Faculty Bibliography

UNLABELLED:With the development of sequencing technology and analytic tools, studying within-species variations enhances the understanding of microbial biological processes. Nevertheless, most existing methods designed for strain-level analysis lack the capability to concurrently assess both strain proportions and genome-wide single nucleotide variants (SNVs) across longitudinal metagenomic samples. In this study, we introduce LongStrain, an integrated pipeline for the analysis of large-scale metagenomic data from individuals with longitudinal or repeated samples. In LongStrain, we first utilize two efficient tools, Kraken2 and Bowtie2, for the taxonomic classification and alignment of sequencing reads, respectively. Subsequently, we propose to jointly model strain proportions and shared haplotypes across samples within individuals. This approach specifically targets tracking a primary strain and a secondary strain for each subject, providing their respective proportions and SNVs as output. With extensive simulation studies of a microbial community and single species, our results demonstrate that LongStrain is superior to two genotyping methods and two deconvolution methods across a majority of scenarios. Furthermore, we illustrate the potential applications of LongStrain in the real data analysis of The Environmental Determinants of Diabetes in the Young study and a gastric intestinal metaplasia microbiome study. In summary, the proposed analytic pipeline demonstrates marked statistical efficiency over the same type of methods and has great potential in understanding the genomic variants and dynamic changes at strain level. LongStrain and its tutorial are freely available online at https://github.com/BoyanZhou/LongStrain. IMPORTANCE/OBJECTIVE:The advancement in DNA-sequencing technology has enabled the high-resolution identification of microorganisms in microbial communities. Since different microbial strains within species may contain extreme phenotypic variability (e.g., nutrition metabolism, antibiotic resistance, and pathogen virulence), investigating within-species variations holds great scientific promise in understanding the underlying mechanism of microbial biological processes. To fully utilize the shared genomic variants across longitudinal metagenomics samples collected in microbiome studies, we develop an integrated analytic pipeline (LongStrain) for longitudinal metagenomics data. It concurrently leverages the information on proportions of mapped reads for individual strains and genome-wide SNVs to enhance the efficiency and accuracy of strain identification. Our method helps to understand strains' dynamic changes and their association with genome-wide variants. Given the fast-growing longitudinal studies of microbial communities, LongStrain which streamlines analyses of large-scale raw sequencing data should be of great value in microbiome research communities.

BACKGROUND/UNASSIGNED:Accurately identifying eating patterns, specifically the timing, frequency, and distribution of eating occasions (EOs), is important for assessing eating behaviors, especially for preventing and managing obesity and type 2 diabetes (T2D). However, existing methods to study EOs rely on self-report, which may be prone to misreporting and bias and has a high user burden. Therefore, objective methods are needed. METHODS/UNASSIGNED:We aim to compare EO timing using objective and subjective methods. Participants self-reported EO with a smartphone app (self-report [SR]), wore the ActiGraph GT9X on their dominant wrist, and wore a continuous glucose monitor (CGM, Abbott Libre Pro) for 10 days. EOs were detected from wrist motion (WM) using a motion-based classifier and from CGM using a simulation-based system. We described EO timing and explored how timing identified with WM and CGM compares with SR. RESULTS/UNASSIGNED:. All had prediabetes or moderately controlled T2D. The median time-of-day first EO (and interquartile range) for SR, WM, and CGM were 08:24 (07:00-09:59), 9:42 (07:46-12:26), and 06:55 (04:23-10:03), respectively. The median last EO for SR, WM, and CGM were 20:20 (16:50-21:42), 20:12 (18:30-21:41), and 21:43 (20:35-22:16), respectively. The overlap between SR and CGM was 55% to 80% of EO detected with tolerance periods of ±30, 60, and 120 minutes. The overlap between SR and WM was 52% to 65% EO detected with tolerance periods of ±30, 60, and 120 minutes. CONCLUSION/UNASSIGNED:The continuous glucose monitor and WM detected overlapping but not identical meals and may provide complementary information to self-reported EO.

The complex nature of microbiome data has made the differential abundance analysis challenging. Microbiome abundance counts are often skewed to the right and heteroscedastic (also known as overdispersion), potentially leading to incorrect inferences if not properly addressed. In this paper, we propose a simple yet effective framework to tackle the challenges by integrating Poisson (log-linear) regression with standard error estimation through the Bootstrap method and Sandwich robust estimation. Such standard error estimates are accurate and yield satisfactory inference even if the distributional assumption or the variance structure is incorrect. Our approach is validated through extensive simulation studies, demonstrating its effectiveness in addressing overdispersion and improving inference accuracy. Additionally, we apply our approach to two real datasets collected from the human gut and vagina, respectively, demonstrating the wide applicability of our methods. The results highlight the efficacy of our covariance estimators in addressing the challenges of microbiome data analysis. The corresponding software implementation is publicly available at https://github.com/yimshi/robustestimates.

