@article {pmid41851157,
year = {2026},
author = {Serventi, L and Huang, C and Hofmann, R},
title = {Exploring pea soaking water as alternative to synthetic fertilizer: growth and microbial analysis of pea and tomato plants.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41851157},
issn = {2045-2322},
abstract = {Synthetic fertilizers deplete soil microbiome. Organic fertilizers lack specific nutrients for plant growth. A fertilizer that delivers essential nutrients to plants without deteriorating soil is lacking. This study investigated the viability of using pea soaking water (PSW) as substitute for synthetic fertilizers to enhance the growth of pea and tomato plants. Traits included plant growth stages, shoot and root weight, estimated chlorophyll content, and soil microbial populations. Pea plants exhibited consistent growth stages and rates of development across treatments, whereas tomato plants displayed treatment-dependent growth variations and differences in rates of development. Synthetic fertilizer (NPK) and PSW treatments increased shoot weight and chlorophyll content in both pea and tomato plants, compared with their controls. Interestingly, PSW produced comparable shoot growth to synthetic fertilizer in both crops. Root weights were similar in response to both fertilizer treatments in tomato but only increased in response to synthetic fertilizer in pea plants. Soil microbial analysis highlighted differences in Lactobacillus amount with soil supporting pea plants having higher bacteria counts. Notably, Lactobacillus amounts were reduced by 48% in the synthetic fertilizer treatment, but not by PSW, compared with the control, for tomatoes only. These findings suggest that PSW is a potential alternative to synthetic fertilizer to sustainably support plant growth. Replacement of synthetic fertilizer with PSW could reduce the environmental impact of agriculture by promoting healthy soil microbiota and preventing eutrophication, as well as reducing reliance on fertilizers. Further research is needed to explore its effect on crop yield, and applicability across crop species, field, and environmental conditions.},
}

@article {pmid41851187,
year = {2026},
author = {Su, X and Jin, J and Huang, Y and Hou, H and Li, Z and Cao, C and Wang, X and Li, F and Deng, Z and Zhang, M},
title = {Tumor-suppressing multi-enterobacteria enhance the anti-PD-1/PD-L1 efficacy in microsatellite stable colorectal cancer.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41851187},
issn = {2045-2322},
support = {Y-HR2019-0295//Beijing Xisike Clinical Oncology Research Foundation/ ; 2024AFD426//Joint Fund Project for Innovation and Development of Hubei Provincial Natural Science Foundation/ ; },
abstract = {UNLABELLED: Gut microbiome plays a pivotal role in modulating immunotherapy responses in colorectal cancer (CRC) treatment. While individual enterobacteria have been identified as enhancers of anti-PD-1/anti-PD-L1 therapy, the synergistic effects of multiple probiotic strains remain insufficiently explored. In this study, we investigated the therapeutic potential of Tumor-Suppressing Multi-Enterobacteria (TSME), a consortium of nine beneficial intestinal probiotic strains, in enhancing anti-PD-1/anti-PD-L1 therapy for microsatellite stable (MSS) CRC. Using a tumor-bearing mouse and employing techniques including flow cytometry, immunohistochemistry, ELISA, and genomic sequencing, we found that TSME significantly improved the efficacy of immune checkpoint inhibitors (ICIs) by optimizing tumor immune and microbe microenvironment. Specifically, the addition of TSME increased CD8[+] T cell infiltration and reshaped cytokine profiles, including reducing pro-inflammatory cytokines (IL-17, IL-1β, IL-6, and TNF-α) while elevating anti-inflammatory factors (IFN-γ). Moreover, TSME significantly up-regulated key immune pathways, including TNF signaling, cytokine-cytokine receptor interaction, and JAK-STAT signaling. In addition, TSME restructured the gut microbiome, increasing the abundance of beneficial bacteria such as Akkermansia and Alistipes. These findings highlight the synergistic effect of the multi-strain probiotics in enhancing ICI efficacy. Well-formulated probiotic consortia offer a promising strategy for enhancing immunotherapy outcomes in MSS CRC and advancing broader implementation of microbiome-assisted precision oncology.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44494-5.},
}

@article {pmid41877288,
year = {2026},
author = {Wei, G and Liu, M and Huang, L and Chen, C},
title = {Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41877288},
issn = {2524-4671},
support = {32272831//National Natural Science Foundation of China/ ; },
abstract = {UNLABELLED: Fungi are crucial components of the pig gut microbiome, influencing host immunity and metabolism. However, the investigation about gut fungi via metagenomic sequencing remains challenging due to analytical complexity. Here, we characterized pig gut fungal profiles using 750 metagenomes collected from public repositories and our previous datasets based on a comprehensive collection of fungal reference genomes, and revealed dynamic compositional changes of pig gut fungi from birth to market (7d, 14d, 21d, 28d, 35d, 70d, and 140d). Weaning significantly shaped the gut fungal community, affecting key fungi like Lachancea kluyveri and Kazachstania slooffiae. Inter-kingdom interaction analysis revealed significant correlations between fungi and bacteria, such as between L. kluyveri and Lactobacillus amylovorus (r = -0.48) and between K. slooffiae and Lactobacillus johnsonii (r = 0.75). We identified 87 diarrhea-associated fungal species at the significance threshold of LDA > 2.0 in three experimental piglet cohorts. In antibiotic-free piglets, fungal species from Saccharomyces and Aspergillus, some of which have been considered as potential probiotics, were enriched in healthy individuals, whereas in antibiotic-treated groups, Saccharomyces spp. and K. slooffiae were higher in diarrheal piglets. Notably, K. slooffiae were negatively correlated with the pathogen M. circinelloides, suggesting a protective role during gut dysbiosis. This study provides a foundation for developing fungal-based interventions to improve pig health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00551-y.},
}

