@article {pmid42766739,
year = {2026},
author = {Tolman, NJ and Choi, W and Coulter, R and Snyder, ME and Sharma, L and Qin, S and Morrell, ED and Mikacenic, C and Alder, JK and Wang, X and Tabary, M and Zhang, Y and Inman, K and Britton, N and Methe, B and Benos, PV and Bon, J and Robinson, K and Dela Cruz, C and Nguyen, MH and Morris, A and Biswas, PS and Bain, W and Kitsios, GD},
title = {Candida in the lower respiratory tract induces barrier disruption in mice and predicts poor outcomes in mechanically ventilated humans.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {39},
pages = {e2608378123},
doi = {10.1073/pnas.2608378123},
pmid = {42766739},
issn = {1091-6490},
support = {R01 HL176668//HHS | NIH (NIH)/ ; IK2 BX004886//United States Department of Veterans Affairs Biomedical Laboratory R&D Services/ ; R38 HL150207//HHS | NIH (NIH)/ ; T32 HL110849//HHS | NIH (NIH)/ ; R01 HL164177//HHS | NIH (NIH)/ ; R01 DK104680//HHS | NIH (NIH)/ ; R01 HL169265//HHS | NIH (NIH)/ ; R01 HL149676//HHS | NIH (NIH)/ ; S10OD028483//HHS | NIH (NIH)/ ; },
mesh = {Animals ; Humans ; Mice ; *Candida albicans/pathogenicity ; *Respiration, Artificial/adverse effects ; *Candidiasis/microbiology ; Male ; Disease Models, Animal ; Neutrophils ; Female ; *Lung Injury/microbiology ; Mice, Inbred C57BL ; Lung/microbiology ; },
abstract = {Candida albicans (Calb) in the lower respiratory tract (LRT) is considered a rare cause of pneumonia, yet its frequent recovery from LRT secretions of mechanically ventilated patients associates with poor clinical outcomes. To determine whether Calb contributes to lung injury, we conducted a translational investigation spanning two independent, prospective human cohorts, murine models of lung injury, and in vitro assays. In critically ill patients, Calb was the most abundant fungus in LRT specimens, and its detection associated with increased markers of lung injury, prolonged mechanical ventilation, and increased mortality. In a murine model, intratracheal Calb was sufficient to disrupt the air-blood barrier and recruit neutrophils, effects markedly attenuated with heat-killed Calb. Neutrophil depletion led to uncontrolled fungal growth, systemic dissemination and mortality, with surviving mice exhibiting worsened barrier disruption, demonstrating that neutrophils support pathogen control while lung injury is driven by the live organism. Calb induced lung epithelial cytotoxicity as well as barrier disruption in human alveolar epithelial cells at air liquid interface. Yeast-locked mutants without hyphal morphogenesis demonstrated attenuated barrier disruption in human alveolar cells and diminished lung injury in mice, despite higher fungal burden. In human cohort data, LRT microbiome profiles with high Calb abundance and codominant bacterial pathogens predicted worse mortality, and mouse models confirmed that Calb amplifies lung barrier disruption when followed by Pseudomonas aeruginosa inoculation, an effect requiring hyphal morphogenesis. These findings establish that LRT Calb causes direct air-blood barrier disruption through hyphal morphogenesis and amplifies bacterial lung injury, challenging the prevailing view of Candida as an innocent respiratory bystander.},
}

Animals
Humans
Mice
*Candida albicans/pathogenicity
*Respiration, Artificial/adverse effects
*Candidiasis/microbiology
Male
Disease Models, Animal
Neutrophils
Female
*Lung Injury/microbiology
Mice, Inbred C57BL
Lung/microbiology

@article {pmid42766821,
year = {2026},
author = {Hogan, R and Chuntova, N and Ait Abdelmalek, I and Lavallée-Rodrigue, K and Thériault, ER and Guenoun, Z and Boulette, J and Coveny, V and Castillo-Nehme, A and Massicotte, S and Gauthier, L and Savard, D and Tunc, A and Leclair, JL and Mechawar, F and Cotocea, I and Jacmin-Park, S and Borduas-Pagé, S and Juster, RP},
title = {Stress and Resilience Study (STARS) Protocol: A Multimethod Investigation of Minority Stress, Allostatic Load and Cognition in LGBTQ+ Adults.},
journal = {Biopsychosocial science and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/PSY.0000000000001528},
pmid = {42766821},
issn = {2998-8756},
support = {FRN 171374//Canadian Institutes of Health Research Sex and Gender Science Chair/ ; },
abstract = {BACKGROUND: Lesbian, gay, bisexual, transgender, and queer (LGBTQ+) people face significant stigma, a structural and social determinant of health that contributes to persistent health disparities. Minority stress theory proposes that both proximal and distal stressors adversely impact health and well-being, while protective factors act as buffers. This study aims to identify mechanisms through which minority stress and protective factors influence physical and mental health in LGBTQ+ adults and to determine whether these processes differ across subgroups as well as in comparison to cisgender heterosexual adults. We hypothesize that greater levels of minority stress will be linked to increased AL, decreased microbiota diversity, and diminished cognitive performance. We further hypothesize that protective factors will moderate these associations.

METHODS: The cross-sectional design aims to recruit a minimum of 360 participants, including diverse LGBTQ+ and cisgender heterosexual subgroups. Data collection will include psychosocial questionnaires, biomarkers assayed from saliva, blood, and stool samples, and a semi-structured interview assessing medical and health history.

DISCUSSION: STARS and the resulting biobank are among the first to integrate psychosocial, cognitive, and multi-system biological measures within LGBTQ+ health research. We will analyze LGBTQ+ subgroups separately rather than as a single heterogeneous population, allowing identification of subgroup-specific risk and protection. Findings are expected to inform the development of targeted, biologically grounded interventions to reduce health disparities in LGBTQ+ communities.},
}

@article {pmid42767039,
year = {2026},
author = {Zheng, B and Hu, Y and Saiqin, G and Zheng, B and Xiang, X},
title = {Aquatic-derived bioactive peptides: molecular mechanisms, digestive fate, and precision nutrition.},
journal = {Food chemistry},
volume = {530},
number = {},
pages = {151204},
doi = {10.1016/j.foodchem.2026.151204},
pmid = {42767039},
issn = {1873-7072},
abstract = {Aquatic-derived peptides (ADPs) are bioactive peptides from fish, shellfish, algae, and aquatic by-products. Reported biochemical activities include antioxidant, ACE-inhibitory, and mineral-binding properties, with immunomodulatory and metabolic functions reported. However, an integrated understanding linking peptide structure, bioavailability, and systemic functions remains incomplete. This review summarizes advances from 2020 to 2026 across in silico, in vitro, animal, and human studies, integrating peptidomics, molecular simulations, transport biology, and multi-omics. Particular attention is given to potential pathways through which ADPs may influence the gut-brain, gut-liver, gut-bone, and gut-skin axes. Emerging delivery strategies, including nanoencapsulation, hydrogel-based carriers, and targeted-release systems, are discussed for peptide stability and gastrointestinal delivery. Finally, we summarize challenges in structural standardization, human mechanistic validation, and regulatory considerations, and discuss future directions including AI-assisted peptide design and precision nutrition. Overall, current evidence supports sequence-dependent bioactivity and selected digestive and transport effects, whereas causal multi-organ and individualized responses remain insufficiently validated in humans.},
}

@article {pmid42767075,
year = {2026},
author = {Arachchilage, PW and Tao, W},
title = {Sustaining thermo-alkaline anaerobic digestion at high organic loading rates by ammonia recovery in a high-rate recirculation line.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126957},
doi = {10.1016/j.watres.2026.126957},
pmid = {42767075},
issn = {1879-2448},
abstract = {Thermophilic anaerobic digestion at high organic loading rates (OLRs) may be inhibited by ammonia. This study coupled thermophilic co-digestion of food waste and sludge with vacuum stripping of ammonia in a recirculation line. OLR increased stepwise from 0.7 to 7.0 g VS/Lreactor/d over 223 d of semi-continuous operation at 55 °C. Starting at OLR 4.0 g/L/d, 25% of working volume in three digesters was replaced once a day with vacuum-stripped digestate having pH 9.80 ± 0.09. Digestate replacement immediately decreased ammonia concentration but resulted in robust alkaline conditions at OLR 5.0-7.0 g/L/d. Methane production in the controls without vacuum stripping stabilized around 2.40 L/L/d for 46 d at OLR 5.0 g/L/d, then began to collapse when total ammonia nitrogen exceeded 1983-2273 mg/L, followed by sharp accumulation of volatile fatty acids to 95.9-308 mmol/L and pH drop to 5.51-5.77. The treatment digesters maintained total ammonia nitrogen below 1018-1085 mg/L while methane production rate increased from 2.83 L/L/d at OLR 5.0 g/L/d to 3.34 L/L/d at OLR 6.5 g/L/d. The treatment digesters became unstable upon daily shocks of pH 8.52-8.64 at OLR 7.0 g/L/d. Digestate microbiome was dominated by fermentative bacteria in genus Defluviitoga and ammonia-tolerant hydrogenotrophic Methanothermobacter. These anaerobic thermophiles were viable upon 5-h vacuum stripping of digestate boiling at pH 9.22-9.80, 65 °C and 25-27 kPa. Methanothermobacter had a strong syntrophic association with Defluviitoga. The interwoven effect of OLR, pH and concentrations of acetic acid, propionic acid and ammonia drove microbial community restructuring and process failure.},
}

@article {pmid42767102,
year = {2026},
author = {Motamedi, H and Derakhshan-Sefidi, M and Kuhestani-Dehaghi, B},
title = {Gut microbiota regulation of the IL-6/STAT3 pathway: Linking hematopoiesis to colorectal cancer progression.},
journal = {International immunopharmacology},
volume = {189},
number = {},
pages = {117452},
doi = {10.1016/j.intimp.2026.117452},
pmid = {42767102},
issn = {1878-1705},
abstract = {BACKGROUND AND AIM: Chronic gut microbiota-driven inflammation fuels colorectal cancer (CRC) progression, but how microbial signals influence systemic immunity and tumor growth remains poorly defined. This review synthesizes evidence on gut microbiota regulation of the interleukin-6 (IL-6)/signal transducer and activator of transcription 3 (STAT3) pathway as the central mechanistic link connecting intestinal dysbiosis, altered hematopoiesis, and CRC progression. Other inflammatory pathways and therapies are discussed only as they intersect with this core axis.

METHODS: A structured search of PubMed, Web of Science, and Scopus (January 2015-December 2024) was performed using CRC, microbiota, IL-6, and STAT3 terms. Included studies provided direct evidence from human CRC tissues, CRC cell lines, or relevant animal models.

RESULTS: Pathobionts such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis directly activate STAT3, whereas beneficial commensals like Clostridium butyricum suppress IL-6/STAT3 signaling. Microbial metabolites-including tryptophan derivatives, short-chain fatty acids, and 4-hydroxybenzeneacetic acid-fine-tune STAT3 activation via host receptors (e.g., aryl hydrocarbon receptor, GPR43). Beyond local effects, chronic IL-6/STAT3 signaling systemically reprograms hematopoiesis: gut-derived inflammatory signals reach the bone marrow, activating STAT3 in hematopoietic stem and progenitor cells and skewing differentiation toward myeloid lineages. This drives expansion of immunosuppressive polymorphonuclear myeloid-derived suppressor cells that infiltrate tumors, inhibit cytotoxic T cell and natural killer cell activity, and enable immune evasion.

CONCLUSION: The microbiota-IL-6/STAT3 interface establishes a gut-bone marrow-tumor axis linking dysbiosis to altered hematopoiesis and CRC progression. Integrative strategies targeting this axis hold promise but require further safety evaluation.},
}

@article {pmid42767106,
year = {2026},
author = {Oliveira, JAVC and Moreira, MIS and Coelho, CPES and Belmok, A and Cena, JA and Dame-Teixeira, N},
title = {Ammonia-oxidizing archaea in host-associated environments and the oral microbiome: Ecological evidence and molecular detection.},
journal = {Archives of oral biology},
volume = {192},
number = {},
pages = {106769},
doi = {10.1016/j.archoralbio.2026.106769},
pmid = {42767106},
issn = {1879-1506},
abstract = {OBJECTIVE: Ammonia-oxidizing archaea (AOA) are key contributors to environmental nitrogen cycling. Reliable detection methods are needed to investigate these low-abundance microorganisms. This review aims to: (1)synthesize and contextualize the evidence on AOA, with an emphasis on the oral microbiome; and (2)evaluate primer sets targeting the amoA gene (encoding ammonia monooxygenase) to support the selection of molecular markers for future investigations of AOA in oral samples.

DESIGN: A narrative review with an exploratory in silico primer analysis was performed. Evidence of AOA detection across environmental and host-associated microbiomes was synthesized, including AOA findings in oral microbiome studies. Published amoA-targeting primer pairs developed for environmental communities were evaluated against reference genomes representing AOA lineages reported in human-associated samples. Reference amoA coding sequences were retrieved from genomes and aligned with each primer pair to compare primer-template compatibility, annealing characteristics, and sequence mismatches across AOA representatives.

RESULTS: AOA was predominantly detected in the oral microbiome based on molecular detection and does not yet distinguish active oral residents from transient organisms or environmental exposure. AOA-related sequences, including signatures assigned to Nitrososphaerota, have been found in oral and caries-associated samples. Although their residency is plausible, stability and metabolic activity still have to be studied. For that, an exploratory analysis showed good performance of four primers, but also the need of more reference sequences to have definitive information.

CONCLUSIONS: Current evidence remains insufficient to define the ecological or functional role of AOA in the oral microbiome. Broader in silico assessment and experimental validation in oral samples are required before specific primer sets can be recommended.},
}

@article {pmid42767155,
year = {2026},
author = {Xu, P and Li, L and Zhang, Y and Jiang, Q and Zhang, Y and Wu, X and Xu, Y},
title = {Threshold effects of organic amendment on acidic red soil remediation: Community assembly and core microbiome-mediated metabolic coupling.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130999},
doi = {10.1016/j.jenvman.2026.130999},
pmid = {42767155},
issn = {1095-8630},
abstract = {To identify the ecological threshold and microbial mechanisms underlying organic amendment (OA)-mediated remediation of acidic red soils, pak choi was employed as a model plant, and a gradient of digestate-derived OA from 0% to 25% was established. This study integrated soil-plant assessment, community assembly modeling, metagenome-assembled genomes (MAGs), and metabolic network analysis. Both soil functioning and plant growth exhibited nonlinear responses. The optimal OA rate was found to be 15%, which increased the soil quality index and pak choi biomass by 92% and more than 13-fold compared to the control group. In contrast, a 25% OA rate elevated electrical conductivity, induced secondary salinity stress, and reduced productivity and economic returns. Under the 15% OA treatment, the microbial community showed the strongest deviation from neutral community model predictions, indicating that neutral processes had limited explanatory power for community assembly, while deterministic processes associated with altered soil conditions may have played a more important role in community reorganization. Accordingly, core functional MAGs (e.g., MAG302, MAG299, MAG321) were significantly enriched under this treatment, with a total relative abundance 17.3 times that of the control group. These MAGs harbored key genes involved in C, N, P, and S cycling (bglB, atoB, narG, nirK, nosZ, gcd, pst, sqr), suggesting functional complementarity in organic matter degradation, denitrification, phosphorus mobilization, and sulfide oxidation, thereby supporting efficient nutrient turnover and system function. Deviation from this threshold resulted in reduced core MAG enrichment and metabolic network synergy. Overall, this study provides genome-resolved targets for functional strain isolation and synthetic community construction, as well as a mechanistic basis for optimizing OA rates and developing microbiome-based precision remediation strategies.},
}

@article {pmid42767176,
year = {2026},
author = {Delican, D and Kılıçkaya, O and Ozden, O and Ensari, Y},
title = {Novel L-Asparaginases from the human gut microbiome: Genome mining, biochemical characterization, and in vitro anti-leukemic activity.},
journal = {Bioorganic chemistry},
volume = {182},
number = {},
pages = {110550},
doi = {10.1016/j.bioorg.2026.110550},
pmid = {42767176},
issn = {1090-2120},
abstract = {L-asparaginase is essential for acute lymphoblastic leukemia treatment; however, current Escherichia coli and Erwinia chrysanthemi formulations face significant limitations, including immunogenicity, glutaminase-associated toxicity, and short plasma half-life. The human gut microbiome represents an unexplored reservoir of therapeutic enzymes that may offer superior biocompatibility due to host-commensal co-evolution. We employed a systematic genome-mining approach to screen human gut metagenomic data for novel L-asparaginase candidates. Five candidate enzymes from the genera Bacteroides, Ruminococcus, Clostridium, and Prevotella were identified using virtual screening. These enzymes were subsequently codon-optimized and heterologously expressed in E. coli, thereby validating our computational selection strategy. Biochemical characterization revealed optimal activity at alkaline pH (8.0-9.0), robust performance at physiological temperature (37 °C), and excellent storage stability. Ruminococcus_seq7 exhibited exceptional kinetic properties (Km = 0.53 ± 0.19 mM; Vmax = 78.6 ± 5.59 U/mg), whereas Bacteroides_seq104 showed intermediate kinetics (Km = 2.04 ± 0.57 mM; Vmax = 75.4 ± 5.75 U/mg). These lead candidates demonstrated complementary anti-leukemic profiles: Ruminococcus_seq7 showed broad-spectrum activity against T-cell leukemias (IC50: 5.1-8.6 U/mL for Jurkat, MOLT-4, and THP-1), while Bacteroides_seq104 exhibited remarkable potency against THP-1 cells (IC50 = 0.9 U/mL) and successfully overcame resistance in REH cells (IC50 = 36.9 U/mL). Both enzymes maintained >95% viability in healthy HUVEC cells. This study provides proof-of-concept for the discovery of therapeutic enzyme from the human gut microbiome. The identified L-asparaginases exhibited favorable biochemical properties, potent and selective anti-leukemic activity, and enhanced safety profiles. The absence of glutaminase activity and high biocompatibility position these gut microbiome-derived enzymes as promising biotherapeutic scaffolds for next-generation leukemia treatment, pending further optimization of substrate affinity to meet clinical standards.},
}

@article {pmid42767184,
year = {2026},
author = {Zhang, K and Gong, Z and Chen, M and Arain, MA and Zohaib, M and Zhang, L},
title = {Ellagic acid in poultry nutrition: emerging roles in gut health, immunity, and sustainable production.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107792},
doi = {10.1016/j.psj.2026.107792},
pmid = {42767184},
issn = {1525-3171},
abstract = {Ellagic acid (EA), is a naturally occurring polyphenolic compound abundant in pomegranate, berries, walnuts, and various agro-industrial by-products, and has attracted increasing interest as a potential phytogenic feed additive for poultry. Its importance arises from the need for effective natural alternatives to antibiotic growth promoters that can simultaneously support bird health, productivity, and production sustainability. This review synthesizes evidence from peer-reviewed studies identified through systematic searches of major scientific databases using combinations of keywords related to EA, poultry, gut health, immunity, oxidative stress, inflammation, growth performance, meat quality, and sustainable production. Relevant peer-reviewed studies were selected based on their direct relevance to EA-mediated physiological, intestinal, immunological, and productive responses in poultry. Literature indicates that EA exerts antioxidant, anti-inflammatory, antimicrobial, and immunomodulatory activities through regulation of oxidative stress responses, inflammatory signaling, intestinal barrier function, and gut microbial communities. Emerging evidence further suggests potential benefits for growth performance, feed efficiency, meat quality, and product stability, while nutrigenomic studies indicate that EA can modulate genes involved in immunity, metabolism, antioxidant defense, and intestinal function. However, its practical application is constrained by limited bioavailability, variable responses, dose optimization, and insufficient long-term evidence. Therefore, this review aims to critically evaluate the mechanistic basis and poultry-specific evidence for EA as a phytogenic feed additive, with particular emphasis on gut-microbiota interactions, immune regulation, oxidative stress and inflammation, productive performance, and highlights the prospects and limitations for sustainable poultry production.},
}

@article {pmid42767274,
year = {2026},
author = {Su, JB},
title = {Letter to the Editor: The Gut Microbiome-Endocrine Axis in Obesity: Mechanisms and Therapeutics.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70772},
pmid = {42767274},
issn = {1440-1746},
abstract = {Obesity therapeutics is rapidly evolving, and mechanistic frameworks linking the gut microbiome to systemic metabolism are essential for clinical translation. In this letter, I commend the invited review by Mao et al., which elegantly integrates mechanistic insights across the gut-brain, gut-adipose, and gut-pancreas axes, and we propose three extensions to strengthen its clinical relevance. First, I highlight the bidirectional interplay between GLP-1 receptor agonists (GLP-1 RAs)-now first-line obesity pharmacotherapy-and the gut microbiome: GLP-1 RAs enrich Akkermansia muciniphila and short-chain-fatty-acid-producing taxa, while baseline microbiome composition modulates individual drug responsiveness. Second, I argue for greater attention to upper gastrointestinal microbial niches and synthetic biology approaches, including engineered Clostridium butyricum strains that secrete GLP-1 locally within the intestinal lumen. Third, I emphasize the circadian dimension of the gut-endocrine axis-time-restricted feeding restores microbial diurnal oscillations-and its integration with phenotype-guided precision medicine (e.g., "hungry gut," "hungry brain," and "emotional hunger" subtypes). Incorporating these perspectives would transform the review into a practical roadmap for personalized obesity intervention.},
}

@article {pmid42767300,
year = {2026},
author = {Ding, MQ and Zhang, ZR and Wang, JY and He, L and Ding, J and Zhang, LY and Zhao, L and Ren, NQ and Wu, WM and Yang, SS},
title = {Corn Straw Co-Feeding Enhances Polystyrene Biotransformation in Mealworms through Redox Regulation and Gut Microbiota-Host Interactions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125731},
doi = {10.1016/j.envres.2026.125731},
pmid = {42767300},
issn = {1096-0953},
abstract = {Plastic-degrading insects ("plastivores") have emerged as promising biological systems for mitigating plastic pollution, yet the mechanisms linking dietary supplementation, gut microbiota, and host physiology remain poorly understood. Here, we investigated the effects of corn straw (CS) co-feeding on the biotransformation of polystyrene (PS) microplastics (Mw 142.6 kDa) versus PS plus natural lignocellulose-containing diet CS at a 4:1 (w/w) ratio versus CS as sole at 25.0 ±0.5 °C for 32 days by yellow mealworms (Tenebrio molitor). Compared with a PS-only diet, CS co-feeding increased PS removal efficiency from 47.3% to 58.5% and enhanced the specific PS consumption rate by 38%. Stable-isotope analysis (with a Δδ[13]C of 1.60‰), gel permeation chromatography (GPC), and Fourier transform infrared spectroscopy (FTIR) confirmed enhanced PS depolymerization and biotransformation. CS co-feeding elevated gut ROS levels by approximately 30% while maintaining antioxidant homeostasis. Integrated metabolomic, microbiome, metatranscriptomic, and host transcriptomic analyses revealed coordinated shifts in redox metabolism, microbial activity, and host signaling pathways. The results suggest that redox regulation and gut microbiota-host interactions jointly contribute to enhanced PS biotransformation during CS co-feeding.},
}

@article {pmid42767344,
year = {2026},
author = {Gruber, I and Edinger, M and Poeck, H and Meedt, E and Holler, E and Herr, W and Koelbl, O and Wolff, D and Weber, D},
title = {Early Broad-Spectrum Antibiotic Exposure Is Associated with Increased Relapse after Myeloablative TBI-Based Allogeneic Hematopoietic Cell Transplantation.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.09.037},
pmid = {42767344},
issn = {2666-6367},
abstract = {BACKGROUND: Broad-spectrum antibiotics are frequently administered during the peri-transplant period in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT). Antibiotic exposure can disrupt the intestinal microbiota and may influence immune recovery and post-transplant outcomes. However, the impact of antibiotic timing on relapse risk after myeloablative total body irradiation (TBI)-based conditioning remains poorly defined.

OBJECTIVE: To investigate whether the timing of therapeutic antibiotic exposure is associated with relapse and other transplantation outcomes in adults undergoing myeloablative TBI-based allo-HCT.

STUDY DESIGN: We retrospectively analyzed 160 adults with acute myeloid leukemia (n = 59) or acute lymphoblastic leukemia (n = 101) undergoing first allo-HCT following myeloablative TBI (8 or 12 Gy). Therapeutic antibiotic exposure was classified as early (initiation before stem cell infusion on Day 0; observed range, Day -20 to -1) or non-early (initiation on Day 0 or thereafter during the initial hospitalization for allo-HCT, or no systemic therapeutic antibiotic exposure during this hospitalization). Endpoints were cumulative incidence of relapse (CIR) and non-relapse mortality (NRM). Associations were evaluated using multivariable models adjusted for disease status, age, diagnosis, and TBI dose. Fine-Gray regression was used for relapse and NRM and Cox regression for OS and PFS. Sensitivity analyses included adjustment for calendar year, ATG use, gut decontamination strategy, and institutional antibiotic protocol era, landmark analyses at Days +30 and +60, and assessment of interactions between early antibiotic exposure and clinically relevant factors.

RESULTS: Median follow-up was 9.8 years. Forty-five patients (28.1%) received early and 115 (71.9%) non-early therapeutic antibiotics. Baseline characteristics were broadly comparable between groups. Early antibiotic exposure was associated with a higher unadjusted CIR than non-early exposure (1-year: 40% vs. 17%; 2-year: 45% vs. 23%; Gray's test P = .006), whereas unadjusted NRM was similar (2-year: 16% vs. 15%; Gray's test P = .690). In multivariable Fine-Gray analyses, early antibiotic exposure was associated with a higher subdistribution hazard of relapse (SDHR 2.00, 95% CI, 1.16-3.43; P = .013), but not with NRM or GVHD. No statistically significant interactions between early antibiotic exposure and disease status, diagnosis, age, or TBI dose were observed. Cause-specific Cox regression confirmed the association between early antibiotic exposure and relapse (CSHR 2.06, 95% CI, 1.20-3.56; P = .009). The association remained consistent after adjustment for calendar year, gut decontamination strategy, ATG use, and the institutional antibiotic protocol era and in landmark analyses at Days +30 and +60. Early antibiotic exposure was associated with inferior OS (HR 1.66, 95% CI, 1.05-2.62; P = .030) and PFS (HR 1.75, 95% CI, 1.12-2.75; P = .014).

