@article {pmid42607425,
year = {2026},
author = {Wan, PJ and He, JC and Lai, FX and Wang, WX and Lin, YJ and Hu, Y and Chen, Y and Chen, H and Liu, F and Wei, Q and Fu, Q},
title = {Environmental impact of long-term Bt rice cultivation on soil microbiomes: insights from 15-year field monitoring and interpretable machine learning.},
journal = {Environment international},
volume = {215},
number = {},
pages = {110457},
doi = {10.1016/j.envint.2026.110457},
pmid = {42607425},
issn = {1873-6750},
abstract = {Understanding the long-term ecological consequences of genetically modified crops is essential for evaluating ecosystem stability under agricultural intensification. Here, we combined 15 years of continuous field observations with interpretable machine learning to examine how Bacillus thuringiensis (Bt) rice cultivation influences soil bacterial communities. Across all samples, α- and β-diversity metrics showed no significant differences between Bt and non-Bt soils, whereas temporal variation, crop growth stage (before sowing and after harvest), and particularly soil depth emerged as dominant drivers of microbial community structure. Using an Elastic Net model, we identified a set of microbial taxa (including ASV1403 Corynebacteriales, ASV4837 Oscillospirales, and ASV893 Micrococcales) that consistently contributed to the discrimination of Bt and non-Bt soils, despite exhibiting minimal abundance differences in conventional differential analyses. These taxa may reflect subtle but ecologically relevant shifts associated with long-term Bt rice cultivation, although their functional roles require further validation. Overall, our results indicate that Bt rice exerts limited influence on soil bacterial community structure relative to broader temporal and edaphic controls. By integrating long-term ecological monitoring with interpretable machine learning, this study provides a data-driven and transparent framework for environmental risk assessment of genetically modified crops and highlights the importance of spatiotemporal variability in shaping soil microbiome responses under agricultural management. One-sentence summary: Long-term field evidence shows that Bt rice has minimal effects on soil bacterial communities, with temporal and depth-related factors dominating microbial variation.},
}

@article {pmid42607433,
year = {2026},
author = {Kito, S and Goto, S and Goto, T and Ogasawara, S and Yoshihara, H and Kitaori, T and Banno, C and Ogawa, S and Kojima, R and Matsumoto, Y and Komura, M and Takahashi, S and Hirayama, M and Sugiura-Ogasawara, M},
title = {Endometrial microbiota composition, but not chronic endometritis or hysteroscopy, predicts euploid miscarriage in unexplained RPL: associations with live birth and miscarriage outcomes.},
journal = {Journal of reproductive immunology},
volume = {177},
number = {},
pages = {104950},
doi = {10.1016/j.jri.2026.104950},
pmid = {42607433},
issn = {1872-7603},
abstract = {Recurrent pregnancy loss (RPL) is a multifactorial condition, and reliable predictors of miscarriage remain limited. This observational cohort study investigated whether hysteroscopy, chronic endometritis (CE), and endometrial microbiome analysis can predict pregnancy outcomes in women with unexplained RPL. Ninety-nine patients with at least two previous miscarriages were enrolled, excluding those with antiphospholipid syndrome, chromosomal abnormalities in either partner, uterine anomalies, or a history of aneuploid miscarriage. CE was diagnosed by CD138-positive endometrial stromal cells, and affected patients received doxycycline 200 mg/day for 14 days. The primary outcome was cumulative live birth assessed in pregnancies resulting in either live birth or euploid miscarriage in relation to hysteroscopic findings, CE, and microbiome composition. The presence of Fusobacterium and Campylobacter was negatively associated with cumulative live birth. Focusing on Lactobacillus species, L. jensenii was positively associated with live birth. Additionally, the incidence of euploid miscarriage was significantly higher among cases with Lactobacillus abundance < 98% and the presence of Fusobacterium and Campylobacter. In contrast, CD138-positive cell counts and hysteroscopic findings were not predictive of pregnancy outcomes, and no associations were observed between the microbiome and hysteroscopic findings. However, the relative abundance of Lactobacillus tended to be lower when CD138-positive cell counts were higher. These findings suggest that Lactobacillus composition, as well as the presence of Fusobacterium and Campylobacter in the endometrial microbiome, may be associated with pregnancy outcomes, indicating that microbiome profiling could provide useful prognostic information for patients with unexplained RPL.},
}

@article {pmid42607770,
year = {2026},
author = {Ji, X and Zhang, S and Wang, H and Yuan, L and Mulama, PI and Yu, J and Wang, W and Liu, S and Zhang, J and Li, M and Liu, W},
title = {Gut microbiome facilitates black soldier fly-mediated bioconversion under zinc stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135651},
doi = {10.1016/j.biortech.2026.135651},
pmid = {42607770},
issn = {1873-2976},
abstract = {The microbiome plays an important role in manure transformation in the black soldier fly (BSF), yet the mechanisms by which it promotes host tolerance to zinc stress remain poorly understood. Here, we show that the gut microbiome promotes larval growth using a controlled zinc-supplemented wheat bran model. High dietary zinc significantly impairs BSF larval growth and development and results in a pronounced reduction in gut length. Using germ-free and gnotobiotic BSF larvae, we find that zinc-induced growth arrest is significantly alleviated by inoculation with Pediococcus acidilactici strain AH1, Bacillus cereus strain AH3, Klebsiella pneumoniae strain AH4, or a consortium of three isolates. Metatranscriptomic analysis reveals that key microbial pathways, including peptidoglycan synthesis and degradation, microbial defense systems, biofilm formation, and zinc metabolism, are upregulated under zinc stress. Moreover, the microbiome facilitate dietary zinc fraction redistribution and reduced host zinc accumulation. Microbial reconstitution further activates host antioxidant responses and mitigates zinc-induced oxidative damage. Together, these findings highlight the critical role of the microbiome in zinc tolerance of BSF larvae, providing insights for future efforts to explore microbiome-assisted optimization of BSF-mediated bioconversion under zinc stress conditions.},
}

@article {pmid42607790,
year = {2026},
author = {Ge, H and Cui, M and Liu, Y and Wu, X and Huang, C and Zhang, L and Fang, H},
title = {Changes in the gut microbiome and neurotransmitters induced by mancozeb.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128977},
doi = {10.1016/j.envpol.2026.128977},
pmid = {42607790},
issn = {1873-6424},
abstract = {Mancozeb is widely used as a broad-spectrum fungicide, and its potential effects on the gut-liver-kidney axis remain incompletely understood. In this study, we used an experimental oral exposure model to identify dose-associated effects and underlying mechanisms associated with mancozeb exposure. Following exposure to mancozeb at doses of 1, 10, and 100 mg/kg body weight, the fungicide was found to accumulate primarily in the digestive system (including the colon, cecum, and their contents) and feces of mice. Mancozeb exposure may exert adverse effects on the biomarkers related to liver function in mice, as evidenced by elevated activities of alanine aminotransferase and aspartate aminotransferase, increased malondialdehyde levels, and reduced activities of superoxide dismutase and glutathione peroxidase. Additionally, it caused significant shortening of the small intestine and increased intestinal permeability, reflected by elevated wet weight and dry-to-wet ratio of fecal particles, along with increased serum levels of creatinine, blood urea nitrogen, uric acid, and lipopolysaccharide. Mancozeb also markedly altered the gut microbiota structure, leading to an increased relative abundance of Lachnospiraceae_NK4A136_group (1.01-1.71-fold) and Ileibacterium (2.21-5.54-fold). Furthermore, mancozeb promoted the accumulation of acetylcholine, histamine release, and elevated levels of indole compounds in intestinal tissues. Transcriptomic analysis revealed upregulation of immune-related genes and downregulation of genes involved in drug metabolism. These results suggest that mancozeb exposure may affect gut microbiota composition, neurotransmitter and metabolite profiles, and the expression of functional genes related to immunity and detoxification. This study provides critical insights for the dietary health risk assessment of mancozeb.},
}

@article {pmid42607815,
year = {2026},
author = {Kim, H and Diederich, M},
title = {Gut microbiome crosstalk in acute myeloid leukemia: mechanisms, treatment-associated dysbiosis, and translational opportunities.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {118369},
doi = {10.1016/j.bcp.2026.118369},
pmid = {42607815},
issn = {1873-2968},
abstract = {Acute myeloid leukemia (AML) is accompanied by perturbations of the intestinal microbiome, but causal relationships remain incompletely defined because most patient data are cross-sectional and confounded by age, diet, antibiotic exposure, hospitalization, neutropenia, and chemotherapy. This review evaluates current evidence for AML-microbiome crosstalk, considering patient microbiome/metabolome associations; AML mouse and cell models; treatment-induced dysbiosis during induction chemotherapy and antimicrobial exposure; and microbiome-targeted interventions. The strongest AML-specific mechanistic evidence implicates intestinal barrier injury, microbial translocation/lipopolysaccharide (LPS) signaling, depletion of short-chain fatty acid (SCFA)-producing bacteria, altered propionate and butyrate availability, and bile-acid remodeling, including preclinical AML-inhibitory activity of chenodeoxycholic acid. Evidence for indoles, hydrogen sulfide, serotonin, precision probiotics, dietary interventions, time-restricted feeding, methionine restriction, and curcumin is more preliminary or extrapolated from non-AML cancer models. Fecal microbiota transplantation restores microbial diversity after induction therapy in early clinical trials, but infection-prevention and survival benefits remain unproven, and safety is a central concern in neutropenic and hematopoietic stem cell transplantation (HSCT) patients. We describe mechanistic gaps and propose a translational scheme that recommends longitudinal sampling, compartment-specific metabolite measurements, antimicrobial surveillance, and trial designs that distinguish microbiome restoration from clinical efficacy.},
}

@article {pmid42607817,
year = {2026},
author = {Agnihotram, B and Mutiu, I and Chiou, H and McGowen, K and Mazewski, C},
title = {The role of the gut-brain axis and polyphenolic compounds in glioblastoma.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110484},
doi = {10.1016/j.jnutbio.2026.110484},
pmid = {42607817},
issn = {1873-4847},
abstract = {Polyphenols are metabolites derived from plant-based sources studied in cancer research for their anti-inflammatory, antioxidant, and antiproliferative properties. While previous studies have focused more on their impact on gastrointestinal diseases like inflammatory bowel disease and malignancies such as colon cancer, there is less attention on their role in neurological diseases and malignancies more distant from the gastrointestinal tract, like brain cancer. Recent work indicates potential for polyphenols to beneficially modulate the gut microbiome and improve neurological disorders through the gut-brain axis. Glioblastoma (GBM), classified as a grade 4 brain tumor by the World Health Organization, poses significant challenges with inefficient conventional treatments that yield a low five-year survival rate. Recent meta-analyses demonstrate the potential of various plant foods to reduce the risk of glioma. However, specific dietary recommendations for brain cancer remain elusive, and the mechanisms of action of plant foods and their compounds, as well as their impact through the gut-brain axis, must still be explored. This review will discuss the impact of polyphenols on the gut-brain axis and analyze the potential benefits of implementing them as preventive and therapeutic GBM interventions with relation to the gut microbiome.},
}

@article {pmid42607848,
year = {2026},
author = {Chen, E and Cao, G and Song, Z},
title = {Novel immunotherapeutic strategies for colorectal cancer treatment: Advances, challenges, and future directions.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189688},
doi = {10.1016/j.bbcan.2026.189688},
pmid = {42607848},
issn = {1879-2561},
abstract = {Immunotherapy has reshaped the treatment landscape of colorectal cancer (CRC), with the clearest and most durable benefit established in mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) disease. However, framing CRC immunotherapy simply as "MSI-H responsive versus microsatellite stable (MSS) resistant" is no longer sufficient. Recent studies indicate that a subset of proficient mismatch repair (pMMR) colon cancers, particularly in the neoadjuvant setting, can mount clinically meaningful responses to immune checkpoint blockade, suggesting that disease stage, local immune organization, and treatment timing critically influence immunotherapy sensitivity. In parallel, emerging evidence has expanded the relevant immune landscape beyond the tumor bed itself, showing that spatially organized stromal and adipose niches can actively divert tumor-reactive lymphocytes and promote immune escape. These advances shift the central challenge in CRC immunotherapy from simply identifying new agents to defining when and in whom immune resistance is reversible, and which biological bottlenecks-such as vascular dysfunction, myeloid suppression, and spatial immune exclusion-must be overcome. In this context, alternative checkpoint inhibitors, bispecific antibodies, cellular therapies, vaccines, nanotechnology-enabled platforms, and microbiome-targeted approaches remain important, but their translational maturity and evidentiary support differ substantially. Biomarker development is likewise evolving from static genomic classification toward dynamic and mechanism-informed stratification incorporating circulating tumor DNA (ctDNA), chromosomal instability, immune architecture, and treatment-induced response trajectories. This review synthesizes recent advances in CRC immunotherapy while emphasizing evidence hierarchy, biomarker-guided patient selection, and the mechanistic basis of combination strategies. We argue that the next phase of CRC immunotherapy will depend less on the indiscriminate addition of novel agents and more on the rational deployment of immunotherapy across molecularly, spatially, and temporally defined disease states.},
}

@article {pmid42608078,
year = {2026},
author = {Lee, J and Aponte Rolón, B and de Lorimier, P and Ané, JM and Benucci, GMN and Carrell, AA and Chai, YN and Chandrasoma, J and Geerdes, N and Infante, V and Kristy, B and Martin, S and Pascoe, I and Patra, R and Radmer, L and Rush, TA and Shita, NS and Suratt, A and Suthers, PF and Cregger, MA and Howe, A and Lebeis, S and Scheller, HV},
title = {Rethinking the soil core microbiome.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71509},
pmid = {42608078},
issn = {1469-8137},
support = {DE-AC02-05CH11231//Joint BioEnergy Institute/ ; DE-FC02-07ER64494//Great Lakes Bioenergy Research Center/ ; DE-SC0018409//Great Lakes Bioenergy Research Center/ ; DE-SC0018420//DOE Center for Advanced Bioenergy and Bioproducts Innovation/ ; ERKP886//Center for Bioenergy Innovation/ ; },
abstract = {The concept of a core microbiome emerged from host-associated research to describe microbial members or functions conserved across clearly defined spatial, temporal, and biological boundaries. In soil- and plant-associated microbiome research, however, the term has increasingly shifted toward analytically defined subsets selected using study-specific thresholds or criteria. Synthesizing recent literature and cross-site analyses of bioenergy crop field soils, we show that the original biological meaning of the core microbiome has been blurred by dataset-specific analytical criteria. Taxa designated as 'core' were highly sensitive to methodological choices and often reflected explanatory value rather than conserved biological membership. Moreover, many studies that identify taxonomic 'core' members interpret their significance in functional terms, suggesting that functional conservation may be the biological interest. Taxonomic conservation may not be the most biologically meaningful target in highly heterogeneous soil and rhizosphere systems, where functional conservation may persist despite taxonomic turnover. Accordingly, 'core microbiome' should be reserved for microbial components explicitly demonstrated to be conserved across defined spatial, temporal, and environmental dimensions and linked to conserved ecological functions, while taxa selected for explanatory value are better described as 'explanatory subsets of taxa'. Greater terminological precision will improve cross-study comparability and strengthen ecological inference in plant-soil microbiome research.},
}

@article {pmid42608251,
year = {2026},
author = {Yang, S and Cress, BF},
title = {Disarming a pathogen with programmable phage-derived particles.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.07.013},
pmid = {42608251},
issn = {1878-4380},
abstract = {Shiga toxin-producing Escherichia coli (STEC) presents a therapeutic dilemma because antibiotic treatment induces prophage-encoded Shiga toxin expression. Galtier et al. engineer phage-derived particles with programmable cell specificity, genetic cargo, and CRISPR guide RNAs that destroy stx while killing STEC in animal models.},
}

@article {pmid42608540,
year = {2026},
author = {Romero-Lopez, M and Naik, M and Thoene, M and Anderson-Berry, A},
title = {Nutritional management at 22-23 weeks gestational age: evidence and knowledge gaps.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42608540},
issn = {1530-0447},
abstract = {With advancing medical capabilities, survival of infants born at 22-23 weeks' gestation is increasing. However, specific recommendations for nutrition support for these infants are lacking. This review examines the unique characteristics of infants born at 22-23 weeks' gestation that impact parenteral and enteral nutrition support, highlighting the lack of evidence and knowledge gaps for optimal practices. Current recommendations developed for extremely or very low birth weight infants may be unsuitable for infants born at 22-23 weeks' gestation due to important differences in anatomy, physiology, body composition, and metabolic capabilities. Key challenges include severely limited intraluminal digestion, profound immune and microbiome immaturity, and reduced metabolic tolerance to parenteral nutrition provision based on current recommendations, none of which are addressed by recommendations developed for larger, more mature preterm populations. Until more specific studies for infants 22-23 weeks gestation are conducted, clinicians must carefully tailor nutritional support for this vulnerable population given their functional and maturational limitations. IMPACT: Survival of infants born at 22-23 weeks gestation is increasing, but currently available nutrition support recommendations may be inadequate due to the unique physiological, metabolic, and gastrointestinal characteristics that are not accounted for in current parenteral and enteral nutrition support recommendations. This review synthesizes available evidence and identifies critical knowledge gaps in nutrition support management specific to infants born at 22-23 weeks' gestation. We provide a framework to guide individualized clinical decision-making and establish research priorities and collaborative efforts in infants born at 22-23 weeks' gestation.},
}

@article {pmid42608579,
year = {2026},
author = {Cordazzo Vargas, B and Martino, C and Dilmore, AH and Metcalf, JL and Burcham, ZM and Lahti, L and Bektanov, A and Borman, T and Salomaa, V and Niiranen, T and Havulinna, AS and Gregor, R and Eyal, S and Meijler, MM and Mizrahi, I and Song, SJ and Bartko, A and Dorrestein, PC and Morton, JT and McDonald, D and Knight, R and Shenhav, L},
title = {Joint-RPCA: domain-aware multi-omics integration for systems microbiology.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {42608579},
issn = {1744-4292},
support = {DP2AI185753//HHS | NIH | NIAID | Division of Microbiology and Infectious Diseases (DMID)/ ; 75D30120C09795//HHS | Centers for Disease Control and Prevention (CDC)/ ; DP1AT010885,U19AG063744//HHS | National Institutes of Health (NIH)/ ; 952914//EC | Horizon 2020 Framework Programme (H2020)/ ; },
abstract = {Integrating multi-omics data is essential for microbiome research, as microbial communities are shaped by and respond to interdependent processes, including taxonomic composition, metabolite production and utilization, and gene expression. However, accurately capturing ecosystem-wide patterns across these modalities is statistically challenging due to differences in scale, sparsity, and compositionality. While a growing number of multi-omics methods have emerged, they differ in their mathematical objectives and modeling assumptions, which in turn shape how biological patterns are represented and interpreted. This underscores the need for tools that explicitly account for the statistical properties of microbial ecosystems. Here, we present Joint Robust Principal Component Analysis (Joint-RPCA), a method designed with these statistical properties in mind and broadly applicable to multi-omics settings with similar challenges. Built on the OptSpace matrix completion framework, Joint-RPCA assumes an underlying shared low-rank structured component across modalities to identify shared variation and cross-modal associations from matched samples. Within this setting and under these statistical assumptions, Joint-RPCA showed stronger performance than the benchmarked general-purpose methods in phenotype separation and feature association tasks, achieving up to sixfold improvement in classification accuracy and over 100-fold faster runtimes. Applied to real-world datasets, including the Integrative Human Microbiome Project (iHMP), mammalian gut microbiomes, and decomposition studies, Joint-RPCA reveals replicable and interpretable multi-omic patterns, offering a scalable and domain-aware solution for systems-level microbiome analysis. Joint-RPCA is available in both Python (https://github.com/biocore/gemelli) and R (https://bioconductor.org/packages/mia).},
}

@article {pmid42608826,
year = {2026},
author = {Broughton, MG and Oba, PM and Mioto, JC and Bauer, LL and Koziol, SA and Panda, C and Pourafshar, S and Dilger, RN and Loman, BR and Swanson, KS},
title = {Effects of a Mushroom-Based β-Glucan Blend on the Gastrointestinal Health and Immune Function of Healthy Adult Cats.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag259},
pmid = {42608826},
issn = {1525-3163},
abstract = {Mushroom complex (MC) is a blend of mushroom water extracts including β-glucans and bovine colostrum that may provide benefits to cats. The objective of this study was to test the effects of MC supplementation on gut health and immune function outcomes of adult cats. Twenty healthy adult cats (7.40±1.54 yr old; 4.25±0.62 kg) were used in a randomized, blinded, placebo-controlled study using a completely randomized design. After a 3-wk wash-in phase, cats were assigned to one of two treatment groups (n = 10/group) and fed for 12 wk: placebo consisting of cellulose, rice bran, liver, and natural food coloring or a MC consisting of mushroom (turkey tail mushroom, red reishi, and lion's mane) water extracts and bovine colostrum. Each treatment (900 mg/d) was top-dressed on the diet. Fecal samples [characteristics, metabolites, microbiota, immunoglobulin (Ig) A] and blood samples (serum chemistry, hematology, oxidative stress markers, immunoglobulins) were collected after the wash-in phase (wk 0) and after 6 and 12 wk. Data were analyzed using the GLIMMIX model of SAS, with P < 0.05 accepted as significant and P < 0.10 as trends. Fecal characteristics (pH, dry matter, scores, frequency) were not affected by treatment, but treatment-time interactions (P < 0.05) were observed for serum IgA and blood urea nitrogen (BUN). Serum IgA increased over time in controls but decreased over time in cats fed MC. Serum BUN tended to increase in all cats over time but to a higher level in cats fed MC. Serum triglycerides were lower (P < 0.05) in cats fed MC. Fecal ammonia, isovalerate, and total branched-chain fatty acids were greater (P < 0.05) in cats fed MC than controls. A treatment-time interaction (P < 0.05) was observed for alpha diversity measures (Fisher's Alpha, Shannon Diversity Index, Observed Features), with all being reduced over time but to a lower extent in cats fed MC. The weighted PCoA plot for fecal beta diversity highlighted a significant treatment-time interaction, with some shifts to the microbiome being observed. The relative abundance of fecal Ruminococcus torques remained fairly stable over time in controls but increased in cats fed MC, while fecal Fusobacterium remained stable in cats fed MC but was decreased in controls. Over 30 bacterial genera were affected by time. Our results suggest that without affecting fecal characteristics, MC supplementation slightly modified fecal microbiota and metabolite concentrations and reduced serum triglycerides of cats.},
}

@article {pmid42608952,
year = {2026},
author = {Cai, T and Tamanini, I and Odorizzi, K and Ceccato, T and Botti, S and Gallelli, L and Mazzoli, S and Palmieri, A and Bjerklund Johansen, TE},
title = {Microbiota-derived short-chain fatty acids are associated with symptoms in chronic prostatitis/chronic pelvic pain syndrome through the production of proinflammatory cytokines: Results from a comparative study.},
journal = {Urologia},
volume = {},
number = {},
pages = {3915603261476871},
doi = {10.1177/03915603261476871},
pmid = {42608952},
issn = {1724-6075},
abstract = {In recent years we have witnessed increasing interest for the role of microbiota in the pathophysiology and management of prostatic diseases. However, there are several aspects to comprehend. Here, we aim to assess the gut microbiota composition and faecal microbiota-derived short-chain fatty acids production (SCFAs) in the pathogenesis of CP/CPPS. All patients with CP/CPPS attending our urology centre, were enrolled in this study, and underwent urological examination, microbiological evaluation, intestinal microbiota analysis and measurement of interleukins in semen. A cohort of subjects who had undergone intestinal microbiota investigation for various reasons but did not exhibit any symptoms of urological disease, was used as control group. Laboratory data from the two groups were analysed in terms of gut microbiota composition and levels of SCFAs. We enrolled 37 patients and 45 controls. In the CP/CPPS patient group, the mean levels of interleukins were: IL-8 934 pg/ml, IL-10 64 pg/ml, IL-6 871 pg/ml. In this patient group, we found higher levels of Bifidobacteriaceae and Bacteroidaceae and lower levels of Prevotella and Lactobacillus with a Firmicutes/Bacteroides mean ratio at 0.27. The control group had a normal Firmicutes/Bacteroides mean ratio (1.6). The two groups showed a significant difference in total SCFAs levels (p = 0.001) and in particular regarding indole-3-propionic acid (p = 0.003) and butyric acid (p < 0.001). A statistically significant correlation was found between the levels of IL-8 and a decreasing SCFAs production (p < 0.001). A difference in gut microbiota between patients with CP/CPPS and controls, together with a reduction in faecal levels of microbiota-derived short-chain fatty acids and decreased IL-8 levels in semen, might be part of the pathophysiological mechanism in CP/CPPS.},
}

@article {pmid42608979,
year = {2026},
author = {Wang, P and Wang, C and Zhang, Y and Bi, L and Zhao, H and Xu, Z and Wang, Z and Sheng, Y and Cui, Y},
title = {Topical Application of Indole-3-Acetic Acid, Present in S. epidermidis Supernatant, Alleviates Atopic Dermatitis in Mice at Least via the Aryl Hydrocarbon Receptor Signalling Pathway.},
journal = {Experimental dermatology},
volume = {35},
number = {8},
pages = {e70329},
doi = {10.1111/exd.70329},
pmid = {42608979},
issn = {1600-0625},
support = {201920102303//Peking Union Medical College/ ; 2024-ZX-019//Project of Integrated Traditional Chinese Medicine Collaboration "Flagship" Department Development/ ; ZRJY2023-GG14//China-Japan Friendship Hospital Youth Science and Technology Excellence Project/ ; 2208085Y25//Outstanding Youth Project of Natural Science Foundation of Anhui Province/ ; 2022YFC3602002//China National Key R&D Program of China/ ; 2022-NHLHCRF-LX-02-03//National High-Level Hospital Clinical Research Funding/ ; },
mesh = {Animals ; *Dermatitis, Atopic/drug therapy/metabolism/microbiology ; *Indoleacetic Acids/administration & dosage/pharmacology/therapeutic use/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism/antagonists & inhibitors ; *Staphylococcus epidermidis/metabolism ; Signal Transduction/drug effects ; Mice ; Humans ; Skin Microbiome ; Skin/metabolism/microbiology ; Keratinocytes/metabolism ; Administration, Topical ; Disease Models, Animal ; Female ; Molecular Docking Simulation ; },
abstract = {Dysbiosis of the skin microbiome, characterised by Staphylococcus aureus overgrowth and imbalance of commensals such as Staphylococcus epidermidis (S. epidermidis), is closely associated with atopic dermatitis (AD). However, the therapeutic relevance of defined S. epidermidis-associated indole metabolite, especially indole-3-acetic acid (IAA), in AD-like inflammation remains incompletely characterised. Here, we investigated the role of IAA, a tryptophan-derived metabolite enriched in the culture supernatant of the tested S. epidermidis strain, in AD-like inflammation. Public transcriptomic analyses suggested impaired AHR-associated and tryptophan-metabolism signatures in AD skin, particularly in lesional skin, while human metagenomic data indicated AD-associated staphylococcal alterations. Targeted metabolomics identified IAA as an enriched indole metabolite in S. epidermidis culture supernatant. In an MC903-induced AD-like mouse model, cutaneous IAA levels and S. epidermidis abundance were reduced. Topical IAA attenuated AD-like phenotypes, improved barrier-related proteins and reduced inflammatory indices. These protective effects were diminished by the AHR antagonist CH223191. Molecular docking predicted a possible interaction between IAA and AHR, and in vitro assays showed that IAA modulated keratinocyte AHR-associated inflammatory and barrier-related responses. Together, our findings support IAA as a microbiome-associated postbiotic candidate for AD management, at least partly through AHR-associated signalling.},
}

Animals
*Dermatitis, Atopic/drug therapy/metabolism/microbiology
*Indoleacetic Acids/administration & dosage/pharmacology/therapeutic use/metabolism
*Receptors, Aryl Hydrocarbon/metabolism/antagonists & inhibitors
*Staphylococcus epidermidis/metabolism
Signal Transduction/drug effects
Mice
Humans
Skin Microbiome
Skin/metabolism/microbiology
Keratinocytes/metabolism
Administration, Topical
Disease Models, Animal
Female
Molecular Docking Simulation

@article {pmid42609075,
year = {2026},
author = {Pugazhendhi, S and Murugesan, T and Sehgal, R},
title = {Beyond Pathogen or Commensal: Emerging Evidence on Blastocystis in Food, Environment, and Human Health.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {15353141261479390},
doi = {10.1177/15353141261479390},
pmid = {42609075},
issn = {1556-7125},
abstract = {BACKGROUND: Blastocystis sp. is a predominant anaerobic eukaryote of the human gastrointestinal tract, with carriage rates exceeding 50% in some populations, particularly in low- and middle-income countries, using molecular methods. Despite its widespread occurrence, its clinical importance continues to be a matter of debate because of its genetic diversity [having 44 subtypes (STs)] and its varied associations with host pathology.

