Jessica R. McCann

BACKGROUND: Obesity and weight loss in adults have been associated with distinct metabolome and gut microbiome features, but the extent to which those associations apply to adolescent stages remain unclear. METHODS: The Pediatric Obesity Microbiome and Metabolism Study (POMMS) enrolled 220 adolescents aged 10–18 with severe obesity (OB) and 67 individuals who were healthy weight controls (HWCs). Blood, stool, and clinical measures were collected at baseline and after a 6-month obesity intervention for the OB group. Metabolomic profiling in serum using targeted quantitative mass spectrometry and microbiome profiling in stool were performed, and those features were assessed for associations with BMI, insulin resistance, and inflammation. Fecal microbiome transplants (FMT) were performed on germ-free mice using samples from both groups to assess effects on weight gain and metabolic pathways. RESULTS: Adolescents with OB exhibited higher serum branched-chain amino acid (BCAA) but lower branched-chain ketoacid (BCKA) levels compared with HWC. This pattern was sex- and age-dependent and differed from adults with obesity who show elevated levels of both BCAA and BCKA. Longitudinal analysis identified metabolic and microbial features correlated with changes in health measures during the intervention. The fecal microbiomes of adolescents with OB and HWC had similar diversity but differed in membership and functional potential. FMT from both OB and HWC donors had similar effects on mouse body weight, but specific taxa were linked to weight gain in recipients of FMT. CONCLUSION: Adolescents with OB have unique metabolomic adaptations and microbiome signatures compared with their HWC counterparts and adults with OB. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT03139877 (Observational Study) and NCT02959034 (Repository). FUNDING SUPPORT: American Heart Association Grants: 17SFRN33670990, 20PRE35180195; National Institute of Diabetes and Digestive and Kidney Diseases Grant: R24-DK110492.

Many human-targeted medications have been found to impact the composition of patients’ gastrointestinal microbiomes, which has been proposed as an unrecognized source of drug side effects, comorbidities, and reduced treatment efficiencies. However, current methods to detect such drug effects on the microbiome largely rely on patient sample analysis or in vitro high-throughput screening - which are both laborious and resource intensive. To accelerate the systematic discovery of drug effects on the microbiome, we designed machine learning (ML) workflows on existing data from high-throughput experiments to predict which drugs can inhibit the growth of 40 commensal microbes in monocultures. We employed these models to predict potential effects of thousands of investigational drugs and found that up to 60% of these drugs are predicted to inhibit the growth of at least one commensal microbe. Using prospective in vitro validations, our workflows enabled us to uncover two non-antibiotic drugs, the recently approved chemotherapeutic Entrectinib and the clinical drug candidate PSI-697, to have previously unknown growth inhibition effects on multiple commensal microbes. Furthermore, we show that resistance to the effects of these drugs is mediated by BamB and TolC, implicating these drugs as potential agents to exacerbate antibiotic resistance. We further validated that Entrectinib significantly reduces microbial richness in a synthetic microbial model community. Taken together, our ML-assisted workflow and future extensions can accelerate the systematic discovery of microbiome-drug interactions, with implications for safer drug development and molecular microbiome engineering.

BACKGROUND Towards improving outcomes for adolescents with obesity, we aimed to define metabolic and microbiome phenotypes at baseline and post-weight loss intervention. METHODS The Pediatric Obesity Microbiome and Metabolism Study enrolled 220 adolescents aged 10-18 with severe obesity (OB) and 67 healthy weight controls (HWC). Blood, stool, and clinical measures were collected at baseline and after a 6-month intervention for the OB group. Serum metabolomic and fecal microbiome data were analyzed for associations with BMI, insulin resistance, and inflammation. Fecal microbiome transplants were performed on germ-free mice using samples from both groups to assess weight gain and metabolomic changes. RESULTS Adolescents with OB exhibited elevated serum branched-chain amino acids (BCAA) but reduced ketoacid metabolites (BCKA) compared to HWC. This pattern was sex- and age-dependent, unlike adults with OB, who showed elevated levels of both. The fecal microbiomes of adolescents with OB and HWC had similar diversity but differed in membership and functional potential. FMT from OB and HWC donors had similar effects on mouse body weight, with specific taxa linked to weight gain in FMT recipients. Longitudinal analysis identified metabolic and microbial features correlated with changes in health measures during the intervention. CONCLUSION Adolescents with OB have unique metabolomic adaptations and microbiome signatures compared to their HWC counterparts and adults with OB. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT03139877 (Observational Study) and NCT02959034 (Repository) FUNDING SOURCES American Heart Association Grants: 17SFRN33670990, 20PRE35180195 National Institute of Diabetes and Digestive and Kidney Diseases Grant: R24-DK110492

Amino acids are indispensable substrates for protein synthesis in all organisms and incorporated into diverse aspects of metabolic physiology and signaling. However, animals lack the ability to synthesize several of them and must acquire these essential amino acids from their diet or perhaps their associated microbial communities. The essential amino acids therefore occupy a unique position in the health of animals and their relationships with microbes. Here we review recent work connecting microbial production and metabolism of essential amino acids to host biology, and the reciprocal impacts of host metabolism of essential amino acids on their associated microbes. We focus on the roles of the branched-chain amino acids (valine, leucine, and isoleucine) and tryptophan on host-microbe communication in the intestine of humans and other vertebrates. We then conclude by highlighting research questions surrounding the less-understood aspects of microbial essential amino acid synthesis in animal hosts.

