Michael H. Woodworth

Antipsychotic medications are widely prescribed and associated with increased infection risk, but underlying mechanisms remain unclear. We examined if antipsychotic-induced microbiome and metabolome alterations impair colonization resistance. Using a murine model, we evaluated haloperidol, olanzapine, risperidone, and quetiapine through longitudinal microbiome profiling, untargeted metabolomic fingerprinting, behavioral testing, and enteric infection challenge. Antipsychotic exposure induced persistent behavioral changes and increased susceptibility to Citrobacter rodentium, with quetiapine and olanzapine producing the greatest weight loss. Microbiome sequencing revealed treatment-specific shifts in beta diversity without consistent alpha diversity changes, while untargeted metabolomic analysis demonstrated robust, drug-specific metabolic reprogramming, particularly in lipid and sterol pathways. Although microbial compositional changes did not fully account for functional outcomes, their integration with metabolomics data revealed disrupted bacterial taxa-metabolite networks and loss of homeostatic metabolic modules. These results provide a potential mechanistic link between the disruptive effects of antipsychotics on the microbiome and impaired colonization resistance.

Metagenomic data provide evidence that bacteriophage (phage) abound in the enteric microbiomes of humans. However, the contribution of these viruses in shaping the bacterial composition of the gut microbiome and how these phages are maintained remain unclear. We performed experiments with 756 combinations of 54 Escherichia coli and nine phage isolates from four fecal microbiota transplantation (FMT) doses and five laboratory phages as samples of non-dysbiotic human enteric microbiota. We also developed a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our experiments predict that as a consequence of the production of the O antigen, most of the E. coli in the human enteric microbiome will be resistant to infections with the array of co-occurring phages. Our modeling suggests that phages are maintained in these enteric communities due to the high rates of transition between the O antigen-resistant and -sensitive states. Based on our observations and predictions from this theory, we postulate that the phage found in the human gut are likely to play a little role in shaping the strain composition of E. coli of healthy individuals. Although we only investigated E. coli , the mechanism of resistance described here is shared among most of the gram-negative bacteria. Evidence is provided that, as a consequence of O antigen-mediated resistance, the genetically diverse array of bacteriophage in the gut microbiome of humans plays little or no role in determining the densities and distribution of the genetically diverse strain E. coli in this habitat. Our mathematical model predicts and our experiments support the hypothesis that the phage present in the gut microbiome are maintained by replication on the minority of sensitive bacteria generated by the leakiness of O antigen-mediated resistance. IMPORTANCE: Bacteriophages (phages) are abundant in the human gut, yet whether these viruses shape the bacterial communities living there remains unresolved. Using Escherichia coli and phages isolated from the stool of healthy fecal microbiota transplantation (FMT) donors, together with a mathematical model, we show that the vast majority of gut E. coli are resistant to co-occurring phages because they express the O antigen, a surface structure that masks the receptors phages use to attach. Despite this widespread resistance, phages persist by replicating on a small, continually regenerated subpopulation of sensitive cells, a phenomenon we term leaky resistance. These findings suggest that phages play a little role in determining which E. coli strains dominate the healthy human gut. Because the O antigen is broadly expressed across gram-negative bacteria, this mechanism likely extends well beyond E. coli and helps explain why isolating therapeutic phages against many pathogens is difficult.

Clostridioides difficile infection (CDI) is facilitated by gut microbiome disruption and associated metabolic disturbances. While many prior studies have focused on the microbial composition of CDI stool, fewer have explored the fecal metabolome using untargeted high-resolution metabolomics (HRM). To characterize the metabolic phenotype of CDI, we performed untargeted HRM on stool samples from 55 CDI patients and 72 healthy controls. CDI was associated with marked alterations in stool metabolites, mapping to 14 significantly dysregulated pathways, including tryptophan metabolism, bile acid metabolism, short-chain fatty acid metabolism, and fatty acid oxidation. These findings suggest that CDI is associated with a distinct fecal metabolic milieu that may promote inflammation, impair colonization resistance, and facilitate C. difficile replication. Our results corroborate previous studies and support further investigation of the role of microbial and immune signaling in CDI as well as metabolic biomarkers and therapeutic targets. IMPORTANCE: As we learn more about the essential role of gut microbes in human health and disease, there is an effort to identify and characterize stool biomarkers that distinguish patients with microbiome-associated disease from healthy individuals. Clostridioides difficile infection contributes to excess healthcare burden and is tightly linked to disruption of the gut microbiome (usually by use of antimicrobials). We compared the metabolome of healthy stool and C. difficile -infected stool to identify metabolites that correlate with disease and may support the development of improved diagnostic tests for C. difficile infection. In comparing these two groups, we found chemical pathways that strongly correlate with disease and others more associated with healthy stool, including bile acid biosynthesis, tryptophan metabolism, and carnitine activation.