@article {pmid42071032,
year = {2026},
author = {Wang, H and Wang, F and Guo, Q and Zou, B and Li, P and Xu, X and He, J and Jiang, S and Yue, J},
title = {Dynamic changes in gut microbiota and discovery of prognostic biomarkers in locally advanced pancreatic cancer during chemoradiotherapy.},
journal = {Clinical and experimental medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42071032},
issn = {1591-9528},
support = {82272753//National Natural Science Foundation of China/ ; ZF004//Collaborative Academic Innovation Project of Shandong Cancer Hospital/ ; },
abstract = {UNLABELLED: Pancreatic cancer has an exceptionally poor prognosis, with the majority of cases diagnosed at an advanced stage. Concurrent chemoradiotherapy (CCRT) remains the standard of care for locally advanced pancreatic cancer (LAPC); however, its therapeutic efficacy is limited. Emerging evidence suggests that the gut microbiota is an important modulator of cancer progression and treatment response. Nevertheless, the dynamic changes in the gut microbial ecosystem in LAPC patients undergoing CCRT remain poorly understood. This study aimed to characterize longitudinal alterations in the gut microbiota during CCRT, identify candidate microbiome-based prognostic markers, and explore their potential associations with host responses. This longitudinal study included 16 patients with LAPC. Fecal and peripheral blood samples were collected at three predefined time points: before CCRT initiation, during CCRT, and after CCRT completion. Gut microbiota composition and community structure were analyzed using 16 S rRNA sequencing targeting the V3–V4 region. Bioinformatic analyses were performed to assess taxonomic distribution, alpha and beta diversity, and microbial co-occurrence patterns. The prognostic relevance of microbial features was further evaluated using machine learning models integrating clinical parameters to predict overall survival. CCRT was associated with dynamic changes in specific microbial taxa across multiple taxonomic levels, with marked inter-individual heterogeneity in microbiota responses. In addition, microbial co-occurrence network complexity was reduced during treatment. Certain microbial taxa during CCRT showed associations with tumor-related serum biomarkers. Using integrated machine learning models, we identified candidate microbiota-based prognostic markers. In particular, Bifidobacterium and Bacteroides were associated with survival prediction, achieving areas under the receiver operating characteristic curve (AUC) of 0.833 and 0.722, respectively. CCRT is associated with longitudinal alterations in the gut microbiome of patients with LAPC, involving both compositional and structural changes. These findings suggest that microbiome dynamics may have potential value as exploratory prognostic indicators. However, given the limited sample size and observational design, further validation in larger cohorts and mechanistic studies are required before clinical application.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10238-026-02158-8.},
}

@article {pmid42075347,
year = {2026},
author = {Núñez-Muñoz, LA and Vargas-Hernández, BY and García-Sierra, MC and Calderón-Pérez, B and Xoconostle-Cázares, B and Ruiz-Medrano, R},
title = {Bacterial and Fungal Communities Associated with the Ectomycorrhizospheric Soil and Stem Endosphere of the Mycoheterotrophic Plant Monotropa uniflora.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081145},
pmid = {42075347},
issn = {2223-7747},
support = {CBF-2025-3383//Secretaría de Ciencia Tecnología e Innovación/ ; CF-2023-G-731//Secretaría de Ciencia Tecnología e Innovación/ ; },
abstract = {The mycoheterotrophic plant Monotropa uniflora relies on fungal symbionts for carbon and nutrient acquisition. However, its interactions with other microbial groups, beyond ectomycorrhizal fungi, remain unexplored. Here, we characterized bacterial and fungal communities associated with M. uniflora across two compartments: ectomycorrhizospheric soil linked to the mycorrhizal network and the surface-sterilized lower stem endosphere. Microbial community composition was assessed using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. Fungal richness was consistently higher in ectomycorrhizospheric soil than in the stem endosphere, whereas bacterial alpha diversity showed no consistent differences between compartments. Multivariate analyses suggested compartment-associated patterns in both bacterial and fungal community composition. Ectomycorrhizospheric soil was dominated by saprotrophic fungal taxa and bacterial groups with predicted metabolic potential, including taxa associated with iron, sulfur and nitrogen cycling. In contrast, the lower stem endosphere was enriched in bacterial taxa commonly associated with anaerobic and nitrogen-related metabolisms. Functional predictions further suggested an increase of carbon fixation-related pathways in rhizosphere-associated bacterial communities. Together, these results indicate that M. uniflora is associated with distinct and structured microbial assemblages across soil and internal plant compartments, highlighting the predicted functional potential of bacterial communities in nutrient- and carbon-related processes in mycoheterotrophic plant-soil systems alongside fungal partners.},
}

@article {pmid42075353,
year = {2026},
author = {Aleynova, OA and Ananev, AA and Nityagovsky, NN and Suprun, AR and Beresh, AA and Dubrovina, AS and Kiselev, KV},
title = {Ability of Different Bacteria from Grapevine to Colonize Arabidopsis thaliana Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081151},
pmid = {42075353},
issn = {2223-7747},
support = {22-74-10001-П//the Russian Science Foundation/ ; },
abstract = {This study investigates the impact of inoculating seeds with bacterial endophytes isolated from Vitis amurensis Rupr. on endophytic community composition in Arabidopsis thaliana (L.) Heynh. Ten bacterial isolates of the genera Agrobacterium, Bacillus, Curtobacterium, Erwinia, Frondihabitans, Gordonia, Pantoea, Pseudomonas, Sphingomonas, and Xanthomonas were applied to seeds and some visible phenotypic effects were observed on plant growth after two weeks. High-throughput sequencing of 16S rRNA revealed that the native endophytic microbiome of A. thaliana was dominated by Gammaproteobacteria, Actinomycetes, Bacteroidia, and Alphaproteobacteria. The key families were Microscillaceae, Chitinophagaceae, Rhizobiaceae, Rhodanobacteraceae, Nocardioi-daceae, Nocardiaceae, Xanthomonadaceae, Devosiaceae, Microbacteriaceae, Crocinitomi-caceae, Pseudomonadaceae, Solimonadaceae, Comamonadaceae, Caulobacteraceae, and Micrococcaceae. Arabidopsis seed inoculation with Agrobacterium sp. R8SCh-B12, Curtobacterium sp. P7SA-B3, and Gordonia aichiensis P6PL2 significantly reduced alpha diversity (Shannon index) and altered beta diversity relative to controls, indicating strong community restructuring. These three isolates, along with Pseudomonas sp. R8SCh-B2, Sphingomonas sp. RA62c-B5, Xanthomonas sp. R7SCh-B6, and Bacillus velezensis AMR25, successfully colonized the plant tissues, as evidenced by significant increases in genus-specific amplicon sequence variants, ASVs (up to 17,820-fold for Curtobacterium sp. ASV33). In contrast, Pantoea sp. P7SCH-B5, Erwinia sp. R8SCh-B3, and Frondihabitans sp. RA62c-B2 failed to colonize A. thaliana, despite being applied to the seeds, suggesting the existence of mechanisms restraining colonization. These findings demonstrate that only a subset of grapevine-derived endophytes can effectively colonize A. thaliana, and that successful colonization correlates with significant shifts in the native microbiome, even in the absence of overt phenotypic changes. This emphasizes the importance of strain-specific compatibility in plant-endophyte interactions. Thus, we report the first descriptions of several novel endophytes that colonized Arabidopsis plants and establish a convenient model to investigate plant-bacterial interactions.},
}

