Yoshiki Vázquez‐Baeza
A5024143614- Gut microbiota and health
- Metabolomics and Mass Spectrometry Studies
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Nutritional Studies and Diet
- Clostridium difficile and Clostridium perfringens research
- Diet and metabolism studies
- Inflammatory Bowel Disease
- Bioinformatics and Genomic Networks
- Food Security and Health in Diverse Populations
- Nutrition, Genetics, and Disease
- Epigenetics and DNA Methylation
- Scientific Computing and Data Management
- Probiotics and Fermented Foods
- Liver Disease Diagnosis and Treatment
- Helicobacter pylori-related gastroenterology studies
- Gene expression and cancer classification
- Cystic Fibrosis Research Advances
- Genetics, Bioinformatics, and Biomedical Research
- Meta-analysis and systematic reviews
- Microscopic Colitis
- Advanced Graph Neural Networks
- Dermatology and Skin Diseases
- Mycobacterium research and diagnosis
- Advanced Numerical Analysis Techniques
Jacobs (United States)
2019-2025
University of California, San Diego
2016-2025
University of California, San Francisco
2022
La Jolla Bioengineering Institute
2020
University of Colorado Boulder
2013-2015
Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, the data contains many zeros. Although we are typically interested in comparing relative abundance taxa ecosystem two or more groups, can only measure taxon specimens obtained ecosystems. Because comparison specimen is not equivalent ecosystems, this presents a special challenge. Second, because (as...
Abstract Background As microbial ecologists take advantage of high-throughput sequencing technologies to describe communities across ever-increasing numbers samples, new analysis tools are required relate the distribution microbes among larger communities, and use increasingly rich standards-compliant metadata understand biological factors driving these relationships. In particular, Earth Microbiome Project drives needs by profiling genomic content tens thousands samples multiple environment...
The bacteria that colonize humans and our built environments have the potential to influence health. Microbial communities associated with seven families their homes over 6 weeks were assessed, including three moved home. differed substantially among homes, home microbiome was largely sourced from humans. microbiota in each identifiable by family. Network analysis identified as primary bacterial vector, a Bayesian method significantly matched individuals dwellings. Draft genomes of human...
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging integrate extent of microbial molecular diversity in stool remains unknown. Using standardized protocols Earth Microbiome Project sample contributions over 10,000 citizen-scientists, together with an open research network, we compare specimens primarily United States, Kingdom, Australia one another environmental samples. Our results show...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Abstract Background It is now apparent that the complex microbial communities found on and in human body vary across individuals. What has largely been missing from previous studies an understanding of how these over time within To extent to which it considered, often assumed temporal variability negligible for healthy adults. Here we address this gap by profiling forehead, gut (fecal), palm, tongue 85 adults, weekly 3 months. Results We skin (forehead palm) varied most number taxa present,...
QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular platform, which it has replaced. facilitates comprehensive and fully reproducible data science, improving accessibility to diverse users by adding multiple user interfaces. can be combined with Qiita, an open-source web-based re-use available for meta-analysis. The following basic protocol describes how install single computer analyze sequence data, from processing of raw DNA reads through...
Advances in sequencing technologies have enabled novel insights into microbial niche differentiation, from analyzing environmental samples to understanding human diseases and informing dietary studies. However, identifying the taxa that differentiate these can be challenging. These issues stem compositional nature of 16S rRNA gene data (or, more generally, taxon or functional data); changes relative abundance one influence apparent abundances others. Here we acknowledge inferring properties...
Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) that often fails standard antibiotic therapy. Despite its widespread recent use, however, little known about the stability of fecal following FMT.Here we report on short- and long-term changes provide kinetic visualization composition in patients with multiply CDI were refractory to therapy treated using FMT. samples collected from four before up 151 days after FMT, daily...