Doyle V. Ward

Gut microbiome differences in Alzheimer’s disease (AD) are typically cataloged taxon by taxon, yet bacterial competition and cross-feeding make species’ roles dependent on the entire community. We analyzed 274 stool metagenomes from 119 older adults (18 with AD) as communities, retaining 22 recurring across 1,000 runs. Using our AI framework, we identified 15 species differing in abundance in AD, particularly the commensal Phocaeicola vulgatus (Cohen’s d –0.91, 95% CI [-1.23, –0.59]), a finding robust to repeated sampling. It correlated negatively with its sister species, Phocaeicola dorei ( r –0.57), suggesting possible niche competition; this replicated in an independent cohort ( r –0.43). P. vulgatus was depleted in AD and the opportunistic pathogen Bacteroides fragilis enriched, shifting their balance toward B. fragilis ( d –0.70), a modestly reproduced AD-associated pattern ( d –0.24). Our findings suggest that AD-associated gut microbiome variation extends beyond taxon-specific abundance to the balance between specific species within a community matrix.

Background: Prophylactic oral azithromycin vs. placebo reduced maternal, but not neonatal, mortality/sepsis in the A-PLUS Randomized Trial. While prophylactic intrapartum azithromycin reduces maternal mortality/sepsis, it may promote antimicrobial resistance (AMR) in commensal bacteria,. Methods: Randomly selected women and their infants participating in A-PLUS were enrolled in a longitudinal cross-sectional sub-study to assess the presence of azithromycin resistance in selected bacteria in nasal cultures. Staphylococcus aureus and Streptococcus pneumoniae were cultured on selective agar, then azithromycin-containing agar to select for azithromycin resistant bacteria, identified biochemically. Azithromycin susceptibility was assessed by E-test. Nasal cultures were collected from women and infants between August 11, 2021 and September 18, 2023 during labor/day 1, day 7, 6 weeks, and 3, 6 and 12 months after delivery. Results: The study enrolled 911 women and 915 liveborn infants at 8 sites in 7 countries. Azithromycin resistance in S aureus was higher and azithromycin susceptibility was lower in women receiving azithromycin compared with those receiving placebo on day 7 (P < 0.001), 6 weeks (P < 0.001) and 3 months (P = 0.009) after delivery. Azithromycin resistance in S aureus was also higher and azithromycin susceptibility was lower 6 weeks after delivery (P < 0.001) in infants born to women receiving azithromycin, Azithromycin resistance in S. pneumoniae was too sparse to interpret. Conclusions: There was an increase in prevalence of azithromycin resistance (or reduction in azithromycin susceptibility) in commensal nasal S. aureus between day 7, 6 weeks and 3 months in women exposed to azithromycin vs. placebo and only at 6 weeks in infants exposed to azithromycin vs. placebo. These differences between the azithromycin and placebo groups were no longer detected at 6 and 12 months post-partum in the women and after 6 weeks through 12 months in the infants.

Background/Objectives: Enterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrheal illness worldwide, resulting in approximately 380,000 deaths annually, with significant morbidity in children and travelers to endemic regions. ETEC infection begins with the attachment of the bacterium to the small intestine via filamentous colonization factors (CF), followed by the production of heat-labile (LT) and heat-stable (ST) toxins that induce watery diarrhea. Targeting CF to prevent ETEC attachment is challenging due to strain heterogeneity. Methods: In previous studies, we developed a class-switched human monoclonal antibody, 68–90, expressed as secretory IgA (SIgA) in rice for cost-effective and stable storage. Rice-produced SIgA exhibited comparable binding efficiency to CfaE, a component of CF, compared to CHO-produced SIgA in vitro. Results: In this work, we showed that oral administration of 68–90 SIgA to Aotus nancymaae did not alter gut microbiome distribution or show signs of systemic exposure. Conclusions: These findings suggest that oral delivery of ETEC-specific SIgA is safe and does not disrupt the gut microbial population, highlighting its potential as an effective and targeted therapeutic strategy.