@article {pmid42075357,
year = {2026},
author = {Sun, C and Ge, Z and Yang, X and Xie, X and Liang, X and Shen, L and Ren, J and Zhang, Y},
title = {Silicon Combined with Activated Carbon Enhances Salt Tolerance in Strawberry (Fragaria × ananassa) by Reinforcing Ion-Redox Homeostasis and Reshaping the Rhizosphere Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081154},
pmid = {42075357},
issn = {2223-7747},
support = {2021C02066-7//Crop New Variety Breeding of Zhejiang Province/ ; SY202304//the Local Science and Technology Cooperation Project of Zhejiang Academy of Agricultural Sciences/ ; 2025SNJF029//the Zhejiang "Sannong Jiufang" Science and Technology Collaboration Program/ ; 2023Z112//the Ningbo Municipal Major Special Project/ ; },
abstract = {Soil salinity severely constrains strawberry production by disrupting ion homeostasis and provoking oxidative injury. This study investigated whether soluble silicon (Si) and activated carbon (AC) act to enhance salt tolerance in strawberry (Fragaria × ananassa). Under NaCl stress, plants showed pronounced growth inhibition, increased Na[+] accumulation and a deteriorated K[+]/Na[+] balance, accompanied by elevated reactive oxygen species (ROS) and lipid peroxidation. In contrast, combined AC + Si treatment consistently provided the strongest protection, improving seedling vigor and survival. Relative to NaCl alone, AC + Si increased shoot and root fresh weight by 67.5% and 78.5%, reduced shoot Na[+] by 59.1%, and lowered shoot H2O2 and MDA by 62.6% and 66.5%, respectively, indicating marked improvement in ion-redox homeostasis. Beyond plant responses, AC-containing treatments alleviated salt-induced increases in soil electrical conductivity, coinciding with a clear restructuring of the rhizosphere bacterial community and enrichment of putatively beneficial taxa. Transcriptome profiling further supported coordinated reprogramming of ion transport, redox control and stress-responsive signaling pathways under the AC + Si regime. Collectively, the results indicated that Si and AC co-application enhances strawberry salt tolerance through an integrated soil-plant-microbiome mechanism that stabilizes ion homeostasis and reinforces redox homeostasis.},
}

@article {pmid42075461,
year = {2026},
author = {Rueda Foronda, JA and Ríos López, JS and Múnera Porras, LM and Pino Rodriguez, NJ},
title = {Climate Variability Under ENSO Reshapes the Coffea arabica Rhizosphere Microbiome While Preserving a Conserved Bacterial Core.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081259},
pmid = {42075461},
issn = {2223-7747},
support = {202143210//Universidad de Antioquia/ ; },
abstract = {Climate variability is a major driver of belowground microbial assembly, yet its effects on rhizosphere microbiomes in perennial crops remain insufficiently resolved. We investigated how macroclimatic oscillations associated with the El Niño-Southern Oscillation (ENSO) influence bacterial communities in the rhizosphere of Coffea arabica. Using 16S rRNA amplicon sequencing across five sampling campaigns covering El Niño, La Niña, and Neutral phases in the Colombian Andes, together with multivariate and variance-partitioning analyses, we quantified the relative contributions of climatic and edaphic factors to rhizosphere community structure. PERMANOVA across three dissimilarity metrics showed that the ENSO explained 11-17% of β-diversity, exceeding the contribution of intra-annual seasonality (6-12%). Ordination analyses indicated moderate compositional differentiation with considerable overlap among ENSO groups, consistent with gradual community turnover under contrasting hydroclimatic conditions. Rainfall and soil pH emerged as the main edaphic correlates of community composition, although their independent effects were no longer significant after accounting for the ENSO phase and season. Despite these shifts, the rhizosphere remained dominated by Acidobacteriota, Actinobacteriota, and Proteobacteria, and a prevalence-defined core microbiome (genera detected in ≥85% of samples) was maintained across climatic phases and seasons. These results indicate that, within the explained fraction of variation, macroclimatic variability contributed more to rhizosphere bacterial turnover than local edaphic heterogeneity, while a conserved prevalence-defined bacterial core may contribute to taxonomic stability in climate-sensitive coffee systems.},
}

@article {pmid42075467,
year = {2026},
author = {Tiwari, P and Park, KI},
title = {Plant-Associated Microbiomes: Crosstalk and Engineering to Improve Nutrient Use Efficiency (NUE) in Crops of Global Importance.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/plants15081265},
pmid = {42075467},
issn = {2223-7747},
abstract = {Global climate change is rapid and poses an alarming threat to agricultural production, significantly impacting economies. Modern agriculture has strongly emphasized improving nutrient availability in crops to address rising malnutrition and contribute to global food security. However, abiotic stresses, including warmer temperatures, drought, waterlogging stress, and elevated CO2, have critical direct and indirect effects on nutrient availability in plants. This systematic review was conducted in accordance with the PRISMA guidelines. The literature survey followed a time period of 2-5 months, during which the conceptualization, analysis, writing, and editing of the article were conducted. In the present era, it is essential to adopt measures to improve the nutritional value [enhance Nutrient Use Efficiency (NUE)] and nutrient management of plant-based foods. Plant-associated microbiomes have co-evolved with their plant counterparts and perform essential functions in nutrient acquisition, including microbial sensing and cross-talk with the plant host, nutrient uptake and sharing, and signaling mechanisms. In natural and agricultural ecosystems, plant microbiomes offer major opportunities and can be harnessed to sustainably supply essential plant nutrients and improve NUE in crops of global importance. Crop-associated microbiomes can be precisely tailored to achieve targeted outcomes, enhancing nutrient acquisition and utilization via microbiome engineering. However, bridging knowledge gaps, understanding microbial colonization, plant-microbiome dynamics, and adopting precise editing approaches are crucial to boost sustainable outcomes and crop productivity. By elucidating plant microbiome crosstalk and microbe-microbe signaling, a better understanding of microbe-mediated nutrient acquisition in plants can be achieved, defining key implications in global food security.},
}