SCOPE: This review summarizes recent findings (2021-2026) on the epidemiology, transmission, pathogenicity, host-microbiome interactions, and subtype-specific characteristics of Blastocystis, with emphasis on its dual role in human health.

KEY FINDINGS: Current evidence indicates that Blastocystis may be either pathogenic or completely commensal, depending on diverse factors. It may be a reflection of a particular gut ecosystem, including higher bacterial diversity and ecological stability. Certain virulence mechanisms of the parasite can disrupt immune responses and epithelial integrity. Virulence related to STs and other factors may be responsible for the shift from asymptomatic colonization to disease, along with the immune status of the host and microbial environment. Blastocystis may be beneficial in healthy conditions, but may cause increased complications in dysbiosis states. Transmission of the infection may be from contaminated water, edible plants, and animal products.

CONCLUSION: Understanding the dual roles of Blastocystis requires comprehensive studies that address subtype-specific behavior and context-dependent host interactions. The present review presents a broad overview of the parasite and further directions for research.},
}

@article {pmid42609092,
year = {2026},
author = {Matteoli, C and Mazzone, A and Verna, R},
title = {Laboratory Medicine in Immune Checkpoint Inhibitor-Induced Autoimmune Disorders: Baseline Assessment, Diagnostic Algorithms, Monitoring, and Predictive Biomarkers.},
journal = {Annals of laboratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.3343/alm.2025.0733},
pmid = {42609092},
issn = {2234-3814},
abstract = {Immune checkpoint inhibitors (ICIs) have substantially improved clinical outcomes across multiple malignancies, but they can disrupt self-tolerance and induce immune-related adverse events resembling autoimmune disorders. In many cases, laboratory abnormalities precede overt clinical manifestations, placing laboratory medicine at the center of baseline evaluation, early recognition, diagnostic confirmation, longitudinal monitoring, and treatment follow-up. This review provides a laboratory-focused overview of ICI-induced autoimmune disorders, focusing on baseline laboratory assessment, monitoring strategies during therapy, organ-specific diagnostic algorithms, ICI-specific toxicity patterns, and candidate predictive biomarkers. Particular attention is paid to endocrine, hepatic, metabolic, cardiac, rheumatologic, and neurologic toxicities and to pre-analytical and analytical issues that can confound interpretation. The potential contribution of digital tools and artificial intelligence to accelerating laboratory-based detection is also discussed. Standardized laboratory pathways integrating baseline testing, reflex and confirmatory algorithms, trend-based surveillance, and multidisciplinary interpretation can improve safety and support personalized decisions regarding immunotherapy continuation and management.},
}

@article {pmid42609106,
year = {2026},
author = {Atashi, A and Seo, H and Tajdozian, H and Sarafraz, F and Shuvo, MSH and Kim, S and Song, HY},
title = {Evaluation of Microbiome Therapeutic Candidates for Carbapenem-Resistant Enterobacteriaceae Associated with Capsule Biosynthesis.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604012},
doi = {10.4014/jmb.2604.04012},
pmid = {42609106},
issn = {1738-8872},
mesh = {*Carbapenem-Resistant Enterobacteriaceae/drug effects/metabolism/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Bacterial Capsules/metabolism/drug effects ; Microbial Sensitivity Tests ; Klebsiella pneumoniae/drug effects ; *Microbiota ; Lactobacillus/metabolism ; Carbapenems/pharmacology ; Enterobacteriaceae Infections/therapy/microbiology ; Animals ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) are life-threatening multidrug-resistant superbugs with severely limited treatment options, highlighting the urgent need for next-generation therapeutics that employ novel mechanisms of action. Microbiome-based therapies have emerged as a promising alternative, with several development pipelines actively progressing. In this study, a comprehensive evaluation of efficacy and safety based on mechanistic evidence is critical for the optimal selection of therapeutic candidate strains. So, we evaluated Lactobacillus and Bacillus candidate strains for activity against CRE, assessing their efficacy and safety in the context of mechanistic insights. Cell-free supernatants derived from these strains exhibited dose-dependent growth inhibition and time-dependent bactericidal activity against carbapenem-resistant Klebsiella pneumoniae. All candidate strains exhibited acceptable safety profiles with no hemolytic activity, although bile salt deconjugation and antibiotic susceptibility patterns varied by strain. Mechanistic analyses revealed that treatment with cell-free supernatants significantly reduced the production of capsular polysaccharide (CPS) and downregulated the CPS biosynthesis-related gene galF, thereby enhancing susceptibility to human serum killing. Additionally, a strong correlation was observed between antibacterial potency and CPS suppression, and two relatively superior candidate strains were prioritized based on their dual functional advantages. Collectively, these findings provide a robust mechanistic rationale for strain prioritization and support the strategic advancement of capsule suppression-based microbiome therapeutics for controlling CRE infections into preclinical and clinical development.},
}

*Carbapenem-Resistant Enterobacteriaceae/drug effects/metabolism/genetics
*Anti-Bacterial Agents/pharmacology
Humans
*Bacterial Capsules/metabolism/drug effects
Microbial Sensitivity Tests
Klebsiella pneumoniae/drug effects
*Microbiota
Lactobacillus/metabolism
Carbapenems/pharmacology
Enterobacteriaceae Infections/therapy/microbiology
Animals

@article {pmid42609162,
year = {2026},
author = {Cabral, JVM and Laughinghouse, HD and Paulino, JM and Gama, WA},
title = {Ariadnema polymorpha gen. et sp. nov. (Scytonemataceae, Cyanobacteria): A new heterocytous cyanobacterium with true and false branching from ruins in the Brazilian Atlantic Forest.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70225},
pmid = {42609162},
issn = {1529-8817},
support = {APQ-1285-2.03/22; APQ-1449-2.03/24//Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {A novel heterocytous Cyanobacterium, Ariadnema polymorpha gen. et sp. nov., was observed in the northern Brazilian Atlantic Forest (BAF), a globally significant biodiversity hotspot that has microbiome diversity yet to be explored. Isolated from ancient sugarcane mill ruins within the BAF, the new genus (strain CCAPE130) exhibits a unique morphology, including inverted Y true branching, coupled with scytonematoid and tolypothricoid false branching within the same trichome, an unusual morphology among heterocytous cyanobacteria. A polyphasic taxonomic approach, integrating detailed morphological characterization, transmission electron microscopy (TEM) ultrastructure analysis, 16S rRNA gene sequencing, and 16S-23S ITS rRNA region sequencing, was employed. Phylogenetic analysis using maximum likelihood and Bayesian inference placed CCAPE130 as a sister clade to the Symphyonema and Mastigocladopsis genera, which were previously associated with Symphyonemataceae, a family originally diagnosed by true Y-branching but now merged into the false-branched family Scytonemataceae. Structural comparisons of the 16S-23S ITS rRNA region D1-D1' showed variations, and the Box B region exhibited structural similarities with related lineages despite nucleotide differences. This research represents a phylogenetic analysis of Scytonemataceae specimens with true and false branching from the Americas, validating A. polymorpha as a new genus and species. Our results significantly enhance our understanding of Scytonemataceae phylogeny and underscore the rich, often overlooked, cyanobacterial diversity present in tropical forest regions, such as the Brazilian Atlantic Forest.},
}

@article {pmid42609329,
year = {2026},
author = {Qin, P and Tuersong, W and Tao, Z and Huang, B and Tan, L and Liu, H and Zhao, J and Hu, M},
title = {Metagenomic profiling of pathogens and antibiotic resistome in influent of six municipal wastewater treatment plants: a descriptive analysis of plant-specific microbial hazards.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780611},
pmid = {42609329},
issn = {1664-302X},
abstract = {INTRODUCTION: Wastewater treatment plants (WWTPs) serve as critical nodes for monitoring urban biological hazards, yet the raw influent-the primary entry point for pathogens and antibiotic resistance genes (ARGs)-remains less characterized compared to treated effluent, particularly at the level of individual facilities, as most prior studies have pooled samples or focused on post-treatment matrices.

METHODS: In this descriptive study, we performed metagenomic sequencing on influent samples collected from six municipal WWTPs, with each plant treated as an independent unit to profile its specific microbial community, pathogen composition, and antibiotic resistome.

RESULTS: Across all samples, a total of 853 bacterial and 232 eukaryotic pathogen species were identified. An exploratory risk index, calculated by integrating species abundance with established risk group classifications, assigned the highest heuristic score to Tangxun Lake (2150), reflecting its concurrent enrichment of both enteric and respiratory pathogens. The pathogen distribution exhibited plant-specific patterns: enteric pathogens including Escherichia coli, Vibrio cholerae, and Campylobacter jejuni were predominantly detected in Huangpu road and Nantaizi Lake, whereas respiratory pathogens such as Mycobacterium tuberculosis and Legionella pneumophila were more abundant in Xinzhuang, Jinyang, and Tangxun Lake. A core set of ARGs-comprising multidrug efflux pumps, β-lactamases, and tetracycline resistance genes-was consistently present across all six facilities, collectively accounting for approximately 60% of the total ARG abundance detected. In addition, exploratory correlations between mobile genetic elements (e.g., plasmids and transposases) and clinically relevant ARGs were observed across the dataset, warranting further investigation.

DISCUSSION: By generating plant-specific hazard inventories rather than pooled averages, this study provides a descriptive baseline that enables facility-specific surveillance prioritization.},
}

@article {pmid42609357,
year = {2026},
author = {Zhao, S and Wang, X and Wu, D and Yang, Y and Yang, Y and Shangguan, Y and Li, J},
title = {Influence of carbon-based organic fertilizer on soil microorganisms and vegetable growth in Sb-As co-contaminated soil: a synergistic mechanism of promotion and detoxification.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1823671},
pmid = {42609357},
issn = {1664-462X},
abstract = {BACKGROUND: Antimony (Sb) and arsenic (As) co-contamination threatens crop production and food safety. Carbon-based organic fertilizers may simultaneously improve soil fertility, regulate microbial communities, and reduce metal(loid) mobility, but their performance in Sb-As co-contaminated vegetable systems remains unclear.

METHODS: A pot experiment with pak choi was conducted to compare different carbon-based amendments, including magnesium sulfate-loaded biochar-based organic fertilizer (CBOF-M). Soil chemistry, pore-water elements, enzyme activities, rhizosphere microbial communities, plant growth, and elemental accumulation were evaluated.

RESULTS: Carbonaceous amendments reduced Sb mobility but increased As solubility. CBOF-M increased soil carbon, produced the highest plant biomass, reduced Sb translocation to edible tissues, and enriched Bacteroidota and Gemmatimonadota. Structural equation modeling identified an indirect microbiome-mediated pathway and a direct enzyme-mediated nutrient-cycling pathway.

CONCLUSION: Magnesium sulfate-loaded biochar-based organic fertilizer produced a promotion-detoxification synergy, although As mobilization remains a key constraint requiring formulation-specific control.},
}

@article {pmid42609382,
year = {2026},
author = {Sandhya, M and Priyadharshini, E and Anand, T and Tharmalingam, N and Senthilraja, G},
title = {Antimicrobial resistance in plant-associated microbial communities: mechanisms, ecology, and one health implications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1778342},
pmid = {42609382},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) has emerged as a major global challenge threatening human, animal, plant and the environment health. Although AMR has been extensively studied in clinical and veterinary sectors, its emergence and dissemination in plant-based agricultural systems remains comparatively underexplored despite of the widespread use of antibiotics, fungicides and other antimicrobial compounds in crop production. These practices exerts selective pressure on plant associated microbial communities, promoting the evolution and dissemination of antimicrobial resistance genes (ARGs) across interconnected environmental compartments including soil, water, plants and food systems highlighting the importance of one health. This review synthesizes current knowledge on the occurrence, mechanisms and ecological drivers of AMR in plant associated microbial communities. It discusses resistance mechanism in bacterial and fungal plant pathogens, the role of soil, rhizosphere, and phyllosphere microbiomes as reservoirs and transmission hubs for ARGs and evidence from global and regional studies illustrating the complexity of AMR in agricultural ecosystems. The review also evaluates emerging sustainable alternatives to conventional antimicrobial use including phage therapy, microbiome engineering, RNA-based biopesticides, CRISPR-based technologies, and nanotechnology based approaches, which have the potential to reduce chemical reliance and mitigate selection pressure for resistance. Overall, integrating plant health into one health governance frameworks, strengthening AMR surveillance in agricultural systems, and promoting sustainable disease management strategies are essential for limiting the spread of resistance and safeguarding agricultural productivity, ecosystem integrity and public health.},
}

@article {pmid42609388,
year = {2026},
author = {Hou, X and Xu, H and Zhu, L and Ding, S and Shao, Y and Zhang, M and Lin, X},
title = {Integrating tongue coating microbiome, tongue coating metabolomics, and exhaled breath metabolomics via machine learning to identify chronic atrophic gastritis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1910978},
pmid = {42609388},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic atrophic gastritis (CAG) is a precancerous gastric condition with limited non-invasive diagnostic options. Alterations in the oral microbiome and its localized metabolic profiles may provide early multi-omics signatures of disease progression.

METHODS: We performed 16S rRNA gene sequencing of tongue coating samples, along with untargeted metabolomics of both tongue coating and exhaled breath condensate (EBC) in 139 patients, including 99 patients with CAG and 40 with chronic non-atrophic gastritis (CNAG) serving as a disease comparison group. The tongue coating microbiome, tongue coating metabolome, and systemic breath volatile profiles were comprehensively characterized. The clinical cohort was randomly partitioned into a training set and an independent validation test set in a 7:3 ratio. Unsupervised PCA algorithm was implemented for metabolic clustering, and LASSO regression was applied for cross-domain feature integration.

RESULTS: CAG patients exhibited significant tongue coating microbiome dysbiosis, characterized by the enrichment of g__Arthrobacter, Veillonella, and Streptococcus, and depletion of Prevotella and Haemophilus compared to the CNAG disease comparison group. Metabolomic profiling of the tongue coating uncovered pronounced metabolic alterations, mapped via unsupervised PCA scores (PC1: 49.5%; PC2: 5.7%), identifying 56 differential tongue coating metabolites that were predominantly upregulated and significantly enriched in alanine, aspartate, and glutamate metabolism pathways. Concurrently, EBC metabolomics mapped via PCA coordinate configurations (PC1: 18.8%; PC2: 8.2%) detected 73 differential metabolites based on unadjusted Student's t-test (p < 0.05), with a majority (56/73) being significantly downregulated, reflecting systemic metabolic variations. To bridge these high-dimensional cross-domain interactions, an optimized 26-feature panel was filtered via LASSO regression. A generalized linear Logistic Regression classifier excelled in discriminating CAG from the CNAG disease comparison group, achieving a top-tier Area Under the Curve (AUC) of 0.8667 (95% CI: 0.748-0.954), an accuracy of 78.6%, and a sensitivity of 90.0% on the independent 7:3 test set, consistently outperforming complex non-linear ensemble tree algorithms. Calibration curve and decision curve analysis (DCA) further confirmed robust fit metrics (Brier Score = 0.1634) and substantial clinical net benefit on the held-out test cohort.

CONCLUSION: This study establishes an advanced, regularized linear machine learning framework, demonstrating that a streamlined 26-feature panel of tongue coating and exhale profiles offers a transparent, non-invasive triage tool for chronic atrophic gastritis. These tightly synchronized local and systemic multi-source trajectories provide crucial insights into oral-gastric microbial interactions and host-microbiome co-metabolism in CAG.},
}

@article {pmid42609392,
year = {2026},
author = {Wang, C and Berube, L and Curran, M and Pompeii, ML and Hu, L and Barua, S and Li, H and St-Jules, DE and Schoenthaler, A and Segal, E and Bergman, M and Popp, CJ},
title = {Associations between the gut microbiome and diet, body composition, and glycemic profiles: a cross-sectional post-hoc analysis of the Personal Diet Study.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1851439},
pmid = {42609392},
issn = {2296-861X},
abstract = {BACKGROUND: The gut microbiome is implicated in obesity and type 2 diabetes (T2D), but how diet, body composition, glycemic status, and self-efficacy factors relate to the microbiome in high-risk individuals is not well characterized. The purpose of this post-hoc analysis is to examine the relationship between the gut microbiome and obesity-related metabolic factors, including body composition, resting energy expenditure (REE), and glycemic variability (GV).

METHODS: Data for this post-hoc cross-sectional analysis were obtained from adults with prediabetes and obesity enrolled in The Personal Diet study, a 6-month behavioral weight loss study. Pre-intervention assessments (n = 95) included the collection of fecal microbiome profile, demographics, socioeconomic status, physical and metabolic characteristics [fat mass, fat free mass (FFM), continuous glucose monitoring-derived GV, REE], self-efficacy and dietary intake. Gut bacterial alpha diversity, beta diversity, and genus level abundances were associated with these host and lifestyle variables using multivariate regression, permutational multivariate analysis of variance, and correlation analyses.

RESULTS: Participants were a mean age of 58 years old, mostly female (75.8%), with a mean BMI of 34.6 kg/m[2] and mean HbA1c of 5.7%. Higher FFM was associated with greater alpha diversity, whereas higher BMI was associated with lower diversity (p < 0.05). Dietary factors were the most consistent correlates of gut microbial beta diversity. At the genus level, associations were observed for sex, metformin use, BMI, protein intake, and REE. The Prevotella/Bacteroides ratio was positively associated with total energy, sugar, and carbohydrate intake (g/day) and negatively associated with monounsaturated fat intake (g/day). Glycemic measures and self-efficacy were not associated with any genera.

CONCLUSION: In adults with prediabetes and obesity, the gut microbiome at baseline was most strongly associated with diet, with additional associations observed for body composition and selected host characteristics. These findings underscore diet as a key correlate of gut microbiome structure in a high-risk metabolic population and support further development of microbiome-informed precision nutrition strategies for obesity prevention and management.},
}

@article {pmid42609412,
year = {2026},
author = {Chooklin, S and Chuklin, S},
title = {The Metabolic Legacy of Acute Pancreatitis: Post-Pancreatitis Diabetes Mellitus.},
journal = {Clinical and experimental gastroenterology},
volume = {19},
number = {},
pages = {635877},
pmid = {42609412},
issn = {1178-7023},
abstract = {Post-pancreatitis diabetes mellitus after acute pancreatitis (PPDM-A) is increasingly recognized as a distinct metabolic complication rather than a simple subtype of type 2 diabetes. This narrative review summarizes current evidence on PPDM-A, with emphasis on terminology, diagnostic timing, epidemiology, pathophysiology, risk factors, clinical phenotypes, screening, prevention, and long-term follow-up. A structured literature search was conducted in PubMed/MEDLINE, Scopus, and Google Scholar to identify relevant studies. PPDM-A may develop after mild, moderately severe, or severe acute pancreatitis, although the risk is greatest in patients with pancreatic necrosis, recurrent attacks, exocrine pancreatic dysfunction, obesity, dyslipidemia, fatty liver disease, metabolic comorbidities, and marked in-hospital glycemic variability. A major diagnostic challenge is distinguishing transient stress hyperglycemia and previously unrecognized diabetes from incident PPDM-A. Formal diagnosis should generally be established no earlier than 90 days after the index episode of acute pancreatitis to minimize misclassification due to transient stress-related dysglycemia. Follow-up assessment should combine fasting plasma glucose and HbA1c, whereas a 75-g oral glucose tolerance test (OGTT) may provide greater sensitivity during early recovery, particularly when HbA1c is unreliable, results are borderline or discordant, or isolated postprandial dysglycemia is suspected. Current evidence indicates that PPDM-A develops through interacting pathogenic domains, including pancreatic endocrine injury with impaired β-cell reserve, metabolic dysregulation characterized by insulin resistance and persistent inflammation, exocrine pancreatic dysfunction with nutritional consequences, and emerging mechanisms involving gut microbiome alterations, bile acid-FGF19 signaling, and extracellular vesicle-mediated communication. Available data support a trajectory-based model in which some patients recover normal glucose metabolism, some develop persistent intermediate dysglycemia, and others progress to overt diabetes over months or years. Structured post-discharge surveillance, risk-stratified follow-up, assessment of exocrine dysfunction, and prevention of recurrent pancreatic injury are essential for improving early detection, reducing diagnostic misclassification, and optimizing long-term clinical outcomes.},
}

@article {pmid42609458,
year = {2026},
author = {Xing, Q and Chen, J and Liu, R and Li, W and Chen, K and Liu, X},
title = {Research Advances on the Molecular Structural Basis and Mechanisms of Quercetin and Its Derivatives in Improving Insulin Resistance.},
journal = {Drug design, development and therapy},
volume = {20},
number = {},
pages = {626825},
pmid = {42609458},
issn = {1177-8881},
mesh = {*Quercetin/pharmacology/chemistry/analogs & derivatives ; Humans ; *Insulin Resistance ; Animals ; Structure-Activity Relationship ; Molecular Structure ; Signal Transduction/drug effects ; },
abstract = {Insulin resistance is a core pathological link in metabolic diseases such as type 2 diabetes, and its prevention and treatment are current research hotspots. Quercetin, a natural flavonoid, has significant potential to improve insulin resistance through its anti-inflammatory, antioxidant, and metabolic regulatory activities. This review systematically examines literature published between 2020 and 2025 from the PubMed, Web of Science, and Scopus databases, focusing on original mechanistic studies in cellular and animal models of insulin resistance. Our synthesis reveals two mechanistic clusters: quercetin directly activates insulin signaling via the insulin receptor substrate 1/Phosphatidylinositol 3-kinase /Protein Kinase B pathway, enhances muscle glucose uptake through AMP-activated protein kinase-dependent glucose transporter 4 translocation. Indirect mechanisms include gut microbiome modulation with increased short-chain fatty acid production, suppresses hepatic inflammation and targeting of transcription factors. Critically, a clear efficacy hierarchy among derivatives was identified: glycosides show superior bioavailability compared to the aglycone, while methylated derivatives exhibit enhanced stability but divergent effects on peroxisome proliferator-activated receptor γ signaling. Major unresolved challenges include the low oral bioavailability of quercetin aglycone, the lack of systematic structure-activity relationship models, and the absence of rigorous human trials. The review concludes that chemical derivatization and advanced delivery systems offer promising strategies, but clinical translation requires an integrated framework combining systematic structure-activity profiling, mechanistic target selection, and validated human studies.},
}

*Quercetin/pharmacology/chemistry/analogs & derivatives
Humans
*Insulin Resistance
Animals
Structure-Activity Relationship
Molecular Structure
Signal Transduction/drug effects

@article {pmid42609478,
year = {2026},
author = {Li, T and Yao, D and Cheng, F and Mou, X and Bian, Q},
title = {The Scalp Microbiome-Hair Axis: Mechanisms and Therapeutic Translation.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1409},
pmid = {42609478},
issn = {2639-5274},
abstract = {Hair loss is common and can markedly impair quality of life, yet the contribution of the scalp microbiome to alopecia remains fragmented across disease subtypes and mechanistic levels. This review aims to construct a clinically relevant and mechanistically coherent framework for the scalp microbiome-hair axis. We first summarize the composition and physiological functions of the scalp microbiome, including its roles in barrier integrity, immune regulation, and nutrient metabolism. We then compare dysbiosis patterns across androgenetic alopecia, alopecia areata, seborrheic dermatitis-associated hair loss, and folliculitis/scarring alopecia. This comparison identifies a shared pathogenic layer-barrier disruption, innate immune activation, altered lipid or metabolite processing, and impaired anagen support-together with subtype-selective mechanisms, including immune-privilege collapse in alopecia areata, androgen-lipid-microbiome coupling in androgenetic alopecia, Malassezia-centered inflammatory ecology in seborrheic dermatitis, and infection/biofilm-driven injury with fibrosis in scarring disease. We further organize the available evidence into a 3-tier signaling cascade linking upstream microbial triggers to midstream NF-κB, JAK-STAT, PI3K/AKT, and Wnt/β-catenin integration and downstream outcomes such as stem-cell quiescence, dermal papilla dysfunction, vascular regression, immune-privilege loss, and fibrosis. We also evaluate probiotics, postbiotics, and engineered microbial systems, whose potential benefits may arise from coordinated anti-inflammatory, ecological, regenerative, and pro-angiogenic effects. However, translation is limited by methodological heterogeneity, weak causal evidence, strain stability, targeted delivery, manufacturing quality control, and regulatory uncertainty. Overall, this framework clarifies shared and subtype-specific roles of scalp dysbiosis and defines priorities for precision, microbiome-guided alopecia therapy.},
}

