Citations

Background: Staphylococcus aureus causes bloodstream and skin infections in humans. The prevalence of multidrug-resistant S. aureus strains means new antibiotics are needed. A novel antimicrobial drug named SK-03-92, a synthetic aromatic organic stilbenoid compound, kills S. aureus cells within 30 min, but an increase in both biofilm formation and persister cells occurs. SK-03-92 treatment downregulates transcription of the biofilm regulating protein regulator (brpR) gene and biofilm regulating protein sensor (brpS) gene in S. aureus. BrpR/BrpS system may be a LytTR regulatory system tied to biofilm formation, creation of persister cells, and late-stage competence in S. aureus. The aim of this study was to determine what biofilm, late-stage competence, and persister-associated genes were regulated in a brpR mutant compared to wild-type strains. Methods: In this study, involvement of BrpR in regulating other genes was assessed by comparing transcriptional changes in a brpR mutant strain to the S. aureus parent strain via RNA sequencing (RNA-Seq). Bioinformatic analysis was then performed on the RNA-Seq data to assess what biochemical pathways might be involved. Results: From these analyses, 440 genes were identified that had significant differences in transcript abundance when comparing the brpR mutant to wild-type strains. Quantitative reverse transcription polymerase chain reaction analysis confirmed bacA, icd, metE, and pdhA transcript levels were lower, whereas alr and mraY were higher in the brpR mutant versus wild-type strain. Furthermore, an enzymatic assay targeting NADH production from the pyruvate dehydrogenase complex showed lower levels in the mutant compared to wild-type strain. Conclusions: Overall, the study demonstrated several biosynthetic pathways tied to biofilm formation and late-stage competency may be regulated by BrpR and some potential leads for the mechanism of action of the SK-03-92 drug were uncovered.

ABSTRACT Background Bile acid (BA) malabsorption (BAM) is a common cause of chronic diarrhoea and may occur in some patients due to abnormalities of the gut microbiota. Effects of probiotics on faecal secretory BAs, particularly the primary BA, chenodeoxycholic acid, are unclear. Aim/Methods We conducted a randomized, double‐blind, placebo‐controlled trial of the De Simone formulation 8‐strain probiotic in 24 patients previously diagnosed with BAM. Patients were randomized to 3 weeks of the probiotic (900 billion bacteria) or placebo (maltose), both administered three times daily. Symptoms, serum 7 α C4, faecal primary BAs, intestinal permeability by 13 C‐mannitol‐lactulose test (0.1 and 1 g of the sugars respectively) over 24 h, faecal short chain fatty acids (SCFA), microbiome, and metabolome were assessed at baseline and post‐intervention. Results Data from 22 patients were included. Probiotic supplementation was associated with a significant decrease in % faecal primary BAs (chenodeoxycholic acid and cholic acid) with median change from baseline −5.7 [IQR −10.3, 0.9]% compared to 9.8 [IQR 0.2, 20.6]% on placebo ( p = 0.012). The faecal microbiome was significantly different in the probiotic group after intervention, driven by probiotic‐specific species. There were no significant differences in symptoms, intestinal permeability, or SCFA. However, there was a numerical difference in the changes from baseline in 0‐2 h 13 C‐mannitol excretion −1.9 [−13.9, 4.2] mg for the probiotic and 1.0 (−0.5, 12.7) mg for placebo ( p = 0.084). Conclusions The De Simone formulation probiotic induced significant microbiome and metabolome changes in patients with BAM, ultimately leading to a decrease in % faecal primary BAs and possible reduction in intestinal permeability. Clinical Trials.gov registration NCT #06609148, January 2, 2025.

