Biology subjects

Chu, N. D.

Publications and source records attributed to Chu, N. D..

3 recordsLinked to original sources

bioRxiv2019

Progressive shifts in the gut microbiome reflect prediabetes and diabetes development in a treatment-naive Mexican cohort

Type 2 diabetes (T2D) is a global epidemic that affects more than 8% of the worlds 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 microbiome in T2D progression remains uncertain. Associations between microbiome composition and diabetes are confounded by medication use, diet, and obesity. Here we present data on a treatment-naive cohort of 405 Mexican individuals across varying stages of T2D severity. Associations between gut bacteria and more than 200 clinical variables revealed a defined set of bacterial genera that were consistent biomarkers of T2D prevalence and risk. Specifically, gradual increases in blood glucose levels, beta cell dysfunction, and the accumulation of measured T2D risk factors was correlated with the relative abundances of four bacterial genera. In a cohort of 25 individuals, T2D treatment - predominantly metformin - reliably returned the microbiome to the normoglycemic community state. Deep clinical characterization allowed us to broadly control for confounding variables, indicating that these microbiome patterns were independent of common T2D comorbidities, like obesity or cardiovascular disease. Thus, our work provides the first solid evidence for a direct link between the gut microbiome and T2D in a critically high-risk population. Whether or not these T2D-associated changes in the gut contribute to the etiology of T2D or its comorbidities remains to be seen.

systems biology↗

bioRxiv2019

Dynamic colonization of microbes and their functions after fecal microbiota transplantation for inflammatory bowel disease

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 recipient and persist in sufficient quantity and for a long enough period of time to result in a clinical benefit. But few studies have comprehensively profiled the colonization and persistence of transferred microbes along with the transfer of their microbial and immune functions. Using 16S, metagenomic, and immunoglobulin A (IgA) sequencing, we analyzed hundreds of longitudinal microbiome samples from a randomized controlled trial of 12 patients with ulcerative colitis who received fecal transplant or placebo for 12 weeks. We uncovered a range of competitive dynamics among donor and patient strains, showing that persistence of transferred microbes is far from static. Indeed, one patient experienced dramatic loss of donor bacteria 10 weeks into the trial, coinciding with a bloom of pathogenic bacteria and worsening clinical symptoms. We similarly evaluated transfer of microbial functions, including desired ones like butyrate production and unintended ones like antibiotic resistance. By profiling bacteria coated with IgA, we identified IgA-coated bacteria associated with inflammation, and we found that microbial interactions with the host immune system can be transferred across people. This transfer of immune function is likely critical for gut microbiome therapeutics for immune-related diseases. Our findings elucidate the colonization dynamics of gut microbes as well as their functions in the context of FMT to treat a complex disease--information that may provide a critical foundation for the development of more-targeted therapeutics.

microbiology↗

bioRxiv2018

Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in public receptors

BackgroundThe adaptive immune system maintains a diversity of T cells capable of recognizing a broad array of antigens. Each T cells specificity and affinity for antigens is determined by its T cell receptors (TCRs), which together across all T cells form a repertoire of tens of millions of unique receptors in each individual. Although many studies have examined how TCR repertoires change in response to disease or drugs, few have explored the temporal dynamics of the TCR repertoire in healthy individuals.\n\nResultsHere we report immunosequencing of TCR {beta} chains (TCR{beta}) from the blood of three healthy individuals at eight time points over one year. TCR{beta} repertoires from samples of all T cells and memory T cells clearly clustered by individual, confirming that TCR{beta} repertoires are specific to individuals across time. This individuality was absent from TCR{beta}s from naive T cells, suggesting that these differences result from an individuals antigen exposure history. Many characteristics of the TCR{beta} repertoire (e.g., alpha diversity, clonality) were stable across time, although we found evidence of T cell expansion dynamics even within healthy individuals. We further identified a subset of \"persistent\" TCR{beta}s present across all time points, and these receptors were rich in clonal and public receptors.\n\nConclusionsOur results revealed persistent receptors that may play a key role in immune system maintenance. They further highlight the importance of longitudinal sampling of the immune system and provide a much-needed baseline for TCR{beta} dynamics in healthy individuals. Such a baseline should help improve interpretation of changes in the TCR{beta} repertoire during disease or treatment.

immunology↗