@article {pmid42609554,
year = {2026},
author = {Alaskar, MK and Alonazi, M and Ben Bacha, A and Alamri, AM and Amina, M and Al Musayeib, NM and Abuaish, S and El-Ansary, AK},
title = {Effects of artichoke extracts and probiotic on maternal immunological activation, valproic acid-induced oxidative stress, and gut leakiness in a rat model of autism.},
journal = {Open life sciences},
volume = {21},
number = {1},
pages = {20251355},
pmid = {42609554},
issn = {2391-5412},
abstract = {Maternal health during pregnancy is a leading factor influencing offspring risk. This study investigated whether postnatal dietary supplementation could reduce oxidative stress and gut leakiness in a rat model of autism spectrum disorder (ASD). Male rat pups were prenatally exposed to valproic acid (VPA) or lipopolysaccharide (LPS) to induce ASD-like conditions. A total of 54 offspring of Wistar albino rats were divided into nine groups to evaluate various postnatal treatments, including an artichoke-based prebiotic (AR), probiotics (Pro), and omega-3 fatty acids (ω3). The experimental design also included control groups (saline, VPA-only, and LPS-only), as well as a protective regimen in which AR was administered both prenatally and postnatally. Oxidative stress and gut permeability "leakiness" were assessed using Enzyme-Linked Immunosorbent Assay (ELISA). Prenatal exposure to VPA and LPS was associated with increased oxidative stress levels in brain homogenates, accompanied by a significant decrease in glutathione (GSH). Additionally, elevated plasma levels of gut permeability biomarkers were observed. In the VPA model, treatment with artichoke-derived prebiotics - administered either prenatally, postnatally, or in combination with probiotics - effectively improved oxidative stress markers, as evidenced by a significant increase in GSH levels. Conversely, similar interventions in the LPS-induced maternal immune activation model did not significantly ameliorate oxidative stress, although a modest increase in GSH levels was noted. Plasma levels of gut permeability biomarkers did not show significant improvement in either model following treatment with artichoke-derived probiotics alone or in combination with probiotics and omega-3 fatty acids. However, intestinal fatty acid-binding protein levels were significantly reduced in all treatment groups across both models. In contrast, lipopolysaccharide-binding protein (LBP) levels were not significantly reduced by artichoke extract monotherapy in either model, although combination therapy with probiotics and/or omega-3s led to significant reductions in LBP. These results support the use of both VPA and LPS as complementary models for studying ASD. The VPA model, characterized by direct and predictable neurotoxic effects, appears to be more suitable for evaluating preventive interventions. In contrast, the LPS model more accurately captures the complex immune-inflammatory mechanisms implicated in ASD, highlighting the need for broader and more individualized treatment strategies. The differing responses to artichoke-based interventions in these models underscore the importance of considering ASD etiology when designing dietary and microbiome-targeted therapies.},
}

@article {pmid42609576,
year = {2026},
author = {Ai, R and Xu, XY and Khan, A and Geng, JM and Tan, WH and Wang, YF and Liu, L},
title = {Polysaccharides from Elsholtzia rugulosa: structural characteristics and treating functional dyspepsia via gut microbiome in conjunction with targeting the PI3K/Akt/cGMP-PKG pathways.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1833860},
pmid = {42609576},
issn = {2296-861X},
abstract = {BACKGROUND: Functional dyspepsia (FD) is a common gastrointestinal disorder characterized by symptoms such as epigastric pain, bloating, and nausea. Current treatments have limited efficacy and significant side effects. Elsholtzia rugulosa, a traditional medicinal plant, is used to treat gastrointestinal disorders, and its polysaccharides (ERP) may offer therapeutic potential for FD.

OBJECTIVE: This study aimed to characterize the structural properties of Elsholtzia rugulosa polysaccharides (ERP) and explore their mechanism in treating FD.

MATERIALS AND METHODS: Neutral ERP-N and acidic ERP-A were isolated from Elsholtzia rugulosa. Their structural features were analyzed, and FD rats were treated with ERP. Gastric pathology, gut microbiota, and the PI3K/Akt/cGMP-PKG pathway were evaluated. RAW264.7 cells were used to assess ERP's immunomodulatory effects.

RESULTS: Structural Analysis: ERP-N (13,415 Da) and ERP-A (3,691 Da) exhibited distinct monosaccharide compositions and linkages. Therapeutic Effects: ERP improved FD symptoms, reduced inflammation, regulated gut microbiota, and activated the PI3K/Akt/cGMP-PKG pathway in rats. Immunomodulatory Activity: ERP-N promoted the secretion of nitric oxide (NO), TNF-α, and IL-6 in RAW264.7 cells, demonstrating immunomodulatory effects.

CONCLUSION: ERP may alleviate FD in association with gut microbiota modulation and changes in the PI3K/Akt/cGMP-PKG-related pathway. ERP-N also exhibits immunomodulatory activity, supporting the traditional use of Elsholtzia rugulosa in gastrointestinal health and offering potential for FD therapy development.},
}

@article {pmid42609585,
year = {2026},
author = {Rocha, MAD and Bagatin, E and Dréno, B and Gontijo, G and Ribeiro, BM and Almeida, LMC},
title = {The Role of Dermocosmetics in Acne Management: Implications for Clinical Practice in Brazil.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {612901},
pmid = {42609585},
issn = {1178-7015},
abstract = {Acne is a prevalent skin condition worldwide, affecting diverse populations, including Brazil. Although acne guidelines are well established for topical and/or systemic medications, recommendations regarding dermocosmetics, which have become increasingly important in acne management, remain limited. This review examines the role of dermocosmetics within acne treatment protocols and provides practical guidance for their integration into skincare routines alongside conventional therapies. Six dermatology experts conducted structured PubMed literature searches (2012-2024) and discussed the findings during expert meetings focused on acne management and dermocosmetics in the Brazilian context. Despite increasing evidence of benefit, the role of dermocosmetics remains underreported, with systemic treatments predominating. Acne pathophysiology is complex with four main pillars: hyperkeratinization of the pilosebaceous gland infundibulum, inflammation, overactivity of sebaceous glands, and microbiome imbalance in the context of an altered skin barrier. Advances in acne microbiome research highlight the importance of targeting dysbiosis, with new treatments exploring pre-, pro-, and postbiotics and bacteriophages. Dermocosmetics containing key active ingredients can address these multifactorial targets of acne, including excessive sebum production, hyperkeratinization, inflammation, and skin barrier and microbiome imbalance. They have been shown in clinical studies to be beneficial as monotherapy for mild cases, as maintenance therapy, or as adjuncts to acne medications. Due to their safety and tolerability profile, dermocosmetics are especially valuable for specific populations, such as pregnant women and prepubertal patients. Published evidence and expert clinical consensus support integrating dermocosmetics into daily routines to enhance acne control, patient adherence, and quality of life. Effective patient education on skincare regimens prevents treatment-related issues and optimizes outcomes. Incorporating dermocosmetics and improving patient education may further optimize these benefits.},
}

@article {pmid42609601,
year = {2026},
author = {Park, MR and Bae, M},
title = {Metatranscriptomic characterization of active microbial communities in strawberry hydroponic drainage effluent.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1909518},
pmid = {42609601},
issn = {1664-302X},
abstract = {Hydroponic cultivation systems improve water and nutrient use efficiency; however, little is known about the active microbial communities inhabiting hydroponic drainage effluent. This study employed metatranscriptomic sequencing to characterize active microbial communities present in drainage effluent collected from strawberry cultivation beds within a commercial recirculating hydroponic system. Drainage effluent samples were collected during the spring and winter cultivation periods and subjected to RNA-based metatranscriptomic analysis. Following quality filtering, de novo assembly, and taxonomic classification, bacterial, fungal, and viral-associated transcripts were analyzed to characterize active microbial communities within the drainage environment. Metatranscriptomic sequencing generated 65.2 million and 53.2 million paired-end reads from the spring and winter samples, respectively. Taxonomic classification revealed distinct microbial profiles between the two analyzed drainage samples. Bacterial transcripts represented the dominant classified component in both samples. The spring sample exhibited a relatively diverse bacterial community composed of multiple taxa, whereas the winter sample was strongly dominated by Serratia marcescens and Serratia proteamaculans. Fungal community composition also differed between samples, with a greater representation of yeast-associated fungi in the winter sample. Viral-associated transcripts were detected in both samples and were primarily represented by bacteriophage-related sequences. A large proportion of transcripts remained unclassified, particularly in the spring sample, highlighting the limited representation of hydroponic drainage microorganisms in current reference databases. Although the study was limited to a single commercial production site, the findings should be interpreted as site-specific observations rather than representative characteristics of strawberry hydroponic systems in general. Nevertheless, the study provides an initial metatranscriptomic characterization of active microbial communities inhabiting strawberry hydroponic drainage effluent under commercial cultivation conditions and establishes a baseline dataset for further comparative investigations involving multiple hydroponic production systems. These findings provide baseline information on active microbial and viral assemblages associated with hydroponic drainage effluent and demonstrate the utility of metatranscriptomics for characterizing microbial communities in recirculating cultivation systems.},
}

@article {pmid42609619,
year = {2026},
author = {Everett, E and Gore, HM and Kallepalli, S and Duffield, KR and Flor-Weiler, L and Marino, J and Ramirez, JL},
title = {Cordyceps and Beauveria infections drive species-specific microbiome dysbiosis in the mosquito Aedes aegypti.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1879658},
pmid = {42609619},
issn = {1664-302X},
abstract = {With the rising prevalence of vector-borne diseases and insecticide resistance in mosquitoes, alternative vector control strategies are urgently needed. Fungal entomopathogens offer a promising approach with a decreased likelihood of resistance development in mosquito populations. However, the mechanisms by which each fungus contributes to host mortality remain poorly understood, and the potential role of microbiome disruption as a secondary pathogenic mechanism has received limited attention. We evaluated the impact of four entomopathogenic fungal species (Beauveria bassiana, Cordyceps javanica, C. cateniannulata, and C. amoenerosea) on the microbiome of the yellow fever mosquito (Aedes aegypti) colonized with a defined, field-derived bacterial community. Whole-body bacterial communities were profiled using high throughput 16S rRNA amplicon sequencing, and community structure was assessed through alpha diversity metrics, beta diversity analysis, hierarchical clustering, and linear discriminant analysis effect size (LEfSe). All four fungal species successfully infected the mosquito; however, their effects on the mosquito microbiome were species-specific. Cordyceps javanica and C. cateniannulata reduced community evenness without significantly affecting species richness, a pattern consistent with a dominance-driven dysbiosis rather than broad bacterial loss. Infections by C. amoenerosea significantly increased total bacterial load and drove strong enrichment of the opportunistic genus Pandoraea, suggesting epithelial disruption or immune dysregulation as possible contributing factors. Beta diversity analysis indicated partial community-level restructuring across all fungal infections. B. bassiana showed a distinct genus-level compositional response, with enrichment of core symbiotic taxa and depletion of Chryseobacterium and Kluyvera, which was different from the Enterobacteriaceae-dominated shifts seen across infections with Cordyceps species. LEfSe analysis identified Kluyvera and Burkholderia as the strongest genus-level discriminators of infection state, suggesting potential utility as microbiome-based indicators of successful fungal colonization. These key findings were independently validated using EdgeR and batch-corrected MaAsLin2 analyses, with Pandoraea enrichment under C. amoenerosea and Burkholderia depletion under C. cateniannulata confirmed by both methods. Taken together, these results show that entomopathogenic fungi restructure the Ae. aegypti microbiome in a species-specific manner, inducing community destabilization and opportunistic bacterial enrichment that likely contribute to the detrimental effects of fungal infection. These results provide a mechanistic insights for the selection and development of fungal biopesticides for mosquito control.},
}

@article {pmid42609637,
year = {2026},
author = {Yu, ZN and Zhou, XS and Yang, L and Luan, Y and Geng, TB and Wang, R and Zhang, RJ and Huang, C},
title = {The gut-heart axis: a review of the mechanisms and therapeutic prospects of gut microbiota and their metabolites in cardiovascular disease.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1909679},
pmid = {42609637},
issn = {2297-055X},
abstract = {The gut microbiota, a vital virtual organ, communicates bidirectionally with the host cardiovascular system via its intricate metabolic network, forming the gut-heart axis. This review systematically clarifies the causal relationship between gut dysbiosis and the pathogenesis of cardiovascular diseases CVD), moving beyond epidemiological associations to solid causal evidence from preclinical and clinical studies. We focus on dissecting the pathophysiological mechanisms of key microbiota-derived metabolites, including trimethylamine N-oxide, short-chain fatty acids, phenylacetylglutamine, and secondary bile acids, and elaborate on their specific regulatory pathways in the development of atherosclerosis, hypertension, heart failure, and thrombosis. Finally, this review comprehensively evaluates the application potential and clinical challenges of gut microbiota-targeted therapeutic strategies, including dietary interventions, prebiotics/probiotics, fecal microbiota transplantation, and novel pharmacological agents targeting microbial metabolic pathways.},
}

@article {pmid42609641,
year = {2026},
author = {Zhang, Y and Li, J and Luo, Y and Liu, S and Liu, J},
title = {Integrative analysis of gut microbiota, plasma metabolome, and gene expression identifies causal mediators in Graves' disease pathogenesis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1704766},
pmid = {42609641},
issn = {1664-302X},
abstract = {BACKGROUND: Graves' disease (GD) is characterized by hyperthyroidism and is influenced by genetic and environmental factors. The "gut-thyroid axis" establishes a connection between the gut microbiota and GD, yet the underlying potential mechanisms remain unclear. This study employed Mendelian randomization to investigate the causal relationships between the gut microbiota and GD, aiming to identify key microbial taxa and their metabolites, as well as to explore the regulatory roles of relevant genes in the pathogenesis of GD.

METHODS: We utilized the two-sample Mendelian randomization (MR) approach to evaluate the causal effects of gut microbiota and plasma metabolites on GD. Mediation analysis was conducted to explore the associations of metabolites in linking gut microbiota to GD. Additionally, we employed bioinformatics tools to identify GD-regulating genes within the gut microbiome and validated their expression levels in peripheral blood mononuclear cells from GD mouse models.

RESULTS: Mendelian randomization analysis identified eight gut microbes associated with GD, six of which were positively correlated with an increased risk, while two were negatively correlated. Additionally, 56 plasma metabolites exhibited potential causal relationships with GD; of these, 27 were positively associated with risk and 29 were negatively associated. Mediation analysis revealed that three bacteria influenced GD through five plasma metabolites. Specifically, the mannose to glycerol ratio and 1-(1-enyl-palmitoyl)-GPC (p-16:0) mediated the effect of Dialister on GD. Gamma-glutamylthreonine mediated the effect of Oscillospira on GD, whereas the ratios of acetylcarnitine (C2) to propionylcarnitine (C3) and adenosine 5'-diphosphate (ADP) to ornithine mediated the effect of MollicutesRF9 on GD. These microbiota regulate plasma metabolites, thereby affecting GD. TAGAP and HERC3 were significantly upregulated in the peripheral blood mononuclear cells of GD mice induced by recombinant adenovirus Ad-TSHR289, while NCEH1 and LYN were significantly downregulated, indicating their potential role in the regulation of GD.

CONCLUSION: This study reveals that the composition of gut microbiota and its related metabolites promote the development of GD through the modulation of gene expression in peripheral blood mononuclear cells. Our findings have significant implications for the advancement of gut microbiota-based diagnostic techniques and targeted therapies for GD.},
}

@article {pmid42609673,
year = {2026},
author = {Zhang, F},
title = {The epigenetic-immune-microbiome axis in early life: reprogramming the origins and endotypes of pediatric asthma.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1835821},
pmid = {42609673},
issn = {1664-3224},
mesh = {Humans ; *Asthma/immunology/genetics/microbiology/etiology ; *Epigenesis, Genetic/immunology ; Animals ; *Microbiota/immunology ; Female ; Immunity, Innate ; Trained Immunity ; Pregnancy ; Child ; Prenatal Exposure Delayed Effects/immunology ; Developmental Origins of Health and Disease ; },
abstract = {Pediatric asthma is a highly heterogeneous inflammatory syndrome characterized by distinct immune endotypes. The inception of asthma predominantly occurs during the first 1,000 days of life, a critical window of immunological plasticity. Within this critical window, the developing immune system is continuously shaped by dynamic interactions between environmental exposures, the microbiome, and host genetics. Recent advances highlight the epigenetic-immune-microbiome axis as the central mechanism orchestrating these interactions. This review provides a comprehensive synthesis of how prenatal maternal imprinting (including maternal immune activation, nutrition, and psychological stress) and postnatal "second hits" (such as respiratory viral infections and gut-lung microbial dysbiosis)trigger the epigenetic reprogramming of airway epithelial cells and innate/adaptive immune cells. We specifically emphasize the paradigm of "trained immunity" in macrophages and dendritic cells, alongside the hyperactivation of group 2 innate lymphoid cells (ILC2s), as fundamental drivers of asthma pathogenesis. In parallel, we outline the epigenetic and metabolic networks (immunometabolism) that govern T-cell polarization (Th1/Th2/Th17/regulatory T cells) and airway mucosal barrier dysfunction. Finally, we evaluate the translational potential of these multi-omics signatures, discussing how non-invasive approaches like nasal epigenomic profiling may eventually aid in stratifying clinical endotypes and inform the development of future mechanism-based therapeutics.},
}

Humans
*Asthma/immunology/genetics/microbiology/etiology
*Epigenesis, Genetic/immunology
Animals
*Microbiota/immunology
Female
Immunity, Innate
Trained Immunity
Pregnancy
Child
Prenatal Exposure Delayed Effects/immunology
Developmental Origins of Health and Disease

@article {pmid42609699,
year = {2026},
author = {Xu, L and Li, Y and Feng, Y and Zhang, Y and Cai, J},
title = {The bidirectional gut microbiota-inflammation axis in gestational diabetes mellitus: pathogenesis, long-term outcomes, and therapeutic perspectives.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1902704},
pmid = {42609699},
issn = {1664-2392},
mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology/therapy/etiology ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; *Inflammation/microbiology ; *Dysbiosis ; Probiotics/therapeutic use ; Animals ; },
abstract = {Gestational diabetes mellitus (GDM) is a highly prevalent metabolic disorder of pregnancy that carries immediate and long-term health risks for both mothers and their offspring. Emerging evidence implicates maternal gut microbiota dysbiosis as a critical contributor to the onset and progression of GDM, primarily through the induction of chronic low-grade systemic inflammation. This review synthesizes recent advances in understanding the compositional shifts in the maternal gut microbiota-including depletion of short-chain fatty acid-producing taxa such as Bifidobacterium and Faecalibacterium, and enrichment of pro-inflammatory genera-and examines how these changes compromise intestinal barrier integrity, promote microbial metabolite translocation, and subsequently activate innate immune pathways. The resultant elevation of pro-inflammatory cytokines directly impairs insulin signaling, exacerbating insulin resistance and fueling a vicious cycle between dysbiosis and metabolic deterioration. Beyond the peripartum period, this review highlights the emerging concept of transgenerational programming, whereby maternal GDM-associated dysbiosis and inflammation may shape the offspring's microbiome, immune set-point, and metabolic trajectory, predisposing them to later-life metabolic and neurodevelopmental disorders. Finally, we critically evaluate current microbiota-targeted interventions, including probiotics, synbiotics, and dietary modifications, and discuss the sources of heterogeneity in clinical trial outcomes. By integrating these mechanistic and translational insights, this review proposes a conceptual framework for early risk stratification and personalized management of GDM, emphasizing that effective clinical translation requires moving beyond one-size-fits-all probiotic trials toward stratified, microbiome-guided strategies.},
}

Humans
Female
*Diabetes, Gestational/microbiology/therapy/etiology
Pregnancy
*Gastrointestinal Microbiome/physiology
*Inflammation/microbiology
*Dysbiosis
Probiotics/therapeutic use
Animals

@article {pmid42609768,
year = {2026},
author = {Wu, L},
title = {Targeting metabolic inflammation in type 2 diabetes mellitus through exercise: multi-level mechanisms of insulin resistance reversal and precision clinical translation - a review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1886943},
pmid = {42609768},
issn = {1664-3224},
mesh = {Humans ; *Diabetes Mellitus, Type 2/metabolism/therapy/immunology ; *Insulin Resistance ; *Inflammation/metabolism/therapy ; *Exercise ; Animals ; Precision Medicine ; *Exercise Therapy/methods ; },
abstract = {Insulin resistance (IR) remains the central pathophysiological driver of type 2 diabetes mellitus (T2DM) and is inadequately targeted by current pharmacotherapies. Emerging evidence in immunometabolism identifies metabolic inflammation (meta-inflammation) as a critical mechanistic bridge between chronic nutrient excess and IR progression, primarily through IKKβ/NF-κB and JNK signaling cascades, NLRP3 inflammasome activation, mitochondrial dysfunction, and lipotoxicity. Exercise intervention counteracts these processes via coordinated multi-tiered mechanisms, including AMPK-mediated insulin sensitization, myokine-driven anti-inflammatory modulation, mitophagy-based mitochondrial quality control, liver-muscle-adipose metabolic crosstalk, and epigenetic reprogramming of inflammatory transcriptional responses. However, clinically significant interindividual variability in exercise responsiveness-termed exercise non-response-limits the effectiveness of population-averaged prescription guidelines. This heterogeneity is attributable to genetic polymorphisms, baseline inflammatory burden, gut microbiota composition, and suboptimal exercise protocol design. This review synthesizes mechanistic evidence linking meta-inflammation, exercise, and IR, and proposes a precision exercise medicine framework integrating multi-omics phenotyping (genomics, metabolomics, and microbiome profiling) with data-driven clinical decision-support tools. This approach aims to translate mechanistic insights into individualized therapeutic strategies for the long-term management of T2DM.},
}

Humans
*Diabetes Mellitus, Type 2/metabolism/therapy/immunology
*Insulin Resistance
*Inflammation/metabolism/therapy
*Exercise
Animals
Precision Medicine
*Exercise Therapy/methods

@article {pmid42609812,
year = {2026},
author = {Lu, YT and Lee, CY and Wang, SH and Hsin, CH and Li, YX and Lu, YC and Yang, SF and Chen, YY and Chang, TH},
title = {Microbiota and Mycobiota Dysbiosis in Sinonasal Fungus Ball: A Paired Lesional and Contralateral Analysis.},
journal = {Laryngoscope investigative otolaryngology},
volume = {11},
number = {4},
pages = {e70534},
pmid = {42609812},
issn = {2378-8038},
abstract = {OBJECTIVES: Fungus ball (FB) is a unilateral form of fungal rhinosinusitis, but it remains unclear whether associated microbial dysbiosis is restricted to the lesional sinus or extends across the sinonasal cavity. This study aimed to determine whether bacterial and fungal dysbiosis in maxillary sinus FB is spatially localized by comparing paired lesional and contralateral-normal sites within the same individuals.

METHODS: This prospective paired-sample study enrolled 14 adults with surgically confirmed unilateral maxillary sinus FB at a tertiary referral center. Middle-meatal swabs were obtained from lesional and contralateral-normal sides during endoscopic sinus surgery. Bacterial and fungal communities were profiled using 16S rRNA gene and internal transcribed spacer (ITS) sequencing. Alpha and beta diversity, taxonomic composition, predicted functional pathways, and bacterial-fungal co-occurrence networks were analyzed.

RESULTS: Lesional sinuses showed significantly reduced bacterial alpha diversity compared with contralateral-normal sides (Wilcoxon p < 0.001) and distinct bacterial beta diversity (PERMANOVA p = 0.003). Fungal beta diversity also differed between sites (p = 0.001), whereas fungal alpha diversity was preserved. Lesional communities showed enrichment of anaerobic and pathobiont taxa, including Haemophilus, Enterococcus, and Pseudomonas, with reduced relative abundance of Staphylococcus. Although Aspergillus abundance was similar bilaterally, network analysis suggested altered Aspergillus-associated connectivity in lesional samples, consistent with a shift in inferred interaction topology rather than increased Aspergillus abundance. Predicted functional analysis further suggested pathway differences that may reflect altered local metabolic conditions.

CONCLUSION: In this cohort, microbial dysbiosis in maxillary sinus FB appeared to be spatially localized, with patterns suggestive of anaerobe enrichment and ecological reorganization centered on Aspergillus. These findings are compatible with the standard surgical emphasis on fungal mass removal and restoration of sinus drainage/aeration, but the microbiome-based relevance of aeration requires confirmation in larger studies.

LEVEL OF EVIDENCE: 3.},
}

@article {pmid42609856,
year = {2026},
author = {Salmona, M and Benattia, A and Meignin, V and Marie Ferré, V and Jouenne, F and Lorillon, G and Le Goff, J and Mourah, S and Tazi, A},
title = {No detectable infectious agents in Langerhans cell histiocytosis with lung involvement.},
journal = {ERJ open research},
volume = {12},
number = {4},
pages = {},
pmid = {42609856},
issn = {2312-0541},
abstract = {Shotgun metagenomics of pulmonary and extrapulmonary Langerhans cell histiocytosis lesions revealed no infectious pathogens and no microbiome differences from control lung tissue, which does not support an infectious role in disease pathogenesis https://bit.ly/4liJHfO.},
}

@article {pmid42609904,
year = {2026},
author = {Wu, Z and Xu, T and Zhao, L and Zhou, Y and Yu, T},
title = {Hyperuricemia is associated with periodontal ligature dysbiosis in a murine model of experimental periodontitis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2716991},
pmid = {42609904},
issn = {2000-2297},
abstract = {BACKGROUND: Hyperuricemia (Hu) is a systemic metabolic disorder implicated in inflammatory conditions and has been epidemiologically associated with an increased prevalence of periodontitis. However, whether Hu is associated with periodontal microbial dysbiosis in experimental periodontitis remains unclear.

OBJECTIVE: This exploratory pilot study aimed to investigate whether Hu is associated with periodontal dysbiosis in experimental periodontitis by characterizing the diversity, taxonomic composition, and predicted functional potential of ligature-associated microbiota using 16S rRNA sequencing.

