@article {pmid42238434,
year = {2026},
author = {Basson, AR and Katz, J and Nguyen, V and Singh, D and Menghini, P and Gomez-Nguyen, A and Sieg, J and Bell, M and Thamma, K and Ponzani, G and Osme, A and Rodriguez-Palacios, A and Cominelli, F},
title = {A Randomized Controlled Trial Comparing Soy-Pea Protein to Animal Protein in Adults with Crohn's Disease.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.20.26353678},
pmid = {42238434},
abstract = {BACKGROUND AND AIMS: Diet plays a critical role in managing Crohn's disease (CD) inflammation. We assessed whether dietary replacement of animal protein (AnimalP) by soy-pea protein (SoyP) decreases the pro-inflammatory potential of gut microbiota and intestinal inflammation in CD patients.

DESIGN: In an open-label, randomized controlled feeding trial at University Hospitals Cleveland Medical Center, CD participants and healthy controls were randomized (1:1) to a soy-pea or animal protein diet for 7-days. Primary outcomes were the absolute difference (Δd7-d0) in; Crohn's Disease Activity Index (CDAI) score and fecal myeloperoxidase (MPO). Secondary outcomes included fecal calprotectin (FC) and high-sensitivity C-reactive protein (hsCRP). Murine fecal transplantation experiments were performed to determine the inflammatory potential of diet-altered gut microbiota.

RESULTS: The study randomized 66 participants, of whom 60 were included in the final analysis (n=31 CD, n=29 HC). After 7 days, CD participants assigned to the SoyP diet were more likely than those assigned to the AnimalP diet to demonstrate reductions in fecal MPO (RR=2.30, 95% CI: 1.04-4.85, P=0.032) and HBI (RR=4.68, 95% CI: 1.22-17.98, P=0.009). The association between SoyP and reduced fecal MPO remained significant after Bonferroni adjustment (FWER-adjusted P=0.006). A similar directional trend was observed for CDAI (RR=1.52, 95% CI: 0.89-2.58, P=0.135), although this did not reach statistical significance. No participants experienced worsening of CDAI. The exploratory post hoc rank-based CDAI-MPO composite score was lower in the CD-SoyP versus CD-AnimalP group (median [IQR]: 5 [4-6] vs 8 [7-9]; P=0.012). Stratified analyses demonstrated significant reductions in fecal MPO among CD participants with lower baseline disease activity (CDAI <150; P<0.0001), but not among those with higher disease activity (P=0.799).

CONCLUSION: Short-term addition of plant-based soy-pea protein within a controlled diet was associated with reductions in objective inflammatory markers in CD, with evidence of greater effects among participants with lower baseline disease activity. ClinicalTrials.gov, Number NCT04065048.},
}

@article {pmid42358320,
year = {2026},
author = {Banchi, P and Mila, H and Selma-Royo, M and Tal, S and Péron, F and Gaillard, V},
title = {Correction: The perinatal microbiota in dogs and cats: a narrative review from human research to veterinary practice.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1866749},
doi = {10.3389/fvets.2026.1866749},
pmid = {42358320},
issn = {2297-1769},
abstract = {[This corrects the article DOI: 10.3389/fvets.2026.1817504.].},
}

@article {pmid42358325,
year = {2026},
author = {de Souza, RBMDS and Fernandes, EL and Santos, LNA and da Silva Lima, L and Silva, HL and de Oliveira, SG and Félix, AP},
title = {Effects of a single-cell protein source from Paecilomyces variotii on diet digestibility and palatability and intestinal functionality of adult dogs.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1787800},
pmid = {42358325},
issn = {2297-1769},
abstract = {INTRODUCTION: This study aimed to evaluate the effects of a single-cell protein (SCP) source from Paecilomyces variotii on the apparent total tract digestibility (ATTD) of macronutrients and energy, diet palatability, fecal fermentative metabolites, and microbiota in dogs.

MATERIALS AND METHODS: Five extruded diets containing 0, 4, 8, 12, and 16% of SCP were manufactured. To isolate the metabolizable energy (ME) and the ATTD of the SCP, an additional test diet was manufactured containing 80% of the 0% diet and 20% of SCP. In Experiment I, 15 adult Beagle dogs were distributed in a randomized block design with 5 diets (0 to 16% SCP) and two periods of 21 days each, totaling 6 repetitions/treatment. In Experiment II, for the palatability test, 16 adult dogs were used, comparing the diets: 0 vs. 4% SCP; 0% vs. 8% SCP; and 4% vs. 16% SCP. In Experiment III, the SCP digestibility was estimated by the substitution method with 12 adult Beagle dogs.

RESULTS: The SCP presented ATTD of dry matter (DM) = 64.3%; ATTD of crude protein = 83.9%; ATTD of acid-hydrolyzed ether extract = 78.3%; and ME of 3843.3 kcal/kg. The ATTD of DM, organic matter, gross energy and the ME of the diets decreased linearly as the dietary inclusion of SCP increased (0 to 16% SCP; p < 0.05). There was a quadratic effect in fecal concentrations of propionate, butyrate, and total short-chain fatty acids, and a linear increase in isobutyrate and total branched-chain fatty acids, with the dietary inclusion of SCP (p < 0.05). Animals fed the 8% SCP diet presented an increase in alpha-diversity indexes (p < 0.05). Dogs fed the 4% SCP diet presented higher fecal abundance of Lactobacillus and Limosilactobacillus, when compared to the 0% group (p < 0.05). Besides, a higher fecal abundance of Lactobacillus and Butyricicoccus and lower abundance of Enterococcus, and Enterocloster was observed in dogs fed the 8% SCP diet compared to the 0% group (p < 0.05).

CONCLUSION: These results demonstrate that the dietary inclusion of 4 and 8% SCP promotes less impact on diet digestibility and may beneficially modulate the fecal microbiome and its metabolites in dogs, without affecting diet palatability.},
}

@article {pmid42358347,
year = {2026},
author = {Fang, X and Wang, M and Yalikun, K and Luo, X and Jiang, X and Nasser, MI and Liu, C and Pu, L},
title = {Relationship between oral microbiota and chronic kidney disease: facts and perspectives.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2687208},
pmid = {42358347},
issn = {2000-2297},
abstract = {BACKGROUND: The human microbiome comprises the microorganisms inhabiting the body, with the oral cavity representing the second most densely colonized site after the colon. Periodontal disease-associated oral bacteria are more common in patients with kidney disorders than in the general population. Oral dysbiosis disrupts host-microbiota homeostasis and promotes destructive periodontal inflammation, which has been linked to chronic kidney disease (CKD). However, current interventional evidence, including randomized controlled trials, remains limited by small sample sizes, short follow-up, heterogeneous periodontal interventions, inconsistent renal endpoints, limited blinding, and inadequate adjustment for confounders such as smoking, glycemic control, and medication use. Thus, causality between oral microbiota modulation and CKD progression remains unproven.

METHODS: This review synthesizes current evidence on the mechanisms by which oral microbiota influence various forms of nephropathy, with a particular focus on the impact of periodontitis (PD) on the progression of renal disease.This review summarizes evidence on mechanisms by which oral microbiota and periodontitis may contribute to nephropathy and renal disease progression.

RESULTS: Oral dysbiosis may affect CKD through systemic inflammation, endothelial dysfunction, and oxidative stress. It may also promote abnormal IgA1 glycosylation in IgA nephropathy and contribute to immune dysregulation and persistent inflammation in glomerulonephritis.

CONCLUSION: Periodontitis-associated oral dysbiosis may contribute to renal disease pathogenesis and progression. Clarifying these mechanisms could support preventive and therapeutic strategies for patients with nephropathy.},
}

@article {pmid42358426,
year = {2026},
author = {Mishra, AK and Tiwari, S},
title = {Topic: boron toxicity in semi-arid crops: the overlooked metalloid in abiotic stress.},
journal = {Physiology and molecular biology of plants : an international journal of functional plant biology},
volume = {32},
number = {6},
pages = {1325-1349},
pmid = {42358426},
issn = {0971-5894},
abstract = {Boron (B) is an essential micronutrient, yet its excess induces phytotoxicity, especially in semi-arid and alkaline soils, severely constraining crop productivity. This review delineates the physiological, biochemical, and molecular responses of plants to B toxicity, highlighting oxidative stress, membrane disruption, metabolic imbalance, and photosynthetic impairment as primary consequences. Multi-omics studies, including transcriptomics, proteomics, and metabolomics, have identified key components of B tolerance, such as BOR and NIP transporters, antioxidant enzymes, and stress-inducible proteins. Proteomic investigations reveal tissue-specific responses, with the upregulation of detoxification proteins, SA-dependent defence proteins, and transcriptional regulators like RING1B, which is also implicated in stem cell maintenance. Emerging evidence underscores the role of epigenetic modifications, DNA methylation, and histone acetylation in modulating B-responsive gene expression. However, the absence of high-resolution spatial mapping of B toxicity zones and limited access to high-throughput phenotyping platforms hinder progress in breeding resilient genotypes. Additionally, the interplay between B toxicity and climate change remains underexplored, despite its likely influence on B solubility and plant uptake. Advancements in nanotechnology and microbiome engineering present novel strategies for mitigation, including nano-sensors for real-time B detection, nano-formulations for controlled delivery, and beneficial microbes for enhancing plant tolerance. Integrating these tools with precision breeding and systems biology offers a sustainable framework to counteract B toxicity. This review advocates for a transdisciplinary approach combining spatial analytics, molecular insights, and ecological resilience to manage B toxicity and ensure long-term agricultural sustainability.},
}

@article {pmid42358480,
year = {2026},
author = {Flores, GD and Damon, ZF and Ford, M and Gancz, NN and Savoca, PW and Esfand, SM and Chu, KA and Querdasi, FR and McCann, CF and Westman, JG and Labus, JS and Clewett, D and Parr, AC and Hsiao, EY and Jacobs, J and Silvers, J and Callaghan, BL},
title = {A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.},
journal = {Brain, behavior, & immunity - health},
volume = {55},
number = {},
pages = {101275},
pmid = {42358480},
issn = {2666-3546},
abstract = {Caregiving-related early adversities (crEAs) are potent risk factors for the development of internalizing psychopathology (e.g., depression, anxiety). Alterations to the dopaminergic mesocorticolimbic system, which supports the construction of reward-related experiences, are commonly observed following crEA exposure and are thought to mediate this risk. Indeed, many internalizing disorders are characterized by disruptions in how reward-related information is represented and used to guide affective and motivational states. Critically, the effects of crEA on mesocorticolimbic functioning may be shaped by input from peripheral systems, such as the gut microbiome, though such bottom-up signaling has been markedly understudied in humans. The Teen Bugs study was thus developed to identify gut microbiome-dependent metabolic pathways linking crEA exposure to mesocorticolimbic functioning and internalizing symptoms in adolescents, a group that experiences a disproportionate incidence of psychopathology relative to other age groups and is underrepresented in the gut microbiome literature. Adolescents aged 12-15 years, with and without histories of crEA exposure, will be followed across three timepoints over five years. At each timepoint, participants will complete a semi-structured clinical interview, a reward-guided decision-making task, and self-report questionnaires assessing mental health, previous caregiving experiences, reward-related behaviors, as well as developmental and lifestyle factors. Participants will also undergo multimodal neuroimaging that leverages MRI-based proxy markers of dopaminergic neurobiology and provide stool and blood samples for metagenomic and metabolomic profiling, respectively. This integrative design has the potential to clarify developmentally salient mechanisms that may serve as novel therapeutic targets for youth most at risk of, or already experiencing, internalizing psychopathology.},
}

@article {pmid42358596,
year = {2026},
author = {Kent, J and Chao, J and Liao, W and Singla, S},
title = {Exploring the Gut Microbiome's Association in Psoriasis and Psoriatic Arthritis: A Scoping Review.},
journal = {Journal of psoriasis and psoriatic arthritis},
volume = {},
number = {},
pages = {24755303261464171},
pmid = {42358596},
issn = {2475-5311},
abstract = {INTRODUCTION: Psoriasis (PsO) and psoriatic arthritis (PsA) are chronic inflammatory conditions treated with primarily immune-modulating medication. However, interest is growing in gut microbiome therapies. Studies have reported altered gut microbiota in PsO/PsA and explored probiotics and fecal microbiota transplantation (FMT) as potential therapies. This review synthesizes global studies on the microbiome's associations in PsO/PsA.

METHODS: We conducted a scoping literature review to understand the association between gut microbiota in PsO and PsA patients. Pubmed was used to identify 4,126 published manuscripts between 2015-2025. Thirty studies were included, encompassing 749,275 participants, with balanced gender representation and ages ranging from 18 to 76 years. These studies included 21 case-control studies, 1 case-series, 2 genome-wide analyses, 5 clinical trials, and 1 retrospective review.

RESULTS: Eighteen studies reported significant gut microbiome differences in PsO/PsA vs healthy controls. Variation in the Firmicutes/Bacteroides (F/B) ratio was of interest, with one study suggesting a low F/B ratio and five studies suggesting an elevated F/B ratio in PsO. A higher F/B ratio was linked to increased acetate production. Acetate and propionate, key short-chain fatty acids (SCFAs), were associated with modulation of the IL-23/Th17 axis in psoriasis and activation of keratinocytes. The role of therapeutics targeting the gut microbiome was explored. Ustekinumab and tofacitinib altered gut microbiome composition. Probiotic and FMT interventions showed mixed outcomes. Six of eight probiotic studies reported increased SCFA producing species and/or reduced inflammatory markers. FMT improved immune markers in mice but had no significant benefit in human trials.

CONCLUSION: Alterations in the microbiome linked to inflammation and immune response, suggest the microbiome as a potential therapeutic target for PsO/PsA.},
}

@article {pmid42358748,
year = {2026},
author = {Shah, SAUR and Tang, B and He, D and Ahmad, M and Nabi, G and Wang, C and Fan, F and Zheng, J and Wang, K and Hao, Y},
title = {Sex and social group altered the gut microbiome and fecal metabolome in the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis).},
journal = {Current zoology},
volume = {72},
number = {3},
pages = {395-408},
pmid = {42358748},
issn = {1674-5507},
abstract = {Factors like sex, diet changes, hormone levels, and stressors disrupt animals' symbiotic bacterial communities. Maintaining healthy bacterial communities is particularly challenging for social species, as group membership, social relationships, microbial transfer, and social stressors influence their microbiotas. This study investigated the influence of sex and social dynamics on the gut microbiome and associated metabolites in the captive Yangtze finless porpoise (YFP), employing 16S rRNA gene sequencing and ultra-high-performance liquid chromatography with tandem mass spectrometry-based metabolomic analyses. The present study reveals that sex and social grouping, that is, male-male (MM), female-female (FF), and male-female (MF) groups, significantly influence the alpha and beta diversity in the captive YFP. The phylum Firmicutes were increased considerably in the FF social group, while Proteobacteria, Cyanobacteria, and Fusobacteriota were significantly increased in the MM group, while Desulfobacterota were risen considerably in the MF group. The genera Macrococcus, Clostridium_sensu_stricto_13, and Cetobacterium were considerably raised in the MM group, Paeniclostridium and Turicibacter were substantially raised in the FF group, while the genus Peptostreptococcaceae were substantially raised in the MF group. The current research also presented significant metabolite variations in the sex and social groups which significantly altered the metabolic pathways such as bile secretion, glycerophospholipid metabolism, protein digestion and absorption, citrate cycle, and carbohydrate digestion in the captive YFPs. Additionally, the research identified a significant correlation between the gut microbiome and fecal metabolome across different sex and social groups. In conclusion, this research highlights the connection between changes in fecal microbiota and host metabolism in captive YFP. It shows how sex and social group dynamics affect both metabolic and bacterial variations, offering valuable insights for improving health and social welfare management in captive YFPs.},
}

@article {pmid42358754,
year = {2026},
author = {Liu, C and Wu, Z and Li, D and He, J and Li, G and Wei, F},
title = {Disentangling host identity and storage time effects on gut microbiota composition in captive migratory birds using absolute and relative quantification.},
journal = {Current zoology},
volume = {72},
number = {3},
pages = {441-450},
pmid = {42358754},
issn = {1674-5507},
abstract = {Understanding how gut microbiota support migratory birds is essential; yet, fecal sample freshness is often a challenge, particularly for rare species that cannot be captured directly. Here, we collected fecal samples from multiple captive migratory bird species at Nanchang Zoo and grouped them by post-defecation time (0, 1, 2, and 4 h). Using both relative and absolute quantification, we assessed the effects of host identity, short-term storage, and their interaction on gut microbiota composition. Species identity and quantification method significantly shaped microbiota profiles. Absolute quantification revealed Firmicutes (763,405.73 copies/μL) and Proteobacteria (340,231.03 copies/μL) as dominant in Grey-crowned Cranes, whereas relative quantification indicated Firmicutes (96.74%) predominated in Swan Geese and Proteobacteria (30.30%) in Black-necked Cranes. Red-crowned Cranes showed higher species richness than Black Swans and Swan Geese, with a significantly greater Shannon index than the latter. PCoA demonstrated clear interspecific differences, especially between crane and waterfowl lineages. Storage time had no significant effects on alpha and beta diversity across 6 species, except for reduced richness in Swan Geese at 2 and 4 h. While overall community structure was stable, a few conditionally rare taxa displayed time-sensitive shifts shortly after defecation. Our findings highlight that both host identity and quantification approach are critical determinants of avian gut microbiota profiles and emphasize that fecal sample freshness mainly affects rare taxa. This study provides methodological insights for optimizing fecal sampling protocols in field-based microbiome research on migratory birds.},
}

@article {pmid42358885,
year = {2026},
author = {Benites-Goñi, H and Cabrera, D and Mauricio-Vilchez, C and Munive-Degregori, A and Espinoza-Carhuancho, F and Mayta-Tovalino, F},
title = {A Scientometric Exploration of Helicobacter Pylori in Cancer Gastric: Impact, Trends, and Collaboration Dynamics.},
journal = {International journal of preventive medicine},
volume = {17},
number = {},
pages = {17},
pmid = {42358885},
issn = {2008-7802},
abstract = {BACKGROUND: Helicobacter pylori (Hp) has been widely linked to various gastric pathologies, including gastric cancer (GC). Understanding how scientific production in this area has been structured, developed, and impacted is key to guiding future research and clinical strategies. To scientometrically explore the oncological literature related to Hp and GC, evaluating its volume, impact, collaboration, and thematic evolution between 2019 and 2025.

METHODS: A descriptive scientometric study with an exploratory approach was conducted. The search was performed in Scopus on June 7, 2025, using the strategy with Boolean operators and broad terms related to Hp and GC. Documents published between January 2019 and June 2025 were selected. The analysis was performed using SciVal, Bibliometrix (R), and VOSviewer, exploring performance indicators, collaborative networks, and thematic evolution. The report was guided by the Reporting and Measurement of Items for Bibliometric or Scientometric Studies in Health Sciences (RAMIBS) guideline.

RESULTS: A total of 4573 documents discussed were obtained from 1445 sources. The number of documents obtained each year declined on average (-8.74%), with an average of 14.09 citations per document (high collaboration rate at 20%), with high impact authors (P. Malfertheiner, h-index 99, countries such as China, Japan, and United States), and the leading journals of Helicobacter and Gastroenterology for productivity and impact in the field. The amount of output was highly concentrated based upon Bradford's Law (46 core journals identified) and there was a strong bibliographic core (in co-citation), whilst thematic evolution showed that the focus of scholarship has evolved from virulence factors focused to integrative approaches around antimicrobial resistance, microbiome, and artificial intelligence.

CONCLUSIONS: The field of research on Hp and GC is an established and collaborative domain currently undergoing a methodological change. The study presents the roadmap that provides guidance for future scientific production and making editorial and clinical decisions.},
}

@article {pmid42358948,
year = {2026},
author = {Fu, J and Shan, J and Xu, H and Zhu, Z and Yang, P and Wang, Q and Han, J and Cao, G},
title = {Altered GABA and secondary bile acids in Guillain-Barré syndrome: association with gut dysbiosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1849216},
pmid = {42358948},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Guillain-Barre Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Bile Acids and Salts/metabolism/blood ; Male ; *gamma-Aminobutyric Acid/metabolism/blood ; Adult ; Middle Aged ; Metabolomics/methods ; Metabolome ; Metagenomics ; Feces/microbiology ; Aged ; },
abstract = {OBJECTIVE: Guillain-Barré syndrome (GBS) is a rare, immune-mediated inflammatory disease of the complex peripheral nervous system that often follows acute infections, and may also be associated with long-term 'silent infections'. Long-term "silent infections" can alter the gut microbiota, which in turn may contribute to immune-mediated inflammatory diseases. Emerging evidence suggests that gut dysbiosis and altered serum metabolites are associated with GBS, but the causative link between GBS and gut microbiota remains unclear. Therefore, this study aimed to evaluate the association between gut microbiota structure and serum metabolic profile in GBS.

METHODS: Untargeted metabolomics profiling of serum and metagenomics sequencing of stool samples were performed to capture the global metabolic and microbial differences between GBS subjects and healthy controls. Multivariate statistical analyses, including PLS-DA, were applied to identify distinct clustering patterns and differential abundances of metabolites and gut microbiota. Pearson's correlation analysis was used to estimate the correlations between abundance of gut microbiota and serum metabolic profile. Seven different media were used to isolate the potential pathogens from GBS stool samples.

RESULTS: The metabolome data revealed that gamma-aminobutyric acid (GABA) metabolism and secondary cholic acid metabolism were perturbed in GBS. Specifically, GABA was increased significantly (approximately 14.3-fold), while multiple secondary cholic acids (methyl deoxycholate, glycodeoxycholic acid, glycolithocholic acid, taurolithocholic acid, and coprocholic acid) were decreased significantly in GBS subjects. Regarding the gut microbiota identified via metagenomic sequencing of stool samples, Ligilactobacillus salivarius, Enterocloster bolteae, and the opportunistic pathogenic Klebsiella pneumonia were notably more abundant in GBS subjects, while Bacteroides sp., Roseburia hominis and Paraprevotella xylaniphila were decreased significantly. In addition, pathogens such as K. pneumoniae were also isolated from GBS subjects. Further analysis of the metagenomic data revealed enrichment of prokaryotic genes involved in the GABA biosynthesis pathway, while genes associated with secondary cholic acid metabolism pathways were decreased in gut microbiome in GBS subjects. On this basis, correlation analysis revealed that changes in GABA were associated with altered levels of gut microbes including Enterococcus species, Ligilactobacillus salivarius and Enterocloster bolteae, whereas changes in secondary cholic acids were positively correlated with altered levels of Bacteroides species and Roseburia species.

CONCLUSION: GABA metabolism and secondary cholic acid metabolism were significantly disturbed in GBS subjects, potentially resulting from the dysbiosis of the gut microbiota. K. pneumonia and other no gut microbes were significantly enriched and isolated in GBS and may contribute to the inflammatory response in this immune-mediated inflammatory disease. These findings also suggest that GABA may be a promising biomarker for the diagnosis of GBS and that modulation of gut microbiota might impact the clinical course of GBS.},
}

Humans
*Dysbiosis/microbiology/metabolism
*Guillain-Barre Syndrome/microbiology/metabolism/blood
*Gastrointestinal Microbiome
Female
*Bile Acids and Salts/metabolism/blood
Male
*gamma-Aminobutyric Acid/metabolism/blood
Adult
Middle Aged
Metabolomics/methods
Metabolome
Metagenomics
Feces/microbiology
Aged

@article {pmid42359004,
year = {2026},
author = {Bai, Z and Lin, X and Wang, B and Li, Z and Qu, X and Hou, Y},
title = {Periodontitis as a potential amplifier of diabetes-related genitourinary complications: evidence gradients and mechanistic insights into the inflammation-microvascular injury axis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1843576},
pmid = {42359004},
issn = {2235-2988},
mesh = {Humans ; *Periodontitis/complications ; *Inflammation ; *Diabetes Complications ; Diabetic Nephropathies ; Male ; *Diabetes Mellitus, Type 2/complications ; Urinary Tract Infections/etiology ; Erectile Dysfunction/etiology ; Oxidative Stress ; },
abstract = {Periodontitis is increasingly recognized as a chronic systemic inflammatory burden that may be associated with greater vulnerability to selected diabetes-related genitourinary complications through overlapping inflammatory and microvascular pathways. This review integrates current epidemiological, mechanistic, and clinical evidence and proposes a conceptual "oral-metabolic-genitourinary axis" to describe potential links between periodontal inflammation and diabetic kidney disease (DKD), diabetes-related erectile dysfunction (ED), and recurrent urinary tract infections (UTIs). Available evidence is strongest for renal endpoints: observational studies and recent cohort data suggest associations between periodontitis and albuminuria, renal function decline, or dialysis risk in patients with type 2 diabetes. In contrast, evidence for ED and recurrent UTIs remains limited, with much of the support derived from mechanistic inference and indirect clinical observations. The proposed biologically plausible pathways include amplification of chronic low-grade systemic inflammation, endothelial and microvascular dysfunction, oxidative stress, advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling, and microbiome interactions involving the oral-gut-genitourinary axis. These proposed associations and pathways may be modified or intensified by poor glycemic control, obesity, smoking, vitamin D deficiency, and gut dysbiosis. Clinically, periodontal therapy has been associated with improved glycemic control and may improve selected inflammatory or renal-related surrogate indicators, suggesting that oral health management could be considered a supportive component of multidisciplinary diabetes care. Overall, periodontitis is best viewed at present as a plausible amplifying factor rather than a confirmed independent cause of these outcomes, and this hypothesis requires confirmation in large prospective cohorts, randomized trials, and multi-omics studies.},
}

Humans
*Periodontitis/complications
*Inflammation
*Diabetes Complications
Diabetic Nephropathies
Male
*Diabetes Mellitus, Type 2/complications
Urinary Tract Infections/etiology
Erectile Dysfunction/etiology
Oxidative Stress

@article {pmid42359007,
year = {2026},
author = {Lu, J and Bi, S and Gao, Y and Zhang, Y and Zhang, T and Sun, M and He, M and Chen, X and Yang, B},
title = {Evaluation of electroacupuncture acupoint selection's potential in the treatment of inflammatory bowel disease: an investigation using a mouse gut microbiome and metabolomics model.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1830455},
pmid = {42359007},
issn = {2235-2988},
mesh = {Animals ; *Electroacupuncture/methods ; *Inflammatory Bowel Diseases/therapy/chemically induced/pathology ; *Acupuncture Points ; Disease Models, Animal ; Mice ; Metabolomics ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; Dextran Sulfate ; Colon/pathology ; Male ; Interleukin-1beta/metabolism ; Body Weight ; Interleukin-6/metabolism ; },
abstract = {Electroacupuncture (EA) serves as an effective complementary therapy in the treatment of inflammatory bowel disease (IBD) within traditional Chinese medicine, with the therapeutic efficacy significantly influenced by the selection of specific acupoints. However, the regulatory mechanisms by which certain acupoints exhibit therapeutic benefits in IBD remain poorly understood. The research project intends to explore the mechanisms of action and regulatory variations in the treatment of IBD by the points Dachangshu (BL25), Tianshu (ST25), and Shangjuxu (ST37). This study used a sodium dextran sulfate-induced IBD mouse model to assess the therapeutic efficacy of three acupoints by evaluating body weight, colon morphology, inflammatory cytokines, gut microbiota, and metabolites. The results indicate that electroacupuncture of these three acupoints did not significantly alter IL-1β levels, but all three acupoints reduced IL-6 levels, with the most significant reduction observed at the Dachangshu acupoint. Furthermore, electroacupuncture treatment improved the structural characteristics of intestinal tissue and slowed the rate of weight loss. In IBD mice, electroacupuncture of three acupoints was associated with significant alterations in the intestinal microbiota and metabolic pathways. The majority of the metabolic pathways involved by these three acupoints are related to lipid, amino acid, and energy metabolism. Additionally, different acupuncture stimulation points also exhibited their own unique metabolic characteristics. These findings provide preliminary correlative evidence for the clinical application of acupuncture point selection in the treatment of IBD.},
}

Animals
*Electroacupuncture/methods
*Inflammatory Bowel Diseases/therapy/chemically induced/pathology
*Acupuncture Points
Disease Models, Animal
Mice
Metabolomics
*Gastrointestinal Microbiome
Cytokines/metabolism
Dextran Sulfate
Colon/pathology
Male
Interleukin-1beta/metabolism
Body Weight
Interleukin-6/metabolism

@article {pmid42359371,
year = {2026},
author = {Zhang, K and Paul, KC and Jacobs, JP and Lin, Y and Kwon, D and Nianogo, R and Bronstein, JM and Keener, AM and Yu, Y and Folle, AD and Jones, DP and Ritz, B},
title = {Integration of the serum metabolome and gut microbiome underscores the importance of altered lipid metabolism and potential immune modulation in Parkinson's Disease.},
journal = {Brain disorders (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {},
pmid = {42359371},
issn = {2666-4593},
abstract = {INTRODUCTION: Single-omics studies have deepened our understanding of disease-related molecular processes, though integrated approaches are needed to uncover cross-system interactions. We previously reported changes in the serum metabolome and gut microbiome in Parkinson's disease (PD). To build on these findings, we conducted a multi-omics integration analysis to examine the interplay between the gut microbiome and human metabolism in PD.