CONCLUSION: In adults with acute leukemia undergoing myeloablative TBI-based allo-HCT, early therapeutic antibiotic exposure was associated with increased relapse incidence and inferior survival, without detectable associations with GVHD or NRM. These observational findings support an association between antibiotic timing and leukemia control but do not establish causality or justify withholding clinically indicated antibiotic therapy. Prospective studies integrating detailed antibiotic exposure data, immune reconstitution analyses, and microbiome profiling are needed to determine whether antibiotic timing contributes to post-transplant relapse risk.},
}

@article {pmid42767355,
year = {2026},
author = {Zhang, W and Yu, Y and He, L and Gong, C and Zha, S and Yao, H and Yu, H and Shi, W and Dong, Y and Liu, G},
title = {Bioaccumulation of Three Typical Antibiotics in the Edible Bivalve Tegillarca granosa: Potential Mechanisms and Human Health Implications.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129194},
doi = {10.1016/j.envpol.2026.129194},
pmid = {42767355},
issn = {1873-6424},
abstract = {Marine bivalves may be exposed to various terrigenous antibiotics, while empirical evidence supporting antibiotic accumulation and potential health risks remains limited. Thus, the accumulation of three typical antibiotics, ciprofloxacin (CIP), erythromycin (ERY), and oxytetracycline (OTC), in an edible bivalve species, blood clam (Tegillarca granosa), was measured in this study. Moreover, microbiological target hazard quotients (mTHQs) and dietary exposure doses of the human gut microbiota (DEGMs) were estimated to assess food safety risks to consumers. Furthermore, the detoxification processes, oxidative status, and energy metabolism in the gill and hepatopancreas were analyzed to explore their potential associations with antibiotic accumulation. Obtained data demonstrated that 28 days of exposure to environmentally realistic levels resulted in significant antibiotic accumulation in blood clams. Fortunately, the mTHQs of antibiotics were far below the critical value, suggesting a low likelihood of direct inhibition of the human intestinal microbiota. Nevertheless, as the DEGM value exceeded the lower boundary of the minimal selective concentration, consuming CIP-contaminated clams may pose a potential concern about antibiotic resistance selection in the intestinal microbiome. Additionally, the contents (or activity) of detoxification enzymes, the expressions of detoxification genes, and the levels of oxidative stress of detoxification organs were all notably altered by antibiotic exposure. Moreover, significant shifts in energy supply were also detected in antibiotic-treated clams. Overall, these findings suggest that antibiotic accumulation in blood clams mag be associated with alterations in detoxification, oxidative status, and energy metabolism, providing insights into the potential toxicological and food safety implications of antibiotic exposure in bivalves.},
}

@article {pmid42767827,
year = {2026},
author = {Nikitina, D and Suk, KT and Torre, A and Idilman, R and Alvares-da-Silva, MR and Lauridsen, MM and Fagan, AC and Kreivenaite, E and Sharma, SP and Nielsen, EJ and Turan, D and Jahagirdar, V and Michalczuk, MT and Khoruts, A and Bojja, SH and Lee, HW and Skieceviciene, J and Sikaroodi, M and Kupcinkas, J and Gillevet, PM and Bajaj, JS},
title = {Hospitalisation in cirrhosis is linked to distinct gut microbiome structural and functional profiles: a multinational metagenomic study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339378},
pmid = {42767827},
issn = {1468-3288},
abstract = {BACKGROUND: Hospitalisations represent major clinical events in cirrhosis, yet prediction based on clinical variables alone remains limited.

OBJECTIVE: Given the role of the gut microbiome in disease progression, we evaluated whether gut metagenomic profiles are associated with 90-day hospitalisation and provide additional prognostic information beyond clinical features in a multinational outpatient cirrhosis cohort.

DESIGN: We enrolled 679 outpatients with cirrhosis from seven countries and performed stool metagenomic profiling, including taxonomic, functional pathway and antibiotic resistance gene (ARG) analyses, with 90-day follow-up. Machine learning models were developed using clinical and microbiome features for predicting non-elective hospitalisations.

RESULTS: 25% of patients required hospitalisation within 90 days. Hospitalised patients had more advanced cirrhosis, lower microbial diversity which was consistent across countries despite marked variation in microbial composition. Diet had a modest influence on microbiome structure. After adjustment for country, disease severity, cirrhosis aetiology and treatment, 19 bacterial species remained independently associated with hospitalisation, including enrichment of Enterococcus faecium and Veillonella rogosae and depletion of multiple commensal taxa. Functional profiling demonstrated coordinated taxonomic-functional alterations focusing on complex carbohydrate degradation pathways, glycan biosynthesis, lipid and nucleotide salvage pathways and association with antimicrobial resistance mechanisms. The combined clinical-microbiome model significantly outperformed both the clinical-only (area under the curve (AUC) 0.79) and microbiome-only (AUC 0.74) models, achieving an AUC of 0.84.

CONCLUSION: Gut microbiome composition and function are associated with short-term hospitalisation risk and provide additional prognostic information beyond clinical variables in a multicountry cohort. Hospitalisation, regardless of country, is characterised by loss of short-chain fatty acid-producing taxa, functional shifts, ARG and pathway changes.},
}

@article {pmid42767852,
year = {2026},
author = {Crossley, P and Feehily, C},
title = {The who, how, and when of mother-infant microbial sharing.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.07.015},
pmid = {42767852},
issn = {1878-4380},
abstract = {The establishment of the infant gut microbiome is strongly linked to health outcomes throughout life. Recently, Mueller et al. reported that the majority of strains shared between a mother and an infant are gut-derived, as opposed to vaginally derived, and strain sharing could be observed into the second year of life.},
}

@article {pmid42767975,
year = {2026},
author = {Burge, K and Velsko, IM and Salazar-García, DC and Uriarte, MH and Lomba Maurandi, J and Warinner, C},
title = {Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70201},
pmid = {42767975},
issn = {1755-0998},
support = {//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; //National Science Foundation/ ; },
mesh = {Animals ; *Microbiota ; *Mouth/microbiology ; *Gene Library ; Humans ; *DNA, Ancient ; Sequence Analysis, DNA ; DNA, Single-Stranded/genetics ; Neanderthals ; *Metagenomics/methods ; },
abstract = {DNA library construction methods can affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few studies have examined how library protocols shape ancient microbial community reconstruction. Here, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from 12 Neanderthals and two Chalcolithic humans, prepared using implementations of the Gansauge et al. and Meyer and Kircher protocols, respectively, and sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication and taxonomic profiles across normalization strategies to assess protocol-specific biases. Double-stranded libraries retained a significantly higher proportion of sequenced reads throughout data processing (dsLib 72.1%, ssLib 37.9%), a higher proportion of oral reads (dsLib 9.78%, ssLib 6.75%), significantly longer median oral DNA read lengths (dsLib 57.5 bp, ssLib 50.5 bp) and more GC-rich fragments (dsLib 60.5% GC, ssLib 52.5% GC). In contrast, ssLibs exhibited slightly higher Shannon diversity and a greater proportion of unique reads. Despite these differences, species richness and overall community composition was not significantly different between protocols, with individual and preservation status explaining the most variance. Stratifying reads by length (< 50 bp vs. ≥ 50 bp) resulted in different classification rates but only had minor effects on diversity estimates. Together, these results demonstrate that dsLib and ssLib protocols impose distinct trade-offs and library choice should be guided by study-specific goals.},
}

Animals
*Microbiota
*Mouth/microbiology
*Gene Library
Humans
*DNA, Ancient
Sequence Analysis, DNA
DNA, Single-Stranded/genetics
Neanderthals
*Metagenomics/methods

@article {pmid42768105,
year = {2026},
author = {Dong, D and Walsh, AM and Vatanen, T and Weingart, G and Khdhiri, M and Stampfer, MJ and Vehik, K and Franzosa, EA and Huttenhower, C and Wang, DD and , },
title = {Gut microbiome maturation in early childhood interacts with host genetics to predict type 1 diabetes risk.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {42768105},
issn = {2522-5812},
abstract = {Prospective evidence linking early-life microbiome development and host genetics with type 1 diabetes (T1D) risk is limited. Here, we describe how gut microbiome maturation and host genetics influence T1D risk in the TEDDY study. We analysed 12,151 longitudinal metagenomes and host genetic data from 887 children at high genetic risk for T1D followed for up to 6 years. We identify three microbiome maturational patterns: Early Matured, Late Matured and Early Plateaued, driven primarily by non-linear changes in species from the Bifidobacterium and Ruminococcus genera. The Early Matured pattern is enriched in galactose metabolism and exhibits higher production of aromatic amino acids and B-group vitamins at early follow-ups, whereas the Early Plateaued pattern has increased microbial production of branched-chain amino acids. Notably, the Early Plateaued pattern is associated with a threefold elevated risk of T1D, whereas other patterns are not associated with T1D risk. Furthermore, we find that host genetic variants related to antimicrobial and antiviral immune responses modify the association between the Late Matured pattern and T1D risk. These findings highlight the role of early microbial exposures and host genetics in T1D susceptibility.},
}

@article {pmid42768289,
year = {2026},
author = {DeVito, A and Kimm-Drapeau, AL and Higgins, WJ and Montecillo, M and Bernstein, MN and Wright, S and Li, C and Bal, I and Dadhania, DM and Selbach, F and Lee, JR},
title = {Serial Blood Microbiome Profiles in Kidney Transplant Recipients Reveal Evidence of Circulating Gut and Non-Gut Derived Microbial DNA.},
journal = {Transplant infectious disease : an official journal of the Transplantation Society},
volume = {},
number = {},
pages = {e70323},
doi = {10.1111/tid.70323},
pmid = {42768289},
issn = {1399-3062},
support = {R21 AI 173849/NH/NIH HHS/United States ; R01DK139249/NH/NIH HHS/United States ; R01AI184528/NH/NIH HHS/United States ; UL1TR002384//National Center for Advancing Translational Sciences of the National Institutes of Health/ ; 539291308//German Research Foundation/ ; },
abstract = {BACKGROUND: In this study, we sought to investigate the utility of 16S rRNA gene sequencing of whole blood in kidney transplant recipients and to assess a link between the gut microbiota and the blood microbiota.

METHODS: We recruited 63 kidney transplant recipients who provided 163 whole blood specimens over the first 140 days after transplantation. We profiled the blood microbiome using 16S rRNA gene sequencing of the V4-V5 hypervariable region. We additionally evaluated the gut microbiota via metagenomic sequencing in a subset of kidney transplant recipients who had matched blood specimens.

RESULTS: We generated a median of 19 959 sequences per blood specimen. We discovered that most whole blood microbiome profiles consisted of mitochondrial DNA (mean relative blood abundance greater than 99%) with minimal microbial DNA detected. Out of the 163 blood specimens, 83 (51%) had detectable microbial 16S rRNA sequences and there were 92 distinct taxa detected at the genus level. Among the 51 kidney transplant recipients, blood microbial 16S sequences were persistently detected in 10 kidney transplant recipients over time, intermittently detected in 29 kidney transplant recipients over time, and not detected in 12 kidney transplant recipients over time. Among 76 matched blood-fecal specimens, 9 blood specimens had detectable gut microbial 16S sequences, which were also detected in 3 of the 9 fecal specimens.

CONCLUSION: Our study finds minimal detection of bacterial DNA in the blood microbiome in kidney transplant recipients and evidence of gut bacterial DNA in the bloodstream of kidney transplant recipients.},
}

@article {pmid42768305,
year = {2026},
author = {Avershina, E and Birkeland, EE and Bucher-Johannessen, C and Rounge, TB},
title = {CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734649},
pmid = {42768305},
issn = {1949-0984},
mesh = {Humans ; *Interspersed Repetitive Sequences ; *Bacteria/genetics/classification/immunology/isolation & purification/virology ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems ; Plasmids/genetics ; Feces/microbiology ; Middle Aged ; Metagenome ; Norway ; Female ; Diet ; Bacteriophages/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we constructed an extended microbiome resource comprising 1.7 K prokaryotic mOTUs, 19.5 K viral vOTUs, and 24.2 K plasmid PTUs, using fecal shotgun metagenomes from 1034 adults over 55 y of age residing in South-East Norway. We also recovered 74.2 K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with the human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Plasmid MGEs were more often targeted by Type II CRISPR-Cas cassettes, whereas viruses were more likely to be targeted by Type I CRISPR-Cas cassettes. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. CRISPR-Cas cassettes mirrored microbiome associations to human demographic and lifestyle factors and enabled the recovery of dairy-associated B. animalis. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome and their contribution to microbial ecosystem dynamics.},
}

Humans
*Interspersed Repetitive Sequences
*Bacteria/genetics/classification/immunology/isolation & purification/virology
*Gastrointestinal Microbiome/genetics
*CRISPR-Cas Systems
Plasmids/genetics
Feces/microbiology
Middle Aged
Metagenome
Norway
Female
Diet
Bacteriophages/genetics
Gastrointestinal Tract/microbiology

@article {pmid42768312,
year = {2026},
author = {Rosenn, EH and Zuniga, M and Lipshitz, M and Fox, E and Engel, M and Pasinetti, GM},
title = {The cervicovaginal gut microbiota axis as a key determinant of systemic physiology.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726648},
pmid = {42768312},
issn = {1949-0984},
mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; *Cervix Uteri/microbiology ; *Microbiota ; },
abstract = {The gut and vaginal microbiomes are both essential to human health, yet they have largely been studied in isolation. Gut microbiota are central to host metabolism, immunity, and the gut-brain axis, while the vaginal microbiome, typically dominated by Lactobacillus species, protects against infection and shapes reproductive outcomes. Although dysbiosis at either site has been linked to systemic disease, the possibility that these communities are interrelated and that the vaginal microbiome could serve as a clinically accessible proxy for systemic microbial states remains underexplored. This represents a clear gap in the literature. In this review, we examine physiological connections between digestive and genitourinary systems, explore how endocrine and immune networks exert dual control across compartments, and analyze correlations between dysbiosis and disease states. We then consider emerging technologies for microbiome analysis and their clinical and translational implications, including the potential for vaginal microbiome profiling to function as a diagnostic surrogate for the gut and as a complementary biomarker platform for prediction of neurologic disease risk. By building a systems-level understanding of the joint immuno-microbial interactome, evaluating advances in computational and omics-based technologies, and situating these tools within emerging healthcare frameworks, we argue that the cervicovaginal-gut microbiota axis is a unique and understudied source for medical discovery.},
}

Humans
Female
*Vagina/microbiology/immunology
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology
*Cervix Uteri/microbiology
*Microbiota

@article {pmid42768338,
year = {2026},
author = {Torki, S and Qorbani, M and Ejtahed, HS and Etebarian, A},
title = {Alterations of oral microbiome in oral potentially malignant disorders: a systematic review.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {42768338},
issn = {1472-6831},
mesh = {Humans ; *Microbiota ; *Mouth Neoplasms/microbiology ; *Mouth/microbiology ; Leukoplakia, Oral/microbiology ; Lichen Planus, Oral/microbiology ; *Precancerous Conditions/microbiology ; Oral Submucous Fibrosis/microbiology ; },
abstract = {BACKGROUND AND OBJECTIVES: Oral potentially malignant disorders (OPMDs), including conditions such as Oral lichen planus, Oral leukoplakia, Proliferative verrucous leukoplakia and Oral submucous fibrosis are associated with an increased risk of oral squamous cell carcinoma. Emerging evidence suggests that alterations in the oral microbiome may contribute to the pathogenesis of these disorders and their malignant transformation. This systematic review aimed to synthesize current evidence on oral microbiome composition and diversity in patients with OPMDs.

METHODS: A comprehensive literature search of PubMed, Scopus, Web of Science, and Google Scholar was conducted to identify eligible human studies published through August 2025. Studies evaluating oral microbiome profiles in patients with clinically and/or histopathologically diagnosed oral potentially malignant disorders (OPMDs) were included. Data on study characteristics, sampling and analytical methods, microbial diversity, and differentially abundant taxa were extracted independently by two reviewers. Risk of bias was assessed using the Newcastle-Ottawa Scale. Owing to substantial clinical and methodological heterogeneity, findings were synthesized qualitatively.

RESULTS: A total of 56 studies were included, comprising 30 studies of Oral lichen planus, 9 of Oral leukoplakia, and 17 examining other OPMDs. 16srRNA sequencing was mostly used and whole unstimulated saliva was the most frequently collected specimen. The most prevalent microbial phyla identified in OPMD patients included Firmicutes, Proteobacteria, and Fusobacteria, but the direction and magnitude of changes varied across OPMD subtypes and sampling methods. Several studies reported an increase in pathogenic species such as Porphyromonas and Prevotella, while commensal bacteria like Streptococcus were less abundant. Findings concerning microbial richness and diversity were inconsistent.

CONCLUSIONS: Oral microbial dysbiosis is a common feature of oral potentially malignant disorders; however, a reproducible microbial signature has not yet been established. Substantial heterogeneity in study design, sampling strategies, and analytical approaches limits causal inference and clinical applicability. Future standardized longitudinal studies are needed to clarify the role of the oral microbiome in malignant transformation and its potential utility as a prognostic biomarker.

TRIAL REGISTRATION: Prospero registration number: CRD42024516735.},
}

Humans
*Microbiota
*Mouth Neoplasms/microbiology
*Mouth/microbiology
Leukoplakia, Oral/microbiology
Lichen Planus, Oral/microbiology
*Precancerous Conditions/microbiology
Oral Submucous Fibrosis/microbiology

@article {pmid42768386,
year = {2026},
author = {Pateriya, D and Tanwar, A and Sharma, VK},
title = {Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
pmid = {42768386},
issn = {1757-4749},
support = {INSACOG//Biotechnology Industry Research Assistance Council/ ; BT/PR50613/MED/32/981/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {The human microbiome serves as a reservoir of antibiotic resistance genes (ARGs), collectively known as the resistome, which has crucial implications for human health. However, the distribution of ARGs across diverse bacterial taxa and their variation across populations, disease states, and body sites remain less well understood. Here, we comprehensively profiled the human resistome using genomic and metagenomic data. Our analysis included 4,744 species-representative gut bacterial genomes and 452 oral bacterial genomes, along with gut metagenomic data from 10,230 individuals across 58 studies encompassing 5,388 healthy and 4,842 disease-associated samples, including underexplored non-Western cohorts. Our analysis revealed variation in the gut resistome across population groups and countries. The oral microbiome exhibited a distinct resistome profile with lower ARG prevalence compared to the gut. Across multiple datasets, ARG abundance was generally higher in inflammatory bowel disease samples compared to healthy samples. Pathogenic taxa such as Enterobacter, Citrobacter, Escherichia, and Klebsiella carried the highest number of ARGs, including clinically relevant ARGs, whereas abundant commensals like Bacteroides and Prevotella contributed to the baseline resistome. Notably, population-level differences in ARG composition appeared to be linked to microbial community structure. Shared ARGs between commensal and pathogenic bacteria provided clues to horizontal gene transfer. These findings provide crucial insights into the ecological and population-level factors shaping the gut resistome, highlighting the roles of both pathogens and commensals in the maintenance and dissemination of antimicrobial resistance.},
}

@article {pmid42768390,
year = {2026},
author = {Macey, MC and Ilieva, V and Stephens, BP and Tatton, B and Balcha, E and Schwenzer, SP and McGenity, TJ and Miruts, H and Gomez, F and Cavalazzi, B and Olsson-Francis, K},
title = {Metagenomic insights into the taxonomic and metabolic diversity of the microbiome of Lake Karum in the Danakil Depression, Ethiopia.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42768390},
issn = {2524-6372},
support = {Grant agreement No 871149//Europlanet 2024 RI project - Expert Exchange/ ; Grant Agreement No 654208//Europlanet 2020 RI project - Transnational Access/ ; Expanding Excellence in England, grant number 124.18//Research England/ ; },
abstract = {BACKGROUND: Hypersaline environments are dynamic ecosystems, the chemistry of which is significantly influenced by climate change, which in turn impacts the microbiota and biogeochemical processes. This study investigates the microbiome of Lake Karum, a hypersaline lake in the Danakil Depression, Ethiopia, with a particular focus on genome-based potential of climate-relevant biogeochemical processes.

RESULTS: The microbiomes of Lake Karum sediments and waters were dominated by halophilic Archaea (Halobacteriota) and Bacteria (Bacteroidota, Pseudomonadota, and Cyanobacteriota), with significant variation in community composition among sites, reflecting geochemical heterogeneity. Despite these taxonomic differences, sediment and water metagenomes exhibited broadly overlapping functional gene profiles. Genes involved in denitrification, carbon monoxide oxidation, osmotic stress tolerance, and utilisation of osmolytes were widespread and predominantly affiliated with Halobacteriales, indicating their pivotal role in nitrogen and carbon cycling. Genome‑resolved analyses revealed substantial intrageneric variation in metabolic potential within dominant halobacterial lineages as well as bacterial candidate phyla, including Candidatus Bipolaricaulota and Candidatus Salsurabacteriota, which encode genes linked to trace-gas metabolism and nitrogen cycling. Notably, a high‑quality metagenome‑assembled genome assigned to the Candidatus Salsurabacteriota was recovered that possesses novel combinations of functional genes not previously reported for this lineage.

CONCLUSION: This study provides a comprehensive genome‑resolved assessment of the taxonomic and functional diversity of the Lake Karum microbiome and identifies microbial taxa with the potential to drive key carbon, nitrogen, and sulfur cycling processes in a hypersaline lake. By revealing previously unrecognised metabolic capabilities within bacterial candidate phyla and highlighting intrageneric functional heterogeneity among dominant halophilic Archaea, this work advances understanding of how hypersaline microbial communities contribute to biogeochemical cycling in extreme environments.},
}

@article {pmid42768438,
year = {2026},
author = {Melby, MC and Timlin, CL and McCracken, FB and Rojas, CA and Carchedi, C and White, B and Cassibry, L and Blake, A and Coon, CN},
title = {Impacts of a fresh-frozen dog food on fecal consistency and microbiome in colony dogs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag303},
pmid = {42768438},
issn = {1525-3163},
abstract = {Fresh-frozen dog diets are becoming increasingly popular among pet owners, but little is known regarding the impact of this diet on canine gut health and the microbiome. This study evaluated the impacts of a fresh-frozen versus an extruded kibble diet on the fecal consistency, metabolites, and microbiome in 16 adult Labrador Retrievers (average age 4.2 ± 0.26 years; average weight: 25.7 kg ± 3.18 kg) over the course of 6 months. Dogs were randomly assigned to one of the two diets in a parallel design. Feces were collected at baseline, 3 months, and 6 months for short-chain fatty acid, ammonia, and microbiome analyses. An additional sample was collected at 1 month for microbiome analysis. Fecal microbiome was analyzed via 16S rRNA gene sequencing. Fecal consistency scores were recorded daily, and body weights and body condition scores were recorded weekly. Data were analyzed across time and treatments using a repeated measures ANOVA. Results showed that fecal consistency was improved in the dogs fed the fresh diet, with differential changes detected shortly after the transition phase onto the test diets (P < 0.01). Fecal butyrate concentrations were greater in the fresh group (P < 0.01), and fecal valerate concentrations fluctuated more in the kibble group while the fresh group remained more consistent over time (P = 0.05). No differences were observed in fecal moisture, pH, ammonia, or other fecal short-chain or branched-chain fatty acids. General dog health was not negatively impacted by either diet, as observed through weight maintenance and veterinary wellness exams. Diet type impacted fecal microbiome composition, as shown by differences in beta diversity between the fresh and kibble groups (P < 0.01). Additionally, microbiomes of dogs fed a fresh diet were enriched in short-chain fatty acid producers such as Turicibacter sanguinis, Ruminococcus, and Clostridium compared to dogs fed kibble. Overall, the fresh diet increased fecal consistency and fecal butyrate, though other fecal parameters were not different.},
}

@article {pmid42768445,
year = {2026},
author = {Due, EM and Munezero, O and Burrough, ER and Burkey, TE and Fernando, SC and Gabler, NK},
title = {Effect of dietary fiber and tributyrin on nursery pig health, performance, bacteriome, and volatile fatty acid concentration.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag302},
pmid = {42768445},
issn = {1525-3163},
abstract = {Dietary fiber and volatile fatty acid (VFA) metabolites have been shown to improve intestinal health and reduce post-weaning diarrhea in pigs. Therefore, the current study was conducted to evaluate the impact of insoluble and soluble dietary fiber sources and butyrate on the intestinal health and growth performance of nursery pigs. It was hypothesized that insoluble and soluble dietary fiber sources or butyrate supplementation would improve nursery pig performance and enteric health. Over two replicates, a total of 610 weaned pigs were assigned to one of five dietary treatments (n = 17 pens/treatment): 1) control diet (CON), 2) wheat bran (WB), 3) beet pulp (BP), 4) corn distiller's dried grains with solubles (DDGS), and 5) CON plus 0.20% tributyrin. Diets were fed in two phases (14 and 28 days). Pigs were confirmed positive for rotavirus A, B, and C and F18 enterotoxigenic Escherichia coli (E. coli). There was no effect of dietary fiber or tributyrin on the proportion of pigs with normal, soft, or liquid fecal consistency in weeks 1, 2, or 3 of the study (P > 0.10). There were no significant differences in average daily gain (ADG), average daily feed intake (ADFI), or gain-to-feed ratio (G:F) among treatments in phase 1 (P > 0.10). Tributyrin tended to increase ADFI in phase 2 compared to CON and BP (P = 0.063), and increased ADFI overall compared to CON (P = 0.031), but had no significant effect on final body weight (P > 0.10). Dietary treatment did not affect ileal, colonic, or fecal VFA concentrations on days 7, 10, or 42. However, on day 22, CON pigs had greater fecal acetate, propionate, valerate, and total VFA concentrations than one or more fiber treatments (P < 0.05), with butyrate tending to be greater than WB (P = 0.080). Bacterial community analysis revealed no effect of dietary fiber treatment on alpha diversity, except for DDGS, where day 14 and day 42 communities differed (P = 0.014). Beta-diversity analysis identified distinct clustering between time points (P = 0.001) and between treatments (P = 0.024) using the Bray Curtis dissimilarity matrix. Overall, although bacterial community composition was affected, the inclusion of wheat bran, beet pulp, corn DDGS, or tributyrin did not significantly impact intestinal health, pathogen load, VFA concentration, or growth performance in nursery pigs.},
}

@article {pmid42768897,
year = {2026},
author = {Watson, CD and Lem, AJ and Bissett, A and Cando-Dumancela, C and Gardner, MG and Hodgson, RJ and Liddicoat, C and Peddle, SD and Breed, MF},
title = {Restoration Plantings Promote Functional Recovery of Soil Fungi.},
journal = {Molecular ecology},
volume = {35},
number = {18},
pages = {e70552},
pmid = {42768897},
issn = {1365-294X},
support = {LP240100073//Australian Research Council/ ; UOWX2101//Ministry of Science and Innovation, New Zealand/ ; //Australian Government under the National Environmental Science Program's Resilient Landscapes Hub/ ; },
mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; Soil/chemistry ; Biodiversity ; Ecosystem ; *Environmental Restoration and Remediation ; Phosphorus/analysis ; },
abstract = {The global scale of biodiversity loss and land degradation has prompted the establishment of ambitious international restoration agreements, with the goal of returning biodiverse and functional ecosystems. Restoration interventions are often vegetation focused, and while they yield positive, measurable outcomes, they do not always lead to whole ecosystem recovery. Although soil microbiota such as fungi are integral ecosystem components (e.g., as symbionts, decomposers and drivers of nutrient cycling), they are largely absent from restoration planning and monitoring. Therefore, how fungi respond to ecosystem restoration, especially over longer time scales, is largely unknown. Here, we show trends of reduced dominance of soil fungal pathotrophs across a restoration chronosequence 6 years after initial sampling. This decline in soil fungal pathotrophs is consistent with continued functional recovery, despite little evidence of additional whole-community fungal recovery. Fungal community composition was also strongly associated with soil properties, particularly phosphorus, consistent with persistent land-use legacies constraining further recovery. The observed change in fungal functional composition is consistent with previous studies reporting higher relative abundance of pathotrophic fungi in ecologically degraded sites. Our study provides valuable insights into how soil fungal communities respond to restoration plantings and highlights the importance of repeated sampling. Our findings also demonstrate the value of considering both taxonomic and functional indicators when assessing ecosystem recovery.},
}

*Soil Microbiology
*Fungi/genetics/classification
Soil/chemistry
Biodiversity
Ecosystem
*Environmental Restoration and Remediation
Phosphorus/analysis

@article {pmid42768967,
year = {2026},
author = {Kang, L and Jia, YJ and Jiang, N and Hu, DM and Mao, JF},
title = {Weed control, maize (Zea mays L.) metabolism, and rhizosphere microbiome of hollow mesoporous silica nanoparticles loaded with S-metolachlor and ZnO quantum dots.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71268},
pmid = {42768967},
issn = {1526-4998},
support = {//the Excellent Postdoctoral Program of Xinjiang Uygur Autonomous Region/ ; },
abstract = {BACKGROUND: Conventional pesticide formulations employ large amounts of organic solvents, raising concerns regarding their environmental contamination, pesticide residues, and potential toxicity to non-target organisms. Hollow mesoporous silica nanoparticles (HMSNs) are non-toxic to both animals and plants, making them a suitable candidate for pesticide loading and delivery studies.