METHODS: A mouse model combining potassium oxonate-induced Hu with ligature-induced periodontitis was established. Male C57BL/6 mice were allocated to normouricemia with periodontitis (NuP), hyperuricemia with periodontitis (HuP), and allopurinol-treated hyperuricemia with periodontitis (HuP+Allo) groups. Ligature-associated microbiota were analyzed by 16S rRNA gene sequencing. Correlations between microbial alterations and biochemical parameters were evaluated using redundancy analysis.

RESULTS: Hu significantly increased microbial diversity and evenness, as indicated by higher Shannon index (P = 0.007) and Shannoneven index (P = 0.002), but did not affect community richness. At the phylum level, Hu increased the Firmicutes/Bacteroidota ratio and Proteobacteria abundance while decreasing Bacteroidota and Actinobacteriota. At the genus level, Hu enriched potentially pathogenic taxa, including Streptococcus and Escherichia-Shigella. Allopurinol partially reversed these changes. Redundancy analysis revealed that microbial shifts were significantly correlated with serum uric acid (R[2]  = 0.711, P = 0.040) and creatinine (R[2]  = 0.695, P = 0.035). Functional prediction suggested that Hu was associated with higher predicted abundances of NOD-like receptor signalling and lower predicted abundance of IL-17 signalling pathways.

CONCLUSION: These exploratory findings suggest that Hu may be associated with dysbiotic remodeling of the periodontal ligature microbiota in experimental periodontitis, linking systemic metabolic disturbance with local microbial imbalance and inflammatory pathway alteration. These alterations were partially reversed by allopurinol and correlated with serum uric acid and creatinine, providing mechanistic insight into how Hu may aggravate periodontal tissue destruction.},
}

@article {pmid42610718,
year = {2026},
author = {Mohd Arshad, N and Kiraman, SK and Sufian, SA and Ahmad, HF},
title = {Draft genome sequence of Staphylococcus epidermidis strain UMP2601 isolated from environmental water.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0047926},
doi = {10.1128/mra.00479-26},
pmid = {42610718},
issn = {2576-098X},
abstract = {We report the draft genome sequence of Staphylococcus epidermidis strain UMP2601 (2,469,061 bp, GC content of 32.03%) isolated from an environmental water sample. The organism was cultured on nutrient agar under aerobic conditions.},
}

@article {pmid42610727,
year = {2026},
author = {Calderón, LL and Garzon, SAC},
title = {Identification of Differentially Abundant Microorganisms Associated with Sjögren's Syndrome: A 16S rRNA Sequencing Data Mining Approach.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag094},
pmid = {42610727},
issn = {1574-6968},
abstract = {Manifestations of Sjögren's syndrome (SS) considerably affect the quality of life. Owing to the multifactorial nature of the syndrome, some individuals present alterations in oral microbiota profiles. This study analysed the oral cavity microbiota profiles of 242 samples -168 from pSS group and 74 from control group- using metabarcoding technique based on sequencing of 16S rRNA gene. Data processing, amplicon sequence variants, and taxonomic assignment were performed using DADA2. Statistical and microbial diversity analyses were performed using phyloseq in R. Alpha and beta diversity metrics were evaluated, as well as the identification of enriched taxa using Linear discriminant analysis Effect Size (LEfSe) analysis. Results revealed no significant differences in the composition and structure of the microbiota between groups. However, differential abundance analysis allowed the identification of 27 microbial taxa, including species Actinomyces dentocariosa; genera Streptococcus, Leptotrichia, Veillonella, Fusobacterium, and Alloprevotella; and phyla Actinobacteriota and Fusobacteriota, in pSS group. Although no direct associations have yet been established between oral microbiota and SS, some of the identified genera have been documented to possess pathogenic factors that induce immune responses. Accordingly, this study lays the groundwork for future analyses of oral microbiota profiles in SS to identify potential microbial biomarkers of disease.},
}

@article {pmid42610782,
year = {2026},
author = {Agrawal, K and Kumar, N and Singh, A and Lu, C and Leung, MF},
title = {Artificial intelligence in food and nutrition science: a paradigm-centric review of computational frameworks and system-level integration.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo02990f},
pmid = {42610782},
issn = {2042-650X},
abstract = {Precision nutrition on a global scale necessitates an understanding of food not as static collections of so-called macronutrients but rather as dynamic and heterogeneous biochemical matrices. These complex non-linear interactions between food composition, gastrointestinal digestion and the human microbiome are difficult to capture using traditional empirical experimental methods. This review articulates a paradigm-based framework that reconceptualizes artificial intelligence (AI) in food and function science, from generic industrial applications to the computational modeling of physiological and biochemical phenomena. We specifically explore critical integrations of Physics-Informed Neural Networks (PINNs) with established data-driven methods to circumnavigate the epistemological limitations of entirely data-driven models within standardized frameworks (e.g., INFOGEST), assessing their use in simulating gastrointestinal mass transfer and dissolution kinetics to achieve predictive accuracies up to R[2] = 0.91 in complex protein digestibility matrices. Finally, we demonstrate how Microbial Community-scale Metabolic Modeling (MCMM) and multimodal machine learning mechanistically couple specific dietary inputs with unique microbiome responses, yielding up to 95% diagnostic accuracy in differentiating diet-responsive metabolic states and individualized postprandial glycemic outcomes. We also emphasize the importance of Graph Neural Networks (GNNs) in rationally designing bioactive peptides, and Artificial Neural Networks (ANNs) for the optimization of microencapsulation, which have demonstrated the capacity to reduce physical experimental formulation trials by over 60%. Furthermore, we evaluate AI's emerging role in precision aquaculture, where computer vision and predictive models yield 94-99% accuracy in disease detection and reduce feed conversion ratios by up to 11%. This review discusses the need to connect computational intelligence and food function, delineating a path toward autonomous metabolically-aware food ecosystems whilst identifying important research gaps in mechanistic interpretability, data standardization, and cultural bias underpinning precision nutrition.},
}

@article {pmid42610803,
year = {2026},
author = {Lin, H and Deng, X and Yang, Y and Zhang, R and Wang, YD and Chen, WD},
title = {Amino acid metabolic reprogramming by gut microbiota: a novel metabolic checkpoint in the tumor microenvironment.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2719116},
doi = {10.1080/19490976.2026.2719116},
pmid = {42610803},
issn = {1949-0984},
mesh = {Humans ; *Amino Acids/metabolism ; *Tumor Microenvironment ; Metabolic Reprogramming ; *Gastrointestinal Microbiome/physiology ; *Neoplasms/metabolism/microbiology ; Animals ; Dysbiosis/microbiology ; },
abstract = {The gut microbiota plays a crucial role in human health, significantly influencing various physiological functions such as amino acid metabolism, which is essential for maintaining homeostasis and preventing disease. Recent progress in gut microbiota research has highlighted the intricate relationships between gut microbial communities and host amino acid metabolism, particularly in the context of cancer. This review focuses on consolidating the latest advances regarding how gut microbiota-mediated amino acid metabolism contributes to cancer development and progression. While dysbiosis has been implicated in various diseases, such as metabolic disorders, autoimmune conditions, and neurodegenerative diseases, this review specifically examines the evidence linking gut microbiota and amino acid metabolism to cancer. Current studies suggest that alterations in gut microbial composition can lead to imbalances in amino acid availability and metabolism, thereby influencing systemic inflammation, oxidative stress, and immune responses that may promote tumorigenesis. Despite these insights, significant challenges remain, including identifying specific microbial strains, deciphering their metabolic pathways, and understanding their complex interactions with host factors in cancer progression. This review aims to summarize recent preclinical and clinical investigations elucidating the mechanisms linking the gut microbiota, amino acid metabolism, and cancer, and to evaluate potential therapeutic strategies targeting the gut microbiome to modulate amino acid metabolism and improve cancer treatment outcomes. By highlighting the gut microbiota as a promising target for innovative oncological therapies, this review provides insights into microbiome-based interventions targeting amino acid-related pathways in cancer.},
}

Humans
*Amino Acids/metabolism
*Tumor Microenvironment
Metabolic Reprogramming
*Gastrointestinal Microbiome/physiology
*Neoplasms/metabolism/microbiology
Animals
Dysbiosis/microbiology

@article {pmid42611027,
year = {2026},
author = {Luo, Y and Feng, A and Li, Y and Ren, Y and Ma, T and Jiang, Y},
title = {High-Throughput Sequencing-Assisted Microbial Profiling and Koch's Postulates Validation Identify Fusarium pernambucanum as the Causal Agent of Fruit Rot in Idesia polycarpa.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-09-25-0311-R},
pmid = {42611027},
issn = {0031-949X},
abstract = {Idesia polycarpa is an economically important tree species valued for urban greening and oil production owing to its oil-rich fruits and high levels of unsaturated fatty acids. The increasing incidence of fruit diseases has become a major constraint on its cultivation; however, the microbial dynamics during disease progression and the primary causal agent remain unclear. In this study, diseased fruits were collected from Sichuan Province, China, a region with frequent disease outbreaks, and categorized into five disease stages based on symptom severity, including initial infection (S1), advancing infection (S2), severe infection (S3), blackening (S4), and necrosis (S5). High-throughput sequencing (HTS) of bacterial 16S rRNA gene and fungal ITS regions from S1, S3, and S5 samples revealed limited variation in bacterial communities across disease stages, whereas fungal communities exhibited pronounced compositional shifts, including a progressive enrichment of Fusarium spp., a well-known group of plant pathogens. Subsequent fungal isolation, morphological characterization, molecular phylogenetics analyses, and pathogenicity assays identified F. pernambucanum as the causal agent of fruit rot. This study elucidates HTS-based microbial profiling during fruit rot, and the results guided pathogen identification based on Koch's postulates, providing insights into disease diagnosis and management in I. polycarpa.},
}

@article {pmid42611050,
year = {2026},
author = {Liu, Y and Wang, L and Cai, B},
title = {Recent advances in the defense mechanisms of arbuscular mycorrhizal fungi in antibiotic-contaminated soil ecosystems.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42611050},
issn = {1432-072X},
support = {NO. LH2023C088//the Natural Science Foundation of Heilongjiang Province of China/ ; NO. HST2022TR002//the Scientific Research Project on Ecological Environmental Protection in Heilongjiang Province/ ; },
mesh = {*Mycorrhizae/drug effects/physiology/growth & development/metabolism/genetics ; *Soil Microbiology ; *Anti-Bacterial Agents/pharmacology/metabolism ; *Soil Pollutants/metabolism ; Ecosystem ; Symbiosis ; Soil/chemistry ; Plants/microbiology ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) are important soil symbionts that support plant nutrient acquisition, stress tolerance, and soil ecosystem stability. The increasing accumulation of antibiotic residues in agricultural soils may inhibit AMF spore germination, hyphal development, and root colonization, thereby weakening mycorrhizal functions and plant-soil feedback. This review summarizes recent advances in AMF responses to antibiotic stress in soil ecosystems and proposes a five-layer defense framework: external interfacial barriers, intracellular metabolic detoxification, antioxidant defense system activation, molecular regulation, and symbiont-level cooperative defense. We emphasize that the evidentiary strength supporting these mechanisms varies across different validation levels. Some responses, such as changes in colonization, hyphal growth, antioxidant enzyme activity, and rhizosphere or hyphosphere microbial communities, have been experimentally observed in antibiotic-contaminated systems. By contrast, several intracellular detoxification and regulatory processes, including pathways mediated by cytochrome P450s (P450s), glutathione S-transferases (GSTs), UDP-glycosyltransferases (UGTs), and transporters, remain primarily inferred from AMF genomic resources, host-symbiont studies, and fungal or plant xenobiotic metabolism studies. Current research is still limited by short-term experimental designs, a strong focus on tetracycline, insufficient molecular validation, and a lack of predictive models. Future studies should integrate multi-omics, single-cell approaches, and artificial intelligence-assisted modelling to identify key functional genes, distinguish direct AMF responses from host- or microbiome-mediated effects, and improve the application of AMF in sustainable remediation of antibiotic-contaminated soils.},
}

*Mycorrhizae/drug effects/physiology/growth & development/metabolism/genetics
*Soil Microbiology
*Anti-Bacterial Agents/pharmacology/metabolism
*Soil Pollutants/metabolism
Ecosystem
Symbiosis
Soil/chemistry
Plants/microbiology

@article {pmid42611081,
year = {2026},
author = {Alahmed, SGK and Janakiev, T and Jović, M and Kruščić, K and Nikolić, M and Stanković, D and Al-Mamoori, AMJ and Dimkić, I},
title = {Diversity and functional traits of indigenous microbiome in Hilla agricultural soils: implications for biocontrol and bioremediation.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42611081},
issn = {1573-0972},
support = {451-03-33/2026-03/200178//Ministry of Science, Technological Development and Innovation of Serbia/ ; TERRA_MADRE 7455//Program PRISMA of the Science Fund of the Republic of Serbia/ ; },
mesh = {*Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Biodegradation, Environmental ; *Microbiota/genetics ; *Archaea/classification/genetics/isolation & purification ; Agriculture ; Soil/chemistry ; Phylogeny ; Biodiversity ; Metals/analysis ; DNA, Bacterial/genetics ; Soil Pollutants/analysis ; },
abstract = {Indigenous bacterial and archaeal communities in agricultural soils were analyzed to provide a basis for biocontrol and bioremediation solutions to be reintroduced in affected areas. Samples from five agricultural soils in Hilla province, Iraq, were analyzed by inductively coupled plasma mass spectrometry for total and bioavailable metals. Bacterial community was identified using 16S rRNA metabarcoding and a cultivable approach. Plant growth-promoting, metal tolerance, and antifungal activities were evaluated on the established culture collection. Chemical analysis revealed elevated levels of nickel (Ni) and lithium (Li) among microelements, and sodium (Na) and phosphorus (P) among analyzed macroelements. 16S rRNA gene metabarcoding analysis showed significant differences in the composition and structure of bacterial and archaeal communities among samples. The most represented genera in the total bacterial community were Bacillus, Peribacillus, Acinetobacter, and Pseudomonas. The most abundant archaeal genera were Hallorussus, Halolamina, and Halarchaeum, detected only at the R5 site. Redundancy analysis indicated potential associations of taxa with micro- and macroelements, such as the positive correlation of Halomicrobium, Halorussus, Halomicrobiaceae, Natronomonas, Halolamina, Aliifodinibius, and Trabulsiella with Na and Fe. Based on the RDA, a negative correlation between Longimicrobiaceae and zinc (Zn) was detected for the first time, to the best of our knowledge. The culturable community was dominated by Bacillus, Mesobacillus, Arthrobacter, and Exiguobacterium. Among all isolates, Bacillus cabrialesii/inaquosorum R2-NA-6, Bacillus licheniformis R4-NA-3, Paenibacillus barcinonensis/taichungensis R4-TSA-5, Bacillus salacetis R4-NA-5, and Peribacillus simplex R2-TSA-2 showed in vitro the most promising combination of PGP traits, metal tolerance, and antifungal activity against most phytopathogenic fungi. The combination of beneficial traits makes these isolates excellent candidates for the further testing and potential development of multifunctional bioinoculants aimed at restoring degraded soils and reducing chemical pesticide use.},
}

*Soil Microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Biodegradation, Environmental
*Microbiota/genetics
*Archaea/classification/genetics/isolation & purification
Agriculture
Soil/chemistry
Phylogeny
Biodiversity
Metals/analysis
DNA, Bacterial/genetics
Soil Pollutants/analysis

@article {pmid42611121,
year = {2026},
author = {Tomar, SS and Khairnar, K},
title = {SARS‑CoV‑2 Associated Shifts in the Upper Respiratory Tract Mycobiome in Non-hospitalized Cases.},
journal = {Mycopathologia},
volume = {191},
number = {5},
pages = {},
pmid = {42611121},
issn = {1573-0832},
support = {OLP-57//CSIR-NEERI/ ; },
mesh = {Humans ; *COVID-19/microbiology ; SARS-CoV-2 ; *Mycobiome ; Male ; *Fungi/classification/genetics/isolation & purification ; Female ; India ; Metagenomics ; Adult ; Middle Aged ; *Respiratory System/microbiology ; },
abstract = {SARS‑CoV‑2 infection is associated with marked changes of the upper respiratory tract mycobiome. URT mycobiome Changes in non-hospitalized patients however, remains poorly defined. We performed shotgun metagenomic sequencing of 95 upper respiratory tract swab samples from 48 symptomatic SARS‑CoV‑2-positive individuals and 47 healthy controls from central India. Fungal diversity and community structure were compared using alpha- and beta-diversity analyses, while differential taxa were identified using prevalence-based testing and a Directional Significance Score (DSS). SARS‑CoV‑2-positive samples showed significantly higher fungal alpha diversity than controls, with increased Shannon diversity (p = 0.000319) and Simpson diversity (p = 0.017). Beta-diversity analysis showed significant separation between groups for both Bray-Curtis and Jaccard distances (PERMANOVA p = 0.001), with significant dispersion effects as well (PERMDISP p = 0.001). DSS analysis showed certain fungal taxa associated with the SARS-CoV-2 group, including enrichment of Candida orthopsilosis, Malassezia furfur, Aspergillus glaucus, Aspergillus terreus, and Aspergillus niger, while Malassezia arunalokei, Aspergillus chevalieri, and Aspergillus sydowii were enriched in controls. These findings indicate that SARS‑CoV‑2 infection is associated with URT mycobiome dysbiosis and enrichment of clinically relevant opportunistic fungi in community cases.},
}

Humans
*COVID-19/microbiology
SARS-CoV-2
*Mycobiome
Male
*Fungi/classification/genetics/isolation & purification
Female
India
Metagenomics
Adult
Middle Aged
*Respiratory System/microbiology

@article {pmid42611156,
year = {2026},
author = {Husain, KH and Khan, H and Thakkar, B and Bungish, M and Vaziri, H},
title = {Chronotherapy in Inflammatory Bowel Disease: Biological Rationale, Human Evidence, and a Clinical Implementation Framework.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42611156},
issn = {1573-2568},
abstract = {Inflammatory bowel disease (IBD) is a chronic condition driven by a dysregulated immune response to the gut microbiome in genetically susceptible individuals. This process may be influenced by the circadian rhythm, the body's internal 24-h clock that coordinates physiology with the day-night cycle. Disruption of this rhythm, whether from behavior or intrinsic dysfunction, can disturb intestinal homeostasis and promote inflammation. Chronotherapy applies this concept clinically by aligning medical treatment with circadian timing to optimize efficacy and reduce adverse effects. There is growing evidence suggesting the importance of this approach for drug metabolism, immune activity, and symptom patterns, offering a new dimension of personalization beyond medication choice alone. This review summarizes the biological links between circadian regulation and intestinal inflammation, highlights emerging human data supporting time-based treatment strategies, and proposes a practical framework for integrating chronotherapy into routine IBD management. By considering when a therapy is delivered in addition to what therapy should be used, clinicians may enhance treatment response, limit toxicity, and improve overall disease control.},
}

@article {pmid42611234,
year = {2026},
author = {Zhu, Y and Deng, X and Wang, Q and Song, H and Wang, L and Zhou, D and Gao, C and Gardea-Torresdey, JL and White, JC and Zhao, L},
title = {SiO2@CuO Nanozyme Reinforces Plant-Microbiome Synergies for Simultaneous Yield Enhancement, Nutritional Fortification, and a Beneficial Soil Legacy.},
journal = {ACS nano},
volume = {20},
number = {32},
pages = {22762-22777},
doi = {10.1021/acsnano.6c06987},
pmid = {42611234},
issn = {1936-086X},
support = {2026ZD1211704//Jing-Jin-Ji Regional Integrated Environmental Improvement-National Science and Technology Major Project/ ; CX (23)3015//Independent Innovation Fund for Agricultural Science and Technology in Jiangsu Province/ ; },
mesh = {*Microbiota/drug effects ; *Copper/chemistry/pharmacology ; *Silicon Dioxide/chemistry/pharmacology ; Soil Microbiology ; Soil/chemistry ; *Zea mays/growth & development/microbiology/drug effects/metabolism ; Rhizosphere ; Seeds ; },
abstract = {Plant associated microbes play pivotal role in promoting host fitness and health. However, modern agricultural practices, such as agrochemicals use and domestication are eroding plant-microbe partnership. Here, we show that nanoenabled seed priming strengthens plant-microbe interactions, enhancing the plant holobiont performance. We found that SiO2@CuO nanozymes (NZs) with peroxidase (POD)-like activities, as seed priming agent, initiate earlier and stronger seed respiration and boost exudates release (sugars, amino acids, and fatty acids), creating a nutrient-rich and transiently hypoxic spermosphere microenvironment. Field trials revealed that by day 40, rhizosphere microbiome diversity increased, with enrichment of functional taxa involved in carbon and nitrogen metabolism, as determined by 16S rRNA and metagenomic sequencing. Throughout the growing season, above-ground tissues in the nanopriming group consistently outperformed the hydropriming control in photosynthetic pigment content and plant height. At harvest, without additional fertilizers or other inputs, nanopriming increased maize yield by 8.1% and improved kernel nutritional quality: starch (21.0%), protein (24.5%), and iron (24.2%). Soil nutrient availability (N, P, K, Ca) and cation exchange capacity also increased, indicating the improved soil quality. Notably, the soil from nanopriming group confers the subsequent maize crop with better drought tolerance and enhanced P uptake capacity, compared to the soil from hydropriming group, indicating beneficial legacy effect. This study demonstrates that a simple seed nanopriming can steer a positive feedback loop between plant and microbe, cascading into multifaceted holobiont benefits. This offers a sustainable strategy to harness plant microbiomes and promote sustainable and climate resilient agriculture.},
}

*Microbiota/drug effects
*Copper/chemistry/pharmacology
*Silicon Dioxide/chemistry/pharmacology
Soil Microbiology
Soil/chemistry
*Zea mays/growth & development/microbiology/drug effects/metabolism
Rhizosphere
Seeds

@article {pmid42611342,
year = {2026},
author = {Li, Y and Ye, Y and Yao, Z and Li, Y and Gao, P and Sun, Z and Wei, Y and Zhou, K and Guo, B and Zhao, Y and Lai, Q},
title = {Integrated Physiological, Transcriptomic, and Gut Microbial Responses of Chinese Mitten Crab (Eriocheir sinensis) to Acute Salinity Stress.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {28},
number = {5},
pages = {},
pmid = {42611342},
issn = {1436-2236},
support = {2025XT0206//the Central Public-interest Scientific Institution Basal Research Fund CAFS/ ; XJRC-2025-ZZB-ZDXQ-011//the Xinjiang Major Demand Talent Support Program Project/ ; },
mesh = {Animals ; *Brachyura/microbiology/physiology/genetics ; *Salt Stress ; *Transcriptome ; *Gastrointestinal Microbiome ; Gills/metabolism/enzymology ; Salinity ; Hemolymph ; Ammonia/metabolism ; Sodium-Potassium-Exchanging ATPase/metabolism ; Aquaculture ; },
abstract = {The development of aquaculture in saline waters provides a potential strategy for expanding aquatic food production under conditions of freshwater scarcity. However, the specific mechanisms by which economically valuable crustaceans respond to acute salinity stress remain unclear. Here, we investigated the survival and physiological responses of Chinese mitten crabs (Eriocheir sinensis) following acute exposure to a range of salinity levels (0.2‰, 5‰, 20‰, 25‰, and 30‰). After 48 h of exposure, the survival rates were 100%, 100%, 80%, 56.7%, and 26.7% in the 0.2‰, 5‰, 20‰, 25‰, and 30‰ groups, respectively, with survival decreasing significantly at salinities of 20‰ and above. Acute salinity exposure altered gill enzyme activities and hemolymph physiological parameters, with reduced Na[+]/K[+]-ATPase activity and increased carbonic anhydrase activity, osmolality, and ammonia content under the higher-salinity treatments. To characterize the molecular and microbial responses to extreme salinity exposure, gill transcriptomic and gut microbiome analyses were conducted in the 0.2‰ control group and the 30‰ treatment group. Transcriptomic analysis identified differential expression patterns associated with ion transmembrane transport, acid-base regulation, calcium homeostasis, and chitin-related processes. Gut microbiome analysis showed marked changes in microbial community structure, including the enrichment of Candidatus Hepatoplasma, Marinifilum, and Sulfitobacter and the reduced relative abundance of Candidatus Bacilloplasma and Shewanella in the 30‰ group. Tax4Fun analysis predicted significant differences in several microbial functional categories related to metabolism. These results indicate that acute high-salinity stress disrupts ion regulation and acid-base balance, inhibits key ion-transport enzymes, and alters the intestinal microbial community, accompanied by changes in predicted microbial phenotypes and functional profiles. This multi-omics analysis provides physiological and microbial insights into the acute response of E. sinensis to elevated salinity and may inform the culture and health management of this economically important species in saline waters.},
}

Animals
*Brachyura/microbiology/physiology/genetics
*Salt Stress
*Transcriptome
*Gastrointestinal Microbiome
Gills/metabolism/enzymology
Salinity
Hemolymph
Ammonia/metabolism
Sodium-Potassium-Exchanging ATPase/metabolism
Aquaculture

@article {pmid42611344,
year = {2026},
author = {Almeida, KA and de Fátima Pereira, P and Guimarães, RA and Afridi, MS and da Silva, JCP and Andrade, B and Quensen, J and Tiedje, J and de Souza, JT and Talamini, V and de Arruda Carvalho, E and de Medeiros, FHV},
title = {Rhizosphere microbiome and calcium synergy drive suppression of Ceratocystis paradoxa in tropical coconut soils.},
journal = {Archives of microbiology},
volume = {208},
number = {11},
pages = {},
pmid = {42611344},
issn = {1432-072X},
mesh = {*Soil Microbiology ; *Calcium/pharmacology/metabolism ; Soil/chemistry ; *Microbiota ; *Rhizosphere ; Hydrogen-Ion Concentration ; *Cocos/microbiology ; *Bacteria/classification/genetics/isolation & purification/drug effects ; Plant Diseases/microbiology/prevention & control ; Calcium Carbonate/pharmacology ; Tropical Climate ; *Cercozoa ; },
abstract = {Ceratocystis paradoxa is a polyphagous, soil-borne pathogen that threatens various crops worldwide. This study evaluated soil suppressiveness against C. paradoxa and identified key biotic and abiotic factors involved. Suppressiveness was assessed using banana peel baits, followed by comparative analysis of microbial communities and soil physicochemical properties in five suppressive and five conducive soils. Suppressive soils exhibited higher culturable bacterial populations and enrichment of Actinobacteria, Proteobacteria, Firmicutes, and Acidobacteria, particularly Solirubrobacter, Actinoplanes, and Conexibacter. Favorable physicochemical traits included higher pH, calcium content, cation exchange capacity, base saturation, and sand content. Calcium carbonate amendments enhanced suppressiveness, particularly at pH 7.0. Transferring the microbiota from suppressive soils to conducive subsoils, combined with calcium carbonate, also induced suppressiveness. These results highlight the synergistic role of microbial communities and soil chemistry, particularly pH and calcium in pathogen suppression. Calcium promoted microbial activity and stabilized pH, contributing to reduced disease incidence. This integrated strategy offers a promising avenue for sustainable management of C. paradoxa in tropical agriculture through microbiome manipulation and soil amendments.},
}