Context: Large numbers of US adults are vaccinated, but COVID-19 vaccine hesitancy remains high. Health centers funded by the Health Resources and Services Administration (HRSA) have played a major role in COVID-19 vaccinations and have the potential to vaccinate even larger numbers of people. Objective: To identify U.S. counties with low COVID-19 vaccination rates and high rates of vaccine hesitancy, explore the characteristics of these counties and health center presence in these areas, and identify priority health centers for targeted vaccine outreach. Study Design: Cross-sectional geospatial analysis of county-level COVID-19 vaccination rates and COVID-19 vaccination hesitancy. Bivariate Local Moran’s I using GeoDa software to identify clusters of counties with low COVID-19 vaccination rates and high rates of COVID-19 vaccine hesitancy. Geographic Information Systems (GIS) mapping to overlay health centers with county-level data. Setting or Dataset: U.S. counties; vaccine hesitancy data from U.S. Department of Health & Human Services Office of the Assistant Secretary for Planning and Evaluation (ASPE); vaccination rates from the Centers for Disease Control and Prevention (CDC); and data on Health Center Program awardees from the HRSA. Population studied: U.S. Counties (n=2,825) for which data on COVID-19 vaccination and COVID-19 vaccine hesitancy are available; and HRSA-funded health centers, excluding Puerto Rico and Pacific Islands (n=1,559). Outcome Measures: COVID-19 vaccine hesitancy and COVID-19 vaccination rates. Results: We identified 219 counties that are part of clusters of high rates of vaccine hesitancy and low COVID-19 vaccination rates. In general, these counties have higher rates of poverty, larger percentages of black and Hispanic populations, and are located in the Southeast (Alabama, Georgia) and West Virginia. Sixty health center awardees are located within these counties, serving almost 700,000 patients. Conclusions: While almost one-half of US adults have been vaccinated, younger adults have much lower rates of vaccination and large numbers are still unvaccinated. Further, vaccine rates vary by race and ethnicity, with less than one-fifth of Hispanic and black adults having been vaccinated. Targeting areas with high rates of vaccine hesitancy and low vaccination rates supports strategic planning, optimizes finite resources, and better assists health centers in creating culturally competent outreach addressing vaccine hesitancy.

Objective: The purpose of this study was to establish a biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification.Methods: A total of 223 adolescents aged 10 to 18 years with BMI ≥95th percentile were enrolled, along with 71 healthy weight participants. Clinical data, fasting serum, and fecal samples were collected at repeated intervals over 6 months. Herein, the study design, data collection methods, and interim analysis—including targeted serum metabolite measurements and fecal 16S ribosomal RNA gene amplicon sequencing among adolescents with obesity (n = 27) and healthy weight controls (n = 27)—are presented.Results: Adolescents with obesity have higher serum alanine aminotransferase, C‐reactive protein, and glycated hemoglobin, and they have lower high‐density lipoprotein cholesterol when compared with healthy weight controls. Metabolomics revealed differences in branched‐chain amino acid–related metabolites. Also observed was a differential abundance of specific microbial taxa and lower species diversity among adolescents with obesity when compared with the healthy weight group.Conclusions: The Pediatric Metabolism and Microbiome Study (POMMS) biorepository is available as a shared resource. Early findings suggest evidence of a metabolic signature of obesity unique to adolescents, along with confirmation of previously reported findings that describe metabolic and microbiome markers of obesity.

