About

Uma Nayak is an Assistant Professor in the Department of Genome Sciences at the University of Virginia School of Medicine. She holds a Ph.D. in Nutrition from Sri Padmavati Mahila Viswavidyalayam, India. Her research interests focus on infant and maternal nutrition, contributing to the understanding of nutritional needs and health outcomes in these populations. Her academic and professional background supports her role in advancing research in genome sciences related to nutrition and health.

Research topics

• Medicine
• Biology
• Genetics
• Evolutionary biology
• Demography
• Computational biology
• Microbiology
• Bioinformatics
• Gastroenterology
• Internal medicine
• Endocrinology

Selected publications

• Decrease in Incidence of Diarrhea Due to <i>Cryptosporidium</i> in Bangladeshi Children Is Associated With an Increase in Anti-<i>Cryptosporidium</i> Antibody Avidity

  The Journal of Infectious Diseases · 2025-06-09 · 2 citations

  articleOpen access

  BACKGROUND: Cryptosporidium is a cause of diarrhea morbidity and mortality in infants in low- and middle-income countries. METHODS: A cohort of children was followed longitudinally in a high-transmission-intensity community in Bangladesh. RESULTS: Diarrhea attributed to Cryptosporidium (cryptosporidiosis) decreased from a peak of 0.19 episodes per child at 1-2 years to 0.05 episodes per child at 3-4 years of age (P = .0064). Notably, the decrease in cryptosporidiosis was not accompanied by a decline in subclinical infections. Using an episode-based analysis confirmed that the parasite burden declined with repeated infections (P < .0001 from the mixed-effects model included data from all infection frequencies; Cq value of the first and fourth infections (last reinfection with >10 cases): Cq 28.65 ± 5.533 versus 32.42 ± 4.046). There was also a decrease in the time required to clear a parasitic infection: longer infections (>1 month) occurred in 43% of the first infections compared to 24% in the fourth infections (P = .00017 from the mixed-effects model). The avidity of anti-Cp23 and anti-Cp17 plasma IgG increased in older children who had fewer diarrheal infections (ratio of the avidity index after the first infection versus that in the older repeatedly infected children: 1.81 ± 1.02 for anti-Cp23 IgG P > .0001 and 1.14 ± 0.35 anti-Cp17 IgG P = .0056). CONCLUSIONS: Our results are consistent with the development of an anti-Cryptosporidium adaptive immune response over repeated infections (average number of previous infections at 4 years, 2.42 ± 1.24) characterized by an increase in anti-Cryptosporidium antibody avidity that is associated with a decrease in cryptosporidiosis but not in subclinical Cryptosporidium infections. Clinical Trials Registration. NCT02764918.

  PublisherOA PDFDOI

• Fecal microbiota transplantation promotes type 2 mucosal immune responses with colonic epithelium proliferation in patients with recurrent Clostridioides difficile

  JCI Insight · 2025-11-18 · 2 citations

  articleOpen access

  BACKGROUNDFecal microbiota transplantation (FMT) is the most effective therapy for recurrent Clostridioides difficile infection (rCDI), yet its mechanism of action remains poorly understood.METHODSWe report the results of a clinical trial of patients undergoing FMT therapy for rCDI (n = 16), which analyzed colon biopsies, plasma, PBMCs, and stool at the time of FMT and 2-month follow-up. Plasma and colon biopsy samples were also collected from healthy controls for comparison with patients with rCDI. Microbiome composition, colonic gene expression, and immune changes were evaluated through high-throughput sequencing and immunoprofiling via flow cytometry.RESULTSNo patients experienced recurrence at follow-up. FMT significantly altered the intestinal microbiome but had no significant impact on the systemic immune system. In contrast, FMT promoted broad changes in colonic transcriptional profiles compared with both pre-FMT and healthy control biopsies, inhibiting genes associated with proinflammatory signaling and upregulating type 2 immunity and proliferative pathways (Myc and mTORC1). FMT increased expression of IL-33 and the type 2 immune EGFR family ligand amphiregulin, potentially explaining upregulation of Myc and mTORC1 pathways. Spatial transcriptomics demonstrated that these changes were localized to the colonic epithelium. Comparison of transcriptional profiles with available single-cell gene sets determined that post-FMT biopsies were enriched in signatures associated with proliferative cell types while repressing signatures of differentiated colonocytes.CONCLUSIONWe conclude that FMT promotes proliferation of the colonic epithelium in patients with rCDI, which may drive regeneration and protect against subsequent CDI.TRIAL REGISTRATIONClinicaltrials.gov NCT02797288.FUNDINGThis work was funded by grants from the NIH.