*Soil Microbiology
*Calcium/pharmacology/metabolism
Soil/chemistry
*Microbiota
*Rhizosphere
Hydrogen-Ion Concentration
*Cocos/microbiology
*Bacteria/classification/genetics/isolation & purification/drug effects
Plant Diseases/microbiology/prevention & control
Calcium Carbonate/pharmacology
Tropical Climate
*Cercozoa

@article {pmid42611469,
year = {2026},
author = {Xu, H and Liu, Q and Duan, Y and Zheng, Y and Hua, M and Zhang, W and Pan, B},
title = {Electroactive Materials for Anaerobic Bioenergy and Bioproduct Recovery from Wastewater: Decoding Tripartite Interfaces in Microbial Electron Transfer.},
journal = {Environmental science & technology},
volume = {60},
number = {32},
pages = {22097-22118},
doi = {10.1021/acs.est.6c06562},
pmid = {42611469},
issn = {1520-5851},
support = {22406086//National Natural Science Foundation of China/ ; 2021YFA1201703//National Key Research and Development Program of China/ ; 021114380230//AI & AI for Science Project of Nanjing University/ ; 2024ZB691//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {*Wastewater ; Electron Transport ; Anaerobiosis ; },
abstract = {Anaerobic wastewater valorization via methanogenesis (bioenergy) and chain elongation (bioproducts) is central to the circular water economy, yet it is fundamentally hindered by thermodynamic constraints and sluggish syntrophic kinetics. While electroactive materials (EAMs) are increasingly deployed to modulate microbial electron transfer (MET), the current understanding remains fragmented and largely phenomenological. This Critical Review establishes a unified multiscale mechanistic framework centered on tripartite interfaces. At the biotic-biotic interface, we demonstrate how EAMs alleviate thermodynamic bottlenecks to steer bidirectional syntrophic fluxes, challenging the oversimplified causal view of direct interspecies electron transfer. At the material-biotic interface, we reframe EAMs from static bioconductors to dynamic mediators, analyzing how their intrinsic solid-state physics and surface redox chemistry govern interfacial charge kinetics. At the intraextracellular interface, we reveal how EAMs regulate transmembrane electron fluxes to reprogram central carbon routing, imposing a biosynthetic trade-off where EAMs replace biological conduits to conserve cellular energy. Critical knowledge gaps are further exposed, spanning biotic/abiotic conductivity confounding, taxonomic overestimation of Geobacter, and material biogeochemical decay. Finally, a roadmap is provided that advocates rational design of self-healing EAMs, synthetic electrogenetic microbiome engineering, artificial intelligence-enabled reactor intensification, and life-cycle sustainability assessments. This Review conceptualizes EAMs as active, adaptive physicochemical regulators, laying the groundwork for programmable material-microbe biohybrids.},
}

*Wastewater
Electron Transport
Anaerobiosis

@article {pmid42611567,
year = {2026},
author = {Jesaveluk, B and Ellenberg, P and Hearps, AC and Tachedjian, G},
title = {The Impact of the Vaginal Microbiome and Microbial Metabolites on HIV Transmission at the Female Reproductive Tract Epithelial Barrier.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {96},
number = {2},
pages = {e70312},
doi = {10.1111/aji.70312},
pmid = {42611567},
issn = {1600-0897},
support = {GNT1164982//National Health and Medical Research Council/ ; GNT1117748//NHMRC Senior Research Fellowship/ ; //Australian Government Research Training Program Scholarship/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology/virology/immunology ; *HIV Infections/transmission/immunology/microbiology ; *Microbiota/immunology ; *Lactobacillus ; *Vaginosis, Bacterial/microbiology/immunology ; Epithelial Cells/virology ; *HIV-1/physiology ; },
abstract = {Despite major advances in biomedical HIV prevention strategies, almost 50% of the 1.3 million new HIV infections in 2024 occurred in women and girls through heterosexual transmission. Choice in HIV prevention modalities is needed throughout a women's lifespan to increase pre-exposure prophylaxis uptake; however, there is a paucity of topical, on-demand options. To establish HIV infection, the virus translocates across the epithelial barrier of the upper and lower female reproductive tract to infect CD4 + HIV target cells in the submucosa. The vaginal microbiome modulates this process. Women colonised with an optimal Lactobacillus-dominated vaginal microbiota are more protected against acquiring HIV compared to women with a non-optimal vaginal microbiota including bacterial vaginosis (BV), characterised by an overgrowth of diverse anaerobes and a paucity of beneficial lactobacilli. Optimal Lactobacillus spp. produce ∼1% lactic acid, which in women with a Lactobacillus-dominant microbiota acidifies the vaginal pH to less than 4.5, inactivates HIV, exerts antimicrobial effects against BV-associated bacteria, directly inhibits inflammatory responses elicited from cervicovaginal epithelial cells and blocks HIV translocation in vitro. Beneficial properties of optimal vaginal lactobacilli and/or lactic acid can potentially be exploited in vaginal delivery strategies to help prevent vaginal dysbiosis and its adverse sexual and reproductive outcomes including HIV.},
}

Female
Humans
*Vagina/microbiology/virology/immunology
*HIV Infections/transmission/immunology/microbiology
*Microbiota/immunology
*Lactobacillus
*Vaginosis, Bacterial/microbiology/immunology
Epithelial Cells/virology
*HIV-1/physiology

@article {pmid42611801,
year = {2026},
author = {Jang, JY and Lee, J and Yun, H and Yang, J},
title = {A Tri-Source Microbiome Dataset from Human Sleep Environments: Saliva, Pillow Dust, and Bedroom Air.},
journal = {Lifestyle genomics},
volume = {},
number = {},
pages = {1},
doi = {10.1159/lfg/adlag001},
pmid = {42611801},
issn = {2504-3188},
abstract = {Despite the established importance of the human microbiome in health, the integrated microbial exposures occurring within the sleep environment remain poorly understood. Sleep represents a critical period of prolonged exposure to indoor microbial reservoirs, yet no study has simultaneously examined the connectivity between environmental sources and the human oral microbiome. We present a novel, tri-source microbiome dataset characterizing microbial communities from co-located saliva, pillow dust, and bedroom air collected from healthy participants in real-world sleep environments. Samples were collected under standardized protocols and analyzed using 16S rRNA gene amplicon sequencing (V3-V4 region). Rigorous quality control and bioinformatic processing were applied to generate high-resolution amplicon sequence variants. Alpha diversity analysis revealed that pillow dust serves as the most diverse and stable microbial reservoir, exhibiting significantly higher species richness and phylogenetic diversity than saliva or air (p < 0.05). Beta diversity analysis showed distinct clustering by sample type, with indoor air and pillow dust exhibiting closer microbial similarity to each other than to saliva. Notably, significant genus-level correlations were identified between air and pillow dust (e.g., Brevitalea, Gardnerella) and between pillow dust and saliva (e.g., Actinomyces, Bifidobacterium), suggesting potential microbial exchange through gravitational settling and physical contact. This tri-source dataset provides a unique resource for investigating host-environment microbial interactions during rest. Our findings highlight the sleep environment as a significant exposome factor that may influence oral microbiome dynamics, offering new avenues for research into respiratory health, built environment science, and human exposome studies.},
}

@article {pmid42611994,
year = {2026},
author = {Birla, P and Yang, L and Shan, W and Minamisawa, S and Dhaygude, O and Manoj, H and Lee, AJ and Ferri, J and Zheng, Y and Northcutt, A and Fan, H and Beauregard, H and Zeng, Z and Smith, KN and Shaikh, FY and Sears, CL and Pardoll, DM and Housseau, F},
title = {Select intratumoral riboflavin-auxotrophic Enterococcus species enhance cell surface MR1 expression and MAIT TCR activation in lung cancer.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {34},
pages = {e2617943123},
doi = {10.1073/pnas.2617943123},
pmid = {42611994},
issn = {1091-6490},
support = {Commonwealth//Commonwealth Foundation for Cancer Research Foundation/ ; BKI//JHU | Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University | Bloomberg ~ Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University (Bloomberg ~ Kimmel Institute for Cancer Immunotherapy)/ ; },
mesh = {Humans ; *Mucosal-Associated Invariant T Cells/immunology/metabolism ; *Lung Neoplasms/immunology/microbiology/metabolism/genetics ; *Enterococcus/metabolism/immunology ; *Receptors, Antigen, T-Cell/metabolism/immunology ; *Histocompatibility Antigens Class I/metabolism/genetics/immunology ; *Minor Histocompatibility Antigens/metabolism/genetics/immunology ; *Riboflavin/metabolism ; Lymphocyte Activation/immunology ; *Carcinoma, Non-Small-Cell Lung/immunology/microbiology ; Ribitol/analogs & derivatives ; Uracil/analogs & derivatives ; },
abstract = {Mucosal-associated invariant T (MAIT) cells are innate-like T cells capable of MR1-dependent immune surveillance, but how intratumoral bacteria modulate MR1 expression in human lung tumors remains unclear. We studied intratumoral MAIT cells from paired single-cell RNA and TCR sequencing datasets of tumor-infiltrating CD3 T cells isolated from non-small cell lung cancer tumors in patients receiving neoadjuvant PD-1 blockade therapy. MAIT cells were subclustered to identify conventional MAIT-associated TCR clonotypes, which were then used to examine how bacterial exposure impacts cell-surface MR1 expression and downstream MAIT TCR activation. We found that select intratumoral Enterococcus species (spp.) did not directly activate MAIT cells but enhanced MR1-dependent MAIT activation in the presence of exogenous 5-OP-RU by increasing cell-surface MR1 expression on antigen-presenting cells including dendritic cells, B cells, and mononuclear phagocytes. This increase in MR1 cell surface expression is modulated through a posttranscriptional mechanism consistent with altered intracellular processing and trafficking of MR1. These findings reveal a role for tumor-associated bacteria in modulating MR1-dependent innate-like T cell activation and provide a basis for future studies examining whether this process influences response to immune checkpoint blockade.},
}

Humans
*Mucosal-Associated Invariant T Cells/immunology/metabolism
*Lung Neoplasms/immunology/microbiology/metabolism/genetics
*Enterococcus/metabolism/immunology
*Receptors, Antigen, T-Cell/metabolism/immunology
*Histocompatibility Antigens Class I/metabolism/genetics/immunology
*Minor Histocompatibility Antigens/metabolism/genetics/immunology
*Riboflavin/metabolism
Lymphocyte Activation/immunology
*Carcinoma, Non-Small-Cell Lung/immunology/microbiology
Ribitol/analogs & derivatives
Uracil/analogs & derivatives

@article {pmid42612036,
year = {2026},
author = {Asbury, MR and Guedez, A and Lee, J and Mercer, EM and Kasaba, F and Rangipour, Z and Kellner, JD and Lacaze-Masmonteil, T and Samara, J and Leijser, LM and Lebel, C and Zein, H and Hendson, L and Murguía Favela, L and McNagny, K and Giesbrecht, GF and Sycuro, L and Alshaikh, B and Arrieta, MC},
title = {Exploring the Early-Life Microbiomes of Preterm Infants and Their Childhood Health Outcomes (The BLOOM Study): Protocol for a Prospective, Observational Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e95658},
doi = {10.2196/95658},
pmid = {42612036},
issn = {1929-0748},
mesh = {Humans ; Prospective Studies ; Infant, Newborn ; *Infant, Premature ; Infant ; Female ; *Gastrointestinal Microbiome/physiology ; Male ; Child, Preschool ; Alberta ; *Microbiota ; Child Development ; Feces/microbiology ; },
abstract = {BACKGROUND: Establishment of the gut microbiome during the first years of life is critically important for long-term health and development. In preterm infants, microbial colonization is disrupted due to their developmental immaturity and the myriad of pre- and postnatal exposures. Unfortunately, this places them at an elevated risk for adverse health outcomes into childhood (eg, asthma and impaired neurodevelopment). Understanding the developmental trajectory of the microbiome in preterm infants, the factors predicting these microbial patterns, and the links to childhood health can offer opportunities to develop interventions and optimize health.

OBJECTIVE: BLOOM (Begin a Life of Health With Observation and Optimization of the Microbiome) is a prospective, observational cohort study that aims to examine how early-life microbiomes shape the health and development of preterm infants into childhood (eg, asthma and neurodevelopment).

METHODS: Infants (<37 weeks gestation) and their families are recruited from 4 neonatal intensive care units in Calgary, Alberta, Canada. Maternal stool and weekly infant stool, urine, and human milk samples are collected during the first 2 months postnatally; participants are then followed up at 3 months, 1 year, and 3 years corrected age for continued data (eg, nutrition, medications, medical history, and home environment) and sample collection (stool, urine, nasal swabs, hair, and blood). Additional clinical testing (eg, allergen skin prick test) and questionnaires (eg, Ages & Stages Questionnaires, Third Edition) are administered to assess health outcomes and developmental milestones.

RESULTS: Study recruitment and data/sample collection for BLOOM commenced in 2019; as of May 2026, we have enrolled 245 participants, and recruitment is ongoing. An initial characterization of early-life microbiome profiles for the first 105 infants enrolled in BLOOM was published online in December 2025.

CONCLUSIONS: BLOOM is a large, comprehensive prospective cohort study and biobank aimed at measuring the microbiome development of preterm-born children. This cohort will address significant research priorities through characterizing the patterns of microbiome development in preterm infants over the first 3 years postnatally and correlating these with health outcomes (eg, immune development, asthma and allergy risks, and neurodevelopment). It is anticipated that the results can be leveraged to identify factors and altered microbiome patterns underlying disease risk, design intervention strategies (eg, microbial therapeutics) for later clinical testing, and generate novel hypotheses of possible underlying mechanisms linking microbiome development to health.},
}

Humans
Prospective Studies
Infant, Newborn
*Infant, Premature
Infant
Female
*Gastrointestinal Microbiome/physiology
Male
Child, Preschool
Alberta
*Microbiota
Child Development
Feces/microbiology

@article {pmid42612400,
year = {2026},
author = {Ramesh, A and Subbarayan, R and Shrestha, R and Krishnamoorthy, L and Radhakrishnan, A},
title = {Bifidobacterium and the gut-immune axis: Mechanistic insights and therapeutic potential.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128686},
doi = {10.1016/j.micres.2026.128686},
pmid = {42612400},
issn = {1618-0623},
abstract = {Gut-immune axis is a bidirectional network that links the intestinal microbiota to host immune homeostasis. Among commensal microbes, Bifidobacterium species are prominent modulators of mucosal and systemic immunity through strain-specific metabolic, structural, and receptor-mediated mechanisms. This narrative review synthesizes mechanistic, preclinical, and clinical evidence on how Bifidobacterium influences immune regulation, epithelial barrier integrity, and inflammation, emphasizing strain specificity and host context. Bifidobacterium exerts immunomodulatory effects through acetate production, exopolysaccharides, tryptophan-derived indoles, and extracellular vesicles, which regulate dendritic cells, macrophage polarization, secretory IgA, tight junction integrity, and Treg/Th17 balance. These effects are highly strain-dependent and are influenced by diet, obesity, host genetics, and disease state. Preclinical and clinical evidence suggests potential benefits in antibiotic-associated dysbiosis, inflammatory bowel disease, cancer therapy response, early life immune maturation, and selected metabolic and neuroimmune disorders, although the outcomes remain heterogeneous. Bifidobacterium should be viewed as a diverse group of immunomodulatory microbes rather than a uniform probiotic genus. Its therapeutic potential depends on the strain selection, host context, and ecological interactions within the gut microbiome. Precision and strain-resolved approaches supported by multi-omics and clinical validation are required to translate these perspectives into routine practice.},
}

@article {pmid42612504,
year = {2026},
author = {Liu, Y and Zhang, C and Zhang, Y and Pang, J and Zhang, J and Li, J and Shi, H and He, X and Kang, Y and Shen, J},
title = {Multivariable-adjusted multi-omics signatures reveal gut microbial functional alterations and metabolic dysregulation in intrinsic capacity decline.},
journal = {The journal of nutrition, health & aging},
volume = {30},
number = {10},
pages = {100945},
doi = {10.1016/j.jnha.2026.100945},
pmid = {42612504},
issn = {1760-4788},
abstract = {BACKGROUND: Intrinsic capacity (IC) decline is inherently correlated with aging, yet distinguishing specific IC-related biomarkers from general physiological aging markers remains a significant challenge. We aimed to identify multi-omics signatures associated with IC decline after adjustment for relevant covariates and to explore the functional pathways potentially involved in IC decline.

METHODS: We analyzed 110 fecal (metagenomics) and 121 serum (untargeted metabolomics) samples from older adults at Beijing Hospital. Multivariable models were applied adjusting for age, sex, Charlson Comorbidity Index (CCI), fish intake, and fruit intake frequency. Differential analyses and network-based mediation approaches were used to assess microbiome-metabolome-IC associations.

RESULTS: After multivariable adjustment, 57 bacterial species and 56 serum metabolites were associated with IC status. The normal IC group showed enrichment of multiple taxa, including Lactobacillus zeae and Paenibacillus glucanolyticus. IC decline was associated with concurrent alterations in amino acid and carnitine-related metabolic pathways, including changes in L-serine, Cysteine, N6,N6,N6-trimethyl-L-lysine, and carnitine C5-OH. Network-based mediation analysis identified overlapping associations among senescence-related metabolites (N1,N8-diacetylspermidine), dietary-derived microbial products (3-(3-hydroxyphenyl)-3-hydroxypropanoic acid), and secondary bile acids (3-epideoxycholic acid), suggesting a structured microbiome-metabolome architecture linked to IC variation.

CONCLUSIONS: This study identifies a multi-omics signature associated with IC decline after adjustment for major demographic, clinical, and dietary factors. The findings reveal concurrent alterations in circulating metabolites related to nutrient and carnitine metabolism, alongside compositional and functional differences in the gut microbiome. Together, these parallel findings characterize a multi-omics profile associated with functional decline. These results provide hypotheses for future validation in longitudinal studies.},
}

@article {pmid42603875,
year = {2026},
author = {Getachew, T and Birri, DJ and Ashenafi, M and Tigu, F and Bez, C and Bertani, I and Venturi, V and Desalegn, A},
title = {The bacterial microbiota of the spontaneously fermented Ethiopian honey wine, Tej.},
journal = {Journal of food science and technology},
volume = {63},
number = {9},
pages = {1691-1699},
pmid = {42603875},
issn = {0022-1155},
abstract = {UNLABELLED: The honey wine (Tej) is the most widely consumed traditionally fermented alcoholic beverage in Ethiopia. Different classes of microorganisms including lactic acid bacteria and yeasts have been reported to be involved in its fermentation. The microbial composition of Tej differs based on the raw materials and additives used by the producers. The purpose of this study was to assess the bacterial composition and diversity of Tej . Six Tej samples were collected from small-scale and household Tej producers in Addis Ababa, Ethiopia, and bacterial diversity was analyzed by 16S rRNA amplicon library sequencing. From the examined samples, 68.5% of the sampled Tej had a pH value of ≤ 3.8. The titratable acidity ranged from 0.4 ± 0.1 to 1.2 ± 0.4, with a significant difference observed at p-value = 0.001. The alcohol content (%, v/v) varied between 10.1 ± 0.7 and 12.0 ± 0.9. Firmicutes and Proteobacteria were the two most predominant taxa, with Firmicutes dominating 99.9% of the three Tej samples and being the second most prevalent taxon in the other two samples. The two dominant genera identified were Lactobacillus and Zymomonas. These findings revealed the importance of evaluating the role of different consortia of microorganisms in the production of Tej and assessing its quality.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-025-06372-2.},
}

@article {pmid42603897,
year = {2026},
author = {Tran, V and Lee, C},
title = {Concurrent Acute Pyelonephritis in a Mother-Infant Dyad: A Case Report.},
journal = {Cureus},
volume = {18},
number = {7},
pages = {e112745},
pmid = {42603897},
issn = {2168-8184},
abstract = {Acute pyelonephritis is an infection of the kidney that affects both adult and pediatric populations. We describe the case of a 31-year-old mother and her infant boy diagnosed with pyelonephritis due to the same organism. Both patients harbored risk factors that increased their susceptibility to infection; however, more importantly, maternal-to-neonatal transmission of microbiota is thought to play a large role in the neonate's infection. This case highlights the importance of and the clinical implications of maternal and neonatal microbiomes.},
}

@article {pmid42603926,
year = {2026},
author = {Vazirzadeh, M and Vatankha, ML and Morales, MA and Zaman, MS and Tamayo, EJS and Kelly, KJ},
title = {Camel milk-based probiotics: functional properties, gut health benefits, and emerging implications for the gut-brain axis-a comprehensive review.},
journal = {Journal of food science and technology},
volume = {63},
number = {9},
pages = {1648-1663},
pmid = {42603926},
issn = {0022-1155},
abstract = {UNLABELLED: Camel milk is gaining scientific interest for its unique composition, including bioactive proteins, high antimicrobial peptides (lactoferrin, lysozyme), immunomodulatory components, and lower allergenic potential compared to bovine milk, positioning it as a promising matrix for probiotic delivery. Probiotics support gut homeostasis and may influence the gut-brain axis via microbial metabolites (SCFAs, GABA), immune modulation, and neuroactive compound production. This review critically assesses current evidence on camel milk-based probiotics, emphasizing functional properties, effects on gut microbiota, gastrointestinal benefits, and emerging implications for the gut-brain axis (inflammation reduction, metabolic signaling, neurotransmitter pathways). Drawing from in vitro studies, animal models (e.g., colitis, EAE, diabetes), and limited human trials, we evaluate translational relevance. Preliminary findings suggest benefits in gut health, microbiota modulation, and potential neuroprotection, but strain specificity, mechanistic details, and robust clinical efficacy remain limited. Significant knowledge gaps persist regarding optimal strains, dosing, and long-term effects. Rigorous, well-designed preclinical and clinical studies are essential to validate health claims and support development of camel milk-based functional products targeting gut and potential neurological health.

