A5043464127- Gut microbiota and health
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Bioinformatics and Genomic Networks
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Infection Control and Ventilation
- Gene expression and cancer classification
- Adipose Tissue and Metabolism
- Dental Research and COVID-19
- Metabolism, Diabetes, and Cancer
- Autism Spectrum Disorder Research
- Dental Health and Care Utilization
- ICT in Developing Communities
- Regulation of Appetite and Obesity
- Amino Acid Enzymes and Metabolism
- Meta-analysis and systematic reviews
- Antibiotic Use and Resistance
- Immune Response and Inflammation
- Dermatology and Skin Diseases
- Neurological Disorders and Treatments
- SARS-CoV-2 detection and testing
- COVID-19 epidemiological studies
- Drug Transport and Resistance Mechanisms
- Mobile Health and mHealth Applications
University of California, San Diego
2019-2024
Alzheimer’s Disease Neuroimaging Initiative
2023
Union Bank of Switzerland
2023
Jacobs (United States)
2022
The University of Texas at Austin
2022
United International University
2010-2014
Autism spectrum disorder (ASD) is a neurodevelopmental characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, we developed Bayesian differential ranking algorithm to identify ASD-associated molecular taxa profiles 10 cross-sectional microbiome datasets 15 other datasets, including dietary patterns, metabolomics, cytokine human...
Abstract Diabetes represents a spectrum of disease in which metabolic dysfunction damages multiple organ systems including liver, kidneys and peripheral nerves 1,2 . Although the onset progression these co-morbidities are linked with insulin resistance, hyperglycaemia dyslipidaemia 3–7 , aberrant non-essential amino acid (NEAA) metabolism also contributes to pathogenesis diabetes 8–10 Serine glycine closely related NEAAs whose levels consistently reduced patients syndrome 10–14 but...
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.
Abstract The composition of the microbial community in intestine may influence functions distant organs such as brain, lung, and skin. These microbes can promote disease or have beneficial functions, leading to hypothesis that gut explain co-occurrence intestinal skin diseases. Here, we show reverse occur, directly alters microbiome. Disruption dermis by wounding digestion dermal hyaluronan results increased expression colon host defense genes Reg3 Muc2 , changes behavior bacteria. Enhanced...
Many tools for dealing with compositional ' 'omics' data produce feature-wise values that can be ranked in order to describe features' associations some sort of variation. These include differentials (which specified covariates) and feature loadings variation along a given axis biplot). Although prior work has discussed the use these 'rankings' as starting point exploring log-ratios particularly high- or low-ranked features, such exploratory analyses have previously been done using custom...
Colorectal cancer (CRC) is driven by genomic alterations in concert with dietary influences, the gut microbiome implicated as an effector disease development and progression. While meta-analyses have provided mechanistic insight into patients CRC, study heterogeneity has limited causal associations. Using multi-omics studies on genetically controlled cohorts of mice, we identify diet major driver microbial metabolomic differences, reductions α diversity widespread changes cecal metabolites...
Microbiome data are sparse and high dimensional, so effective visualization of these requires dimensionality reduction. To date, the most commonly used method for reduction in microbiome is calculation between-sample microbial differences (beta diversity), followed by principal-coordinate analysis (PCoA). Uniform Manifold Approximation Projection (UMAP) an alternative that can reduce beta diversity distance matrices. Here, we demonstrate benefits limitations using UMAP on data. Using real...
SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic antagonistic effects of specific bacterial taxa on viral prevalence infectivity. We set out to test whether communities predict occurrence a hospital setting.We collected 972 samples from hospitalized patients with COVID-19, their health care providers, surfaces before, during, after admission. screened...
Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive web tool visualizing trees in context microbiome, metabolome, other community data scalable to with well over 500,000 nodes. EMPress provides novel functionality-including ordination integration animations-alongside many standard tree visualization features thus simplifies exploratory analyses forms 'omic data.IMPORTANCE Phylogenetic are integral...
This study identifies physiological habitats using quantitative magnetic resonance imaging (MRI) to elucidate intertumoral differences and characterize microenvironmental response targeted cytotoxic therapy. BT-474 human epidermal growth factor receptor 2 (HER2+) breast tumors were imaged before during treatment (trastuzumab, paclitaxel) with diffusion-weighted MRI dynamic contrast-enhanced measure tumor cellularity vascularity, respectively. Tumors stained for anti-CD31, anti-ɑSMA,...
How benign liver steatosis progresses to nonalcoholic steatohepatitis (NASH), fibrosis, and hepatocellular carcinoma (HCC) remains elusive. NASH progression entails diverse pathogenic mechanisms relies on complex cross-talk between multiple tissues such as the gut, adipose tissues, liver, brain. Using a hyperphagic mouse fed with Western diet (WD), we aimed elucidate kinetics of hepatic extrahepatic alterations during NASH-HCC progression, well regression.
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.
Quantifying the differential abundance (DA) of specific taxa among experimental groups in microbiome studies is challenging due to data characteristics (e.g., compositionality, sparsity) and study designs repeated measures, meta-analysis, cross-over). Here we present BIRDMAn (
Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (COVID-19), their health care providers, hospital surfaces before, during, after admission. screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities 16S rRNA gene amplicon sequencing, contextualized massive diversity this dataset a meta-analysis over...
E-healthcare or telemedicine applications are being widely deployed across the globe to provide healthcare remote locations. This paper proposes deployments at patient side that target urban and rural population in Bangladesh. In this regard, addresses existing facilities socio-economic condition of these two categories identify potential applications. The core proposed is a generic unit amenable different requirements deployment scenarios. Provisions for individual group discussed both...
Abstract Many tools for dealing with compositional “’omics” data produce feature-wise values that can be ranked in order to describe features’ associations some sort of variation. These include differentials (which specified covariates) and feature loadings variation along a given axis biplot). Although prior work has discussed the use these “rankings” as starting point exploring log-ratios particularly high-or low-ranked features, such exploratory analyses have previously been done using...
Gut dysbiosis, defined as pathogenic alterations in the distribution and abundance of different microbial species, is associated with neuropathic pain a variety clinical conditions, but this has not been explored context neuropathy people HIV (PWH). We assessed gut diversity dysbiosis PWH without (PWoH), some whom reported distal (DNP). DNP was graded on standardized, validated severity scale. The microbiome characterized using 16S rRNA sequencing phylogenetic tree construction. Songbird...
Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from can identify when infected have touched and they been present in hospital rooms or schools. However, the sensitivity specificity of surface sampling a method detecting presence positive individual, well guidance...
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 Autism is a highly heritable neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in autism, with dozens cross-sectional microbiome other omic studies revealing autism-specific profiles along GBA albeit little agreement composition or magnitude. To explore functional architecture we developed an age sex-matched Bayesian differential ranking algorithm that identified...
Abstract Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive tool visualizing trees in context microbiome, metabolome, etc. community data scalable beyond modern large datasets like Earth Microbiome Project. EMPress provides novel functionality—including ordination integration animations—alongside many standard tree visualization features, thus simplifies exploratory analyses forms ‘omic data.
Adverse changes in the gut microbiome with aging are an emerging mediator of arterial dysfunction, which contributes to cardiovascular disease (CVD) development. We investigated therapeutic potential enhancing bioavailability gut-derived short-chain fatty acids (SCFAs; produced from dietary fiber) for improving age-related dysfunction. performed microbial whole-genome sequencing young (3 months) versus old (24 male C57BL/6N mice explore bacterial taxonomic abundance and functional pathways...