Gary D. Wu

Clostridioides difficile causes severe disease in adults but commonly colonizes infants asymptomatically. The consequences of early-life colonization on host development remain unknown. In a neonatal mouse model, C. difficile colonization drove proinflammatory and tissue repair responses in the intestinal epithelium, enriching injury-associated intestinal stem cell populations and skewing differentiation toward secretory lineages. Despite transient colonization, exposure to C. difficile early in life led to persistent changes into adulthood. Epithelial responses were toxin dependent, as colonization with nontoxigenic strains or maternal vaccination with a C. difficile –targeted messenger RNA–lipid nanoparticle vaccine protected neonates. Human infant intestinal epithelial cells were sensitive to C. difficile toxins, and biopsies from colonized infants exhibited altered intestinal stem cell behavior. This study redefines C. difficile as an underappreciated early-life pathogen with lasting effects on host development.

Glucuronidation is an important detoxification pathway that operates in balance with gastrointestinal microbial β-glucuronidase (GUS) activity, which can regenerate bioactive metabolites from their glucuronidated forms. How this host-microbe interaction shapes the distribution and pool of glucuronidated metabolites (i.e., the glucuronidome) remains poorly understood. In this study, we employed pattern-filtering data science approaches in conjunction with untargeted LC-MS/MS metabolomics to map the glucuronidome in urine, serum, and colon/fecal samples from gnotobiotic and conventional mice, and in humans. We find that microbial colonization and GUS activity compress the colonic glucuronidome and expand urinary glucuronidome diversity, revealing a compartmental redistribution of glucuronidated metabolites. Reverse metabolomics of known glucuronidated chemicals and glucuronidation pattern filtering searches in public metabolomics datasets exposed the diversity of glucuronidated metabolites in human and mouse ecosystems. In summary, we present a glucuronidation fingerprint resource that provides broader access to and analysis of the glucuronidome. Together, this work establishes a scalable analytical framework and provides mechanistic insight into how microbial activity reshapes systemic glucuronidation, with implications for drug metabolism, diet-microbe interactions, and biomarker discovery.

Tangible and intangible barriers to healthy eating (e.g., lack of food preparation equipment and lack of time, respectively) may prevent households from utilizing accessible food to produce nutritious meals; yet their role in food and nutrition insecurity remains unclear. Participants (n=184) were from the Community Health, Access to Nutrition, and Grocery Experiences (CHANGE) Study (2024), a cross-sectional needs assessment conducted in a primarily non-Hispanic Black, low-income, and urban community. Food and nutrition insecurity were measured using a validated 18-item survey and a validated one-item screener, respectively. Barriers were assessed using a validated 8-item survey (range 0-8). Weighted multivariable log-binomial regression models estimated prevalence ratios (PR) (reference group: no barriers); multiple imputation addressed missing data. Barriers were common (66.0%), with intangible (63.4%) being more prevalent than tangible (17.8%). Over half of the participants experienced food (51.4%) or nutrition (41.6%) insecurity. Higher barrier scores were associated with food (Score of 1-4: aPR=1.79, 95% CI [1.29-2.48]; Score of 5-8: 2.20, 95% CI [1.55-3.12]) and nutrition (Score of 5-8: 2.09, 95% CI [1.10-4.00]) insecurity. Tangible barriers were associated with a greater prevalence of food and nutrition insecurity than intangible barriers. Addressing barriers to healthy eating may reduce food and nutrition insecurity in high-risk communities.