Background: Malnutrition and antimicrobial-resistant infections are major causes of morbidity and mortality in low-income countries. These conditions have been associated with the gut microbiome, although little is known about the acceptability of microbiota therapies such as fecal microbiota transplantation (FMT). We explored the acceptability of FMT among health care providers (HCPs) and patients in Addis Ababa, Ethiopia. Methods: In this qualitative study, we purposively sampled patients with bacterial infections and acute malnutrition, caregivers, and HCPs at two hospitals. Eight focus group discussions were held. Amharic and English discussion guides covered knowledge of FMT and perceived barriers or facilitators for uptake. Data were transcribed and translated into English when necessary. MAXQDA software was used for a thematic analysis, with trained researchers closely reading transcripts to identify issues, develop a codebook, iteratively code data, and assess intercoder agreement. Description, comparison, and categorization were conducted to discern core themes, and validity checks ensured that findings were grounded in the data. Results: HCPs indicated a general willingness to prescribe FMT, provided that there was sufficient evidence supporting its efficacy and safety and they were confident on patient adherence. Patient acceptability of FMT was categorized along a continuum from those who were unconvinced, persuadable, amenable, and accepting of salvage treatment. Conclusions: FMT may be acceptable for HCPs and patients in Addis Ababa, although interventions are needed to enhance acceptance among some groups, such as marketing it as standard medication, obtaining endorsement by religious leaders, providing multiple formulations, and/or providing thoughtful health communication.

More than 850 million individuals worldwide, accounting for 10–15% of the adult population, are estimated to have chronic kidney disease. Each of these individuals is host to tens of trillions of microorganisms that are collectively referred to as microbiota — a dynamic ecosystem that both influences host health and is itself influenced by changes in the host. Available evidence supports the existence of functional connections between resident microorganisms and kidney health that are altered in the context of specific kidney diseases, including acute kidney injury, chronic kidney disease and renal stone disease. Moreover, promising data from preclinical studies suggest that targeting of gut microbial pathways may provide new therapeutic opportunities for the treatment of kidney disease. This Roadmap describes current understanding of the mechanisms by which microorganisms regulate host organ function, the effects of kidney disease on the gut microbiome, and how these insights may contribute to the development of microbe-targeted therapeutics. We highlight key knowledge gaps that remain to be addressed and strategies for addressing these, outlining both the promise and the potential pitfalls of leveraging our understanding of the gut microbiota to better understand and treat kidney disease.

Objectives: Sponge-Sticks (SS) and ESwabs are frequently utilized for detection of multidrug-resistant organisms (MDROs) in the environment. Head-to-head comparisons of SS and ESwabs across recovery endpoints are limited. Design: We compared MDRO culture and non-culture-based recovery from (1) ESwabs, (2) cellulose-containing SS (CS), and (3) polyurethane-containing SS (PCS). Methods: Known quantities of each MDRO were pipetted on a stainless-steel surface and swabbed by each method. Samples were processed, cultured, and underwent colony counting. DNA was extracted from sample eluates, quantified, and underwent metagenomic next-generation sequencing (mNGS). MDROs underwent whole genome sequencing (WGS). MDRO recovery from paired patient perirectal and PCS-collected environmental samples from clinical studies was determined. Setting: Laboratory experiment, tertiary medical center, and long-term acute care facility. Results: Culture-based recovery varied across MDRO taxa, it was highest for vancomycin-resistant Enterococcus and lowest for carbapenem-resistant Pseudomonas aeruginosa (CRPA). Culture-based recovery was significantly higher for SS compared to ESwabs except for CRPA, where all methods performed poorly. Nucleic acid recovery varied across methods and MDRO taxa. Integrated WGS and mNGS analysis resulted in successful detection of antimicrobial resistance genes, construction of high-quality metagenome-assembled genomes, and detection of MDRO genomes in environmental metagenomes across methods. In paired patient and environmental samples, multidrug-resistant Pseudomonas aeruginosa ( MDRP) environmental recovery was notably poor (0/123), despite detection of MDRP in patient samples (20/123). Conclusions: Our findings support the use of SS for the recovery of MDROs. Pitfalls of each method should be noted. Method selection should be driven by MDRO target and desired endpoint.