PURPOSE/UNASSIGNED:The purpose of this study is to describe diabetes distress and related factors among Chinese Americans with type 2 diabetes in New York City (NYC). METHODS/UNASSIGNED:We conducted a secondary data analysis of the baseline data from three research studies conducted among community-dwelling Chinese American adults with type 2 diabetes. Diabetes Distress Scale (DDS) was used to measure sources of diabetes distress including emotional-, regimen-, interpersonal-, and physician-related distress. A score of 2 or greater indicates moderate diabetes distress or higher. Patient Health Questionnaire-2 (PHQ-2) was used to measure depressive symptoms. Participants' sociodemographic information was also collected. Descriptive statistics were used to describe diabetes distress, and logistic least absolute shrinkage and selection operator (LASSO) regression was used to examine factors associated with diabetes distress level. RESULTS/UNASSIGNED:Data from 178 participants (mean age 63.55±13.56 years) were analyzed. Most participants were married (76.40%), had a high school degree or less (65.73%), had a household annual income < $25,000 (70.25%), and reported limited English proficiency (93.22%). About 25.84% reported moderate or higher overall distress. The most common sources of distress were emotional burden (29.78%), followed by regimen- (28.65%), interpersonal- (18.54%), and physician-related distress (14.04%). Participants who were younger, female, limited English proficient, and had elevated depressive symptoms were more likely to have higher diabetes distress. CONCLUSION/UNASSIGNED:Diabetes distress is prevalent among Chinese immigrants with type 2 diabetes, especially emotional- and regimen-related distress. Given the known link between diabetes distress and poor glycemic control, it is critical to screen for diabetes distress at primary care clinics and incorporate psychological counseling in diabetes care in this underserved population.

In this article, we present a flexible model for microbiome count data. We consider a quasi-likelihood framework, in which we do not make any assumptions on the distribution of the microbiome count except that its variance is an unknown but smooth function of the mean. By comparing our model to the negative binomial generalized linear model (GLM) and Poisson GLM in simulation studies, we show that our flexible quasi-likelihood method yields valid inferential results. Using a real microbiome study, we demonstrate the utility of our method by examining the relationship between adenomas and microbiota. We also provide an R package "fql" for the application of our method.

BACKGROUND:Recent studies have demonstrated considerable interindividual variability in postprandial glucose response (PPGR) to the same foods, suggesting the need for more precise methods for predicting and controlling PPGR. In the Personal Nutrition Project, the investigators tested a precision nutrition algorithm for predicting an individual's PPGR. OBJECTIVE:This study aimed to compare changes in glycemic variability (GV) and HbA1c in 2 calorie-restricted weight loss diets in adults with prediabetes or moderately controlled type 2 diabetes (T2D), which were tertiary outcomes of the Personal Diet Study. METHODS:The Personal Diet Study was a randomized clinical trial to compare a 1-size-fits-all low-fat diet (hereafter, standardized) with a personalized diet (hereafter, personalized). Both groups received behavioral weight loss counseling and were instructed to self-monitor diets using a smartphone application. The personalized arm received personalized feedback through the application to reduce their PPGR. Continuous glucose monitoring (CGM) data were collected at baseline, 3 mo and 6 mo. Changes in mean amplitude of glycemic excursions (MAGEs) and HbA1c at 6 mo were assessed. We performed an intention-to-treat analysis using linear mixed regressions. RESULTS:We included 156 participants [66.5% women, 55.7% White, 24.1% Black, mean age 59.1 y (standard deviation (SD) = 10.7 y)] in these analyses (standardized = 75, personalized = 81). MAGE decreased by 0.83 mg/dL per month for standardized (95% CI: 0.21, 1.46 mg/dL; P = 0.009) and 0.79 mg/dL per month for personalized (95% CI: 0.19, 1.39 mg/dL; P = 0.010) diet, with no between-group differences (P = 0.92). Trends were similar for HbA1c values. CONCLUSIONS:Personalized diet did not result in an increased reduction in GV or HbA1c in patients with prediabetes and moderately controlled T2D, compared with a standardized diet. Additional subgroup analyses may help to identify patients who are more likely to benefit from this personalized intervention. This trial was registered at clinicaltrials.gov as NCT03336411.