Background: Malnutrition significantly impacts surgical outcomes yet is difficult to identify preoperatively. Few studies have investigated the association between comprehensive body composition assessment and malnutrition in males and females separately. This study evaluates sex-specific associations between preoperative imaging-derived body composition features and malnutrition in abdominal surgery patients. Methods: This cross-sectional study included patients who underwent a preoperative abdominal computed tomography scan and elective abdominal surgery at a single institution (2018–2021). A deep learning algorithm quantified five muscle groups and two fat depots from CT scans. Clinical malnutrition was diagnosed by registered dietitians using standardized criteria. Sex-specific associations between imaging features and malnutrition were evaluated using logistic regression. Results: Among 1143 patients, 20.2% had clinical malnutrition, with prevalence varying by procedure type (3.5–38.2%). Malnutrition was associated with reduced muscle volume for both sexes; however, myosteatosis was only associated with malnutrition in females. In males, malnutrition was associated with decreased psoas volume (OR: 0.58, 95% CI [0.41–0.82]), decreased quadratus lumborum volume (OR: 0.52, 95% CI [0.35–0.77]), and reduced erector spinae attenuation (OR 0.58, 95% CI [0.41–0.82]). In females, decreased psoas volume (OR 0.56, 95% CI [0.41–0.77]) and attenuation (OR 0.59, 95% CI [0.44–0.79]) were associated with malnutrition. Both sexes showed increased subcutaneous fat attenuation (males: OR 1.58, 95% CI [1.22–2.04]; females: OR 1.96, 95% CI [1.54–2.50]) and visceral fat attenuation (males: OR 1.43 95% CI [1.07–1.90]; females: OR 1.68 95% CI [1.29–2.20]) associated with malnutrition. Conclusions: Males and females exhibit distinct body composition features associated with clinical malnutrition. Comprehensive analysis of muscle and fat characteristics reveals these sex-specific relationships, providing foundational knowledge for future development of predictive tools to enable earlier identification of patients at higher nutrition-related surgical risk.

γδ T cells maintain intestinal immune homeostasis, but their contributions to human ulcerative colitis (UC) are poorly understood. We characterized γδ T cells in intestinal biopsies obtained from patients with UC and healthy donors using single-cell RNA sequencing, T cell receptor profiling, and mass cytometry. UC reduced CD103 ⁺ Vγ4Vδ1 ⁺ γδ intraepithelial lymphocytes (γδ IELs) and increased γδ T cell subsets with stemlike phenotypes expressing TCF-1 (T cell factor 1) and PD-1 (programmed cell death receptor 1) or effector-like phenotypes expressing granzyme B, perforin, and T-bet in the lamina propria. γδ T cell composition changes in UC correlated with decreased expression of epithelial BTNL3 and BTNL8 and increased BTN3A1 and BTN3A3 , suggesting altered recruitment and activation. Clinical improvement recovered γδ IELs and reduced inflammation-associated subsets. Inflammation-associated changes were observed in peripheral blood γδ T cells. Thus, distinct γδ T cell subsets in different niches exert protective or pathogenic functions in UC.

Glucuronidation is an important detoxification pathway that operates in balance with gastrointestinal microbial β-glucuronidase (GUS) enzymes that can regenerate active metabolites from their glucuronidated forms. Although significant progress has been made in characterizing GUS enzymes, methods to comprehensively define the glucuronidome – the collection of glucuronidated metabolites – remain limited. In this study we employed pattern-filtering data science approaches alongside untargeted LC-MS/MS metabolomics to map the glucuronidome in urine, serum, and colon/fecal samples from gnotobiotic and conventional mice. Our findings reveal microbiome-driven shifts in the glucuronidome, highlighting how differential GUS activity can influence host metabolite profiles. Reverse metabolomics of known glucuronidated chemicals and glucuronidation pattern filtering searches in public metabolomics datasets exposed the diversity of glucuronidated metabolites in human and mouse ecosystems. In summary, we present a new glucuronidation fingerprint resource that provides broader access to and analysis of the glucuronidome. By systematically capturing glucuronidation patterns, this resource enhances unknown metabolite annotation efforts and provides new insights into the dynamic relationship between the host and bacterial biotransformation activities.

Dissemination of organisms from the gut microbiota is a major contributor to sepsis and critical illness. Patients with cirrhosis are prone to systemic infections and are commonly prescribed the carbohydrate lactulose to manage hepatic encephalopathy (HE) ¹ . Commensal metabolism of lactulose is believed to reduce pathobiont colonization through short-chain fatty acid production, but its direct effects on gut pathobionts remain unexplored ² . Here, we show that lactulose consumption unexpectedly selects for mutations in Escherichia coli lactose (lac) operon regulation, enhancing its metabolic fitness and colonization capacity. This is mediated by selection for constitutive expression of the lac operon through mutations in its regulatory components. Using in vitro systems, murine models, and clinical samples, we demonstrate that these mutations enable E. coli to exploit lactulose as a carbon source, bypassing host carbohydrate metabolism and increasing its intestinal colonization. Despite its long-standing use in HE treatment, we find that lactulose has a paradoxical association with risk of infection hospitalization in patients with cirrhosis in a large epidemiologic study. The emergence of lactulose-adapted E. coli strains could be suppressed by a dietary oligosaccharide that competitively inhibits lactulose uptake. These findings reveal a mechanism by which dietary substrates exert selective pressure on the microbiome, with implications for diet-based strategies to modulate microbial evolution and infection risk.