RESULTS: HMSNs with an average particle size of 165 nm were synthesized using a self-template method. Fluorescein isothiocyanate was successfully conjugated to the HMSNs to enable the investigation of their transport and distribution in maize. The S-metolachlor (S-met) loading efficiencies of HMSN and HMSN@ZnO quantum dots (QDs) carriers were 18.7% and 10.7%, respectively. Application of nanocarriers did not adversely affect weed control efficacy, maize growth, or plant antioxidant enzymatic activity. No detrimental effect of the nanocarriers was observed on crop and weed control, and no clear differences were observed in metabolites and soil microbial dynamics. HMSN@S-met@ZnO QDs treatment increased the proportions of lysobacter and blastococcus compared to the control, whereas the EC treatment exhibited a relatively different distribution pattern for sphingobacterium and pseudomonas. Actinophytocola algeriensis and sphingomicrobium were selectively enriched in nanocarriers-based treatments relative to the control and conventional S-met EC treatment. The active microbial community was predominantly composed of species affiliated with entotheonella and pseudomonas based on the metatranscriptomic species profiling.

CONCLUSION: The nanocarrier formulations were safe for maize and maintained effective weed control, and significantly modulated metabolites of maize plants and the microbial community composition in the soil. © 2026 Society of Chemical Industry.},
}

@article {pmid42768978,
year = {2026},
author = {Boettcher, SR and Kenney, RM and Everson, NA and Kashat, I and Soyad, A and Tengler, G and Ramesh, M and Veve, MP},
title = {Clinical Experience with Oral Fecal Microbiota Spores (Vowst®) in a Health System Specialty Pharmacy.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajhp/zxag293},
pmid = {42768978},
issn = {1535-2900},
abstract = {PURPOSE: To describe clinical experience and patient outcomes with orally administered fecal microbiota spore (FMS) capsules, live-brpk, for prevention of recurrent Clostridioides difficile infection (rCDI) after workflow implementation into a local health-system specialty pharmacy (HSSP) model.

SUMMARY: rCDI carries substantial morbidity, and the approval of orally administered FMS capsules introduced a novel prevention option with new challenges in medication access, prior authorization, and cost. To meet this need, an HSSP workflow was adapted to support acquisition of FMS for adults receiving a prescription order. Over the period from June 1, 2023, through December 31, 2024, a total of 72 FMS prescriptions were generated for 50 patients, of which 29 (58%) ultimately obtained the medication. Patients reflected a real-world population, the median (IQR) age was 70 (55-79) years, 55% were men, the median (IQR) number of previous CDI episodes (including the proximal episode) was 2 (1-3), and 25% were immunocompromised. Among patients who received FMS, rCDI occurred in 2 (7%) patients at eight weeks. Of the 21 prescriptions obtained through the HSSP, 62% required a single prior authorization (PA) attempt, and the median (IQR) time to dispensing from prescription generation was 16 (12-20) days. Copayments ranged from $0 to >$2,500, with most patients (18, 86%) receiving FMS for less than $6.

CONCLUSION: Implementation of an adapted HSSP FMS medication workflow resulted in medication access for more than half of patients and offers a practical, adaptable model for integrating high-cost microbiome therapies into specialty pharmacy practice.},
}

@article {pmid42769362,
year = {2026},
author = {McKelvey, MC and Einarsson, GG and Carson, J and Kadoom, A and Brown, RR and Campbell, C and Jackson, A and McDowell, C and Clarke, M and Copeland, F and Ferguson, K and McLeese, RH and Convery, R and Hill, AT and De Soyza, A and Shahidi, M and Kelly, M and Carroll, M and Gatheral, T and Anwar, M and Duckers, J and Flight, W and Hurst, JR and Ionescu, AA and Loebinger, MR and Sullivan, AL and Chalmers, JD and Downey, DG and Tunney, MM and O'Neill, B and McAuley, DF and Elborn, JS and Bradley, JM and Taggart, CC},
title = {Effects of hypertonic saline and/or carbocisteine on sputum rheology in bronchiectasis: CLEAR-EME.},
journal = {ERJ open research},
volume = {12},
number = {5},
pages = {},
pmid = {42769362},
issn = {2312-0541},
abstract = {BACKGROUND: Mucoactives such as hypertonic saline (HTS) and carbocisteine are widely used in the treatment of bronchiectasis, though there is insufficient evidence to support their use. The aim of this mechanistic sub-study, embedded within the CLEAR trial, was to characterise the properties of sputum from patients with bronchiectasis and to assess whether treatment with HTS and/or carbocisteine altered these properties.

METHODS: In CLEAR, patients were randomised to receive HTS, carbocisteine, HTS plus carbocisteine or standard care, and sputum samples were collected at randomisation (baseline) and at 2 and 8 weeks post-randomisation. Sputum viscoelasticity was determined by rotational plate rheometry. Biomarkers were quantified by ELISA and microbiome composition was assessed by next-generation sequencing. The primary outcome was differences in sputum viscoelasticity between groups at 2 weeks following the commencement of treatment.

RESULTS: Sputum viscoelastic properties were not reduced by 2 or 8 weeks of treatment with HTS and/or carbocisteine (n=6-15 per group). Sputum biomarker levels and bacterial community composition were similar across groups at 2 or 8 weeks. At baseline, viscoelasticity (crossover point σc) was positively correlated with interleukin-8 (r=0.49, p=0.012) and greater relative bacterial dominance (r=0.35, p=0.041).

CONCLUSIONS: These data do not support the use of HTS or carbocisteine to alter sputum viscoelasticity, inflammatory marker levels or bacterial community composition in patients with bronchiectasis.},
}

@article {pmid42769424,
year = {2026},
author = {Yang, Y and Jia, W and Xie, J and Qiu, J and Li, C and He, C and Luo, M and Zhao, L and Wang, Y},
title = {Microbiome network remodeling is associated with soil lipid metabolism in safflower under different cropping system-location combinations: an omics-based dissection.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1898896},
pmid = {42769424},
issn = {1664-302X},
abstract = {This study investigated differences in safflower rhizosphere soil microbiota and metabolic functions among three planting pattern-location combinations (PLMEs): soybean-safflower rotation at Chenghai (CH), tobacco-safflower rotation at Longpan (ZYHY), and apple orchard intercropping at Lijiang (LJ). Each PLME comprised 6 plots. Bacterial α-diversity was significantly higher in the CH system, whereas fungal α-diversity peaked under the ZYHY system. Correlation analysis showed that bacterial α-diversity was negatively correlated with available potassium, while fungal α-diversity was negatively correlated with catalase activity. Microbial community structures significantly varied among the different PLMEs, with redundancy analysis indicating that bacterial variation was mainly explained by electrical conductivity, while fungal variation was mainly explained by available phosphorus. Under the adopted network-construction procedure, sample-specific subnetwork analysis suggested that the bacterial subnetworks in CH were more topologically complex and stable, while the fungal subnetworks in ZYHY were more complex than those in other treatments; no marked differences in fungal subnetwork stability were observed. These findings remain exploratory. Although dominant microbial taxa were unchanged, their relative abundances varied notably. Non-targeted metabolomics analysis identified significant shifts in glycerophospholipid metabolism, with five key metabolites, including L-serine, phosphatidylethanolamine, and lecithin, serving as biomarkers strongly correlated with genera such as Gaiella, Microlunatus, and Mortierella. An exploratory structural equation modeling analysis revealed significant positive associations of bacterial α-diversity and bacterial network complexity with glycerophospholipid metabolism, and a significant negative association of fungal network complexity with glycerophospholipid metabolism. Overall, our results suggest that the CH system is associated with higher bacterial diversity, greater microbial network stability, and alterations in key metabolic pathways. Future studies involving direct measurements of plant growth, yield, and disease incidence are required to validate whether such rhizosphere changes are associated with agronomic benefits.},
}

@article {pmid42769442,
year = {2026},
author = {Xu, J and Mei, W and Shi, J and Li, J and Liu, M and Yang, Z and Tian, N and Hu, Y},
title = {Rhizosphere microbial diversity analysis reveals enrichment of biocontrol taxa in healthy tobacco plants and yields novel antagonists against Phytophthora nicotianae.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1889242},
pmid = {42769442},
issn = {1664-462X},
abstract = {INTRODUCTION: Tobacco black shank (TBS), caused by Phytophthora nicotianae, is a devastating disease. Current control relies heavily on chemical pesticides, which pose risks of resistance and environmental pollution. Biological control using rhizosphere microorganisms offers a sustainable alternative. However, the relationship between the composition of the rhizosphere microbiome and its suppressive activity against P. nicotianae has not yet been systematically elucidated.

METHODS: High-throughput sequencing was used to compare the differences in rhizosphere microbiota of healthy and diseased plants from multiple field sites in Yunnan, China, combined with culture-dependent isolation and screening of antagonistic microorganisms against P. nicotianae.

RESULTS: No significant differences in bacterial or fungal diversity were found between healthy and diseased rhizosphere soils. Despite this overall similarity in diversity, healthy rhizosphere soil was significantly enriched in biocontrol genera, including Pseudomonas, Paenibacillus, and Massilia. A total of 204 bacterial and 95 fungal strains were isolated, among which 64 bacteria and 41 fungi exhibited antagonistic activity against P. nicotianae. Four strains (710, 733, 1088, and 1145) showed the strongest inhibitory effects and were identified as Bacillus amyloliquefaciens, Yokenella sp., Metapseudomonas resinovorans, and Bacillus subtilis, respectively. Moreover, the soluble metabolites and volatile metabolites produced by these strains also inhibited P. nicotianae. Notably, this study provides the first evidence that Y. regensburgei and M. resinovorans function as biocontrol agents against P. nicotianae, with mycelial inhibition rates reaching 72.29% and 38.96%, respectively.

DISCUSSION: These results reveal the enrichment of specific biocontrol taxa in healthy tobacco rhizosphere and identify Y. regensburgei and M. resinovorans as novel antagonists against P. nicotianae. This study expands the strain library for TBS biological control and provides promising candidates for developing green management strategies.},
}

@article {pmid42769480,
year = {2026},
author = {Zhang, X and Sun, C and Yang, B},
title = {Microbiome-based nutrition and the gut-muscle axis: emerging perspectives for athletic performance and recovery.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1927715},
pmid = {42769480},
issn = {2296-861X},
abstract = {The gut microbiota has emerged as a significant regulator of exercise adaptation, recovery, and skeletal-muscle function, giving rise to the idea of the gut-muscle axis as a potential target in sports nutrition. This review summarizes current data on how microbiome-targeted nutritional approaches, such as probiotics, prebiotics, synbiotics, post-biotics, and polyphenol-rich dietary interventions, effect physiological processes related to athletic performance. Human research suggests that certain therapies may enhance endurance capacity, recuperation, gastrointestinal health, immunological function, and body composition, however, these advantages are typically strain-, formulation-, and population-specific. Further experimental evidence indicates that microbial metabolites, especially urolithins and short-chain fatty acids, may control anabolic signaling, inflammatory responses, mitochondrial function, and redox balance via pathways involving AMPK, PGC-1α, and associated molecular networks. However, there is still no direct validation of these pathways in human athletes, and the majority of mechanistic information comes from cellular and animal models. The translation of existing findings into evidence-based sports nutrition recommendations is further constrained by significant variation in study design, intervention characteristics, participant populations, and outcome measures. More robust longitudinal human investigations incorporating strain-resolved microbiome profiling, microbial metabolomics, and standardized physiological and performance outcomes are needed in order to identify effective intervention strategies and establish causal mechanisms.},
}

@article {pmid42769587,
year = {2026},
author = {Pourbahrighesmat, S and Tojjari, A and Laliotis, G and Saeed, A},
title = {Interkingdom microbiome physiology in colorectal cancer: barrier dysfunction, immune-metabolic signaling, and therapeutic resistance.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1922297},
pmid = {42769587},
issn = {1664-042X},
abstract = {Colorectal cancer develops within a physiologically altered intestinal ecosystem. Epithelial barrier disruption, chronic inflammatory signaling, immune remodeling, and metabolic rewiring reshape host-microbial interactions in this niche. Although most colorectal cancer microbiome reviews have emphasized bacterial taxa, the gut ecosystem is inherently multi-kingdom, comprising bacteria, fungi, bacteriophages, and other viral elements that interact with one another and with the host. In this review, we propose that the clinically relevant unit of the colorectal cancer microbiome is often not a single organism but a configured interkingdom whose functional output depends on local physiology. Throughout, we distinguish human observational associations from mechanisms demonstrated in experimental models and from prospectively validated clinical effects. We synthesize evidence linking the bacteriome, mycobiome, and phageome to colorectal carcinogenesis, immune modulation, metabolic signaling, and therapeutic response. We highlight context-dependent mechanisms, including the paradoxical effects of Fusobacterium nucleatum, fungal regulation of myeloid and inflammasome pathways, phage-mediated control of bacterial virulence, and cross-kingdom metabolic circuits involving butyrate, succinate, bile acids, lactate, and arginine. We further propose, as a conceptual framework requiring longitudinal validation, that therapeutic resistance may sometimes reflect a treatment-selected ecological state rather than the action of a single resistance-conferring microbe. Finally, we address the reproducibility challenges raised by low-biomass intratumoral microbiome studies and outline minimum methodological standards for future multi-kingdom investigations. A framework centered in physiology, attentive to contamination, and organized around interactions may improve biomarker development and support rational microbiome-directed strategies in colorectal cancer.},
}

@article {pmid42769625,
year = {2026},
author = {Baram, S and Sarathi, A and Bakke, M and Arumugam, M and Pedersen, AML},
title = {Oral health and oral microbiota composition in patients with Parkinson's disease: a case‒control study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2726612},
pmid = {42769625},
issn = {2000-2297},
abstract = {INTRODUCTION: Parkinson's disease (PD) is associated with motor and non-motor dysfunctions that may influence oral homeostasis. An altered microbiota has been linked to PD, yet oral microbial changes remain poorly characterized. This case‒control study aimed to determine if the oral microbiota, the oral health status, and salivary secretion differ between patients with PD and matched controls.

MATERIALS AND METHODS: Forty participants (20 with PD and 20 controls) underwent standardized oral examinations, neurological scoring (Hoehn & Yahr; UPDRS II-III), and measurements of unstimulated (UWS) and stimulated whole saliva (SWS) flow rates. Microbial profiling of SWS samples and dorsal tongue scrapes was performed using long-read 16S rRNA gene sequencing (V1-V8). Alpha/beta diversity and differential abundance analyses were performed.

RESULTS: Patients with PD exhibited significantly lower UWS flow rates, higher plaque scores, and higher prevalence of xerostomia and drooling. Dental status and gingival inflammation did not differ between the groups. Microbial richness and Shannon diversity were lower in tongue scrapes from the PD group, but not in saliva samples. Veillonella, Prevotella and Streptococcus dominated the microbiota in both groups. Fusobacterium periodonticum and pseudoperiodonticum were consistently more enriched in both saliva and tongue microbiota of patients with PD.

CONCLUSION: Patients with PD have lower UWS flow rates and a shift toward a more anaerobic, biofilm-adapted oral ecosystem, particularly on the tongue. The tongue microbiome may potentially serve as a sensitive biomarker of PD-related dysbiosis.},
}

@article {pmid42769647,
year = {2026},
author = {Zhao, X and Wang, H and Liu, Y and Cao, L},
title = {Beyond the tumor microenvironment: a hierarchical immune-circuit model of immune checkpoint blockade resistance.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1919294},
pmid = {42769647},
issn = {2234-943X},
abstract = {Immune checkpoint blockade (ICB) produces durable tumor control in a subset of patients, yet resistance is usually interpreted through tumor-intrinsic lesions or suppression within the tumor microenvironment (TME). We propose that ICB resistance can also be organized as failure of a multiscale antitumor immune circuit comprising local immune execution, regional immune education in tumor-draining lymph nodes (TDLNs), and systemic immune calibration by the host. In this model, "hierarchical" denotes nested functional dependence rather than one-way anatomical control: local killing depends probabilistically on antigen visibility, access, and a renewable supply of tumor-reactive cells; nodal priming depends on competent dendritic-cell licensing and host immune fitness; and reciprocal feedback can propagate or repair failure across compartments. We first define the canonical CD8-dominant substrate that ICB can amplify, including cross-presentation, costimulation, progenitor-exhausted T-cell maintenance, trafficking, and target-cell recognition, while retaining alternative CD4, natural killer, intratumoral antigen-presenting-cell, and tertiary lymphoid routes. We then evaluate local, regional, and systemic resistance mechanisms, four directional feedback axes, and context-dependent patterns in pancreatic cancer, melanoma, non-small-cell lung cancer, microsatellite-stable colorectal cancer, hepatocellular carcinoma, and prostate cancer. Evidence from animal perturbation, human spatial and clonal studies, and clinical trials supports individual circuit components but remains heterogeneous. Randomized perioperative regimens demonstrate disease- and setting-specific benefit, whereas negative randomized results and mixed or limiting early-phase signals across innate agonism, stromal or metabolic targeting, radiotherapy combinations, and systemic conditioning constrain therapeutic extrapolation. We therefore present compartment-resolved biomarkers and adaptive trial designs as research hypotheses, not a validated classifier or standard-care algorithm. The framework will be useful only if prespecified multiscale measurements improve prediction beyond tumor-only models and if mechanism-matched interventions produce the expected pharmacodynamic repair before clinical benefit is attributed to the circuit.},
}

@article {pmid42769662,
year = {2026},
author = {Goodall, T and Jones, B and Thorpe, AC and Griffiths, RI and Gweon, HS and Read, DS and Pywell, R and Busi, SB},
title = {Antimicrobial resistance as a signature of soil restoration across a 143-year chronosequence.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag250},
pmid = {42769662},
issn = {2730-6151},
abstract = {Restoring agriculturally degraded habitats to species-rich grasslands is a vital conservation objective. During restoration, how the soil resistome matures alongside microbial community composition and function remains unclear. Here, we tested two competing hypotheses: whether the soil resistome co-occurs through a microbial structural maturation, in which soil restoration is associated with higher-order biotic interactions, or whether antimicrobial resistance (AMR) is instead associated with the competitive pressures and high bacterial taxonomic richness found in disturbed, eutrophic arable land. Using a unique land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly following the cessation of agricultural activity. Our results demonstrate that AMR abundance increases significantly with restoration age, reaching a maximum in >143-year-old soils. The strongest predictor of this rise in AMR abundance was an increasing microbial eukaryotic signature rather than increasing microbial density, suggesting that resistome expansion is not associated with generalized spatial competition, but rather, co-occurs with structural maturation of the microbiome. We observed an order of magnitude increase in antibiotic biosynthetic potential, dominated by the emergence of streptomycin clusters. Microbial reorientation during soil maturation mirrors the expansion of a core resistome comprised of ancient, intrinsic mechanisms, such as Major Facilitator Superfamily (MFS) efflux pumps and RNA Polymerase-Binding Protein A (RbpA) target protection, in older soils. We demonstrate that endogenous AMR is a hallmark of healthy, restored soil ecosystems rather than a marker of anthropogenic soil degradation.},
}

@article {pmid42769680,
year = {2026},
author = {Zelca, E and Gudra, D and Karklina, D and Ustinova, M and Lunge, M and Fridmanis, D and Rumba-Rozenfelde, I and Daugule, I},
title = {New Insights into the Composition of the Early-Life Gut Microbiome: A Metagenomic Analysis of Fecal Samples in Children Up to 18 Months of Age.},
journal = {Pediatric gastroenterology, hepatology & nutrition},
volume = {29},
number = {5},
pages = {359-373},
pmid = {42769680},
issn = {2234-8646},
abstract = {PURPOSE: To determine the gut microbiome composition and associated factors in infants.

METHODS: Cross-sectional study was conducted in primary healthcare centers including healthy children up to 18 months of age. Parents of children answered a questionnaire and bring a fecal sample of their child. Fecal samples were analyzed using shotgun sequencing. The relative abundances of taxonomic profile were detected and compared with associated factors.

RESULTS: In the study were included 91 children. The most abundant taxonomic units belonged to phyla: Bacillota, Bacteroidota, Actinobacteria. In contrast, the most abundant species were Bifidobacterium longum and Bifidobacterium breve, demonstrating an age-appropriate microbial composition. The viral fraction mainly consisted of bacteriophages, with the most abundant viral family being Tospoviridae. Nevertheless, more than 50 rather new taxonomic entities were observed to cause shifts in the taxonomic units of the infant gut microbiome in association with perinatal antibacterial therapy, type of delivery, feeding type in the first 6 months of life. Higher relative abundance of Kitasatospora spp. MMS16 BH015 was associated with C-section and antibacterial treatment during delivery. A total of 302 antimicrobial resistance genes were identified, the most frequently encountered genes were associated with glycopeptide antibiotic resistance: vanG, vanT, vanW, vanY and adeF. The distribution of ARGs did not differ among different age groups.

CONCLUSION: Metagenomic sequencing provides broader insights into the composition of the gut microbiome, emphasizing the presence of unusual species associated with environmental and perinatal factors. Perinatal antibacterial treatment may have a greater impact on the infant microbiome than was previously estimated.},
}

@article {pmid42769727,
year = {2026},
author = {González, M and Galarza-Arévalo, GE and Garzón-Romero, C and Romero, MP},
title = {Antimicrobial Strategies for Chronic Cutaneous Ulcers: From Preclinical Nanotechnology to Clinical Practice.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {624310},
pmid = {42769727},
issn = {1178-2013},
mesh = {Humans ; Chronic Disease ; Biofilms/drug effects ; Wound Healing/drug effects ; *Skin Ulcer/therapy/microbiology/drug therapy ; Animals ; Nanotechnology/methods ; Nanomedicine ; *Anti-Infective Agents/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Chronic cutaneous ulcers represent a growing global public health challenge, affecting an estimated 1-2% of the population in high-income countries and imposing a substantial socioeconomic burden through prolonged hospitalizations, repeated outpatient visits, increased risk of amputation, and significant impairment of patients' quality of life. Standard wound care centered on debridement, moisture-balancing dressings, and systemic antibiotics fails to resolve a large proportion of cases, particularly those complicated by polymicrobial biofilm infection and antimicrobial resistance, underscoring an urgent need for more effective therapeutic strategies. Despite the growing body of work on individual therapeutic modalities, no prior review has jointly evaluated clinically validated adjunct therapies and preclinical nanoplatform evidence for chronic cutaneous ulcers within a single, biofilm-ecology-centered framework, the gap this review addresses. This review critically evaluates current clinical and preclinical advances in the treatment of chronic cutaneous ulcers, with a focus on novel therapeutic modalities and emerging nanotechnology-based approaches. Clinically, the available evidence indicates that low-intensity ultrasound, electrical microcurrent therapy, photodynamic therapy, regenerative biomaterials, oxygen-based interventions, and advanced topical therapies may improve wound contraction, reduce microbial burden, relieve pain, and enhance tissue repair when used as adjuncts to standard care. At the preclinical level, metallic, polymeric, inorganic, and hybrid nanoplatforms can simultaneously target resistant bacteria and biofilms, stimulate angiogenesis, regulate inflammatory signaling, and support extracellular matrix remodeling. Recent advances in ulcer therapy are moving the field beyond passive wound coverage toward mechanism-driven treatments that actively modulate the chronic wound microenvironment. Despite this progress, current clinical evidence remains inconsistent and is often limited by small patient cohorts and non-standardized protocols. This highlights the pressing need for rigorous translational research to incorporate multifunctional bioactive platforms into well-supported, ulcer-specific therapeutic strategies.},
}

Humans
Chronic Disease
Biofilms/drug effects
Wound Healing/drug effects
*Skin Ulcer/therapy/microbiology/drug therapy
Animals
Nanotechnology/methods
Nanomedicine
*Anti-Infective Agents/therapeutic use
Anti-Bacterial Agents/therapeutic use

@article {pmid42769745,
year = {2026},
author = {Ratnadewi, N and Husin, F and Mose, JC and Syamsunarno, MRAA and Irianti, S},
title = {Gut and Gastric Dysbiosis in Hyperemesis Gravidarum: A Scoping Review of Microbiome-Targeted Evidence and Translational Pathways.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {632969},
pmid = {42769745},
issn = {1179-1411},
abstract = {BACKGROUND: Hyperemesis gravidarum (HG) is defined by severe nausea and/or vomiting beginning in early pregnancy, impaired ability to eat or drink normally, and a marked restriction of daily activities. Although gastrointestinal dysbiosis has been proposed in HG, its role remains uncertain within the emerging growth differentiation factor 15 (GDF15)-centered model of susceptibility.