Background The Azithromycin Prevention in Labor Use Study (A-PLUS), a large, multi-national randomized trial, was performed to evaluate the improvement of maternal and newborn outcomes following a single dose of azithromycin (AZ) given during labor. However, the immediate and long-term impact of this single dose on the microbiome and the development or prevalence of antimicrobial resistance are unknown. We designed a sub-study to assess AZ resistance of bacterial isolates from clinical infections and of three target bacteria (Staphylococcus aureus, Streptococcus pneumoniae, and Escherichia coli) from the serial surveillance of the nasopharynx and rectum. Additionally, the serially surveilled samples will be evaluated for changes to the microbiome and the resistome of the nasopharynx and rectum. Methods and Analysis As part of the large, randomized APLUS trial, maternal and neonatal clinical infections were monitored for up to 42 days postpartum, and samples collected for culture using site-specific routine methods. For this sub-study, cultured bacterial isolates will be assessed for AZ resistance using an antibiotic susceptibility method. Additionally, a random subset of maternal-neonatal dyads from the main trial will be selected for serial surveillance with aseptic swab collections of the nasopharynx and the rectum at baseline, and subsequently at 1-week, 6-weeks, 3-months, 6-months, and 12-months postpartum. The serial samples will undergo selective culturing of sentinel bacterial species and screened for AZ resistance. An additional set of serial samples will be stored for future microbiome and resistome analyses. Ethics and Dissemination The study protocol was reviewed, and ethics approval obtained from all the relevant ethical review boards at each research site. All participants will provide informed written consent prior to their enrollment. Results of the trial will be disseminated through peer-reviewed publications, presentations at relevant conferences, and at dissemination meetings with the ministries of health and local stakeholders at each research site. Trial Registration NCT03871491.

A 34-year-old male presented with recurrent fever, arthralgia, and rash. He had two prior hospitalizations for suspected vasculitis and meningococcal meningitis at age 13 years. Positive blood cultures for Neisseria gonorrhoeae established the diagnosis of disseminated gonococcal infection. Complement studies showed low total (CH50) and alternative pathway (AP50) activity and low levels of all alternative and terminal complement proteins and the complement inhibitors factor H and factor I (FI), suggesting uninhibited complement activation and complement consumption. A homozygous nonsense mutation leading to a premature stop codon (p.Arg474*, or R456X) in CFI predicted complete FI deficiency, which was confirmed by immunoblotting. The patient’s serum contained IgG against reduction-modifiable protein and the lipoproteins H.8 and lipidated azurin, which are targets for blocking antibodies against gonococci and meningococci, respectively. This report underscores the importance of considering FI deficiency in patients with invasive neisserial infections, vasculitis-like manifestations, and consumptive complementopathy.

Alzheimer’s Disease Analysis Model Generation 1 (ADAM-1) is a multi-agent reasoning large language model (LLM) framework designed to integrate and analyze multimodal data, including microbiome profiles, clinical datasets, and external knowledge bases, to enhance the understanding and classification of Alzheimer’s disease (AD). By leveraging the agentic system with LLM, ADAM-1 produces insights from diverse data sources and contextualizes the findings with literature-driven evidence. A comparative evaluation with XGBoost revealed a significantly improved mean F1 score and significantly reduced variance for ADAM-1, highlighting its robustness and consistency, particularly when utilizing human biological data. Although currently tailored for binary classification tasks with two data modalities, future iterations will aim to incorporate additional data types, such as neuroimaging and peripheral biomarkers, and expand them to predict disease progression, thereby broadening ADAM-1’s scalability and applicability in AD research and diagnostic applications.