Objective: To establish a biorepository of clinical, metabolomic, and microbiome samples from adolescents with obesity as they undergo lifestyle modification. Methods: We enrolled 223 adolescents aged 10-18 years with Body Mass Index ≥ 95 ^th percentile, along with 71 healthy weight participants. We collected clinical data, fasting serum, and fecal samples at repeated intervals over 6 months. Here we present our study design, data collection methods, and an interim analysis, including targeted serum metabolite measurements and fecal 16S rRNA gene amplicon sequencing among adolescents with obesity (n=27) and healthy weight controls (n=27). Results: Adolescents with obesity have higher serum alanine aminotransferase, C-reactive protein, and glycated hemoglobin, and lower high-density lipoprotein cholesterol when compared with healthy weight controls. Metabolomics revealed differences in branched chain amino acid related metabolites. We also observed differential abundance of specific microbial taxa and lower species diversity among adolescents with obesity when compared with the healthy weight group. Conclusions: The Duke Pediatric Metabolism and Microbiome Study biorepository is available as a shared resource. Early findings suggest evidence of a metabolic signature of obesity unique to adolescents, along with confirmation of previously reported findings describing metabolic and microbiome markers of obesity. Clinical Trial Registration: Biorepository: NCT02959034 Observational Trial: NCT03139877 What is already known about this subject?: The intestinal microbiome plays an important role in adult obesity and regulation of metabolism. Although it is well-established that obesity has its roots in childhood, very little is known about the role of the microbiome in pediatric obesity and how it changes during adolescence. What are the new findings in your manuscript?: This manuscript provides details of a new shared biorepository including clinical data, stool samples and plasma samples from a diverse cohort of 223 adolescents with obesity followed longitudinally over 6 months during a weight management intervention, as well as 71 adolescents with healthy weight as a comparison group. Interim analyses suggest that adolescents with obesity have microbiome signatures and metabolite profiles similar to adults, however key differences in microbial communities and metabolic by-products are identified. How might your results change the direction of research or focus of clinical practice?: The POMMS biorepository will be available for investigators to use in future research, to elucidate the underlying mechanisms of obesity and related chronic health conditions. Preliminary data reveal metabolite profiles that suggest adolescence may be a window of metabolic plasticity and disease reversibility Microbiome and metabolomic signatures suggest potential biomarkers that may serve as prognostic or predictive factors in disease remission, or targets for future therapeutics.

Previous studies have demonstrated the presence of microbial DNA in the fetal environment. However, it remains unclear whether this DNA represents viable bacteria and how it relates to the maternal microbiota across body sites. We studied the microbiota of human and mouse dyads to understand these relationships, localize bacteria in the fetus, and demonstrate bacterial viability. In human preterm and full-term mother-infant dyads at the time of cesarean delivery, the oral cavity and meconium of newborn infants born as early as 24 weeks of gestation contained a microbiota that was predicted to originate from in utero sources, including the placenta. Using operative deliveries of pregnant mice under highly controlled, sterile conditions in the laboratory, composition, visualization, and viability of bacteria in the in utero compartment and fetal intestine were demonstrated by 16S rRNA gene sequencing, fluorescence in situ hybridization, and bacterial culture. The composition and predicted source of the fetal gut microbiota shifted between mid- and late gestation. Cultivatable bacteria in the fetal intestine were found during mid-gestation but not late gestation. Our results demonstrate a dynamic, viable mammalian fetal microbiota during in utero development.

Accumulating evidence suggests a connection between asthma development and colonization with nontypeable Haemophilus influenzae (NTHi). Specifically, nasopharyngeal colonization of human infants with NTHi within 4 weeks of birth is associated with an increased risk of asthma development later in childhood. Monocytes derived from these infants have aberrant inflammatory responses to common upper respiratory bacterial antigens compared to those of cells derived from infants who were not colonized and do not go on to develop asthma symptoms in childhood. In this study, we hypothesized that early-life colonization with NTHi promotes immune system reprogramming and the development of atypical inflammatory responses. To address this hypothesis in a highly controlled model, we tested whether colonization of mice with NTHi on day of life 3 induced or exacerbated juvenile airway disease using an ovalbumin (OVA) allergy model of asthma. We found that animals that were colonized on day of life 3 and subjected to induction of allergy had exacerbated airway disease as juveniles, in which exacerbated airway disease was defined as increased cellular infiltration into the lung, increased amounts of inflammatory cytokines interleukin-5 (IL-5) and IL-13 in lung lavage fluid, decreased regulatory T cell-associated FOXP3 gene expression, and increased mucus production. We also found that colonization with NTHi amplified airway resistance in response to increasing doses of a bronchoconstrictor following OVA immunization and challenge. Together, the murine model provides evidence for early-life immune programming that precedes the development of juvenile airway disease and corroborates observations that have been made in human children.

Summary: Mycobacterium tuberculosis proteins that are exported out of the bacterial cytoplasm are ideally positioned to be virulence factors; however, the functions of individual exported proteins remain largely unknown. Previous studies identified Rv0199 as an exported membrane protein of unknown function. Here, we characterized the role of Rv0199 in M. tuberculosis virulence using an aerosol model of murine infection. Rv0199 appears to be a member of a Mce‐associated membrane (Mam) protein family leading us to rename it OmamA, for orphaned Mam protein A. Consistent with a role in Mce transport, we showed OmamA is required for cholesterol import, which is a Mce4‐dependent process. We further demonstrated a function for OmamA in stabilizing protein components of the Mce1 transporter complex. These results indicate a function of OmamA in multiple Mce transporters and one that may be analogous to the role of VirB8 in stabilizing Type IV secretion systems, as structural similarities between Mam proteins and VirB8 proteins are predicted by the Phyre 2 program. In this study, we provide functional information about OmamA and shed light on the function of Mam family proteins in Mce transporters.