GRAPHICAL ABSTRACT: The graphical abstract illustrates camel milk-derived probiotics as modulators of the gut-brain axis through interconnected pathways. Central mechanisms include microbiota modulation, synthesis of neuroactive compounds (SCFAs, GABA, neurotransmitters), immune regulation, and anti-inflammatory effects. Bidirectional communication between gut and brain occurs via neural, endocrine, and metabolic routes, with potential therapeutic applications for mental health disorders including depression, anxiety, and cognitive impairment.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-026-06765-x.},
}

@article {pmid42604017,
year = {2026},
author = {Wu, Y and Xie, L and Li, S and Ye, J and Zhu, Z and Zhang, Y and Chen, F},
title = {Ecosystem settings and urbanization shape microbial communities and antibiotic resistance genes on coastal microplastics.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100655},
pmid = {42604017},
issn = {2666-5174},
abstract = {Coastal wetlands are increasingly contaminated by microplastics that provide long-lived substrates for microbial colonization, yet the joint effects of ecosystem settings and urbanization on plastisphere communities and their resistomes remain poorly understood. Here, we used a 2 × 2 factorial design across mangrove and sandy-beach sediments under rural and urban influence, combined with metagenomic profiling, to characterize microplastic-associated microbiota and antibiotic resistance genes (ARGs). Microbial communities on microplastics showed clear separation between mangroves and sandy shores, with additional shifts along the rural-urban gradient, indicating context-dependent plastisphere assembly. Urbanization substantially increased richness in mangrove plastispheres, whereas effects on sandy beaches were weak or inconsistent and largely confined to low-abundance taxa. In situ exposure yielded a diverse ARG repertoire (>1 000 ARGs), and ARG composition showed significant ecosystem × human-impact interactions, with urban mangrove microplastics hosting the highest ARG diversity. Genus-ARG co-occurrence networks showed denser bacteria-ARG association patterns in mangrove than in sandy-beach plastispheres, with a limited number of genera statistically associated with multiple ARGs. These results suggest that plastisphere communities and resistomes varied across ecosystem settings and urbanization contexts, with urban mangrove microplastics showing relatively higher ARG diversity and stronger bacteria-ARG co-occurrence patterns. These findings highlight the need for habitat-specific monitoring of microplastic-associated resistance.},
}

@article {pmid42604251,
year = {2026},
author = {Zhang, B and Jiang, X and Zhao, H and Wang, B},
title = {BileActome reveals community-assembled bile acid metabolism in the rumen microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag205},
pmid = {42604251},
issn = {2730-6151},
abstract = {Microbial bile acid metabolism is an important link between microbiomes and host physiology, but its genetic basis remains difficult to resolve from genome and metagenome data. This is largely because existing annotation resources are not designed for the high sequence diversity and functional complexity of microbial bile acid genes. Here we present BileActome, a reusable annotation resource developed specifically for microbial bile acid metabolism. BileActome defines 27 experimentally supported gene families, including bile salt hydrolases, bile acid-inducible operon genes, and microbial hydroxysteroid dehydrogenases. Its design prioritizes experimentally supported functional sites when available and conserved domain features otherwise, while also distinguishing key functional subtypes. We applied BileActome to 1693 high-quality rumen metagenome-assembled and isolate genomes and validated its performance using controlled in vitro rumen fermentations under three bile acid interventions. In metagenomic gene-catalog analyses, BileActome enabled pathway-level interpretation of microbial responses to bile acid exposure, with the most reproducible responses centered on Bai-associated gene families. At genome scale, it generated a phylogeny-informed map of bile acid metabolic potential that was broader and more informative than Kyoto Encyclopedia of Genes and Genomes (KEGG)-based annotation. Further analyses of genomes, local gene organization, and genome-level guilds showed that bile acid metabolism in the rumen is modular, phylogenetically structured, and distributed across different microbial members. Deconjugation and oxidation/epimerization-related functions were widespread, whereas complete bile acid-inducible systems were less common. Together, these findings support a community-assembled model of bile acid metabolism and establish BileActome as an open and reproducible framework for studying specialized microbial functions in complex ecosystems.},
}

@article {pmid42604380,
year = {2026},
author = {Hu, D and Wang, H and Groß, V and Burns, A and Urich, T},
title = {Summer drought impacts micropredator abundance and microbial food web structure in a rewetted fen peatland.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag169},
pmid = {42604380},
issn = {2730-6151},
abstract = {Summer drought significantly affects soil microbiome diversity and functioning, and metabolic interactions in wetland ecosystems, yet its effects on the microbial food web are less understood. We investigated the dynamics of bacterivorous microorganisms and prey bacteria (PBac) in a rewetted fen peatland before, during, and after a summer drought using small subunit ribosomal RNA (SSU rRNA) gene sequencing and quantitative metatranscriptomics. We identified bacterivores including bacteria (e.g. Myxobacteria), protists, and nematodes, as well as Ca. Patescibacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota archaea (PD) having a host-dependent lifestyle. In addition, bacteriophage transcripts were enumerated. The summer drought increased the diversity of bacterivorous protists (BPro) and bacteria (BBac) in the fen, along with decreases in the water level and increases in redox potential. The SSU rRNA transcripts abundance for all bacterivores (with the exception of the PD) increased during the drought, reaching a peak in October. The transcript abundance of all bacterivores remained above predrought level for at least four months after the drought ended. This became more evident when assessing the bacterivore-to-prey-bacteria ratios, with the ratios of aerobic BBac, BPro, and nematode to PBac increasing by more than two-fold compared to predrought. In contrast, the PD and bacteriophage-to-prey ratios remained rather stable. This study provides a holistic view of the diversity and composition of bacterivores in a fen peat microbiome, including the PD and bacteriophages, and suggests a long-lasting impact of summer drought on bacterivore and food web dynamics. The strong responses of aerobic bacterivores may lead to changes in ecosystem functioning through modulated trophic interactions in a changing climate.},
}

@article {pmid42604383,
year = {2026},
author = {Song, G and Cheng, F and Qiao, Z and Ge, F and Bi, Y},
title = {Phycosphere microbiome contributes to ecological dominance of diatoms: a comparative study of Cyclotella atomus and Ulnaria ulna.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag211},
pmid = {42604383},
issn = {2730-6151},
abstract = {Diatoms play a crucial role in aquatic ecosystems, yet the mechanisms underlying their long-term dominance remain poorly understood. This study investigated the relationship between diatom ecological persistence and their phycosphere bacterial communities by comparing the long-term dominant species Cyclotella atomus with the short-term dominant species Ulnaria ulna. 16S rRNA gene sequencing combined with predictive functional profiling revealed that the bacterial community associated with C. atomus was more diverse, stable, and interconnected than that associated with U. ulna. Taxonomic analysis identified key bacterial taxa such as Gemmatimonas, Sphingobium, and Pseudorhodoferax enriched in C. atomus. Co-occurrence network analysis demonstrated higher microbial interaction complexity in C. atomus, enhancing functional redundancy and ecosystem stability. Functional predictions indicated significant enrichment in carbohydrate metabolism (glycosaminoglycan degradation, pentose/glucose interconversion) and stress response pathways (betaine biosynthesis, xenobiotic metabolism by cytochrome P450) in the C. atomus microbiome, supporting a mutualistic relationship in which diatom-derived extracellular polymeric substances sustains specialized bacteria that reciprocate with vitamin B12, phytohormones, and chemical defenses. Based on these results, a mutually reinforced symbiotic cycle model was proposed to illustrate how the diatom and its phycosphere microbiome established a resilient holobiont capable of prolonged ecological dominance. The bacterial community associated with each diatom species exhibited host specificity and contributed to the maintenance of host dominance. These findings highlight the critical role of microbial partnerships in diatom success, offering new insights for predicting phytoplankton community dynamics and managing aquatic ecosystems.},
}

@article {pmid42604542,
year = {2026},
author = {Sepúlveda, AMG and da Conceição Jesus, E and Molina, YC and Buttrós, VH and Carvalho, LQ and Pasqual, M and Dória, J},
title = {Strawberry micropropagation simplifies endomicrobiome and highlights potential for in vitro biotization with beneficial rhizobacteria.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70278},
pmid = {42604542},
issn = {1438-8677},
support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
abstract = {Strawberry micropropagation produces uniform, disease-free planting material. However, repeated in vitro subculturing can simplify the endophytic microbiome, reducing plant vigour and acclimatization success. This study investigated the impact of successive in vitro generations on the endomicrobiome of Fragaria × ananassa cv. San Andreas and determined if targeted biotization with beneficial rhizobacteria can enhance plant performance. Profiled endophytic bacterial and fungal communities were analysed in the mother plant and across three in vitro generations using amplicon sequencing of the 16S rRNA gene and ITS markers. Ten plant growth-promoting bacterial strains were tested in vitro. The most effective strains were combined into consortia, and their impact on growth, survival and phenolic and flavonoid accumulation was assessed under in vitro and ex vitro acclimatization conditions. Successive subcultures simplified the endophytic assemblage. The mother plant exhibited substantially higher bacterial alpha-diversity than in vitro generations, with richness and Shannon diversity declining significantly (P <0.001) across all subcultures. In vitro biotization with A. brasilense Ab-V5 and A. brasilense Ab-V6 increased total dry biomass from 190.63 mg in the control to 216.75 mg and 209.11 mg, respectively. Under ex vitro conditions, several inoculated treatments achieved 100% survival compared with 75% in the non-inoculated control. Prolonged in vitro maintenance reduces the complexity of the strawberry endomicrobiome by imposing a selective bottleneck. Targeted introduction of beneficial bacteria partially compensates by enhancing growth, survival and secondary metabolite accumulation, supporting microbiome-assisted strategies to improve tissue culture performance and ex vitro establishment.},
}

@article {pmid42604698,
year = {2026},
author = {Zhou, Y and Zhang, L and Li, Q and Wang, H and Shi, H and Zhao, Y and Xiao, X and Zhang, Y},
title = {Prenatal Exposure to Organophosphate Esters and Infantile Neurobehavior: Integrating the Gut Microbiome and Metabolome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125494},
doi = {10.1016/j.envres.2026.125494},
pmid = {42604698},
issn = {1096-0953},
abstract = {Organophosphate esters (OPEs) are widely used flame retardants and plasticizers. Given their structural similarity to neurotoxic organophosphorus pesticides, concerns have been raised regarding their potential developmental neurotoxicity. However, epidemiologic evidence remains limited, and the roles of gut microbial and metabolic perturbations in these associations are not well characterized. We analyzed 404 mother-child pairs from the Shanghai Maternal-Child Pairs Cohort. OPE concentrations were quantified in cord serum. Meconium samples were profiled for gut microbiota and metabolomics, and behavioral development at 2 years was assessed using the Strengths and Difficulties Questionnaire. Generalized linear models, negative-binomial hurdle regression, SHapley Additive exPlanations, high-dimensional mediation analysis, metabolome-wide association analysis, meet-in-the-middle analysis, and pathway enrichment analysis were applied. A doubling of cord serum tris(2-butoxyethyl) phosphate (TBEP) concentration was associated with a 0.09-point increase in the conduct problem score at age 2 years (95% confidence interval [CI]: 0.02, 0.16). A doubling of TBEP concentration was also associated with 7.9% higher Chao1 richness (95% CI: 2.8%, 14.1%) and 8.7% higher ACE richness (95% CI: 3.5%, 14.1%). A doubling of Chao1 and ACE richness was associated with 0.27-point (95% CI: 0.12, 0.42) and 0.31-point (95% CI: 0.15, 0.46) increases in conduct problem scores, respectively. Alpha diversity indices and Collinsella were identified as potential mediators of the TBEP-conduct problem association. Integrated metabolomic analyses further implicated five pathways, particularly catecholamine biosynthesis and tyrosine metabolism. Enrichment scores for these pathways were positively associated with Chao1, ACE, and Collinsella. Prenatal TBEP exposure was associated with greater behavioral problems in early childhood. Altered neonatal gut microbiota and related metabolic pathways may partly underlie this association.},
}

@article {pmid42604878,
year = {2026},
author = {Yang, F and Tian, L and Xia, Y and Ye, C and Wu, H and Wang, H and Wang, Y and Guo, S and Guo, N and Yang, J and Sun, J and Li, Y and Tao, Z and Xiong, X and Huang, X and Xu, T and Liu, X and Shang, Y and Guo, Y},
title = {Geographical distribution and seasonality of insect species and gut microbiota of fly larvae from 65 real cases in China.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {42604878},
issn = {1437-1596},
support = {82402196//National Natural Science Foundation of China/ ; 82572150//National Natural Science Foundation of China/ ; 2024JJ6546//Natural Science Foundation of Hunan Province/ ; },
abstract = {Forensic entomology can be pivotal for minimum postmortem interval (PMImin) estimation. Case-based studies can support forensic investigations and guide laboratory research, but systematic data from real cases in China remain limited. In this study, 65 forensic entomology cases collected from 2017 to 2024 in two regions of China, Beijing and Hunan, were analyzed to characterize necrophagous insect occurrence patterns and larval gut microbiota. A total of 30 colonizing insect species from 11 families were identified. Lucilia sericata, Chrysomya megacephala, and Sarcophaga crassipalpis were the most frequently recorded species. Diptera, especially Calliphoridae and Sarcophagidae, were mainly associated with shorter postmortem intervals, whereas coleopteran taxa were more often observed in longer-interval cases. In addition, insect occurrence showed clear geographical distribution and seasonality: L. sericata and S. crassipalpis predominated in Beijing cases, whereas C. megacephala and Sarcophaga peregrina were more frequent in Hunan cases. Overall species diversity was highest in summer, whereas only Calliphora vicina and Aldrichina grahami were observed in winter. 16S rRNA gene sequencing of larval gut microbiota revealed a stable core microbiome across diverse cases and species, including Ignatzschineria, Clostridium, Peptostreptococcus, Vagococcus, and Peptoniphilus. This study provides regional forensic entomology reference data and characterizes the gut microbiota of fly larvae collected directly from human remains in police casework, offering a useful basis for future forensic investigations and laboratory studies.},
}

@article {pmid42604919,
year = {2026},
author = {Shi, C and Zhang, H and Liu, Y and Zhou, G and Zhou, Y and Yan, Y and Huang, X and Yang, X and Chen, L and Lü, F},
title = {Tobacco intercropping with Allium crops reshapes soil microbiome-metabolome interactions and improves plant health and tobacco leaf quality.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42604919},
issn = {1471-2229},
support = {32160517//National Natural Science Foundation of China/ ; 2021XM15//he Key R&D Project of Guizhou Tobacco Company/ ; },
mesh = {*Nicotiana/growth & development/physiology/metabolism/microbiology ; *Plant Leaves/physiology/metabolism ; *Soil Microbiology ; *Microbiota ; *Metabolome ; *Allium/growth & development ; Plant Diseases/virology ; *Crop Production/methods ; },
abstract = {BACKGROUND: Intercropping systems play important roles in improving soil conditions, enhancing crop performance and suppressing soil-borne diseases. However, the mechanisms by which tobacco-Allium intercropping regulates soil microecology, tobacco growth and leaf quality remain insufficiently understood. In this study, tobacco monoculture and tobacco intercropping systems with onion, garlic or Chinese chive were established to evaluate tobacco agronomic traits, disease occurrence, cured leaf chemical composition and defence-related enzyme activities. Soil physicochemical properties, microbial community structure and metabolomic profiles were further analysed and integrated using a multi-omics approach.

RESULTS: Compared with tobacco monoculture, the tobacco-garlic intercropping treatment (CG) showed the most pronounced effects. CG alleviated soil acidification and increased the contents of available phosphorus and available potassium. The incidence and disease index of tobacco mosaic virus disease (TMVD) were significantly reduced by 27.91% and 31.77%, respectively. CG also significantly improved tobacco agronomic traits and enhanced the activities of phenylalanine ammonia-lyase (PAL), polyphenol oxidase (PPO) and superoxide dismutase (SOD) by 146.50%, 162.65% and 248.87%, respectively. In cured tobacco leaves, total nitrogen, nicotine and reducing sugar contents increased by 20.57%, 28.22% and 10.49%, respectively. In addition, CG significantly increased potassium content and improved the potassium-to-chloride ratio by 55.46%. Correlation analysis showed that intercropping promoted the enrichment of beneficial bacterial genera, including Gemmatimonas and Sphingomonas, and enhanced functional pathways associated with linoleic acid metabolism, nucleotide metabolism, purine metabolism, pyrimidine metabolism, and the biosynthesis of antibiotics and other secondary metabolites.

CONCLUSIONS: Tobacco-Allium intercropping, especially tobacco-garlic intercropping, improved tobacco growth and cured leaf chemical quality and reduced field TMVD occurrence. These effects were associated with changes in rhizosphere soil properties, microbial communities and metabolites.},
}

*Nicotiana/growth & development/physiology/metabolism/microbiology
*Plant Leaves/physiology/metabolism
*Soil Microbiology
*Microbiota
*Metabolome
*Allium/growth & development
Plant Diseases/virology
*Crop Production/methods

@article {pmid42605004,
year = {2026},
author = {Umashankar, B and Pankonien, I and Amaral, M and Ooi, CY and Jardé, T and Waters, SA},
title = {Cystic Fibrosis and Colorectal Cancer Risk: Reprogramming of the Intestinal Epithelial Niche and Cell-State Plasticity in the CFTR Modulator Era.},
journal = {Cell proliferation},
volume = {},
number = {},
pages = {e70272},
doi = {10.1111/cpr.70272},
pmid = {42605004},
issn = {1365-2184},
support = {NHMRC_APP1188987//National Health and Medical Research Council/ ; //Sydney Children Hospital Network Foundation/ ; //Luminesce Alliance Research/ ; },
abstract = {Cystic fibrosis (CF) has shifted from a fatal paediatric lung disease to a multi-organ, lifespan-spanning disorder in which gastrointestinal (GI) complications and malignancies are increasingly prominent. With improved survival into mid- and late adulthood, aided by newborn screening, optimised nutrition and the advent of highly effective CF transmembrane conductance regulator (CFTR) modulators, implementation of colonoscopic surveillance has highlighted a several-fold increase in early-onset colorectal cancer (CRC) and a broader spectrum of intestinal pathology. In parallel, work in mouse models, human tissue and patient-derived intestinal organoids now places the CFTR at the centre of a complex epithelial compartment that integrates ion and pH homeostasis, mucus biology, microbiota, redox balance and immune/stromal function. In this review, we advance the hypothesis that CF may be conceptualised as a niche-centric hereditary CRC predisposition syndrome, in which germline CFTR dysfunction chronically destabilises epithelial identity in addition to increasing mutational burden. We synthesise evidence that CFTR loss remodels stem cell regulation, promotes hypoxia and oxidative stress, perturbs microbial ecosystems, drives chronic immune activation and stromal remodelling, and induces epithelial-mesenchymal plasticity (EMP) and DNA-damage vulnerability, collectively creating a pre-neoplastic intestinal ecosystem. We situate this model within contemporary CRC frameworks that emphasise cell-state transitions, hybrid epithelial-mesenchymal (E/M) states and specialised stromal niches, and we distinguish it from oncofoetal reprogramming, an APC-driven programme that CF does not clearly recapitulate. We propose that CF may provide a naturally occurring human context in which chronic epithelial stress sustains EMP-like pressure, a concept that requires direct validation in human CF intestinal tissue. Finally, we consider how CFTR modulators, microbiome-directed therapies and redox-targeted interventions might re-programme the CF intestinal niche and outline experimental and clinical strategies needed to determine whether early, ecosystem-level correction can prevent GI cancers in this high-risk population.},
}

@article {pmid42605204,
year = {2026},
author = {Tan, W},
title = {Evolution and Mechanistic Insights of Immunometabolism in Metabolic Diseases and Infections.},
journal = {Scandinavian journal of immunology},
volume = {104},
number = {2},
pages = {e70141},
doi = {10.1111/sji.70141},
pmid = {42605204},
issn = {1365-3083},
mesh = {Humans ; Animals ; *Metabolic Diseases/immunology/metabolism ; Metabolic Reprogramming ; Trained Immunity ; Immunity, Innate ; *Infections/immunology/metabolism ; Glycolysis ; TOR Serine-Threonine Kinases/metabolism ; Inflammation/immunology/metabolism ; *Energy Metabolism ; },
abstract = {Immunometabolism, an emerging field exploring metabolic reprogramming and functional regulation in immune cells, offers a lens for understanding complex diseases. This review delineates core concepts, key signalling nodes-emphasising the mechanistic target of rapamycin (mTOR) as an integrator of metabolic and immune signals-research and intervention strategies across metabolic and infectious diseases. Immune cells display metabolic plasticity: At rest, they depend mainly on mitochondrial oxidative phosphorylation, but swiftly shift to aerobic glycolysis upon activation to fuel effector functions. Pro-inflammatory subsets like Th1 cells and M1 macrophages lean heavily on glycolysis, whereas regulatory T cells favour fatty acid oxidation. Central pathways-glycolysis, the tricarboxylic acid (TCA) cycle, and amino acid metabolism-directly shape immune activation and inflammation via intermediates and regulatory enzymes. For example, succinate and itaconic acid are critical in inflammation control, while fatty acid and cholesterol metabolism dictate immune cell fate. In metabolic disorders such as obesity, diabetes, fatty liver disease, and atherosclerosis, immune metabolic reprogramming is the main driver of chronic low-grade inflammation and tissue injury. During infection, a metabolic tug-of-war ensues: Pathogens hijack host metabolism for survival, and the host counters by reprogramming its own metabolism. The idea of "trained immunity" highlights how metabolism-epigenetics crosstalk endows innate immunity with memory-like capacity. These insights inform therapeutic avenues-modulating metabolic pathways, nutritional interventions, and microbiome targeting-with wide potential. Challenges remain, including the complexity of in vivo networks and the need for precise interventions. Yet advances in single-cell multi-omics and metabolic flux analysis will deepen mechanistic understanding and enable breakthroughs in precision strategies.},
}

Humans
Animals
*Metabolic Diseases/immunology/metabolism
Metabolic Reprogramming
Trained Immunity
Immunity, Innate
*Infections/immunology/metabolism
Glycolysis
TOR Serine-Threonine Kinases/metabolism
Inflammation/immunology/metabolism
*Energy Metabolism

@article {pmid42605348,
year = {2026},
author = {Dai, Q and Deng, H and Wang, J and Shi, J and Ding, J and Gao, Y and Sun, W and Shen, Y and Wang, X and Lou, C},
title = {Neoadjuvant Hepatic Arterial Infusion Chemotherapy with FOLFOX Plus Tislelizumab for Resectable Hepatocellular Carcinoma Beyond the Milan Criteria: Efficacy, Safety and Biomarker Exploration.},
journal = {Journal of hepatocellular carcinoma},
volume = {13},
number = {},
pages = {615120},
pmid = {42605348},
issn = {2253-5969},
abstract = {PURPOSE: This study aimed to evaluate the efficacy and safety of hepatic arterial infusion chemotherapy of oxaliplatin, fluorouracil, and leucovorin (FOLFOX-HAIC) combined with tislelizumab as a neoadjuvant regimen in patients with resectable hepatocellular carcinoma (HCC) beyond the Milan criteria, and to explore predictive biomarkers of treatment response.

RESULTS: 26 patients completed neoadjuvant therapy, with a median tumor size of 6.35cm. The objective response rate according to mRECIST criteria reached 57.7%, and the disease control rate was 96.2%. 22 patients underwent radical surgery, and 10 patients (10/22, 45.5%) achieved major pathological response (residual viable tumor ≤10%). Six patients (27.3%) achieved complete pathological response, and 25 patients (96.2%) experienced at least one treatment-related adverse events (TRAEs) The most common TRAEs were elevated transaminases (76.9%), HAIC-related pain (34.6%). Transcriptomic analysis revealed that differential genes between responding and non-responding tumors primarily involved pathways related to bile acid secretion and fatty acid metabolism. Metabolomic analysis showed elevated serum chenodeoxycholic acid (CDCA) in non-responders and elevated tumor glycocholic acid (GCA). Microbiome analysis further confirmed increased abundance of bile acid metabolism-related bacteria such as bacteroides in non-responders. Serum interleukin-6 (IL-6) levels after neoadjuvant therapy were correlated with treatment response.

CONCLUSION: FOLFOX-HAIC combined with tislelizumab as neoadjuvant therapy for HCC beyond the Milan criteria demonstrates favorable anti-tumor efficacy and controllable toxicity. The level of GCA in tumor, peripheral blood CDCA, IL-6, and fecal bacteroides may hold the potential to serve as a composite biomarker panel to predict pathological response and treatment sensitivity.},
}

@article {pmid42605509,
year = {2026},
author = {Xiao, L and Fu, C and Santos, IR and Duarte, CM and Liu, J and Zhou, L and Zhou, M and Dang, R and Lin, J and Xiao, K and Luo, Y and Han, G},
title = {Microbial Decomposition of Lignin to Methane Reduces Net Blue Carbon Benefit Across China's Saltmarshes.},
journal = {Global change biology},
volume = {32},
number = {8},
pages = {e71059},
doi = {10.1111/gcb.71059},
pmid = {42605509},
issn = {1365-2486},
support = {2022YFF0802101//National Key Research and Development Program in China/ ; U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 41991330//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Methane/metabolism ; *Lignin/metabolism ; China ; *Wetlands ; Carbon/metabolism ; *Microbiota ; Biodegradation, Environmental ; },
abstract = {CH4 emissions from mangrove, saltmarsh, and seagrass ecosystems partially offset carbon sequestration, potentially diminishing the climate mitigation capacity of these blue carbon habitats. However, a mechanistic understanding of the processes governing CH4 production potential across large spatial scales remains limited. By integrating incubation-based measurements from 116 sites, we reveal significant ecosystem-specific differences in CH4 production potential, with saltmarshes emerging as CH4 production hotspot relative to mangroves and seagrass meadows. Using an integrated analytical approach encompassing more than 30 environmental, biogeochemical, and microbial parameters, we demonstrate that CH4 production potential converges on sediment organic carbon availability, particularly plant-derived carbon, as a key regulatory axis. Additionally, metagenome-assembled genomes (MAGs) recovered from saltmarshes show a functional bias toward lignin degradation, thereby fueling downstream CH4 production via methylotrophic pathways. Lignin-addition and stable carbon isotope experiments further provide supportive evidence that lignin decomposition enhances Chinese saltmarsh CH4 production potential, revealing a pathway that may reduce net blue carbon benefit. Together, these findings underscore that saltmarsh plant-derived lignin is less stable than conventionally assumed, as microbial processing redirects stored carbon toward CH4 production, challenging current blue carbon accounting frameworks at a continental scale within China.},
}

*Methane/metabolism
*Lignin/metabolism
China
*Wetlands
Carbon/metabolism
*Microbiota
Biodegradation, Environmental

@article {pmid42605689,
year = {2026},
author = {Núñez-Belmar, J and Leyrer, J and Beltrán, V and Borie, E and Fernández-Gil, F},
title = {Beyond bactericidal surfaces: interfacial selectivity as a design principle for implant biomaterials.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/08927014.2026.2715441},
pmid = {42605689},
issn = {1029-2454},
abstract = {Within seconds of placement, an adsorbed conditioning film replaces the implant's manufactured substrate and becomes the true interface host cells and microorganisms encounter. Conventional strategies engineered to kill or suppress bacteria therefore act on an interface neither party meets, helping explain the inconsistent clinical performance of broadly bactericidal designs. We propose interfacial selectivity, the capacity of a surface to favor beneficial over detrimental interactions, as a unifying design framework for implant biomaterials, and show how interfacial physicochemistry can be programmed to discriminate between colonizers. The implant boundary is viewed as three coupled interfaces: implant-film, film-microbiome, and film-host. Shared drivers, surface energy, charge, hydration, and multiscale topography, govern all three, so modifications intended to deter pathogens also influence commensal colonization, soft-tissue sealing, and osteoimmune balance. A regime map of interfacial forces reinterprets functionalization strategies within a common selectivity space, and a proposed selectivity index, applied here to published data for three archetypal surfaces, reorients evaluation from short-term killing toward the balance between host-beneficial and pathogen-beneficial outcomes. We derive transferable design principles, propose a minimum reporting standard, identify methodological gaps limiting translation, and argue that genomic and multi-omic calibration could enable patient-specific implementation across dental, percutaneous, and orthopedic implants.},
}

@article {pmid42605778,
year = {2026},
author = {},
title = {Gut Microbiome Metabolism Links High Fat Diets to Immunotherapy Efficacy.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {OF1},
doi = {10.1158/2159-8290.CD-RW2026-071},
pmid = {42605778},
issn = {2159-8290},
}

@article {pmid42605963,
year = {2026},
author = {Zhang, S and Wang, M and Chen, J and Zhu, Y and Zhu, B and Xu, Z and Liao, Y and Wang, Y},
title = {Highly Sensitive Spatial Host-Microbiome Transcriptomics in FFPE Tissues via Iterative Hydrogel Expansion.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77219},
doi = {10.1002/advs.77219},
pmid = {42605963},
issn = {2198-3844},
support = {2026ZD0556100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; TD2024015//Hangzhou Leading Innovation and Entrepreneurship Team Project/ ; 2024SSYS0022//Key R&D Program of Zhejiang/ ; },
abstract = {Spatial transcriptomics (ST) of archival formalin-fixed paraffin-embedded (FFPE) tissues is fundamentally limited by a trade-off between spatial resolution and transcriptomic sensitivity due to severe molecular crowding and RNA degradation. Here, we present Ex-spRandom, a highly sensitive platform that overcomes this limitation by directly converting diverse, fragmented RNA biotypes into stably anchored cDNA through the integration of random-primed in situ cDNA synthesis chemistry with interpenetrating polymer network (IPN)-based tissue expansion chemistry. This physicochemical synergy physically decrowds the dense FFPE matrix, directly converting highly fragmented host and microbial RNAs into stably anchored cDNA. Consequently, Ex-spRandom improves spatial signal confinement while enabling the detection of nearly 10,000 median genes per 50-µm spatial bin. Leveraging this synergistic high resolution and sensitivity, the platform captures over 44,000 unique host genes, enabling the precise delineation of continuous neurodevelopmental trajectories in the complex embryonic eye. Furthermore, Ex-spRandom achieves simultaneous, spatial profiling of host epithelial architecture and microbial transcript signals in the colon, detecting over 150,000 unique microbial genes. Ultimately, this scalable platform establishes a framework for sensitive, cross-kingdom spatial profiling in archival FFPE tissues.},
}