METHODS: In a community-based study of 113 PD patients from rural California, microbiome profiles were obtained via 16S rRNA gene sequencing of fecal samples. Serum metabolomic profiles were generated using untargeted high-resolution LC-MS. Residual matrices of metabolomics data were extracted after adjusting for age, sex, racial minority status, and study wave. We identified PD-associated bacterial genera and summarized their abundance using principal component analysis. Using this summary score as the dependent variable, we performed partial least squares (PLS) regression to identify serum metabolites associated with the PD-related gut microbiome. Pathway enrichment analysis was then conducted on selected metabolite features from the PLS model.

RESULTS: We identified 266 metabolite features and annotated 29 metabolic compounds associated with PD-related microbes (p < 0.1). Enrichment analysis revealed perturbed pathways in lipid metabolism, including fatty acid activation and metabolism, linoleate metabolism, and glycerophospholipid metabolism, as well as carbohydrate metabolism such as hexose phosphorylation and starch/sucrose metabolism.

CONCLUSION: Our multi-omics integration analysis revealed that PD-associated gut microbiota are involved in host lipid metabolism, immune-related pathways, and potentially vitamin B-mediated regulation of kynurenine pathway metabolism, providing insights into potential microbiome-metabolome interactions in PD pathophysiology.},
}

@article {pmid42359619,
year = {2026},
author = {Chen, Z and Li, G and Tang, X and Liu, X},
title = {Cardiovascular Adverse Events Associated with Immune Checkpoint Inhibitors from the Perspective of Gut Microecology: Potential Roles and Research Advances of the Gut Microbiota.},
journal = {Journal of cardiovascular pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1097/FJC.0000000000001842},
pmid = {42359619},
issn = {1533-4023},
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized cancer immunotherapy by significantly improving the prognosis of patients with various malignancies. Despite their clinical benefits, ICIs are increasingly recognized for inducing cardiovascular adverse events (CVAEs), including severe toxicities such as myocarditis, which pose substantial challenges in oncology practice. Emerging evidence highlights the gut microbiota as a critical regulator of host immunity, potentially influencing the development and progression of ICI-associated cardiovascular toxicities. This review comprehensively examines the current understanding of the interplay between gut microbiota and ICI-associated CVAEs. We systematically analyze the incidence, pathophysiological mechanisms, diagnostic criteria, and prognosis of major cardiovascular toxicities linked to ICIs. Furthermore, we explore the immunomodulatory functions of the gut microbiome that may underlie these adverse events, emphasizing microbiota-mediated systemic immune dysregulation and cardiovascular-specific toxicity pathways. We also discuss future research directions and the clinical implications of integrating gut microbiota modulation into the management of ICI-associated cardiovascular complications. By synthesizing multidisciplinary insights, this review aims to provide a theoretical foundation and research framework to advance both basic and clinical studies in this emerging field.},
}

@article {pmid42359789,
year = {2026},
author = {Lakey, BD and Wozniak, KJ and Britton, RA and Tabor, JJ},
title = {Mucin-derived sugars act as metabolic brakes controlling growth initiation in Akkermansia muciniphila.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2691334},
pmid = {42359789},
issn = {1949-0984},
mesh = {*Mucins/metabolism/chemistry ; Animals ; Humans ; *Akkermansia/growth & development/metabolism ; Mice ; Gastrointestinal Microbiome ; Polysaccharides/metabolism ; *Dietary Sugars/metabolism ; Colon/microbiology ; Citric Acid Cycle ; *Verrucomicrobia/growth & development/metabolism ; },
abstract = {Akkermansia muciniphila is a key member of the gut microbiota and plays important roles in host metabolism and health. In the colon, A. muciniphila extracts nutrients from oligosaccharide-rich mucin glycans that comprise the mucosa. However, this environment is complex and shaped by dietary inputs, microbiome metabolism, and mucin glycan composition varying across hosts, gastrointestinal regions, and physiological states. How strains of A. muciniphila integrate these nutrient signals into growth initiation and niche colonization remains unclear. Here, we compare physiological responses of a human- and mouse-derived strain of A. muciniphila, finding that dietary sugars differentially affect these isolates, suggesting host-associated tuning of metabolic capacity. In contrast, several mucin-derived sugars impose a conserved, concentration-dependent delay in growth initiation, implicating the lag phase as a critical metabolic checkpoint for growth. Genetic suppressor analysis identified sugar kinases and a component of the tricarboxylic acid cycle as genetically encoded control points linking glycan sugar exposure to the energy balance required for growth. These findings demonstrate that mucin-derived sugars function as both nutrients and metabolic stressors, regulating growth initiation. We propose that A. muciniphila employs metabolic "brakes" to coordinate growth with mucin composition, putatively linking host glycan landscapes to microbial physiology and ecological fitness within the mucus layer.},
}

*Mucins/metabolism/chemistry
Animals
Humans
*Akkermansia/growth & development/metabolism
Mice
Gastrointestinal Microbiome
Polysaccharides/metabolism
*Dietary Sugars/metabolism
Colon/microbiology
Citric Acid Cycle
*Verrucomicrobia/growth & development/metabolism

@article {pmid42359815,
year = {2026},
author = {Delgado Ocaña, S and Herrera, G and Guzmán, D and Self, DW and Cuesta, S},
title = {Gut Proteobacteria glycine metabolism regulates neuroplasticity, motivation, and reinstatement of cocaine self-administration in mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2693397},
pmid = {42359815},
issn = {1949-0984},
mesh = {Animals ; Mice ; *Glycine/metabolism ; *Cocaine/administration & dosage/adverse effects ; Male ; Self Administration ; *Motivation ; Mice, Inbred C57BL ; *Proteobacteria/metabolism ; *Neuronal Plasticity ; *Gastrointestinal Microbiome ; Humans ; *Cocaine-Related Disorders/metabolism/microbiology ; Nucleus Accumbens/metabolism ; Escherichia coli/metabolism/genetics ; },
abstract = {Addiction is a chronic and relapsing disorder that affects millions of people worldwide; nonetheless, currently available FDA-approved treatments are limited in number and effectiveness. In past years, the gut-brain axis has emerged as a key modulatory factor associated with different psychiatric disorders, including addiction. Working in mice, we have shown that cocaine exposure alters the composition of the gut microbiome, increasing the abundance of Proteobacteria. This microbial shift, in turn, leads to a depletion in host glycine levels, altering cocaine-induced transcriptional changes in the Nucleus Accumbens (NAc) and facilitating the development of behavioral sensitization and conditioned place preference. Among the behavioral models to study psychostimulant use disorders, cocaine self-administration (SA) remains the most translational. Therefore, here we investigated whether Proteobacteria-induced glycine depletion can affect cocaine SA in mice. Using the human Escherichia coli HS and the glycine-uptake-deficient mutant E. coli HS ΔCycA, we build upon our previous findings and demonstrate that the ability of gut Proteobacteria to use glycine during cocaine SA shapes the trajectory and long-term neurobehavioral plasticity induced by the drug. Furthermore, we show that this bacterial-induced glycine depletion impacts the NAc proteome, altering its vulnerability to undergo molecular adaptations across different stages of the SA paradigm. Altogether, our findings show that the gut microbiome, and particularly the Proteobacteria phylum, is a crucial factor influencing short and long-term adaptation underlying motivation and cocaine-seeking behaviors.},
}

Animals
Mice
*Glycine/metabolism
*Cocaine/administration & dosage/adverse effects
Male
Self Administration
*Motivation
Mice, Inbred C57BL
*Proteobacteria/metabolism
*Neuronal Plasticity
*Gastrointestinal Microbiome
Humans
*Cocaine-Related Disorders/metabolism/microbiology
Nucleus Accumbens/metabolism
Escherichia coli/metabolism/genetics

@article {pmid42359986,
year = {2026},
author = {Wang, X and Meng, H and Yuan, B and Liu, D and Dong, Y and Zhang, F and Cao, H and Li, D and Yang, J and Sun, J and Wang, Y and Chen, B and Yan, J},
title = {Short-Chain Fatty Acids as Potential Mediators of NSAIDs' Effects on Arthritis Pain Relief.},
journal = {Pain research & management},
volume = {2026},
number = {1},
pages = {e9190926},
pmid = {42359986},
issn = {1918-1523},
support = {BJ2023052//The Grants of Top Talent Support Program for Young and Middle-Aged People of Wuxi Committee of Health/ ; 82370809//National Natural Science Foundation of China/ ; 32101033//National Natural Science Foundation of China/ ; BK20210060//Natural Science Foundation of Jiangsu Province/ ; K2023004//The Key Research Project of Health Commission of Jiangsu Province/ ; CXTD2021003//Key Discipline Construction Program of Wuxi Commission of Health/ ; K20253003//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research Program/ ; },
mesh = {Animals ; *Fatty Acids, Volatile/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/therapeutic use/pharmacology ; Male ; Rats ; Diclofenac/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Gastrointestinal Microbiome/drug effects ; Celecoxib/pharmacology/therapeutic use ; Tramadol/pharmacology/therapeutic use ; Disease Models, Animal ; *Osteoarthritis/drug therapy ; *Pain/drug therapy/etiology ; },
abstract = {BACKGROUND: Nonsteroidal anti-inflammatory drugs (NSAIDs) are the preeminent choice for treating osteoarthritis (OA) and have demonstrated the ability to regulate the gut microbiome. This study aims to explore the possibility that pharmacologically modified microbiome plays a role in improvement of arthritis.

METHOD: Rats with the right knee joint subjected to anterior cruciate ligament transection (ACLT) surgery were randomly allocated to eight groups. Four weeks after the procedure, the rats were given an intervention with saline (NS), celecoxib (CE), diclofenac (DF), and tramadol (TM). The rats were executed after 6 weeks of intervention, serum was used to evaluate the levels of inflammation and pain-related factors (IL-1β, IL-6, TNF-α, LPS, CGRP, and NGF), rat joints were used to assess local inflammation in the joints (MyD88) and the effect of the drug on the cartilage (Micro CT, Safranin O-Fast Green stain), Von Frey fibrous filaments were used to assess the sensation of pain in rats, and the differences in feces for the gut microbiome and short-chain fatty acids (SCFAs) were compared by 16S rRNA sequencing and gas chromatographic analyses.

RESULT: Rats treated with CE, DF, and TM experienced significant relief from joint pain, but the analgesic effect of CE and DF was significantly weakened after the combined application of antibiotics, while the effect of TM on pain remained after the application of antibiotics. The expression of MyD88 in the articular cartilage was somewhat reduced by CE and DF. Additionally, the gas analysis showed a significant increase in the SCFA content in the feces of the drug-intervention group.

CONCLUSION: NSAID-induced changes in gut microbiota structure and the subsequent increase in SCFA production may contribute to their pain-alleviating effects in rats. Although to a lesser extent, NSAIDs can also slightly reduce localized inflammation in the joints.},
}

Animals
*Fatty Acids, Volatile/metabolism
*Anti-Inflammatory Agents, Non-Steroidal/therapeutic use/pharmacology
Male
Rats
Diclofenac/pharmacology/therapeutic use
Rats, Sprague-Dawley
Gastrointestinal Microbiome/drug effects
Celecoxib/pharmacology/therapeutic use
Tramadol/pharmacology/therapeutic use
Disease Models, Animal
*Osteoarthritis/drug therapy
*Pain/drug therapy/etiology

@article {pmid42359989,
year = {2026},
author = {Oprea, OG and Balmus, IM and Ilie, T and Plavan, G and Nicoara, MN and Gorgan, L and Trifan, A and Stoica, B and Tamba, BI and Ciobica, A and Ciorpac, M},
title = {Natural products modulate social behavior and gut microbiota in a valproic acid-induced zebrafish model of autism spectrum disorder.},
journal = {Biomolecules & biomedicine},
volume = {},
number = {},
pages = {},
doi = {10.17305/bb.2026.14302},
pmid = {42359989},
issn = {2831-090X},
abstract = {Natural products rich in honey- and plant-derived bioactive compounds are increasingly investigated as modulators of the gut-brain-microbiome axis, a pathway implicated in autism spectrum disorder (ASD)-related behavioral and gastrointestinal alterations. This study evaluated whether two novel formulations, a honey-based product (API) and a plant extract-based product (MOD), modulate exploratory, anxiety-like, and social behavior and intestinal microbiota composition in an adult valproic acid (VPA)-induced zebrafish model of ASD. Adult wild-type zebrafish were assigned to control, VPA (300 μM), API (500 mg/L), MOD (500 mg/L), VPA+API, and VPA+MOD groups. Behavioral outcomes were assessed using the novel tank test and a T-maze social behavior test, while intestinal microbiota was profiled by 16S rRNA gene sequencing using an Oxford Nanopore platform. VPA exposure induced mild locomotor and anxiety-like behavioral alterations, whereas API and MOD further modified exploratory and social behavioral readouts in both healthy and VPA-treated zebrafish. Both formulations increased the time spent near the social stimulus; however, this finding should be interpreted cautiously because treatment-associated hypolocomotion and altered exploratory activity may influence T-maze performance. Microbiota profiling revealed a Pseudomonadota-dominated community across all groups, with descriptive treatment-associated shifts in secondary phyla and diversity patterns, particularly in combined VPA+API and VPA+MOD groups. However, no significant differences in alpha diversity, beta diversity, or genus-level abundance remained after multiple-testing correction. These findings suggest that API and MOD may modulate behavioral outcomes in adult zebrafish exposed to VPA, while their effects on gut microbiota remain exploratory and require validation in larger, adequately powered studies.},
}

@article {pmid42359998,
year = {2026},
author = {Boon, D and O'Rourke, B and Carmody, M and Woods, DF and Gloe, A and Platero-Rochart, D and Sánchez-Murcia, PA and McGlacken, GP and Reen, FJ},
title = {Coumarins Disrupt Cell-Cell Communication and Virulence in Priority Pathogens: Targeting the PQS Signalling System in Pseudomonas aeruginosa.},
journal = {Microbial biotechnology},
volume = {19},
number = {7},
pages = {e70404},
pmid = {42359998},
issn = {1751-7915},
support = {12/RC/2275_2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/IP/1315/SFI_/Science Foundation Ireland/Ireland ; 21/FFP-A/8784/SFI_/Science Foundation Ireland/Ireland ; SFI 15/RI/3221/SFI_/Science Foundation Ireland/Ireland ; 21/RI/9705/SFI_/Science Foundation Ireland/Ireland ; ILP-POR-2019-004/HRBI_/Health Research Board/Ireland ; GOIPG/2021/692//Irish Research Council for Science, Engineering and Technology/ ; //Medizinische Universität Graz/ ; },
mesh = {*Pseudomonas aeruginosa/drug effects/pathogenicity/physiology/metabolism/genetics ; *Quorum Sensing/drug effects ; *Coumarins/pharmacology/metabolism ; Virulence/drug effects ; *Signal Transduction/drug effects ; Biofilms/drug effects/growth & development ; *Quinolones/metabolism ; Pyocyanine/metabolism ; *Cell Communication/drug effects ; Umbelliferones/pharmacology/metabolism ; },
abstract = {Cell-to-cell communication in microbial systems is known for its vital role in cellular signalling and gene expression. A specific form termed Quorum Sensing (QS) has received considerable attention since its discovery in the marine symbiont Aliivibrio fischeri. QS-controlled microbial functions are associated with bacterial virulence, pathogenicity, host-microbe interactions, and biofilm development. Interference in these signalling systems can modulate microbial virulence and pathogenicity, and microbial infection caused by drug-resistant pathogens. Plant-derived phytochemicals are considered a promising candidate, with coumarins emerging as significant plant-derived signalling molecules shaping microbiome dynamics and pathogen behaviours from a broad spectrum of ecosystems. Here we explored the role of natural and synthetic coumarin compounds in the control of signalling and virulence traits in Pseudomonas aeruginosa and other priority bacterial pathogens, including the fungal opportunist Aspergillus fumigatus. We uncovered an important 'hydroxylation-bias' favouring coumarin, umbelliferone (7-OH), and 6-hydroxy-coumarin (6-OH) in the specific competitive inhibition of the Pseudomonas Quinolone Signal (PQS), associated with reduced activity of a PqsR translational fusion and suppression of pyocyanin production. Conversely, while esculetin (6,7-OH) was most effective at Acyl Homoserine Lactone (AHL) QS biosensor inhibition, it did not affect PQS production. Anti-biofilm activity of coumarins against P. aeruginosa was independent of initial attachment but linked to changes in exopolysaccharide production. As the very real threat posed by antimicrobial resistance persists, these data support a role for phytochemicals such as coumarins in delivering an ecological solution to dysbiosis in the host-microbe interaction.},
}

*Pseudomonas aeruginosa/drug effects/pathogenicity/physiology/metabolism/genetics
*Quorum Sensing/drug effects
*Coumarins/pharmacology/metabolism
Virulence/drug effects
*Signal Transduction/drug effects
Biofilms/drug effects/growth & development
*Quinolones/metabolism
Pyocyanine/metabolism
*Cell Communication/drug effects
Umbelliferones/pharmacology/metabolism

@article {pmid42360048,
year = {2026},
author = {Mauri, M and Unger, K and Gershenzon, J and Allen, RJ and Agler, MT},
title = {Bacterial degradation of a plant toxin and nutrient competition with commensals trade off to constrain pathogen growth.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0006426},
doi = {10.1128/msystems.00064-26},
pmid = {42360048},
issn = {2379-5077},
abstract = {Healthy plant leaves potentially host both commensal bacteria and opportunistic pathogens, which, under some circumstances, may cause disease. The interactions between commensals and opportunistic pathogens are generally poorly understood, but such understanding is crucial for developing effective biocontrol strategies. In Arabidopsis thaliana, isothiocyanates (ITCs) are defense metabolites that suppress most bacteria; commensals are especially affected as they do not express ITC resistance genes. The ITC hydrolase SaxA detoxifies ITCs, making it an important virulence factor for bacterial and fungal pathogens. To investigate pathogen-commensal interactions based on SaxA-mediated ITC degradation, we used five ITC-sensitive bacterial commensals and the opportunistic pathogen Pseudomonas viridiflava 3D9 (PS). All strains were isolated from healthy A. thaliana leaves. PS degrades 4-methylsulfinylbutyl-ITC (4MSOB-ITC) with SaxA. We examined commensal growth in the presence of 4MSOB-ITC, both in monoculture and in coculture with PS or a saxA-deficient mutant (PSKO). We used the growth data to develop a generalizable consumer-resource mathematical model incorporating ITC toxicity, ITC degradation, and nutrient use. We predicted and confirmed experimentally that the extent to which SaxA benefits the pathogen depends on its effects on commensals. In some contexts, commensal rescue and the resultant nutrient competition limit pathogen growth. In addition, we tested in silico how commensal ITC susceptibility, pathogen ITC degradation rates, and growth parameters affect the trade-off between SaxA-mediated virulence (strong pathogen growth) and commensal rescue (commensal growth). Our findings suggest that the effects of microbial traits-traditionally viewed as either virulence or plant-beneficial factors-are constrained in the microbiome context. This underscores the need to reconsider how such traits are classified in the context of plant-microbiome interactions.IMPORTANCEHealthy plant leaves host a variety of bacteria; these can be beneficial, but some (opportunistic pathogens) can also be harmful under certain conditions. To design effective biocontrol strategies to sustainably protect plants, it is important to understand how opportunistic pathogens thrive as part of a healthy leaf microbiome. Plant defense metabolites, such as isothiocyanates (ITCs), which kill commensal leaf bacteria, and bacterial ITC resistance mechanisms, such as the ITC hydrolase SaxA, which are often expressed in pathogens and degrade ITCs, may play key roles in the plant microbiome composition. In this study, we explore how SaxA-mediated ITC degradation by a pathogen also benefits diverse ITC-sensitive commensals and how this, in turn, could shape microbiome stability and plant health. Using mathematical modeling based on growth data from Pseudomonas viridiflava with diverse commensals, we find that interaction dynamics can be explained by ITC detoxification and nutrient competition. We predict and experimentally confirm that conditions exist under which SaxA favors commensal growth so strongly that the pathogen is outcompeted for resources, thus not benefiting from its own virulence factor. Our findings suggest that the effects of microbial traits, including virulence factors, are context-dependent, especially when functioning as a public good in a community context like SaxA. Moreover, we propose that this concept, which has been known from antibiotic-degrading microbes, may be worth considering as well when studying plant-pathogen interactions under natural conditions where the commensal microbiome might play an important role in plant disease outcomes.},
}

@article {pmid42360058,
year = {2026},
author = {Puhachova, M and Klair, HK and Hariharan, B and Imtiaz, I and Zambrano Valenzuela, JJ and Alradi, EHA and Gbobbo, E and Zahoor, F and Shah, H and Kale, V and Narasimhan, N and Jamaleddin Ahmad, FA},
title = {Extending the Eisenbarth Model: Stage 0 as a Provisional Framework for Early Risk Stratification and Prevention in Type 1 Diabetes.},
journal = {Journal of diabetes research},
volume = {2026},
number = {1},
pages = {e9970365},
pmid = {42360058},
issn = {2314-6753},
mesh = {Humans ; *Diabetes Mellitus, Type 1/prevention & control/immunology/diagnosis/genetics ; Autoantibodies/immunology/blood ; Disease Progression ; Animals ; Risk Assessment ; Autoimmunity ; Risk Factors ; Biomarkers ; Genetic Predisposition to Disease ; Early Diagnosis ; },
abstract = {BACKGROUND: Type 1 diabetes (T1D) is an autoimmune disease characterized primarily by T cell-mediated pancreatic β-cell destruction, with islet autoantibodies serving as important biomarkers of autoimmune activity and risk progression. Early detection of immune imbalances before seroconversion may help identify individuals at increased risk before established autoimmunity develops. In this review, the proposed "Stage 0" construct is framed as a hypothesis-driven, preautoimmune research construct rather than an established clinical stage.

OBJECTIVE: This narrative review evaluates the proposed Stage 0 construct as a hypothesis-driven, preautoimmune conceptual framework for T1D, summarizes genetic, environmental, metabolic, and immunological factors that may precede islet autoantibody seroconversion, and outlines research priorities for risk stratification and prevention.

METHODS: This review searched PubMed and Google Scholar using MeSH and free-text terms to identify studies on early T1D pathogenesis, genetics, immunity, omics, metabolism, biomarkers, screening, and prevention. English-language human studies, mechanistic studies, reviews, and selected animal studies were included when relevant to early T1D biology. The SANRA framework was used to assess methodological quality.

KEY CONTENT AND FINDINGS: This review discusses Stage 0 as a proposed preautoimmune phase and evaluates factors that may affect T1D progression, including early signs of inflammation, metabolic changes, gut dysbiosis, and β-cell stress. Polygenic and HLA-based risk scores may improve disease prediction, but their performance differs across ancestries and requires population-specific validation. The evidence remains strongest for genetic risk and islet autoantibody status, whereas many preautoantibody biomarkers remain exploratory and require replication. Prevention strategies are reviewed across immune-modulating, antigen-specific, metabolic, microbiome-oriented, and screening-linked pathways.