METHODS: Guided by PRISMA-ScR, this scoping review searched PubMed/MEDLINE, Scopus, Web of Science, publisher websites, and reference lists for contemporary evidence published between 1 January 2021 and 2 May 2026. Pre-2021 foundational publications were excluded from the charted evidence map and included-study count and were cited only as methodological or biological background.

RESULTS: Thirty-six sources of evidence were synthesized across five thematic domains. Direct human studies identified associations between HG and altered microbial diversity or composition, as well as gastric Helicobacter pylori exposure, but taxonomic findings were inconsistent and no reproducible diagnostic signature emerged. Mendelian randomization implicated Coprococcus 2, Ruminococcus, and Turicibacter, whereas observational studies could not resolve whether dysbiosis preceded symptoms or followed vomiting, dietary restriction, medication exposure, or hospitalization. Pregnancy-context and mechanistic studies supported plausible pathways involving bile acids, short-chain fatty acids, intestinal barrier function, inflammation, and gut-brain signaling, but these remain indirect for HG. GDF15-centered endocrine susceptibility had the strongest mechanistic support. Pregnancy probiotic and prebiotic studies provided safety and proof-of-concept data, while HG-specific efficacy evidence remained insufficient.

CONCLUSION: Current evidence supports dysbiosis as an associated modifier, consequence, or endotype marker rather than an established independent cause of HG. Priority studies should use Windsor-compatible definitions, early longitudinal sampling, harmonized sequencing and metabolomic methods, concurrent assessment of GDF15 and nutritional status, and biologically stratified trials of confirmed H. pylori infection or reproducible functional dysbiosis.},
}

@article {pmid42769873,
year = {2026},
author = {McGovern, CJ and Tako, E},
title = {Microbial exopolysaccharides as bioactive modulators of intestinal health: a systematic review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1885879},
pmid = {42769873},
issn = {2296-861X},
abstract = {Microbial exopolysaccharides (EPS) are secondary metabolites produced and secreted by microorganisms during fermentation. Their structure and physicochemical properties depend on the microbial strain and growth conditions, making them highly versatile for application in the food industry. Current investigations have expanded to include their use as a bioactive compound, providing health benefits to the host without the introduction of live microorganisms, as in the case with probiotics. This systematic review analyzed 28 in vivo studies to assess the effects of EPS on intestinal health. Evidence suggests that EPS modulates the gut microbiome, enhances intestinal epithelium integrity, alters inflammatory biomarkers, affects colonic morphology, and increases short-chain fatty acid (SCFA) production. Overall, this systematic review primarily focuses on colonic health, with limited consideration of the role of EPS during small intestinal digestion. The findings support the potential of microbial exopolysaccharides as bioactive macromolecules that may improve intestinal health. This systematic review has been registered with the International Prospective Register of Systematic Reviews database (PROSPERO) (ID: CRD420261292367).},
}

@article {pmid42769920,
year = {2026},
author = {Zhang, L and Yin, Y and Li, R and Wang, G and Li, L and Yu, Y and Lu, W},
title = {Space radiation health risks to hematopoietic, neural, and gastrointestinal systems in astronauts.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1926972},
pmid = {42769920},
issn = {2296-2565},
mesh = {Humans ; *Astronauts ; *Space Flight ; *Cosmic Radiation/adverse effects ; *Gastrointestinal Tract/radiation effects ; Animals ; *Hematopoietic System/radiation effects ; *Radiation Exposure/adverse effects ; *Nervous System/radiation effects ; },
abstract = {The rapid progress in global deep space exploration presents astronauts with a complex space radiation environment that substantially exceeds that of near-Earth orbit. Space radiation primarily consists of galactic cosmic rays (GCRs) and solar particle events (SPEs), which exhibit strong penetrative capability and considerable biological damaging potential. These factors may induce persistent oxidative stress, mitochondrial dysfunction, DNA double-strand breaks, and repair pathway challenges. This review examines the impacts of space radiation on the hematopoietic, neural, and gastrointestinal systems. Human spaceflight observations indicate that exposure to space radiation may be associated with bone marrow suppression, reduced lymphocyte counts, diminished thymic output, and immune dysfunction, which may heighten susceptibility to infection and inflammation. Preclinical animal model research indicates that even low doses of space-relevant radiation may induce cognitive decline, memory deficits, anxiety-like behaviors, and neurodegenerative alterations, though these findings remain to be validated in human astronauts. Proposed mechanisms include impaired hippocampal synaptic plasticity, neuroinflammatory activation, and mitochondrial energy metabolism imbalance. Radiation has been shown to compromise the intestinal epithelial barrier, induce intestinal stem cell senescence, and disturb gut microbiome equilibrium in preclinical models. These gastrointestinal alterations may potentially exacerbate neurocognitive dysfunction and promote chronic inflammation via the gut-brain axis, based on mechanistic evidence from animal studies. Currently, there remains an insufficient systematic understanding of the cumulative effects, sex differences, and individual susceptibility associated with long-term low-dose composite radiation exposure. Integrating aerospace medicine is imperative to address these knowledge gaps and safeguard astronaut health during future deep-space missions.},
}

Humans
*Astronauts
*Space Flight
*Cosmic Radiation/adverse effects
*Gastrointestinal Tract/radiation effects
Animals
*Hematopoietic System/radiation effects
*Radiation Exposure/adverse effects
*Nervous System/radiation effects

@article {pmid42769962,
year = {2026},
author = {Duraj, J and Kowalczyk, K and Żelechowska, P and Agier, J},
title = {Immune-nutritional interactions in endometriosis: current evidence and future perspectives in disease management.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1940772},
pmid = {42769962},
issn = {1664-3224},
mesh = {Humans ; Female ; *Endometriosis/immunology/diet therapy/metabolism/etiology ; Animals ; Disease Management ; *Nutritional Status ; Diet ; Gastrointestinal Microbiome ; Diet, Mediterranean ; },
abstract = {Endometriosis is a chronic estrogen-dependent inflammatory disorder affecting approximately 10% of women of reproductive age. It remains a major contributor to chronic pelvic pain, infertility, and reduced quality of life. Despite considerable advances in elucidating its genetic, hormonal, and immunological basis, current therapeutic strategies frequently provide incomplete symptom relief, may be associated with adverse effects, and fail to prevent disease recurrence. Therefore, increasing attention has been directed toward modifiable environmental factors, particularly nutrition, as supplementary strategies for disease management. This review comprehensively examines the evidence connecting dietary patterns and bioactive food components with the immunopathogenesis of endometriosis. It explores the potential role of nutrition in modulating key biological processes involved in endometriosis pathophysiology and progression, including immune dysregulation, chronic inflammation, oxidative stress, angiogenesis, estrogen metabolism, and gut microbiota imbalance. Particular emphasis is placed on the Mediterranean diet and selected dietary components, such as omega-3 fatty acids, vitamin D, resveratrol, epigallocatechin-3-gallate, and probiotics, as well as dietary interventions like low-FODMAP and gluten-free diets. The findings are discussed in relation to mechanistic evidence and emerging observations. Substantial clinical data supporting specific dietary interventions are scarce, and most dietary guidelines are based on preliminary research. Future investigations that incorporate nutritional interventions alongside immune profiling, microbiome analysis, and multi-omics technologies may facilitate the development of individualized nutritional strategies as adjuncts within the framework of precision medicine for women affected by endometriosis.},
}

Humans
Female
*Endometriosis/immunology/diet therapy/metabolism/etiology
Animals
Disease Management
*Nutritional Status
Diet
Gastrointestinal Microbiome
Diet, Mediterranean

@article {pmid42770043,
year = {2026},
author = {Wuopio, J and Graells, T and Lin, YT and Schillemans, T and Moll, JM and Eklund, AC and Nielsen, HB and Larsson, A and Engström, G and Orho-Melander, M and Johnson, LS and Ärnlöv, J},
title = {Associations between sodium intake and gut microbiota composition.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1889723},
pmid = {42770043},
issn = {2296-861X},
abstract = {INTRODUCTION: High salt intake is associated with adverse health outcomes. Emerging evidence highlights the importance of the gut microbiome in human health, but large-scale human data on salt intake and the microbiome are limited. We examined the cross-sectional association between estimated 24-h sodium excretion (est24hNa) and the gut microbiome in a population-based cohort.

METHODS: We included 9,220 participants from the Swedish SCAPIS cohort with available shotgun metagenomic sequencing of fecal samples and urine analyses. We estimated the 24-h sodium excretion using the Kawasaki formula. Alpha diversity was assessed using the Shannon and inverse Simpson indices, and beta diversity using Bray-Curtis dissimilarity. Functional potential was evaluated using Gut Microbial Modules. Associations were analyzed using mixed linear regression models.

RESULTS: Alpha diversity was inversely associated with est24hNa, but associations were attenuated after adjustment for BMI and were not significant in fully adjusted models. Beta diversity was associated with est24hNa, although the explained variance was small (R2 < 0.001). Higher est24hNa was associated with 75 microbial species, including lower abundance of 27 species and higher abundance of oral-associated taxa such as Streptococcus spp. and Veillonella. It was also associated with increased abundance of pathways involved in microbial energy metabolism and carbohydrate fermentation.

CONCLUSION: Higher est24hNa was associated with selected gut microbiome features, including a higher abundance of several oral-associated taxa and differences in inferred functional capacity for energy metabolism and carbohydrate fermentation. These findings identify microbial patterns associated with sodium exposure that may be relevant to cardiometabolic health.},
}

@article {pmid42770647,
year = {2026},
author = {Mishra, S and Saxena, S},
title = {Probiotics as Functional Dietary Interventions for Gut Health, Immune Modulation, and Overall Well-Being: A Systematic Review.},
journal = {Clinical pediatrics},
volume = {},
number = {},
pages = {99228261480530},
doi = {10.1177/00099228261480530},
pmid = {42770647},
issn = {1938-2707},
abstract = {BACKGROUND: The pediatric gut microbiome influences immune maturation, neurodevelopment, and disease susceptibility. Probiotic supplementation has been investigated across multiple childhood conditions, yet strain-specific efficacy remains inconsistent.

OBJECTIVE: The objective of this review is to systematically evaluate strain-specific probiotic interventions in children and assess clinical efficacy, safety, and mechanistic pathways.

METHODOLOGY: A systematic review was conducted following PRISMA 2020 guidelines. PubMed, Scopus, and Web of Science were searched for studies (2006-2024).

RESULTS: Strong evidence supports Lactobacillus rhamnosus GG and Saccharomyces boulardii for acute diarrhea. Mixed strains show moderate benefit in atopic dermatitis. Adjunct probiotic therapy improves Helicobacter pylori eradication rates. Evidence in asthma and autism spectrum disorder remains preliminary.

CONCLUSION: Significant heterogeneity in strains, dosing, and study design limits generalizability. Probiotic efficacy in pediatrics is strain and condition-specific. Standardized RCTs and precision microbiome approaches are required.},
}

@article {pmid42770724,
year = {2026},
author = {Zhang, Y and Elsheikha, HM and Zheng, W-B and Nan, F-L and Liu, R and Zhang, X-X and Yang, L-H and Li, Y and Ma, H},
title = {An atlas of colonization factors in the mouse gut microbiome reveals phylogenetically structured repertoires and infection-stage-associated variation during Toxoplasma gondii infection in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0194026},
doi = {10.1128/spectrum.01940-26},
pmid = {42770724},
issn = {2165-0497},
abstract = {Colonization factors (CFs) comprise CF-associated gene families related to microbial establishment, persistence, host interaction, and gut ecological fitness, but their organization and variation in the mouse gut microbiome remain poorly defined. We integrated the Mouse Gut Genome Catalogue and the Mouse Gut Protein Catalogue, clustered at 90% amino acid identity, to define CF repertoires. A total of 79 conserved CF families, comprising over 2.4 million homologs, were identified across 112,951 genomes from 2,824 microbial species. Species-level CF-associated gene profiles exhibited a clear phylogeny-associated pattern and separated microbial species into two groups with distinct genome-scale functional profiles. Across the cecum and small intestine, CF profiles differed among control, acute, and chronic infection groups in dominant CF abundance, diversity, richness, and overall composition. CF profiles were significantly concordant with taxonomic profiles and associated with microbial community variation. Differential abundance analyses identified tissue- and stage-associated CF features. Exploratory machine-learning analyses showed high classification performance across all feature sets in the cecum, with the genus-level model yielding the highest median performance, whereas species- and genus-level taxonomic profiles provided stronger discrimination than CF profiles in the small intestine. This study provides a reference-based atlas of CF-associated gene repertoires and a CF-centered framework relating these repertoires to microbial phylogeny, genome-scale functional profiles, and infection-stage-associated variation in a murine Toxoplasma gondii infection model. CF-associated gene profiles can complement taxonomic and functional descriptions of the mouse gut microbiome, although the biological roles of individual CF-associated genes require experimental validation.IMPORTANCEStudies of the mouse gut microbiome commonly emphasize taxonomic composition, whereas the ecological traits associated with microbial establishment and persistence in the murine intestine remain less well characterized. By profiling CF-associated gene repertoires across control, acute, and chronic infection groups in mice, we show that infection-stage-associated differences in murine gut microbial community structure are accompanied by differences in colonization- and fitness-associated gene profiles. CF composition was associated with microbial community structure and functional potential, and CF-based features captured intestinal-region- and infection-stage-associated variation within this mouse data set. The principal contribution of this study is a reference-based, CF-centered framework that complements conventional taxonomic and functional profiling in murine infection models and provides a foundation for future mechanistic investigations of microbial colonization.},
}

@article {pmid42770729,
year = {2026},
author = {Mao, M and Wu, Y and Ye, L and Su, X and Zhang, J and Cui, S and Wang, C and Xu, S and Jian, Y and Qin, L and Zhu, B},
title = {Impact of plant sex on endophytic microbial diversity and community assembly in dioecious species.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0097626},
doi = {10.1128/spectrum.00976-26},
pmid = {42770729},
issn = {2165-0497},
abstract = {Dioecious plants show marked sexual dimorphism in morphology, physiology, defense, and life-history allocation, yet differences in endophytic microbiomes remain understudied. We compared endophytic bacterial and fungal communities between male and female individuals of four dioecious species-Eucommia ulmoides, Taxus wallichiana var. mairei, Ginkgo biloba, and Morus alba-by high-throughput sequencing of bark (E. ulmoides and T. wallichiana var. mairei) and leaves (G. biloba and M. alba). Sex significantly influenced the assembly of bacterial and fungal communities in all species. Bacterial alpha diversity (Shannon index) was significantly higher in males than females for E. ulmoides, T. wallichiana var. mairei, and M. alba. The bacterial phylum Spirochaetota was only detected in male samples of E. ulmoides, G. biloba, and M. alba, while the fungal genera Albophoma and Striaticonidium were detected only in female samples across all four species. Acidobacteria were significantly enriched in males of E. ulmoides and T. wallichiana var. mairei, whereas the fungal genus Sporidesmium was more abundant in females of T. wallichiana var. mairei and M. alba. Despite these sex-driven differences, dominant endophytic composition was similar between sexes: Actinobacteriota and Proteobacteria were the most prevalent bacterial phyla, whereas Ascomycota and Basidiomycota were the most prevalent fungal phyla across all samples. Co-occurrence analysis indicated stronger links between Actinobacteriota or Proteobacteria and other phyla than among remaining phyla. These results enhance understanding of sex-associated endophytic communities in dioecious plants and may inform studies on plant sex differentiation and potential plant-microbiome associations.IMPORTANCEPlant sex influences physiology, defense, and resource allocation, but its effects on internal microbial communities remain poorly understood. We compared endophytic bacteria and fungi in male and female Eucommia ulmoides, Taxus wallichiana var. mairei, Ginkgo biloba, and Morus alba using high-throughput sequencing and found consistent sex-associated differences in microbial diversity and specific taxa (e.g., Spirochaetota enriched in males; Albophoma and Striaticonidium enriched in females). These results indicate that sex is a reproducible driver of endophyte community assembly across diverse hosts. Recognizing sex-specific microbiomes has practical implications for conservation, forest and crop health management, and targeted bioprospecting, and underscores the need to include host sex as a key factor in ecological, functional, and evolutionary studies of plant-microbe interactions.},
}

@article {pmid42770768,
year = {2026},
author = {Speare, L and Rosales, SM},
title = {mGem: The two-decade evolution of in vivo coral microbiome manipulations.},
journal = {mBio},
volume = {},
number = {},
pages = {e0167826},
doi = {10.1128/mbio.01678-26},
pmid = {42770768},
issn = {2150-7511},
abstract = {Over the past two decades, microbiome manipulations have emerged as a strategy to bolster coral fitness. Here, we provide a timeline of two decades of research on in vivo coral microbiome manipulation studies aimed at improving coral health. A summary of coral hosts, probiotic taxa, and how experimental design varies across studies is synthesized to identify commonly used taxa and research gaps. This review highlights methodological challenges and identifies opportunities to advance probiotic development and translate microbial interventions into practical tools for coral restoration and reef management.},
}

@article {pmid42771082,
year = {2026},
author = {Jangid, C and Kumari, K and Joshi, R and Hamza, M and Dalal, J},
title = {Characterisation of microbial succession for the estimation of PMI and PMSI in terrestrial and aquatic environments.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {42771082},
issn = {1556-2891},
support = {200510192313//University Grant Commission/ ; },
abstract = {Decomposition is a continuous yet environmentally friendly process, and accurate estimation of the postmortem interval (PMI) and postmortem submersion interval (PMSI) remains a major challenge in forensic investigations. Recent developments in sequencing technologies have demonstrated great potential in the use of microbial communities in determining the time since death. Here, we investigated microbial community succession in human remains via 16 S rRNA gene sequencing and estimated the potential use of bacterial succession for estimating the PMI and PMSI. Distinct temporal shifts in microbial community composition were observed during aquatic and terrestrial decomposition, indicating predictable succession patterns associated with decomposition progression. Regression modeling under leave-one-out cross-validation demonstrated encouraging predictive performance, with the aquatic PMSI model based on ridge regression achieving an R[2] of 0.861 (MAE = 2.45 days), whereas the terrestrial PMI model using random forest regression achieved an R[2] of 0.768 (MAE = 2.60 days). Integration of microbial succession data with standardized decomposition scoring systems. These findings provide preliminary proof-of-concept evidence that microbial succession patterns can support PMI and PMSI estimation in forensic investigations. To the best of our knowledge, this represents the first forensic microbiome investigation of human terrestrial and aquatic decomposition for PMI and PMSI estimation in India.},
}

@article {pmid42771917,
year = {2026},
author = {Li, D and Xie, M and Chen, X and Li, T and Wang, A and Jiang, S and Xie, X},
title = {Proteins and microorganisms reveal that feed and substrate exert different effects on the growth and development of juvenile Chinese horseshoe crabs.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {61},
number = {},
pages = {102030},
doi = {10.1016/j.cbd.2026.102030},
pmid = {42771917},
issn = {1878-0407},
abstract = {In recent years, the population of Chinese horseshoe crabs (Tachypleus tridentatus) has declined sharply. As a living fossil of the ocean, they have an extremely slow growth cycle. To protect this endangered species, research has focused on identifying the optimal conditions required for its growth and development. Previous studies have focused on analyzing the optimal feed for T. tridentatus at various life stages. However, the optimal conditions required for the growth and development of first instar juveniles remain unclear. Furthermore, there is a lack of accurate and effective knowledge regarding the cultivation of first instar juveniles in aquaculture. Therefore, this study investigates the effects of feed and substrate on juvenile growth and development. Four experimental groups were established: a no-substrate, no-feeding group (WK group), a no-substrate, oyster feeding group (WS group), a group with sandy-mud substrate but no feeding (SNK group), and a group with sandy-mud substrate and oyster feeding (SNS group). The results were analyzed based on experimental records, proteomics, and microbiomics data. The results indicated that the SNS group exhibited the highest molting rate, as well as the highest weights for both first- and second instar juvenile horseshoe crabs. This indicates that the combined effect of oysters and the substrate is far greater in molting rates than the effect of either alone. Based on the proteomic results, under sandy-mud substrate conditions, oyster feeding induced substantial accumulation of mannosyl-oligosaccharide 1,2-alpha-mannosidase IA-like and Spartin, while reducing creatinase accumulation. With oyster feeding, the addition of sandy-mud substrate led to substantial accumulation of juvenile hormone acid O-methyltransferase-like isoform X1 and thromboxane-A synthase-like. Consistent with the microbiome results, juvenile horseshoe crabs in the SNS group exhibited higher average relative abundances of intestinal bacteria including Vibrionaceae, Thalassobius, and Defluviimonas.},
}

@article {pmid42761814,
year = {2026},
author = {Meng, X and Li, L and Hao, R and Lin, Z and Liu, K and Chi, G and Ren, J and Liu, R and Gao, Y and Yu, X and Tong, X},
title = {Shared oral microbiome signatures linking periodontitis and autoimmune thyroiditis: NHANES 2009-2012.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2728750},
pmid = {42761814},
issn = {2000-2297},
abstract = {OBJECTIVE: To examine the association between periodontitis severity and autoimmune thyroiditis (AIT) in a nationally representative US sample and to explore oral microbiome features shared between the two conditions.

METHODS: We analyzed adults from NHANES 2009-2012 with complete periodontal examinations, thyroid autoantibodies, and oral microbiome data (n = 1,346). Periodontitis was classified using CDC/AAP case definitions. AIT was defined as positivity for thyroid peroxidase antibodies (TPOAb ≥ 9 IU/mL) and/or thyroglobulin antibodies (TgAb ≥ 4 IU/mL). Survey-weighted multivariable logistic regression estimated adjusted odds ratios (aORs) and 95% confidence intervals (CIs). Oral microbiome diversity and differentially abundant genera were compared between groups.

RESULTS: In the fully adjusted model, mild and severe periodontitis were associated with higher odds of AIT compared with periodontally healthy individuals (mild: aOR 2.15, 95% CI 1.20-3.84; severe: aOR 2.77, 95% CI 1.22-6.28), whereas moderate periodontitis was not significantly associated (aOR 1.47, 95% CI 0.63-3.43). Genera enriched in both AIT and periodontitis included Fusobacterium, Bergeyella, Johnsonella, and Prevotella_2. Fusobacterium abundance increased across periodontal severity categories and showed a weak inverse correlation with TPOAb, whereas TT3 and FT3 showed weak positive correlations with Fusobacterium.

