A5006621565- Gut microbiota and health
- Metabolomics and Mass Spectrometry Studies
- Rheumatoid Arthritis Research and Therapies
- Traditional Chinese Medicine Studies
- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Diet and metabolism studies
- Clostridium difficile and Clostridium perfringens research
- Mycobacterium research and diagnosis
- Food Security and Health in Diverse Populations
- Monoclonal and Polyclonal Antibodies Research
- Systemic Lupus Erythematosus Research
- Viral gastroenteritis research and epidemiology
- Pediatric Hepatobiliary Diseases and Treatments
- Tryptophan and brain disorders
- Molecular Biology Techniques and Applications
- Nutritional Studies and Diet
- Hepatitis C virus research
- Pancreatic and Hepatic Oncology Research
- Liver Diseases and Immunity
- Microbial Natural Products and Biosynthesis
- Microbial Metabolites in Food Biotechnology
- Liver Disease Diagnosis and Treatment
- Protein Tyrosine Phosphatases
- Forensic and Genetic Research
Mayo Clinic
2020-2025
University of Minnesota Rochester
2024
WinnMed
2022-2023
Mayo Clinic in Arizona
2020-2021
Hamad Medical Corporation
2018-2021
Indian Institute of Chemical Biology
2015-2018
Academy of Scientific and Innovative Research
2017
Abstract Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift microbial genomics from few genome comparisons large-scale pan-genome studies at different scales of phylogenetic resolution. Pan-genome provide framework for estimating the genomic diversity dataset, determining core (conserved), accessory (dispensable) unique (strain-specific) gene pool species, tracing horizontal gene-flux across strains providing insight into species...
Abstract Providing insight into one’s health status from a gut microbiome sample is an important clinical goal in current human research. Herein, we introduce the Gut Microbiome Health Index (GMHI), biologically-interpretable mathematical formula for predicting likelihood of disease independent diagnosis. GMHI formulated upon 50 microbial species associated with healthy ecosystems. These are identified through multi-study, integrative analysis on 4347 stool metagenomes 34 published studies...
Abstract Background Rapid advances in the past decade have shown that dysbiosis of gut microbiome is a key hallmark rheumatoid arthritis (RA). Yet, relationship between and clinical improvement RA disease activity remains unclear. In this study, we explored patients with to identify features are associated with, as well predictive of, minimum clinically important (MCII) activity. Methods We conducted retrospective, observational cohort study on diagnosed 1988 2014. Whole metagenome shotgun...
Recent advancements in translational gut microbiome research have revealed its crucial role shaping predictive healthcare applications. Herein, we introduce the Gut Microbiome Wellness Index 2 (GMWI2), an enhanced version of our original GMWI prototype, designed as a standardized disease-agnostic health status indicator based on taxonomic profiles. Our analysis involves pooling existing 8069 stool shotgun metagenomes from 54 published studies across global demographic landscape (spanning 26...
The community composition of the human microbiome is known to vary at distinct anatomical niches. But little about nature variations, if any, genome/sub-genome levels a specific microbial across different present report aims explore, as case study, variations in gene repertoire 28 Prevotella reference genomes derived from body-sites human, reported earlier by Human Microbiome Consortium.The pan-genome for remains "open". On an average, 17% predicted protein-coding genes any particular genome...
Abstract Background Dysbiosis of the gut microbiome is frequent in intensive care unit (ICU), potentially leading to a heightened risk nosocomial infections. Enhancing has been proposed as strategic approach mitigate potential adverse outcomes. While prior research on select probiotic supplements not successfully shown improve microbial diversity, fermented foods offer promising alternative. In this open-label phase I safety and feasibility study, we examined kefir an initial step towards...
Abstract Background Rheumatoid arthritis (RA) is a chronic, autoimmune disorder characterized by joint inflammation and pain. In patients with RA, metabolomic approaches, i.e., high-throughput profiling of small-molecule metabolites, on plasma or serum has thus far enabled the discovery biomarkers for clinical subgroups, risk factors, predictors treatment response. Despite these recent advancements, identification blood metabolites that reflect quantitative disease activity remains an...