Background: The increasing incidence of inflammatory bowel disease (IBD) presents significant medical and societal challenges. A well‐designed IBD database is crucial for both epidemiological studies and clinical management. However, inconsistencies between regional databases hinder cross‐institutional and international research, especially between Eastern and Western societies.Methods: We developed a new IBD database, the 301 IBD database, integrating the IBD clinical characteristics from the Penn IBD database (USA) and the latest IBD guidelines and consensus and clinical practices of the Chinese PLA General Hospital (PLAGH). We applied this database to analyze clinical data of IBD inpatients at PLAGH from 2008 to 2023.Results: The 301 IBD database contains 490 items in 6 sections including demographic characteristics, personal history, clinical phenotype, disease activity, laboratory tests and examinations, and treatment. Features of the 301 IBD database include inpatient focus, biochemical indicators and opportunistic infection focus, and more about ulcerative colitis (UC)‐associated complications. Single‐center analysis revealed an increasing hospitalization trend, from 2.35% in 2008 to 3.94% in 2023. We found that the clinical characteristics of our UC inpatients are predominantly male (62.5%), extensive lesions (55.1%), low usage of biologics (4.1%), and a high incidence of UC‐CRC (3.0%). The clinical characteristics of CD inpatients included male predominance (68.39%), early onset age (35.43 ± 14.75‐year‐old), and high rate of surgery (25.81%).Conclusion: The 301 IBD database, integrating Eastern and Western clinical data, provides a valuable tool for IBD clinical research. Future international, multicenter collaborations are expected to further enhance its utility.

The gut microbiota plays a critical role in human health and disease. Microbial community assembly and succession early in life are influenced by numerous factors. In turn, assembly of this microbial community is known to influence the host, including immune system development, and has been linked to outcomes later in life. To date, the role of host-mediated nutritional immunity and metal availability in shaping microbial community assembly and succession early in life has not been explored in depth. Using a human infant cohort, we show that the metal-chelating protein calprotectin is highly abundant in infants. Taxa previously shown to be successful early colonizers of the infant gut, such as Enterococcus , Enterobacteriaceae, and Bacteroides, are highly resistant to experimental metal starvation in culture. Lactobacillus , meanwhile, is highly susceptible to metal restriction, pointing to a possible mechanism by which host-mediated metal limitation shapes the fitness of early colonizing taxa in the infant gut. We further demonstrate that formula-fed infants harbor markedly higher levels of metals in their gastrointestinal tract compared to breastfed infants. Formula-fed infants with high levels of metals harbor distinct microbial communities compared to breastfed infants, with higher levels of Enterococcus , Enterobacter, and Klebsiella , taxa which show increased resistance to the toxic effects of high metal concentrations. These data highlight a new paradigm in microbial community assembly and suggest an unappreciated role for nutritional immunity and dietary metals in shaping the earliest colonization events of the microbiota. IMPORTANCE: Early life represents a critical window for microbial colonization of the human gastrointestinal tract. Surprisingly, we still know little about the rules that govern the successful colonization of infants and the factors that shape the success of early life microbial colonizers. In this study, we report that metal availability is an important factor in the assembly and succession of the early life microbiota. We show that the host-derived metal-chelating protein, calprotectin, is highly abundant in infants and successful early life colonizers can overcome metal restriction. We further demonstrate that feeding modality (breastmilk vs formula) markedly impacts metal levels in the gut, potentially influencing microbial community succession. Our work suggests that metals, a previously unexplored aspect of early life ecology, may play a critical role in shaping the early events of microbiota assembly in infants.