BACKGROUND:Emerging evidence suggests the potential mediating role of microbiome in health disparities. However, no analytic framework can be directly used to analyze microbiome as a mediator between health disparity and clinical outcome, due to the non-manipulable nature of the exposure and the unique structure of microbiome data, including high dimensionality, sparsity, and compositionality. METHODS:Considering the modifiable and quantitative features of the microbiome, we propose a microbial causal mediation model framework, SparseMCMM_HD, to uncover the mediating role of microbiome in health disparities, by depicting a plausible path from a non-manipulable exposure (e.g., ethnicity or region) to the outcome through the microbiome. The proposed SparseMCMM_HD rigorously defines and quantifies the manipulable disparity measure that would be eliminated by equalizing microbiome profiles between comparison and reference groups and innovatively and successfully extends the existing microbial mediation methods, which are originally proposed under potential outcome or counterfactual outcome study design, to address health disparities. RESULTS:Through three body mass index (BMI) studies selected from the curatedMetagenomicData 3.4.2 package and the American gut project: China vs. USA, China vs. UK, and Asian or Pacific Islander (API) vs. Caucasian, we exhibit the utility of the proposed SparseMCMM_HD framework for investigating the microbiome's contributions in health disparities. Specifically, BMI exhibits disparities and microbial community diversities are significantly distinctive between reference and comparison groups in all three applications. By employing SparseMCMM_HD, we illustrate that microbiome plays a crucial role in explaining the disparities in BMI between ethnicities or regions. 20.63%, 33.09%, and 25.71% of the overall disparity in BMI in China-USA, China-UK, and API-Caucasian comparisons, respectively, would be eliminated if the between-group microbiome profiles were equalized; and 15, 18, and 16 species are identified to play the mediating role respectively. CONCLUSIONS:The proposed SparseMCMM_HD is an effective and validated tool to elucidate the mediating role of microbiome in health disparity. Three BMI applications shed light on the utility of microbiome in reducing BMI disparity by manipulating microbial profiles. Video Abstract.

OBJECTIVES/OBJECTIVE:Although technology-supported interventions are effective for reducing chronic disease risk, little is known about the relative and combined efficacy of mobile health strategies aimed at multiple lifestyle factors. The purpose of this clinical trial is to evaluate the efficacy of technology-supported behavioral intervention strategies for managing multiple lifestyle-related health outcomes in overweight adults with type 2 diabetes (T2D) and chronic kidney disease (CKD). DESIGN AND METHODS/METHODS:, age ≥40 years), T2D, and CKD stages 2-4 were randomized to an advice control group, or remotely delivered programs consisting of synchronous group-based education (all groups), plus (1) Social Cognitive Theory-based behavioral counseling and/or (2) mobile self-monitoring of diet and physical activity. All programs targeted weight loss, greater physical activity, and lower intakes of sodium and phosphorus-containing food additives. RESULTS:Of 256 randomized participants, 186 (73%) completed 6-month assessments. Compared to the ADVICE group, mHealth interventions did not result in significant changes in weight loss, or urinary sodium and phosphorus excretion. In aggregate analyses, groups receiving mobile self-monitoring had greater weight loss at 3 months (P = .02), but between 3 and 6 months, weight losses plateaued, and by 6 months, the differences were no longer statistically significant. CONCLUSIONS:When engaging patients with T2D and CKD in multiple behavior changes, self-monitoring diet and physical activity demonstrated significantly larger short-term weight losses. Theory-based behavioral counseling alone was no better than baseline advice and demonstrated no interaction effect with self-monitoring.

Recent studies have suggested that the temporal dynamics of the human microbiome may have associations with human health and disease. An increasing number of longitudinal microbiome studies, which record time to disease onset, aim to identify candidate microbes as biomarkers for prognosis. Owing to the ultra-skewness and sparsity of microbiome proportion (relative abundance) data, directly applying traditional statistical methods may result in substantial power loss or spurious inferences. We propose a novel joint modeling framework [JointMM], which is comprised of two sub-models: a longitudinal sub-model called zero-inflated scaled-Beta generalized linear mixed-effects regression to depict the temporal structure of microbial proportions among subjects; and a survival sub-model to characterize the occurrence of an event and its relationship with the longitudinal microbiome proportions. JointMM is specifically designed to handle the zero-inflated and highly skewed longitudinal microbial proportion data and examine whether the temporal pattern of microbial presence and/or the non-zero microbial proportions are associated with differences in the time to an event. The longitudinal sub-model of JointMM also provides the capacity to investigate how the (time-varying) covariates are related to the temporal microbial presence/absence patterns and/or the changing trend in non-zero proportions. Comprehensive simulations and real data analyses are used to assess the statistical efficiency and interpretability of JointMM. This article is protected by copyright. All rights reserved.