  PublisherOA PDFDOI

• Predicting Stunted Growth in Two Year Old Bangladeshi Children via the Super Learner

  Journal of Data Science · 2025-01-01

  articleOpen access

  Stunted growth in children is a worldwide issue which may cause long term problems for individuals stunted as early as two years of age. However, predicting stunted growth with accuracy is quite complex, but machine learning poses a distinct advantage in this regard. While several techniques are available for predictive modeling, the Super Learner stands out as an ensemble method that integrates multiple algorithms into a single predictive model with enhanced performance. In this study, the Super Learner model, comprising generalized linear model, bagged trees, random forests, conditional random forest, stochastic gradient boosting, Bayesian additive regression trees, neural networks, and model averaged neural networks, achieved high performance with high area under the receiver operating characteristic curve, Brier Score, and the minimum of precision and recall values. However, after analyzing the results from cross validation, the final model selected was the Bayesian additive regression trees. Within the final model, the height-for-age z-score at one year, income, expenditure, anti-lipopolysaccharide antibody at week 6 and at week 18, plasma retinol binding protein at week 6, plasma soluble cluster designation 14 at week 18, fecal Reg 1B at week 12, vitamin D at week 18, mother’s weight and height at enrollment, fecal calprotectin at week 12, fecal myeloperoxidase at week 12, number of days of diarrhea through the first year of life, and the number of days of exclusive breastfeeding through the first year of life emerged as the top important variables for predicting stunted growth at two years of age.

  PublisherOA PDFDOI

• Pulmonary Function and Survival 1 Year After Dupilumab Treatment of Acute Moderate to Severe Coronavirus Disease 2019: A Follow-up Study From a Phase 2a Trial

  Open Forum Infectious Diseases · 2024-01-02 · 4 citations

  articleOpen access

  Abstract Background We previously conducted a phase 2a randomized placebo-controlled trial of 40 subjects to assess the efficacy and safety of dupilumab use in people hospitalized with coronavirus disease 2019 (COVID-19) (NCT04920916). Based on our preclinical data suggesting that downstream pulmonary dysfunction with COVID-19 induced type 2 inflammation, we contacted patients from our phase 2a study at 1 year for assessment of post-COVID-19 conditions. Methods Subjects at 1 year after treatment underwent pulmonary function tests, high-resolution computed tomographic imaging, symptom questionnaires, neurocognitive assessments, and serum immune biomarker analysis, with subject survival also monitored. The primary outcome was the proportion of abnormal diffusion capacity for carbon monoxide (DLCO) or 6-minute walk test (6MWT) at the 1-year visit. Results Of those survivors who consented to 1-year visits (n = 16), subjects who had originally received dupilumab were less likely than those who received placebo to have an abnormal DLCO or 6MWT (Fisher exact P = .011; adjusted P = .058). As a secondary endpoint, we saw that 16% of subjects in the dupilumab group died by 1 year compared to 38% in the placebo group, though this was not statistically significant (log-rank P = .12). We did not find significant differences in neurocognitive testing, symptoms, or chest computed tomography between treatment groups but observed a larger reduction in eotaxin levels in those who received dupilumab. Conclusions In this observational study, subjects who received dupilumab during acute COVID-19 hospitalization were less likely to have a reduced DLCO or 6MWT, with a nonsignificant trend toward reduced mortality at 1 year compared to placebo.