@article {pmid42075560,
year = {2026},
author = {Cho, WS and Thillaichidambaram, M and Jeon, S and Kim, GR and Lee, SU and Lee, SH and Kim, YJ and Lee, ES and Kim, Y and Kang, D and Kim, SY},
title = {Lung Microbiome Dysbiosis in Pulmonary Fibrosis Induced by Multi-Walled Carbon Nanotubes and Bleomycin in Rats.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {4},
pages = {},
doi = {10.3390/medicina62040688},
pmid = {42075560},
issn = {1648-9144},
support = {This study was supported by the 2023 overseas training grant from Pusan National University Yangsan Hospital.//Pusan National University Yangsan Hospital./ ; },
mesh = {Animals ; *Pulmonary Fibrosis/microbiology/chemically induced/physiopathology/etiology ; *Bleomycin/adverse effects ; Rats, Wistar ; Rats ; *Dysbiosis/microbiology/etiology/physiopathology ; *Nanotubes, Carbon/adverse effects ; Female ; *Microbiota/drug effects ; *Lung/microbiology/physiopathology ; Bronchoalveolar Lavage Fluid/microbiology ; Disease Models, Animal ; RNA, Ribosomal, 16S ; },
abstract = {Background and objectives: Occupational and environmental inhalation exposures, including high-aspect-ratio carbon nanotubes, can trigger pulmonary fibrosis (PF). The relationship between exposure-specific fibrogenic pathways (granulomatous inflammation versus diffuse epithelial injury) and lung microbiome dysbiosis remains incompletely understood. We therefore compared lung microbiome alterations in rat PF models induced by multi-walled carbon nanotubes (MWCNTs) and bleomycin. Materials and Methods: Female Wistar rats received a single intratracheal instillation of vehicle, MWCNTs (750 μg/rat), or bleomycin (1 mg/rat). At day 28, fibrosis and inflammation were evaluated by histopathology and bronchoalveolar lavage fluid (BALF) profiling. Lung microbial communities were characterized by 16S rRNA gene sequencing (V3-V4). Seventeen lung samples passed stringent quality control and were analyzed (control n = 5; bleomycin n = 7; MWCNT n = 5). Results: Both agents induced PF with increased profibrotic signaling, but with distinct pathological signatures: MWCNTs produced localized granulomatous lesions and a robust neutrophilic response (25% of BALF cells), whereas bleomycin caused diffuse interstitial remodeling. Bleomycin increased microbial richness (alpha diversity; p < 0.05) and significantly shifted community structure (beta diversity; p < 0.05), while MWCNT exposure showed comparatively limited changes in global diversity. The relative abundance of Pseudogracilibacillus (including P. marinus) was higher in the bleomycin group than in controls, whereas Facklamia tabacinasalis and Corynebacterium maris were more abundant in the MWCNT group. Across samples, Proteobacteria abundance was inversely correlated with BALF TGF-β, MCP-1, and neutrophil proportion. At the species level, Pseudogracilibacillus marinus was positively correlated with BALF TGF-β, while Facklamia tabacinasalis and Corynebacterium maris were positively correlated with MCP-1, CINC-3, and neutrophil proportion (Spearman; p < 0.05). Conclusions: Mechanistically distinct fibrogenic exposures generate exposure-linked lung microbiome signatures that track with host inflammatory and profibrotic responses. These signatures may support biomarker development for environmentally and occupationally relevant PF and motivate longitudinal and functional studies to clarify causality.},
}

Animals
*Pulmonary Fibrosis/microbiology/chemically induced/physiopathology/etiology
*Bleomycin/adverse effects
Rats, Wistar
Rats
*Dysbiosis/microbiology/etiology/physiopathology
*Nanotubes, Carbon/adverse effects
Female
*Microbiota/drug effects
*Lung/microbiology/physiopathology
Bronchoalveolar Lavage Fluid/microbiology
Disease Models, Animal
RNA, Ribosomal, 16S

@article {pmid42075665,
year = {2026},
author = {Cazacu, SM and Streba, CT and Constantin, C and Ionele, CM and Rogoveanu, I and Popescu, AV and Florescu, MM},
title = {The Overlap Between Crohn's Disease and Intestinal Tuberculosis: A Never-Ending Story.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {4},
pages = {},
doi = {10.3390/medicina62040794},
pmid = {42075665},
issn = {1648-9144},
mesh = {Humans ; *Crohn Disease/diagnosis/physiopathology ; *Tuberculosis, Gastrointestinal/diagnosis/physiopathology ; Diagnosis, Differential ; },
abstract = {The prevalence of Crohn's disease has increased over the last few decades, even in developing countries, whereas that of intestinal tuberculosis has decreased, which places both diseases at an epidemiological crossroads. Crohn's disease and intestinal tuberculosis share many clinical, endoscopic, imaging, and pathological features, which sometimes make differential diagnosis very difficult; an accurate diagnosis is, however, very important since an erroneous treatment can worsen the evolution or delay proper therapy. The association between past TB infection and Crohn's disease can make the diagnosis especially hard. This review summarizes current data on specific features that allow differentiation between Crohn's disease and intestinal tuberculosis, paying particular attention to the microbiome, clinical signs, endoscopy, cross-sectional imaging, bacteriological, and immunological findings detailed. The importance of computerized models and scores for the differentiation is also detailed, because common features may make the differentiation based on a single criterion difficult.},
}

Humans
*Crohn Disease/diagnosis/physiopathology
*Tuberculosis, Gastrointestinal/diagnosis/physiopathology
Diagnosis, Differential

@article {pmid42075741,
year = {2026},
author = {Raut, N and Chaudhary, AA and Patil, H and Shidhaye, S and Khobragade, R and Umekar, M and Ali, MAM and Trivedi, R},
title = {Antimicrobial Consumption and Resistance Dynamics Across Healthcare Level: Global Evidence and Stewardship Implications.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040414},
pmid = {42075741},
issn = {2076-0817},
support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; },
mesh = {Humans ; *Antimicrobial Stewardship ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial ; Global Health ; Delivery of Health Care ; },
abstract = {BACKGROUND/OBJECTIVES: Antimicrobial resistance (AMR) is a critical global public health challenge driven by inappropriate and excessive antimicrobial use (AMU) across human, animal, and environmental sectors.