CONCLUSION: Existing evidence supports additional research into preautoimmune biological alterations prior to the emergence of autoantibodies; however, Stage 0 should not be recognized as a clinical stage at this time. Standard biomarkers, ancestry-inclusive risk models, and prospective validation are essential before Stage 0 screening is considered for routine practice. Future research should determine whether this provisional framework can be translated into ethical, evidence-based screening and prevention pathways.},
}

Humans
*Diabetes Mellitus, Type 1/prevention & control/immunology/diagnosis/genetics
Autoantibodies/immunology/blood
Disease Progression
Animals
Risk Assessment
Autoimmunity
Risk Factors
Biomarkers
Genetic Predisposition to Disease
Early Diagnosis

@article {pmid42360164,
year = {2026},
author = {Sahu, BK and Panda, SK and Mallick, U and Panda, SH and Sahu, MC},
title = {The role of probiotics in restoring and maintaining vaginal microbiome health: a review.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0001126},
doi = {10.1128/iai.00011-26},
pmid = {42360164},
issn = {1098-5522},
abstract = {The vaginal microbiome is an important aspect of female reproductive health. The dominant microbial species of this ecosystem, Lactobacillus, offers protection from vaginal infections by maintaining lower pH levels and reducing potential pathogen colonization. Dysbiosis, or imbalance of the vaginal microbial ecosystem, has been associated with both common infections, such as bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), and urinary tract infections (UTIs), and obstetric complications, including gestational diabetes, preterm labor, and obstetric anemia. This review provides an overview of the composition and function of the vaginal microbiota, emphasizing the role of Lactobacillus and other beneficial microbes and their mechanisms of action, including lactic acid and hydrogen peroxide production, competitive adherence, and immune modulation. Evidence from clinical trials supports the efficacy of these strains in reducing recurrence of BV, VVC, and UTIs. Additionally, emerging research shows promise for probiotic use in managing reproductive conditions such as gestational diabetes mellitus, preterm labor, and obstetric anemia. The review also discusses safety considerations, particularly in immunocompromised individuals, and the expanding interest in non-Lactobacillus genera like Bifidobacterium and Bacillus. Targeted probiotic interventions have great potential for restoring and maintaining a healthy vaginal microbiome, preventing recurrent infections, and helping improve reproductive outcomes. However, in order to incorporate these approaches in clinical practice, probiotic strains, delivery method, and dosage all need standardization.},
}

@article {pmid42360210,
year = {2026},
author = {Sayfitdinkhazhaev, ZF and Zhukova, NG and Israilova, GM and Zhukova, IA and Masenko, AY and Gaponova, OV},
title = {[Parkinson's disease associated with a mutation in the glucocerebrosidase gene].},
journal = {Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova},
volume = {126},
number = {6},
pages = {17-22},
doi = {10.17116/jnevro202612606117},
pmid = {42360210},
issn = {1997-7298},
mesh = {Humans ; *Glucosylceramidase/genetics ; *Parkinson Disease/genetics ; *Mutation ; alpha-Synuclein/metabolism ; },
abstract = {Parkinson's disease (PD) is one of the most socially significant neurodegenerative disorders due to its high prevalence and progressive nature. The key link in PD pathogenesis is the accumulation of the pathological alpha-synuclein. However, neuroinflammation, oxidative stress, mitochondrial dysfunction, and dysregulation of the brain-gut-microbiome axis also contribute significantly to the development of the disease. The etiology of PD remains controversial. This review of modern medical literature, covering domestic and foreign papers, summarizes recent studies on GBA1 gene mutations in PD patients. It showed that the prevalence of GBA1 gene mutations varies by geographical location. In addition, mutations in the GBA1 gene potentiate alpha-synuclein accumulation, lysosomal and mitochondrial dysfunction, and affect neuroinflammation in PD. The mechanisms of action of modern targeted therapies for PD associated with GBA1 gene mutations are described.},
}

Humans
*Glucosylceramidase/genetics
*Parkinson Disease/genetics
*Mutation
alpha-Synuclein/metabolism

@article {pmid42360315,
year = {2026},
author = {Paila, B and Asok, S and Suresh, AK},
title = {Physicochemical stability and protein corona profiling on the interaction of iron oxide nanoparticles with human tears.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5tb02620b},
pmid = {42360315},
issn = {2050-7518},
abstract = {The integration of nanotechnology into ophthalmology represents a promising frontier for the development of precision diagnostics and therapeutics aimed at enhancing ocular health. While the systemic interactions of iron oxide nanoparticles (IONPs) with blood plasma have been extensively studied, their biomolecular interactions within the ocular environment, particularly human tears, remain largely unexplored. In this study, we comprehensively investigate the physicochemical behaviour and proteomic corona interactions of IONPs upon exposure to human tear extracts. Dynamic light scattering (DLS) revealed a modest increase in hydrodynamic diameter from ∼115 ± 3.3 nm to ∼139 ± 0.7 nm, accompanied by a reduction in the zeta potential (ZP) from ∼-36 ± 1.7 mV to ∼-29 ± 1 mV, likely due to protein adsorption. Proteomic profiling via liquid chromatography-mass spectrometry (LC-MS/MS) identified that 25 tear proteins got adsorbed onto the IONPs when compared to tear alone samples with 91 proteins, revealing the association of Lysozyme C, Lactotransferrin, Mammaglobin B, Lipocalin-1, keratins, immunoglobulins, opiorphin propeptide, Keratin II, Protein S100 and mesothelin proteins implicated in bacteriolysis, iron transport, transcriptional regulation, immune response, the cytoskeleton, tissue integrity, nucleotide binding, inflammation regulation, skin tissue formation, endogenous inhibition, microbiome homeostasis and signal transduction. These findings provide protein dynamics of the ocular nano-bio interface, emphasizing the influence of tear protein composition on IONPs. Our results highlight how tear protein corona formation defines the physicochemical stability of IONPs within the human tear environment and provide a basic understanding of these alterations, which may influence IONP-based ocular therapeutic systems.},
}

@article {pmid42360481,
year = {2026},
author = {Bhandari, R and Wills, Z and Harris, J and Salie, M and Ankrah, NYD and Wong, AC and Eastman, K and Ringbauer, J and Striegler, RK and Kang, DS},
title = {Rare Taxa and Stochastic Drift Drive the Microbiome Assembly of the Invasive Pest Drosophila suzukii, While Host Filtering Structures the Grape Sour Rot Community.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02819-x},
pmid = {42360481},
issn = {1432-184X},
abstract = {Understanding the processes that shape microbial community structure is a central challenge in ecology. The relative importance of deterministic and stochastic processes in driving the microbiome assembly and composition remains poorly understood across diverse animal and plant hosts. Here, we characterized the bacterial (16 S rRNA) and fungal (ITS rRNA) communities in invasive pest spotted wing Drosophila (SWD, Drosophila suzukii) and sour-rot-affected grapes from seven California vineyards using high-throughput sequencing. We found that while the bacterial microbiome of male and female SWD was compositionally similar, these communities were entirely distinct from those on sour rot-affected grapes, indicating strong host-specific filtering. SWD also harbored substantially higher microbial density and greater diversity compared to grapes. Ecological modeling revealed a fundamental divergence in assembly mechanisms: SWD communities were predominantly shaped by stochastic processes, with a neutral model explaining 40% of the variation. In contrast, sour-rot-affected grape communities were structured by a combination of stochastic and deterministic factors. Importantly, taxa that deviated from neutral predictions, thereby indicating selection, were primarily classified as rare or intermediate in abundance. This suggests that low-abundance taxa may act as keystone drivers of dysbiosis during rot development. These results highlight the differing assembly rules governing a vector-host system: the mobile vector acts as a stochastic reservoir, promoting pathogen dispersal, while the sessile host imposes strict environmental filtering. This underscores the critical role of rare taxa in shaping community structure and ecosystem stability in SWD and its host grapes.},
}

@article {pmid42360674,
year = {2026},
author = {Olenik, M and Güderer, İ and Wang, Y and Alvi, T and Pandey, P and Dönertaş, HM},
title = {Design and analysis strategies for robust microbiome ageing research.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70397},
pmid = {42360674},
issn = {1873-3468},
support = {P2021-00-007//Carl-Zeiss-Stiftung/ ; },
abstract = {The gut microbiome changes systematically with age and associates with age-related morbidity and mortality, establishing it as a candidate biomarker and intervention target for ageing. Realising this potential requires methodological rigour, as distinguishing genuine biological signals from methodological artefacts remains challenging given variable findings across cohorts. This review provides an integrated framework for human microbiome-ageing research, organised around five methodological challenges that will collectively strengthen causal inference. We examine how age-associated factors can correlate with chronological age and may confound the microbiome-age associations, while selection biases shape old-age cohorts towards healthier profiles. We address within-host temporal dynamics and between-individual heterogeneity that require appropriate sampling to distinguish age-related signatures from transient states, and validation strategies that separate ageing from batch effects in predictive models. Mendelian randomisation provides causal leverage when triangulated with longitudinal and interventional evidence. Throughout, we examine how design choices determine the limits of analytical inference. The review concludes with a practical checklist, equipping researchers to strengthen reproducibility, improve generalisability and advance microbiome-based metrics towards validated indicators of biological ageing.},
}

@article {pmid42360706,
year = {2026},
author = {Glynn, VM and Lawrence, EC and Cleves, PA and Barrett, RDH},
title = {Symbiont identity impacts prokaryotic microbiome dynamics during heat stress in a model system for corals.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icag086},
pmid = {42360706},
issn = {1557-7023},
abstract = {The coral microbiome is highly complex, and interactions between microbiome members have been proposed as an important component of coral thermotolerance. However, establishing causal links among specific microbiome members remains difficult in corals because these communities are diverse and difficult to manipulate experimentally. We used Aiptasia, an emerging coral model system, to test how algal symbiont identity influences the structure and dynamics of the prokaryotic microbiome during heat stress. We generated clonal Aiptasia lines hosting two well-defined strains of photosynthetic algae in the family Symbiodiniaceae. We exposed these animals to an acute thermal stress assay while tracking prokaryotic dynamics with 16S sequencing. Among heat-stressed animals, algal strain was the strongest driver of prokaryotic community composition. We also identified line-associated indicator taxa that may be linked to differences in bleaching resistance. Finally, the more thermally sensitive host-algal association showed greater inter-sample dissimilarity in prokaryotic community structure under heat stress, suggesting that sustained microbiome variability may characterize more stress-sensitive cnidarian holobionts. These results suggest algal symbionts may shape bleaching responses not only through effects on host physiology, but also through their influence on prokaryotic microbiome dynamics.},
}

@article {pmid42361106,
year = {2026},
author = {Pal, NK and Kibria, MK and Noor, T and Ahmed, MF and Islam, MS and Ahmed, MF and Latif, MA and Ali, M and Noman, MA and Kundu, D and Sharma, O and Mollah, MNH},
title = {In-silico identification of bacterial key-genes directly or indirectly associated with the development and progression of colorectal cancer for exploring anti-bacterial agents.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0343565},
pmid = {42361106},
issn = {1932-6203},
mesh = {*Colorectal Neoplasms/microbiology/drug therapy/genetics/pathology ; *Anti-Bacterial Agents/pharmacology ; Humans ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; *Gastrointestinal Microbiome/genetics/drug effects ; Disease Progression ; *Genes, Bacterial ; *Bacteria/genetics/drug effects ; },
abstract = {Colorectal cancer (CRC), which includes malignancies of the colon and rectum, constitutes a major global health challenge. Though there are several drugs that targets CRC-related genes/proteins, but their performance is not yet reach to the satisfactory level. Moreover, their effectiveness gradually decreases over time with long-term use, a phenomenon known as drug resistance. Therefore, it is required to explore new alternative candidate drugs against CRC. Several studies recommended CRC-related dysregulated host-genes guided candidate drugs. However, microbiome guided drug discovery particularly targeting bacterial key genes (bKGs) within CRC-associated gut microbiota remains very limited. This study aims to identify bKGs as antibacterial targets within CRC-associated bacterial taxa for exploring anti-bacterial agents. At first, we analysed a 16S rRNA-seq profile dataset that contained 24 CRC and 50 healthy samples, where beta diversity analysis results showed significant differences in bacterial compositions between CRC and HC groups. Differential abundance analysis with threshold values at |log2FC| > 1.0 and adjusted p-value < 0.05 identified 42 significantly altered bacterial taxa of which Bacteroides fragilis, Bacteroides ovatus, Bacteroides uniformis, and Flavonifractor plautii were prioritized based on effect size and published literature reporting their association with CRC. Further, an integrative subtractive genomics and protein-protein interaction (PPI) network analyses was used to identify top-ranked 10 essential bKGs (ribD, ribBA, murA, alr, hisI, hisE, hisD, hisG, hisH, and hisB) from these four CRC-associated bacterial taxa as putative antibacterial targets. Finally, three candidate drug molecules (Sulfasalazine, Aminoglutethimide, and Tipiracil) were recommended as the preliminary bKGs-guided candidate anti-bacterial agents for CRC through molecular docking and ADME/T analyses. Further experimental and clinical validation is required to establish these compounds as the effective drugs targeting the bKGs for CRC. Thus, these findings may provide insights for developing innovative anti-bacterial treatment approach relevant to CRC.},
}

*Colorectal Neoplasms/microbiology/drug therapy/genetics/pathology
*Anti-Bacterial Agents/pharmacology
Humans
RNA, Ribosomal, 16S/genetics
Computer Simulation
*Gastrointestinal Microbiome/genetics/drug effects
Disease Progression
*Genes, Bacterial
*Bacteria/genetics/drug effects

@article {pmid42361405,
year = {2026},
author = {Sun, Z and Wang, T and Lasky-Su, JA and Litonjua, AA and Weiss, ST and Chavarro, JE and Liu, YY},
title = {Intrapartum caesarean delivery and childhood BMI trajectories in relation to the infant gut microbiome in the VDAART prospective birth cohort.},
journal = {EBioMedicine},
volume = {129},
number = {},
pages = {106347},
doi = {10.1016/j.ebiom.2026.106347},
pmid = {42361405},
issn = {2352-3964},
abstract = {BACKGROUND: The rising global health crisis of childhood overweight and obesity is potentially influenced by caesarean delivery (CD), but it remains a subject of ongoing debate. The gut microbiome, which is affected by delivery mode and can impact body weight, might play a role in this issue. However, the complex relationship between them remains poorly understood.

METHODS: We analysed data from a randomised, double-blind, placebo-controlled trial VDAART cohort, including BMI percentiles from 683 children aged 2-8 years and 1672 stool samples collected between 3 months and 5 years (all data in this study were collected between May 2010 and February 2018). To evaluate how CD relates to BMI trajectories, we conducted permutation testing and discussed the effect of confounding factors. We then used PERMANOVA, random forest classification, and Generalised Microbe Phenotype Triangulation (GMPT) to explore the role of the gut microbiota in mediating this relationship.

FINDINGS: Compared with vaginal delivery, intrapartum CD (iCD) rather than antepartum CD (aCD) was associated with a higher BMI percentile trajectory (Δ = 31.8%; 95% CI, 16.25%-47.55%; P = 0.001, Permutation test), and this was observed only among female children. Moreover, delivery mode was significantly associated with early-life gut microbiota, with effects also limited to females (F = 2.15 and 2.47 at months 3-6 and at age 1; P = 0.035 and 0.007, PERMANOVA). Random Forest models using early microbiota data can predict later overweight/obesity, performing best among iCD-born females (AUROC = 0.88; 95% CI, 0.83-0.94 for age 2), indicating an optimal intervention window before age one. Finally, GMPT identified 24 early-life taxa potentially mediating iCD-related overweight/obesity risk (11 preventive; 13 permissive), including Bacteroides ovatus, Bifidobacterium bifidum, Clostridium leptum, Eggerthella lenta, etc. INTERPRETATION: Our results indicate that CD types and children's sex are key factors in this interaction, offering a possible explanation for the ongoing debate about whether CD is linked to childhood overweight/obesity, and providing valuable insights for future intervention strategies.

FUNDING: This work was supported by the National Institutes of Health.},
}

@article {pmid42361802,
year = {2026},
author = {Fink, T and Rybniker, J and Bollenbach, T},
title = {Predicting antimicrobial resistance for precision medicine.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.031},
pmid = {42361802},
issn = {1934-6069},
abstract = {Antibiotics are among medicine's greatest successes, but resistance evolution threatens their continued efficacy. Decades of research have deepened our understanding of the mechanisms and evolutionary dynamics of antimicrobial resistance. More recently, advances in machine learning (ML) and artificial intelligence (AI) show promise in predicting antimicrobial resistance in pathogens based on rapid whole-genome sequencing and other accessible data. In this perspective, we highlight advances in understanding the mechanisms and spread of antimicrobial resistance. We discuss how this knowledge, coupled with ML- and AI-based approaches, can inform the prediction of resistance and a precision-medicine strategy that targets pathogenic bacteria specifically, thereby limiting resistance evolution and collateral damage to the microbiome. These accurate predictions of bacterial vulnerabilities will enable the adaptation of classical antimicrobial treatments with adjuvants, as well as the use of novel, narrow-spectrum therapeutics. Implementing these strategies, while also identifying key challenges, will help bring this strategy into clinical practice.},
}

@article {pmid42362124,
year = {2026},
author = {Chen, R and Zhan, Z and Zhang, S and Tang, S and Qin, H and Deng, Z and Gao, J},
title = {Duality of Bacteroides cross-feeding networks in health and disease.},
journal = {Pharmacological research},
volume = {230},
number = {},
pages = {108327},
doi = {10.1016/j.phrs.2026.108327},
pmid = {42362124},
issn = {1096-1186},
abstract = {Bacteroides species occupy central positions in gut microbial cross-feeding networks as dominant degraders of dietary and host-derived glycans. By releasing diffusible metabolites, Bacteroides can support beneficial commensals and host homeostasis, yet the same interactions may be co-opted under dysbiotic conditions to promote opportunistic expansion, disease progression, or therapeutic resistance. These divergent outcomes arise from context-dependent network structures, strain-level heterogeneity, and spatial organization rather than intrinsic microbial traits. Despite growing mechanistic insight, clinical translation remains limited by poor reproducibility, insufficient strain-level resolution, overreliance on association studies, and single-species frameworks that neglect network behavior. Here, we synthesize recent advances in the molecular architecture of Bacteroides-mediated cross-feeding, including polysaccharide utilization loci (PULs), spatially deployed surface enzymes, and outer membrane vesicles (OMVs), as well as their ecological dynamics and functional consequences, and critically evaluate why these interactions fail to yield predictable clinical outcomes. We propose a shift toward network-based microbiome therapeutics, highlighting predictive metabolic modeling, cross-feeding-guided consortium design, improved spatiotemporal resolution, and targeted modulation of host-microbe interfaces as key future directions. The principal novelty of this review lies in reframing Bacteroides cross-feeding networks, rather than individual species, as the fundamental unit of microbiome therapeutics, and in tracing this network logic from molecular mechanisms through ecological dynamics to a concrete, experimentally addressable translational roadmap. Embracing cross-feeding networks as therapeutic units may enable more reproducible, mechanism-driven, and personalized microbiome interventions.},
}

@article {pmid42362173,
year = {2026},
author = {Pan, T and Yang, H and Yang, C and Zhao, Y},
title = {Non-antibiotic drug-induced microbiotoxicity as a pharmacological variable.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {112220},
doi = {10.1016/j.cbi.2026.112220},
pmid = {42362173},
issn = {1872-7786},
abstract = {Traditional pharmacology typically explains individual differences in efficacy and toxicity through the host's genetic background, drug-metabolizing enzymes, transporter activity, dietary exposure, and comorbidities; however, these factors alone are insufficient to fully account for the clinically prevalent phenomena of "same drug, different efficacy" and "same drug, different toxicity." Recent studies have shown that the gut microbiota not only directly participates in drug biotransformation but also continuously influences drug exposure, therapeutic efficacy, and susceptibility to adverse reactions through the reshaping of metabolite profiles, alterations in barrier function, regulation of mucosal immunity, and the restructuring of the host's absorption, distribution, metabolism, and excretion systems. Based on this, this article begins at the conceptual level of pharmacomicrobiomics and microbiotoxicity to systematically review the primary mechanisms by which non-antibiotic drugs induce gut microbiota disruption. It integrates representative evidence from metabolic, neuropsychiatric, gastrointestinal, anticancer, and immunomodulatory drugs, and further discusses their clinical significance in therapeutic stratification, toxicity prediction, infection risk assessment, and the design of microbiome interventions. Current evidence suggests that microbiotoxicity induced by non-antibiotic drugs is not merely a concomitant phenomenon but should be incorporated as a critical variable within the pharmacological explanatory framework. Future drug evaluations should not be limited to the host target organs and traditional pharmacokinetic processes but should also fully consider their impact on the host microbiome to advance more predictive and intervention-oriented precision medicine.},
}

@article {pmid42362546,
year = {2026},
author = {Vemuganti, V and Kang, JW and Zhang, Q and McGregor, ER and Hilser, JR and Aquino-Martinez, R and Harding, S and Harpt, JL and Beck, KR and Bussan, H and Kuehn, JF and Deming, Y and Studer, R and Johnson, SC and Asthana, S and Zetterberg, H and Blennow, K and Engelman, CD and Allayee, H and Anderson, RM and Ulland, TK and Bäckhed, F and Bendlin, BB and Rey, FE},
title = {Gut bacterial metabolite imidazole propionate potentiates Alzheimer's disease pathology.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74744-z},
pmid = {42362546},
issn = {2041-1723},
abstract = {The gut microbiome modulates metabolic and neurovascular processes implicated in Alzheimer's disease and related dementias (ADRD), but the underlying mechanisms remain unclear. Here, we identify the bacterial metabolite imidazole propionate (ImP) as a modifier of ADRD pathology. In a cohort of 1196 cognitively unimpaired adults, higher plasma ImP levels were associated with lower preclinical cognitive scores and biomarkers of ADRD, both cross-sectionally and longitudinally. Fecal metagenomic analysis linked putative ImP producers to ADRD phenotypes. Genome-wide integrative analysis revealed a locus on chromosome 12 associated with both plasma ImP levels and AD risk in humans, supporting a host genetic contribution to ImP regulation and a causal role of this metabolite in AD. In mice, chronic ImP administration exacerbated AD-like pathology. ImP impaired brain endothelial barrier and promoted tau hyperphosphorylation in primary neurons, an effect blocked by glycogen synthase kinase-3β inhibition. Together, this study links ImP to hallmarks of neurodegeneration and suggests that targeting ImP may represent a potential strategy to modify ADRD risk.},
}

@article {pmid42362550,
year = {2026},
author = {Falshaw, N and Ducarmon, QR and King, A and Grundler, F and Mesnage, R},
title = {Remodelling of the gut virome after long-term fasting.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42362550},
issn = {2055-5008},
mesh = {*Fasting ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/genetics/classification/isolation & purification ; Humans ; Metagenomics/methods ; Bacteria/virology/classification ; Feces/virology/microbiology ; Bacteroides/virology ; Faecalibacterium/virology ; },
abstract = {Long-term fasting is a promising strategy to restore metabolic health. Emerging evidence suggests that the gut microbiome may mediate some of fasting benefits, but the role of its viral component remains poorly understood. Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n = 89 individuals, n = 241 samples) before and after 9.8 days of fasting (~ 250 kcal/day) as well as one and three months afterwards. Fasting induced a transient loss of viral diversity and a shift toward increased representation of virulent phages. External dataset validation identified 49 phages showing reproducible directional changes during fasting. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium-associated phages and enrichment of Bacteroides-associated phages. Cross-domain network analyses revealed denser viral-bacterial networks at the end of fast, with enriched connections to butyrate producers, suggesting phages may participate in the fasting-induced restructuring of microbial networks involving health-associated taxa. Collectively, these findings indicate that fasting remodels the gut virome cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and occurring in parallel with improvements in cardiometabolic markers.},
}

*Fasting
*Virome
*Gastrointestinal Microbiome
Bacteriophages/genetics/classification/isolation & purification
Humans
Metagenomics/methods
Bacteria/virology/classification
Feces/virology/microbiology
Bacteroides/virology
Faecalibacterium/virology

@article {pmid42362661,
year = {2026},
author = {Ichikawa, S and Shimura, A and Kikuchi, A and Sanda, R and Sasayama, K and Nonoue, K and Tamura, H and Kano, T and Shimada, Y},
title = {Gut microbiome composition and predicted functions relate to growth and behavior in a Japanese preschool cohort.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59018-4},
pmid = {42362661},
issn = {2045-2322},
abstract = {Early childhood is a period of rapid brain maturation and gut microbiome assembly, when emerging behavioral difficulties can shape later mental health and learning trajectories. Microbiota-gut-brain communication has been implicated in neurodevelopment through microbial metabolites and immune signaling. However, most pediatric evidence comes from high-risk or clinically referred cohorts, and gut microbiome-related correlates of typical behavioral variation in community-based preschool children remain poorly defined. In a cross-sectional sample of typically developing Japanese preschool children, we observed exploratory nominal associations between behavioral variation within normative ranges and gut microbiome composition and predicted functions. Internalizing domains showed candidate links with taxa and predicted pathways related to inflammatory potential and nucleotide biosynthesis, whereas somatic complaints and withdrawn behavior showed nominal associations with lower predicted respiratory and fermentative activity. Sleep-related difficulties showed multiple representative nominal pathway-level associations, including pathways related to methyl-donor and heme biosynthesis, while externalizing domains showed candidate links with predicted cell-envelope and carbohydrate-remodeling pathways. In contrast, age, height, and weight tracked expected maturation-related microbiome features, indicating that behavioral associations were not simple proxies of growth. Together, these findings provide an exploratory profile of microbiome-behavior correlations in a low-risk Japanese preschool cohort and highlight pathway-level candidates that may interface with neurodevelopment.},
}

@article {pmid42362797,
year = {2026},
author = {Mizuno, K and Chretien, B and Nishida, K and Ito, T and Kawashima, H and Ando, Y},
title = {Vonoprazan is associated with a phenotype-specific increase in cholangitis reporting in immune checkpoint inhibitor-treated patients: a VigiBase pharmacovigilance study.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42362797},
issn = {1435-5922},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) can cause immune-related adverse events (irAEs), including cholangitis, a rare but clinically severe hepatobiliary phenotype. Whether potassium-competitive acid blockers (PCABs) such as vonoprazan are associated with hepatobiliary adverse-event reporting among ICI-treated patients remains unclear.

METHODS: We performed a READUS-PV-compliant case-noncase disproportionality analysis using VigiBase, the WHO global individual case safety report database (inception through December 1, 2025; MedDRA v27.1). Adjusted reporting odds ratios (aRORs) were estimated for composite liver injury and a custom cholangitis-related endpoint for vonoprazan, proton pump inhibitors (PPIs), and histamine-2 receptor antagonists (H2RAs). The primary analysis was restricted to ICI-exposed reports and adjusted for age, sex, region, hepatotoxic co-medications, and ICI class. Sensitivity analyses addressed treatment intensity, microbiome-modifying co-medications, regional restriction, endpoint definition, sparse-data bias, and ICI subgroup. Six additional irAE categories were analyzed as comparator outcomes.