CONCLUSION: Periodontitis severity was associated with AIT in this cross-sectional NHANES analysis, and Fusobacterium emerged as a shared genus associated with both periodontal status and thyroid autoimmunity. Longitudinal and interventional studies are warranted to assess causality.},
}

@article {pmid42761980,
year = {2026},
author = {Assaf, S and Lio, P},
title = {The Active Shelf: A Clinician's Guide to Active Dermatologic Care for Atopic Dermatitis.},
journal = {The Journal of clinical and aesthetic dermatology},
volume = {19},
number = {7},
pages = {33-37},
pmid = {42761980},
issn = {1941-2789},
abstract = {Key therapeutic options for dermatologic care frequently extend beyond prescription medications to include evidence-based, over-the-counter (OTC) topicals that meaningfully influence disease pathophysiology. We introduce the concept of active dermatologic care (ADC), which encompasses nonprescription topical products with biologically active compounds that support and modulate key skin disease processes and can be routinely incorporated into comprehensive dermatologic care plans. We expand upon the recent concept of categorizing OTC active ingredients for acne based on their mechanisms of action and apply it to atopic dermatitis. The pathophysiologic pillars of itch, barrier dysfunction, acid mantle disruption, dysbiosis, and inflammation are each considered as potential therapeutic targets for ADC.},
}

@article {pmid42762145,
year = {2026},
author = {Yi, TW and Kumar, P and Karwasra, R and Sharma, N and Behare, MH and Linkang, X and Abdelkarim Maki, MA and Khanna, K},
title = {Biopolymeric Approaches for Colon Cancer Treatment: A Comprehensive Review of Polysaccharide-based Delivery Systems.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {235},
pages = {},
doi = {10.3791/70872},
pmid = {42762145},
issn = {1940-087X},
mesh = {Humans ; *Polysaccharides/chemistry/administration & dosage ; *Colonic Neoplasms/drug therapy ; *Drug Delivery Systems/methods ; Animals ; *Antineoplastic Agents/administration & dosage/chemistry ; Drug Carriers/chemistry ; },
abstract = {Globally, colon cancer remains one of the leading causes of mortality. Multidrug resistance, systemic toxicity, and poor tumor selectivity significantly limit conventional chemotherapy. This review highlights the need for localized therapy to increase efficacy and minimize systemic side effects. Colon-targeted drug delivery systems (CDDS) are designed and developed to overcome these challenges. Both natural and synthetic polysaccharides act as carriers in CDDS because of their biodegradability, biocompatibility, pH- and enzyme-responsiveness, and mucoadhesive properties. Polysaccharides such as chitosan, dextran, pectin, alginate, and hyaluronic acid have been formulated into nanoparticles, microparticles, and hydrogels, enabling controlled and site-specific delivery. These carriers deliver chemotherapeutics, nucleic acids, and immunotherapeutics, as well as theranostic agents that combine imaging and therapy. Preclinical evidence demonstrates significant translational potential for polysaccharide-based CDDS. However, clinical trials remain limited, which highlights the gap between laboratory findings and clinical applications. Major challenges in colon-targeted drug delivery include variability in polysaccharide sources and quality, difficulties in large-scale manufacturing, and regulatory challenges. Addressing these challenges will be essential to move towards commercialization and clinical adoption. Personalized therapy through microbiome profiling, integration with nanotechnology and bioinformatics, and smart, biosensor-responsive carriers will be the focus going forward. Polysaccharide-based CDDS provide safer, more effective, and more personalized treatment with continued research to optimize delivery and overcome existing limitations.},
}

Humans
*Polysaccharides/chemistry/administration & dosage
*Colonic Neoplasms/drug therapy
*Drug Delivery Systems/methods
Animals
*Antineoplastic Agents/administration & dosage/chemistry
Drug Carriers/chemistry

@article {pmid42762163,
year = {2026},
author = {Silva-Magaña, MA and Mora-Flores, LP and Pita-Galeana, MA and Hernández-Lemus, E and de Anda-Jáuregui, G},
title = {A network dynamical simulation model for the study of antibiotic resistance in microbial communities.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734703},
doi = {10.1080/19490976.2026.2734703},
pmid = {42762163},
issn = {1949-0984},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Bacteria/drug effects/genetics ; Computer Simulation ; Models, Biological ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; },
abstract = {Antibiotic resistance emerges from ecological and evolutionary processes occurring within complex microbial communities. Interactions among microorganisms can shape the pathways through which resistance traits spread and persist, yet many theoretical approaches treat microbial populations as homogeneous compartments. Here we present a simulation-based network dynamical model that represents microbial communities as ecological association networks. In this formulation, nodes correspond to bacterial populations, metapopulations, or taxon-level ecological units, while resistant counterparts represent state-expanded subpopulations associated with the same ecological unit. Edges represent co-occurrence-based ecological proximity rather than direct physical contacts or confirmed horizontal gene transfer events. Using stochastic simulations across multiple network topologies, we explore how structural properties of microbial communities influence the emergence and persistence of resistance. Parameter sweeps across transmission probability, initial resistance fraction, and antibiotic intervention timing allow us to characterize regimes in which resistance either remains localized or spreads through the community. The model produces time series of resistant and susceptible states and snapshots of evolving network configurations, enabling qualitative comparison across simulation scenarios. Our results show that network structure strongly modulates resistance dynamics. Highly clustered networks tend to trap resistance within local neighborhoods, whereas heterogeneous networks with hub nodes facilitate rapid dissemination. Antibiotic perturbations can either suppress resistance or paradoxically accelerate its expansion depending on network topology and intervention timing. These findings should be interpreted as qualitative results from a minimal proof-of-concept model, not as a direct reconstruction of plasmid transfer, species replacement, or patient-specific microbiome responses.},
}

*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
*Bacteria/drug effects/genetics
Computer Simulation
Models, Biological
*Drug Resistance, Bacterial
*Drug Resistance, Microbial

@article {pmid42762368,
year = {2026},
author = {Cirak, S and Grieshaber, V and Müller, P and Chao, CM},
title = {The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing.},
journal = {Molecular and cellular pediatrics},
volume = {13},
number = {1},
pages = {},
pmid = {42762368},
issn = {2194-7791},
abstract = {In severe childhood-onset neuromuscular disease (NMD), ventilatory muscle weakness and ineffective airway clearance drive recurrent infections and chronic colonization that is often culture-negative, polymicrobial, or both. The lung microbiome framework offers a unifying model: altered microbial immigration, elimination, and growth can produce dysbiosis with pathobiont expansion and antimicrobial resistance (AMR). We propose that pediatric NMD may follow a distinct developmental trajectory in which early-life secretion stasis, viral insults, and frequent antibiotics perturb immune-microbiome crosstalk during lung growth, potentially "imprinting" long-term community structure. However, NMD-specific airway microbiome data remain sparse because most studies rely on culture or upper-airway sampling. Oxford Nanopore Technologies (ONT) long-read sequencing enables real-time metagenomics with AMR gene detection and can deliver same-day profiles (as short as ~ 6 h from sample to result in optimized workflows), but requires robust low-biomass controls and, in some settings, polishing or hybrid strategies to mitigate higher per-read error. A major limitation of metagenomic sequencing of respiratory samples is the high proportion of host DNA, bacterial reads may account for only about 1-5% of the total sequencing reads. We review microbiome principles relevant to pediatric NMD, summarize current evidence, and outline ONT-enabled study designs and translational priorities.},
}

@article {pmid42762400,
year = {2026},
author = {Cunha, B and Alter, A and Berschback, M and Park, S and Gold, S and Schneider, Y},
title = {Rethinking Restrictive Diets in IBD: Toward an Inclusion-Focused Nutritional Paradigm.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42762400},
issn = {1534-312X},
mesh = {Humans ; *Inflammatory Bowel Diseases/diet therapy ; Elimination Diets ; Diet, Mediterranean ; Diet, Carbohydrate-Restricted ; Diet, Gluten-Free ; FODMAP Diet ; },
abstract = {PURPOSE OF REVIEW: Patient-initiated elimination diets are widely adopted by those with inflammatory bowel disease (IBD), yet the evidence supporting their long-term use remains limited and their risks are increasingly recognized. Some common elimination diets utilized by patients include the specific carbohydrate diet (SCD), low-FODMAP diet, and gluten-free and dairy-free diets. This narrative review critically examines the role of self-initiated restrictive dietary strategies in IBD management, evaluating the evidence for and against common elimination-based approaches, and contrasts these with emerging data supporting more inclusive dietary patterns.

RECENT FINDINGS: Sustained elimination diets carry meaningful risks: malnutrition, micronutrient deficiency, sarcopenia, gut microbial dysbiosis, food anxiety, and avoidant/restrictive food intake disorder (ARFID). Current evidence demonstrates that the Mediterranean diet performs comparably to more restrictive approaches in inducing symptomatic remission, and generally is not associated with adverse nutritional and psychosocial consequences. Contemporary recommendations from several gastrointestinal societies discourage long-term elimination diets and favor inclusive, nutritionally adequate patterns, particularly the Mediterranean diet, as a preferred dietary framework for most patients with IBD, though supporting evidence remains largely observational and randomized controlled trial data are limited. We propose a paradigm shift from dietary exclusion toward inclusion, diversity, and nutritional adequacy, with registered dietitians as essential partners in IBD care. When elimination is clinically indicated, it should be time-limited, goal-directed, and followed by structured food reintroduction. Moving beyond restriction represents not a retreat from dietary focus, but its maturation, aligning nutritional guidance with the principles of patient-centered, evidence-based disease management.},
}

Humans
*Inflammatory Bowel Diseases/diet therapy
Elimination Diets
Diet, Mediterranean
Diet, Carbohydrate-Restricted
Diet, Gluten-Free
FODMAP Diet

@article {pmid42762419,
year = {2026},
author = {Negi, R and Sharma, B and Darshani, P and Thakur, SS and Ratnasari, A and Barwant, MM and Tomar, P and Yadav, N and Yadav, AN},
title = {Revitalization of plant growth-promoting plant allied microbes: an eco-friendly approach for agricultural and environmental sustainability.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {42762419},
issn = {2676-8607},
abstract = {Plants are increasingly recognized as metaorganisms because they harbor diverse and dynamic microbial communities that establish intricate symbiotic associations and collectively regulate plant growth, development, and adaptation to changing environmental conditions. Plant-associated microorganisms colonize distinct ecological niches, including the rhizosphere, phyllosphere, endosphere, and surrounding soil, where they contribute to nutrient acquisition, phytohormone production, disease suppression, and tolerance to biotic and abiotic stresses. These multifunctional interactions have positioned plant growth-promoting (PGP) plant-allied microbes as promising alternatives to chemical fertilizers and pesticides for sustainable agriculture. However, despite significant advances in plant microbiome research, information on the diversity, functional mechanisms, agricultural applications, emerging technologies, and translational challenges of PGP microbes remains dispersed across the literature, limiting a comprehensive understanding of their potential for sustainable crop production. To address this gap, this review synthesizes recent advances in the ecology, functional mechanisms, and agricultural significance of plant growth-promoting plant-allied microbes, with particular emphasis on their roles in improving nutrient availability, enhancing crop productivity, suppressing phytopathogens, and increasing plant resilience to environmental stresses. The review further discusses recent developments in microbial consortia, microbiome engineering, omics-based technologies, and advanced bioformulation strategies, while critically evaluating challenges associated with commercialization, formulation stability, environmental variability, regulatory frameworks, and farmer adoption. Finally, future research priorities and technological innovations required for the successful integration of microbial-based solutions into climate-resilient agricultural systems are highlighted. This review provides a comprehensive and up-to-date perspective that supports the development and sustainable implementation of plant-allied microbial technologies for environmentally responsible agriculture and long-term food security.},
}

@article {pmid42762752,
year = {2026},
author = {Gomes, BPFA and Francisco, PA and Lima, AR and Godoi-Jr, EP and Fagundes, PIG and Passini, MRZ and Bronzato, JD and Lopes, EM and Chen, T and Paster, BJ},
title = {Unraveling microbial heterogeneity in post-treatment endodontic infections via 16S rRNA gene profiling.},
journal = {Archives of oral biology},
volume = {192},
number = {},
pages = {106767},
doi = {10.1016/j.archoralbio.2026.106767},
pmid = {42762752},
issn = {1879-1506},
abstract = {OBJECTIVES: This study aimed to characterize the intraradicular bacteriome of post-treatment endodontic infections using high-throughput 16S rRNA gene sequencing and to assess inter-individual microbial heterogeneity through a disaggregated ecological analysis.

DESIGN: Endodontic samples were collected from single root canals of 10 female patients requiring retreatment. The V3-V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Amplicon sequence variants were generated using DADA2-based processing. Microbial communities were characterized using relative-abundance profiles, Bray-Curtis, Hellinger, and CLR-transformed Aitchison distances, together with Local Contribution to Beta Diversity (LCBD), Species Contribution to Beta Diversity (SCBD), and Baselga's abundance-based beta-diversity partitioning.

RESULTS: Proteobacteria and Firmicutes predominated, although their relative contributions varied substantially among individuals, with greater heterogeneity at genus and species levels. Desulfobulbus predominated in R3, R10, R17, and R19, Enterococcus in R5 and R11, Haemophilus in R15 and R22, and Streptococcus in R21, whereas R20 showed a more distributed polymicrobial profile. Streptococcus oralis subsp. dentisani clade 398 showed the highest mean relative abundance, while Parvimonas micra had the highest prevalence despite relatively low abundance. R21, R22, and R20 showed the greatest beta-diversity contributions. Community differences were driven predominantly by balanced changes in taxon abundance rather than abundance gradients. The species-level core was limited and threshold-dependent.

CONCLUSION: Post-treatment endodontic infections exhibited highly individualized microbial profiles and substantial inter-individual variation, with a limited species-level core. These findings highlight the ecological complexity of microbial communities present after endodontic treatment and support comprehensive infection control during retreatment.},
}

@article {pmid42762890,
year = {2026},
author = {Ibrahim, F},
title = {Rapidly Fermentable Prebiotic Substrates: Benefits, FODMAP Effects and Host Tolerance.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {105130},
doi = {10.1016/j.clnesp.2026.105130},
pmid = {42762890},
issn = {2405-4577},
abstract = {Rapidly fermentable prebiotic substrates occupy a contradictory position in human nutrition. In microbiome and functional-food research, low molecular weight non-digestible carbohydrates such as inulin, fructo-oligosaccharides, galacto-oligosaccharides are added to foods and supplements to promote bifidogenic, metabolic and gastrointestinal benefits. In parallel, clinical nutrition often restricts the same substrates as FODMAPs to reduce symptoms in irritable bowel syndrome and related disorders of gut-brain interaction, while food-science research seeks to reduce raffinose-family oligosaccharides because of their flatulence-producing and antinutritional effects. This review examines these contradictory framings and asks whether the same rapidly fermentable substrates should be understood as beneficial prebiotics, symptom-provoking FODMAPs, or tolerance-limiting food components. It argues that the physiological effects of these substrates are not fixed properties of the compounds alone but also arise from interactions between intrinsic fermentability and host context. Rapidly fermentable substrates may support beneficial microbial and metabolic responses in tolerant individuals, but may contribute to gas production, osmotic effects, luminal distension, symptom generation or even immune activation in susceptible contexts. Future research should move beyond defining prebiotic efficacy primarily by enrichment of selected bacterial taxa. Instead, each substrate should be tested through dose-response studies that establish both beneficial and tolerance thresholds across healthy individuals and clinically relevant phenotypes. Future studies should also examine prebiotics within a host-ecology framework, testing whether benefit depends less on maximising microbial stimulation and more on maintaining a controlled, spatially contained and clinically tolerable microbiome.},
}

@article {pmid42762960,
year = {2026},
author = {Fukuda, T and Takagaki, M and Nakamura, H and Ozaki, T and Kadono, Y and Kawabata, S and Terada, E and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Kishima, H},
title = {Role of gut microbiome modulation in the attenuation of aging-related neuroinflammation in early brain injury after subarachnoid hemorrhage.},
journal = {Brain research},
volume = {},
number = {},
pages = {150559},
doi = {10.1016/j.brainres.2026.150559},
pmid = {42762960},
issn = {1872-6240},
abstract = {Early brain injury (EBI) critically determines post-subarachnoid hemorrhage (SAH) outcome, with worse prognosis in older patients. Aging confers exaggerated inflammation, possibly via gut microbiome (GM) alterations. We investigated whether GM alterations contribute to aging-related worsening of post-SAH EBI and whether GM modulation can reduce this inflammatory vulnerability. Young (8-12 weeks) and aged (17-20 months) male C57BL/6 mice underwent experimental SAH. Neurological scores, brain water content, neuronal degeneration, blood-brain barrier permeability, and inflammation were assessed. A combined GM modulation protocol consisting of antibiotic pretreatment, fecal microbiota gavage from young donors, and subsequent co-housing with young mice was performed in aged recipient mice. Compared to young mice, aged mice exhibited higher mortality, worse neurological scores, increased neuronal degeneration, and enhanced neutrophil infiltration, neutrophil extracellular trap (NET) formation, and microglial TNF-α expression. Absolute brain water content was lower in aged mice than in young mice, with a similar age-related difference also observed in sham animals. GM analysis revealed reduced diversity, decreasedFirmicutes, and increasedProteobacteriain aged mice. The GM modulation intervention shifted the GM composition toward that of young mice and was associated with reduced neuronal injury, neutrophil infiltration, NET formation, and microglial inflammation; however, neurological scores and brain water content did not improve at 24 h. These findings indicate that aging is associated with greater post-SAH vulnerability and enhanced neuroinflammation, while GM modulation reduces specific neuroinflammatory and neurodegenerative components of EBI without demonstrating improvement in overall functional outcome at 24 h. The gut-brain axis constitutes a potential therapeutic target for improved SAH outcomes in older adults.},
}

@article {pmid42763148,
year = {2026},
author = {De Troyer, T and De Windt, K and Pomian, B and De Paepe, E and Plekhova, V and Vanhaecke, L},
title = {Design of experiments-driven optimization of dual ultra-high-performance liquid chromatography high resolution mass spectrometry for integrated fecal metabolomics and lipidomics.},
journal = {Analytica chimica acta},
volume = {1422},
number = {},
pages = {346087},
doi = {10.1016/j.aca.2026.346087},
pmid = {42763148},
issn = {1873-4324},
mesh = {*Feces/chemistry ; Chromatography, High Pressure Liquid/methods ; *Metabolomics/methods ; *Lipidomics/methods ; Liquid Chromatography-Mass Spectrometry/methods ; *Lipids/analysis ; Mass Spectrometry ; Humans ; },
abstract = {Recently, feces has gained increased attention in metabolomics and lipidomics research due to its ability to reflect complex diet-host-microbiome interactions. Traditionally, these analyses rely on separate workflows, resulting in longer analysis times and increased instrument load. To address these limitations, we present a dual ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (dual UHPLC-HRMS) approach. As a first step, two previously validated single UHPLC-HRMS methods for metabolomics and lipidomics, each demonstrating robust chromatographic separation of compounds, covering a broad physicochemical range (LogP -5.30 to 21.90), were selected. To integrate both workflows into the dual platform, thirteen critical LC-MS parameters were systematically optimized using a Design of Experiments (DoE). The parameters encompassed ion generation, transmission and detection, injection-related factors, unified column oven conditions, and source geometry. This approach enabled a robust dual workflow, achieving a 21% reduction in analysis time. Targeted evaluation demonstrated consistent detection of 287 metabolites (260 with CV<20%) and 162 lipids (144 with CV<20%), thereby outperforming the single methods, which detected 272 metabolites (232 with CV<20%) and 145 lipids (116 with CV<20%), respectively. Untargeted analysis further demonstrated increased coverage, with an additional 1652 metabolite and 3966 lipid features detected with the dual method without compromising repeatability of the feature signal intensities (79.4% vs. 81.2% for metabolomics and 87.4% vs. 82.7% for lipidomics, with CV<30%). Our novel dual UHPLC-HRMS workflow enhances analytical throughput, while also improving fecal metabolome and lipidome coverage and repeatability, offering a robust and cost-effective solution for large-scale studies.},
}

*Feces/chemistry
Chromatography, High Pressure Liquid/methods
*Metabolomics/methods
*Lipidomics/methods
Liquid Chromatography-Mass Spectrometry/methods
*Lipids/analysis
Mass Spectrometry
Humans

@article {pmid42763326,
year = {2026},
author = {Shirazi Nia, R and Lu, J and De Vega, D and Poudine, N and Pan, C and Zhou, F and Ji, J and Giamas, G},
title = {Beyond the blood-brain barrier: humanised mice, the missing link in glioblastoma research.},
journal = {Oncogene},
volume = {},
number = {},
pages = {},
pmid = {42763326},
issn = {1476-5594},
abstract = {Glioblastoma (GBM) remains a major challenge in neuro-oncology, associated with a high rate of mortality despite decades of intensive research and therapeutic advancements, underscoring the urgent need for innovative preclinical platforms that can more accurately recapitulate the biological and pathological features of human disease. While conventional animal models have contributed to our understanding of GBM biology and the evaluation of treatment efficacy, they fail to capture the full complexity and heterogeneity of the tumour microenvironment (TME). Ex vivo models are associated with certain advantages in this context; however, they can not mirror the complex dynamic and multicellular interactions present in living organisms, particularly the critical treatment barriers unique to the central nervous system: the blood-brain barrier (BBB), blood-cerebrospinal fluid barrier (BCSFB) and blood-meningeal barrier (BMB). In response to these limitations, humanised mouse models have emerged as an advanced platform capable of faithfully mimicking the molecular, pathological and immunological features of human GBM. These models enable the replication of complex in vivo crosstalk between the immune system and the TME, while preserving the relevant treatment barriers that govern drug delivery to the brain. Accumulating evidence indicates that humanised mouse models closely reproduce the infiltration of human immune components into the TME, enabling the study of clinically relevant interactions that contribute to therapeutic resistance and treatment failure in GBM. This review aims to provide a comprehensive and systematic overview of the currently employed humanised mouse models in GBM research, highlighting their applications and comparative advantages. Finally, we evaluate the opportunities and challenges associated with each model and discuss future directions to increase the translational relevance and predictive power of preclinical GBM research. Humanised mouse models provide a valuable translational platform combining the human immune system and PDX orthotopic engraftment. Compared to conventional models and ex vivo models, these models can reproduce the complex cross-talk between tumour cells and the immune system, tumour heterogeneity, immunosuppressive TME, as well as complex in vivo interactions such as brain-specific barriers, including BBB, BCSFB and BMB. Future implementation of the human gut microbiome in these models has the potential to further increase translational relevance and precision in GBM research. Created in BioRender.com.},
}

@article {pmid42763356,
year = {2026},
author = {Kasprowicz-Furmańczyk, M and Chmielnicki, W and Zdanowska, N and Owczarczyk-Saczonek, A},
title = {The Role of the Microbiome in Lichen Sclerosus: Pathophysiological Insights and Therapeutic Implications.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42763356},
issn = {2193-8210},
abstract = {Lichen sclerosus (LS) is a chronic inflammatory and fibrotic dermatosis of unclear etiology, traditionally considered an autoimmune disorder. Emerging evidence suggests that microbiome dysbiosis may contribute to disease pathogenesis by modulating local immune responses and tissue remodeling. This narrative review synthesizes current data on the skin, genital, and gut microbiome in LS, focusing on potential mechanistic links between microbial imbalance and immune activation. Available studies consistently show alterations in microbial composition; however, findings remain heterogeneous because of the small sample sizes, methodological variability, and predominantly cross-sectional designs. Despite these limitations, accumulating data indicate that microbial dysbiosis may influence key immunological pathways involved in LS, including T-cell activation and chronic inflammation. In particular, mucosa-associated invariant T (MAIT) cells are proposed as a potential mechanistic bridge between microbial-derived signals and immune dysregulation, although their role in LS remains unclear. These observations support a conceptual model of LS as a microbiome-modulated inflammatory and fibrotic disorder rather than a purely autoimmune condition. Clinically, microbiome profiling and targeted modulation may offer novel diagnostic and therapeutic opportunities. Future research should prioritize longitudinal and interventional studies, ideally incorporating multi-omics approaches, to clarify causality and facilitate translation into clinical practice.},
}

@article {pmid42763436,
year = {2026},
author = {Alberdi, A and Ramirez, J and Gaun, N and Horisberger, Z and Wang, B and Trivedi, U and Bogri, A},
title = {LMDmapper: an open-source desktop tool for spatial mapping of laser microdissection samples.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {257},
pmid = {42763436},
issn = {2732-5121},
abstract = {Laser microdissection (LMD) enables researchers to isolate targeted microsamples from microscopy slide specimens for downstream molecular analyses. While traditionally employed for isolating eukaryotic cells from complex tissues, LMD is starting to be used for micro-scale spatial microbiome analyses, which require the precise location of the microsamples to be tracked for downstream spatial analyses. To address this need, we present LMDmapper, an open-source desktop application that allows designing, tracking and logging micron-scale spatial microsample data and metadata from LMD sessions. The software parses Leica Database LIF image files (containing stage coordinates), imports laser microdissection CSV exports (containing image pixel coordinates), transforms and maps image pixel coordinates into stage coordinates, and presents the resulting cut points together with user-defined plate layouts and collection metadata. LMDmapper supports a variety of microdissection designs, including multiple slides, specimens, collection plates and plate layouts. The application is implemented in TypeScript using Electron, React, Vite, and fast-xml-parser. LMDmapper outputs include a metadata CSV linking microsample identifiers to plate positions, collection information, image labels, pixel coordinates and stage coordinates, as well as the possibility to create overview images of the specimens, and automatically calculating distances between cutting points and regions of interest. With these capabilities, LMDmapper is intended as a practical bridge between microscope-side laser microdissection records and downstream spatial omics sample tracking.},
}

@article {pmid42763526,
year = {2026},
author = {Palanivel, M and Narayana, JK and Chotirmall, SH},
title = {Axial Connectivity of the Lung Microbiome: A Review of Interorgan Crosstalk.},
journal = {Comprehensive physiology},
volume = {16},
number = {5},
pages = {e70269},
pmid = {42763526},
issn = {2040-4603},
abstract = {The classic organ-centric model of human physiology is rapidly giving way to a unified approach embracing the human body as an integrated network of bidirectional interorgan communication. The human microbiome serves as a fundamental mediator of this shift, regulating immune homeostasis, barrier integrity and metabolic signaling across organs. While the lung maintains a characteristic low-biomass microbiome in dynamic equilibrium, any disruption primes local and systemic immune responses contributing to disease. Beyond the well-described gut-lung axis, crosstalk between the lung and other distal organ systems is lesser recognized; however, increasingly acknowledged as a key under-appreciated contributor to respiratory disease including extrapulmonary complications. This review synthesizes current established evidence on axial connectivity of the lung microbiome across the gut, brain, skin, heart, kidney, and liver, and finds that such crosstalk is predominantly, though not exclusively gut-mediated. Direct lung-organ interactions are described for several axes; however, they remain preliminary. Across these lung-axial systems, common pathophysiological mechanisms emerge, including dysbiosis-induced depletion of microbial metabolites, immunomodulation, and barrier perturbations, all linking pulmonary disease with neuroinflammation, gastrointestinal deficits, and cardiac, renal, hepatic, and dermatological abnormalities. We assess how therapeutic modulation of interorgan systems offers promising avenues for improved risk stratification and novel therapeutics. Recognizing microbiome-mediated pulmonary-organ crosstalk represents an emerging conceptual framework in respiratory medicine, repositioning microbial communities as key modulators of extrapulmonary disease.},
}

@article {pmid42764218,
year = {2026},
author = {Huang, QY and Xiang, HR and Tu, HK},
title = {[Current research status of the intratumoral microbiome and evolution of detection technologies].},
journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]},
volume = {48},
number = {9},
pages = {1124-1138},
doi = {10.3760/cma.j.cn112152-20260303-00105},
pmid = {42764218},
issn = {0253-3766},
support = {82574197//National Natural Science Foundation of China/ ; K20230085//Healthy Zhejiang One Million People Cohort/ ; },
mesh = {Humans ; *Microbiota ; *Tumor Microenvironment ; *Neoplasms/microbiology/pathology ; Metagenomics ; Bacteria/isolation & purification ; },
abstract = {As a core functional component of the tumor microenvironment, the regulatory role of intratumoral microbiome in tumorigenesis and progression has become as a frontier research direction in oncology. Microorganisms such as bacteria, fungi, and viruses participate in the regulation of tumor biological mechanisms through multiple pathways, including metabolite secretion, induction of genomic instability, and remodeling of the immune microenvironment; their species composition and abundance characteristics exhibit distinct cancer-type specificity, and their impact on patient prognosis is highly context-dependent. Current detection systems for the intratumoral microbiome mainly encompass in situ detection technologies, metagenomic sequencing, and computational pathology-driven intelligent detection, each with its own advantages and limitations, among which intelligent detection centered on deep learning is gradually overcoming the technical bottlenecks of identifying low-abundance microbial signals, achieving accurate quantification, and resolving spatial distribution. In the future, with the deep integration of three-dimensional pathological imaging, spatial omics, and multi-modal foundation models, intratumoral microbiome research will advance toward the in-depth development of multi-dimensional data integration, providing innovative ideas and technical pathways for elucidating the regulatory mechanisms between microorganisms and the host and for developing precision diagnostic and treatment strategies based on individual microecological characteristics.},
}