METHOD: This narrative review synthesizes recent evidence on antimicrobial utilization and resistance patterns. A structured search of PubMed, Scopus, and Web of Science was conducted for studies published between 2015 and 2025. Eligible sources included surveillance reports, registry-based analyses, and clinical studies. Data were qualitatively analyzed to identify key trends and regional variations.

RESULT: Marked geographical variation in AMR was observed. Carbapenem resistance in Escherichia coli remains low globally (2-3%) but is higher in Southeast Asia (17-18%) and India (~40%). Klebsiella pneumoniae shows consistently high resistance (>40% globally; ~54% in India), while Pseudomonas aeruginosa exhibits stable resistance levels (35-45%). Resistance prevalence increases from primary to tertiary care settings, reflecting greater antimicrobial exposure. Vulnerable populations-including pediatric, elderly, pregnant, and immunocompromised patients-face higher risks of antimicrobial exposure and adverse outcomes, including nephrotoxicity, hepatotoxicity, and microbiome disruption. WHO AWaRe data indicate a global shift toward increased use of Watch-category antibiotics. Stewardship interventions, such as audit and feedback, prescribing restrictions, rapid diagnostics, and decision support systems, effectively reduce inappropriate AMU.

CONCLUSIONS: Integrated, data-driven antimicrobial stewardship and robust surveillance systems are essential to mitigate the global burden of AMR.},
}

Humans
*Antimicrobial Stewardship
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Drug Resistance, Bacterial
Global Health
Delivery of Health Care

@article {pmid42075766,
year = {2026},
author = {Piloto-Sardiñas, E and Rodríguez, I and Santos, HA and Paulino, PG and Corona-González, B and Cabezas-Cruz, A},
title = {Ecological Frameworks of Pathogen-Pathogen and Pathogen-Microbiome Interactions Within the Tick Holobiont.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040440},
pmid = {42075766},
issn = {2076-0817},
mesh = {Animals ; *Ticks/microbiology ; *Microbiota ; *Host-Pathogen Interactions ; Symbiosis ; *Tick-Borne Diseases/microbiology ; },
abstract = {Ticks harbor complex microbial communities composed of symbionts, commensals, and tick-borne pathogens (TBPs). Together, these microorganisms form the tick holobiont. Within this system, the tick's physiological architecture structures microbial communities by distributing microorganisms across distinct tissues. This compartmentalization creates spatially distinct ecological niches, which in turn shape how microbial communities assemble and interact. In this review, we integrate ecological theory with current knowledge of tick microbiome research to examine how pathogen-pathogen and pathogen-microbiome interactions emerge within these tissue-structured microbial communities. We first outline how baseline ecological filters, including tick species, developmental stage, tissue identity, vertical transmission, and environmental context, shape the microbiome configuration through community assembly processes. We then examined how TBPs, as high-impact colonizers, can further modify microbial networks by altering host-mediated selective pressures, influencing interaction topology, and reshaping community stability. Based on these observations, we propose a dual selective pressure framework in which (i) baseline ecological structuring processes and (ii) pathogen-associated selective pressures interact to determine the microbial network configuration and functional outcomes within the tick holobiont. These interacting forces may drive shifts in diversity, modularity, keystone taxa emergence, and network resilience, ultimately influencing vector competence. This review frames the microbial communities within the tick holobiont as spatially structured ecological systems shaped by multilevel selective pressures. This conceptual foundation provides a coherent framework for understanding microbial interactions in arthropod vectors and highlights avenues for mechanistic research and microbiome-based strategies to mitigate tick-borne diseases.},
}

Animals
*Ticks/microbiology
*Microbiota
*Host-Pathogen Interactions
Symbiosis
*Tick-Borne Diseases/microbiology

@article {pmid42075777,
year = {2026},
author = {Lagos, I and Pérez de Arce, E and Faggiani, I and D'Amico, F and Zilli, A and Furfaro, F and Massironi, S and Cicerone, C and Solitano, V and Parigi, TL and Peyrin-Biroulet, L and Danese, S and Allocca, M},
title = {The Role of Microbiota and Fecal Transplantation in Inflammatory Bowel Disease.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/pathogens15040451},
pmid = {42075777},
issn = {2076-0817},
mesh = {*Fecal Microbiota Transplantation/methods ; Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/therapy/microbiology ; Crohn Disease/therapy/microbiology ; Colitis, Ulcerative/therapy/microbiology ; Feces/microbiology ; Treatment Outcome ; },
abstract = {Inflammatory bowel diseases (IBDs), including ulcerative colitis (UC) and Crohn's disease (CD), are consistently associated with alterations in gut microbial communities, although the extent and characteristics of these alterations vary across studies, supporting a potential role of the microbiota in disease pathogenesis and therapeutic modulation. We conducted a systematic review to synthesize current evidence on microbiota alterations in IBD and the clinical application of fecal microbiota transplantation (FMT). A total of 118 studies were included (76 focused on microbiota profiling and 42 evaluated FMT as therapy). Across heterogeneous study designs and microbial characterization methods, reduced microbial diversity was the most consistently reported alteration, generally more pronounced in CD than in UC. Depletion of Faecalibacterium prausnitzii-a key butyrate producer with anti-inflammatory properties-was commonly reported, often accompanied by functional impairment in short-chain fatty acid production. Microbial patterns were frequently associated with mucosal inflammation and varied across disease phenotypes; these patterns have been increasingly explored as predictors of treatment response and relapse, although mechanistic interpretation remains limited and causal relationships are difficult to establish. Evidence from randomized controlled trials suggests potential efficacy of FMT in UC, particularly with intensive or repeated protocols, whereas data in CD remain limited and heterogeneous, with signals of benefit often appearing transient. FMT was generally well tolerated, but long-term safety data remain scarce. Emerging multi-omic approaches are reshaping the field by integrating taxonomic and functional insights, with potential implications for risk stratification, diagnosis, prognosis, and therapeutic optimization. Further standardized, longitudinal, and mechanistically oriented studies are required to translate microbiome research into clinically actionable strategies in IBD.},
}