RESULTS: Among 295,671 ICI-exposed reports, 1098 co-reported vonoprazan and 1186 reports met the cholangitis-related endpoint. Cholangitis was reported in 35 of 1098 vonoprazan-exposed reports (3.19%) versus 0.39% of ICI reports without vonoprazan. Vonoprazan was associated with increased cholangitis reporting (aROR 2.79; 95% CI 1.93-4.02; P < 0.001; E-value 5.02), whereas PPIs and H2RAs showed no significant association. The association persisted across sensitivity analyses, including Western Pacific restriction, microbiome- and treatment-intensity adjustment, and PD-1/PD-L1 monotherapy. Comparator irAE associations were modest and heterogeneous.

CONCLUSIONS: Vonoprazan was associated with a phenotype-specific increase in cholangitis reporting among ICI-treated patients, a pattern absent with PPIs or H2RAs and unmatched across comparator irAEs. Prospective clinical validation is warranted.},
}

@article {pmid42362941,
year = {2026},
author = {Tan, W},
title = {Microbiome and cancer immunotherapy: a bibliometric analysis.},
journal = {Journal of the Egyptian National Cancer Institute},
volume = {38},
number = {1},
pages = {},
pmid = {42362941},
issn = {2589-0409},
mesh = {Humans ; Bibliometrics ; *Immunotherapy/methods ; *Neoplasms/therapy/immunology/microbiology ; *Microbiota/immunology ; },
abstract = {OBJECTIVE: To systematically analyze the global research landscape, collaboration patterns, knowledge flow pathways, and frontier trends in the synergistic effects between the microbiome and cancer immunotherapy.

METHODS: A systematic bibliometric analysis of publications on the synergistic effects between the microbiome and cancer immunotherapy (2010-2026) was performed using the Web of Science Core Collection. After deduplication, 3,058 publications were analyzed with CiteSpace 6.3.1 (co-citation, keyword burst, timeline), VOSviewer 1.6.19 (co-authorship, co-occurrence networks), and bibliometrix R package 4.4.1 (dual-map overlay, knowledge flow).

RESULTS: Annual publications grew at an average rate of 23.0%, reaching 715 in 2025. China and the United States contributed 60.1% of global output, with MD Anderson Cancer Center, Shanghai Jiao Tong University, and Paris-Saclay University serving as core collaboration hubs. Three major academic lineages (fundamental mechanisms, clinical translation, tumor-specific research) and three knowledge flow pathways (mathematical modeling → molecular genetics; clinical medicine → molecular biology; ecology → molecular biology) were identified, shaping distinct research paradigms. Hotspots evolved from "gut microbiota-ICIs" toward "oral microbiota," "engineered bacteria," and "precision prediction."

CONCLUSION: The field has transitioned from mechanistic exploration to precision intervention, with multidisciplinary integration and clinical translation as future priorities. The identified knowledge flow pathways and academic lineages provide a framework for understanding the intellectual structure of this rapidly evolving domain.},
}

Humans
Bibliometrics
*Immunotherapy/methods
*Neoplasms/therapy/immunology/microbiology
*Microbiota/immunology

@article {pmid42363045,
year = {2026},
author = {Li, X and Wang, G and Huang, W and Xiao, R and Wang, J and Ke, L and Wu, C and Chen, L and Wang, B},
title = {Geographic patterns and soil-to-bark microbial transmission shape microbiome assembly in tea trees.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09111-7},
pmid = {42363045},
issn = {1471-2229},
support = {NO. 32060697//National Natural Science Foundation of China/ ; NO. 202401BD070001-009//Yunnan Fundamental Research Projects/ ; },
abstract = {BACKGROUND: Understanding the ecological links in the microbiome of Camellia sinensis is vital for exploring beneficial interactions between microorganisms and economically important woody plants.

RESULT: This study investigates the characteristics of microbial communities, source-sink dynamics, driving factors, and functional differentiation of tea tree bark and bulk soil in the primary tea-producing regions of Yunnan, China (City of Pu'er, Lincang, and Xishuangbanna). Using amplicon sequencing, FEAST source tracking, and functional prediction, we analyzed microbial community differences and ecological roles. Findings revealed that bulk soil may served as the microbial reservoir for bark, sharing all bark bacteria and 68.09% of bark fungi in Pu'er, with minimal reverse flow. Soil harbored higher alpha diversity dominated by Chloroflexi, Acidobacteriota, and Sordariomycetes, while bark selectively enriched Gammaproteobacteria, Cyanobacteriia, and Lecanoromycetes. Plant type mainly influenced bark bacterial communities (R²=76.49%, P < 0.001), whereas geographic location significantly impacted soil bacterial composition (R²=45.72%, P < 0.001) and fungi in both bark (R²=63.06%, P < 0.001) and soil (R²=78.84%, P < 0.01). Total nitrogen (TN) and organic matter (OM) in bulk soil emerged as the predominant factors influencing community variation both for niches of soil and bark. Functional differentiation was observed, with soil microbiomes primarily engaged in chemoheterotrophy and nutrient cycling, while bark microbiomes were more involved in carbon fixation and stress resistance. LEfSe analysis identified 30 bacterial and 64 fungal biomarkers (LDA ≥ 4, P < 0.05), including Xanthobacteraceae in soil and Pleosporaceae in bark.

CONCLUSIONS: This study highlights soil's crucial role as a microbial reservoir and the impact of niche-specific factors, providing a framework to understand how microbial diversity is maintained and regulated along the Soil-Bark Continuum in tea plants.},
}

@article {pmid42363135,
year = {2026},
author = {Öz, ÖF and Seval, MM and Doğan, Ö and Varli, B and Çetinkaya, ŞE and Dökmeci, F},
title = {Elevated urinary succinate in women with symptom-defined overactive bladder without clinically recognized cardiometabolic disease: a cross-sectional study.},
journal = {BMC women's health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12905-026-04596-8},
pmid = {42363135},
issn = {1472-6874},
abstract = {BACKGROUND: Overactive bladder (OAB) is a symptom-defined syndrome, and its metabolic correlates remain incompletely understood. This study investigated whether urinary tricarboxylic acid cycle metabolites differ between women with symptom-defined probable OAB and controls without clinically recognized cardiometabolic disease.

METHODS: In this cross-sectional clinic-based study, women aged 18 years and older attending a gynecology outpatient clinic were enrolled. Participants with self-reported cardiometabolic disease or related medication use were excluded. Probable OAB was defined by an Overactive Bladder Awareness Tool Version 8 score of 8 or higher. Midstream urine samples were analyzed for succinate and malate by gas chromatography-mass spectrometry and normalized to urinary creatinine. Group comparisons, Spearman correlations, multivariable log-linear regression, sensitivity analyses, and exploratory receiver operating characteristic analyses were performed.

RESULTS: A total of 186 women were included, comprising 81 with OAB and 105 controls. Women with OAB were older, had slightly higher body mass index, higher parity, and were more frequently postmenopausal. Urinary succinate and malate levels were higher in the OAB group. After adjustment for age, body mass index, parity, and menopausal status, OAB remained associated with higher urinary succinate (adjusted geometric mean ratio, 1.69; 95% CI, 1.34-2.12) and malate (1.25; 95% CI, 1.02-1.52). Succinate showed modest exploratory discrimination (AUC, 0.678), whereas malate showed limited discrimination (AUC, 0.560).

CONCLUSIONS: Urinary succinate was higher in women with symptom-defined probable OAB even after adjustment for major demographic covariates, while the association with malate was weaker. These findings are hypothesis-generating and require confirmation in adequately powered, prospectively phenotyped cohorts with standardized metabolic, dietary, and urinary microbiome assessment.},
}

@article {pmid42363297,
year = {2026},
author = {Wang, Y and Liu, M and Dogra, SK and Vidal, K and Godin, JP and Darwish, N and Wei, X and Reymond, L and Li, Q and Dong, J and Vyllioti, AT and Bettler, J and Kennedy, E and Wang, K and Zhai, Q and O'Regan, J and Samuel, TM and Cai, W},
title = {Effects of an infant formula containing a whey protein concentrate on feeding tolerance and markers of intestinal immune defense in Chinese infants.},
journal = {BMC nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40795-026-01395-0},
pmid = {42363297},
issn = {2055-0928},
abstract = {BACKGROUND: Human milk (HM) bioactive components can have immune modulatory functions, impact the gut microbiome, and may result in functional benefits when added to infant formula (IF). In this single-arm, prospective, intervention study, we tested the effectiveness of an IF with a whey protein concentrate co-enriched in α-lactalbumin, milk fat globule membrane (MFGM), and Sn-2 palmitate resulting in protein and lipid profiles observed in HM. The outcomes tested were feeding tolerance, Bifidobacteria abundance, and intestinal and immune health of Chinese infants.

METHODS: Predominantly formula-fed (FF) and breastfed (BF) infants were enrolled between 3 and 28 days and assigned to the FF (N = 60) or BF (N = 60) group, per their feeding practice, for 6 weeks. The primary endpoint was Infant Gastrointestinal Symptom Questionnaire (IGSQ) index score assessed using a validated IGSQ-13 questionnaire after 6 weeks of intervention; non-inferiority of FF vs BF was tested. Secondary endpoints included fecal Bifidobacteria abundance assessed using shotgun metagenomics sequencing; fecal short chain fatty acids (SCFAs) analyzed by ultra-performance liquid chromatography-tandem mass spectrometry; fecal markers of immune response, inflammation, intestinal barrier integrity (secretory immunoglobulin A sIgA), cytokines, calprotectin, α1 antitrypsin, lipocalin-2) assessed using enzyme-linked immunosorbent assay; stool consistency assessed using gastrointestinal (GI) diary; anthropometric assessments; quality of life; physician reported adverse events; and use of medications.

RESULTS: Good GI tolerance was observed in both groups at V2 (mean ± SD IGSQ score FF: 19.9 ± 7.4; BF: 16.8 ± 4.2); difference of means 1.35 [95% CI: -1.312, 4.012]). After 6 weeks, Bifidobacterium genus relative abundance was not significantly different between the groups. Total SCFAs were significantly higher (p < 0.05) in the FF versus BF group, driven by increased levels of valeric and propanoic acids (p < 0.05 for both). The IGSQ domain scores, stool consistency, fecal markers of immunity, inflammation, and intestinal barrier integrity (except lipocalin-2 which was significantly higher in BF vs FF), anthropometric Z-scores, common illnesses, antibiotic use, and adverse events were not significantly different between groups at week 6.

CONCLUSIONS: Our results support the effectiveness of this tested infant formula in supporting good GI tolerance, growth, specific intestinal and immune health markers, and Bifidobacteria abundance similar to that of the BF group.

TRIAL REGISTRATION: NCT04880083 (2021-05-06).},
}

@article {pmid42363299,
year = {2026},
author = {Karim, R and Legeay, J and Bammou, M and Hijri, M and Ahmed, B},
title = {Host genotype and edaphic factors shaped bacterial communities associated with native and endemic medicinal Artemisia species in arid environment.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00920-9},
pmid = {42363299},
issn = {2524-6372},
support = {AS-77//OCP Group/ ; 151STPR07-4//UM6P Seed Grant/ ; },
abstract = {BACKGROUND: Plant-associated microbiomes are key contributors to plant nutrition and stress tolerance, particularly in arid ecosystems where extreme abiotic conditions strongly shape plant-microbe interactions. Despite this, the abiotic drivers of microbiome assembly across different plant compartments in wild medicinal species from these environments remain poorly understood. In this study, we investigated bacterial community structure across multiple niches, including bulk soil, rhizosphere, root, and shoot, in three wild Artemisia species (Artemisia herba-alba Asso., Artemisia negrei L., and Artemisia mesatlantica Maire), the latter two being endemic to arid regions of Morocco.

RESULTS: Using amplicon sequencing, we observed diverse bacterial associations with each plant niche harboring distinct taxa. Host plant species significantly influenced bacteriome composition (p = 0.026), particularly in Artemisia mesatlantica, which hosted the most specific bacterial taxa compared to its other relatives. Plant compartment emerged as key drivers of belowground bacterial community assembly with additional structuring by host species and edaphic factors. Soil pH, calcium carbonate content, organic matter and electrical conductivity were strongly correlated with shifts in bacterial diversity and composition, emphasizing the role of soil physicochemical properties as an environmental filter under extreme alkaline and arid conditions. Despite these species- and environment-specific variations, a conserved core bacteriome was identified across all Artemisia species, and compartments except shoot, comprising of Bacillus, Microvirga and Rhizobium.

CONCLUSION: Our results demonstrate that the interplay between host identity and soil properties orchestrates distinct, yet functionally coherent bacterial communities in wild Artemisia species. Bacterial taxa identified as core are well-known for their roles in plant growth promotion, biocontrol and production of bioactive secondary metabolites. The persistence of this core bacterium comprising of Bacillus, Microvirga and Rhizobium suggests a stable association across hosts and compartments, potentially reflecting conserved ecological roles, although functional contributions were not directly assessed in this study. Overall, our findings reveal how the interplay between soil properties and host identity shapes the assembly of distinct, yet compositionally consistent bacterial communities in wild medicinal Artemisia species.},
}

@article {pmid42363400,
year = {2026},
author = {ChandoMal, U and Jayramdass, B and Kumari, N and Huna, },
title = {Methodological Considerations in Interpreting Biliary Microbiome and Gallbladder Carcinogenesis.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70548},
pmid = {42363400},
issn = {1440-1746},
}

@article {pmid42363746,
year = {2026},
author = {Raval, NP and Roy, D and Ansari, A and Goswami, S and Regonda, V and Shete, O and Adhikary, K and Verma, S and Ghosh, TS},
title = {Overlapping gut microbiome signatures in aging and disease are characterized by enrichment of medication-associated oral microbes in the gut.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70391},
pmid = {42363746},
issn = {1873-3468},
support = {DST/INSPIRE/FELLOWSHIP/2023/IF230228//Department of Science and Technology, Ministry of Science and Technology, India/ ; EMDR/CAREP-2023-0000572//Indian Council of Medical Research/ ; BT/RLF/Re-entry/55/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {Biological aging is associated with gut microbiome alterations, including depletion of commensals and enrichment of disease-linked pathobionts. However, the extent to which these changes overlap with disease-associated microbiome signatures remains unclear. Here, we re-examined 45 454 gut microbiomes (141 studies) to quantify overlap between aging-associated microbiome alterations and six major diseases. Cardiometabolic diseases showed the greatest overlap, followed by colorectal cancer. We identified 15 microbes enriched with aging and depleted in health, of which > 50% belonged to oral-associated Streptococcus, Veillonella and Rothia clades. Review of two population-level cohorts (6029 subjects) revealed reproducible associations between these microbes and seven cardiometabolic disease-linked medications. We further discuss their medication associations and propose strategies to deconfound medication- and disease-associated microbiome signatures in aging studies.},
}

@article {pmid42363850,
year = {2026},
author = {Galib, FA and Kafi, AA and Hasnat, S and Sakif, TI and Hoque, MN and Rahman, MM and Gupta, DR and Islam, T},
title = {Genome sequence of Enterobacter vonholyi H2G27 isolated from the gut of Bangladesh's national fish, Tenualosa ilisha.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0031826},
doi = {10.1128/mra.00318-26},
pmid = {42363850},
issn = {2576-098X},
abstract = {The 4.7-Mbp complete genome of Enterobacter vonholyi strain H2G27, isolated from Bangladesh's national fish, hilsa shad (Tenualosa ilisha), was assembled into two contigs. Analysis confirmed a nonpathogenic profile and identified an antimicrobial bottromycin biosynthetic gene cluster. These findings highlight the strain's probiotic potential for sustainable aquaculture management.},
}

@article {pmid42363855,
year = {2026},
author = {Pham, EQ and Gaulke, CA and Eisen, JA and Dandekar, S},
title = {Metagenome-assembled genomes recovered from the gut microbiomes of simian immunodeficiency virus-infected rhesus macaques.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0042826},
doi = {10.1128/mra.00428-26},
pmid = {42363855},
issn = {2576-098X},
abstract = {Rhesus macaques are widely used model organisms for studying human biology, yet relatively few metagenome-assembled genomes (MAGs) are available from their microbiome. Here, we report 159 MAGs recovered from simian immunodeficiency virus-infected macaques, including those treated either with antiretroviral therapy or 10-hydroxystearic acid.},
}

@article {pmid42363861,
year = {2026},
author = {Gallego, S and Matthews, AE and Gates, V and Sharma, K and Baiz, MD},
title = {Complete genome sequence of a yellow-pigmented Pantoea sp. XAF26B01_ASV70 isolated from blue-winged warbler feces.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0012126},
doi = {10.1128/mra.00121-26},
pmid = {42363861},
issn = {2576-098X},
abstract = {We report the genome assembly of a yellow-pigmented Pantoea sp. isolated from blue-winged warbler feces in Western New York, USA. Long read sequencing yielded a complete circular chromosome and three circular plasmids. The largest plasmid encodes a carotenoid biosynthesis (crt) gene cluster consisting of crtE, crtX, crtY, crtI, and crtB.},
}

@article {pmid42363866,
year = {2026},
author = {Haag, L and Dietz-Ziegler, S and Schwarz, J and Kaiser, G and Rühle, J and Hebel, J and Lesk, T and Lajqi, T and Müller, J and Schoppmeier, U and Fundel, R and Molnar, K and Fortmann, I and Poets, CF and Hauke, J and Okun, JG and Wolff, D and Zemlin, M and Härtel, C and Gille, C and Köstlin-Gille, N},
title = {Early antibiotic exposure and vaccine immune responses in preterm infants: potential sex-specific differences.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2694122},
pmid = {42363866},
issn = {1949-0984},
mesh = {Humans ; Female ; Male ; *Anti-Bacterial Agents/administration & dosage/adverse effects ; *Infant, Premature/immunology ; Infant, Newborn ; Prospective Studies ; *Gastrointestinal Microbiome/drug effects ; Sex Factors ; Antibodies, Bacterial/blood ; Infant ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; *Vaccines/immunology ; },
abstract = {Neonatal sepsis represents a major risk in preterm infant care, resulting in widespread early-life antibiotic exposure. While the latter has been linked to immune maturation in term-born neonates, its impact on preterm immune development remains unclear. The aim of this prospective observational study was to investigate the effect of early antibiotic exposure on vaccine titers at a corrected age of four months. To achieve this, blood and stool samples were analyzed from 69 preterm infants (<32 weeks gestational age; 35 with 34 without antibiotic exposure during the first postnatal week) at postnatal day 14 and again at four months corrected age. We assessed vaccine-induced antibody titers against Bordetella pertussis and Haemophilus influenzae, immune cell profiles (flow cytometry), gut microbiome composition (16S rRNA sequencing), and plasma amino acid and acylcarnitine levels (tandem mass spectrometry). Preterm infants exposed to early antibiotics showed reduced antibody titers following vaccination, with differences appearing more pronounced in girls. Antibiotic-exposed girls displayed increased monocytes and myeloid-derived suppressor cells (MDSCs), both of which inversely correlated with antibody titers. Early antibiotic exposure was associated with differences in microbial community types at postnatal day 14, with Klebsiella-dominated and Bifidobacteria-lacking communities occurring more frequently in antibiotic-exposed infants. Antibiotic-exposed girls exhibited distinct metabolomic alterations, including elevated levels of two unsaturated fatty acids that negatively correlated with monocyte and MDSC abundance. Our findings suggest that early antibiotic exposure impairs vaccine responses in preterm infants and indicates a potentially sex-specific susceptibility. Antibiotic-driven changes in the microbiome and metabolome may sustain suppressive innate immune cell populations, which may in turn weaken adaptive responses to vaccination.},
}

Humans
Female
Male
*Anti-Bacterial Agents/administration & dosage/adverse effects
*Infant, Premature/immunology
Infant, Newborn
Prospective Studies
*Gastrointestinal Microbiome/drug effects
Sex Factors
Antibodies, Bacterial/blood
Infant
Feces/microbiology
Bacteria/classification/genetics/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
*Vaccines/immunology

@article {pmid42363883,
year = {2026},
author = {Ravikumar, P and Ravindran, A and Raman, K},
title = {Deciphering global patterns of marine microbial community assembly and network stability.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0047026},
doi = {10.1128/msystems.00470-26},
pmid = {42363883},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial community ecology seeks to unravel the patterns and processes that govern the diversity, assembly, and functional stability of microbial assemblages across global ecosystems. In recent years, the increased availability of sequencing data from large-scale ocean microbiome projects has made it feasible to study microbial community assembly and its underlying mechanisms across global marine environments. In this study, we have investigated species richness patterns, community assembly mechanisms, and interaction patterns of marine bacterial communities by analyzing 16S ribosomal RNA amplicon sequencing data from 4,611 samples collected from ocean microbiome projects. Using neutral community models, the iCAMP framework, and co-occurrence network analyses, we showed that stochastic processes drive microbial community assembly across all latitude zones. In the polar zone, dispersal limitation was the primary driver of community assembly, compared with temperate and tropical communities, where dispersal limitation and selection played an important role. Polar microbial communities exhibited the highest modularity and network robustness, but were more vulnerable to hub removal. Although previous studies have attributed the higher stability of polar communities to environmental filtering, our analyses reveal that the resilience of the community is dependent on a few central taxa. By classifying the genera as generalists and specialists, we further highlight the role played by the specialist taxa in maintaining the stability of the marine microbial community, especially under the pressures of climate change and global warming. In general, our findings offer a latitudinal perspective on the stability of the ocean bacterial community, with implications for understanding their responses to environmental disturbances.

IMPORTANCE: Marine microbes play a vital role in sustaining food webs, cycling nutrients, and regulating Earth's climate. However, we still lack a global understanding of how these microbial communities form, interact, and remain stable under environmental change. By analyzing over 4,600 ocean samples from across the globe, using integrative approaches like neutral models, iCAMP, and network analysis, we have dissected the processes driving bacterial community assembly across different latitude zones and identified that the relative contributions of deterministic and stochastic processes vary significantly. This latitudinal variation in the assembly mechanisms highlights the complexity of the dynamics of the bacterial community in the ocean. Importantly, identifying the pivotal role of specialist taxa in upholding community stability underlines the vulnerability of these ecosystems to disturbances that could disrupt key microbial interactions. Understanding these microbial dynamics is critical for conserving ocean health and sustaining the processes that govern global ecosystems.},
}

@article {pmid42363993,
year = {2026},
author = {Jia, Y and Liu, KL and Huang, SC},
title = {Gut microbiota and meat quality in ruminants: a review of mechanisms and microbiota-targeted interventions.},
journal = {Food science of animal resources},
volume = {46},
number = {1},
pages = {},
pmid = {42363993},
issn = {2636-0780},
support = {KC25119//Xuzhou Cutting-Edge Technology Research Program/ ; XSZR202512//Xuzhou Vocational College of Bioengineering University-Level Project/ ; 23KJB360017//Basic Research Project of the Natural Science Foundation of the Jiangsu Higher Education Institutions/ ; KC23037//Basic research program young talents in science and Technology project of Xuzhou/ ; 2025SJYB0894//General Program of Philosophy and Social Science Research in Jiangsu Universities/ ; },
abstract = {The quality of ruminant meat (e.g., beef and lamb) is a vital source of high-quality protein and essential nutrients for humans, and is gaining global consumer attention. As a crucial nexus in ruminant physiology, the complex gut microbiota plays a pivotal role in determining meat quality by driving nutrient conversion, controlling systemic signaling cascades, and acting as a key regulator of immune balance. Research shows a close association between gut microbiota and meat quality indicators, such as color, flavor, tenderness, pH value, and water-holding capacity (WHC). The underlying mechanisms involve modulating energy metabolism and fat deposition, regulating fatty acid synthesis, supporting protein turnover, and reducing oxidative stress. Moreover, multi-omics technologies are gradually revealing how gut microbes influence meat quality. These insights also help develop targeted intervention strategies, including feed formulation optimization (e.g., supplementation with prebiotics or functional additives), probiotic and enzyme inhibitor application, and targeted regulation of microbial metabolic pathways. This paper systematically reviews the compositional characteristics of the ruminant gut microbiota, evaluates key indicators of meat quality, and explores the mechanisms regulating meat quality alongside microbiota-targeting intervention strategies, providing theoretical references and practical approaches for the green, efficient production of high-quality ruminant meat.},
}

@article {pmid42364055,
year = {2026},
author = {Xu, Q and Sun, L and Han, X and Zhang, Q and Jiang, W and Zhu, S},
title = {Multi-kingdom gut microbiota analyses define bacterial-fungal interplay in multiple type 2 diabetes cohorts.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42364055},
issn = {1869-1889},
abstract = {The role of the gut microbiome in type 2 diabetes (T2D) remains incompletely defined, particularly across microbial kingdoms and diverse populations. Here, we conducted a meta-analysis of 3,857 fecal metagenomes from six international cohorts, profiling bacteria, fungi, archaea, and viruses. Using supervised machine-learning models trained on harmonized multi-kingdom profiles with cross-cohort validation, we identified conserved alterations in T2D, characterized by reduced bacterial and viral diversity and increased fungal and archaeal diversity. A cross-kingdom panel of 33 microbial markers derived from these models achieved robust diagnostic performance (AUR-OC=0.82), outperforming single-kingdom models. Notably, Saccharomyces cerevisiae was consistently depleted in T2D and inversely correlated with glycemic indices. In mice, oral S. cerevisiae supplementation improved glucose tolerance and insulin sensitivity while reducing the abundance of Eggerthella lenta and Klebsiella pneumoniae, bacterial taxa previously linked to adverse metabolic and inflammatory phenotypes. Together, our findings highlight the diagnostic value and mechanistic relevance of multi-kingdom microbial signatures in T2D and position S. cerevisiae as a potential fungal probiotic candidate for metabolic intervention.},
}

@article {pmid42364134,
year = {2026},
author = {Vacaru, RP and Didilescu, AC and Scannapieco, FA},
title = {Oral Health, Periodontitis, and Respiratory Diseases: Biological Pathways.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70126},
pmid = {42364134},
issn = {1600-0765},
abstract = {Poor oral hygiene and periodontitis influence lung diseases such as pneumonia, chronic obstructive pulmonary disease (COPD), COVID-19, and asthma. The normal lung is not sterile, with a distinct microbial ecosystem that is spatially varied along the respiratory tract. The biogeography of the lung microbiome is balanced between microbial microaspiration from the oral-pharynx and clearance. The mouth is an important reservoir for respiratory pathogens including Streptococcus pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, and Staphylococcus aureus, as well as oral microbes (Porphyromonas, Prevotella, Fusobacterium, etc.). Poor oral hygiene and periodontitis increase the bacterial load that can be aspirated, and the host produces pro-inflammatory components that enhance microbial virulence and compromize epithelial integrity. Both poor oral hygiene and periodontitis have been associated with pneumonia, particularly in hospitals and nursing home settings. Periodontitis may also facilitate viral pneumonia (including COVID-19) by altering receptor expression and immune function. Periodontitis correlates with COPD severity and exacerbation frequency through pathways involving matrix metalloproteinases and cytokines. Periodontitis also is associated with asthma and acute exacerbations. Inflammation shapes the lung microbiome by impacting microbial nutrient availability through vascular leakage, inducing changes to epithelial cells which facilitate bacterial adherence, and inducing the production of cytokines, leading to mucus overproduction, inhibition of phagocytosis, and enhancement of microbial pathogen virulence. Multiple biological pathways have been examined in vitro that suggest how "the oral-lung axis" influences pneumonia, COPD, and asthma. Periodontal treatment and effective oral hygiene should be well integrated into medical care to prevent and manage respiratory diseases.},
}

@article {pmid42364158,
year = {2026},
author = {Liu, C and Lin, Y and Li, Y and Liu, T and Yang, S and Chang, M and Du, Y and Li, X and Lv, Y and Ji, J and Ma, S and Guan, S},
title = {Differential Effects of Prenatal Depression and Anxiety on Infant Sleep: Dual-Pathway Mechanisms Involving the HPA Axis and the Gut-Brain Axis.},
journal = {Sleep},
volume = {},
number = {},
pages = {},
doi = {10.1093/sleep/zsag171},
pmid = {42364158},
issn = {1550-9109},
abstract = {STUDY OBJECTIVES: Prenatal psychological distress is associated with adverse offspring outcomes, including infant sleep disturbances and altered gut microbiota, yet the mediating roles of neonatal gut microbiome and tryptophan metabolism remain underexplored.

