Browsing by Author "Huang, Hu"

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    Data from "Diverse Bacterial Communities Exist on Canine Skin and are Impacted by Cohabitation and Time"
    (2016-11-17) Johnson, Timothy; Torres, Sheila; Danzeisen, Jessica; Clayton, Jonathan; Ward, Tonya; Knights, Dan; Huang, Hu; joh04207@umn.edu; Johnson, Timothy
    This related study sampled 40 dogs from 20 households over the course of three seasons. Three skin sites were examined. The goal of the study was to determine if a core skin microbiome exists in dogs across time and body site, and if cohabitation impacts sharing of the skin microbiome. This dataset is a part of the Torres_Johnson Canine Microbiome Study.
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    Discovering genetic drivers in acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation
    (2019-05) Huang, Hu
    Acute graft-versus-host disease (GVHD) is one of the major complications after allogeneic hematopoietic stem cell transplantation (allo-HCT) that cause non-relapse morbidity and mortality. Although the increasing matching rate of the human leukocyte antigen (HLA) genes between donor and recipient (DR) has significantly reduced the risk of GVHD, clinically significant GVHD remains as a transplantation challenge, even in HLA-identical transplants. Candidate gene studies and genome-wide association studies have revealed susceptible individual genes and gene pairs from DR pairs that are associated with acute GVHD; however, the roles of genetic disparities between donor and recipient remain to be understood. To identify genetic factors linked to acute GVHD, we investigated the classical HLA and non-HLA genes and conducted a genome-wide clinical outcome association study. Assessment of 4,646 antigen recognition domain (ARD)-matched unrelated donor allo-HCT cases showed that the frequency of mismatches outside the ARD in HLA genes is very low when the DR pairs are matched at ARD. Due to the low frequency of amino acid mismatches in the non-ARD region and their reportedly weak alloimmune reactions, we suggest that the non-ARD sequence mismatches within the ARD-matched DR pairs have limited influence on the development of acute GVHD, and may not be a primary factor. The genome-wide clinical outcome association study between DR pairs observed multiple autosomal minor histocompatibility antigens (MiHAs) restricted by HLA typing, though their association with acute GVHD outcome was not statistically significant. This result suggests that HLA mismatching outweighs other genetic mismatches as contributors to acute GVHD risk. In the cases of female donors to male recipients, we identified the significant association of the Y chromosome-specific peptides encoded by PCDH11Y, USP9Y, UTY, and NLGN4Y with the acute GVHD outcome. Additionally, we developed a machine learning-based genetic variant selection algorithm for ultra-high dimensional transplant genomic studies. The algorithm successfully selected a set of genes from over 1 M genetic variants, all of which have evidence to be linked to the transplant-related complications. This work offers evidence and guidance for further research in acute GVHD and allo-HCT and provides useful bioinformatics and data mining tools for transplant genomic studies.
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    Relationships between cecum, ileum and litter bacterial microbiomes in a commercial turkey flock, and the impact of penicillin treatment on early bacterial community establishment
    (2015-10-19) Danzeisen, Jessica; Clayton, Jonathan; Huang, Hu; Knights, Dan; McComb, Brian; Hayer, Shivdeep; Johnson, Timothy; joh04207@umn.edu; Johnson, Timothy
    Gut health is paramount for commercial poultry production, and methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associations of these populations with the poultry farm environment, since these bacteria are thought to drive metabolism and prime the host immune system. In this study, a single flock of commercial turkeys was followed over the course of twelve weeks to examine bacterial microbiome inhabiting the ceca, ileum, and corresponding poultry litter. Furthermore, the effects of low-dose, growth-promoting penicillin treatment (50 g/ton) in feed on the ileum bacterial microbiome were also examined during the early brood period. The cecum and ileum bacterial communities of birds shifted independently but in parallel to one another over time, with distinct bacterial populations harboring each site. Corresponding poultry litter more closely represented the ileal bacterial populations than cecal bacterial populations, and also changed parallel to ileum bacterial populations over time. Penicillin applied at low doses in feed significantly enhanced early weight gain in commercial poults, and this correlated with predictable shifts in the ileum bacterial populations in control versus treatment groups. Overall, this study demonstrates the dynamic shifts in the turkey gastrointestinal microbiome during development, the correlations between bacterial populations in the gastrointestinal tract and the litter environment, and the impact of low-dose penicillin on the modulation of bacterial communities in the ileum. Alternatives to low-dose antibiotics would benefit by mimicking these effects in the gut, among others.