*Fecal Microbiota Transplantation/methods
Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/therapy/microbiology
Crohn Disease/therapy/microbiology
Colitis, Ulcerative/therapy/microbiology
Feces/microbiology
Treatment Outcome

@article {pmid42075987,
year = {2026},
author = {Choińska, R and Nasiłowska, J and Wojtczak, A and Lewandowski, W and Świsłocka, R},
title = {Isoxanthohumol and Its Derivatives: Antioxidant Activity and Effects on the Gut Microbiota.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081311},
pmid = {42075987},
issn = {1420-3049},
support = {2020/39/B/NZ9/01894//National Science Centre/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Xanthones/pharmacology/chemistry ; Humans ; *Antioxidants/pharmacology/chemistry ; Humulus/chemistry ; Animals ; Flavonoids/pharmacology/chemistry ; Propiophenones/chemistry/pharmacology ; Flavanones/chemistry/pharmacology/metabolism ; },
abstract = {Isoxanthohumol (IX) is a prenylated flavonoid derived from hop cones (Humulus lupulus) that is gaining increasing recognition for its potential biological effects. Despite numerous studies on its precursor, xanthohumol, studies on IX remain limited. Of particular interest is its metabolism, particularly its biotransformation by gut microbiota to 8-prenylnaringenin (8-PN), a potent phytoestrogen, which indicates the complex nature of its biological activity and potential health implications. This review summarizes the current state of knowledge on IX and its derivatives, covering their microbial metabolism, their impact on the gut microbiome, and the metabolic consequences of this conversion. Furthermore, it examines the relationship between the molecular structure of IX and its derivatives and their biological activity, highlighting existing research gaps and the need for further research on the safety and therapeutic potential of these compounds.},
}

*Gastrointestinal Microbiome/drug effects
*Xanthones/pharmacology/chemistry
Humans
*Antioxidants/pharmacology/chemistry
Humulus/chemistry
Animals
Flavonoids/pharmacology/chemistry
Propiophenones/chemistry/pharmacology
Flavanones/chemistry/pharmacology/metabolism

@article {pmid42076028,
year = {2026},
author = {Karczmarzyk, A and Wojcieszyńska, D and Nowak, A and Smułek, W and Guzik, U},
title = {Berberine Toxicity Profile in Experimental Models as a Basis for Assessing Its Biological Safety.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081350},
pmid = {42076028},
issn = {1420-3049},
mesh = {*Berberine/toxicity/pharmacology ; Oxidative Stress/drug effects ; Animals ; },
abstract = {Berberine, a natural alkaloid, is a substance widely used in natural medicine. However, there is a significant knowledge gap regarding the potential negative effects of higher environmental concentrations of berberine resulting from its use as a supplement. Therefore, the aim of this study was to assess its toxicity towards microorganisms and organisms from various trophic levels. The results indicate that berberine may influence the reorganization of bacterial membranes, thereby negatively impacting the environmental microbiome. However, oxidative cell damage, a phenomenon commonly described in the literature, was not demonstrated. At the concentrations used, berberine may even have a protective effect. The analysis of toxicity towards Tetrahymena, Selenastrum, and Heterocypris indicated a similar level of berberine toxicity across these organisms, suggesting that the toxic effect is not species-dependent and that the mechanism of toxicity is probably based on universal cellular mechanisms.},
}

*Berberine/toxicity/pharmacology
Oxidative Stress/drug effects
Animals

@article {pmid42076046,
year = {2026},
author = {Toydemir, S and Merey, G},
title = {Biochemistry of Human Gut Microbiota: Related Diseases and Dietary Interactions.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {8},
pages = {},
doi = {10.3390/molecules31081369},
pmid = {42076046},
issn = {1420-3049},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology/metabolism ; *Diet ; Inflammatory Bowel Diseases/microbiology/metabolism ; Obesity/microbiology/metabolism ; },
abstract = {The human gut microbiota represents a complex and dynamic ecosystem of trillions of microorganisms that play a fundamental role in maintaining physiological homeostasis, regulating metabolism, and modulating the immune system. This narrative review explores the biochemical intricacies of the gut microbiome, focusing on the dominant phyla (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Fusobacteria) and their specific contributions to host health. A critical emphasis is placed on the metabolic outputs of these microorganisms, such as short-chain fatty acids (SCFAs) like butyrate, which serve as vital energy sources and anti-inflammatory signaling molecules. Conversely, the review examines how dysbiosis, the disruption of microbial balance, is mechanistically linked to the pathogenesis of diverse conditions, including obesity, diabetes mellitus, inflammatory bowel disease (IBD), and gout. Furthermore, it highlights the profound impact of dietary interventions on microbial architecture, notably, how non-digestible carbohydrates promote beneficial taxa and eubiosis, while high-fat and high-sugar diets drive metabolic endotoxemia and systemic inflammation. By synthesizing current knowledge on microbial biotransformations of proteins and polyphenols, this work underscores the bidirectional relationship between nutrition and the microbiome. Ultimately, understanding these biochemical interactions is essential for developing targeted probiotic, prebiotic, and nutritional strategies to prevent and manage chronic metabolic and inflammatory disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology
Dysbiosis/microbiology/metabolism
*Diet
Inflammatory Bowel Diseases/microbiology/metabolism
Obesity/microbiology/metabolism