METHODS: This prospective birth cohort study enrolled 2288 mother-infant pairs, using questionnaires to assess prenatal anxiety/depression and infant sleep patterns up to 12 months. A 112-pair sub-cohort underwent multi-omics analyses: meconium microbiota profiling via 16S rRNA sequencing and cord blood tryptophan metabolite quantification via LC-MS/MS. LASSO regression, mediation analyses, and XGBoost modeling were applied.

RESULTS: Results showed prenatal depression-only was a significant risk factor for infant sleep disturbance (fully adjusted OR = 1.53, 95% CI:1.04-2.25), with a stronger effect in female infants (OR = 2.11, p = 0.022). Cord blood cortisol partially mediated this link (ACME = -7.47, 95% CI: [-14.82, -0.12], p = 0.048). Prenatal anxiety correlated with reduced meconium microbial alpha-diversity, lower Bifidobacterium abundance, and decreased 3-HAA/serotonin levels, which were associated with sleep disturbance; serial mediation confirmed the gut microbiota-tryptophan metabolism pathway. The XGBoost predictive model achieved an AUC of 0.727, with microbial diversity, Streptococcus abundance, dopamine, and 3-HAA as top contributors.

CONCLUSIONS: This study identifies distinct mediating pathways for depression and anxiety, providing targets for personalized infant sleep health interventions.},
}

@article {pmid42364257,
year = {2026},
author = {Foster, WS and Nowosad, CR},
title = {Germinal center responses at barrier organ sites.},
journal = {Current opinion in immunology},
volume = {101},
number = {},
pages = {102807},
doi = {10.1016/j.coi.2026.102807},
pmid = {42364257},
issn = {1879-0372},
abstract = {In this review, we detail the features of barrier germinal centers (GC) that form in tertiary lymphoid structures (TLSs) within non-immune organs that host a local microbiome, and posit a framework of immunity where TLS-GCs created at barrier sites are a key part of normal humoral immunity, and that they form the first layer of an intended multi-layered and increasingly defensive adaptive immune system, providing complementary tissue-specific responses, alongside the local secondary lymphoid organ network and systemic immune responses.},
}

@article {pmid42364261,
year = {2026},
author = {Abuhassan, Q and Atoom, AM and Ganesan, S and Panigrahi, R and Kumar, VR and Sharma, V and Chauhan, AS and Shodikulova, G},
title = {The microbiome-epigenome axis: Regulation of host genome function across development and disease.},
journal = {Cancer treatment and research communications},
volume = {48},
number = {},
pages = {101299},
doi = {10.1016/j.ctarc.2026.101299},
pmid = {42364261},
issn = {2468-2942},
abstract = {The gut microbiome is increasingly recognized as a metabolically active regulator of host gene expression, translating environmental exposures-particularly diet-into epigenetic signals that shape development, immunity, metabolism, and disease susceptibility. This narrative review synthesizes current evidence for a microbiome-epigenome axis in which microbial metabolites and regulatory molecules modulate DNA methylation, histone modifications, non-coding RNA networks, RNA epitranscriptomic marks, and higher-order chromatin organization. Short-chain fatty acids act as histone deacetylase inhibitors, acyl-CoA donors, and regulators of histone acetyltransferase activity; microbially derived B vitamins influence one-carbon metabolism and S-adenosylmethionine availability; and bile acids, indoles, trimethylamine-N-oxide, and extracellular vesicle cargo signal through host metabolic, immune, and transcriptional pathways. Evidence from germ-free and recolonization models, genetic perturbation studies, in vitro systems, and human cohorts indicates that microbial signals exert particularly strong effects during developmental windows of heightened epigenetic plasticity, contributing to immune tolerance, trained innate immunity, and long-term metabolic programming. Dysbiosis may disrupt these regulatory circuits and promote inflammatory bowel disease, colorectal cancer, cardiometabolic and atherosclerotic disorders, and neurodevelopmental or neurodegenerative conditions. By integrating microbial metabolism with chromatin regulation, RNA-based control, and genome topology, this review highlights the microbiome as a dynamic epigenetic interface between environment and host physiology. Key challenges include establishing causality in humans, resolving temporal and tissue-specific mechanisms, and developing longitudinal multi-omics studies with functional validation. Targeted microbiome modulation may ultimately restore epigenetic homeostasis and support precision prevention and therapy.},
}

@article {pmid42364275,
year = {2026},
author = {Muizelaar, W and Sloth, JJ and Fromberg, A and Jensen, SN and Dijkstra, J and Zaccaria, E},
title = {Temporal dynamics of bromoform metabolite formation and microbial responses during in vitro rumen fermentation with Asparagopsis taxiformis.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {7},
pages = {101879},
doi = {10.1016/j.animal.2026.101879},
pmid = {42364275},
issn = {1751-732X},
abstract = {This study investigated the temporal dynamics of bromoform (CHBr3) dehalogenation from Asparagopsis taxiformis and its effects on fermentation characteristics and microbial composition in an in vitro batch culture system, generating data relevant to the safety and efficacy assessment of A. taxiformis as a methane (CH4) inhibitor. Per treatment, six bottles were incubated with individual rumen fluid from three rumen fistulated lactating Holstein-Friesian dairy cows, with duplicate bottles per biological replicate (3 biological × 2 technical replicates). These bottles were used for continuous measurement of gas production, spot CH4 measurements at 0, 1, 2, 4, 8, 12, 24, 36, 48, 60, and 72 h of incubation, as well as for sampling (at 72 h) of volatile fatty acids (VFAs), CHBr3 metabolites, total bromine, iodine and arsenic concentration, and microbiome composition. Substrate (0.5 g DM) comprised 60% grass and 40% corn (DM basis) with or without 0.01 g DM A. taxiformis (Asparagopsis and Control, respectively). Samples for CHBr3 metabolites, bromine, iodine, arsenic, and microbiome analyses were taken to study changes over time (at 1, 2, 4, 8, 12, 24, 36, 48, and 60 h) from extra bottles incubated at the same starting time containing the Asparagopsis treatment. Cumulative gas production was not affected by the addition of A. taxiformis, while cumulative CH4 production was reduced by 94 and 78% after 24 and 72 h of fermentation, respectively. Total VFA concentration and molar proportion of acetate decreased, and molar proportion of propionate increased in Asparagopsis compared to Control. After 1 h of fermentation, only 5.3% of the added CHBr3 was detectable, and it was below the detection limit after 8 h. The concentration of dibromomethane (CH2Br2) increased markedly within 1 h and remained relatively stable up to 72 h of fermentation. No bromomethane was detected. The lack of stoichiometric conversion between CHBr3 and CH2Br2 suggests that additional, unidentified brominated metabolites may have formed. Total bromine, iodine, and arsenic concentrations remained relatively stable over time. Supplementation of A. taxiformis resulted in large shifts in microbial community, including a decrease in the relative abundance of archaeal and ciliate species. Longitudinal microbiome analyses confirmed a progressive microbial community restructuring over time. The shifts in bacterial community generally indicate an adaptation to elevated hydrogen concentrations or alternative fermentation pathways. Further in vivo research is needed on the absorption, metabolism, distribution, and excretion of CHBr3 and its derivatives in ruminants, including potential metabolism in organs beyond the rumen.},
}

@article {pmid42364328,
year = {2026},
author = {Wang, S and Chen, X and Wu, Z and Zhao, Q and Teng, Y and Yang, Q and Zhang, H and Wang, Y},
title = {Exploring the multi-barrier repair effects of Codonopsis pilosula water extract in improving rhubarb-induced intestinal dysfunction in mice based on the tryptophan metabolism-AhR pathway.},
journal = {International immunopharmacology},
volume = {186},
number = {},
pages = {117065},
doi = {10.1016/j.intimp.2026.117065},
pmid = {42364328},
issn = {1878-1705},
abstract = {BACKGROUND: The intestine is the core digestive and absorptive organ and the largest immune barrier. Intestinal dysfunction impairs physiological function, but current treatments remain suboptimal because of its complex etiologies. This study investigated whether Codonopsis pilosula water extract (CPWE) repairs intestinal mucosal barrier damage in mice and elucidated the underlying mechanisms.

MATERIALS AND METHODS: Intestinal dysfunction was induced in male ICR mice by continuous gavage with rhubarb water extract to establish a diarrhea model. The efficacy of CPWE was evaluated by measuring body weight, fecal water content, and the small intestinal propulsion rate. Histopathological changes in intestinal tissues were examined using H&E and AB-PAS staining. Intestinal barrier damage was assessed by immunofluorescence and Western blotting. Furthermore, transcriptomic and microbiome sequencing were employed to explore the specific mechanisms by which CPWE repairs intestinal mucosal barrier damage.

RESULTS: CPWE effectively alleviated rhubarb-induced diarrhea and restored the intestinal mucosal barrier in mice. It increased onula occludens-1 (ZO-1) and occludin (OCLN) expression, promoted mucin 2 (MUC2) secretion, reduced the proportions of Th1 and Th17 cells in the colonic lamina propria, and modulated gut microbial composition. These changes were associated with regulation of tryptophan metabolism and aryl hydrocarbon receptor (AhR) signaling, consistent with a role in maintaining the integrity of the mechanical, chemical, immune, and biological barriers.

CONCLUSIONS: These findings suggest that CPWE ameliorates rhubarb-induced intestinal barrier dysfunction through multi-barrier repair associated with tryptophan metabolism and AhR signaling. This study provides a theoretical basis for multi-component strategies in diarrhea-related intestinal injury and supports the application of traditional Chinese medicine in precision treatment of intestinal diseases.},
}

@article {pmid42364363,
year = {2026},
author = {Sanabani, SS},
title = {The skin microbiome: from historical ecology to therapeutic frontiers.},
journal = {Anais brasileiros de dermatologia},
volume = {101},
number = {4},
pages = {501393},
doi = {10.1016/j.abd.2026.501393},
pmid = {42364363},
issn = {1806-4841},
abstract = {BACKGROUND: Human skin, the body's largest organ, hosts a diverse ecosystem of bacteria, fungi, viruses, and mites collectively known as the skin microbiome. This microbiome supports cutaneous homeostasis through barrier defense, immune education, and metabolic functions.

OBJECTIVE: To narratively review the historical evolution of skin microbiome research, synthesize current knowledge on its composition, biogeography, and functional roles in health and disease, and highlight emerging microbiome-based therapeutic strategies in dermatology.

METHODS: This review integrates seminal historical works with contemporary evidence from culture-independent sequencing and multi-omic investigations of the skin microbiome, identified through a selective search of recent dermatology and microbiome literature.

RESULTS: Modern molecular and multi-omic approaches have revealed microbial diversity across sebaceous, moist, and dry skin niches and clarified key functions of the skin microbiome, including colonization resistance, immune modulation, metabolite production, and participation in the gut-skin axis. Dysbiosis of these communities is linked to inflammatory conditions such as atopic dermatitis, acne vulgaris, psoriasis, and chronic wounds. A growing body of work supports microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and microbiome engineering, as promising personalized strategies.

STUDY LIMITATIONS: As a narrative review, this work may be subject to selection bias and does not provide a quantitative synthesis of all available studies on the skin microbiome.

CONCLUSIONS: By integrating historical context with mechanistic insights from modern microbiome research, this review underscores the skin microbiome as a central ecological determinant of cutaneous health and disease and provides a framework for translating microbiome science into clinical applications and precision dermatology.},
}

@article {pmid42364402,
year = {2026},
author = {Li, J and Shahbaz, Z and Feng, X and Han, X and Wang, M and Du, W and Xu, J and Li, X and You, J and Liang, D and Xiang, X and Wang, L},
title = {Effect of Chinese gallnuts tannic acids on the growth performance, intestinal morphometry and microbiome of broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107279},
doi = {10.1016/j.psj.2026.107279},
pmid = {42364402},
issn = {1525-3171},
abstract = {The rise in global restrictions on antibiotic growth promoters have intensified the search for sustainable and safe alternatives. Phytogenic feed additives (PFAs) have emerged as promising contestants because of their diverse biological properties. This research studied the potential effects of herbal extracts as the standardized PFA containing tannic acids derived from Chinese gallnuts on intestinal morphometry, growth performance and cecal microbiota. For this purpose, 224 one-day-old male Ross 308 broiler chicks were allocated to 28 cages, with eight birds per cage and seven replicate cages per treatment, in a 35-day trial. The four dietary treatments were: negative control (NC) without antibiotic growth promoters, NC + avilamycin at 100 g/t, NC + colistin sulfate at 100 g/t, and NC + Chinese gallnuts tannic acids (CGTA) at 200 g/t. The growth performance indices were observed during the whole production cycle. The intestinal morphometry was observed on the day 35. The dietary inclusion of CGTA significantly improved feed conversion ratio (FCR) during 0 to 10 and 0 to 21 days as compared to NC diet treatment. Moreover, the European Production Efficiency Factor (EPEF) of 441 was also observed numerically higher in the CGTA supplementation treatment. Additionally, the intestinal morphometric analysis revealed a substantial rise in both the duodenal and jejunum height of villus and a decrease in epithelial thickness in both duodenum and jejunum, indicating the enhanced absorptive capacity and gut integrity. Crypt depth and goblet cell numbers were not affected significantly. Notably, microbiota analysis showed no significant differences in alpha or beta diversity. In conclusion, dietary supplementation of CGTA at 200 g/t improved feed efficiency and intestinal morphometry in broilers, without altering the community of cecal microbiota.},
}

@article {pmid42364408,
year = {2026},
author = {Xu, Z and Liu, Y and Wang, Y and Zhao, J and Wang, Y and Chen, L and Hou, D},
title = {Association between gut microbiota and white matter microstructural damage in tuberculous meningitis patients.},
journal = {Tuberculosis (Edinburgh, Scotland)},
volume = {160},
number = {},
pages = {102793},
doi = {10.1016/j.tube.2026.102793},
pmid = {42364408},
issn = {1873-281X},
abstract = {BACKGROUND: Tuberculous meningitis (TBM), the most severe form of tuberculosis, may involve the gut-brain axis. This study investigated the link between TBM, brain white matter integrity measured by diffusion tensor imaging (DTI), and the gut microbiome.

METHODS: 22 TBM patients and 31 healthy controls underwent MRI and provided fecal samples. Gut microbiota (16S rRNA sequencing), fecal metabolites (metabolomics), and DTI metrics (FA, MD, RD, AD) were analyzed. Tract-based spatial statistics and correlation analyses were employed.

RESULTS: TBM patients showed lower gut microbiota α-diversity. The abundance of the Escherichia genus correlated negatively with FA and positively with MD in specific white matter tracts. Metabolomics revealed elevated acetic acid in TBM patients, which correlated with both Escherichia abundance and DTI metrics. KEGG analysis indicated altered arginine and proline metabolism pathways.

CONCLUSION: TBM is associated with differences in gut microbiota composition. Higher relative abundance of Escherichia is linked to white matter microstructural damage, potentially mediated by specific bacterial metabolites.},
}

@article {pmid42364424,
year = {2026},
author = {Chambers, LM and Spakowicz, D and Chalif, J and O'Connor, R and Kistenfeger, Q and Mehra, Y and Mohssen, M and Abdeen, C and Haight, P and Nagel, C and Neff, R and Cohn, D and Copeland, LJ and Backes, F and Cosgrove, C and Hays, J and Dravillas, C and McLaughlin, E and O'Malley, D},
title = {PRO-PLATINUM: A randomized, double-blind, placebo controlled study to investigate the efficacy of a probiotic intervention on the gut and vaginal microbiome of ovarian cancer patients undergoing treatment with platinum chemotherapy.},
journal = {Gynecologic oncology},
volume = {211},
number = {},
pages = {74-78},
doi = {10.1016/j.ygyno.2026.06.016},
pmid = {42364424},
issn = {1095-6859},
abstract = {BACKGROUND: PRO-PLATINUM evaluates whether a 5-strain probiotic formulation can favorably modulate the gut microbiome during platinum-based chemotherapy in ovarian cancer (OC), while assessing feasibility, safety, and translational correlates of response and toxicity.

PATIENTS AND METHODS: PRO-PLATINUM is an IRB-approved, randomized, double-blind, placebo-controlled trial enrolling 124 patients with stage II-IV or platinum-sensitive recurrent high-grade OC receiving platinum-based chemotherapy. The study opened to enrollment in February 2026. Participants are randomized 1:1 to a 5-strain probiotic (WBF-038) or placebo, stratified by newly diagnosed advanced versus recurrent disease. The intervention contains inulin and five microbial strains: Akkermansia muciniphila, Anaerobutyricum hallii, Clostridium beijerinckii, Clostridium butyricum, and Bifidobacterium infantis, and is administered orally twice daily beginning within seven days of cycle 1 and continuing through seven days after the completion of cycle 6. Eligible patients must have ECOG performance status 0-2, adequate organ function, and no major probiotic-related contraindications. Stool, blood, and vaginal samples are collected at baseline, cycle 3, and cycle 6; tumor tissue is collected at surgery when available. The primary endpoint is change in gut microbiome composition by whole-genome metagenomic sequencing. Secondary endpoints include intervention adherence, biospecimen feasibility, recurrence-free survival, and overall survival. Exploratory endpoints include toxicity, postoperative infections, stool consistency, diet, medication and antibiotic exposure, quality of life, symptom burden, serum metabolomic and immune profiling, vaginal and tumor microbiome composition, and associations between microbial features and clinical outcomes.

CONCLUSIONS: PRO-PLATINUM will evaluate treatment feasibility and safety and generate prospective translational data to inform future microbiome-directed strategies to improve treatment tolerance, quality of life, and outcomes in OC patients.},
}

@article {pmid42364535,
year = {2026},
author = {Juárez-Campusano, YS and Tellez-Garcia, AA and Arellano-Carbajal, F and Acevedo-Whitehouse, K},
title = {Transcriptomic changes in the gut mucosa of fasting northern elephant seal pups reveal immune modulation during early microbiome establishment.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {60},
number = {},
pages = {101920},
doi = {10.1016/j.cbd.2026.101920},
pmid = {42364535},
issn = {1878-0407},
abstract = {Fasting is an integral component of the life-history of many species. Following abrupt weaning, northern elephant seal pups (Mirounga angustirostris) undergo an extended post-weaning fast of approximately 60 days. During this period, enteric bacterial diversity increases, suggesting that host immune regulation may facilitate the establishment of microbial communities. However, the molecular processes occurring within the intestinal mucosa during this transition remain poorly understood. To investigate these mechanisms, we characterized transcriptional changes in the enteric mucosa of male and female northern elephant seal pups sampled at weaning and after one month of fasting. Total RNA isolated from rectal swabs was sequenced and aligned to the Mirounga angustirostris reference genome. Differential gene expression and gene set enrichment analyses were used to identify genes and pathways associated with fasting and sex-specific responses. Fasting was accompanied primarily by transcriptional downregulation, including genes involved in antimicrobial defense, inflammation, protein turnover, and epithelial remodeling. In contrast, several genes associated with B-cell activity and immune recognition were upregulated. Gene Set Enrichment Analysis revealed coordinated activation of immune-regulatory pathways indicating dynamic modulation of intestinal immunity rather than generalized immune suppression. Pronounced sex-specific differences were also observed. Male pups exhibited transcriptional patterns consistent with enhanced immune tolerance, whereas females showed broader immune-pathway activation, including enrichment of pro-inflammatory and stress-response pathways. Several non-coding RNAs also displayed sex-specific changes in expression. Together, these findings suggest that fasting induces transcriptional remodeling of the gut and may contribute to immune regulation during a critical period of microbiome establishment in northern elephant seal pups.},
}

@article {pmid42364562,
year = {2026},
author = {Linh, TC and Duc, CKT},
title = {Indirect pharmacology of phytopolyphenols: The role of intermediate substances in cross-organ regulation and phenotypic outcomes.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {159},
number = {},
pages = {158466},
doi = {10.1016/j.phymed.2026.158466},
pmid = {42364562},
issn = {1618-095X},
abstract = {BACKGROUND: Dietary polyphenols exhibit diverse biological activities, yet many parent compounds rarely reach peripheral target organs at pharmacologically relevant concentrations following oral intake. This discrepancy highlights the need to understand how these compounds exert systemic efficacy.

PURPOSE: This review aims to critically evaluate the concept of "indirect pharmacology" in the context of dietary polyphenols, referring to mechanisms in which biological effects are mediated predominantly through gut microbiota-dependent biotransformation and intermediary signaling molecules rather than direct systemic exposure of the intact parent compounds at pharmacologically relevant concentrations.

STUDY DESIGN: A comprehensive narrative review and conceptual synthesis of current evidence regarding polyphenol-microbiota interactions and their interorgan signaling pathways.

METHODS: The study evaluates key mechanisms, including microbial biotransformation, the modulation of the intestinal barrier, and the multi-layered signaling network of shared mediators across major cross-organ axes. Evidence from in vitro systems, animal models, metabolomic analyses, and available human intervention studies was comparatively evaluated to assess the mechanistic and translational strength of current evidence.

RESULTS: Current evidence suggests that unabsorbed polyphenols undergo extensive microbial biotransformation to generate bioactive mediators, including short-chain fatty acids (SCFAs), secondary bile acids, and specific phenolic derivatives. Together with the modulation of the microbial architecture itself, these mediators reinforce the gut barrier to reduce endotoxemia. By entering the systemic circulation, these metabolites may influence host receptor signaling and interorgan communication across the gut-liver, gut-adipose, and gut-brain axes, thereby contributing to the regulation of systemic inflammation and glucose-lipid metabolism. However, in many cases, causal validation remains incomplete, and the relative contribution of direct versus microbiota-mediated mechanisms is still unresolved.

CONCLUSION: The physiological efficacy of dietary polyphenols is heavily driven by a multi-target, microbiota-mediated regulatory network. Although the indirect pharmacological framework provides an integrative perspective for understanding microbiota-mediated polyphenol activity, substantial translational challenges remain, including interindividual microbiome variability, limited causal validation, and insufficient long-term clinical evidence.},
}

@article {pmid42364737,
year = {2026},
author = {Hajjar, C and Saint-Criq, V and Thomas, M and Butel, MJ and Bazarbachi, A and Abifadel, M},
title = {The lung microbiome in hematopoietic stem cell transplantation: immune interactions, clinical consequences, and emerging interventions.},
journal = {Respiratory medicine},
volume = {261},
number = {},
pages = {109004},
doi = {10.1016/j.rmed.2026.109004},
pmid = {42364737},
issn = {1532-3064},
abstract = {Hematopoietic stem cell transplantation (HSCT) offers curative potential for hematologic malignancies and immune disorders, yet pulmonary complications remain major contributors to non-relapse morbidity and mortality. Traditionally attributed to immune suppression and graft-versus-host disease (GvHD), these complications are increasingly recognized to involve disruption of pulmonary microbial communities. A growing body of clinical and experimental evidence indicates that HSCT-associated perturbations in the lung microbiome, driven by conditioning, antimicrobials, immune injury, and infection, are associated with distinct post-transplant pulmonary phenotypes and, in some cohorts, with mortality risk. Whether these microbial shifts represent causal contributors to lung injury or contextual biomarkers of immune vulnerability remains unresolved, and this distinction carries direct implications for microbiome-targeted intervention. Dysbiotic shifts in the lung have been associated with both infectious and non-infectious complications, including idiopathic pneumonia syndrome, bronchiolitis obliterans syndrome, and fibrotic lung disease. Gut-lung microbial crosstalk may amplify or reflect systemic immune dysfunction, though the directionality of this relationship remains incompletely characterized. Multi-omics approaches, integrating metagenomics, metatranscriptomics, and metabolomics, are beginning to define the host-microbiome interaction signatures that distinguish injury subtypes and predict outcomes. This review synthesizes mechanistic insights into lung microbiome-immune interactions after HSCT, critically appraises the methodological constraints on the current evidence base, and evaluates microbiome-based interventions, including fecal microbiota transplantation, inhaled postbiotics, and precision antimicrobials, as candidate strategies for respiratory protection in transplant recipients, while acknowledging that prospective interventional evidence in this population remains limited.},
}

@article {pmid42364788,
year = {2026},
author = {Araújo, LSA and Franzan, BC and Almeida, MIV and Coelho, IS and Almeida, FQ},
title = {Fecal microbiota of weaned equine and mule foals grazing bermudagrass pastures.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {106070},
doi = {10.1016/j.jevs.2026.106070},
pmid = {42364788},
issn = {0737-0806},
abstract = {BACKGROUND: Weaning is a critical period in the lives of foals. After weaning, forage consumption represents a major challenge for both equine or mule foals.

