A5046171080- Gut microbiota and health
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Cancer-related molecular mechanisms research
- Microbial Community Ecology and Physiology
- Radiomics and Machine Learning in Medical Imaging
- Diet and metabolism studies
- Nutritional Studies and Diet
- Epigenetics and DNA Methylation
- Nutrition, Genetics, and Disease
- Nutrition, Health and Food Behavior
- Enterobacteriaceae and Cronobacter Research
- Lung Cancer Diagnosis and Treatment
- Single-cell and spatial transcriptomics
- Colorectal Cancer Screening and Detection
- Metabolomics and Mass Spectrometry Studies
University of California, San Diego
2020-2024
La Jolla Bioengineering Institute
2023-2024
Micron (United States)
2020-2022
Jacobs (United States)
2020
University of Montana
2020
Danone (France)
2020
Colorado State University
2020
Public interest in the effects of fermented food on human gut microbiome is high, but limited studies have explored association between consumption and large cohorts. Here, we used a combination omics-based analyses to study relationship thousands people using both cross-sectional longitudinal data. We found that consumers subtle differences their microbiota structure, which enriched conjugated linoleic acid, thought be beneficial. The results suggest further specific kinds impacts health...
Abstract In 2020, we identified cancer-specific microbial signals in The Cancer Genome Atlas (TCGA) [1]. Multiple peer-reviewed papers independently verified or extended our findings [2–12]. Given this impact, carefully considered concerns by Gihawi et al. [13] that batch correction and database contamination with host sequences artificially created the appearance of cancer type-specific microbiomes. (1) We tested comparing raw Voom-SNM-corrected data per-batch, finding predictive...
Abstract The pursuit of highly sensitive and specific cancer diagnostics based on cell‐free nucleic acids isolated from minimally invasive liquid biopsies has been an area intense research commercial effort for at least two decades. Most these tests detect cancer‐specific mutations or epigenetic modifications circulating DNA derived tumor cells (ctDNA). Although recent FDA approvals both single multianalyte biopsy companion diagnostic assays are proof the tremendous progress made in this...
One goal of microbial ecology researchers is to capture the maximum amount information from all organisms in a sample. The recent COVID-19 pandemic, caused by RNA virus SARS-CoV-2, has highlighted gap traditional DNA-based protocols, including high-throughput methods authors previously established as field standards. To enable simultaneous SARS-CoV-2 and community profiling, compared relative performance two total nucleic acid extraction protocols with authors' benchmarked protocol. included...
Abstract The cancer microbiome field tremendously accelerated following the release of our manuscript nearly three years ago 1 , including direct validation type-specific conclusions in independent, international cohorts 2,3 and tumor microbiome’s adoption into hallmarks 4 . Disentangling contamination signals from biological is an important consideration for this research field. Therefore, despite numerous, high-impact, peer-reviewed papers that either validated or extended them using data...
One goal among microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by RNA virus SARS-CoV-2, has highlighted gap traditional DNA-based protocols, including high-throughput methods we previously established as field standards. To enable simultaneous SARS-CoV-2 and community profiling, compare relative performance two total nucleic acid extraction protocols our benchmarked protocol. We included...
Abstract Introduction: Links between cancer and microbes date back four millennia (Sepich-Poore et al. 2021. Science). Recently, we found that microbial DNA is detectable in tumor tissues patient blood from many human types (Poore 2020. Nature). These intratumoral bloodborne microbiomes were distinct types, normal malignant tissues, present cell-free plasma samples. However, the practical utility of (cf-mbDNA) as a bona fide liquid biopsy diagnostic, including its applicability early-stage...
Fermented foods have gained much attention due to their proposed gut health benefits from recent clinical trials. However, very few studies explored the effects of fermented foods, especially plant origin, on microbiota composition and functional capacity in large human cohorts. Thus, objective this study was assess whether self-reported food consumption is associated with compositional or microbiome changes a subset individuals American Gut Project (AGP) cohort. Using multi-omics approach...
Abstract Introduction: Human tissues, including tumors, are extensively colonized by taxonomically diverse microbes. Intra-tumoral microbial activity and events of cellular turnover trafficking contribute to shedding nucleic acids into the blood stream. Here we characterized signatures (mbDNA) present in primary-tumor tissue patients affected with different cancer types, particular focus on lung cancer, demonstrated discriminatory power such for identification classification versus other...