  PublisherOA PDFDOI

• Systemic neutrophil degranulation and emergency granulopoiesis in patients with Clostridioides difficile infection

  Anaerobe · 2024-03-20 · 9 citations

  articleOpen access

  Clostridioides difficile infection (CDI) is characterized by neutrophilia in blood, with a high leukocyte count accompanying severe infection. In this study, we characterized peripheral blood neutrophil activation and maturity in CDI by (i) developing a method to phenotype stored neutrophils for disease-related developmental alterations and (ii) assessing neutrophil-associated biomarkers. We stored fixed leukocytes from blood collected within 24 h of diagnosis from a cohort of hospitalized patients with acute CDI. Additional study cohorts included recurrent CDI patients at time of and two months after FMT therapy and a control healthy cohort. We assessed levels of neutrophil surface markers CD66b, CD11b, CD16 and CD10 by flow cytometry. Plasma neutrophil elastase and lipocalin-2 were measured using ELISA, while G-CSF, GM-CSF and cytokines were measured using O-link proteomic technology. CD66b+ neutrophil abundance assessed by flow cytometry correlated well with complete blood counts, establishing that neutrophils in stored blood are sufficiently well-preserved for phenotyping by flow cytometry. Neutrophil abundance was significantly increased in CDI patients compared to healthy controls. Emergency granulopoiesis in acute CDI patients was evidenced by lower neutrophil surface expression of CD10, CD11b and CD16. CD10+ staining of neutrophils started to recover within 3–7 days of CDI treatment. Neutrophil activation and degranulation were higher in acute CDI as assessed by plasma neutrophil elastase and lipocalin-2. Biomarker levels in immunocompetent subjects were associated with recurrence and fatal outcomes. Neutrophil activation and emergency granulopoiesis characterize the early immune response in acute CDI, with plasma degranulation biomarkers predictive of disease severity.

  PublisherDOI

• Genetic Susceptibility to Astrovirus Diarrhea in Bangladeshi Infants

  Open Forum Infectious Diseases · 2024-02-29 · 1 citations

  articleOpen access

  Abstract Background Astroviral infections commonly cause acute nonbacterial gastroenteritis in children globally. However, these infections often go undiagnosed outside of research settings. There is no treatment available for astrovirus, and Astroviridae strain diversity presents a challenge to potential vaccine development. Methods To address our hypothesis that host genetic risk factors are associated with astrovirus disease susceptibility, we performed a genome-wide association study of astrovirus infection in the first year of life from children enrolled in 2 Bangladeshi birth cohorts. Results We identified a novel region on chromosome 1 near the loricrin gene (LOR) associated with astrovirus diarrheal infection (rs75437404; meta-analysis P = 8.82 × 10−9; A allele odds ratio, 2.71) and on chromosome 10 near the prolactin releasing hormone receptor gene (PRLHR) (rs75935441; meta-analysis P = 1.33 × 10−8; C allele odds ratio, 4.17). The prolactin-releasing peptide has been shown to influence feeding patterns and energy balance in mice. In addition, several single-nucleotide polymorphisms in the chromosome 1 locus have previously been associated with expression of innate immune system genes PGLYRP4, S100A9, and S100A12. Conclusions This study identified 2 significant host genetic regions that may influence astrovirus diarrhea susceptibility and should be considered in further studies.

  PublisherOA PDFDOI

• Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

  Nature · 2024 · 480 citations

  • Biology
  • Genetics
  • Evolutionary biology

  in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.