Abstract We previously proposed the Gut Microbiome Wellness Index (GMWI), a predictor of disease presence based on gut microbiome taxonomic profile. As an application this index for food science research, we applied GMWI as quantitative tool measuring prebiotic effect oligosaccharides. Mainly, in vitro anaerobic batch fermentation system, fructooligosaccharides (FOS), galactooligosaccharides (GOS), xylooligosaccharides (XOS), inulin (IN), and 2’-fucosyllactose (2FL), were mixed separately...
Patients with rheumatoid arthritis (RA) can test either positive or negative for circulating anti-citrullinated protein antibodies (ACPA) and are thereby categorized as ACPA-positive (ACPA+) ACPA-negative (ACPA-), respectively. In this study, we aimed to elucidate a broader range of serological autoantibodies that could further explain immunological differences between patients ACPA+ RA ACPA- RA. On serum collected from adult (n = 32), 30), matched healthy controls used highly multiplex...
Gut microbial symbionts have been shown to influence the development of autoimmunity in multiple sclerosis (MS). Emerging research points an important relationship between microbial-IgA interface and MS pathophysiology. IgA-secreting B cells are observed brain, shifts gut bacteria-IgA binding described some patients with MS. However, relationships microbiome host immune response, particularly regarding B-cell-depleting immunomodulation, remain underexplored. This study aimed evaluate...
Abstract A key question in human gut microbiome research is what are the robust structural patterns underlying its taxonomic composition. Herein, we use whole metagenomic datasets from healthy guts to show that such do exist, albeit not conventional enterotype sense. We first introduce concept of mixed-membership enterotypes using a network inference approach based on stochastic block models. find microbiomes across group people (hosts) display nested structure, which has been observed...
The relationship between primary biliary cholangitis (PBC), a chronic cholestatic autoimmune liver disease, and the peripheral immune system remains to be fully understood. Herein, we performed first mass cytometry (CyTOF)-based, immunophenotyping analysis of in PBC at single-cell resolution. CyTOF was on blood mononuclear cells (PBMCs) from patients (n = 33) age-/sex-matched healthy controls obtain cell abundance marker expression profiles. Hierarchical clustering methods were applied...
Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles microbe-microbe and host-microbe interactions. Given the biological significance of SMs current profound interest metabolic functions microbiomes, unbiased identification BGCs from high-throughput metagenomic data could offer novel insights into complex chemical ecology communities. Currently available tools for predicting shotgun metagenomes have several...
Abstract Summary We recently introduced the Gut Microbiome Wellness Index (GMWI), a stool metagenome-based indicator for assessing health by determining likelihood of disease given state one’s gut microbiome. The calculation our wellness index depends on relative abundances health-prevalent and health-scarce species. Encouragingly, GMWI has already been utilized in various studies focusing differences microbiome between cases controls. Herein, we introduce GMWI-webtool, user-friendly browser...
The conglomerate of microorganisms inhabiting various body-sites human, known as the human microbiome, is one key determinants health and disease. Comprehensive pan-genomic functional analysis approach for microbiome components can enrich our understanding about impact on health. By utilizing this we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) - a novel dynamic web-resource that integrates genomic characteristics 1293 complete microbial genomes available from Human...
Abstract The aim of the current study is to review molecular characteristics Neisseria meningitidis ( N. ) in Hamad Medical Corporation, which provider secondary and tertiary care state Qatar. A total 39 isolates from period 2013 2018 were revived identified by Vitek, susceptibility on basis E test was retrieved patient’s files. subjected multilocus sequence typing. most common serogroup (19) W135, 12 isolated blood CSF. ST-11 predominant ST clonal complex causing cases (61.53%). Clonal...
This study aimed to identify plasma proteomic signatures that differentiate active and inactive giant cell arteritis (GCA) from non-disease controls. By comprehensively profiling the proteome of both patients with GCA controls, we proteins (1) distinguish controls (2) associate disease activity in GCA.
Abstract The relationship between Primary Biliary Cholangitis (PBC), a chronic cholestatic autoimmune liver disease, and the peripheral immune system remains to be fully understood. Herein, we performed first mass cytometry (CyTOF)-based, immunophenotyping analysis of in PBC at single-cell resolution. CyTOF was on blood mononuclear cells (PBMCs) from patients (n=33) age-/sex-matched healthy controls obtain cell abundance marker expression profiles. Hiearchical clustering methods were applied...