neuropsychiatric disorders (NPDs), specifically anxiety disorder (ANXD) and/or major depressive (MDD), as defined by DSM-IV or V criteria. The also examined influence of medication use, particularly antidepressants anxiolytics, classified through Anatomical Therapeutic Chemical (ATC) Classification System, on microbiota. Both 16S rRNA gene amplicon sequencing shallow shotgun were performed DNA extracted from 666...
Abstract BACKGROUND The gut microbiome is a potentially modifiable factor in Alzheimer’s disease (AD); however, understanding of its composition and function regarding AD pathology limited. METHODS Shallow-shotgun metagenomic data was used to analyze fecal from participants enrolled the Wisconsin Microbiome Risk Study, leveraging clinical cerebrospinal fluid (CSF) biomarkers. Differential abundance ordinary least squares regression analyses were performed find differentially abundant...
Emerging research suggests that diet plays a vital role in shaping the composition and function of gut microbiota. While significant efforts have been made to identify general patterns linking microbiome, much this lacks representation from low- middle-income countries such as Mexico. Additionally, both microbiome highly complex individualized configurations, there is growing evidence tailoring diets individual microbiota profiles may optimize path toward improving or maintaining health...
<title>Abstract</title> As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient filtration using prior human references can introduce false sex biases and inadvertently permit flow-through of host-specific during bioinformatic analyses, which could be exploited individual identification. To address these issues, we benchmark three methods...
Abstract Background The aim of this study was to identify a gut microbial signature associated with patterns gray matter volume in AD, and validate the by testing it against measures AD pathology cognitive performance. Prior literature suggests that species involved bile acid production inflammation may be implicated signature. Method sample comprised 204 Microbiome Alzheimer’s Risk Study participants (22 10 MCI, 172 CN; 129 Females, 78 APOE+) from Wisconsin Disease Research Center Registry...
Abstract Background Gut microbiome features are known to be different in Alzheimer’s disease (AD) patients compared with cognitively normal. Evidence suggests that the gut microbiota may related pathology of AD. We examined association between and AD phenotypes genotypes. Method Cross‐sectional analysis was performed on filtered count table including 246 participants from Microbiome Risk Study. The taxonomic used analyze differential abundance using BIRDMAn pipeline. To determine differences...
Abstract Background Alzheimer’s disease (AD) is a neurodegenerative disorder with significant environmental factors, including diet, that influence its onset and progression. While the ketogenic diet (KD) holds promise in reducing metabolic risks potentially affecting AD progression, only few studies have explored KD’s molecular impact for markers of therapeutic potential. The BEAM study simultaneously profiled effect on lipidome, blood cerebrospinal metabolome, microbiome both cognitively...
STRUCTURED ABSTRACT INTRODUCTION The ketogenic diet (KD) is an intriguing candidate for neuroprotection in Alzheimer’s disease (AD) given its protective effects against metabolic dysregulation and seizures. diet’s neuroprotective have been shown to be gut microbiome-dependent mice; thus we examined KD-induced changes the microbiome metabolome patients at-risk AD. METHODS We compared low-carbohydrate modified Mediterranean Ketogenic Diet (MMKD) low-fat American Heart Association (AHAD) adults...