Nathaniel D. Chu
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View article: Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease
Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease Open
Fecal microbiota transplantation (FMT)—transferring fecal microbes from a healthy donor to a sick patient—has shown promise for gut diseases such as inflammatory bowel disease. However, unlike pharmaceuticals, fecal transplants are complex…
View article: Daily, Oral FMT for Longterm Maintenance Therapy in Ulcerative Colitis: Results of a single-center, prospective, randomized pilot study.
Daily, Oral FMT for Longterm Maintenance Therapy in Ulcerative Colitis: Results of a single-center, prospective, randomized pilot study. Open
BackgroundFecal microbiota transplantation (FMT) is a promising new strategy in the treatment of Inflammatory Bowel Disease, but long-term delivery systems are lacking. This randomized study was designed as a safety and feasibility study o…
View article: Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort
Progressive Shifts in the Gut Microbiome Reflect Prediabetes and Diabetes Development in a Treatment-Naive Mexican Cohort Open
Type 2 diabetes (T2D) is a global epidemic that affects more than 8% of the world’s population and is a leading cause of death in Mexico. Diet and lifestyle are known to contribute to the onset of T2D. However, the role of the gut microbio…
View article: Predicting human health from biofluid-based metabolomics using machine learning
Predicting human health from biofluid-based metabolomics using machine learning Open
Biofluid-based metabolomics has the potential to provide highly accurate, minimally invasive diagnostics. Metabolomics studies using mass spectrometry typically reduce the high-dimensional data to only a small number of statistically signi…
View article: Daily, Oral FMT for Long-Term Maintenance Therapy in Ulcerative Colitis: Results of a Single-Center, Prospective, Randomized Pilot Study.
Daily, Oral FMT for Long-Term Maintenance Therapy in Ulcerative Colitis: Results of a Single-Center, Prospective, Randomized Pilot Study. Open
This randomized study was designed to assess the safety and feasibility of long-term fecal microbiota transplantation (FMT) in subjects with mild to moderate UC using frozen, encapsulated oral FMT (cFMT). FMT induction was implemented by c…
View article: Predicting human health from biofluid-based metabolomics using machine learning
Predicting human health from biofluid-based metabolomics using machine learning Open
Processed input data sets as well as output files and trained health state predictive models for human diseases using metabolomics of biofluids. These data are associated with the following manuscript: 'Predicting human health from bioflui…
View article: Predicting human health from biofluid-based metabolomics using machine learning
Predicting human health from biofluid-based metabolomics using machine learning Open
Processed input data sets as well as output files and trained health state predictive models for human diseases using metabolomics of biofluids. These data are associated with the following manuscript: 'Predicting human health from bioflui…
View article: Predicting human health from biofluid-based metabolomics using machine learning
Predicting human health from biofluid-based metabolomics using machine learning Open
Biofluid-based metabolomics enables the profiling of thousands of molecules and has the potential to provide highly accurate, minimally invasive diagnostics for a range of health conditions. However, typical metabolomics studies focus on o…
View article: Progressive shifts in the gut microbiome reflect prediabetes and diabetes development in a treatment-naive Mexican cohort
Progressive shifts in the gut microbiome reflect prediabetes and diabetes development in a treatment-naive Mexican cohort Open
Type 2 diabetes (T2D) is a global epidemic that affects more than 8% of the world’s population and is a leading cause of death in Mexico. Diet and lifestyle are known to contribute to the onset of T2D. However, the role of the gut microbio…
View article: Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease
Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease Open
For fecal microbiota transplantation (FMT) to be successful in complex immune diseases like inflammatory bowel disease (IBD), it is assumed that therapeutic microbes and their beneficial functions and immune interactions must colonize the …
View article: Additional file 4: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors
Additional file 4: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors Open
Data for persistence across our time series and sharing across subjects in an independent, large cohort for TCRβs in this study. The columns “aminoAcid”, ‘vGeneName”, “jGeneName”, and “tcr” are the same as for Additional file 3. The column…
View article: Additional file 3: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors
Additional file 3: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors Open
Count, frequency, V, J, and CDR3 amino acid sequence data for high abundance TCRβs in each sample. This is a tab-delimited, gzip-compressed file. The column “tcr” corresponds to a label that identifies a unique combination of CDR3 amino ac…
View article: Additional file 2: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors
Additional file 2: of Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors Open
Table S1. Overall TCRβ-sequencing statistics per sample: sequencing depth, productive TCRβ sequencing depth, fraction of productive TCRβ sequences, unique V genes identified, unique J genes identified, unique CDR3 sequences, unique TCRβs, …
View article: Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors
Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors Open
Background The adaptive immune system maintains a diversity of T cells capable of recognizing a broad array of antigens. Each T cell’s specificity for antigens is determined by its T cell receptors (TCRs), which together across all T cells…
View article: Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in public receptors
Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in public receptors Open
Background The adaptive immune system maintains a diversity of T cells capable of recognizing a broad array of antigens. Each T cell’s specificity and affinity for antigens is determined by its T cell receptors (TCRs), which together acros…
View article: A Mobile Element in <i>mutS</i> Drives Hypermutation in a Marine <i>Vibrio</i>
A Mobile Element in <i>mutS</i> Drives Hypermutation in a Marine <i>Vibrio</i> Open
Bacteria face a trade-off between genetic fidelity, which reduces deleterious mistakes in the genome, and genetic innovation, which allows organisms to adapt. Evidence suggests that many bacteria balance this trade-off by modulating their …
View article: Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations
Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations Open
Fecal microbiota transplantation is a compelling treatment for recurrent Clostridium difficile infections, with potential applications against other diseases associated with changes in gut microbiota. But variability in fecal bacterial com…
View article: Caribbean corals house shared and host‐specific microbial symbionts over time and space
Caribbean corals house shared and host‐specific microbial symbionts over time and space Open
Summary The rise of coral diseases has triggered a surge of interest in coral microbial communities. But to fully understand how the coral microbiome may cause or respond to disease, we must first understand structure and variation in the …