AIMS/OBJECTIVES: This study evaluated the fecal bacterial concentration, composition, diversity and differential abundance in weaned equine and mule foals under rotational grazing on Bermudagrass (Cynodon spp.) pasture.

METHODS: A randomized design was used with equine and mule foals grazing two rotations on three Bermudagrass cultivars (Coastcross, Florakirk, and Tifton-85). Pasture rotation occurred every 20 days. The first rotation was evaluated at 20, 40 and 60 days post-weaning, and the second rotation at 80, 100 and 120 days post-weaning. Eight weaned foals (four equine and four mules) grazed on 3 ha of each cultivar. Fecal samples were collected at the end of each grazing cycle. Bacterial populations were evaluated using culture-based methods and 16S rRNA sequencing. Forage chemical composition, bacterial counts, fecal pH, alpha diversity, and bacterial communities were analyzed using the Kruskal-Wallis's test followed by Dunn's test. Multivariate analyses of Operational Taxonomic Units (OTUs) were performed using PERMANOVA, and differentially abundant OTUs were identified using the LEfSe method.

RESULTS: Equine foals showed higher counts of Lactobacillus and anaerobic bacteria based on culture methods. Sequencing revealed increased relative abundance of lactic acid bacteria, Limosilactobacillus, Ligilactobacillus, Streptococcus and Enterococcus in equine foals. Mules exhibited higher fecal pH and Shannon diversity, with greater abundance of Agathobacter, Ruminococcus, Phascolarctobacterium and Treponema.

CONCLUSION: The results suggest that mule foals may are more resilient to changes in pasture and exhibit adaptive mechanisms related to digestive efficiency and forage utilization in Cynodon pastures.},
}

@article {pmid42364789,
year = {2026},
author = {DiSilvestro, AN and Wesolowski, LT and Williams, BD and Warren, LK and Athrey, G and White-Springer, SH},
title = {Short-term provision of moderate dietary starch alters fecal microbiota but does not exacerbate exercise-induced inflammation in yearling Quarter Horses.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {106071},
doi = {10.1016/j.jevs.2026.106071},
pmid = {42364789},
issn = {0737-0806},
abstract = {BACKGROUND: Energy-dense feeds commonly provided to equine athletes may be high in starch, which alter gastrointestinal microbiota and could promote systemic inflammation.

AIMS/OBJECTIVES: To test the hypothesis that exercise-induced inflammation would be greater in horses receiving a starch- versus fiber-based concentrate.

METHODS: Quarter Horses (mean±SD 16±1mo; 337±30kg) received either a fiber-based control (CON; 7 fillies, 8 geldings) or an isocaloric, isonitrogenous starch concentrate (STARCH; 8 fillies, 7 geldings) for 24d. Fecal metagenomics were evaluated on d0 and 21. Blood inflammatory mediators were quantified on d0, d21, and surrounding a 2-h submaximal exercise test (SET) on d22.

RESULTS: On d21, CON horses had greater Lactobacillaceae (∼5.7% vs. ∼2.4% in STARCH), while STARCH had greater Lachnospiraceae (∼38% vs. ∼32% in CON) but diet alone did not impact inflammatory markers. On d22, CRP increased at 24h post-SET in all horses (P<0.0001). By 48h, CRP returned to pre-SET in STARCH but remained elevated in CON (P=0.0005), resulting in greater CRP in CON than STARCH at 48h (P=0.02). TNFα increased from pre-SET to 1h in STARCH horses (P=0.02), then returned to pre by 6h. In CON horses, TNFα increased at 24h (P=0.04) and remained elevated at 48h (P=0.0005). Throughout the SET, CON had greater IL-10 than STARCH horses (P=0.005). SAA, IL-4, IL-8, and vascular endothelial growth factor (VEGF)-A were differentially impacted by the SET but were unaffected by diet.

CONCLUSION: Contrary to our hypothesis, fiber-fed horses appeared to elicit a more robust acute inflammatory response to exercise than starch-fed horses despite an altered gastrointestinal microbiome.},
}

@article {pmid42364790,
year = {2026},
author = {Kamal, R and Chauhan, A and Bhargava, SK and Dhiman, S and Singh, TG and Kumar, D and Awasthi, A},
title = {Reprogramming chronic wounds: the emerging role of microbiome-targeted therapies in diabetic foot ulcers.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {127137},
doi = {10.1016/j.ijpharm.2026.127137},
pmid = {42364790},
issn = {1873-3476},
abstract = {Diabetic foot ulcers (DFUs) represent one of the most severe complications of diabetes mellitus, frequently leading to chronic infection, delayed wound healing, and lower-limb amputations. Despite advances in wound care, current therapeutic strategies largely rely on broad-spectrum antibiotics and mechanical interventions, which often fail to address the complex biological environment of non-healing wounds. Emerging evidence indicates that DFUs are strongly associated with alterations in the wound microbiome, including microbial dysbiosis, polymicrobial biofilm formation, and persistent inflammatory responses. These factors collectively contribute to impaired tissue regeneration and resistance to conventional therapies. Consequently, microbiome-targeted therapeutic strategies are gaining increasing attention as a promising approach for DFU management. Novel interventions such as bacteriophage therapy, probiotic and postbiotic-based wound dressings, and CRISPR-mediated genome editing provide precise tools for disrupting pathogenic biofilms, attenuating microbial virulence, and overcoming antimicrobial resistance while preserving beneficial microbial communities. In parallel, advances in rapid microbiome diagnostics, smart wound dressings, nanotechnology-based drug delivery systems, and data-driven personalized treatment platforms are enabling more adaptive and targeted wound management. By shifting the perspective from treating DFUs as simple infections to understanding them as complex microbial ecosystems, these emerging strategies offer new opportunities to enhance healing outcomes.},
}

@article {pmid42364834,
year = {2026},
author = {Chen, X and Tan, B and Shao, G and Pan, J and Lu, L and Xiao, Z and Lin, Z and Ji, G and Xu, H},
title = {From Mechanisms to Therapy: Targeting the Gut-Brain Axis in Chronic Gastrointestinal Pain.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108329},
doi = {10.1016/j.phrs.2026.108329},
pmid = {42364834},
issn = {1096-1186},
abstract = {Chronic gastrointestinal pain (CGP) is a common and often difficult-to-manage symptom in disorders of gut-brain interaction (DGBI). Owing to the limited efficacy of current therapeutic approaches in a subset of patients, a better understanding of gut-brain axis (GBA) dysfunction may facilitate the development of improved treatment strategies. This review summarizes the pathophysiological mechanisms underlying CGP, focusing on the contributions of microbial dysbiosis, mucosal immune activation, and neuroendocrine disturbances to peripheral and central nociceptive sensitization. Current therapeutic approaches, including cognitive and behavioral interventions, pharmacological neuromodulation, and microbiome-directed therapies, are critically reviewed with regard to their mechanistic basis and available clinical evidence. In addition, we discuss evidence indicating that plant-derived bioactive compounds have been reported to modulate multiple pathways implicated in CGP, including epithelial barrier dysfunction, visceral hypersensitivity, inflammatory signaling, oxidative stress, and ion channel activity. By integrating advances in psychogastroenterology with emerging findings from natural product research, this review discusses potential complementary strategies for CGP management and the challenges associated with their clinical translation. A deeper understanding of GBA regulation may facilitate the identification of novel therapeutic targets and inform the development of more individualized treatment strategies for CGP, although further preclinical and clinical studies are required to establish their efficacy and safety.},
}

@article {pmid42365026,
year = {2026},
author = {Zhang, S and Le Guennec, A and Shoaie, S and Carpenter, GH},
title = {Urea supplementation is associated with holistic changes in suprathreshold non-volatile flavour perception through oral microbiome carbon metabolism.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00951-z},
pmid = {42365026},
issn = {2396-8370},
abstract = {Urea is a small inorganic compound, readily available in saliva, that can be metabolised by the oral microbiome. We hypothesised that dietary supplementation with urea would increase salivary levels, alter microbial metabolism and, potentially, modify suprathreshold non-volatile flavour perception. A semi-trained panel of 20 participants completed taste evaluations using visual analogue scales for nine tastants, both before and during a 5-day urea supplementation regimen. System-level analysis revealed a significant shift in suprathreshold non-volatile flavour perception during supplementation (PERMANOVA, p = 0.008) even though none of the nine tastants showed significant changes (p > 0.05 or an absolute percentage change greater than 10%) during the intervention. Functional gene completeness analysis, together with [13]C NMR, suggested that the oral microbiome primarily utilises carbon dioxide generated from urease-mediated urea metabolism. Overall, urea supplementation was associated with changes in microbiome carbon-related metabolic pathways and induce holistic level changes in suprathreshold non-volatile flavour perception.},
}

@article {pmid42365232,
year = {2026},
author = {Gao, G and Wei, Z and Zhang, Q and Wang, Y and Zhao, Z and Wang, Y and Bao, H and Lv, Y},
title = {Study on the correlation between respiratory microbiome alterations and disease location/severity in children with Mycoplasma pneumoniae pneumonia.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05319-7},
pmid = {42365232},
issn = {1471-2180},
abstract = {Mycoplasma pneumoniae pneumonia (MPP) is a common form of community-acquired pneumonia in children, potentially involving multiple organ systems. Accumulating evidence suggests that dysbiosis of the respiratory microbiota is associated with various respiratory diseases. Nevertheless, it remains unclear how the respiratory microbiota varies across anatomical sites, interacts with other microbes, and correlates with host immunity in children with MPP compared to non‑MPP respiratory diseases. In this study, we collected and analyzed pharyngeal swabs, sputum, and bronchoalveolar lavage fluid samples from 401 pediatric MPP patients and 287 control subjects (MPP-negative children with other respiratory conditions).Comparative analysis revealed significant respiratory microbiome dysbiosis in MPP patients, with Mycoplasmoides constituting 30.33% of the total microbial community. A discriminative model based on Mycoplasmoides abundance demonstrated excellent performance (AUC = 0.983, sensitivity = 95.3%, specificity = 98.3%). Notably, Mycoplasmoides abundance showed significant negative correlations with Prevotella, Veillonella_A, Staphylococcus, and Rothia, suggesting potential inhibitory effects.Anatomical distribution analysis indicated distinct microbial distributions: Prevotella and Veillonella_A were predominantly enriched in the upper respiratory tract, while Mycoplasmoides showed greater abundance in the lower respiratory tract. Consistency analysis supported the hypothesis of microbial translocation from upper to lower respiratory tract in affected children.Severe MPP cases exhibited significantly higher Mycoplasmoides abundance. For correlations with clinical indicators, both Mycoplasmoides and Streptococcus showed nominal associations. Our findings elucidate the complex interplay between respiratory microbiota in pediatric MPP patients and its association with disease severity and clinical outcomes. This study highlights the need for further research to explore and validate the prognostic relevance of value of these microbial markers.},
}

@article {pmid42365269,
year = {2026},
author = {Fassarella, M and Smidt, H},
title = {Translational human gut microbiome research: What are the missing pieces of the puzzle?.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08490-7},
pmid = {42365269},
issn = {1479-5876},
abstract = {BACKGROUND: Human gut microbiome research has expanded remarkably over the past two decades, revealing the fundamental role of gut microbes in human health and disease. Despite these advances, translation into evidence-based clinical practice and public health implementation remains exceptionally limited. This integrative translational perspective review evaluates human gut microbiome research across four critical aspects: translational successes, barriers to effective translation, applicability of frameworks from other medical disciplines, and strategies to enhance translational progress.

MAIN TEXT: Human gut microbiome research was evaluated through the lens of translational medical research principles, as summarised below. (1) Translational successes in human gut microbiome research are explored by analysing the developmental pathways of major microbiome-based or microbiome-targeted approaches, including faecal microbiota transplantation, probiotics, postbiotics, prebiotics, and dietary interventions, despite overall limited clinical and public health translation. (2) Established translational medical research frameworks served as a foundation to identify missing elements in current human gut microbiome research, including progression through T0-T4 phases, bidirectional knowledge flow, prioritization of unmet patient and societal health needs, patient-centric approaches, stakeholder engagement, and interdisciplinary collaboration. Integration of these principles is discussed in light of the specific characteristics, challenges, and limitations of human gut microbiome research. (3) Translational barriers in human gut microbiome research were analysed beyond limited integration of translational medical principles. These arise from the inherent complexity and high-dimensional nature of the gut microbiome, temporal and inter-individual variability, confounding factors, inconsistent methodological standardization and validation, and fragmentation across research efforts. Collectively, these barriers hinder causal inference, resulting in a low-quality evidence base and limiting effective translation. (4) A framework to advance translational human gut microbiome research is proposed based on the previous findings, including strategic priorities such as education and training in translational research principles for gut microbiome researchers.

CONCLUSIONS: Human gut microbiome research remains largely confined to early translational phases, with progression toward effective translation limited by intrinsic and methodological barriers that hinder causal inference and high-level evidence generation. Integration of core translational medical research principles offers a pathway to bridge these gaps, with education and training of gut microbiome researchers emerging as a key priority for advancing translational progress.},
}

@article {pmid42365322,
year = {2026},
author = {Gong, S and Zhang, Y and Du, W and Zhang, C and Wu, N and Zhang, X and Ren, Z and Zhang, Y and Zhang, P and Zhan, C and Wu, X},
title = {An oral berberine nanocapsule platform orchestrates microbiota for potent gastric cancer chemotherapy.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04674-x},
pmid = {42365322},
issn = {1477-3155},
support = {32101063//National Natural Science Foundation of China/ ; 2025C02056//Pioneer R&D Program of Zhejiang/ ; SLJ0314//Leading Talent of Chinese Medicine in Jiangsu Province/ ; },
abstract = {Systemic chemotherapy for gastric cancer is frequently compromised by debilitating, dose-dependent toxicities, necessitating innovative adjunctive strategies that balance therapeutic efficacy with systemic safety. While natural products represent a promising source of candidates, their clinical translation is frequently hindered by intrinsic pharmacokinetic barriers. To address this, we developed the oral resident binary intestinal therapy (ORBIT) system, an excipient-free nanocapsule platform engineered for prolonged gut residency. Unlike conventional pharmaceutical formulations that depend on synthetic excipients, ORBIT is an excipient-free, self-assembled nanocapsule composed of a high-density dopamine-functionalized hyaluronic acid (hDAHA) shell encapsulating a berberine (BBR) core. This unique architecture provides a protective shield for BBR against premature degradation while utilizing the adhesive properties of the hDAHA shell to enhance gastrointestinal retention. ORBIT enables sustained, pH-responsive drug release, providing robust in situ shielding of the intestinal mucosa against oxaliplatin-induced injury and preserving epithelial barrier integrity. In preclinical gastric cancer models, the ORBIT regimen synergistically potentiates oxaliplatin-mediated tumor suppression while dramatically ameliorating systemic toxicity. Mechanistically, ORBIT administration profoundly remodels the microbiome-immune axis, specifically enriching beneficial commensals such as Akkermansia to drive increased intratumoral infiltration of CD8[+] T cells. This study establishes a new oral nanotherapeutic paradigm for chemo-immunotherapy, presenting a compelling and clinically translatable strategy to optimize gastric cancer treatment outcomes.},
}

@article {pmid42365405,
year = {2026},
author = {Ying, C and Jiajun, Q and Yuyuan, LU and Chongxiang, X and Zhongyuan, X},
title = {Mechanism of Buzhong Yiqi decoction for Hashimoto's thyroiditis: insights from gut microbiota and metabolomics.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {46},
number = {3},
pages = {571-583},
pmid = {42365405},
issn = {2589-451X},
support = {2023-NHLHCRF-BQ-28//National High Level Hospital Clinical Research Funding: Study on the Mechanism of the Gut Microbiota Participating in the Metabolic Regulation Therapy of Hashimoto's Thyroiditis by Buzhong Yiqi decoction/ ; TJF-QN-2023-06//Tongchuan Thyroid Disease Prevention Center 2023 Research Special Youth Project: Study on the Mechanism of Buzhong Yiqi decoction in Treating Hashimoto's Thyroiditis by Improving Gut Mucosal Barrier/ ; 81973855//National Natural Science Foundation of China: Action Mechanism of Buzhong Yiqi decoction in Treating Hashimoto's Thyroiditis Based on Transforming Growth Factor β/Smad Signaling Pathway and the Balance between Treg and Th17 Cells/ ; },
mesh = {Animals ; *Drugs, Chinese Herbal/administration & dosage ; Rats ; *Gastrointestinal Microbiome/drug effects ; Metabolomics ; Humans ; Female ; *Hashimoto Disease/drug therapy/metabolism/microbiology ; Male ; Rats, Sprague-Dawley ; },
abstract = {OBJECTIVE: To investigate the effect of Buzhong Yiqi decoction (BZYQ) and its potential mechanism by conducting a comprehensive analysis of intestinal microbiota and metabolomics in autoimmune thyroiditis (AIT) rats.

METHODS: An AIT model with antibiotic cocktail were established. After 8 weeks of intervention with BZYQ, the levels of anti-thyroid peroxidase antibodies (TPOAb) and thyroglobulin antibodies (TGAb) were measured. Pathological changes were assessed using hematoxylin and eosin staining. Changes of gut microbiota and fecal metabolites were analyzed through 16S RNA sequencing and metabolomics analysis.

RESULTS: BZYQ intervention improved pathological damage of thyroid gland in AIT rats and significantly reduced the levels of anti-thyroid antibodies. Additionally, it had an ameliorative effect on the pathological damage of the colon. Also, BZYQ increased the abundance of Lactobacillus reuteri, reversing the dysbiosis of the gut microbiota. And BZYQ could regulate tryptophan metabolism of tryptophan to reverse metabolic disorders in HT. The correlation analysis indicated a close relationship between tryptophan metabolism and Lactobacillus reuteri.

CONCLUSIONS: BZYQ is a promising therapeutic approach for HT. Its mechanism in treating HT may be associated with the regulation of gut microbiota dysbiosis and the improvement of gut-derived metabolic disorders.},
}

Animals
*Drugs, Chinese Herbal/administration & dosage
Rats
*Gastrointestinal Microbiome/drug effects
Metabolomics
Humans
Female
*Hashimoto Disease/drug therapy/metabolism/microbiology
Male
Rats, Sprague-Dawley

@article {pmid42365572,
year = {2026},
author = {Abebaw, D and Adugna, A and Tegegne, BA and Teffera, ZH and Selabat, B and Kindie, Y and Tilahun, M and Belew, H and Baylie, T and Mengistu, G and Jemal, M and Atnaf, A},
title = {Harnessing the gut microbiome for improved immune checkpoint inhibition in colorectal cancer immunotherapy: a narrative Review.},
journal = {Clinical and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10238-026-02222-3},
pmid = {42365572},
issn = {1591-9528},
abstract = {Colorectal cancer (CRC) remains among the most prevalent and deadliest malignancies worldwide, with limited survival outcomes, particularly in patients with metastatic disease. Despite advances in immunotherapy, immune checkpoint inhibitors (ICIs) have shown efficacy mainly in mismatch repair-deficient (dMMR) CRC, while responses in mismatch repair-proficient (pMMR) microsatellite-stable (MSS) cases remain limited. Emerging evidence highlights the gut microbiome as a critical factor influencing CRC development, progression, and therapeutic response. In particular, the gut microbiota has been shown to affect the efficacy of ICIs, with dysbiosis contributing to treatment resistance and specific microbial taxa enhancing antitumor immune responses. Preclinical and clinical studies have demonstrated that microbiome-based interventions, including probiotics, fecal microbiota transplantation (FMT), dietary modulation, and traditional medicines, can restore immune function by modulating immune cell populations and producing immunoregulatory metabolites. These effects may enhance responsiveness to ICIs and contribute to the suppression of tumor growth. However, we also address key limitations in this field, including inconsistent findings and safety concerns, such as infection risks, to guide future translational efforts. Overall, while microbiome-based interventions represent a promising adjunct to CRC immunotherapy, rigorous clinical trials and mechanistic validation are required before their routine clinical implementation.},
}

@article {pmid42365602,
year = {2026},
author = {Carvalho, OMS and Abukwaik, A and Sultan, O and Koizia, LJ and Harris, BHL},
title = {An OLD DOG teaching us new tricks in ageing biology.},
journal = {The Journal of frailty & aging},
volume = {15},
number = {4},
pages = {100181},
doi = {10.1016/j.tjfa.2026.100181},
pmid = {42365602},
issn = {2260-1341},
}

@article {pmid42357744,
year = {2026},
author = {Jiang, X and Zhang, X and Sun, Y and Liu, S and Chen, X and Zhong, R and Cao, Y and Sun, Q and Wu, S},
title = {Balancing High Yield and Metabolic Health in Dairy Ruminants: The Central Hub Role of the Rumen Microbiota.},
journal = {Veterinary sciences},
volume = {13},
number = {6},
pages = {},
pmid = {42357744},
issn = {2306-7381},
support = {32573272 and U23A20234//National Natural Science Foundation of China/ ; 2025JH-ZRKX-0639//Natural Science Foundation of Xi'an/ ; 2025JCQY049//Agricultural Innovation Technology Project and Key Agricultural Technology Core Research Project/ ; },
abstract = {Modern dairy production has greatly increased milk yield, but high productivity is often accompanied by greater metabolic pressure, particularly during the transition period. Ketosis, fatty liver, and subacute ruminal acidosis are major disorders that limit health, efficiency, and sustainability in high-yielding dairy ruminants. This review examines the rumen microbiota as a central biological interface linking diet, ruminal fermentation, epithelial function, hepatic metabolism, and inflammation. Under homeostatic conditions, the rumen microbiota supports lactation by converting dietary fibre, starch, and nitrogen into volatile fatty acids, microbial protein, and other metabolites required for gluconeogenesis, milk component synthesis, and epithelial maintenance. However, under excessive nutritional or physiological stress, especially high-concentrate feeding and periparturient negative energy balance, this system may shift toward dysbiosis, acid accumulation, lipopolysaccharide release, epithelial barrier impairment, and activation of gut-liver inflammatory pathways. These changes can contribute to the occurrence and interaction of subacute ruminal acidosis, ketosis, and fatty liver. We further summarize key factors affecting rumen microbial stability, including diet structure, host variation, physiological stage, environmental stress, feeding management, and ruminal epithelial volatile fatty acid absorption. Finally, microbiome-oriented strategies, such as gradual dietary transition, nutritional preconditioning, probiotics, postbiotics, functional metabolites, host metabolic support, and epithelial-targeted interventions, are discussed. Maintaining rumen microbial homeostasis should be regarded as a core principle for balancing high milk yield with long-term metabolic health. Future research should move beyond descriptive profiling toward causal validation of host-microbe interactions and the development of microbiome-based early-warning and individualized nutritional management systems.},
}

@article {pmid42357757,
year = {2026},
author = {Ma, L and Qu, J and Li, X and Liu, Y},
title = {Ecological Reassembly of the Milk Microbiome and Its Associated Resistome During the Dry Period in Dairy Cows.},
journal = {Veterinary sciences},
volume = {13},
number = {6},
pages = {},
pmid = {42357757},
issn = {2306-7381},
support = {2023YFD1800100//National Key Research and Development Program of China/ ; No. IFR-06//the Agricultural Science and Technology Innovation Program/ ; },
abstract = {The aim of this study was to characterize the coordinated dynamics of the mammary microbiome, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the dry period, calving, and early lactation. The mammary microbiome undergoes substantial ecological changes across these stages, yet the coordinated dynamics of microbial composition, ARGs, and MGEs remain poorly understood. Here, shotgun metagenomic sequencing was performed on mammary secretion samples collected before dry-off (BM), immediately after calving (ACM), and one month postpartum (AM). The mammary microbiome exhibited a clear "exposure-bottleneck-reassembly" trajectory. BM was characterized by high microbial diversity and the enrichment of environmentally associated taxa, whereas ACM displayed a pronounced immunological bottleneck with markedly reduced microbial diversity and network complexity. During AM, microbial communities partially recovered but remained distinct from the BM state, indicating persistent ecological restructuring after calving. ARGs and MGEs showed parallel dynamics, with broad resistome and mobilome diversity in BM, a sharp contraction in ACM, and a selective re-expansion in AM. Network analysis further revealed maximal ecological complexity in BM, increased ARGs/MGEs connectivity in ACM, and partial stabilization in AM. These findings demonstrate that host physiological transitions, together with dry cow therapy (DCT), drive the coordinated remodeling of the mammary microbiome, resistome, and mobilome across the dry period.},
}

@article {pmid42357793,
year = {2026},
author = {Barahona, ER and Dias, ALG and Egyedy, A and Ametaj, BN},
title = {Intravaginal Probiotics in Transition Dairy Cows: A Randomized Multi-Farm Field Trial on Health and Milk Production.},
journal = {Veterinary sciences},
volume = {13},
number = {6},
pages = {},
pmid = {42357793},
issn = {2306-7381},
support = {2015D00R7//Alberta Ministry of Agriculture and Forestry/ ; },
abstract = {Uterine infections (metritis and endometritis) are a leading cause of culling and reproductive failure in transition dairy cows, and antibiotic-resistant Gram-negative pathogens limit conventional therapy. This randomized, controlled, multi-farm field trial evaluated whether four intravaginal infusions of a host-adapted lactic acid bacteria (LAB) cocktail (Lactobacillus sakei FUA3089, Pediococcus acidilactici FUA3138, P. acidilactici FUA3140; 10[8]-10[9] cfu/dose) at -3, -2, +3, and +4 weeks relative to calving reduce periparturient disease and improve milk production. A total of 526 pregnant cows (426 Holstein, 100 Jersey) from four commercial Alberta farms (automatic-milking, parlor, and certified-organic systems) were block-randomized within farm and parity to TRT1 (saline; n = 175), TRT2 (saline + skim milk; n = 176), or TRT3 (LAB cocktail in saline + skim milk; n = 175). Uterine infection incidence was assessed by Metricheck™ mucus scoring and transrectal ultrasonography at +3 and +4 weeks postpartum. Across the principal peripartum infectious outcomes, TRT3 showed a consistent protective effect: uterine infection incidence was lowest in TRT3 (18.8% vs. 25.1% in pooled controls; OR = 0.69; 95% CI, 0.44-1.09; an approximately 25% relative reduction; exact p = 0.12), and this metritis signal was additionally supported by a repeated-measures mixed model accounting for farm, parity, and week (p = 0.0175), although the Bonferroni-adjusted pairwise contrasts were tendencies (adjusted p ≈ 0.12), and the effect did not differ by parity (treatment × lactation interaction, p = 0.97). Subclinical mastitis was numerically lower in TRT3 than in pooled controls (5.3% vs. 8.9%; OR = 0.57; 95% CI, 0.27-1.24; exact p = 0.16), whereas retained placenta, milk fever, displaced abomasum, and lameness showed no clear cow-level treatment effect in the cow-level exact analyses. Milk yield increased significantly in multiparous cows, which produced 4.6 L/day more milk than TRT1 and 3.22 L/day more than TRT2 over the first 50 days in milk (p < 0.01 for both contrasts; treatment × parity interaction, p = 0.01). No effect was seen on milk composition, uterine involution, or reproductive performance. The trial supports intravaginal LAB as a candidate antibiotic-free prophylactic whose response depends on farm- and cow-level contexts and whose mechanisms require confirmation through microbiological and metabolic measurements.},
}