@article {pmid42076109,
year = {2026},
author = {Bharadwaj, R and Gaspar, C and Moeller, TD and Ward, D and Klempner, MS and Wang, Y and Cavacini, LA},
title = {Impact of Oral Pre-Exposure Secretory IgA Prophylactic Produced in Rice on Gut Microbiome Homeostasis.},
journal = {Pharmaceutics},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/pharmaceutics18040457},
pmid = {42076109},
issn = {1999-4923},
support = {MT21010.006//Naval Medical Research Command's Naval Advanced Medical Development Program/ ; W81XWH-21-2-0018//Combat Readiness - Medical Research Program/ ; INV-010709/GATES/Gates Foundation/United States ; },
abstract = {Background/Objectives: Enterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrheal illness worldwide, resulting in approximately 380,000 deaths annually, with significant morbidity in children and travelers to endemic regions. ETEC infection begins with the attachment of the bacterium to the small intestine via filamentous colonization factors (CF), followed by the production of heat-labile (LT) and heat-stable (ST) toxins that induce watery diarrhea. Targeting CF to prevent ETEC attachment is challenging due to strain heterogeneity. Methods: In previous studies, we developed a class-switched human monoclonal antibody, 68-90, expressed as secretory IgA (SIgA) in rice for cost-effective and stable storage. Rice-produced SIgA exhibited comparable binding efficiency to CfaE, a component of CF, compared to CHO-produced SIgA in vitro. Results: In this work, we showed that oral administration of 68-90 SIgA to Aotus nancymaae did not alter gut microbiome distribution or show signs of systemic exposure. Conclusions: These findings suggest that oral delivery of ETEC-specific SIgA is safe and does not disrupt the gut microbial population, highlighting its potential as an effective and targeted therapeutic strategy.},
}

@article {pmid42076694,
year = {2026},
author = {Sahatsanon, K and Chaweewan, K and Sringarm, K and Arjin, C and Hnokaew, P and Satsook, A and Saman, P and Kim, HW and Patthararangsarith, P and Busayakanit, P and Adeyemi, KD and Sivapirunthep, P and Chaosap, C},
title = {Effects of Host-Specific Multi-Lactic Acid Bacterial Probiotics on Performance, Carcass Traits, Meat Quality, and Gut Microbiome in Fattening Pigs.},
journal = {Veterinary sciences},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/vetsci13040322},
pmid = {42076694},
issn = {2306-7381},
support = {KDS 2022/010//King Mongkut's Institute of Technology Ladkrabang/ ; No. 65-17 Sub Project No. 1//Thailand Institute of Scientific and Technological Research/ ; },
abstract = {This study evaluated the effects of a host-specific multi-lactic acid bacterial (MLAB) probiotic and sex on performance, carcass traits, meat quality, and gut microbiota in fattening pigs. Thirty-two crossbred pigs (10 ± 0.80 weeks; 23.43 ± 0.17 kg) were assigned to a 2 × 2 factorial design with diet (control or MLAB probiotics) and sex (barrow or female). The MLAB supplement consisted of seven lactic acid bacterial strains mixed in equal proportions (≈14.3% each)-Lactobacillus brevis, Lactobacillus reuteri, Weissella cibaria, Lactobacillus paraplantarum, Lactococcus lactis, Lactobacillus pentosus, and Pediococcus pentosaceus-administered at 1 × 10[9] CFU/kg feed for 12 weeks. MLAB probiotic supplementation reduced bone proportion while increasing skin and fat content (p < 0.05), with a treatment × sex interaction for loin eye area (p < 0.05). Meat quality improved in the MLAB group, showing higher ultimate pH and lower cooking loss (p < 0.05), indicating improved water-holding capacity. Female pigs exhibited higher early postmortem pH and protein content (p < 0.05). Microbiome analysis revealed increased abundances of Oxalobacteraceae and Paludibacteraceae and reduced Clostridium sensu stricto 6 (p < 0.05). These results suggest that host-adapted probiotics may support gut microbial balance and improve certain pork quality traits.},
}

@article {pmid42076708,
year = {2026},
author = {Yu, J and Dou, Z and Wang, C and Zhou, S and Shi, H and Zhang, H and Wang, H and Ma, N and Shen, X and Chang, G},
title = {Yeast Culture Enhances Production Performance in Late-Lactation Dairy Cows by Reshaping Rumen Microbiota and Metabolic Pathways.},
journal = {Veterinary sciences},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/vetsci13040336},
pmid = {42076708},
issn = {2306-7381},
support = {2022AAC02072//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; KYT2023004//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Yeast culture (YC), a complex functional feed additive containing fermentation metabolites, has demonstrated potential in dairy production systems. However, its mechanistic effects on rumen function and host metabolism in lactating dairy cattle warrant further investigation. This study evaluated the impacts of YC supplementation on production performance, systemic antioxidant status, and rumen function in late-lactation Holstein cows. Fourteen multiparous Holstein cows (body weight 655 ± 28 kg; days in milk 270.4 ± 1.6 d) were randomly allocated into two groups, a control group (CON, basal diet) and a YC-supplemented group (YC, basal diet + 50 g/d YC), in a 28-day feeding trial. YC supplementation significantly increased dry matter intake (p < 0.01), nutrient digestibility (p < 0.01 for DM, CP, EE, NDF, and ADF), and milk yield (p < 0.05) compared to CON. Systemic antioxidant capacity was enhanced, as evidenced by elevated serum superoxide dismutase activity (p < 0.01) and total antioxidant capacity (p < 0.05). Rumen fermentation was improved with higher concentrations of total volatile fatty acids (p < 0.01) and microbial protein (p < 0.01) and reduced ammonia nitrogen levels (p < 0.01). Macrogenomic analysis revealed a YC-mediated restructuring of the rumen microbiota, characterized by an increased relative abundance of Firmicutes and decreased Bacteroidota. Untargeted metabolomic profiling identified significant alterations in rumen metabolite profiles, with differential metabolites enriched in pyrimidine metabolism and vitamin digestion and absorption pathways. These results indicate that YC supplementation improves production performance in late-lactation dairy cows through multi-faceted mechanisms involving rumen microbial community modulation and metabolic pathway activation, ultimately enhancing nutrient utilization and metabolic efficiency.},
}