@article {pmid42606123,
year = {2026},
author = {Ðuran, I and Tang, WHW and Mamic, P},
title = {The gut microbiome and allograft outcomes: implications for heart transplantation.},
journal = {The Journal of clinical investigation},
volume = {136},
number = {16},
pages = {},
doi = {10.1172/JCI207999},
pmid = {42606123},
issn = {1558-8238},
mesh = {Humans ; *Heart Transplantation/adverse effects ; *Gastrointestinal Microbiome/immunology ; Allografts ; *Graft Rejection/microbiology/immunology ; Immunosuppressive Agents/therapeutic use ; Animals ; *Heart Failure/microbiology/surgery/therapy ; Fecal Microbiota Transplantation ; },
abstract = {Heart transplantation remains the gold standard therapy for patients with end-stage heart failure. However, post-transplant complications are considerable. Emerging evidence implicates the gut microbiome as a modifiable determinant of post-heart transplant outcomes through its influence on host immunity, metabolism, and inflammation. This Review synthesizes current understanding of gut microbiome dysregulation following solid organ transplantation, with particular emphasis on heart transplantation, examining mechanistic links underpinning important complications including allograft rejection, infection, metabolic dysfunction, and cardiac allograft vasculopathy. We critically evaluate bidirectional interactions between the gut microbiome and immunosuppressive drugs, assess the potential for microbiome profiling to serve as a predictive biomarker for post-transplant complications, and examine microbiome-targeted interventions including dietary modification, prebiotics, probiotics, and fecal microbiota transplant. Finally, we propose a translational roadmap to integrate microbiome science into heart transplant care to optimize immunosuppression, predict complications, and improve long-term outcomes for heart transplant recipients.},
}

Humans
*Heart Transplantation/adverse effects
*Gastrointestinal Microbiome/immunology
Allografts
*Graft Rejection/microbiology/immunology
Immunosuppressive Agents/therapeutic use
Animals
*Heart Failure/microbiology/surgery/therapy
Fecal Microbiota Transplantation

@article {pmid42606185,
year = {2026},
author = {Demirci, M},
title = {Asthma Dysbiosis Index: A Universal Airway Microbiome Signature From Multi-Cohort Analysis.},
journal = {Pediatric pulmonology},
volume = {61},
number = {8},
pages = {e71796},
doi = {10.1002/ppul.71796},
pmid = {42606185},
issn = {1099-0496},
}

@article {pmid42606273,
year = {2026},
author = {Al Shuraiqi, A and Al-Ansari, A and Al-Habsi, A and Abed, RMM and Barry, MJ},
title = {Heat-Stress Alters the Effects of Antibiotics on Fish Behavior.},
journal = {Environmental toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1002/tox.70188},
pmid = {42606273},
issn = {1522-7278},
support = {IG/SCI/BIOL/21/01//Sultan Qaboos University/ ; RC/GRG/SCI/BIOL/21/04//Oman, Research and Innovation Authority (RIA)/ ; },
abstract = {Antibiotics are a common contaminant of freshwaters, yet surprisingly understudied compared to other classes of drugs. Even trace concentrations of antibiotics can alter the gut microbiome, in turn affecting multiple systems including physiology, biochemistry, and behavior. Concurrently, climate change is leading to higher average temperatures and more frequent temperature spikes. The microbiome of poikilotherms is also highly sensitive to temperature. Little is known of how these two stressors interact. In this study we investigated the effects of amoxicillin, an antibiotic that is widely used in human and veterinary medicine, on the swimming behavior and predatory avoidance responses of zebrafish at two temperatures, 28°C (normal) and 32°C (heat-stressed). Additionally, we investigated the effects of the two stressors on the gut microbiome and heat shock protein expression. Both temperature and amoxicillin affected key behaviors including boldness, sociability, and swimming speed, with fish exposed to low-dose amoxicillin having higher swimming velocity suggesting a possible hormesis response. Amoxicillin exposure also increased fish boldness, while temperature had the opposite effect. A high temperature also reduced fish sociability. Both stressors also altered zebrafish responses to a conspecific alarm cue and induced heat shock protein gene expression. Heat stress and amoxicillin both altered the fish gut microbiome at the genus level with heat stress alone increasing several genera (e.g., Nordella, Nocardia, Reyranella), while heat stress plus high amoxicillin (20 μg/L) further increased others (e.g., Bradyrhizobium, Legionella, Xanthobacter). Overall alpha diversity (Shannon) changed little, but community composition (ANOSIM) shifted most clearly under high amoxicillin and under heat combined with amoxicillin, indicating dose- and temperature-dependent restructuring of the gut microbiome. Overall, the microbiome is emerging as an important regulator of physiology and behavior that is vulnerable to multiple stressors.},
}

@article {pmid42606298,
year = {2026},
author = {Abbasian, R and Parajuli, B and Yu, L and Durocher, B and Gardner, E and Chodur, E and Dwelley, MK and Ellermeier, CD and Ho, TD and Bosch, DE},
title = {Secreted nuclease effector neutralization by active site mimicry in Bacillota.},
journal = {mBio},
volume = {},
number = {},
pages = {e0151626},
doi = {10.1128/mbio.01516-26},
pmid = {42606298},
issn = {2150-7511},
abstract = {Polymorphic toxins mediate interbacterial antagonism among competitors in the gut microbiome. Nuclease effectors, distantly related to the type VI-secreted Bacteroidales Tde, are enriched in human gut Bacillota. Tde mediates antagonism among Bacillota, and expression of the cognate immunity, Tdi, in recipients is protective. Crystal structures of Tde/Tdi complexes from two Bacillus spp. and Enterococcus quebecensis highlight a conserved mechanism of immunity. Tdi engages Tde with high-affinity, specific binding at an interface that features predominantly polar amino acids. A separate Tdi interface has a very highly conserved P(Φ)4GG motif that structurally mimics and displaces a short helix in Tde's active site, which contains the critical catalytic residues. An isolated P(Φ)4GG motif peptide is sufficient for Tde nuclease activity inhibition at high concentrations. However, key residues at both the polar interface and P(Φ)4GG are required for complete inhibition of nuclease activity and protection against toxicity. We propose a multivalent Tde/Tdi neutralization mechanism where an initial high-affinity interface increases the local concentration of Tdi's P(Φ)4GG motif, enabling it to displace the Tde active site through structural mimicry. The resulting conformational rearrangement of Tde increases its flexibility in solution and susceptibility to proteolysis, which may aid in eliminating the toxic effector.IMPORTANCEBacteria in the gut microbiome compete using toxin secretion systems. Prior research has emphasized the importance of secretion systems in gram-negative bacteria. We describe a class of secreted nuclease effectors (toxins) and protective immunity proteins that are enriched in gram-positive Bacillota in human gut microbiomes. These effector/immunity pairs mediate antagonism among Bacillus and Enterococcus spp. The immunity proteins neutralize the nuclease effector through a unique mechanism of enzymatic active site mimicry. The immunity proteins bind effectors with very high-affinity at an interface with polar residues. The effector undergoes a large conformational change. A very highly conserved motif on the immunity surface competitively displaces an active site short helix and loop that contains the key catalytic residues. This rearrangement of the effector renders it inactive and susceptible to elimination by proteolysis.},
}

@article {pmid42606380,
year = {2026},
author = {Zuo, Y and Su, Z and Guo, J and Zhou, M and Wang, Y and Ni, Z},
title = {Regulatory Mechanisms of Synthetic Microbial Communities on Rhizosphere Microecology to Alleviate Continuous Monoculture Obstacles of Medicinal Plants.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag205},
pmid = {42606380},
issn = {1365-2672},
abstract = {Driven by industrial policies and market expansion, China has formed the world's largest medicinal plant cultivation industry. However, sustainable herbal production is seriously hindered by continuous monoculture obstacles (CMOs), which arise from prolonged single-species successive cultivation and manifest as comprehensive soil degradation featuring autotoxic allelochemical buildup, unbalanced rhizosphere microbiota, impaired soil physicochemical conditions, and frequent soil-borne pathogen outbreaks. Such adverse alterations lower soil enzyme activity, disrupt microbial community homeostasis, and severely impair both the yield and bioactive constituent quality of medicinal plants. Synthetic microbial communities (SynComs), experimentally assembled from defined microbial isolates via precise cultivation and controlled assembly, exhibit promising potential to regulate plant metabolism, optimize nutrient cycling and boost plant stress tolerance, and thus may serve as a feasible strategy to mitigate medicinal plant CMOs. This review took rhizosphere microecology as its core research perspective and summarized CMOs' status, SynComs' significance, construction methods, and their mechanisms in reshaping rhizosphere microecology-focusing on root exudates, nutrient cycling and microbiome dynamics. SynComs adjusted root exudates, participate in carbon/nitrogen/phosphorus cycling, enhance stress/pathogen resistance, and strengthen root immunity via signaling pathways (e.g. jasmonic acid). Existing experimental evidence indicated SynComs may partially repair plant-microbe communication networks impaired under continuous monoculture. Future research should prioritize innovative SynCom designs with keystone microbes, improved assembly techniques, and deeper rhizosphere mechanistic studies to advance sustainable medicinal plant production.},
}

@article {pmid42606596,
year = {2026},
author = {Kwack, KH and Sohn, J and Zhang, L and Li, L and Mullaney, R and Arao, Y and Blackshear, PJ and Kirkwood, KL},
title = {Gut microbiota transmits osteoimmune dysregulation and exacerbates trabecular bone loss in tristetraprolin-deficient mice.},
journal = {Journal of bone and mineral metabolism},
volume = {},
number = {},
pages = {},
pmid = {42606596},
issn = {1435-5604},
support = {R01DE028258/DE/NIDCR NIH HHS/United States ; R01DE028258S1/DE/NIDCR NIH HHS/United States ; R01DE032310/DE/NIDCR NIH HHS/United States ; K99DE034829/DE/NIDCR NIH HHS/United States ; },
abstract = {INTRODUCTION: Tristetraprolin (TTP) is an RNA-binding protein essential for controlling cytokine production, and its deficiency leads to profound skeletal deterioration. Although TTP deficiency is associated with systemic inflammation and microbial dysbiosis, the contribution of the gut microbiota to bone pathology remains poorly defined.

MATERIALS AND METHODS: We investigated whether the microbiome causally modulates osteoimmune mechanisms and bone microarchitecture in TTP-deficient mice. To isolate the effects of the microbiome, we utilized specific pathogen-free (SPF) and germ-free (GF) co-housing mouse models.

RESULTS: Microbial transfer bidirectionally regulated systemic inflammation and the expansion of monocytic myeloid-derived suppressor cells (M-MDSCs), a population with potent osteoclastogenic capacity. Importantly, microbiota transfer was sufficient to induce osteoclast activation and a selective deterioration of trabecular bone microarchitecture in otherwise healthy mice, without affecting overall bone mass. Crucially, the transmission of these osteoimmune and skeletal phenotypes was microbiota-dependent; while a baseline genetic bone deficit persisted in GF TTP-deficient mice, the co-housing-induced M-MDSC expansion and trabecular bone alterations were not observed under GF conditions.

CONCLUSION: Our findings identify a microbiota-dependent osteoimmune axis that amplifies inflammatory bone loss in TTP deficiency. This work establishes the gut microbiome as a mechanistic modifier of bone quality in genetically driven inflammatory disease and highlights microbial targeting as a potential therapeutic strategy for inflammatory bone loss.},
}

@article {pmid42606623,
year = {2026},
author = {Nishihara, N and Tachibana, S and Yamakage, M},
title = {Prebiotic raffinose attenuates surgery-induced delirium-like behaviors through gut microbiota-mediated serotonergic signaling in frail senescence-accelerated mice: an experimental study using SAMP10 mice.},
journal = {Journal of anesthesia},
volume = {},
number = {},
pages = {},
pmid = {42606623},
issn = {1438-8359},
support = {20K17841//Japan Society for the Promotion of Science/ ; 24K12053//Foundation for Promotion of Material Science and Technology of Japan/ ; },
abstract = {BACKGROUND: Postoperative delirium (POD) is a severe neuropsychiatric complication characterized by acute cognitive dysfunction and neuroinflammation, particularly prevalent in frail elderly patients. While the gut-brain axis is recognized as a regulator of neuroinflammation, specific preventive strategies remain limited. We investigated whether preoperative administration of raffinose, a prebiotic trisaccharide, prevents POD-like behaviors through gut microbiota-mediated neuroimmune modulation in frail senescence-accelerated mice.

METHODS: Twenty-six-week-old senescence-accelerated mice (SAMP10) were randomly assigned to control (N), surgery (O), or raffinose-treated surgery (R) groups (n = 5-6 per group, depending on the endpoint). Raffinose (5% w/v) was administered via drinking water for 4 weeks prior to laparotomy under general anesthesia. Delirium-like behaviors were assessed using the open field, Y-maze, and buried food tests at 6 h post-surgery. Serum biomarkers were quantified via ELISA. Gut microbiota composition was analyzed using 16S rRNA sequencing.

RESULTS: Surgery was associated with a numerical reduction in Y-maze spontaneous alternation that showed a large effect size but did not reach conventional statistical significance (O: 4.32 ± 3.46% vs. N: 10.71 ± 5.41%; p = 0.097, Cohen's d = 1.41, 95% CI -0.04 to 2.79), whereas a robust and statistically significant motivational deficit was observed in the Buried Food Test (O: 240.8 ± 116.7 s vs. N: 35.2 ± 25.6 s; p = 0.001, d = 2.52). Raffinose pretreatment was associated with higher Y-maze spontaneous alternation compared with the surgery group (R: 12.4 ± 4.20%; p = 0.034 vs. O, d = 2.10) and with restoration of motivational behavior in the BFT (R: 18.7 ± 4.74 s; p = 0.0006 vs. O, d = 2.77). Systemically, raffinose reduced circulating IL-6 by 56% and preserved gut microbial α- and β-diversity, with significant enrichment of Lactobacillus. Lactobacillus abundance was strongly correlated with preserved serum serotonin (r = 0.72, p = 0.003).

CONCLUSIONS: Prebiotic raffinose attenuates surgery-induced systemic inflammation and preserves cognitive-attentional and motivational performance in frail mice, providing convergent behavioral, biochemical, and microbiome evidence consistent with a gut-microbiota-serotonergic mechanism, which requires direct causal validation in future studies. These findings provide a preclinical rationale for prehabilitation nutritional strategies targeting the gut-brain axis, while acknowledging that individual behavioral readouts differ in the strength of the surgery-induced control-vs-surgery contrast.},
}

@article {pmid42606639,
year = {2026},
author = {Shahbaztabari, N and Shahverdi, M and Taherkhani, S and Hosseini, E and Amjadi, F},
title = {Potential Role of Prebiotics and Probiotics on Oocyte Quality, Embryo Development, Endometrial Health, and Fertility Outcomes in Assisted Reproductive Technologies.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42606639},
issn = {1867-1314},
abstract = {Assisted reproductive technologies (ART) have transformed infertility treatment over recent decades, yet success rates remain inconsistent. Beyond the established embryological and hormonal determinants, emerging research identifies the human microbiome-particularly gut and reproductive tract communities-as a critical regulator of reproductive efficiency. The gut microbiota influences endocrine balance, metabolic signaling, and immune homeostasis, all of which have a direct impact on oocyte maturation, embryo viability, and endometrial receptivity. Dysbiosis, characterized by the depletion of beneficial lactobacilli and an increase in pro-inflammatory bacterial taxa, has been associated with oxidative stress, reduced oocyte competence, and implantation failure. In contrast, a balanced microbiota supports follicular health and hormonal coordination. Prebiotic and probiotic interventions may enhance reproductive outcomes through several complementary mechanisms. By restoring a Lactobacillus-dominant microbial profile, they help stabilize the reproductive tract ecosystem, reinforce epithelial and immune barrier function, and limit the overgrowth of potentially pathogenic species. These changes reduce local inflammation and oxidative stress while promoting the secretion of antimicrobial peptides and bacteriocins that maintain tissue integrity. Collectively, these microbiome-mediated effects can contribute to improved follicular fluid homeostasis, enhanced oocyte competence, better early embryo development, and ultimately higher ART success rates. In conclusion, modulation of the gut-reproductive axis through targeted probiotic or prebiotic therapy represents a promising biological adjunct to assisted reproduction. Further mechanistic studies and large-scale randomized trials are warranted to validate its clinical applicability and optimize therapeutic regimens.},
}

@article {pmid42606819,
year = {2026},
author = {Lee, KJ and Park, JH and Park, H and Kim, MJ and Yoon, H and Kim, JM and Han, SH and Suk, KT},
title = {Phocaeicola coprocola attenuates liver fibrosis by modulating extracellular matrix remodeling.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2718623},
doi = {10.1080/19490976.2026.2718623},
pmid = {42606819},
issn = {1949-0984},
mesh = {Animals ; *Extracellular Matrix/metabolism ; *Liver Cirrhosis/metabolism/therapy/microbiology ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Liver/metabolism/pathology ; Gastrointestinal Microbiome ; Humans ; *Actinobacteria/physiology ; Diet, Western/adverse effects ; },
abstract = {Chronic liver diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD), frequently progress to liver fibrosis, yet effective antifibrotic therapies remain limited. Here, we investigated the therapeutic potential of the commensal bacterium Phocaeicola coprocola using Western diet (WD)-induced MASLD and DDC + TAA-induced fibrosis murine models. In the WD model, P. coprocola administration attenuated hepatic steatosis, reduced lipogenic gene expression, and improved metabolic and histological parameters. In contrast, in the DDC + TAA model of advanced fibrosis, P. coprocola significantly reduced cholestatic markers and fibrosis severity. Mechanistically, these antifibrotic effects occurred independently of broad suppression of inflammatory mediators or upstream TGF-β-Smad signaling, and were instead associated with selective downregulation of extracellular matrix (ECM)-related fibrogenic programs, including Col1a1, Col3a1, and Mmp2. Notably, these effects were observed even in the absence of detectable gut colonization, suggesting that stable engraftment is not required for therapeutic activity. P. coprocola also enhanced colonic epithelial barrier-related gene expression and host-microbial metabolic signaling. In humans, circulating ECM remodeling markers (PIIINP, MMP2, and TIMP1) were associated with fibrosis severity, supporting the translational relevance of ECM-targeted mechanisms. Collectively, these findings identify P. coprocola as a selective modulator of ECM remodeling that uncouples fibrotic output from upstream inflammatory signaling, highlighting its potential as a microbiome-based therapeutic strategy for liver fibrosis across multiple disease etiologies.},
}

Animals
*Extracellular Matrix/metabolism
*Liver Cirrhosis/metabolism/therapy/microbiology
Mice
Male
Disease Models, Animal
Mice, Inbred C57BL
Liver/metabolism/pathology
Gastrointestinal Microbiome
Humans
*Actinobacteria/physiology
Diet, Western/adverse effects

@article {pmid42607235,
year = {2026},
author = {Kharazishvili, K and Hujova, A and Hucl, T and Balounova, K and Vokacova, K and Kroupa, M},
title = {Leukocyte telomere length and gut microbiome profiles in pancreatic ductal adenocarcinoma and at-risk conditions.},
journal = {Biomolecules & biomedicine},
volume = {},
number = {},
pages = {},
doi = {10.17305/bb.2026.14506},
pmid = {42607235},
issn = {2831-090X},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at an advanced stage, highlighting the need for minimally invasive biomarkers capable of distinguishing it from related risk conditions. This study evaluated relative leukocyte telomere length (LTL) and gut microbiome profiles as potential biomarkers for PDAC. The study included 244 participants with PDAC (n = 37), chronic pancreatitis (CP; n = 56), type 2 diabetes mellitus (T2DM; n = 99), or no related risk conditions (controls; n = 52). LTL was measured by monochrome multiplex quantitative polymerase chain reaction (qPCR), while gut microbiome composition was assessed by 16S ribosomal RNA (rRNA) gene sequencing in a subset of participants with PDAC (n = 12), CP (n = 13), and controls (n = 7). LTL varied with age, sex, and smoking status. After adjustment for these factors, patients with PDAC had significantly longer LTL than controls (p = 0.029), whereas differences between PDAC and CP or T2DM were not significant. LTL showed limited ability to discriminate PDAC from controls (area under the receiver operating characteristic curve = 0.651) and was not associated with overall survival. Gut microbiome diversity and taxonomic composition did not differ significantly among the analyzed groups. These findings indicate that LTL has limited utility as a standalone diagnostic or prognostic biomarker for PDAC but may warrant further evaluation as a complementary marker in larger prospective studies. The exploratory microbiome findings also require validation in adequately powered cohorts.},
}

@article {pmid42607346,
year = {2026},
author = {Morizot, C and Halper, J and Breban, M and Gill, T and Loeuille, D and Moulin, D},
title = {Experimental models of spondyloarthritis: Pathophysiological insights and translational challenges.},
journal = {Journal of autoimmunity},
volume = {163},
number = {},
pages = {103607},
doi = {10.1016/j.jaut.2026.103607},
pmid = {42607346},
issn = {1095-9157},
abstract = {Spondyloarthritis (SpA) represents a heterogeneous group of chronic inflammatory rheumatologic diseases, including axial spondyloarthritis (axSpA), psoriatic arthritis (PsA), and SpA associated with inflammatory bowel disease (IBD). These conditions share overlapping clinical manifestations, genetic predisposition-particularly a strong association with HLA-B27-and common immunopathogenic pathways, notably the IL-23/IL-17 axis and tumor necrosis factor (TNF) signaling. Understanding SpA pathophysiology has been greatly facilitated by animal models, which have provided critical mechanistic insights and served as indispensable tools for preclinical drug testing. Among these, rodent models have been particularly informative. However, despite their contributions, no single model reproduces the full clinical spectrum of SpA, which includes axial inflammation, enthesitis, peripheral arthritis, and extra-articular manifestations such as uveitis, psoriasis, and gut involvement. This review provides a comprehensive analysis of rodent SpA models, focusing on their mechanistic underpinnings, key discoveries, and translational relevance. We first summarize the major categories of models before examining the strengths and limitations of each. We highlight how these models have advanced our understanding of the gut-joint axis, IL-23-driven entheseal inflammation, and TNF-dependent pathways, which are now major therapeutic targets. Finally, we discuss emerging strategies to enhance translational fidelity, including humanized mice, microbiome engineering, and integration of multi-omic approaches. These developments are essential to bridge the current gap between experimental findings and clinical applications in SpA.},
}

@article {pmid42603144,
year = {2026},
author = {Feidenhansl, C and Rruci, E and Knödlseder, N and Lomholt, HB and Brüggemann, H},
title = {Differential Quantification of Cutibacterium acnes Phylotypes IA and IB/II on Healthy and Acne-Prone Human Skin.},
journal = {Experimental dermatology},
volume = {35},
number = {8},
pages = {e70347},
pmid = {42603144},
issn = {1600-0625},
support = {LF-OC-21-000826//LEO Fondet/ ; //Kjærsgaard foundation/ ; },
mesh = {Humans ; *Acne Vulgaris/microbiology/drug therapy ; *Skin/microbiology ; Female ; Isotretinoin/therapeutic use ; Polymerase Chain Reaction/methods ; Skin Microbiome ; Adult ; Dermatologic Agents/therapeutic use ; *Propionibacteriaceae/genetics/isolation & purification ; *Propionibacterium acnes/genetics/isolation & purification ; Male ; Young Adult ; Hyaluronoglucosaminidase/genetics ; },
abstract = {Cutibacterium acnes is a common skin bacterium that inhabits sebaceous follicles and comprises multiple phylotypes. Healthy skin is colonized by a C. acnes population dominated by phylotypes IA, IB, and II. In acne, this diversity is reduced, with a predominance of phylotype IA. Quantifying C. acnes phylotypes has been challenging due to the lack of specific methods. Here, we developed a droplet digital PCR (ddPCR) assay that separately quantifies phylotype IA and phylotypes IB/II, based on a difference in the hyaluronidase gene. The method was applied to skin swabs from 14 healthy individuals and 14 acne patients. Healthy skin contained nearly equal amounts of IA and IB/II, whereas acne samples showed a 111-fold predominance of IA over IB/II, due to a marked depletion of IB/II, instead of an increase of IA. After 4-6 months of isotretinoin treatment, C. acnes levels decreased drastically, with phylotype IA reduced by 50-fold. Twelve to 15 months after treatment, both phylotypes rebounded, although IB/II recovered only partially. Taken together, this ddPCR method can quantitatively distinguish the acne-dominant phylotype IA from healthy skin-associated phylotypes IB/II, and is thus a useful tool for skin microbiome studies and specifically for assessing C. acnes dysbiosis in acne.},
}

Humans
*Acne Vulgaris/microbiology/drug therapy
*Skin/microbiology
Female
Isotretinoin/therapeutic use
Polymerase Chain Reaction/methods
Skin Microbiome
Adult
Dermatologic Agents/therapeutic use
*Propionibacteriaceae/genetics/isolation & purification
*Propionibacterium acnes/genetics/isolation & purification
Male
Young Adult
Hyaluronoglucosaminidase/genetics

@article {pmid42603146,
year = {2026},
author = {Zhang, R and Li, H and Wang, C and Yang, G},
title = {Synthetic microbial communities: emerging live biotherapeutics for targeted gut microbiome modulation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2719056},
doi = {10.1080/19490976.2026.2719056},
pmid = {42603146},
issn = {1949-0984},
mesh = {Humans ; Animals ; Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Inflammatory Bowel Diseases/therapy/microbiology ; *Biological Therapy/methods ; *Dysbiosis/therapy/microbiology ; Clostridium Infections/therapy/microbiology ; Colorectal Neoplasms/therapy/microbiology ; Clostridioides difficile ; },
abstract = {Gut microbiome dysbiosis causes various intestinal diseases. However, an undefined composition and potential biosafety risks limit the applicability of traditional fecal microbiota transplantation (FMT). Synthetic microbial communities (SynComs), which are compositionally defined and rationally designed emerging live biotherapeutics, offer a novel alternative to FMT. This review establishes strict boundaries between SynComs and traditional donor-derived preparations, comparatively evaluating "top-down" and "bottom-up" construction strategies. We explored the mechanisms underlying the SynComs-mediated synergistic restoration of intestinal homeostasis via direct targeted antagonism and modulation of the host immune network. Moreover, we systematically evaluated the current research landscape of SynComs in Clostridioides difficile infection, inflammatory bowel disease, and colorectal cancer. This review examines fundamental challenges, including host colonization resistance, chemistry, manufacturing, and control barriers, biosafety risks, and microbiokinetic regulatory frameworks, thereby addressing the translational gap. Our analysis of current literature provides a theoretical basis for the clinical translation of SynComs as emerging live biotherapeutics.},
}

Humans
Animals
Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome
Inflammatory Bowel Diseases/therapy/microbiology
*Biological Therapy/methods
*Dysbiosis/therapy/microbiology
Clostridium Infections/therapy/microbiology
Colorectal Neoplasms/therapy/microbiology
Clostridioides difficile

@article {pmid42603246,
year = {2026},
author = {Lou, J and Liu, H and Xiang, Z and Li, J and Kong, H and Le, X},
title = {Integrated analysis of the diabetic foot ulcer microbiome and host transcriptome supports a microenvironment-microbiota-host repair framework.},
journal = {Endocrine},
volume = {91},
number = {1},
pages = {},
pmid = {42603246},
issn = {1559-0100},
support = {2022RC255//Traditional Chinese Medicine Science and Technology Project of Zhejiang Province/ ; 2025HY0993//Medical and Health Science Program of Zhejiang Province/ ; CXTD202502004//Zhejiang Clinovation Pride/ ; Y202140685, Y202456684//Scientific Research Fund of Zhejiang Provincial Education Department/ ; 2023RC081, 2025KY1395, 2025KY1443//Medical Scientific Research Foundation of Zhejiang Province/ ; 2022-F17//Project of Ningbo Leading Medical & Health Discipline/ ; 2022498346//Zhejiang Medical and Health Science and Technology Project/ ; 2023030615//Ningbo Top Medical and Health Research Program/ ; },
mesh = {Humans ; *Diabetic Foot/microbiology/genetics ; *Microbiota/genetics ; *Transcriptome ; *Wound Healing/genetics/physiology ; Skin Microbiome ; Female ; Male ; },
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) arise from interacting clinical, microbial, and host processes, yet public datasets differ substantially in design, scale, and evidentiary strength.