@article {pmid42358093,
year = {2026},
author = {Öz, M and Üstüner, E and Çifci, S and Dikel, S and İleri, E and Budak, F},
title = {Innovative Field Applications of Probiotics, Prebiotics, and Medicinal Plant Products for Disease Control in Aquaculture.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70227},
doi = {10.1111/jfd.70227},
pmid = {42358093},
issn = {1365-2761},
abstract = {Disease outbreaks and the associated reliance on antibiotics pose major constraints to the sustainability of modern aquaculture. As regulatory pressures increase and consumer demand shifts toward residue-free production, diverse biological interventions are gaining prominence as viable alternatives to chemotherapeutics. These include microbiome-modulating agents (probiotics, classical prebiotics, and synbiotics), alongside a distinctly separate category of functional additives: phytogenics (medicinal plant derivatives), which are valued for their direct bioactive and immunomodulatory properties. This review synthesizes current laboratory and field-based evidence regarding the efficacy, mechanisms, and practical challenges of these functional additives. While in vitro and controlled studies demonstrate clear benefits in immune modulation, competitive exclusion, and gut health, real-world application is frequently hindered by environmental inconsistencies and formulation instability. We critically evaluate the impact of system-specific variables and draw several specific mechanistic inferences: First, the over-reliance on static in vitro assays fundamentally fails to predict in vivo colonization under multifactorial field stress (e.g., thermal and pH fluctuations). Second, thermal degradation during industrial feed extrusion is a primary driver of batch-to-batch inconsistency, rendering advanced microencapsulation and post-coating techniques practically mandatory for viable delivery. Third, the efficacy of functional additives is strictly governed by the culture matrix; while the chemical stability of Recirculating Aquaculture Systems (RAS) yields predictable outcomes, open ponds face severe abiotic fluctuations, and Biofloc Technology (BFT) requires precise Carbon-to-Nitrogen (C:N) stoichiometry to facilitate heterotrophic assimilation. To overcome these limitations, we propose a strategic shift toward next-generation interventions specifically thermal-stable postbiotics, precision phage therapy for niche-clearing, and rigorous multi-omics technologies for molecular validation, replacing purely phenotypic observations. By integrating these specific innovations within a precision digital health framework, this work provides a comprehensive roadmap for standardizing bio-based disease control for sustainable and reproducible aquaculture production.},
}

@article {pmid42358128,
year = {2026},
author = {Lin, JC and Wang, QS and Guo, ZM and Zhang, F and Qiu, CY},
title = {Associations between oral microbiome diversity and rheumatoid arthritis in U.S. adults: NHANES 2009-2012.},
journal = {Acta odontologica Scandinavica},
volume = {85},
number = {},
pages = {360-372},
doi = {10.2340/aos.v85.46064},
pmid = {42358128},
issn = {1502-3850},
mesh = {Humans ; *Microbiota ; Cross-Sectional Studies ; Female ; United States/epidemiology ; *Arthritis, Rheumatoid/microbiology/epidemiology ; Nutrition Surveys ; *Mouth/microbiology ; Male ; Adult ; Middle Aged ; },
abstract = {OBJECTIVE: Although links exist between periodontitis and rheumatoid arthritis (RA), and the gut microbiome has been implicated in RA pathogenesis, the role of oral microbiome diversity in RA remains insufficiently characterized. This study aimed to explore the association between oral microbiome diversity (including alpha and beta diversity) and RA status through a cross-sectional analysis of the National Health and Nutrition Examination Survey (NHANES).

MATERIAL AND METHODS: This cross-sectional study analyzed data from 1,544 participants aged ≥ 20 years derived from the 2009-2012 NHANES cycles. We employed multivariate logistic regression, restricted cubic splines (RCS), receiver operating characteristic (ROC) curve analysis, SHapley Additive exPlanations (SHAP) method and beta diversity assessment (Principal Coordinate Analysis [PCoA] and Permutational Multivariate Analysis of Variance [PERMANOVA]) to examine associations between oral microbiome diversity metrics and RA.

RESULTS: After adjustments, four alpha diversity metrics (observed amplicon sequence variants [ASVs]: OR [95% CI] = 0.996 [0.992, 0.999], P = 0.043; Faith's PD: OR [95% CI] = 0.943 [0.900, 0.988], P = 0.014; Shannon-Wiener index: OR [95% CI] = 0.786 [0.641, 0.965], P = 0.021; Simpson index: OR [95% CI] = 0.127 [0.018, 0.915], P = 0.037) were significantly inversely associated with the presence of RA. This relationship was approximately linear (P for nonlinear > 0.05) and moderated by socioeconomic factors (P for interaction < 0.05). ROC and SHAP analyses revealed that the Simpson index had the highest explanatory capacity for RA. However, beta diversity (Bray-Curtis, UniFrac distances) revealed no significant differences between RA and non-RA groups (all P > 0.05).

CONCLUSIONS: Higher oral microbiome alpha diversity is significantly associated with lower prevalence of RA. Oral microbial diversity may serve as a potential indicator associated with RA status. However, given the cross-sectional nature of this study, longitudinal and interventional studies are warranted to further elucidate causal relationships.},
}

Humans
*Microbiota
Cross-Sectional Studies
Female
United States/epidemiology
*Arthritis, Rheumatoid/microbiology/epidemiology
Nutrition Surveys
*Mouth/microbiology
Male
Adult
Middle Aged

@article {pmid42358148,
year = {2026},
author = {Yuan, SL and Huang, YQ and Li, CT and Xu, DQ and Zheng, X},
title = {[Research progress on the role of the microbiota-gut-liver axis immune pathway in metabolic dysfunction-associated steatotic liver disease].},
journal = {Sheng li xue bao : [Acta physiologica Sinica]},
volume = {78},
number = {3},
pages = {579-591},
doi = {10.13294/j.aps.2025.0075},
pmid = {42358148},
issn = {0371-0874},
mesh = {Humans ; *Liver/immunology ; *Fatty Liver/immunology/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; *Metabolic Diseases/immunology/complications ; Animals ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a widely prevalent chronic liver disease that presents significant challenges to public health and medical care worldwide, yet its underlying mechanisms remain incompletely understood. The gut microbiome plays a crucial role in MASLD. Liver inflammation is a key factor in the onset and progression of this disease, and the gut microbiota significantly influences the liver's immune system and inflammatory responses. This article aims to review how both pro-inflammatory and anti-inflammatory gut microbes regulate liver inflammation by activating liver immunity and enhancing liver immune protection, respectively, through the microbiota-gut-liver axis. This review seeks to provide valuable insights for the improvement and treatment of MASLD.},
}

Humans
*Liver/immunology
*Fatty Liver/immunology/microbiology
*Microbiota
*Gastrointestinal Microbiome
*Metabolic Diseases/immunology/complications
Animals

@article {pmid42358218,
year = {2026},
author = {Wang, L and Song, J and Wang, H and Wang, T and Li, J and Cao, N and Li, Y and Gu, Z and Jiang, X},
title = {Polyphenol-based nanoparticles enhancing doxycycline efficacy for acne therapy.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5tb02875b},
pmid = {42358218},
issn = {2050-7518},
abstract = {Acne is an inflammatory dermatological disorder largely caused by Cutibacterium acnes (C. acnes), which primarily affects the face, neck, chest, and back, leading to skin impairment. This condition is often associated with post-inflammatory erythema, hyperpigmentation, and scarring, as well as psychosocial and emotional distress. Based on the major pathological characteristics of acne with microbiome colonization, and multiple immune responses, we selected doxycycline, a common clinically used antibiotic and anti-inflammatory drug, and epigallocatechin gallate (EGCG), a polyphenol, to construct topically applicable nanoparticles (NPs). The resulting doxycycline-EGCG (DE) NPs significantly reduced the proportion of dead cells in C. acnes-induced HaCaT cells and demonstrated excellent anti-inflammatory effects through inhibition of NF-κB and STAT3 pathways compared to doxycycline alone. Moreover, the DE NPs exhibited better antibacterial efficacy against C. acnes along with improved antioxidant capacity than doxycycline. In an acne-like mouse model, the DE NPs also effectively suppressed skin inflammation and reduced inflammatory cytokine expression. Overall, this work presents a co-assembly strategy driven by covalent and non-covalent interactions, affording polyphenol-based doxycycline NPs with potent anti-inflammatory, antioxidant and antibacterial properties, and offering new opportunities for safe and effective acne local therapy.},
}

@article {pmid42358245,
year = {2026},
author = {Cheng, W and Li, N and Huang, Y and Wei, C and Li, R and Zhang, Y and Chang, Q and Jiang, C},
title = {Regional physicochemical filtering shapes microbiome-metabolome coupling at the Huangshui interface during Nongxiangxing Baijiu fermentation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1869375},
pmid = {42358245},
issn = {1664-302X},
abstract = {INTRODUCTION: Huangshui (HS), the liquid fraction that accumulates at the bottom of fermentation pits, serves as a key ecological interface linking microbial diversity and metabolism between fermented grains and pit mud during fermentation. Although HS is increasingly recognized as a reservoir of microorganisms and flavor precursors, how regional heterogeneity shapes its microbiome-metabolome coupling remains unclear.

METHODS: HS samples derived from nine representative Nongxiangxing Baijiu (NXB) production regions were compared using physicochemical characterization, amplicon sequencing, volatile metabolomics, and ecological association analysis.

RESULTS: The results showed marked regional differences in acidity, nitrogen availability, mineral nutrient content, and organic acid composition, indicating distinct fermentation microenvironments. Lactic acid dominated the acid pool in all samples, whereas short- and medium-chain fatty acids varied substantially among regions, suggesting differences in carbon flux allocation and chain elongation activity. Bacterial communities were dominated by Lactobacillus, methanogenic archaea, and Caproiciproducens, whereas fungal communities were enriched with fermentative yeasts (Pichia, Saccharomyces, and Kazachstania). A total of 162 volatile organic compounds were identified, with esters as the predominant aroma class, showing clear regional differentiation. Furthermore, integrated correlation and network analyses indicated that regional physicochemical factors acted as ecological filters, shaping microbial guild assembly and volatile metabolite patterns.

DISCUSSION: Lactobacillus emerged as a central taxon associated with acid-ester balance, whereas methanogenic and chain-elongating taxa were linked to carbon redistribution and medium-chain fatty acid formation. Further, these findings support the revised view of HS as an active metabolic interface, highlighting its potential for origin discrimination and precise fermentation control in NXB production.},
}

@article {pmid42358248,
year = {2026},
author = {Zuluaga-Quintero, C and Diaz Barrera, LE and Villamil, L},
title = {The dual role of Actinobacteria in aquaculture: a systematic review of metabolic benefits and detrimental effects.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1794932},
pmid = {42358248},
issn = {1664-302X},
abstract = {INTRODUCTION: Actinobacteria are ubiquitous and metabolically versatile members of aquatic microbiomes, yet their roles in aquaculture remain under-characterized compared with other microbial groups. This systematic review synthesizes current evidence on their functional duality in farmed fish systems, integrating both metabolic benefits and detrimental effects.

METHODS: Studies describing Actinobacterial isolates with at least one laboratory validation were systematically collected and critically evaluated. Methodological approaches were examined to distinguish in vitro bioactivity from in vivo effects and to assess taxonomic, genomic, and functional characterization.

RESULTS: Only a minority of studies progressed beyond in vitro screening, and a critical gap in genomic resolution was identified: almost half lacked molecular identification, and most relied solely on partial 16S rRNA sequencing. Streptomyces emerged as the predominant genus, accounting for most reports of both favorable and detrimental effects. Selected Streptomyces strains and their postbiotic fractions showed consistent antagonism against major fish pathogens, including Vibrio harveyi, Aeromonas hydrophila, and Streptococcus agalactiae, through quorum-sensing disruption, antibiofilm activity, nutrient competition, and targeted immunometabolic modulation. Conversely, Streptomyces, together with Nocardia and Mycobacterium, have been associated with geosmin and 2-methylisoborneol production, sporadic opportunistic infections, and putative involvement in tetrodotoxin cycling.

DISCUSSION: These outcomes appear highly context-dependent and reflect ecological adaptations rather than intrinsic hazards. By consolidating evidence on both beneficial and detrimental traits, this review highlights the need for genome-resolved taxonomy and ecologically informed screening pipelines to guide the safe and effective integration of Actinobacteria into aquaculture.},
}

@article {pmid42358249,
year = {2026},
author = {He, L and Huang, Y and Li, H and Zhu, B and Zhang, Z and Wu, J and Zhou, S and Zhan, Q and Wu, K and Wu, F},
title = {Novel insights into gut microbiota alterations in major depressive disorder with suicidal ideation: a metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1843301},
pmid = {42358249},
issn = {1664-302X},
abstract = {INTRODUCTION: Suicidal ideation in major depressive disorder (MDD) is common, yet its biological mechanisms and biomarkers remain unclear. The gut microbiota, a key component of the gut-brain axis, has been implicated, but current evidence is limited.

METHODS: We analyzed fecal samples from 141 participants, including 52 healthy controls (HCs) and 89 first-episode, drug-naïve MDD patients, further classified into suicidal ideation (SI, n = 57) and non-suicidal ideation (NSI, n = 32) groups using the Beck Scale for Suicide Ideation (BSSI). Shotgun metagenomic sequencing with HUMAnN3-based taxonomic and functional profiling was performed. Microbial diversity, differential abundance, and partial correlation analyses with suicidal ideation severity were conducted to identify key microbial taxa associated with suicidal ideation. For functional difference analysis, MaAsLin2 was employed across four levels: KEGG Orthology (KO), KEGG pathways, CAZy, and MetaCyc pathways. Mediation analysis was used to assess potential mediating effects between suicidal ideation and key microbial taxa after adjustment for age, sex, education, and BMI.

RESULTS: No significant differences were observed in overall microbial diversity. Bacteroides cellulosilyticus was enriched in HCs and showed a significant negative association with suicidal ideation severity. Functionally, compared with the NSI group, patients with suicidal ideation exhibited reduced microbial capacities related to peptidoglycan biosynthesis. Mediation analysis further indicated that B. cellulosilyticus may modulate suicidal ideation through pathways involved in carbohydrate transport and metabolism, vitamin K2 biosynthesis, and DNA repair.

CONCLUSION: Bacteroides cellulosilyticus may act as a potentially protective microbial species, negatively regulating suicidal ideation, possibly by enhancing carbohydrate metabolism and short-chain fatty acid production. Notably, this species has received limited attention in the context of psychiatric disorders, highlighting its potential as a novel microbial target. These findings provide new microbiome-based insights into suicidal ideation in MDD.},
}

@article {pmid42358257,
year = {2026},
author = {Mathes, F and Roussel, EG and Cragg, BA and Weightman, AJ and Sass, H and Parkes, RJ and Webster, G},
title = {Surface sediment microbial communities remain viable, culturable, and metabolically active during sequential heating.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1840877},
pmid = {42358257},
issn = {1664-302X},
abstract = {Marine sediments harbour a vast and diverse microbial biomass, yet it remains unclear how temperate surface sedimentary microbial communities transition to deep hot subsurface conditions. To simulate the effects of increasing temperature stress associated with deep burial, an estuarine surface sediment was sequentially heated from 15 °C to 90 °C over 434 days. Total cell counts increased during the first 210 days (42 °C), while FISH-detectable cells remained relatively constant for the first 56 days (15 °C). Overall culturability increased by one order of magnitude for heterotrophs and sulfate reducers, and by three orders of magnitude for methanogens. Subsequent heating from 42 °C to 90 °C resulted in a progressive decline in cell numbers, viability and culturability; however, culturable cells were detected throughout the experiment, including at the highest temperature (90 °C). Surprisingly, cells sampled at 90 °C were culturable across all incubation temperatures (15-90 °C) suggesting different members of the community were capable to grow across this large temperature range. Radiolabelled substrates were rapidly metabolised at 90 °C (≥1 day). Microbial community analysis demonstrated that with increasing temperature, members of the bacterial class Clostridia, mainly the Caldicoprobacteraceae (22.1%) and Peptococcaceae (10.5%) dominated the community. This study demonstrates that a phylogenetically diverse microbial community, originally adapted to temperate near-surface physicochemical conditions, can undergo functional and compositional restructuring and that certain members can become metabolically active under deep, thermally elevated sedimentary environments. This transition is likely mediated by the activation and selective enrichment of a cryptic thermophilic 'seed bank' present within the community and therefore may represent a mechanism of how deep sediments are inoculated with microbes and how the deep hot biosphere is sustained.},
}

@article {pmid42355923,
year = {2026},
author = {Mammadov, RA and Roest, HP and Fuhler, GM and Su, J and Visseren, T and Janssen, HLA and Porte, RJ and Murad, SD and Hansen, BE and van der Laan, LJW and Peppelenbosch, MP},
title = {Association of FUT2 rs601338 Genotype with Colonic Mucosal Microbiome Composition, Post-Transplant Bacteremia, and All-Cause Mortality After Liver Transplantation for Primary Sclerosing Cholangitis: A Retrospective Cohort Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {12},
pages = {},
pmid = {42355923},
issn = {2077-0383},
abstract = {Background/Objectives: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease frequently requiring liver transplantation (LTx). The gut-liver axis, host genetics, and microbial dysbiosis are thought to contribute to disease progression and post-transplant outcomes. The FUT2 rs601338 polymorphism influences mucosal fucosylation, host-microbial interactions, and susceptibility to infection. This study aimed to investigate the association between FUT2 genotype, colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in a retrospective single-center PSC cohort. Methods: This retrospective cohort study included PSC patients who underwent LTx at Erasmus MC University Medical Center (Rotterdam, The Netherlands) between 1987 and 2015. Pre-transplant archival formalin-fixed paraffin-embedded (FFPE) colonic biopsy specimens were available for microbiome analysis. Of 169 transplanted patients, FFPE tissue was available for 98 individuals, and FUT2 rs601338 genotyping was successfully performed in 87 patients. Patients were classified as FUT2 non-secretors (AA, n = 28) and secretors (GA/GG, n = 59). Post-transplant bacteremia was assessed based on clinically indicated blood cultures during follow-up. Colonic mucosal microbiome composition was analyzed using 16S rRNA gene sequencing. Results: FUT2 non-secretors showed a distinct colonic mucosal microbiome profile compared with secretors, characterized by differential abundance of selected taxa within Proteobacteria, Firmicutes, and Bacteroidetes. Post-transplant bacteremia occurred in 30 patients and was more frequent among non-secretors (43%) compared with secretors (15%). Both FUT2 non-secretor status and post-transplant bacteremia were associated with reduced all-cause post-transplant survival in Kaplan-Meier analysis and remained associated with mortality in multivariable regression models. Specific microbial taxa were also showed associations with bacteremia, mortality, and established prognostic scores, including the Amsterdam-Oxford Model and Mayo Risk Score. Conclusions: FUT2 genotype is associated with alterations in colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in PSC patients undergoing liver transplantation. These findings suggest a potential interplay between host genetics, intestinal microbiota, and infectious complications after transplantation. Given the retrospective design, limited sample size, and use of archival FFPE tissue, all findings should be interpreted as exploratory and hypothesis-generating. Prospective multicenter studies using standardized sampling and high-resolution metagenomic approaches are warranted for validation.},
}

@article {pmid42356004,
year = {2026},
author = {Greța-Oanță, AL and Roman, A and Berindan-Neagoe, I and Strilciuc, Ș and Vesa, ȘC and Pop, LA and Trombitaș, VE and Albu, S},
title = {Direct Maxillary Sinus Tissue Analysis for TAS2R38 Polymorphisms: Establishing a Tissue-Based Translational Framework in Odontogenic Rhinosinusitis.},
journal = {Journal of clinical medicine},
volume = {15},
number = {12},
pages = {},
pmid = {42356004},
issn = {2077-0383},
support = {882//Iuliu Hațieganu University of Medicine and Pharmacy/ ; },
abstract = {Background/Objectives: Bitter taste receptors (T2Rs), specifically T2R38, are present in the respiratory epithelium and react with bacterial quorum-sensing molecules to induce an innate immunity response. Although TAS2R38 polymorphisms have been correlated with susceptibility to chronic rhinosinusitis (CRS), they have not yet been explored in odontogenic rhinosinusitis (ORS), a distinct form of CRS with particular microbial and inflammatory features. We aim to establish a proof-of-concept methodology for investigating TAS2R38 genetic variants in ORS using direct maxillary sinus tissue analysis and demonstrate the feasibility of this translational approach. Methods: We conducted a prospective pilot case-control study of 36 ORS patients and 37 controls undergoing septoplasty without sinonasal disease. Maxillary sinus mucosal biopsies were obtained intraoperatively with informed consent. Genomic DNA was extracted using the PureLink Genomic DNA Mini Kit and quantified via NanoDrop spectrophotometry. TAS2R38 haplotypes were determined and classified as taster (PAV/PAV), non-taster (AVI/AVI), or intermediate (PAV/AVI) phenotype. Results: Among fully classifiable canonical TAS2R38 phenotypes (32 ORS patients, 28 controls), distributions were: tasters 12.5% vs. 25.0%, non-tasters 31.3% vs. 25.0%, and intermediate 56.3% vs. 50.0%. AVI/AVI non-taster status was not significantly associated with ORS susceptibility (OR = 1.36, 95% CI: 0.44-4.25; Fisher's exact p = 0.775). Conclusions: This proof-of-concept study demonstrates that genotyping-grade genomic DNA can be recovered from acutely inflamed maxillary sinus mucosa, validating this substrate for future tissue-based expression, functional, and microbiome analyses not obtainable from peripheral samples; germline genotyping itself does not require sinus tissue. The observed difference in non-taster prevalence (31.3% vs. 25.0%) did not reach statistical significance and is reported descriptively. This directional trend is hypothesis-generating only and, given the limited statistical power, does not constitute evidence for an association. The demonstrated feasibility, together with the established biological rationale, supports an adequately powered confirmatory study and lays the foundation for future investigation of taste receptor genetics in ORS pathogenesis, and potentially personalized therapeutic strategies.},
}

@article {pmid42356063,
year = {2026},
author = {Kyrochristou, I and Fousekis, F and Kyrochristou, GD and Schizas, D and Pappas-Gogos, G and Raptis, D and Ioannidis, O and Vlachos, K and Lianos, GD},
title = {Impact of Gut Microbiota on the Clinical Course and Treatment Outcomes of Colorectal Cancer-A Systematic Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {6},
pages = {},
pmid = {42356063},
issn = {1648-9144},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; *Gastrointestinal Microbiome/physiology ; Treatment Outcome ; Prognosis ; Feces/microbiology ; },
abstract = {Background and Perspectives: As colorectal cancer research focuses on improving screening policies and treatment strategies, the gut microbiome is emerging as a novel diagnostic and prognostic biomarker. This systematic review aims to present the available data on the role of gut microbiota in colorectal cancer diagnosis, prognosis, and treatment response. Materials and Methods: A systematic search under the PRISMA recommendation was conducted in PubMed database, until February 2026. Original human studies evaluating associations between gut microbiome composition and CRC diagnosis, survival outcomes, or therapeutic response were included. Both stool- and tissue-based analyses were considered. A qualitative synthesis of the data was performed. Results: Thirty-six studies met the inclusion criteria, encompassing case-control cohorts, prospective survival analyses, and early-phase translational trials. Across populations and sequencing methodologies, gut microbiome alterations were consistently identified, with enrichment of oral-derived anaerobes, particularly Fusobacterium nucleatum, and depletion of beneficial commensal taxa in CRC patients compared with controls. Beta-diversity analyses frequently showed distinct clustering of microbial communities between the CRC and control groups, whereas alpha-diversity findings were heterogeneous. Several stool-based multi-species classifiers demonstrated good to excellent diagnostic performance, particularly when combined with established screening modalities. Tumor-associated microbial signatures were further associated with adverse survival outcomes and, in exploratory cohorts, with differential treatment response. Emerging evidence suggests that the microbiome may represent a modifiable environmental factor, particularly relevant in early-onset CRC. Conclusions: The gut microbiome represents a promising adjunctive biomarker for CRC diagnosis and prognostic stratification, with potential implications for precision oncology. However, methodological heterogeneity and the need for prospective validation currently limit its routine clinical implementation.},
}

Humans
*Colorectal Neoplasms/microbiology/therapy/diagnosis
*Gastrointestinal Microbiome/physiology
Treatment Outcome
Prognosis
Feces/microbiology

@article {pmid42356119,
year = {2026},
author = {Persely, A and Piroska, M and Zoldi, L and Beszedics, B and Juhasz, J and Makra, N and Dunai, ZA and Szabo, D and Tarnoki, DL and Tarnoki, AD},
title = {The Role of Gut Microbiome in Mild Cognitive Impairment: A Twin Study.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {6},
pages = {},
pmid = {42356119},
issn = {1648-9144},
mesh = {Humans ; Male ; *Cognitive Dysfunction/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Aged ; Female ; RNA, Ribosomal, 16S/analysis ; Feces/microbiology ; Aged, 80 and over ; Twins, Monozygotic ; },
abstract = {Background and Objectives: Recent studies have revealed the potential roles of gut microbiota and microbial metabolites in influencing mild cognitive impairment (MCI) and Alzheimer's disease via the gut-brain axis. This relationship has not yet been investigated in monozygotic twin pairs, which represent an ideal model for minimizing genetic confounding. Materials and Methods: Seven twin pairs discordant for ACE and 15 for MoCA were enrolled. Stool samples were subjected to 16S ribosomal RNA-based microbiome analysis. Results: No significant differences in alpha or beta diversity were observed between MCI-discordant twin pairs at the genus or family level. The most robust finding was a significantly lower abundance of Lachnospiraceae in MCI-affected twins, identified independently by ANCOM-BC and LEfSe. Additional exploratory findings included higher abundances of Sutterella, Succinivibrio, Odoribacter, and Ruminococcus. However, several taxa showed opposing patterns between ACE- and MoCA-derived cohorts, highlighting the methodological impact of cognitive instrument selection. Conclusions: The convergent reduction of Lachnospiraceae across two independent analytical methods represents the most substantive finding. The remaining results are exploratory, limited by small sample size, restricted statistical power, and lack of availability to fully control for dietary habits, physical activity, and medication use. Validation in larger longitudinal twin cohorts with a standardized cognitive assessment is warranted.},
}