Humans
*Microbiota
*Tumor Microenvironment
*Neoplasms/microbiology/pathology
Metagenomics
Bacteria/isolation & purification

@article {pmid42764315,
year = {2026},
author = {Shao, Y and Zhang, RF and Wang, Z and Gan, J and Jiang, XJ and Yang, L},
title = {From Dysbiosis to Blood-Brain Barrier Disruption: The Metabolite-Mediated Gut-Brain Axis in Alzheimer's Disease.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42764315},
issn = {1559-1182},
mesh = {Humans ; *Blood-Brain Barrier/metabolism/pathology ; Animals ; *Alzheimer Disease/metabolism/pathology/microbiology ; *Dysbiosis/metabolism ; *Gastrointestinal Microbiome/physiology ; *Brain-Gut Axis/physiology ; *Brain/metabolism ; },
abstract = {Alzheimer's disease (AD) is not merely a central nervous system disorder; rather, it is a systemic condition profoundly influenced by the peripheral internal environment. Recent research has revealed that imbalances in the gut microbiota (GM) and metabolite disturbances contribute to AD onset and progression. Clinical and animal studies have indicated that AD patients commonly exhibit reduced GM diversity, decreased populations of short-chain fatty acid (SCFA)-producing and indole-producing bacteria, disrupted bile acid (BA) profiles, and elevated levels of trimethylamine N-oxide (TMAO) and kynurenine pathway (KP) activity. These alterations not only reflect gut dysbiosis, but also impair blood-brain barrier (BBB) integrity and amplify neuroinflammation by modulating tight junction proteins and inflammatory signaling through their effects on receptors and transporters such as G protein-coupled receptors(GPR41/43), aryl hydrocarbon receptor(AhR), Farnesoid X receptor(FXR)/ Takeda G protein-coupled receptor 5(TGR5), L-type amino acid transporter 1(LAT1), and Major Facilitator Superfamily Domain containing 2A(MFSD2A). From an integrative perspective, these changes -including short-Chain Fatty Acids (SCFAs) deficiency, elevated TMAO and toxic BA levels, overactivation of the KP, and Lipopolysaccharides (LPS) leakage-often act synergistically, collectively forming key pathological nodes in the "metabolic network-BBB-AD" axis. GM-targeted strategies such as dietary interventions, probiotics and fecal microbiota transplantation (FMT) have demonstrated potential in improving metabolite profiles and BBB homeostasis. Future research should utilize induced pluripotent stem cell-derived organoids and multi-omics integration approaches to elucidate the spatiotemporal dynamics of metabolites within the gut-brain axis (GBA), thereby laying the foundation for precise microbiome-based interventions in AD.},
}

Humans
*Blood-Brain Barrier/metabolism/pathology
Animals
*Alzheimer Disease/metabolism/pathology/microbiology
*Dysbiosis/metabolism
*Gastrointestinal Microbiome/physiology
*Brain-Gut Axis/physiology
*Brain/metabolism

@article {pmid42764380,
year = {2026},
author = {Li, L and Lei, S and Ngan, C},
title = {Pathogen-oriented mNGS is not equivalent to microbiome profiling: interpreting BALF mNGS diversity in ARDS.},
journal = {Journal of intensive care},
volume = {14},
number = {1},
pages = {},
pmid = {42764380},
issn = {2052-0492},
support = {25LCYJ34//Health Commission of Sichuan Province Medical Science and Technology Program/ ; },
abstract = {Gao et al. provide valuable data-linking bronchoalveolar lavage fluid metagenomic next-generation sequencing with inflammatory subphenotypes of acute respiratory distress syndrome. We highlight three issues relevant to interpretation: an apparent inconsistency concerning exclusion of samples with no micro-organisms detected, use of a pathogen-oriented workflow for community-level ecological inference, and the distinction between detection yield and diagnostic performance without an independent reference standard. Clarification of sample eligibility, sensitivity analysis including technically valid samples reported as negative by sequencing, and confirmation that sequencing and bioinformatic procedures are validated for quantitative microbiome analysis would strengthen interpretation.},
}

@article {pmid42764750,
year = {2026},
author = {Holmes, A and Matilla, MA},
title = {Toward Sustainable Crop Production in a Changing Climate: Microbiomes, Pathogens, Biostimulants and Biocontrol Innovations.},
journal = {Microbial biotechnology},
volume = {19},
number = {9},
pages = {e70442},
doi = {10.1111/1751-7915.70442},
pmid = {42764750},
issn = {1751-7915},
support = {JHI-A1-1//Scottish Government Environment, Natural Resources and Agriculture Research Program/ ; JHI-A1-2//Scottish Government Environment, Natural Resources and Agriculture Research Program/ ; JHI-D3-1//Scottish Government Environment, Natural Resources and Agriculture Research Program/ ; PID2023-146281NB-I00//Spanish Ministry for Science, Innovation and Universities/ ; },
mesh = {*Climate Change ; *Microbiota ; *Crops, Agricultural/microbiology/growth & development ; Biological Control Agents ; Soil Microbiology ; Biotechnology/methods ; *Crop Production/methods/trends ; Agriculture/methods ; Plant Diseases/microbiology/prevention & control ; },
abstract = {Climate change is recognised as one of the most pressing global challenges, with profound consequences for plant health, agricultural productivity, and food security worldwide. In this opinion article, we discuss recent advances in how climate change affects plant-microbe interactions, soil antibiotic resistance, and plant-associated microbiomes, including shifts in the distribution of plant pathogens. We also examine the influence of land-use practices, including integrated agricultural management, on the physicochemical and microbiological properties of soils under changing climatic conditions. In addition, we critically discuss emerging biological and biotechnological strategies aimed at enhancing plant health and resilience under climate change. These approaches include the rational design of synthetic microbial communities (SynComs), bacteriophage therapy, mycovirus-based biocontrol, antibiotic-producing microbial biocontrol agents, (nano-enabled) microbiome engineering, and extracellular vesicle-mediated RNA delivery systems. Challenges involved in translating laboratory-based discoveries into effective field applications are also discussed. Collectively, current advances highlight the growing potential of microbial biotechnology to reduce reliance on chemical pesticides and fertilisers, while supporting sustainable and integrated crop management under climate-change scenarios.},
}

*Climate Change
*Microbiota
*Crops, Agricultural/microbiology/growth & development
Biological Control Agents
Soil Microbiology
Biotechnology/methods
*Crop Production/methods/trends
Agriculture/methods
Plant Diseases/microbiology/prevention & control

@article {pmid42764800,
year = {2026},
author = {Ruiz, D and Robinson, V and Doucoure, M and Cheema, AR and Ramirez Cabal, C and Saleef Abdul Salam, A and Younes, RA and Song, W and Ibrahim, SA and Ariyo, O and Gupta, RD},
title = {Role of the Reproductive Tract Microbiome in Infertility and Assisted Reproductive Technologies: A Comprehensive Review.},
journal = {Cureus},
volume = {18},
number = {8},
pages = {e114891},
pmid = {42764800},
issn = {2168-8184},
abstract = {The female reproductive tract microbiome has emerged as a potential factor associated with reproductive health, infertility, and outcomes of assisted reproductive technologies (ARTs). Growing interest in host-microbiome interactions has highlighted the potential roles of microbial communities in implantation, immune regulation, and endometrial receptivity. This comprehensive narrative review summarizes current evidence on the reproductive tract microbiome and its relationship with infertility and ART outcomes. Relevant literature was identified from MEDLINE, Embase, and Web of Science from database inception through March 2026, with emphasis on observational, interventional, and mechanistic studies involving human participants or human-derived samples. The review examines microbial communities of the vagina, cervix, endometrium, and fallopian tubes and their associations with infertility, recurrent pregnancy loss, implantation failure, and ART outcomes. Proposed biological mechanisms, including alterations in epithelial barrier integrity, immune modulation, inflammatory signaling, and hormonal-microbial interactions, are also discussed. In addition, the review evaluates emerging microbiome-based diagnostic approaches and potential therapeutic strategies, including antibiotics, probiotics, micronutrient supplementation, and vaginal microbiota transplantation. Current evidence suggests that the reproductive tract microbiome may be associated with reproductive health and fertility outcomes and represents a promising area of translational research. However, substantial methodological heterogeneity, limited high-quality interventional evidence, and the lack of standardized diagnostic criteria currently restrict clinical implementation. Well-designed prospective studies and randomized clinical trials are needed to clarify causal relationships, evaluate microbiome-targeted interventions, and determine whether microbiome-based approaches can improve infertility and ART care.},
}

@article {pmid42764836,
year = {2026},
author = {Dong, C and Tai, J and Ma, Y and Wang, Y and Yang, J},
title = {Anti-inflammatory dietary patterns and cognitive aging in older adults: a scoping review of mechanistic, clinical, and nursing implications.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1952047},
pmid = {42764836},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary patterns with lower inflammatory potential may support cognitive aging, but Mediterranean, Dietary Approaches to Stop Hypertension (DASH), Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND), and dietary inflammatory scores represent non-equivalent exposures, and observational findings have not been consistently confirmed in randomized trials. This scoping review mapped evidence linking whole-diet patterns and dietary inflammatory indices with cognitive aging, measured biological pathways, and clinical interpretation and potential nursing implications.

METHODS: PubMed, Embase, Web of Science Core Collection, and Scopus were searched from inception to 30 June 2026. Eligible studies evaluated dietary patterns or validated inflammatory indices in older adults or cohorts assessed in later life and reported cognitive, dementia, mechanistic, neuroimaging, neuropathological, or implementation outcomes. Evidence was synthesized narratively, with observational and interventional findings considered separately.

RESULTS: Thirty-eight reports were included: 27 longitudinal observational studies, seven randomized intervention reports, three cross-sectional biomarker or neuroimaging studies, and one post hoc analysis. Mediterranean- and MIND-oriented patterns and lower dietary inflammatory potential were recurrently associated with more favorable cognitive outcomes, but findings varied across definitions, populations, measures, and follow-up. Randomized evidence was mixed and not definitive. Fourteen reports measured inflammatory, proteomic, microbiome, neuroimaging, cerebrospinal-fluid, spectroscopy, or neuropathological outcomes, supporting selected biological links without establishing a complete diet-neuroinflammation-cognition pathway. No study evaluated a complete nurse-led or nurse-supported dietary pathway; the nursing framework is author-derived and untested.

CONCLUSION: The evidence is epidemiologically suggestive and biologically plausible, but does not establish that any specific diet prevents dementia. Dietary improvement may be incorporated into individualized multidomain risk reduction, provided that nutritional adequacy, frailty, cultural fit, affordability, and sustained adherence are addressed. Better-contrasted trials, temporally ordered mechanistic studies, and prospective implementation evaluations are needed.},
}

@article {pmid42764917,
year = {2026},
author = {Li, B and Yang, Q and Li, M and He, J and Zhang, Z and Wan, X and Mo, Z and Li, R and Li, S and Xu, W and Gu, M and Huang, H and Li, W and Huang, Z and Yang, H and Chen, WH and Liu, Z},
title = {Gut microbiota-derived 5-HTP penetrates the host blood-brain barrier and ameliorates autism symptoms.},
journal = {Acta pharmaceutica Sinica. B},
volume = {16},
number = {9},
pages = {6168-6184},
pmid = {42764917},
issn = {2211-3835},
abstract = {Autism spectrum disorder (ASD), a highly prevalent neurodevelopmental condition, is increasingly recognized for its strong association with the intestinal microbiome. However, the development of gut microbiota-targeted therapies has been impeded by a limited understanding of the molecular mechanisms underlying interactions between commensal bacteria and the host nervous system. In this study, shotgun metagenomic sequencing and UPLC-MS/MS targeted metabolic analyses identified altered tryptophan metabolites in the gut microbiota of both human ASD patients and ASD mouse models. Notably, we demonstrate that commensal bacteria-derived 5-hydroxytryptophan (5-HTP), metabolite of tryptophan, ameliorates anxiety, stereotypical and repetitive behaviors, as well as social deficits in these mouse models. Furthermore, 5-HTP is capable of crossing the blood-brain barrier and inhibits the overexpression of receptor tyrosine kinase (RTK) ligands, thereby suppressing the downstream RTK/MAPK/ERK signaling cascade. This inhibition subsequently normalizes the excessive stabilization of dendritic spines in the hippocampus in MeCP2 mouse. Our research demonstrates that gut microbiota producing 5-HTP improves ASD symptoms in various ASD animal models, elucidates the molecular mechanisms between gut microbiota and the onset and treatment of ASD, and provides a promising therapeutic approach for ameliorating ASD through the expression of neuron-regulated small molecules by gut indigenous bacteria.},
}

@article {pmid42765047,
year = {2026},
author = {Guo, Q and Liang, F and Chen, P and Zhang, Y and Xie, M and Wan, X and Mao, J and Chen, H and Wu, W and Jiang, D and Wu, S},
title = {Microbiota-Host Interactions in Perimenopausal Syndrome: Mechanisms and Therapeutic Strategies (Review).},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {631942},
pmid = {42765047},
issn = {1179-1411},
abstract = {BACKGROUND: Perimenopausal syndrome (PMS) is common, with more than 70% of perimenopausal women experiencing symptoms such as hot flashes and anxiety. As a key regulator of host physiology, the gut microbiota may play an important role in the pathogenesis of PMS.

OBJECTIVE: This review aimed to synthesize clinical and preclinical evidence on alterations in the gut microbiota during perimenopause, elucidate the potential mechanisms underlying host-microbiota interactions, and summarize and critically evaluate current therapeutic strategies targeting the gut microbiota.

METHODS: A targeted literature search of PubMed and Web of Science was conducted for relevant studies published through July 15, 2026. Search terms covered perimenopause, menopause, gut microbiota, estrobolome, gut-brain axis, metabolomics, female microbiome, ovarian function, probiotics, and fecal microbiota transplantation. Human studies were prioritized, with high-quality animal and mechanistic studies included when clinical evidence was limited.

RESULTS: Few studies have directly examined women with PMS. Findings on gut microbial diversity and changes in specific taxa have been inconsistent across studies, and no reproducible pattern of gut dysbiosis specific to PMS has been established. Current evidence suggests that ovarian aging and fluctuations in sex hormones may reshape the gut microbial ecosystem. In turn, microbial enzymes and metabolites may interact bidirectionally with host endocrine changes by influencing the enterohepatic circulation of estrogens, immune and inflammatory responses, ovarian function, and gut-brain communication. Lifestyle interventions are supported by a relatively substantial body of evidence for symptom improvement, although whether their effects are mediated by the gut microbiota remains unclear. Certain strain-specific probiotics have shown preliminary clinical promise. However, evidence supporting prebiotics, synbiotics, traditional Chinese medicine, acupuncture, plant-derived products, and fecal microbiota transplantation is derived mainly from small clinical studies or preclinical experiments. By distinguishing direct clinical evidence from PMS populations from indirect evidence derived from other populations and experimental studies, this review reveals a central paradox in current research that strong biological plausibility coexists with insufficient clinical causal evidence.

CONCLUSION: The gut microbiota may contribute to the pathogenesis and progression of PMS through the "gut microbiota-estrogen-ovary-immune-brain axis". However, current evidence primarily supports bidirectional associations and biological plausibility. Although microbiota-targeted interventions have potential therapeutic value, the available evidence remains insufficient to support their routine clinical use. Future research should include longitudinal cohort studies using standardized menopausal staging and multicenter randomized controlled trials. Confounding factors such as age, diet, medication use, and hormone therapy should be adequately controlled. Integrated analyses of multiple omics datasets should also be combined with mechanistic studies to establish the causal role and clinical translational potential of the gut microbiota.},
}

@article {pmid42765490,
year = {2026},
author = {Milano, M and Hiram Guzzi, P},
title = {Differential analysis of microbial interaction networks.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag522},
pmid = {42765490},
issn = {1477-4054},
support = {//OFIDIAPlus (Operational Fire Danger preventIon plAtform Plus)/ ; },
mesh = {*Microbiota ; Humans ; Inflammatory Bowel Diseases/microbiology/genetics ; *Gene Regulatory Networks ; *Microbial Interactions ; *Diabetes Mellitus, Type 2/microbiology/genetics ; Female ; Atherosclerosis/microbiology/genetics ; Computational Biology/methods ; },
abstract = {Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities-encoded in patterns of association among microbial gene families-may reveal how these systems reorganize across biological conditions. Here, we present a network-based framework for characterizing microbiome rewiring across conditions. The approach combines condition-specific network inference, differential network analysis, and pathway-level network analysis to identify associations that are gained, lost, or altered between groups, with a specific focus on sex-dependent differences. We apply the framework to inflammatory bowel disease, type 2 diabetes, and atherosclerotic cardiovascular disease (ACVD), comparing male and female-specific microbial gene family networks within each disease context. Across these settings, differential networks flag large numbers of candidate rewired associations; however, permutation testing (sex labels shuffled, group sizes preserved, 500 permutations for gene-family networks, and 1000 for pathway networks) shows that the global amount of apparent rewiring is not greater than expected under the null at the global or edge level in any cohort, and that most edges exclusive to one group are induced by group-specific feature filtering rather than by a genuine change in association ($\sim $80%-83% in ACVD). We therefore present the method as a rigorously validated framework and a cautionary case study: the differential-network machinery is sound, but the headline biological signal in a naive analysis is largely a property of correlation thresholding and, for the longitudinal inflammatory bowel disease (IBD) cohort, of pseudoreplication. The only non-null result across all validations is a SOHPIE-DNA per-taxon test in the IBD disease arm (15 taxa at FDR $< 0.05$), which we report as a single nominal finding requiring independent replication. Code, data, and supplementary information are available at https://github.com/mmilano87/NetMicrobiome.},
}

*Microbiota
Humans
Inflammatory Bowel Diseases/microbiology/genetics
*Gene Regulatory Networks
*Microbial Interactions
*Diabetes Mellitus, Type 2/microbiology/genetics
Female
Atherosclerosis/microbiology/genetics
Computational Biology/methods

@article {pmid42765517,
year = {2026},
author = {Ward, GD and Ruiz-Tabas, Á and Altea-Manzano, P},
title = {Metastatic niche shaped by host factors influences disseminated cancer cell fate.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70471},
pmid = {42765517},
issn = {1873-3468},
support = {DGP_PIDI_2024_02725//Consejería de Universidad, Investigación e Innovación, Junta de Andalucía/ ; //Federation of European Biochemical Societies/ ; PID2023-152426OA-I00//Agencia Estatal de Investigación/ ; ERC-StG-101116912//European Union/ ; },
abstract = {Metastasis is responsible for the vast majority of cancer-related deaths, yet organ selectivity and the fate of disseminated cancer cells remain incompletely understood. While tumor-intrinsic programs have been extensively characterized, increasing evidence indicates that host-related extrinsic factors critically modulate the molecular and cellular landscape of metastatic niches. Aging, dietary habits, microbiome, physical activity, smoking, air pollution, and chronic stress may reshape systemic inflammation, immune surveillance, vascular permeability, stromal composition, extracellular matrix remodeling, and metabolic signaling in organs commonly targeted by metastasis, including bone, lung, liver, and brain. These host-dependent alterations influence disseminated cancer cell homing, extravasation, dormancy, and proliferative outgrowth by reprogramming tissue-resident and recruited cell populations, as well as niche-derived soluble and mechanical cues. In this review, we describe a framework in which metastasis is dynamically codetermined by tumor cell plasticity and host systemic state, contextualized by recent mechanistic insights into how lifestyle and physiological states rewire organ microenvironments to become either permissive or restrictive to metastatic colonization. Understanding these interactions may reveal actionable targets for metastasis prevention and highlight modifiable behaviors as biological determinants of organ susceptibility to metastatic disease.},
}

@article {pmid42765534,
year = {2026},
author = {Gabrielli, M and Bredel, A and Paoli, L and Robinson, SL},
title = {Advancing biosynthetic pathway discovery through short-read-directed long-read sequencing.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6np00020g},
pmid = {42765534},
issn = {1460-4752},
abstract = {Time span of literature: 2020-todayMetagenomic methods have rapidly advanced, enabling the identification of biosynthetic pathways directly from complex microbiome data. Short-read sequencing, while accurate and cost-effective, often generates fragmented assemblies that can lead to incomplete biosynthetic gene cluster (BGC) recovery. Although long-read sequencing offers a solution to the fragmentation problems, technical requirements and higher costs have limited its scalability. Here, we examine BGC fragmentation in short-read sequencing data across large databases of metagenome-assembled genomes (MAGs) and estimate the targeted genome contiguity required to recover 'complete' biosynthetic gene clusters. We argue that the increasing availability of MAGs recovered from short-read metagenomes with recent advancements in ultra-low input DNA amplification for high-fidelity PacBio sequencing-now requiring as little as nanograms of DNA-can be used sequentially to boost biosynthetic pathway discovery. We demonstrate how natural products researchers can benefit from using short-read MAG comparisons to guide targeted long-read re-sequencing efforts with low amounts of input DNA and/or limited financial resources. Our analysis provides strategic recommendations for the broader scientific community on how to best leverage the strengths of short- and long-read sequencing data to efficiently allocate resources and accelerate natural product discovery.},
}

@article {pmid42765606,
year = {2026},
author = {Zhang, J and Xu, S and Chen, C and Wang, Z and Du, W and Hong, L and Asiegbu, FO and Wang, K},
title = {Synthetic microbial community promotes seedling growth of Chinese fir via dissolving phosphorus and modifying rhizosphere microbial community.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag135},
pmid = {42765606},
issn = {1758-4469},
abstract = {Phosphorus (P) is an essential nutrient for plant growth, yet its availability in soil is severely constrained by fixation into insoluble forms that plants cannot directly utilize. Although phosphate-solubilizing microorganisms (PSM) represent a promising strategy to mobilize soil P, the functional potential of endophytic PSM and their synthetic consortia in promoting tree growth remains largely underexplored. In this study, endophytic bacteria were isolated from the roots of Chinese fir (Cunninghamia lanceolata). Among them, 42 isolates were screened for phosphate-solubilizing activity on media containing calcium phosphate, iron phosphate, aluminum phosphate, and organic phosphorus. Six strains with strong solubilizing capacity and no antagonistic interactions were selected to construct a synthetic microbial community (SynCom-P6), which was then applied to local soil and Chinese fir seedlings. Soil available P content initially decreased but subsequently increased from day 7 to day 21 after SynCom-P6 inoculation, indicating effective mobilization of insoluble P in soil. Inoculation with SynCom-P6 significantly enhanced root elongation and biomass accumulation, with both root fresh and dry weights showing marked increases compared to the control. Absolute quantification 16S amplicon and metagenomic sequencing revealed that SynCom-P6 reshaped the rhizosphere bacterial community, enriching beneficial genera such as Massilia and Dyadobacter, and altered functional profiles, including upregulation of hormone signaling and nitrogen fixation related genes. These results demonstrated that the synthetic community not only improved soil P availability but also promoted root growth and modified the rhizosphere microbiome in a beneficial direction. Our findings highlight the potential of endophytic phosphate-solubilizing SynCom-P6 as a promising bio-inoculant for sustainable forestry, reducing the need for chemical P fertilizers while enhancing Chinese fir productivity. Future research should focus on field validation and mechanistic exploration of microbial interactions and functional gene expression.},
}

@article {pmid42765627,
year = {2026},
author = {Liu, W and Ding, J and Sun, Y and Yan, B and Wang, Z and Wang, C and Shu, C and Zhou, JG and Yu, G and Peng, Y and Wang, S},
title = {Composable Visualization of High-Dimensional Biological Data with ggalign.},
journal = {Current protocols},
volume = {6},
number = {9},
pages = {e70453},
doi = {10.1002/cpz1.70453},
pmid = {42765627},
issn = {2691-1299},
support = {//National Natural Science Foundation of China/ ; },
mesh = {*Software ; *Computer Graphics ; *Data Visualization ; Humans ; *Computational Biology/methods ; Multiomics ; },
abstract = {ggalign is an R/CRAN package for creating flexible and composable multi-panel data visualizations. The package extends the ggplot2 grammar of graphics by introducing an integrative framework that supports both data-free and data-aware composition. After five years of continuous development, ggalign has evolved into a comprehensive solution that handles diverse data types and layout structures, including quad, circular, and stack layouts. It was originally designed for general-purpose composable visualization and has been expanded to support multi-omics data integration, extending the application of ggalign to pan-cancer analysis, single-cell transcriptomics, and microbiome studies. This article presents eight basic protocols for constructing complex visualizations using the declarative syntax of ggalign. Basic Protocol 1 describes data-free composition for flexible arrangement of multiple plots; Basic Protocol 2 describes data-aware quad layout for integrating a central plot with surrounding annotations; Basic Protocol 3 describes data-aware circular layout for visualizing ring-structured data; Basic Protocol 4 describes stack layout and nested composition for coordinated display of multi-track graphics; Basic Protocol 5 describes visualization of gene expression matrix heatmaps; Basic Protocol 6 describes visualization of somatic mutation landscapes using ggoncoplot(); Basic Protocol 7 describes circular visualization based on chromosome data, and Basic Protocol 8 describes cross-connection visualization between genes and pathways. The complete package reference is available at https://yunuuuu.github.io/ggalign/, with comprehensive documentation and tutorials at https://yunuuuu.github.io/ggalign-book/, and a gallery of example figures at https://yunuuuu.github.io/ggalign-gallery/. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Data-free composition Basic Protocol 2: Aligning data-aware with quad layouts Basic Protocol 3: Aligning data-aware with circular layouts Basic Protocol 4: Stack layouts and nested composition Basic Protocol 5: Visualizing heatmap of gene expression matrix Basic Protocol 6: Visualizing somatic mutation landscapes using ggoncoplot() Basic Protocol 7: Visualizing circos plots with ggalign Basic Protocol 8: Visualizing observational connections.},
}

*Software
*Computer Graphics
*Data Visualization
Humans
*Computational Biology/methods
Multiomics