Importance: Intestinal multidrug-resistant organism (MDRO) colonization is highly prevalent in long-term acute care hospital (LTACH) patients and is associated with MDRO infection and transmission. However, there are no therapies approved by the US Food and Drug Administration to reduce intestinal MDRO colonization.Objective: To determine the safety and acceptability of fecal microbiota transplantation (FMT) in LTACH patients.Design, Setting, and Participants: This single-center, open-label nonrandomized clinical trial was conducted from April to December 2023 at an LTACH in the Southeastern US with median 50-patient census and 28-day length of stay. Patients with MDRO colonization were identified by perirectal prevalence sampling. Patients colonized with at least 1 target MDRO were approached for informed consent for FMT. FMT recipients were compared with untreated controls with MDRO colonization. Data were analyzed from August 2024 to May 2025.Intervention: Healthy donor fecal microbiota (50-100 g stool and 250 mL normal saline with 9% glycerol) instilled via gastrostomy tube or enema without antibiotic or bowel preparation conditioning.Main Outcomes and Measures: The primary outcome was frequency and severity of adverse events. Solicited adverse events were recorded for 7 days. Unsolicited adverse events were recorded for 6 months. Four weekly perirectal MDRO cultures were performed after FMT.Results: A total of 42 patients, including 10 (mean [SD] age, 63.8 (14.5) years; 7 [70%] female) who received FMT and 32 contemporaneous controls (mean [SD] age, 64.0 [13.7] years; 13 [41%] female) were assessed. In 2 prevalence surveys, 23 of 32 (72%) and 26 of 34 (77%) perirectal cultures grew at least 1 MDRO. Among the FMT group, 5 patients received FMT via gastrostomy alone, 4 via enema alone, and 1 with both routes more than 30 days apart. No serious adverse events were attributed to FMT, and post-FMT solicited adverse events were mild. At final visit, all perirectal cultures from FMT recipients grew at least 1 MDRO. Post hoc analyses found numerically fewer FMT recipients had positive blood culture results (0 individuals vs 6 individuals [19%]; P = .31), pathogen intestinal dominance (2 of 8 individuals [25%] vs 4 of 8 individuals [50%]; P = .61), and 7 fewer days of antibiotic therapy per 1000 patient days (median [IQR], 12.6 [0-25.2] days vs 19.7 [6.5-36.1] days; P = .38) compared with controls in the 6 months after prevalence survey, although these differences were not statistically significant. Accounting for higher baseline FMT recipient antibiotic use, difference-in-differences analysis estimated 26 (95% CI, −64 to 12) fewer days of antibiotic therapy per 1000 patient-days after FMT, although this difference was also not statistically significant.Conclusions and Relevance: In this nonrandomized pilot clinical trial, FMT was acceptable for LTACH patients without related serious adverse events. Although not powered to test these outcomes, this study found potential reductions in bacteremia, intestinal pathogen domination, and antibiotic use associated with FMT, suggesting FMT should be evaluated in larger, randomized trials.Trial Registration: ClinicalTrials.gov Identifier: NCT05780801

The enteric microbiota is an established reservoir for multidrug-resistant organisms that present urgent clinical and public health threats. Observational data and small interventional studies suggest that microbiome interventions, such as fecal microbiota products and characterized live biotherapeutic bacterial strains, could be an effective antibiotic-sparing prevention approach to address these threats. However, bacterial colonization is a complex ecological phenomenon that remains understudied in the context of the human gut. Antibiotic resistance is one among many adaptative strategies that impact long-term colonization. Here we review and synthesize evidence of how bacterial competition and differential fitness in the context of the gut present opportunities to improve mechanistic understanding of colonization resistance, therapeutic development, patient care, and ultimately public health.

While the inhibitory receptor FcγRIIB has been shown to be upregulated on activated CD8 ⁺ T cells in both mice and humans, its effect on T cell fate during infection has not been fully elucidated. We identified an increase in FcγRIIB-expressing CD8 ⁺ T cells in patients with COVID-19 relative to healthy controls as well as in mouse models of viral infection. Despite its well-known role as an Fc receptor, FcγRIIB also ligates the immunosuppressive cytokine Fgl2, resulting in CD8 ⁺ T cell apoptosis. Both chronic LCMV infection in mice and COVID-19 in humans resulted in a significant increase in plasma Fgl2. Transfer of CD8 ⁺ T cells into a Fgl2-replete, but not Fgl2-devoid, environment resulted in elimination of FcγRIIB ⁺ , but not FcγRIIB ^– , CD8 ⁺ T cells. Similarly, plasma Fgl2 was directly proportional to CD8 ⁺ T cell lymphopenia in patients with COVID-19. RNA-Seq analysis demonstrated that Fgl2 was produced by murine virus–specific CD8 ⁺ T cells, with an increase in Fgl2 in CD8 ⁺ T cells elicited during chronic versus acute viral infection. Fgl2 was also upregulated in CD8 ⁺ T cells from patients with COVID-19 versus healthy controls. In summary, CD8 ⁺ T cell production of Fgl2 during viral infection underpinned an FcγRIIB-mediated loss of CD8 ⁺ T cell immunity in both mice and humans.

Brendan J Kelly, Jennie H Kwon, Michael H Woodworth; Reply to Olle et al, The Journal of Infectious Diseases, , jiae576, https://doi.org/10.1093/infdis/jia