Humans
Male
*Cognitive Dysfunction/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology
Aged
Female
RNA, Ribosomal, 16S/analysis
Feces/microbiology
Aged, 80 and over
Twins, Monozygotic

@article {pmid42356129,
year = {2026},
author = {Pilateris, I and Bostanjopoulou, S},
title = {"Brain-First" vs. "Body-First" PD: Definitions and Implications in Everyday Clinical Practice: A Systematic Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {6},
pages = {},
pmid = {42356129},
issn = {1648-9144},
mesh = {Humans ; *Parkinson Disease/physiopathology/diagnosis/classification ; Disease Progression ; Biomarkers ; *Brain/physiopathology ; },
abstract = {(1) Background and Objectives: Parkinson's disease's (PD) underlying pathophysiology still remains incompletely understood, with Braak's hypothesis of ASyn pathology propagation being the most widely accepted. Recently, a novel model has been introduced, proposing two distinct ASyn propagation pathways: a bottom-up trajectory termed Body-first PD, and a central nervous system (CNS)-initiated pathway termed Brain-first PD. This distinction introduces new perspectives in the PD literature landscape regarding diagnosis, prognostic factors and patient management. This study set out to systematically synthesize the current literature comparing Brain-first and Body-first PD, with a focus on clinical characteristics and disease progression, diagnostic biomarkers, and management approaches. (2) Materials and Methods: A systematic literature search was conducted in March 2025 using PubMed, Cochrane Library, DOAJ and Google Scholar. Human observational, diagnostic, and interventional studies published between 2019 and March 2025, including patients with de novo or early PD, were eligible. Pre-motor REM sleep behavioral disorder (RBD) was used as the primary differentiation criterion. Risk of bias was evaluated using the Joanna Briggs Institute (JBI) critical appraisal checklists. Results were synthesized using a narrative approach. (3) Results: Sixteen studies comprising 2107 PD patients met the inclusion criteria. Body-first PD was associated with a higher non-motor symptom (NMS) burden, faster disease progression, and a higher prevalence of cognitive impairment. Additionally, Body-first PD patients exhibited more widespread and symmetrical neurodegeneration, along with electrophysiological and metabolic differences. Distinct biomarker and microbiome profiles were also observed between subtypes. No eligible studies addressing management approaches were identified. (4) Conclusions: In conclusion, the available evidence suggests that Brain-first and Body-first PD may represent two distinct pathophysiological entities, a proposal with great significance for the diagnosis, prognosis and management of PD patients. However, the predominantly cross-sectional nature of the current literature limits causal inference. Future longitudinal and interventional studies are required to clarify the potential clinical implications of this subtype classification theory.},
}

Humans
*Parkinson Disease/physiopathology/diagnosis/classification
Disease Progression
Biomarkers
*Brain/physiopathology

@article {pmid42356145,
year = {2026},
author = {Anton, D and Băciuț, M and Almășan, O},
title = {The Oral-Gut Microbiome Connection in Patients with Periodontitis: A Systematic Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {6},
pages = {},
pmid = {42356145},
issn = {1648-9144},
support = {100418/29.08.2025, SMIS code 350525//Ministry of Investments and European Projects/ ; },
mesh = {Humans ; *Periodontitis/microbiology/physiopathology/complications ; *Gastrointestinal Microbiome/physiology ; Inflammation ; *Mouth/microbiology ; *Microbiota ; },
abstract = {Background and Objectives: This study aims to evaluate the recent literature on the oral-gut connection in the context of periodontal disease, emphasizing the significance of systemic risk associated with chronic inflammation. This review explores whether chronic inflammation resulting from periodontal disease can induce systemic conditions through alterations in the gut microbiome and whether periodontal treatment may contribute to overall health improvement. Materials and Methods: A systematic database search was performed using pre-established search strategies. Searches were conducted in three databases between 1 and 20 October 2025. A total of 578 articles were screened for eligibility based on inclusion and exclusion criteria. Two authors agreed on the selection process used. The methodological quality of the included studies was assessed using the Newcastle-Ottawa scale and the Risk of Bias 2 Tool. Results: Eleven studies were considered eligible for inclusion in the review. The gut microbiome is similar to the oral microbiome in patients with periodontitis. Gut microbial shifts may drive systemic inflammation and metabolic dysfunction. Tooth loss and gum disease are linked to alterations in the gut bacteria, potentially compromising the intestinal barrier permeability. In contrast, the presence of natural teeth may prevent oral-gut bacterial transmission. Changes in the gut microbiota are correlated with improvements in periodontal status after non-surgical periodontal therapy. Conclusions: The evidence presented in this review supports an association between periodontitis, oral-gut microbial alterations, and systemic inflammatory conditions. However, most available studies are observational, limiting causal inference. Targeted modulation of the gut microbiome may represent a promising area for future research, but its clinical applicability remains inconclusive.},
}

Humans
*Periodontitis/microbiology/physiopathology/complications
*Gastrointestinal Microbiome/physiology
Inflammation
*Mouth/microbiology
*Microbiota

@article {pmid42356224,
year = {2026},
author = {Barbazza, S and van der Hoeven, M and Ponce, MC and Weber, AM and Fauzi, MD and Soekarjo, DD and Ryan, EP and Fortin, S and Wieringa, FT},
title = {Addition of Prebiotic Rice Bran to Ready-to-Use Therapeutic Food Modulated Changes in Body Composition Only of 6-23-Month-Old Children During Treatment for Uncomplicated Acute Malnutrition: The Solutions to Enhance Health with Alternative Treatment (SEHAT) Study.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356224},
issn = {2072-6643},
support = {NA//Thrasher Research Fund/ ; },
mesh = {Humans ; *Oryza ; Double-Blind Method ; *Body Composition ; Female ; Male ; Infant ; *Prebiotics/administration & dosage ; Weight Gain ; Food, Processed ; Treatment Outcome ; *Severe Acute Malnutrition/diet therapy ; },
abstract = {Background: Ready-to-use therapeutic foods (RUTFs) have been developed to treat severe acute malnutrition (SAM) in children by promoting rapid weight gain, but the long-term effects have been overlooked. Incorporating prebiotic rice bran into RUTF can enhance balanced weight gain. We hypothesized that children receiving RUTF + rice bran would exhibit increased fat-free mass (FFM) and reduced body fat percentage and abdominal adiposity. Methods: A double-blinded randomized controlled trial (ClinicalTrials.gov:NCT05319717) involving 200 children with different degrees of acute malnutrition compared the effectiveness of RUTF with or without rice bran. Children received treatment for 8 weeks, with another 8 weeks of follow-up. Anthropometry, including skinfolds, was collected every 4 weeks. Results: Compliance was similar in both groups (~21%). Children aged 6 to 23 months receiving RUTF + rice bran gained more FFM than those receiving RUTF alone (p = 0.05 at week 8). Over the 8-week treatment, the fat mass index increased in children receiving RUTF (p = 0.02), but not in those receiving RUTF + rice bran (p = 0.48), although the increase in body fat percentage was similar (p = 0.23). The ratio of abdominal to peripheral skinfolds decreased in both groups during treatment but increased during follow-up, though the difference was not statistically significant. In children aged 24 to 59 months, no significant differences in body composition were observed. The fat-free mass index increased in both groups during treatment but declined afterwards, with significant changes noted in the RUTF + rice bran group. Conclusions: The addition of rice bran to RUTF affected body composition changes during treatment only in younger children, where more lean mass was gained and fat mass gain was limited. Differences in intestinal microbiome maturity might underlie this age difference.},
}

Humans
*Oryza
Double-Blind Method
*Body Composition
Female
Male
Infant
*Prebiotics/administration & dosage
Weight Gain
Food, Processed
Treatment Outcome
*Severe Acute Malnutrition/diet therapy

@article {pmid42356234,
year = {2026},
author = {Eftekhar, MS and Singh, D and Katz, J and Nguyen, V and Menghini, P and Rodriguez-Palacios, A and Cominelli, F and Raffner Basson, A},
title = {Effect of Short-Term Grape Powder Supplementation in Patients with Crohn's Disease: A Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356234},
issn = {2072-6643},
support = {n/a//California Grape Commission/ ; K01DK127008, DK055812, DK091222, DK097948, and P01DK091222//NIH/NIDDK/ ; 1P01DK091222-24/NH/NIH HHS/United States ; 1R21DK118373-24/NH/NIH HHS/United States ; },
mesh = {Humans ; *Crohn Disease/microbiology/diet therapy ; Pilot Projects ; *Vitis ; Adult ; Female ; *Dietary Supplements ; Male ; Feces/microbiology/enzymology ; Powders ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Peroxidase/analysis ; C-Reactive Protein/metabolism/analysis ; },
abstract = {Background: The overall objective of this pilot diet intervention study was to determine the effect of grape powder (GP) supplementation on gut microbiota composition and inflammatory markers in individuals with Crohn's disease (CD). Methods: Adult CD participants were recruited from the Digestive Health Institute at University Hospitals Medical Center, Cleveland. All participants were supplemented with 45 g/day of freeze-dried grape powder (equivalent to ~1.5 cups of fresh grapes) daily for 21 days. The primary outcome was the change in fecal microbiome profiles. Secondary outcomes included the absolute difference (day 21-day 0) in Harvey Bradshaw Index (HBI) score, fecal myeloperoxidase (MPO), and high-sensitivity C-reactive protein (hsCRP). Results: A total of 21 CD participants were included in the final analysis. After 21 days of GP supplementation, more than half of the participants (13, 61.9%) experienced a reduction in fecal MPO, while 80% (17) experienced either a reduction or no change in HBI score. Microbiome analysis revealed modest but directional shifts, including enrichment of Akkermansiaceae, Bacteroidaceae, Tannerellaceae, Rikenellaceae, and Monoglobaceae. While overall community structure did not significantly change at the cohort level, individualized microbiome responses as well as functional pathway shifts were observed following the intervention. Conclusions: Daily supplementation with freeze-dried grape powder for 21 days was safe and well-tolerated in adults with CD and was associated with modest shifts in gut microbiome composition. This study was registered on clinicaltrials.gov (NCT05972694; 5 February 2024).},
}

Humans
*Crohn Disease/microbiology/diet therapy
Pilot Projects
*Vitis
Adult
Female
*Dietary Supplements
Male
Feces/microbiology/enzymology
Powders
*Gastrointestinal Microbiome/drug effects
Middle Aged
Peroxidase/analysis
C-Reactive Protein/metabolism/analysis

@article {pmid42356238,
year = {2026},
author = {Wang, J and Ma, F and Wang, PF and Hung, CH and Wu, KT and Liao, LA and Guo, JY and Hou, CW},
title = {Effects of Probiotic and Dietary Fiber Supplementation on Metabolic Syndrome-Related Features, Mood, and Sleep in Adults with Obesity.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356238},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/administration & dosage ; *Dietary Fiber/administration & dosage ; *Obesity/psychology/complications ; Female ; *Metabolic Syndrome ; Male ; Adult ; Double-Blind Method ; Middle Aged ; *Dietary Supplements ; *Affect/drug effects ; *Sleep/drug effects ; Cholesterol, HDL/blood ; Treatment Outcome ; Sleep Quality ; },
abstract = {Background: Obesity is associated with metabolic dysregulation, mood disturbance, and poor sleep quality. Although dietary fiber and probiotic supplementation have both been proposed as microbiome-targeted strategies for obesity management, their independent and combined effects remain unclear. Methods: In this double-blind, randomized, placebo-controlled 2 × 2 factorial trial, 56 adults with obesity were randomized to placebo, dietary fiber, probiotic, or combined supplementation for 8 weeks. One withdrew during baseline assessment, and 55 participants were included in the intention-to-treat analysis. Outcomes included metabolic syndrome-related indicators, mood assessed by the Profile of Mood State, and sleep quality assessed by the Pittsburgh Sleep Quality Index. Intervention effects were evaluated using factorial ANCOVA with baseline adjustment. Results: No significant dietary fiber × probiotic interactions were detected. Dietary fiber supplementation showed selective favorable effects, mainly on HDL cholesterol and mood-related outcomes. Probiotic supplementation showed a significant main effect primarily on HDL cholesterol but did not remain significant after FDR correction. Sleep-related improvements were observed only in within-group analyses and were not supported by significant factorial ANCOVA effects. Combined supplementation did not provide additional benefits over single-component interventions. Conclusions: Dietary fiber supplementation may have selective favorable effects in adults with obesity, particularly on HDL cholesterol and mood-related outcomes. The absence of additional benefit from combined supplementation suggests that the effectiveness of synbiotic strategies may depend on the compatibility between the selected dietary fiber and probiotic strains.},
}

Humans
*Probiotics/administration & dosage
*Dietary Fiber/administration & dosage
*Obesity/psychology/complications
Female
*Metabolic Syndrome
Male
Adult
Double-Blind Method
Middle Aged
*Dietary Supplements
*Affect/drug effects
*Sleep/drug effects
Cholesterol, HDL/blood
Treatment Outcome
Sleep Quality

@article {pmid42356276,
year = {2026},
author = {Scrivin, R and Martinez, I and Henningsen, K and Slater, G and Henry, R and Anderson, D and Costa, RJS},
title = {Faecal Bacterial and Short-Chain Fatty Acid Profiles in Response to 48 h FODMAP Intervention Prior to Endurance Exercise.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356276},
issn = {2072-6643},
mesh = {Humans ; *Fatty Acids, Volatile/metabolism/analysis ; *Feces/microbiology/chemistry ; *FODMAP Diet ; Male ; *Gastrointestinal Microbiome ; Biomarkers/blood ; *Physical Endurance/physiology ; Young Adult ; Adult ; },
abstract = {Background/Objectives: Short-term low-fermentable oligo-, di-, and monosaccharide and polyol (FODMAP) diets can reduce exercise-associated gastrointestinal symptoms (Ex-GIS); however, their effects on the gut microbiome, short-chain fatty acids (SCFAs), and gastrointestinal biomarkers remain unclear. This study explored the effects of 48 h dietary FODMAP manipulation within a high-carbohydrate diet on faecal bacterial and SCFA profiles, and their relationships with exercise-induced gastrointestinal syndrome (EIGS) biomarkers, Ex-GIS, and performance. Methods: Twelve endurance athletes experiencing Ex-GIS were randomly allocated to a 48 h high-carbohydrate (mean ± SD: 12.1 ± 1.8 g∙d[-1])-high-FODMAP (HC-HFOD) (54.8 ± 10.5 g∙d[-1]) and a 48 h high-carbohydrate-low-FODMAP (HC-LFOD) (3.0 ± 0.2 g∙d[-1]) diet before 2 h of running at 60% V˙O2max, followed by a 1 h distance test (22.9 ± 1.2 °C, 46 ± 8% RH). Baseline faecal samples were collected before exercise trials to determine faecal bacterial and SCFA profiles. Blood samples were collected pre- and post-exercise to determine plasma I-FABP, sCD14, and CRP concentrations. Ex-GIS were recorded every 15 min throughout exercise. Results: Faecal bacterial α-diversity and relative abundance (RA%) at the phylum level were unchanged following both diets, while several family- and genus-level taxa RA% values were changed (p < 0.05), with greater shifts after HC-HFOD. HC-HFOD significantly increased faecal total-SCFA (p = 0.004), acetic (p = 0.002), and butyric (p = 0.028) acid concentrations. Strong positive and negative correlations between bacterial RA% and EIGS biomarkers and Ex-GIS were observed. Strong negative correlations with bacterial RA% and performance were observed. Conclusions: The 48 h HC-HFOD resulted in greater increases in bacterial RA% and SCFA concentrations compared with baseline. Bacterial RA% correlated bidirectionally with EIGS biomarkers and Ex-GIS, alongside strong negative associations with performance.},
}

Humans
*Fatty Acids, Volatile/metabolism/analysis
*Feces/microbiology/chemistry
*FODMAP Diet
Male
*Gastrointestinal Microbiome
Biomarkers/blood
*Physical Endurance/physiology
Young Adult
Adult

@article {pmid42356291,
year = {2026},
author = {Lupu, A and Anton, E and Sasaran, MO and Tarnita, I and Ioniuc, I and Rusu, TE and Moisa, S and Tarca, E and Butnariu, LI and Mitrofan, EC and Nedelcu, AH and Anton, SC and Knieling, A and Morariu, ID and Lupu, VV},
title = {The Role of Microbiota in Type 1 Diabetes: Insights into Dysbiosis and Immune Interactions.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356291},
issn = {2072-6643},
mesh = {Humans ; *Diabetes Mellitus, Type 1/immunology/microbiology ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Animals ; },
abstract = {Type 1 Diabetes (T1D) is a complex autoimmune disorder characterized by immune-mediated destruction of pancreatic β cells, driven by genetic susceptibility and modulated by environmental factors, notably the gut microbiome. Dysbiosis, manifested as reduced microbial diversity, perturbations in the Firmicutes/Bacteroidetes ratio, and compromised short-chain fatty acid production, contributes to T1D pathogenesis through mechanisms involving immune system dysregulation and heightened intestinal permeability. Emerging evidence indicates a relationship between the gut and oral microbiomes, as well as the potential influence of the virome and mycobiome. This narrative review synthesizes the current literature on the intricate interplay between the gut microbial ecosystem, the host immune response, and the development of T1D, highlighting the potential for targeted microbiome-based interventions to ameliorate disease progression. A more nuanced understanding of these multi-kingdom interactions is essential for developing precise therapeutic strategies to prevent or delay T1D onset and to improve patient outcomes through restoration of immune tolerance and gut homeostasis.},
}

Humans
*Diabetes Mellitus, Type 1/immunology/microbiology
*Dysbiosis/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Animals

@article {pmid42356304,
year = {2026},
author = {Thomas, KL and Wahlquist, AE and Clark, WA},
title = {Maternal Pre-Pregnancy Body Mass Index and Its Impact on Short- and Long-Chain Fatty Acid and Microbiome Profiles of Human Breast Milk in Caucasian Women of Northeast Tennessee.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356304},
issn = {2072-6643},
mesh = {Humans ; Female ; *Body Mass Index ; *Milk, Human/microbiology/chemistry ; Adult ; *Microbiota ; Pregnancy ; *Fatty Acids/analysis ; White People ; Maternal Nutritional Physiological Phenomena ; Cohort Studies ; *Fatty Acids, Volatile/analysis ; Lactation ; Young Adult ; },
abstract = {Background: Increasing evidence suggests that breast milk and its bioactive components, including short-chain fatty acids and the milk microbiome, are influenced by maternal nutrition and body mass index (BMI). Bioactive components transferred to the infant through breast milk play a pivotal role in infant growth and development and have indications in the child's future short- and long-term health outcomes. This study aimed to assess the impact of maternal pre-pregnancy BMI (PP-BMI) on human breast milk macronutrient composition, short- and long-chain fatty acid profiles, and breast milk microbiome profiles. Approach: This was an exploratory cohort study of forty-four lactating Caucasian women, two to fourteen weeks postpartum, divided into groups based on pre-pregnancy body mass index (BMI). Study participants signed informed consent, completed health and nutritional surveys, and provided a breast milk sample. Breast milk samples were subjected to proximate analysis, microbiome identification and short- and long-chain fatty acid extraction and analysis. Results: Maternal age, maternal physical activity, infant birth weight, and time of lactation at sample collection were not significantly different between the maternal PP-BMI groups. PP-BMI was significantly different between the two maternal groups. No significant differences were found between the maternal BMI groups concerning nutritional intake. No differences in breast milk microbiomes were observed in alpha diversity and beta diversity between the maternal PP-BMI groups. For long-chain fatty analysis in breast milk samples, myristic acid was significantly higher in the PP-BMI overweight/obese group while stearic acid was significantly higher in the PP-BMI normal-weight group. Butyric, valeric, and isocaproic acid concentrations in HBM were significantly higher in the PP-BMI normal-weight group and lower or undetectable in the PP-BMI overweight/obese group. Conclusions: Data from this exploratory cohort study indicate that maternal diet and pre-pregnancy BMI may be associated with differences in selected HBM fatty acids. There were no significant differences in microbiomes for alpha and beta diversity in breast milk between maternal PP-BMI groups; however, lower relative abundance was observed in the breast milk of the PP-BMI overweight/obese group. These findings should be interpreted in the context of the study's limitations, including convenience recruitment from a Facebook group, the modest sample size, and restriction to Caucasian women from a single geographic region.},
}

Humans
Female
*Body Mass Index
*Milk, Human/microbiology/chemistry
Adult
*Microbiota
Pregnancy
*Fatty Acids/analysis
White People
Maternal Nutritional Physiological Phenomena
Cohort Studies
*Fatty Acids, Volatile/analysis
Lactation
Young Adult

@article {pmid42356326,
year = {2026},
author = {Gong, X and Wang, Y and Chu, W and Zhao, Y and Liu, J and Zou, Q},
title = {Integrated Metabolomic and Microbiome Profiling Reveals Divergent Effects of No- and High-Fat Coffee in Mice.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356326},
issn = {2072-6643},
support = {RX-ZD202510//peking University Health Science Center Luckin Coffee Health Innovation Base/ ; },
mesh = {Animals ; Male ; *Coffee/chemistry ; Mice, Inbred C57BL ; *Metabolomics/methods ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Metabolome ; Multiomics ; Diet, High-Fat ; Chlorogenic Acid/metabolism ; Bacteria/classification/genetics ; *Dietary Fats/administration & dosage ; RNA, Ribosomal, 16S ; },
abstract = {Background/Objectives Coffee is widely consumed worldwide and is rich in bioactive compounds with potential metabolic benefits. Recently, lipid-enriched coffee formulations have gained popularity; however, their biological effects and underlying mechanisms remain poorly understood. Methods In this study, we employed an integrated multi-omics approach to investigate the impact of coffee and high-fat coffee on the plasma metabolome and gut microbiota of C57BL/6J mice. Eighteen male mice were randomly assigned to three groups (n = 6) and received water, coffee, or high-fat coffee by oral gavage daily for 14 days. The plasma metabolome was analyzed via UHPLC-MS/MS, and the gut microbiota was profiled u 16S rRNA gene sequencing. Results Metabolomic analysis revealed distinct clustering patterns among groups. A total of 200 metabolites were significantly altered in the coffee group compared with the water group, while 86 metabolites were altered in the high-fat coffee group compared with the coffee group, with 56 overlapping metabolites suggesting a core metabolic response. Microbiome analysis showed that coffee consumption increased the abundances of Akkermansia and Bifidobacterium and decreased the levels of Ligilactobacillus and Muribaculum. Coriobacteriaceae UCG-002 and Turicibacter were significantly enriched in the high-fat coffee group, whereas Lachnospiraceae NK4A136 group, Mucispirillum and unclassified Lactobacillaceae were reduced. Association analysis highlighted the top 20 metabolites with the highest degree of connection to gut microbial genera, two of which belong to the chlorogenic acid pathway. Conclusions Reduced levels of ferulic acid and 3-hydroxybenzoic acid, two metabolites potentially involved in antioxidant and anti-inflammatory activities, were observed in the high-fat coffee group, suggesting that dietary cream influences microbiota-associated chlorogenic acid metabolism.},
}

Animals
Male
*Coffee/chemistry
Mice, Inbred C57BL
*Metabolomics/methods
*Gastrointestinal Microbiome/drug effects
Mice
*Metabolome
Multiomics
Diet, High-Fat
Chlorogenic Acid/metabolism
Bacteria/classification/genetics
*Dietary Fats/administration & dosage
RNA, Ribosomal, 16S

@article {pmid42356333,
year = {2026},
author = {Bragazzi, NL and Ceylan, Hİ and Rosi, A and Scazzina, F and de Giorgio, A and Dergaa, I and Scoditti, E and Garbarino, S},
title = {The Co-Evolution of Sleep and Diet: Toward an Emerging Framework of Evolutionary Chrononutrition in Circadian-Metabolic Health.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356333},
issn = {2072-6643},
mesh = {Humans ; *Sleep/physiology ; *Biological Evolution ; *Circadian Rhythm/physiology ; *Diet ; *Feeding Behavior/physiology ; Animals ; Energy Metabolism ; },
abstract = {Sleep and dietary behavior are deeply conserved biological processes that co-evolved under ecological pressures shaping human anatomy, metabolism, immunity, cognition, and life history strategies. Major transitions in human dietary ecology, including plant-dominant hominin foraging, increased meat consumption, control of fire and cooking, agricultural domestication, industrialization, and postindustrial globalization, restructured nutrient intake, pathogen exposure, microbial ecology, metabolic demands, and temporal organization of behavior. Emerging evidence from evolutionary genomics, chronobiology, neuroendocrinology, and microbiome science indicates that sleep-feeding interactions represent a conserved adaptive regulatory module optimized for fluctuating energy availability and strong photoperiodic entrainment. Modern environments characterized by widespread availability of highly palatable, energy-dense foods rich in refined carbohydrates, added sugars, and multiple industrial additives, together with artificial light at night, continuous caloric access, sedentary behavior, and psychosocial stress produce a profound evolutionary mismatch destabilizing circadian-metabolic homeostasis. This mismatch is characterized by circadian disruption, temporal misalignment of feeding and sleep behaviors, and, in many populations, insufficient sleep duration. Within this conceptual landscape, the emerging framework of "evolutionary chrononutrition" proposes that metabolic health and sleep integrity depend not only on what humans eat, but critically on when food is consumed in relation to endogenous circadian architecture shaped across deep evolutionary time. This review synthesizes anthropological, physiological, and molecular evidence to develop an integrative evolutionary framework linking sleep and diet to contemporary cardiometabolic, neurodegenerative, inflammatory, and psychiatric disorders, with particular emphasis on how each major dietary transition plausibly altered sleep duration, architecture, circadian timing, neuroendocrine regulation, and the temporal alignment between feeding behavior and biological rhythms.},
}

Humans
*Sleep/physiology
*Biological Evolution
*Circadian Rhythm/physiology
*Diet
*Feeding Behavior/physiology
Animals
Energy Metabolism