@article {pmid42765732,
year = {2026},
author = {Hammer, AJ and Kasschau, KD and Davis Ii, EW and Hoffman, P and Johnson-Camacho, K and Alexiev, A and Anderson, K and Shannon, J and Marriott, LK and Sharpton, TJ},
title = {Polycyclic aromatic hydrocarbons, gut microbiome composition, impulsivity, and attention covary in a human cohort.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0078326},
doi = {10.1128/spectrum.00783-26},
pmid = {42765732},
issn = {2165-0497},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are pervasive environmental pollutants linked to adverse neurobehavioral outcomes, yet the biological pathways coupling exposure to behavior are poorly defined. The gut microbiome is both sensitive to PAH exposure and a modulator of central nervous system function, suggesting it may mediate how PAH exposure influences neurobehavior. We tested whether PAH exposure, gut microbiome composition, and neurobehavioral function covary in a statewide sample of 34 adults stratified into high-impulsivity/poor-attention (HH) and low-impulsivity/fast-attention (LL) groups. Participants wore silicone wristbands for 30 days to passively sample PAH exposure and provided a single fecal sample for 16S rRNA profiling at the end of the wear period. Higher PAH exposure was associated with HH group membership in a sex-dependent manner, with the largest elevations among HH males. At the community level, PAH exposure profiles correlated with microbiome dissimilarity, and HH membership was associated with increased alpha-diversity and altered community composition relative to LL members. At the taxon level, 22 genera were significantly associated with 14 PAH compounds (FDR < 0.1). No individual genera were significantly associated with neurobehavioral group after multiple testing correction. Nevertheless, cross-referencing PAH-responsive genera (FDR < 0.1) against those with nominal neurobehavioral associations (P < 0.05) identified two candidate genera-Hydrogenoanaerobacterium and Methanobrevibacter-whose abundance covaries with both PAH exposure and neurobehavioral phenotype. Both have been independently linked to cognitive or neurological outcomes in prior work. These findings support a three-way relationship among environmental chemical exposure, gut microbiome composition, and neurobehavioral function, establishing an empirical foundation for testing microbiome-mediated links between PAH exposure and neurobehavioral outcomes.IMPORTANCEPolycyclic aromatic hydrocarbon (PAH) exposure is widespread and is associated with impulsivity and attention problems, but how exposure translates into neurobehavioral risk is unclear. The gut microbiome is a plausible intermediary: gut microbes biotransform environmental chemicals and produce metabolites that influence brain function. In a statewide adult cohort, higher PAH exposure associated with with greater impulsivity and poorer attention in a sex-dependent manner, and both PAH exposure and neurobehavioral phenotype were associated with distinct gut microbiome features at the community and taxon levels. We identify candidate genera at the intersection of PAH exposure and neurobehavioral group whose biology independently implicates them in cognitive and neurological function. Because their associations with neurobehavioral phenotype are nominal, we present these genera as hypothesis-generating candidates for future study. By showing that all three domains covary within a single cohort, this work moves beyond pairwise associations toward testable microbiome-targeted and exposure-reduction strategies for PAH-related neurobehavioral risk.},
}

@article {pmid42765765,
year = {2026},
author = {Benot, AO and Waldschmidt, G and Gilvarg, SC and Legge, EOL and Okyere, IJ and Tiyapun, C and Lucas, SK and Vander Yacht, AL and Goff, JL},
title = {Prescribed burns drive lasting changes in soil nitrogen cycling and microbial function.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0085226},
doi = {10.1128/msystems.00852-26},
pmid = {42765765},
issn = {2379-5077},
abstract = {Fire is a major pulse disturbance to soil microbial communities, with broad implications for nutrient cycling; however, regular burning is also a natural and often-essential process maintaining biodiversity in unique and imperiled fire-dependent ecosystems. Prescribed fire is widely used to promote this biodiversity and simultaneously reduce wildfire risk. Although such repeated burning is known to alter surface biodiversity, belowground soil geochemistry, and soil microbial community structure, the functional consequences (i.e., the metabolic capabilities that underlie the ecosystem services soil microorganisms provide) remain underexplored. Here, we examined the effects of 30 years of repeated prescribed fire at the Albany Pine Bush-a fire-dependent, inland pitch pine barren ecosystem of the northeastern United States. Compared with the control stands, we observed that this long-term fire management has led to substantial depletion of inorganic soil nitrogen, specifically nitrate. We found no meaningful differences in the higher-level taxonomic composition of soil prokaryotic or fungal communities; however, analysis of metagenome-assembled genomes assembled from these soils revealed several differentially abundant populations. Furthermore, our metagenomic analysis revealed significant changes in the nitrogen-cycling functional potential, specifically decreased dissimilatory nitrate reduction and denitrification potential in repeatedly burned soils. These functional shifts have important implications for both nutrient cycling and emissions of trace nitrogen gases from these soils. Our results suggest that functionally meaningful changes in the soil microbiome can persist between burn events, even when higher-order community membership appears stable. This may imply that repeated fire can deplete reactive nitrogen emissions from soils by lowering the functional capacity of nitrogen-reducing microbes.IMPORTANCEPrescribed fire is widely used by land managers to reduce wildfire risk and promote biodiversity. While the effects of fire on aboveground processes are well understood, much less is known about how repeated burning influences soil biological properties-including the functional role that soil microorganisms play in nutrient cycling and greenhouse gas production. We addressed this gap by studying soils from the Albany Pine Bush, a rare and endangered ecosystem that has experienced regular prescribed fires for 30 years. Long-term fire management significantly altered soil chemistry, specifically lowering the amount of nitrogen in the soil. In addition, we found that fire management decreased the genetic potential of the soil microbial community to produce nitrogen oxides-potent contributors to climate change. Thus, prescribed fire's contribution to greenhouse gas emissions may involve a complex relationship between direct fire-driven emissions, increased fire resilience of promoted vegetation, and-as suggested by our results-the reduced ability of soil microbes to produce greenhouse gases.},
}

@article {pmid42765877,
year = {2026},
author = {Bonanno, S and Sheta, R and Ramu, T and Verenkar, S and Kim, D and Bessette, E and Pierre, P and Joshi, NS},
title = {Modulating innate immune responses to curli fibers through protein engineering.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0039426},
doi = {10.1128/iai.00394-26},
pmid = {42765877},
issn = {1098-5522},
abstract = {Curli fibers produced by Escherichia coli are functional amyloids that activate Toll-like receptor 2 (TLR2), initiating innate immune responses at mucosal surfaces. While microbiome-derived curli contribute to host-microbe interactions, their intrinsic immunostimulatory activity limits their utility as programmable scaffolds for engineered probiotic systems, and dysregulated TLR2 activation has been associated with inflammatory bowel disease, systemic lupus erythematosus, neurodegeneration, and sepsis. Here, we engineered E. coli Nissle 1917 to produce modified curli fibers designed to reduce TLR2 signaling through two mechanistically distinct strategies: steric shielding via silk-elastin-like protein sequences and direct receptor antagonism via a known TLR2 antagonist, staphylococcal superantigen-like protein 3 (SSL3). Both engineered variants assembled into structurally intact amyloid fibers and exhibited significantly reduced intrinsic TLR2-dependent NF-κB activation in reporter cells. In competitive inhibition assays against structurally diverse TLR2 agonists, the SSL3 fusion achieved near-complete attenuation of TLR2-dependent signaling, maintained under rising agonist load, while steric shielding provided moderate, agonist class-dependent inhibition. In primary human monocyte-derived dendritic cells, the SSL3 fusion robustly attenuated IL-8 secretion and transcriptional induction of IL-8, IL-6, and IL-1β, whereas steric shielding produced only partial attenuation that did not translate to broad inflammatory suppression. These results establish engineered curli as a tunable platform for receptor-specific modulation of innate immune signaling and highlight the broader potential of modular microbial amyloids as programmable interfaces for engineering host-microbe interactions at mucosal surfaces.},
}

@article {pmid42765916,
year = {2026},
author = {Wang, G and Liu, X and Wang, Z and Tian, H and Li, Y and Luo, Y},
title = {Exploring Cervical Cancer-Associated Vaginal and Cervical Microbiota via 16S rRNA Sequencing.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70412},
doi = {10.1002/mbo3.70412},
pmid = {42765916},
issn = {2045-8827},
support = {320.6750.2021-25-5//Wu Jieping Medical Foundation Special Funding for Clinical Research/ ; },
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Middle Aged ; *Vagina/microbiology ; *Cervix Uteri/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; Aged ; China ; DNA, Ribosomal/genetics/chemistry ; Phylogeny ; Lactobacillus/genetics/isolation & purification ; Prevotella/genetics/isolation & purification ; Computational Biology ; },
abstract = {Although the etiology of cervical cancer has been partially established, its pathogenesis remains a key research focus. Specific studies on the genital tract microbiota of cervical cancer patients in Southern China are still scarce. To address this research gap, the present study collected genital tract microbial samples from 16 cervical cancer patients and 16 healthy women. Analysis of cervical cancer-specific microbiota was conducted via 16S rRNA gene sequencing. The study included 32 women (16 cervical cancer patients and 16 healthy controls) aged 45-65 at enrollment. Total genome DNA from samples was extracted using the hexadecyltrimethylammonium bromide (CTAB) CTAB method. The vaginal and cervical microbiota composition was determined by sequencing barcoded 16S rDNA gene fragments (V3-V4), and a comparative bioinformatics analysis of the microbiome was performed. The study revealed a homogeneous microbial composition dominated by Lactobacillus in healthy women, whereas cervical cancer patients exhibited increased diversity with reduced Lactobacillus and enriched Prevotella. No significant differences were observed between sampling sites within each group. Functional predictions linked the cancer-associated microbiota to metabolic pathways and the AEROBACTIN-SYN-PWY pathway. In conclusion, our findings suggest that these specific key microbial taxa and their related metabolic pathways contribute to the pathogenesis of cervical cancer and may serve as promising targets for clinical treatment and intervention.},
}

Humans
Female
*Uterine Cervical Neoplasms/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Middle Aged
*Vagina/microbiology
*Cervix Uteri/microbiology
*Bacteria/classification/genetics/isolation & purification
Sequence Analysis, DNA
DNA, Bacterial/genetics/chemistry
Aged
China
DNA, Ribosomal/genetics/chemistry
Phylogeny
Lactobacillus/genetics/isolation & purification
Prevotella/genetics/isolation & purification
Computational Biology

@article {pmid42765918,
year = {2026},
author = {Gregory, CL and Radja, K and Haak, DC and Bradford, EL and Fell, RD and Walke, JB and Belden, LK},
title = {A metagenomic survey reveals widespread antibiotic resistance genes in honey bee (Apis mellifera) gut bacteria across the United States.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0075526},
doi = {10.1128/aem.00755-26},
pmid = {42765918},
issn = {1098-5336},
abstract = {Antibiotic use has contributed to antibiotic resistance genes (ARGs) accumulating in many environments, including host-associated microbiomes. Managed honey bee gut bacteria may accumulate ARGs, as honey bees are sometimes treated with antibiotics and often live in agricultural landscapes contaminated with antibiotics. We describe the occurrence and distribution of ARGs in honey bee bacterial gut symbionts from 13 apiaries in a transect across the USA from Washington to Virginia. Using metagenomic sequencing, we detected 55 unique ARGs conferring resistance to 14 classes of antibiotics. Of these, 11 ARGs encoded multidrug resistance. ARGs varied among sites, and ARG composition in hives shifted across the transect. Among honey bee gut bacterial genera, ARG occurrence varied, with Gilliamella and Frischella containing the highest proportions of ARGs despite their low relative abundance in the gut community, suggesting specific genera may serve as ARG reservoirs. As tetracycline is the most used antibiotic in beekeeping, we compared the frequency and abundance of tetracycline resistance genes across apiaries. All hives contained tetracycline resistance genes, with tetB and tetM present at all apiaries. Based on qPCR, tetB and tetM abundance varied significantly among apiaries. TetB was higher overall and declined in abundance from Washington to Virginia. We demonstrate that honey bee gut bacteria possess a diversity of ARGs, not all of which are consistent with antibiotic use in beekeeping, ARG frequency varies among bacterial genera in the honey bee gut, and certain ARGs are associated with hive geographic location.IMPORTANCEThe spread of antibiotic resistance genes (ARGs) to bacterial pathogens is a critical issue facing global health. Gut bacterial symbionts of managed honey bees make good bioindicators for ARGs because honey bees interact with potential environmental reservoirs of ARGs and are broadly distributed across the USA, including in both urban and rural environments. Based on our transect across the USA, ARGs were diverse and widely distributed among honey bee gut symbionts, although certain bacterial genera had a higher propensity for accumulating ARGs. Tetracycline resistance genes were most common, and varied in occurrence and abundance across the transect. The abundance of tetB, in particular, increased from east to west along the sampled transect. These large-scale patterns of ARG distribution within a widely dispersed host-associated microbiome system provide a foundation from which to examine the underlying factors driving differences in ARG occurrence and abundance.},
}

@article {pmid42766112,
year = {2026},
author = {Shang, J and Li, L and Dong, C and Wei, Y},
title = {Bacteriophage-bacteria coevolution: from molecular arms races to ecological and applied perspectives.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42766112},
issn = {1432-072X},
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *Biological Coevolution ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; CRISPR-Cas Systems ; *Biological Evolution ; Evolution, Molecular ; },
abstract = {Bacteriophages are the most abundant biological entities, driving bacterial evolution through long-term coevolution. Bacteria have evolved diverse defense strategies against phage, including receptor modification, restriction-modification systems, CRISPR-Cas, abortive infection systems, and newly discovered systems such as BREX, DISARM, CBASS, Thoeris, and Zorya. In response, phages deploy countermeasures such as receptor-binding diversification, anti-CRISPR proteins, DNA modification, and inhibitors targeting host immunity. These interactions generate distinct evolutionary dynamics-arms race and fluctuating selection-shaping microbial population structure and ecological stability. Phage-host coevolution promotes microbial diversity, horizontal gene transfer, and regulates community composition across ecosystems. Understanding these processes is critical for applications like phage therapy, microbiome engineering, and biotechnology. This review summarizes molecular mechanisms of bacterial defense and phage counter-defense, discusses coevolutionary models, highlights ecological and applied implications, and outlines future research directions.},
}

*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
*Biological Coevolution
Gene Transfer, Horizontal
Host-Pathogen Interactions
CRISPR-Cas Systems
*Biological Evolution
Evolution, Molecular

@article {pmid42766174,
year = {2026},
author = {Palanisamy, M and Thalavaipandian, L and Selvaraj, D and Rajamani, K and Babalola, OO and Ramalingam, S},
title = {Unlocking the hidden potential of the genus Salvia through a systematic review of endophytic bacterial and fungal diversity and biotechnological prospects.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42766174},
issn = {1432-072X},
support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; },
mesh = {*Endophytes/classification/genetics/physiology/metabolism/isolation & purification ; *Salvia/microbiology/chemistry/growth & development ; Biotechnology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Fungi/classification/genetics/isolation & purification/metabolism ; Biodiversity ; },
abstract = {The genus Salvia is one of the largest and the most pharmacologically important genera within the family Lamiaceae, which is known for its rich diversity of bioactive compounds, including phenolics and terpenoids. Recent studies have shown that endophytic fungi and bacteria associated with Salvia play important roles in plant growth, development, and chemical composition, which in turn contribute to species adaptability. This review presents a comprehensive, PRISMA-guided systematic review that emphasises the diversity and biotechnological potential of these endophytes. Available evidence indicates that although Salvia-associated endophytes have been widely studied, most research has focused on a single species, namely Salvia miltiorrhiza, with comparatively limited attention to other species and their associated endophytic communities. This review compiles comprehensive, current knowledge on endophyte diversity, tissue-specific distribution, and ecological roles, along with their biotechnological applications related to plant growth promotion, stress tolerance, biocontrol activity, and the production of bioactive compounds. It also highlights the role of endophytes in enhancing host secondary metabolite accumulation, with appropriate citations. Despite significant advances, gaps remain in understanding endophyte diversity across different Salvia species and in linking microbial functions to host-associated metabolic outcomes. This review identifies key knowledge gaps and outlines future directions to advance our understanding of plant-endophyte interactions and to support their effective application in sustainable agriculture and biotechnology.},
}

*Endophytes/classification/genetics/physiology/metabolism/isolation & purification
*Salvia/microbiology/chemistry/growth & development
Biotechnology
*Bacteria/classification/isolation & purification/genetics/metabolism
*Fungi/classification/genetics/isolation & purification/metabolism
Biodiversity

@article {pmid42766561,
year = {2026},
author = {Chen, X and Lei, M and Tang, J and Wang, H and Chen, J and Liu, Y and Li, S and Liu, F and Wang, Y and Li, Z and Dai, Z},
title = {Efficacy, safety, and feasibility of youth-derived fecal microbiota transplantation among adults with type 1 diabetes mellitus: A protocol of Pilot Randomized Controlled Trial.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0343078},
doi = {10.1371/journal.pone.0343078},
pmid = {42766561},
issn = {1932-6203},
mesh = {Humans ; *Diabetes Mellitus, Type 1/therapy/microbiology ; *Fecal Microbiota Transplantation/methods/adverse effects ; Pilot Projects ; Adult ; Double-Blind Method ; Female ; Glycated Hemoglobin/metabolism/analysis ; Male ; Feasibility Studies ; Young Adult ; Randomized Controlled Trials as Topic ; Treatment Outcome ; Blood Glucose ; Adolescent ; Continuous Glucose Monitoring ; Gastrointestinal Microbiome ; Insulin/therapeutic use ; },
abstract = {BACKGROUND: Dysbiosis of gut microbiota plays a key role in type 1 diabetes mellitus (T1DM). Fecal microbiota transplantation represents a novel therapeutic avenue. We hypothesize that youth-derived fecal microbiota transplantation (yFMT) can remodel the gut microecosystem and improve clinical outcomes. This pilot trial aims to assess the feasibility, safety, and preliminary efficacy of yFMT in adults with T1DM.

METHODS AND ANALYSIS: This single-center, randomized, double-blind, placebo-controlled pilot study will enroll adults with T1DM who have suboptimal glycemic outcomes (glycated hemoglobin [HbA1c] of 7.0-14.0% or time in range [TIR] <70%). Following a 17-day run-in period for insulin optimization, continuous glucose monitoring (CGM) wearing, baseline assessments and bowel preparation, participants will be randomly allocated (1:1) to take yFMT or placebo capsules for 6 consecutive days, alongside their standard insulin therapy, and then complete a 12-week follow-up. The primary efficacy endpoint is the change from baseline in the rate of achieving the composite target of TIR > 70% and time below range <4% at 12 weeks post-randomization. Secondary efficacy endpoints include: (1) the change from baseline in the same composite achievement rate at 4 weeks post-intervention; (2) changes from baseline at Weeks 4 and 12 in other glycemic metrics (including HbA1c, fasting plasma glucose, 2-hour postprandial glucose, and additional CGM metrics), C-peptide, immune responses, infection markers, and gut microbiota composition; and (3) changes from baseline at Week 12 in serum metabolomic profiles (bile acids, short-chain fatty acids, and other related metabolites). Feasibility will be assessed through recruitment rate, retention rate, intervention adherence, and acceptability. Safety endpoints include the incidence of adverse events and serious adverse events.

DISCUSSION: Our findings will offer new insight into the feasibility and effects of oral yFMT capsules in adults with T1DM and provide the necessary evidence to power a subsequent multicenter large-scale study. Exploratory biomarker analyses conducted within this study may further pave the way for future individualized microbiome‑based therapeutics.

TRIAL REGISTRATION: Chinese Clinical Trial Registry identifier: ChiCTR2500111955 (November 7, 2025).},
}

Humans
*Diabetes Mellitus, Type 1/therapy/microbiology
*Fecal Microbiota Transplantation/methods/adverse effects
Pilot Projects
Adult
Double-Blind Method
Female
Glycated Hemoglobin/metabolism/analysis
Male
Feasibility Studies
Young Adult
Randomized Controlled Trials as Topic
Treatment Outcome
Blood Glucose
Adolescent
Continuous Glucose Monitoring
Gastrointestinal Microbiome
Insulin/therapeutic use

@article {pmid42761475,
year = {2026},
author = {Yu, Q and Zheng, Y and Li, Y and Li, S and Wu, W and Lan, L and Mao, J and Fang, K and Chen, Z and Gao, YD},
title = {Supragingival plaque microbiome features in allergic rhinitis and allergic asthma and their association with dental caries: a cross-sectional study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2732753},
pmid = {42761475},
issn = {2000-2297},
abstract = {BACKGROUND: Allergic rhinitis (AR) and allergic asthma (AS) are associated with increased risk of dental caries, potentially associated with alterations in the oral microbiome.

OBJECTIVE: To characterize supragingival plaque microbiome features and their associations with caries severity in allergic adults.

DESIGN: This cross-sectional study enrolled patients with cat dander-induced AR or AS, along with age- and sex-comparable normal controls (NC). Supragingival plaque was collected for 16S rRNA gene sequencing. Microbial diversity, ANCOM-BC2 with multiple-testing correction and pseudo-count sensitivity analysis and LEfSe exploratory analysis were performed. Factors of caries severity (DMFT/DMFS) were examined with a random forest model and multivariable negative binomial regression.

RESULTS: A total of 89 participants (32 AR, 46 AS and 11 NC) were included. Allergic patients exhibited significantly higher α-diversity than NC. ANCOM-BC2 analysis identified 24 taxa with an omnibus FDR threshold; a family-resolved, genus-unclassified Prevotellaceae passed the pseudo-count sensitivity analysis. LEfSe analysis identified Treponema and Bacteroidota as AR-enriched taxa, and Actinobacteriota as AS-enriched taxa. Treponema was the top-ranked random forest feature. Among allergic patients, regular dental check-ups were associated with lower DMFT (IRR = 0.47, 95% CI: 0.30-0.75) and DMFS (IRR = 0.34, 95% CI: 0.17-0.69). Corynebacterium abundance was inversely associated with DMFT (IRR = 0.56, 95% CI: 0.31-0.98), and Actinomyces abundance was positively associated with DMFS (IRR = 2.96, 95% CI: 1.07-8.19).

CONCLUSIONS: Plaque microbial communities differed across groups, and selected taxa were associated with caries severity among allergic adults. Future investigations are needed to evaluate temporality and mechanisms.},
}

@article {pmid42761666,
year = {2026},
author = {Berggren, A and Farrell, M and Sun, L and Neilands, J},
title = {Orally ingested Lactobacillus crispatus VPC177 enhances total vaginal Lactobacillus counts-a cross-over exploratory study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1894758},
pmid = {42761666},
issn = {1664-302X},
abstract = {INTRODUCTION: The vaginal microbiome plays a crucial role in vaginal health, and disturbances in the microbial balance can negatively affect female wellbeing. In recent years, there has been growing interest in the use of probiotics and prebiotics to support a healthy vaginal microbiota. However, effects are often strain-specific and should be clinically demonstrated to influence the vaginal microbiota. This study aimed at evaluating the ability of four different orally administered probiotic strains to affect the fecal, and more specifically, the vaginal microbiota in healthy women.

METHODS: In this open-label, cross-over, exploratory study 35 women age 20-63 years consumed four different strains, Lactobacillus crispatus VPC111, Lactobacillus gasseri VPG44, L. crispatus VPC177 and Lactiplantibacillus plantarum HEAL9[®] for 14 days each with a washout period of 14 days between each intervention period. Levels of lactobacilli were assessed in fecal and vaginal samples following each intervention period.

RESULTS: VPC111, VPC177, and HEAL9 all resulted in significant increases in fecal lactobacilli after 14 days intervention compared to baseline (p < 0.05). VPC177 significantly increased vaginal lactobacilli (p = 0.001), whereas VPC111, VPG44, and HEAL9 showed no significant vaginal effects. Post hoc characterization of L. crispatus VPC177 demonstrated that it produces both D- and L-lactate at high levels (9.31 and 4.58 g/L, respectively) and possesses genes associated with bacteriocin production, glycogen utilization, and mucosal adhesion, supporting its potential for antimicrobial activity, carbohydrate metabolism, and colonization of the vaginal environment.

DISCUSSION: These findings demonstrate that probiotic effects on the vaginal microbiota are strain-specific, and that an increase in fecal lactobacilli does not necessarily translate into corresponding changes in the vaginal microbial community. Among the strains evaluated, VPC177 was the most promising candidate for supporting vaginal health through oral probiotic administration.},
}

@article {pmid42761778,
year = {2026},
author = {Cheney, C and Page, E and Yeung, D and White, D},
title = {Clinical evidence and biological mechanisms linking obesity to adverse outcomes in pediatric and adolescent acute lymphoblastic leukemia.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1918955},
pmid = {42761778},
issn = {2234-943X},
abstract = {This review critically evaluated the relationship between obesity and survival outcomes in Acute Lymphoblastic Leukemia (ALL), highlighting key evidence gaps and exploring the biological mechanisms that may contribute to this association. In patients with ALL, obesity is consistently associated with a higher incidence of severe treatment-related toxicities, increased frequency of therapy delays, and reduced event-free survival. This connection is most pronounced in pediatric and adolescent ALL populations, whereas evidence supporting a similar effect in adults remains limited. Proposed biological mechanisms underlying these adverse outcomes include increased bone marrow adiposity, chronic low-grade inflammation, dysregulated insulin signaling and obesity-associated alterations in the gut microbiome. The current body of evidence identifies obesity as a clinically significant risk factor that defines a vulnerable subgroup of ALL patients, supporting the need for enhanced toxicity surveillance, individualized treatment strategies, and optimized supportive care interventions. Elucidation of the biological pathways linking obesity to adverse ALL outcomes may also inform the development of novel therapeutic approaches aimed at mitigating obesity-driven morbidity and mortality in this high-risk population.},
}

@article {pmid42761784,
year = {2026},
author = {Yu, M and Wu, Y and Wang, A and Wang, M and Chen, Y and Ren, H and Zhang, Y and Liu, Y and Wang, S and Fan, X},
title = {Chronic low-grade inflammation drives skeletal aging and neurocognitive decline: inflammaging as a central hub coupling bone-brain aging.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1874465},
pmid = {42761784},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Aging/immunology ; *Inflammation/immunology/metabolism ; *Brain/immunology/metabolism/pathology ; *Cognitive Dysfunction/immunology/metabolism ; *Bone and Bones/metabolism/immunology ; cGAS-STING Signaling Pathway ; Senescence-Associated Secretory Phenotype ; Inflammasomes/metabolism ; },
abstract = {BACKGROUND: Global population aging has driven a marked rise in the co-prevalence of osteoporosis and cognitive impairment, and a bidirectional epidemiological association between the two conditions is now supported by multiple meta-analyses. The shared biological mechanisms underlying this comorbidity, however, remain incompletely defined, and the two disorders continue to be managed within largely separate clinical disciplines.