Objective: To test the effect of physical activity on the gut microbiome and circulating short chain fatty acids among sedentary overweight/obese adults with prediabetes. We hypothesized that randomization to increased physical activity would result in gut microbiome changes. Methods: \We randomized 77 adults with prediabetes and a sedentary lifestyle into one of two groups: 1) Intervention Group: Invited to engage in home-based moderate intensity walking 3x/week for 30 minutes/session in weeks 1-4 and for 45 minutes/session during weeks 5-8 of the 8-week intervention; or 2) Control Group: Maintained habitual physical activity levels. We performed metagenomic sequencing from stool collected at baseline, week 4, and week 8, with short-chain fatty acids (SCFA) measured from serum collected at baseline and week 8. Taxonomic and functional profiling were performed on the metagenomic reads; alpha diversity metrics were subsequently derived. Linear regression assessed the difference in change between the intervention and control groups for alpha-diversity and SCFA levels. Results: We screened 1,533 participants for eligibility and consented 132. Of these, 87 entered the run-in phase and 77 were randomized. Participants were 51.4±8.9 years old, 87.7% female, and 74% non-Hispanic White. Mean fasting glucose was 103.3±13.2 while mean BMI was 34.4±5.7. In comparison to the control group, the intervention group experienced decreased alpha diversity as characterized by Shannon, Richness, and Faith’s diversity indices by week 8 of the intervention (P<0.05). SCFA levels trended towards improvement in the intervention group, but the results were not statistically significant. Functional analysis of KEGG ontologies revealed themes consistent with a microbiome with enhanced metabolic activity and host-relevant metabolic signaling (Figure). Conclusions: Randomization to a walking intervention resulted in modest gut microbiome changes among adults with overweight/obesity and prediabetes.

OBJECTIVE To test the effect of physical activity on the gut microbiome and circulating short-chain fatty acids (SCFAs) among sedentary adults with prediabetes and overweight or obesity. RESEARCH DESIGN AND METHODS In a pilot and feasibility trial, we randomized 77 adults with prediabetes and a sedentary lifestyle into one of two groups: 1) intervention: invited to engage in home-based moderate-intensity walking 3×/week for 30 min/session in weeks 1–4 and for 45 min/session during weeks 5–8 of the 8-week intervention; or 2) control: maintained habitual physical activity levels. We performed metagenomic sequencing from stool collected at baseline, week 4, and week 8, with SCFAs measured from serum collected at baseline and week 8. Taxonomic and functional profiling was performed on the metagenomic reads; α-diversity metrics were subsequently derived. Linear regression assessed the difference in change between the intervention and control groups for α-diversity and SCFA levels. RESULTS We screened 1,533 participants for eligibility and consented 132. Of these, 87 entered the run-in phase, and 77 were randomized. Participants were mean (SD) 51.4 (8.9) years old, 87.7% female, and 74% non-Hispanic White. Mean fasting glucose was 103.3 (13.2) mg/dL, while mean BMI was 34.4 (5.7) kg/m2. Compared with the control group, the intervention group experienced decreased α-diversity as characterized by Shannon, Richness, and Faith diversity indices by intervention week 8 (P &lt; 0.05). Changes in SCFA levels were not statistically significant different in intervention versus control. CONCLUSIONS Randomization to a walking intervention resulted in modest gut microbiome changes among adults with overweight or obesity and prediabetes.

(1) Background: Mammographic breast density (MBD) is a well-established predictor of breast cancer risk, yet the biological mechanisms underlying this association remain incompletely understood. MBD is characterized by alterations in breast stromal architecture, including increased collagen deposition and changes in immune cell composition. Given emerging evidence that the breast harbors a resident microbiome, we investigated whether the breast tissue microbiome correlates with MBD. (2) Methods: Adjacent normal breast tissue was collected under sterile conditions from 33 women undergoing surgery for benign or malignant breast disease. DNA was extracted and subjected to 16S rRNA gene sequencing (Illumina MiSeq). (3) Results: We observed a non-significant trend toward lower α-diversity in high-MBD samples compared to low-MBD samples, p = 0.13. β-Diversity analyses identified a modest association between MBD and microbial community composition (MiRKAT p = 0.049). A random forest-based model incorporating genus-level relative abundances improved prediction of MBD over clinical characteristics alone, identifying Corynebacterium (Actinobacteria) and other genera as key predictors. (4) Conclusions: Breast tissue microbial features vary with mammographic breast density, suggesting a potential association with density-associated breast cancer risk. These exploratory findings warrant validation in larger cohorts to better elucidate biological mechanisms and clinical relevance.