METHODS: We curated eight public DFU cohorts and defined an evidence hierarchy. PRJNA287759 was reprocessed from raw 16 S reads; outcome tests used one baseline sample per patient (74 healed and 15 non-healed/adverse). GSE134431 compared 13 DFU with 8 diabetic foot skin samples using limma. Host discrimination underwent fold-confined leave-one-sample-out validation, 100 repeated nested five-fold analyses, 200 label permutations, and independent rank-score evaluation in GSE80178.

RESULTS: Baseline diversity and community structure did not differ by outcome (Shannon P = 0.159; Observed ASVs P = 0.669; PERMANOVA R2 = 0.0157, P = 0.142). Rothia was the only nominal genus (P = 0.0307), and none survived FDR correction across prevalence thresholds. GSE134431 yielded 2,873 differentially expressed genes with coherent epidermal repair enrichment. Host leave-one-sample-out AUC was 0.990 (95% CI 0.964-1.000), repeated nested-CV median AUC was 0.981 (95% interval 0.952-1.000), and permutation P was 0.00995. The GSE80178 score separated 6 DFU from 3 diabetic foot skin samples (exact P = 0.0238; AUC = 1.000), although this external comparison was small.

CONCLUSIONS: Host expression provides the strongest evidence, whereas microbiome findings remain exploratory. The repair framework synthesizes parallel evidence without demonstrating causal coupling or a clinically deployable biomarker.},
}

Humans
*Diabetic Foot/microbiology/genetics
*Microbiota/genetics
*Transcriptome
*Wound Healing/genetics/physiology
Skin Microbiome
Female
Male

@article {pmid42603266,
year = {2026},
author = {Weng, R and Dong, G and Tang, J and Zhao, Y},
title = {Gut Microbiota and Ischemic Stroke: From Pre-Stroke Dysbiosis and Acute-Phase Changes to Therapeutic Applications.},
journal = {Brain and behavior},
volume = {16},
number = {8},
pages = {e71547},
pmid = {42603266},
issn = {2162-3279},
support = {LCYSSQ20220823091204009 SCRCND202501//Shenzhen Clinical Research Center for Neurological Diseases/ ; //Shenzhen High-level Hospital Construction Fund/ ; },
mesh = {Humans ; *Dysbiosis/complications/microbiology ; *Ischemic Stroke/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Brain-Gut Axis/physiology ; *Brain Ischemia/microbiology ; *Stroke ; },
abstract = {PURPOSE: Ischemic stroke poses a major global health burden, and growing evidence points to the microbiota-gut-brain axis as an important contributor to stroke pathophysiology and recovery. The purpose of this review is to summarize current knowledge on bidirectional gut-brain communication in stroke, establishing gut dysbiosis as an upstream risk factor for stroke onset and examining microbiota dynamics across acute and chronic phases.

METHOD: A comprehensive review of the current literature was conducted to synthesize existing evidence on the mechanisms of gut-brain communication, the influence of host factors, post-stroke complications, and candidate therapeutic interventions targeting the MGBA in ischemic stroke.

FINDING: Gut dysbiosis acts as a risk factor for stroke through TMAO-mediated atherothrombosis, systemic inflammatory priming, and comorbidity-associated dysbiotic pre-conditioning. Following a stroke, dysbiosis is characterized by a depletion of short-chain fatty acid (SCFA)-producing taxa and an expansion of pro-inflammatory bacteria, particularly Proteobacteria and Enterobacteriaceae. Host factors (age, sex, genetics, and comorbidities) shape microbiota signatures and influence outcomes. Furthermore, post-stroke complications-including cognitive impairment, depression, stroke-associated pneumonia, and gastrointestinal dysfunction-are intimately linked to persistent dysbiosis. Mechanistically, the gut microbiota modulates stroke outcomes through immune regulation, metabolite signaling, blood-brain barrier integrity, and vagal pathways. Candidate therapeutic interventions (probiotics/prebiotics, fecal microbiota transplantation, SCFA supplementation, traditional Chinese medicine, and neuromodulation) demonstrate promising neuroprotective and recovery-enhancing effects, predominantly in preclinical models.

CONCLUSION: While targeted interventions like probiotics and dietary fiber supplementation have shown modest benefits in small clinical trials, human clinical evidence remains largely preliminary. The translation of FMT, SCFA supplementation, and neuromodulatory approaches to clinical practice requires validation through rigorous, adequately powered randomized controlled trials. Future precision microbiome medicine demands individualized profiling and phenotype-specific interventions to establish microbiota-targeted strategies as viable adjunctive stroke therapies.},
}

Humans
*Dysbiosis/complications/microbiology
*Ischemic Stroke/microbiology/therapy/physiopathology
*Gastrointestinal Microbiome/physiology
Animals
*Brain-Gut Axis/physiology
*Brain Ischemia/microbiology
*Stroke

@article {pmid42603366,
year = {2026},
author = {Huang, H and Sun, J and Zhai, M and Jiang, C and Zhu, G},
title = {Periodontitis in a Large Cohort of Young Chinese Adults: Associated Factors and Salivary Microbiome-Metabolome Profiles.},
journal = {International dental journal},
volume = {76},
number = {5},
pages = {109813},
doi = {10.1016/j.identj.2026.109813},
pmid = {42603366},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: Periodontitis is a chronic multifactorial inflammatory disease that damages periodontal tissues and is associated with systemic diseases. It shows a global younger onset trend, with rising incidence in Chinese young adults, but studies mostly focus on those ≥35 years, lacking systematic exploration of 18 to 35-year-olds.

METHODS: From December 2024 to May 2025, 2888 adults aged 18 to 35 years were recruited from Tongji Hospital. Periodontitis was diagnosed per the 2018 Classification. Questionnaires collected demographic, physical and mental health, oral hygiene and lifestyle data. Saliva samples underwent 16S rRNA sequencing and untargeted metabolomics. Statistical analyses included independent samples t-test, Mann-Whitney U test, chi-square test and binary logistic regression.

RESULTS: Periodontitis prevalence was 25.00%. Logistic regression identified marital status, suboptimal health, adverse childhood experiences, smoking and alcohol drinking were correlated with periodontitis, while longer per-brushing duration was negatively correlated with periodontitis. Salivary microbiota community richness and composition differed significantly between groups, with higher Fusobacteriota in periodontitis patients. Untargeted metabolomics identified 267 differential metabolites (mainly lipids, amino acids) and enriched metabolic pathways (e.g., nucleotide metabolism). Fusobacteriota was negatively correlated with 5-phosphoribosyl-4-carboxy-5 aminoimidazole.

CONCLUSIONS: Multiple factors were associated with periodontitis in young adults. Salivary microbiota and metabolic abnormalities may be associated with its pathogenesis, providing a scientific basis for prevention and management. The generalizability of these findings was limited by single-center convenience sampling and exploratory multi-omics profiling performed on a small matched subgroup.

CLINICAL RELEVANCE: This study identified a 25% prevalence of periodontitis in Chinese young adults aged 18 to 35 years, clarified its multidimensional associated factors, and revealed salivary microbiome-metabolome perturbations. It provided a scientific basis for the prevention of periodontitis in this young population.},
}

@article {pmid42603438,
year = {2026},
author = {Verma, V and Devi, YL and Devi, TB and Laishram, P and Dinesh, GK and Sarangi, PK and Singh, AK and Prasad, R},
title = {Wheat microbiome interactions under climate change: Mechanisms of abiotic stress tolerance and sustainable crop resilience.},
journal = {Plant physiology and biochemistry : PPB},
volume = {238},
number = {},
pages = {111626},
doi = {10.1016/j.plaphy.2026.111626},
pmid = {42603438},
issn = {1873-2690},
abstract = {Climate change-induced stresses, including drought, heat, and salinity, are increasingly constraining wheat productivity globally and pose a significant threat to global food security. Although beneficial rhizosphere microorganisms are known to enhance wheat stress tolerance, the mechanisms underlying wheat-microbiome interactions under climate-stress conditions remain poorly understood. This review highlights that wheat actively recruits and reshapes stress-resilient microbial communities, particularly members of Bacillus and Pseudomonas, which promote stress adaptation by regulating reactive oxygen species (ROS), phytohormone homeostasis, nutrient acquisition, and stress-responsive signalling pathways. Furthermore, wheat domestication has altered plant-microbe interactions, resulting in substantial differences in microbiome composition and functional potential between modern cultivars and their wild relatives. The wheat rhizosphere is a dynamic ecological interface where roots interact with diverse microbial communities that influence plant growth, nutrient cycling, and resilience to environmental stresses. This review synthesizes current knowledge on the effects of climate change on wheat physiology, growth, and rhizosphere microbiome composition, while examining how soil physicochemical properties shape microbial assembly and function. Particular emphasis is placed on the mechanisms by which beneficial microorganisms alleviate abiotic stress, including modification of root system architecture, antioxidant regulation, indole-3-acetic acid (IAA) production, osmolyte accumulation, nutrient mobilization, and mitigation of stress-induced ethylene through ACC deaminase activity. We also discuss plant-microbe communication networks mediated by root exudates, microbial signalling molecules, and hormonal crosstalk that govern microbial recruitment, colonization, and establishment within the rhizosphere. Recent advances in genomics, transcriptomics, proteomics, metabolomics, and integrated multi-omics approaches have revealed that wheat dynamically restructures its microbiome in response to environmental stress, with host genotype serving as a key determinant of microbial community composition and function. By integrating evidence on soil properties, microbial functional traits, rhizosphere community dynamics, and wheat stress adaptation, this review provides a comprehensive framework for understanding microbiome-mediated stress resilience. Despite considerable progress, significant knowledge gaps remain regarding microbial community stability, functional redundancy, and the long-term field performance of microbial consortia across locations, seasons, and combined stress scenarios. Addressing these challenges through the integration of multi-omics technologies, microbiome-assisted breeding, synthetic microbial consortia, and climate-smart management strategies will be essential for developing resilient and sustainable wheat production systems under changing climatic conditions.},
}

@article {pmid42603583,
year = {2026},
author = {Zhang, X and Li, J and Yang, Z and Zheng, S and Huang, Q and Meng, F and Zhang, Y},
title = {Maternal co-exposure to polystyrene microplastics and DEHP impairs thyroid function in adult rat offspring.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128962},
doi = {10.1016/j.envpol.2026.128962},
pmid = {42603583},
issn = {1873-6424},
abstract = {Maternal combined exposure to polystyrene microplastics (PS-MPs) and di-(2-ethylhexyl) phthalate (DEHP) poses potential risks to offspring endocrine development; however, the combined effects of these two contaminants remain poorly characterized. Pregnant rats were exposed to PS-MPs, DEHP or a combination of both throughout pregnancy and lactation. The hypothalamic-pituitary-thyroid (HPT) axis function and gut microbiota composition were then assessed in adult offspring. Single-contaminant exposure altered thyroid hormone levels and HPT axis gene expression. Co-exposure exacerbated these disruptions, producing greater TSH suppression, elevated thyroid hormone levels, and uniform downregulation of Nis expression in offspring of both sexes. Sex-specific differences in hypothalamic and pituitary gene expression were observed, suggesting that upstream HPT axis regulation was disrupted via sex-divergent mechanisms. The combined exposure also induced morphological disruption of thyroid follicular epithelial cells and elevated oxidative stress markers. In co-exposed offspring, gut microbiome profiling revealed Bacteroides depletion and Enterococcus enrichment as the most prominent taxa-level shifts. The parallel perturbations in gut microbiome composition and HPT axis function across treatment groups support a proposed disruption model of the gut-brain-thyroid axis. Our findings demonstrate that maternal co-exposure to PS-MPs and DEHP induces sex-divergent thyroid endocrine disruption in offspring, driven by a complex integration of additive and synergistic toxicities. Consequently, relying exclusively on single-pollutant models likely underestimates the developmental health threats of real-world plastic mixtures, highlighting the critical need to incorporate mixture interactions and sex-specific vulnerabilities into future environmental risk assessments.},
}

@article {pmid42603665,
year = {2026},
author = {Stewart, GE and Guo, Y and Cao, S},
title = {Emerging bacterial membrane vesicles from microbial messengers to therapeutic nanocarriers.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {115250},
doi = {10.1016/j.jconrel.2026.115250},
pmid = {42603665},
issn = {1873-4995},
abstract = {Bacterial membrane vesicles (BMVs) are nanoscale vesicles that are naturally released by bacteria into the extracellular environment. By retaining the bacterium's membrane and luminal cargo, BMVs represent natural nanocarriers and long-distance messengers capable of influencing human health and disease progression. Depending on the bacterial species of origin, BMVs present important transport roles by carrying diverse native molecular cargo, protecting luminal cargo from degradation, promoting intracellular delivery and cytosolic release, crossing biological barriers, and mediating interactions with host cells. Recently, engineering strategies have emerged to harness these natural nanocarriers for the improved delivery of a wide range of therapeutic cargos, including proteins, antigens, nucleic acids, oncolytic viruses, polymers, and nanoparticles. These engineering strategies include genetic engineering, encapsulation, surface modification, and detoxification methods. Together, these strategies provide features including superior loading efficiency, targeted delivery, controlled release, longer circulation time, and multi-composite delivery approaches. This review discusses BMVs as versatile, multi-functional, and bio-active delivery vehicles along with current preparation methods, delivery routes, engineering strategies, highlighting unique features and challenges for translation.},
}

@article {pmid42603715,
year = {2026},
author = {Altaffer, AL and Weisman, MH and Kaplan, RM and Horváth-Puhó, E and Sørensen, HT and Weiss, PF},
title = {Early life exposures association with later diagnosis of spondyloarthritis: A population-based case-control study.},
journal = {The Journal of rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.3899/jrheum.2026-0087},
pmid = {42603715},
issn = {1499-2752},
abstract = {OBJECTIVE: To assess whether early-life antibiotics are associated with spondyloarthritis (SpA) diagnosed by age 21.

METHODS: In this population-based, matched case-control study, we used Danish live births (1997-2023) restricted to those reaching minimum relevant ages by December 31, 2024: 1-21 years for psoriatic arthritis (PsA), 6-21 years for peripheral/axial SpA and inflammatory bowel disease-associated arthritis (IBD-AA). Cases (n=560) had physician-recorded SpA (peripheral/axial SpA, PsA, or IBD-AA). Controls were matched 1:50 by birth year, sex, and calendar year of diagnosis. Primary exposure was systemic antibiotic use the first year of life; secondary exposures included antibiotic class, number of courses, delivery mode, early upper respiratory tract infection (URTI), and systemic nonbacterial antimicrobials. Conditional logistic regression estimated adjusted odds ratios (aORs); dose-response was tested with the Wald test.

RESULTS: Among cases (median age 16.8 years; 59% peripheral/axial SpA, 28% PsA, 13% IBDAA), 50% received antibiotics, versus 42% of controls. First-year antibiotic exposure was associated with higher odds of SpA (aOR 1.35, 95% CI: 1.14-1.59). Broad-spectrum penicillins had the strongest class-specific association (aOR 1.42, 95% CI 1.19-1.70). Early URTI was independently associated with SpA (aOR 1.88, 95% CI 1.32-2.67); delivery mode and systemic nonbacterial antimicrobials were not. In SpA subgroup analysis, the association with first-year antibiotics was significant only for PsA (aOR 1.75, 95% CI: 1.27-2.41).

CONCLUSION: Antibiotic exposure in the first year of life, particularly broad-spectrum penicillins, was associated with increased odds of SpA by age 21, supporting the hypothesis that early-life microbiome disruption may increase later SpA risk.},
}

@article {pmid42600524,
year = {2026},
author = {Khan, R and Uddin, N and Srivastava, AK and Iqbal, A and Riaz, A and Kamran, A and Xie, X and Yang, S},
title = {Nanoparticles in climate-resilient agriculture: Biological mechanisms, rhizosphere interactions, and yield enhancement under abiotic stress.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128683},
doi = {10.1016/j.micres.2026.128683},
pmid = {42600524},
issn = {1618-0623},
abstract = {Climate change intensifies abiotic stresses that limit crop productivity, requiring innovative strategies to enhance resilience without compromising sustainability. Nanoparticles (NPs) have emerged as potential modulators of plant stress responses by influencing molecular regulation, physiological adaptation, and stress resilience. However, current evidence remains fragmented because studies are dispersed across different NP types, crop species, abiotic stress conditions, and omics platforms, with most investigations conducted under controlled experimental conditions and few integrating molecular responses with agronomic performance. In this study, we synthesize evidence from plant physiology, omics (including transcriptomics, proteomics, metabolomics, and soil microbiome analyses), and agronomic studies to provide an integrated conceptual synthesis linking NPs' physicochemical properties with multi-omics reprogramming and yield-related outcomes under abiotic stress. Collectively, the available evidence indicates that NP size, surface charge, composition, and redox activity strongly influence uptake behavior, intracellular interactions, and signaling intensity, thereby shaping coordinated system-level responses rather than isolated modifications in individual genes, proteins, or metabolites. Across abiotic stresses, NPs modulate stress responses through effects on redox homeostasis, hormonal signaling, ion transport, metabolic flexibility, and rhizosphere interactions. However, their effects vary with NP properties, application conditions, plant species, and stress environments, ranging from stress mitigation to growth inhibition. These responses can improve photosynthetic stability, reproductive performance, and resource allocation, contributing to partial recovery of growth and yield under certain stress conditions. Conversely, excessive or poorly controlled NP exposure disrupts redox balance and growth, underscoring the importance of narrow efficacy windows. We further identify key limitations in the existing literature, including dose and crop specificity, short-term experimental designs, limited field validation, and limited mechanistic linkage between multi-omics responses and agronomic performance, highlighting the need for synchronized multi-omics validation. We contend that future advancements require a transition from proof-of-concept demonstrations to predictive, system-level approaches that integrate multi-omics with developmental stage, environmental context, and yield stability. By reframing NPs as context-dependent modulators of stress resilience rather than universal growth enhancers, this review provides a conceptual foundation for their responsible evaluation and potential application in climate-resilient agriculture.},
}

@article {pmid42600695,
year = {2026},
author = {Merenstein, C and McGinniss, JE and Gallop, R and Whiteside, SA and Pandya, K and Oyster, M and Graham-Wooten, J and Kalman, L and Clausen, E and Cantu, E and Diamond, JM and Bushman, FD and Christie, JD and Collman, RG},
title = {The Early Post-Transplantation Lung Microbiome and CXCL10 are Associated with Chronic Lung Allograft Dysfunction: A Prospective Study with 5-year Follow-Up.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2026.08.009},
pmid = {42600695},
issn = {1600-6143},
abstract = {Chronic lung allograft dysfunction (CLAD) is the major barrier to long-term lung transplantation success. Microbial factors have been linked to CLAD risk, and sequence-based methods have been applied recently to identify potential microbial drivers, though patient heterogeneity and follow-up time have been limitations. We undertook a longitudinal cohort study of 186 patients transplanted for diseases other than cystic fibrosis. Dense lung sampling was done over the first-year and patients were followed for 6.04 (median) years. Bronchoalveolar lavage (BAL) was analyzed by bacterial 16S rRNA gene sequencing and quantification. Post-implantation BAL was assayed for cytokines and metabolomics. Seventy patients (38%) developed CLAD. CLAD development and shorter time-to-CLAD were associated with higher lung bacterial burden particularly 6-months post-transplant, low Streptococcus/Prevotella ratio in lung six-weeks post-transplant, and elevated lung IP10/CXCL10 immediately post-implantation. Each factor associated with distinct CLAD timing. These factors, together with previously-recognized clinical features, stratify patients into groups differing by >3-fold CLAD risk. Thus, increased lung bacteria and altered composition during the first-year post-transplantation and immediate post-implantation IP10/CXCL10 associate with CLAD after transplantation for non-CF lung disease. Early events in the allograft may establish conditions impacting later graft failure, identify potentially modifiable mechanisms of injury, and provide biomarkers of CLAD risk.},
}

@article {pmid42600761,
year = {2026},
author = {Hong, Z and Lu, Z and Shi, R and Zheng, S and Luo, J and Chen, J and Xie, Z and Zheng, JS and Chen, YM and Zhang, Z},
title = {Prospective associations of tea consumption with skeletal muscle mass and strength: Insights from the gut microbiome and proteomics.},
journal = {Pharmacological research},
volume = {231},
number = {},
pages = {108398},
doi = {10.1016/j.phrs.2026.108398},
pmid = {42600761},
issn = {1096-1186},
abstract = {Tea consumption may be associated with skeletal muscle health, but longitudinal evidence based on repeated assessments remains limited. We examined the associations of tea intake and serum biomarkers with repeated skeletal muscle measures and explored whether these associations might be partly explained by multi-omics features. In this prospective cohort, 3408 adults were followed for approximately 12 years. Skeletal muscle mass was measured by dual-energy X-ray absorptiometry, handgrip strength by digital dynamometry, gut microbial taxonomic and functional profiles by shotgun metagenomic sequencing, serum proteins by data-independent acquisition mass spectrometry, and fecal metabolites by targeted UPLC-MS/MS metabolomics. Linear mixed-effects models examined longitudinal associations, and mediation analyses estimated indirect effects. In longitudinal analyses, higher tea consumption frequency was associated with greater appendicular skeletal muscle mass, appendicular skeletal muscle index, and handgrip strength (β: 0.037-0.140; 95% CI: 0.002-0.205). Higher circulating flavan-3-ols showed similar associations with these muscle-related outcomes (β: 0.085-0.174; 95% CI: 0.007-0.254), whereas no significant associations were observed with walking speed. Exploratory multi-omics analyses identified tea-related differences in gut microbial species and functional pathways, fecal metabolites, and circulating proteins, including Gemmiger formicilis, amino acid biosynthesis pathways, fructose 1,6-bisphosphate, VTN, CFI, CNDP1, and ITIH4. Exploratory mediation analyses identified statistical indirect associations involving multi-omics features, with estimated proportions mediated ranging from 4.5% to 19.0%. Overall, higher tea consumption and circulating biomarkers were associated with greater skeletal muscle mass and strength, accompanied by distinct multi-omics features that may provide potential biological links between tea exposure and muscle-related outcomes.},
}

@article {pmid42600831,
year = {2026},
author = {Fabian Plaza, S and Gonzalo Tortella, F and Larama, G and Rodriguez, R and Lebeau, T and Lapie, C and Valdivia, W and Fajardo, E and Fernández-Baldo, M and Hirzel, J and Santoyo, G and Schoebitz, M},
title = {Forest conversion is more strongly associated with soil microbial functioning than chronic trace element exposure in an industrialized coastal Mediterranean ecosystem.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128963},
doi = {10.1016/j.envpol.2026.128963},
pmid = {42600831},
issn = {1873-6424},
abstract = {Forest soils in industrialized coastal zones can experience chronic diffuse trace element (TE) exposure, yet how vegetation replacement influences soil microbial communities under these conditions remains poorly understood. This study compared soils from native sclerophyllous forests and exotic pine plantations in the Hualpén Peninsula Nature Sanctuary (Chile), located near an industrial complex characterized by oil refining, petrochemical, steel, and port activities. Twenty-two soil sites were evaluated for TE concentrations, contamination indices, physicochemical properties, microbial biomass, enzymatic activities, and bacterial community composition using 16S rRNA gene sequencing. Native forest soils contained 89% more organic matter (14.4% vs. 7.6%) and nearly twice the available N (53.6 vs. 26.2 mg kg[-1]) than plantation soils. These soils also exhibited greater respiration and microbial biomass carbon, whereas plantation soils showed higher metabolic quotients (qCO2), indicating lower microbial metabolic efficiency. Soil pH remained acidic in both systems (5.6-5.8). Mn and Zn were the most abundant elements, while contamination factors were highest for Pb, Cr, and Mn, indicating persistent trace element enrichment across the study area. Bacterial communities were dominated by Proteobacteria, Actinobacteriota, and Acidobacteriota, with native forest soils showing significantly higher Faith phylogenetic diversity (p = 0.041). Redundancy analysis revealed that bacterial community structure was more strongly associated with nutrient availability and microbial functional indicators than with trace element enrichment. However, Cr showed a significant secondary association (envfit r[2] = 0.53, p = 0.032). Overall, the results indicate that variation in soil microbial functioning was more closely associated with vegetation type and related soil properties than with chronic trace element enrichment. These findings highlight the importance of considering land-use change, soil quality, and contamination together when evaluating microbial responses in industrially influenced forest ecosystems.},
}