  DOI

• Impact of Nurse-Directed Educational Intervention onKnowledge and Health Promotion Behaviours amongPatients with Sickle Cell Anemia

  African Journal of Biomedical Research · 2024-01-01

  articleOpen access

  The study aimed to assess the knowledge and health promotion behavior of adolescents regarding sickle cell anemia and to evaluate the effectiveness of a nurse-directed intervention. Specific objectives included assessing knowledge in the experimental and control groups, evaluating the effect of the intervention on health promotion behavior, and comparing demographic variables with pretest scores between groups. An interventional research approach with a quasi-experimental design was adopted at Parul Sevashram Hospital, Vadodara. A total of 20 adolescents were selected using simple random sampling. Data were collected through pretest and posttest assessments on knowledge and health promotion behavior. Findings revealed that in the experimental group, 50% of respondents had poor and average knowledge at pretest, whereas post-test results showed 100% had average knowledge. In the control group, 100% of respondents had poor knowledge at pretest; post- test showed 60% attained average knowledge, while 40% remained in the poor category. Regarding lifestyle behavioral changes, in the experimental group, 50% reported a neutral attitude and 40% an agreeable attitude at pretest, whereas post-test results indicated 70% agreed and 30% strongly agreed with positive health behaviors. In the control group, pretest results showed 50% neutral, 30% agreeable, and 20% disagreeable attitudes; posttest results indicated 50% neutral, 40% agreeable, and 10% disagreeable attitudes. The study concludes that nurse-directed intervention was effective in improving both knowledge and health promotion behavior among adolescents with sickle cell anemia in the experimental group compared to the control group.

  PublisherDOI

• Phase III randomized clinical studies to evaluate the immunogenicity, lot-to-lot consistency, and safety of ROTAVAC® liquid formulations (ROTAVAC 5C &amp; 5D) and non-inferiority comparisons with licensed ROTAVAC® (frozen formulation) in healthy infants

  Human Vaccines & Immunotherapeutics · 2023-11-15 · 4 citations

  articleOpen access

  : Clinical Trials Registry of India (CTRI): CTRI/2015/02/005577CTRI/2016/11/007481 and CTRI/2019/03/017934.

  PublisherDOI

• Pulmonary function and survival one year after dupilumab treatment of acute moderate to severe COVID-19: A follow up study from a Phase IIa trial

  medRxiv · 2023-09-02 · 3 citations

  preprintOpen access

  Background: We previously conducted a Phase IIa randomized placebo-controlled trial of 40 subjects to assess the efficacy and safety of dupilumab use in those hospitalized with COVID-19 (NCT04920916). Based on our pre-clinical data suggesting downstream pulmonary dysfunction with COVID-19 induced type 2 inflammation, we contacted patients from our Phase IIa study at 1 year for assessment of Post Covid-19 Conditions (PCC). Methods: Subjects at 1 year after treatment underwent pulmonary function testing (PFTs), high resolution computed tomography (HRCT) imaging, symptom questionnaires, neurocognitive assessments, and serum immune biomarker analysis, with subject survival also monitored. The primary outcome was the proportion of abnormal PFTs, defined as an abnormal diffusion capacity for carbon monoxide (DLCO) or 6-minute walk testing (6MWT) at the 1-year visit. Results: Sixteen of the 29 one-year survivors consented to the follow up visit. We found that subjects who had originally received dupilumab were less likely to have abnormal PFTs compared to those who received placebo (Fisher's exact p=0.011, adjusted p=0.058). We additionally found that 3 out of 19 subjects (16%) in the dupilumab group died by 1 year compared to 8 out of 21 subjects (38%) in the placebo group (log rank p=0.12). We did not find significant differences in neurocognitive testing, symptoms or CT chest imaging between treatment groups but observed evidence of reduced type 2 inflammation in those who received dupilumab. Conclusions: We observed evidence of reduced long-term morbidity and mortality from COVID-19 with dupilumab treatment during acute hospitalization when added to standard of care regimens.

  PublisherOA PDFDOI

Frequent coauthors

• William A. Petri

  University of Virginia

  44 shared

• Rashidul Haque

  International Centre for Diarrhoeal Disease Research

  37 shared

• Josyf C. Mychaleckyj

  University of Virginia

  36 shared

• Beth D. Kirkpatrick

  University of Vermont

  30 shared

• Diane M. Becker

  Johns Hopkins University

  27 shared

• Ruth J. F. Loos

  Novo Nordisk (United States)

  26 shared

• Alan B. Zonderman

  26 shared

• Guanjie Chen

  National Institutes of Health

  25 shared