ABSTRACT Aims To investigate whether the association between the nitrite‐generating capacity of the subgingival microbiome and early cardiometabolic risk biomarkers varies by dietary nitrate intake. Materials and Methods Cross‐sectional data from 668 participants (mean age 31 ± 9 years, 73% women) were analysed. Dietary nitrate intake was calculated from food frequency questionnaires. Subgingival 16S rRNA sequencing (Illumina, MiSeq) and PICRUSt2 estimated microbial genes. The Microbiome‐Induced Nitric Oxide Enrichment Score (MINES) was calculated as a ratio of microbial gene abundances representing enhanced net capacity for NO generation. Adjusted multivariable linear models regressed cardiometabolic risk biomarkers (HbA1c, glucose, insulin, insulin resistance (HOMA‐IR), blood pressure) on nitrate intake and MINES together with a MINES × nitrate intake interaction term. Results Mean nitrate intake was 190 ± 171 mg/day. Significant interactions of MINES and nitrate intake were observed for insulin and HOMA‐IR ( p < 0.05). Among participants with a low MINES, higher nitrate intake was associated with lower HOMA‐IR (1.2 [1.1–1.4] vs. 1.5 [1.3–1.6]; p = 0.002), but levels were similar in those with high MINES ( p = 0.84). Conclusions A biomarker of higher microbial NO‐generating capacity in subgingival plaque is associated with lower insulin and insulin resistance among individuals with lower dietary nitrate intake. Future trials evaluating the cardiometabolic benefits of nitrate‐rich diets should incorporate measures of the entire oral microbiome.

Three previously uncharacterized bacterial species, designated strains BD586 T , BD613 T and BD626 T , isolated from human clinical specimens, were identified at Mayo Clinic, Rochester, Minnesota, USA. Initial identification efforts using matrix-assisted laser desorption ionization-time-of-flight MS and partial 16S rRNA gene sequencing proved inconclusive. Comprehensive analysis involving phenotypic characterization, biochemical assays and whole-genome sequencing was undertaken. The isolates were Gram-negative, motile, facultatively anaerobic rods, occurring singly, in pairs and in short chains; BD613 T additionally formed small aggregates. The isolates tested positive for catalase and negative for oxidase. Their colonies appeared smooth, white, opaque and non-haemolytic. Growth was observed at 35 °C under aerobic, anaerobic and CO₂-enriched conditions, as well as in media with NaCl concentrations up to 10% and at pH 7-9. Phylogenetic relationships were inferred from core gene alignments, average nucleotide identity and digital DNA–DNA hybridization comparisons. Results confirmed the placement of BD586 T , BD613 T and BD626 T within the recently established Dryocola genus, while also indicating their novelty as distinct species. The major cellular fatty acids were C 16:0 and C 17:0 cyclo. Based on these findings, a formal description of three new species, Dryocola mayonis sp. nov. (type strain BD586 T =TSD 474 T , =NCTC 15089 T , =DSM 119465 T ), Dryocola sharpae sp. nov. (type strain BD613 T =TSD 475 T , =NCTC 15090 T , =DSM 119466 T ) and Dryocola baronae sp. nov. (type strain BD626 T =TSD 476 T , =NCTC 15091 T , =DSM 119479 T ), is proposed, and the genus description of Dryocola is emended to refine its genomic, morphological and chemotaxonomic boundaries.