Older adults suffer from a high rate of asymptomatic bacteriuria (ASB), in which urinalysis may appear positive (presence of bacteria, white blood cells, and nitrates), often triggering initiation of antibiotics in acute care settings, without actual urinary tract infection (UTI) present. To investigate the urinary microbiome of older adults being tested for UTI, we enrolled a convenience sample of 250 older adult Emergency Department patients who had microscopic urinalysis ordered as part of their routine clinical care. Urinalysis results were classified as positive or negative, and patients were classified as being symptomatic or asymptomatic based on established diagnostic guidelines. We sought to determine if features of the urinary microbiome differed between positive and negative urinalysis (UAs) and symptomatic and asymptomatic patients with positive UAs. The same urine sample used for clinical testing was sequenced and analyzed for bacterial taxa, metabolic pathways, and known bacterial virulence factors. After exclusion for anatomical abnormalities and filtering for sequencing quality, 152 samples were analyzed (5 negative UAs, 147 positive UAs, among which 68 were asymptomatic, and 79 symptomatic). Positive UA samples showed significantly lower alpha diversity (2.29 versus 0.086, p < 0.01) and distinct community composition based on beta-diversity (PERMANOVA on Bray-Curtis distance p < 0.01). Alpha and beta diversity did not significantly differ between asymptomatic and symptomatic patients. Machine learning classifiers combining clinical covariates other than specific signs and symptoms and microbiome features (taxa, metabolic pathways, or virulence factors) revealed mostly microbiome features as predictive of symptomatic UTI over clinical features.

The role of microbes and their metabolites in modulating tuft cell (TC) dynamics in the large intestine and the relevance of this pathway to infections is unknown. Here, we uncover that microbiome-driven colonic TC hyperplasia protects against Clostridioides difficile infection. Using selective antibiotics, we demonstrate increased type 2 cytokines and TC hyperplasia in the colon but not in the ileum. We demonstrate the causal role of the microbiome in modulating this phenotype using fecal matter transplantation and administration of consortia of succinate-producing bacteria. Administration of succinate production–deficient microbes shows a reduced response in a Pou2f3-dependent manner despite similar intestinal colonization. Finally, antibiotic-treated mice prophylactically administered with succinate-producing bacteria show increased protection against C. difficile–induced morbidity and mortality. This effect is nullified in Pou2f3−/− mice, confirming that the protection occurs via the TC pathway. We propose that activation of TCs by the microbiota in the colon is a mechanism evolved by the host to counterbalance microbiome-derived cues that facilitate invasion by pathogens.

Background The Azithromycin Prevention in Labor Use Study (A-PLUS), a large, multi-national randomized trial, was performed to evaluate the improvement of maternal and newborn outcomes following a single dose of azithromycin (AZ) given during labor. However, the immediate and long-term impact of this single dose on the microbiome and the development or prevalence of antimicrobial resistance are unknown. We designed a sub-study to assess AZ resistance of bacterial isolates from clinical infections and of three target bacteria (Staphylococcus aureus, Streptococcus pneumoniae, and Escherichia coli) from the serial surveillance of the nasopharynx and rectum. Additionally, the serially surveilled samples will be evaluated for changes to the microbiome and the resistome of the nasopharynx and rectum. Methods and Analysis As part of the large, randomized APLUS trial, maternal and neonatal clinical infections were monitored for up to 42 days postpartum, and samples collected for culture using site-specific routine methods. For this sub-study, cultured bacterial isolates will be assessed for AZ resistance using an antibiotic susceptibility method. Additionally, a random subset of maternal-neonatal dyads from the main trial will be selected for serial surveillance with aseptic swab collections of the nasopharynx and the rectum at baseline, and subsequently at 1-week, 6-weeks, 3-months, 6-months, and 12-months postpartum. The serial samples will undergo selective culturing of sentinel bacterial species and screened for AZ resistance. An additional set of serial samples will be stored for future microbiome and resistome analyses. Ethics and Dissemination The study protocol was reviewed, and ethics approval obtained from all the relevant ethical review boards at each research site. All participants will provide informed written consent prior to their enrollment. Results of the trial will be disseminated through peer-reviewed publications, presentations at relevant conferences, and at dissemination meetings with the ministries of health and local stakeholders at each research site. Trial Registration NCT03871491.