AIM AND SCOPE: This review consolidates existing evidence into an integrative immunopathological framework in which inflammaging-the chronic, low-grade, sterile systemic inflammatory state driven by senescent cells and their senescence-associated secretory phenotype (SASP)-is examined as a shared upstream driver that concurrently reconfigures skeletal remodeling and central neuroimmune dynamics through the bone-brain axis. We do not claim to identify novel molecular targets; rather, we synthesize an integrative perspective that has been treated in disciplinary silos.

KEY MECHANISTIC THEMES: At the molecular level, persistently elevated SASP-derived cytokines (IL-6, IL-1β, TNF-α) engage RANKL-dependent osteoclastogenesis in bone and prime microglial neuroinflammation in the central nervous system. Chronic NF-κB signaling and NLRP3 inflammasome activation, amplified in preclinical models by mitochondrial DNA release via the cGAS-STING axis, sustain this dual pathological output. Within the bone-brain axis, bone-derived endocrine signaling is remodeled during aging: osteocalcin (OCN) secretion declines, while osteocyte-derived sclerostin (SOST) rises and may antagonize Wnt/β-catenin signaling in both compartments. Blood-brain barrier disruption and peripheral immune-cell infiltration further amplify central neuroinflammation.

BALANCED APPRAISAL: We explicitly distinguish (i) conceptual hypotheses, (ii) preclinical (cellular and rodent) findings, and (iii) validated human data. Several widely cited mechanisms-including OCN-GPR158-mediated neuroprotection, cGAS-STING-driven neuroinflammation, and microbiome-based longevity signatures-rest predominantly on murine models or single cohorts and require independent human validation. Microglial responses in the aging brain reflect a heterogeneous state space rather than a uniform pro-inflammatory conversion.

THERAPEUTIC IMPLICATIONS: Candidate bone-brain dual-targeting interventions-senolytics (dasatinib plus quercetin), NLRP3 inhibitors, cGAS-STING blockade, GLP-1 receptor agonists, and microbiota-targeted strategies-are discussed with explicit reference to current evidence level, safety concerns, and translational limitations, rather than as established co-therapies. Dual-endpoint randomized trials enriched for elevated inflammaging biomarkers are needed before any of these agents can be positioned for clinical use in bone-brain comorbidity.

CONCLUSION: The inflammaging-centered framework advanced here provides a testable integrative pathophysiological perspective on bone-brain aging comorbidity and a rationale for interdisciplinary "bone-brain integrated" clinical evaluation in older adults, which we frame as an aspirational, hypothesis-generating model rather than an evidence-based standard of care.},
}

Humans
Animals
*Aging/immunology
*Inflammation/immunology/metabolism
*Brain/immunology/metabolism/pathology
*Cognitive Dysfunction/immunology/metabolism
*Bone and Bones/metabolism/immunology
cGAS-STING Signaling Pathway
Senescence-Associated Secretory Phenotype
Inflammasomes/metabolism

@article {pmid42761811,
year = {2026},
author = {Le, Q},
title = {Restructuring the gut microbiota in obesity: molecular mechanisms linking dysbiosis to systemic inflammation and therapeutic opportunities.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1902756},
pmid = {42761811},
issn = {1664-042X},
abstract = {Obesity is characterized by a chronic low-grade inflammatory state that contributes to insulin resistance, type 2 diabetes, and metabolic syndrome. The gut microbiota has emerged as a critical mediator of this inflammatory process through multiple interconnected mechanisms including metabolic endotoxemia, short-chain fatty acid dysregulation, and intestinal barrier dysfunction. This review synthesizes current evidence on the structural and functional alterations of the gut microbiome in obesity, examines the mechanistic pathways linking dysbiosis to systemic inflammation, and critically evaluates therapeutic strategies aimed at restructuring the obese gut microbial community. We focus on three major intervention approaches: fecal microbiota transplantation, probiotic and prebiotic supplementation, and next-generation targeted microbial therapies. Analysis of clinical and preclinical studies reveals that successful microbial restructuring requires not only compositional shifts but also functional restoration of microbial metabolite production, particularly short-chain fatty acids. The evidence supports a model wherein obesity-associated dysbiosis perpetuates chronic inflammation through increased lipopolysaccharide translocation, reduced butyrate production, and compromised intestinal barrier integrity. Restoring microbial eubiosis through targeted interventions offers a promising avenue for resolving chronic low-grade inflammation and improving metabolic health outcomes in obese individuals.},
}

@article {pmid42758536,
year = {2026},
author = {Gracia Alvira, JB and Migotti, S and Tian, X and Nolte, V and Schlötterer, C},
title = {Environmental temperature is a strong driver of subspecies competition in the Drosophila microbiome.},
journal = {eLife},
volume = {15},
number = {},
pages = {},
pmid = {42758536},
issn = {2050-084X},
support = {10.55776/W1225//Austrian Science Fund/ ; 10.55776/PAT7786824//Austrian Science Fund/ ; 10.55776/F91//Austrian Science Fund/ ; Achadapt/ERC_/European Research Council/International ; },
mesh = {Animals ; *Microbiota ; *Temperature ; *Drosophila/microbiology ; *Drosophila simulans/microbiology ; Symbiosis ; },
abstract = {Most microbiome research focuses on the taxonomic composition at the species level to understand the impact of environmental factors, but intraspecific diversity has largely been ignored. To address this significant knowledge gap, we took advantage of the simple, culturable microbiome of Drosophila. First, we documented that natural populations of D. simulans harbor three diverged clades of Lactiplantibacillus plantarum, a key nutritional symbiont. We studied the distinct ecological roles of these three clades by exposing flies with their native microbiome to two temperature regimes in the laboratory. Tracking the three clades within the complete Drosophila microbiome over a period of more than 10 years at two temperatures, we identified strikingly distinct dynamics in response to the selection regime. We confirmed the functional differentiation of the three clades using in vitro growth measurements and in vivo mono-association assays. Our results highlight that environmental selection operates at the subspecies level. Therefore, we conclude that the functional diversification of the microbiome can only be understood when intra- and interspecific diversity is considered.},
}

Animals
*Microbiota
*Temperature
*Drosophila/microbiology
*Drosophila simulans/microbiology
Symbiosis

@article {pmid42758655,
year = {2026},
author = {Ball, RAW and Mohammed, AD and Jolly, A and Johnson, K and Sklenicka, S and Kucherina, M and Peacock, T and Liu, E and Hogan, KM and Baird, M and Peña, MMO and Nagarkatti, P and Nagarkatti, M and Kubinak, JL},
title = {IgA deficiency reveals a microbiota-dependent pathway to gluten sensitivity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2724175},
doi = {10.1080/19490976.2026.2724175},
pmid = {42758655},
issn = {1949-0984},
mesh = {Animals ; *Glutens/adverse effects/immunology ; Mice ; Mice, Knockout ; *IgA Deficiency/microbiology/immunology ; *Gastrointestinal Microbiome ; Immunoglobulin A/genetics ; Intestinal Mucosa/pathology/immunology/microbiology ; Mice, Inbred C57BL ; Intestine, Small/pathology/immunology/microbiology ; Th17 Cells/immunology ; Diet, Gluten-Free ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Celiac Disease/microbiology/immunology ; Ileum/pathology/immunology/microbiology ; },
abstract = {Selective IgA deficiency (sIgAD) is the most common primary immunodeficiency and increases susceptibility to gluten-related enteropathies, but the underlying mechanisms of pathogenesis are unknown. Utilizing IgA[-/-] mice and wild-type controls, we investigated how dietary gluten shapes susceptibility to small intestinal inflammation. We found that IgA[-/-] mice developed gluten-induced villus blunting in the ileum and enhanced Th17 responses. Exposure to a gluten-free diet prevented villus blunting in IgA[-/-] mice. Dietary gluten promoted the expansion of Streptococcus and Desulfovibrio species, depletion of members of the order Lactobacillales, and shifts in microbial metabolic pathways related to lipid metabolism. Next, to determine if gluten sensitivity is microbiota-dependent, germ-free colonization experiments were performed using complete microbiota transfers or mono-colonization with a single Streptococcus species (Streptococcus lutetiensis), both of which were sufficient to recapitulate gluten-sensitive enteropathy. Our findings demonstrate that dietary gluten promotes small intestinal inflammation and mucosal remodeling in IgA-deficient mice through microbiota-dependent mechanisms. This work highlights a key role for sIgA in maintaining immune homeostasis at the diet-microbiota interface and reveals a novel microbial pathway underlying gluten sensitivity.},
}

Animals
*Glutens/adverse effects/immunology
Mice
Mice, Knockout
*IgA Deficiency/microbiology/immunology
*Gastrointestinal Microbiome
Immunoglobulin A/genetics
Intestinal Mucosa/pathology/immunology/microbiology
Mice, Inbred C57BL
Intestine, Small/pathology/immunology/microbiology
Th17 Cells/immunology
Diet, Gluten-Free
Bacteria/classification/genetics/isolation & purification/metabolism
*Celiac Disease/microbiology/immunology
Ileum/pathology/immunology/microbiology

@article {pmid42758711,
year = {2026},
author = {Emfietzoglou, M and Bantounou, MA and Osmani, S and Narimatsu, T and Baroutis, KG and Varsamidaki, A and Skondra, D and Papaconstantinou, D and Theodossiadis, P and Chatziralli, I and Miller, JW and Vavvas, DG},
title = {Shotgun metagenomic profiling of the fecal microbiome in Lamp2 knockout mice reveals limited genotype-associated differences under standard housing.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357009},
doi = {10.1371/journal.pone.0357009},
pmid = {42758711},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; Mice ; Male ; Mice, Knockout ; *Metagenomics/methods ; *Lysosomal-Associated Membrane Protein 2/genetics ; Genotype ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; Metagenome ; },
abstract = {BACKGROUND: Lysosomal pathways influence host-microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome-lysosome fusion, and pathogenic variants in LAMP2 cause Danon disease. Whether Lamp2 loss alters the gut microbiome in vivo has not been systematically evaluated using methods that profile both taxonomic composition and microbial functional potential, such as shotgun metagenomics.

METHODS: We performed shotgun metagenomic sequencing on 50 fecal samples from male Lamp2 knockout (Lamp2KO) mice and wild-type (WT) littermates sampled at 3, 6, 9, and 12 months under single-genotype cages or mixed-genotype cohousing. Two low-depth libraries (<3 × 105 classified genus-level reads) were excluded from primary inference (primary set: n = 48). We analyzed genus-level alpha diversity, beta diversity, and differential abundance using compositional, cage-aware mixed-effects models and cage-blocked permutation testing. We analyzed functional pathway profiles using copies-per-million abundances with centered-log-ratio transformation and mixed-effects modeling. We controlled multiple testing using the Benjamini-Hochberg false discovery rate.

RESULTS: In the primary set (48 samples from 27 cages), Lamp2KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray-Curtis distances). Primary mixed-effects models detected no genera with differential abundance after false discovery rate correction. Taxonomic profiles were broadly similar between genotypes and were dominated by Bacteroidota and Bacillota. Exploratory within-cage (paired) analyses identified consistent directional differences in a small set of genera, but these signals were not supported by the primary mixed-effects models. Functional pathway profiles were similar between genotypes; one pathway (dTDP-β-L-rhamnose biosynthesis) showed an exploratory association (FDR q < 0.10) within the 50 most abundant pathways.

CONCLUSIONS: In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with Lamp2 deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.},
}

Animals
*Feces/microbiology
Mice
Male
Mice, Knockout
*Metagenomics/methods
*Lysosomal-Associated Membrane Protein 2/genetics
Genotype
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
Metagenome

@article {pmid42758728,
year = {2026},
author = {Imrich, CN and Backman, LRF and Allworth, AP and Andorfer, MC and Paris, JC and Greeley, NM and Fu, B and Balskus, EP and Drennan, CL},
title = {The structural basis of malodorant skatole formation by the glycyl radical enzyme indoleacetate decarboxylase.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {38},
pages = {e2618341123},
doi = {10.1073/pnas.2618341123},
pmid = {42758728},
issn = {1091-6490},
support = {GM126982//HHS | NIH (NIH)/ ; T32ES007020//HHS | NIH (NIH)/ ; 1122374//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; 1144152//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; Gilliam//HHMI (HHMI)/ ; Gates Faculty Scholar Award (OPP1158186)//HHMI (HHMI)/ ; Waterman CHE-20380529//NSF (NSF)/ ; GM145910//HHS | NIH (NIH)/ ; Investigator//HHMI (HHMI)/ ; },
mesh = {*Carboxy-Lyases/metabolism/chemistry ; *Skatole/metabolism/chemistry ; Catalytic Domain ; Models, Molecular ; Cryoelectron Microscopy ; Decarboxylation ; *Bacterial Proteins/chemistry/metabolism ; },
abstract = {Glycyl radical enzymes (GREs) catalyze challenging chemical reactions using a posttranslationally installed glycyl radical cofactor. One such enzyme, indoleacetate decarboxylase (IAD), performs the radical-based decarboxylation of indole-3-acetate (I3A) to form the malodorant molecule skatole. In addition to being an odor nuisance, skatole is a human and livestock lung toxin, a suspected carcinogen, and a mosquito attractant, all of which impact human health, agriculture, food production, and wastewater treatment. Here, we use cryogenic electron microscopy to solve a 2.45-Å resolution structure of IAD from the gut bacterium Olsenella uli. We observe IAD in a homotetrameric form with the substrate I3A bound in all four protomers. The positioning of I3A in the active site is unexpected and is more consistent with a Kolbe-type decarboxylation mechanism, i.e., a decarboxylation initiated by a 1-electron oxidation of the carboxylate moiety rather than being initiated by hydrogen atom transfer (HAT). Previously, a high deuterium content in skatole from IAD assays in D2O was used to support a HAT mechanism over a Kolbe-type mechanism. However, we show here that deuterium content does not necessarily inform on mechanism as IAD can catalyze the exchange of skatole's 3'-methyl hydrogens postturnover. Structural comparisons show that both IAD and hydroxyphenylacetate decarboxylase display structural features that are not found in other characterized GREs, suggesting that they represent a distinct GRE-subclass. Collectively, these insights will inform IAD inhibitor design aimed at decreasing skatole production.},
}

*Carboxy-Lyases/metabolism/chemistry
*Skatole/metabolism/chemistry
Catalytic Domain
Models, Molecular
Cryoelectron Microscopy
Decarboxylation
*Bacterial Proteins/chemistry/metabolism

@article {pmid42758777,
year = {2026},
author = {Briard, M and Guillon, B and Venot, E and Grauso, M and Hennequet-Antier, C and Bruneau, A and Fenaille, F and Castelli, F and Thomas, M and Lezmi, G and Leite-de-Moraes, M and Adel-Patient, K and Saint-Criq, V},
title = {A microbiome-metabolome signature associated with pediatric severe asthma.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0358560},
doi = {10.1371/journal.pone.0358560},
pmid = {42758777},
issn = {1932-6203},
mesh = {Humans ; *Asthma/microbiology/metabolism ; *Microbiota ; *Metabolome ; Female ; Child ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Severity of Illness Index ; Case-Control Studies ; Adolescent ; },
abstract = {BACKGROUND: Severe asthma is a heterogeneous condition encompassing multiple phenotypes. Understanding lung-specific mechanisms in children with severe asthma may enable the development of more precise therapeutic strategies. We previously reported that immune components in bronchoalveolar lavages (BALs) differentiate children with severe asthma from non-asthmatic disease-controls and, frequent from non-frequent exacerbators, among children with severe asthma.

OBJECTIVE: To identify a local signature of severe asthma using complementary multi-omics analyses of BALs. A secondary objective was to evaluate whether bacterial taxa and metabolites discriminate severe asthma subtypes associated with distinct phenotypes or endotypes.

METHODS: BAL microbiome and metabolome were investigated in 20 children with severe asthma and 10 non-asthmatic children using 16S rRNA gene amplicon sequencing and liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS), respectively. Data were analysed separately and through integrative multi-omics approaches.

RESULTS: Compared with controls, BALs from children with severe asthma showed increased alpha-diversity, higher relative abundances of Actinobacteriota, Streptococcus, Moraxella, Corynebacterium, Tropheryma, and Treponema, and an altered polyamine pathway characterized by reduced arginine and increased spermine and spermidine levels. Integrated analyses revealed significant associations between Streptococcus and both spermine and spermidine. Independently, each dataset discriminated severe asthma phenotypes, notably exacerbation frequency and co-occurring atopic dermatitis. Unsupervised clustering of microbiome profiles identified four distinct clusters that may reflect severe asthma endotypes.

CONCLUSIONS: This study identifies a distinct airway microbiome-metabolome signature associated with pediatric severe asthma. Enrichment of specific bacterial taxa, particularly Streptococcus, together with altered polyamine metabolic pathway, highlights microbial-metabolic interactions potentially involved in disease pathophysiology. The ability of microbiome and metabolome profiles to independently and jointly discriminate clinical phenotypes underscores the relevance of multi-omics approaches for diagnosis and follow-up of severe asthma. Our findings support the importance of airway-level profiling to improve mechanistic understanding of severe asthma and inform on future targeted therapeutic strategies.},
}

Humans
*Asthma/microbiology/metabolism
*Microbiota
*Metabolome
Female
Child
Male
Bronchoalveolar Lavage Fluid/microbiology
RNA, Ribosomal, 16S/genetics
Multiomics
Severity of Illness Index
Case-Control Studies
Adolescent

@article {pmid42759240,
year = {2026},
author = {Xu, J and Song, Y and Wu, W and Zhou, H and Wu, Y and Li, C},
title = {The impact of maternal gestational diabetes mellitus on the microbiome of offspring: A systematic review.},
journal = {Journal of reproductive immunology},
volume = {178},
number = {},
pages = {104965},
doi = {10.1016/j.jri.2026.104965},
pmid = {42759240},
issn = {1872-7603},
abstract = {Gestational diabetes mellitus (GDM) adversely affects maternal and offspring health, and the early-life microbiome is implicated in developmental programming. This systematic review quantitatively evaluated the association between maternal GDM and alterations in the gut and oral microbiomes of offspring. We systematically searched PubMed, Web of Science, and Embase (up to August 2025) for eligible studies adopting high-throughput sequencing techniques. Random-effects meta-analysis was performed for alpha diversity metrics, while findings on beta diversity and microbial taxonomy were summarized narratively. Twenty-one studies were included. The meta-analysis revealed no statistically significant differences in gut microbial alpha diversity between infants exposed to maternal GDM and unexposed controls. Beta diversity exhibited substantial inter‑study heterogeneity, with no consistent shifts observed. In infants born to mothers with GDM, several microbial taxa including Gammaproteobacteria, Enterobacteriaceae, Micrococcaceae, Propionibacteriaceae, Rikenellaceae, Megasphaera, Staphylococcus, Collinsella, Rothia, Pelomonas, Veillonella, Shewanellaceae and Prevotella tended to decrease in abundance, whereas Escherichia tended to increase. Notably, no microbial taxon presented consistent abundance changes in three or more studies, and these repeated findings were based on limited evidence. Delivery mode appeared to have minimal influence on offspring gut alpha diversity. Collectively, maternal GDM may not be strongly linked to shifts in offspring gut or oral microbial alpha diversity. However, the consistent dysregulation of specific microbial taxa in GDM-exposed offspring may exert potential impacts on offspring immune and metabolic development. Further longitudinal multicenter investigations are warranted to elucidate the causal relationships and long-term health implications of GDM-induced microbial alterations in children.},
}

@article {pmid42759465,
year = {2026},
author = {Yang, W and Zhu, X and Zhang, J and Chen, Y and Liu, S and Si, T and Zhang, L},
title = {Silicon nanoparticles and jasmonic acid synergistically enhance cadmium phytoextraction by Sedum alfredii via coordinated metal acquisition and stress tolerance.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143556},
doi = {10.1016/j.jhazmat.2026.143556},
pmid = {42759465},
issn = {1873-3336},
abstract = {Cadmium (Cd) phytoextraction requires efficient metal acquisition and translocation without compromising plant growth and detoxification. We investigated the effects of silicon nanoparticles (Si-NPs) and jasmonic acid (JA), applied alone or together, on Cd phytoextraction by Sedum alfredii. The combined treatment increased shoot biomass and total Cd accumulation by 32.6% and 67.4%, respectively. Si-NPs-containing treatments increased rhizosphere available Cd by 5.4-5.9%, promoted Cd uptake and root-to-shoot translocation, and induced Cd- and Si-transport-related genes. JA strengthened antioxidant enzyme activities. The combined treatment further increased phytochelatin and glutathione levels by 152% and 48.7%, respectively, while reducing malondialdehyde by 38.5%. These responses indicate enhanced thiol-mediated detoxification and oxidative protection. Metabolomic and microbiome analyses further revealed compartment-specific responses. The rhizosphere was associated with Cd-mobilization-related metabolites and enrichment of potentially beneficial genera, including Polycyclovorans and Ramlibacter. In contrast, leaves showed enhanced sulfur-thiol metabolism, redox regulation, and secondary metabolism. Multiblock integration linked Cd phytoavailability and accumulation with detoxification and biomass production. Overall, Si-NPs and JA exhibited asymmetric functional complementarity, integrating enhanced Cd acquisition and transport with thiol-centered detoxification and growth maintenance. This accumulation-compatible tolerance strategy provides a mechanistic framework for improving assisted Cd phytoextraction by coordinating Cd flux with whole-plant detoxification capacity.},
}

@article {pmid42759480,
year = {2026},
author = {Hu, F and Liu, X and Zhang, Y and Tan, S and Wang, J and Xia, M and Lu, F and Zhang, Q},
title = {Polylactic acid microplastics enhance copper bioavailability and host-microbiome toxicity during black soldier fly bioconversion of food waste: Mechanisms and multi-level impacts.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143654},
doi = {10.1016/j.jhazmat.2026.143654},
pmid = {42759480},
issn = {1873-3336},
abstract = {Biodegradable microplastics are increasingly entering food waste (FW) streams, yet their effects on heavy metal behavior during black soldier fly larvae (BSFL) bioconversion remain unclear. This study investigated the combined effects of polylactic acid microplastics (PLA-MPs, 1% w/w) and Cu (100-300 mg/kg ww) in a BSFL-based FW conversion system. The 100-200 mg/kg treatments represented upper-range Cu exposure scenarios relevant to Cu-rich food residues. PLA-MPs increased Cu accumulation in larvae by 14-32% and shifted Cu toward more bioactive fractions in larvae and frass, indicating enhanced Cu mobility and bioavailability. Co-exposure intensified oxidative and detoxification responses, depleted glutathione, increased lipid peroxidation, and altered energy metabolism. Transcriptomic analysis indicated activation of xenobiotic metabolism, glutathione-related detoxification, and immune-associated pathways. PLA-MPs and Cu also reshaped gut and frass microbial communities, increased community stochasticity, suppressed dissolved organic matter humification, and reduced substrate stabilization and bioconversion performance. Partial least squares path modeling further linked Cu activation and migration, host physiological stress, and microbial dysbiosis to reduced bioconversion efficiency. Overall, PLA-MPs enhanced Cu bioavailability and amplified multi-level toxicity during BSFL-mediated FW treatment, highlighting potential risks to the safe valorization of contaminated organic waste.},
}

@article {pmid42759613,
year = {2026},
author = {Klingler, AM and Vidyant, S and Pyakurel, S and Viel, KCMF and Good, A and Rochman, Y and Brusilovsky, M and Caldwell, JM and Rothenberg, ME and Azouz, NP},
title = {Loss of kallikrein 5 expression exacerbates allergic skin inflammation including impairing filaggrin processing, promoting Th2 differentiation and inducing dysbiosis.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {100404},
doi = {10.1016/j.mucimm.2026.100404},
pmid = {42759613},
issn = {1935-3456},
abstract = {Atopic dermatitis (AD) is a chronic allergic skin disease with T helper 2 (Th2) cell predominance and epithelial barrier impairment. The serine protease kallikrein (KLK) 5 has an essential role in regulating keratinocyte desquamation and skin renewal. Increased expression and activity of KLK5 is sufficient to induce skin inflammatory responses including AD. We examined the consequences of Klk5 deficiency following exposures to the type 2-provoking agent calcipotriol in mice. Loss of KLK5 exacerbates a spectrum of AD-like responses including increased accumulation of skin eosinophils and langerhans cells, over-expression of an array of cytokines in the skin and exacerbated scratching behavior. Klk5[-/-] mice demonstrated microbiome dysbiosis with enriched actinobacteria and reduced firmicutes in the skin, alteration in skin metabolites involved in the acetyl-CoA pathway and decreased expression of mature filaggrin monomers. Cutaneous application of Cis-Urocanic acid (cUCA) attenuated inflammatory responses highlighting barrier dysfunction as primary mechanism. We reveal an unappreciated role for KLK5 in inhibiting type 2 responses, acting through its roles in filaggrin processing and modulation of the skin microbiome and metabolome. Though KLK5 overactivation is known to contribute to several inflammatory skin disorders, our findings demonstrate that complete loss of KLK5 is also pathogenic in AD-like responses in mice.},
}

@article {pmid42759845,
year = {2026},
author = {Glenn, E and Titus, C and Kasthuriarachchi, T and Burke, K and Chow, D and Lin, C and Liu, E and Zhang, H and Zhang, T and Li, Y},
title = {Maternal-offspring microbiome interface contributes to the impact of maternal use of central nervous system-active drugs on offspring neurodevelopment.},
journal = {Journal of pharmaceutical sciences},
volume = {},
number = {},
pages = {104509},
doi = {10.1016/j.xphs.2026.104509},
pmid = {42759845},
issn = {1520-6017},
abstract = {The prevalence of maternal central nervous system-active medication use has increased over the last two decades, raising questions regarding potential neurodevelopmental consequences for offspring. While most of these substances are known to cross the placenta and enter breast milk, their developmental impact remains unclear. This review synthesizes current evidence identifying the maternal-offspring microbiome interface as a possible conduit for neurodevelopmental programming. We examine how the maternal gut, placental, and breast milk microbiomes establish the foundation for the offspring's early microbial ecosystem, how drug-induced dysbiosis may disrupt these interactions, and how these may impact offspring neurodevelopment. However, isolating specific drug-induced microbial effects from the influence of underlying maternal psychiatric conditions and identifying specific microbial signatures that correlate with resilience or susceptibility in offspring remain a substantial challenge. Current literature relies heavily on preclinical models, highlighting an urgent need for longitudinal human studies to better inform risk-benefit analyses for maternal pharmacotherapy.},
}