ABSTRACTIntroduction/AimsMuscle cramps are a common symptom in amyotrophic lateral sclerosis (ALS). Ameliorating muscle cramps may improve quality of life in devastating diseases like ALS. A traditional Japanese medicine (Kampo, TJ‐68) is widely prescribed in Japan for muscle cramps. However, it is not available in the USA. This study evaluated the safety, tolerability, and efficacy of TJ‐68 in ALS.MethodsThis study was a double‐blind, randomized, placebo‐controlled crossover trial, consisting of four periods, conducted at three centers in the USA. Safety was evaluated using multiple measures. The primary efficacy outcome was the Visual Analog Scale for Muscle Cramps Affecting Overall Daily Activity (item #5 of the Muscle Cramp Scale (MCS)). The secondary outcomes included the remaining items of the MCS and the Clinical Global Impression of Changes (CGIC), among others. The study was planned to enroll 22 participants with ALS within 2 years.ResultsThe enrollment was slow and was completed with 11 participants. There were no serious safety issues and TJ‐68 was well tolerated. Although the primary outcome measure did not reach statistical significance (p = 0.35), several secondary measures showed significant results: MCS #1 triggering of cramps (p = 0.01), MCS #2 cramp frequency (p = 0.03), MCS Additional 1 change of motor behaviors (p = 0.02), and CGIC assessed by the evaluator (p = 0.009). Other outcome measures did not reach statistical significance.DiscussionThe study revealed that N‐of‐1 trial design can detect changes in a small sample size, and TJ‐68 appeared to be safe. Larger studies are needed to confirm the efficacy of TJ‐68.

Abstract Breast cancer is the leading cause of cancer death among women worldwide. Most cases occur in those without identifiable modifiable risk factors, highlighting critical gaps in our understanding of breast cancer biology including the influence of the gut microbiome. Here we studied the gut microbiome with shallow shotgun metagenomic sequencing from preoperative stool samples in a well-characterized clinical cohort of 131 women, median age 59 years, undergoing breast-conserving surgery for benign (n=23), high-risk (n=47), or malignant (n=61) breast disease. Taxonomic profiling was performed with Sourmasth 4.2.4 with GTDBv202 as reference database; functional profiling of metagenomic data employed HUMAnN 3.6 with identified gene families mapped to MetaCyc pathways. Differences in alpha diversity in terms of species richness were observed across diagnosis groups (benign, high-risk, malignant) and was lowest for high-risk lesions (p=0.031). Decreased alpha diversity was also associated with higher body mass index (BMI) (Shannon p=0.12, Inverse Simpson p=0.025). Significant beta diversity differences across diagnosis groups also were seen (Bray-Curtis p=0.044, Jaccard p=0.013) as were differences in association with BMI (Bray-Curtis, Jaccard, both p=0.002). No significant diversity differences associated with age, mammographic breast density or menopausal status were observed. Functional pathway profiling stratified by BMI showed a correlation between increasing BMI and greater relative abundance of genes in nicotinamide adenine dinucleotide (NAD) biosynthesis, folate metabolism, and aromatic amino acid metabolism pathways (p=0.0279, 0.0667 and 0.0860, respectively) - pathways implicated in breast cancer detection, survival and prognosis. Cross-referencing our significantly (FDR &lt;5%) differentially abundant taxonomic findings with these functional pathway data identified enrichment of several Blautia species, linked to NAD biosynthesis via tryptophan metabolism, in patients with higher BMI. We also noted enrichment of Dorea formicigenerans, a species associated with increased breast cancer risk in obese women due to its pro-inflammatory effects, in individuals with a higher BMI. Here we report significant differences in gut microbiome diversity, taxonomy and functional pathway signals in association with BMI in women with breast disease. Differentially abundant species seen with rising BMI may contribute to functional pathways that drive increased breast cancer risk and may provide an actionable target for risk reduction independent of conventional risk reduction strategies. Citation Format: Jack W. Sample, Matteo Redaelli, Stephen Johnson, Tanya L. Hoskin, Marina R. Walther-Antonio, Jun Chen, Tina J. Hieken. Obesity alters cancer-related microbial pathways in women with benign and malignant breast disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2213.