@article {pmid42076832,
year = {2026},
author = {Carracedo Lorenzo, Z and Rizaludin, MS and Wang, J and Berdaguer, R and Brito-López, C and Sánchez-Arcos, C and Garbeva, P and Pieterse, CMJ and Dicke, M and Testerink, C and Kloth, KJ and Karlova, R},
title = {Pseudomonas volatiles shape the root transcriptome and microbiome to promote plant growth under drought.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71203},
pmid = {42076832},
issn = {1469-8137},
support = {024.004.014//NWO Dutch Research Council (NWO/OCW)/ ; },
abstract = {Volatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and plants. While their potential as plant growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remain poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress Arabidopsis seedlings were exposed to VOCs emitted by Pseudomonas strains under control and osmotic stress conditions. Plant biomass and root architecture were evaluated. Root transcriptomics analysis was performed and validated using Arabidopsis mutants and metabolomics. Volatile organic compounds effects were also tested on soil-grown Brassica oleracea and on its rhizosphere microbiome. Pseudomonas VOCs promoted plant growth under both axenic and soil conditions in A. thaliana and in B. oleracea, and under control and drought conditions. Transcriptomics, metabolomics, and functional analysis revealed interactions between Pseudomonas VOCs, glucosinolates, and ABA signalling, as well as a positive association between VOC exposure and coumarin biosynthesis. VOC treatment also reshaped the rhizosphere microbiome under drought, leading to a community composition more similar to that of well-watered plants. Overall, Pseudomonas VOCs promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation.},
}

@article {pmid42076857,
year = {2026},
author = {Yang, Z and Zhou, W and Chen, P and Dai, Z and Feng, G and Limpens, E and Zhang, L},
title = {Phosphorus fertilizer forms orchestrate contrasting plant-microbe recruitment strategies in the rhizosphere of field grown wheat.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71231},
pmid = {42076857},
issn = {1469-8137},
support = {ZR2021MC042//Natural Science Foundation of Shandong Province/ ; 2024YFE0105000//National Key Research and Development Program of China/ ; PC2024B02003//Pinduoduo-China Agricultural University Research Fund/ ; 32130094//National Natural Science Foundation of China/ ; 42277112//National Natural Science Foundation of China/ ; },
abstract = {Plants engage in intricate interactions with rhizosphere microbes. These interactions are crucial for plant nutrient acquisition and productivity, but the mechanisms by which different nutrient forms shape rhizosphere microbes to enhance nutrient utilization under field conditions remain unclear. We investigated the rhizosphere bacterial communities of wheat and their functions across key growth stages in response to different phosphorus (P) fertilizer forms in a 4-yr field experiment, integrating 16S rRNA gene sequencing, metatranscriptomic sequencing, and soil chemical analyses. In the field, the three P fertilizer forms showed comparable P use efficiency (PUE) over 4 years. At the three-leaf stage, insoluble P fertilizer increased root-associated citrate concentrations, enriched carboxylate-associated bacteria (e.g. Bacillus, Solirubrobacter, and Nitrospira), and resulted in higher transcript abundance of genes involved in citrate metabolism and P acquisition. Polymeric P fertilizer enhanced soil phosphatase activity, increased root-associated succinate concentrations, and had higher transcript abundance of genes involved in succinate metabolism and complex polysaccharide degradation. Soluble P fertilizer increased soil available P and enriched Devosia, favored glycoprotein degradation, while showing a limited response to P mobilization processes. This study suggests that, under field conditions, different P fertilizer forms shape distinct rhizosphere bacterial communities to improve PUE by altering root-associated carboxylate release.},
}

@article {pmid42076882,
year = {2026},
author = {Hayashi, I and Sánchez-Pinillos, M and Toju, H},
title = {Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories.},
journal = {Ecology letters},
volume = {29},
number = {5},
pages = {e70388},
doi = {10.1111/ele.70388},
pmid = {42076882},
issn = {1461-0248},
support = {202302//Kyoto University CeLiSIS Program (23CeLiSIS-02)/ ; JPMJCR23N5//Core Research for Evolutional Science and Technology/ ; 24KJ1454//Japan Society for the Promotion of Science/ ; 202302//New Energy and Industrial Technology Development Organization/ ; JPMJFR2048//Fusion Oriented REsearch for disruptive Science and Technology/ ; },
mesh = {Stochastic Processes ; *Microbiota ; Ecosystem ; },
abstract = {Biological community dynamics arise from both deterministic and stochastic processes. While species' responses to environmental factors define attractors of community structure, stochasticity, particularly during early assembly, can redirect ecological trajectories. However, quantifying such roles of stochasticity in community assembly has remained challenging. We tracked community assembly in two multi-replicated experimental systems, each with four levels of founding community size, analysing > 3000 samples across four time points. Stronger initial stochasticity led to greater divergence of both population- and community-level consequences. Strikingly, conspicuous differentiation into alternative trajectories of community assembly occurred when the absolute number of founding prokaryotic cells was less than the order of 10[4]. Thus, quantitative differences in stochasticity produced qualitative differences in community fate. These results demonstrate that early stochastic events can have enduring impacts on ecological dynamics. Deeper quantitative insights into stochasticity will reorganise our views on biological invasions, agroecosystem microbiome management, and therapeutics of human-associated microbiomes.},
}

Stochastic Processes
*Microbiota
Ecosystem

@article {pmid42077003,
year = {2026},
author = {Bukovac, J and Husain, M and Sapper, T and O'Dell, A and Bittoni, M and Gastier, H and Chebbi, A and Hockenhull, V and Dohar, Z and Moon, J and Tabung, F and Verschraegen, C and Wu, R and Kendra, K and Yang, Y and Volek, J and Spakowicz, D},
title = {How the Ketogenic Diet Shapes the Microbiome to Influence Cancer Immunotherapy Outcomes: An Exploration of Clinical Trials and Their Results.},
journal = {Nutrition and cancer},
volume = {},
number = {},
pages = {1-30},
doi = {10.1080/01635581.2026.2658807},
pmid = {42077003},
issn = {1532-7914},
abstract = {Ketogenic dietary interventions (KDIs) are increasingly explored as adjuncts in oncology due to their metabolic and immunomodulatory effects. One mechanism by which KDIs are expected to modulate the immune system is by altering the gut microbiome, which has been shown to affect treatment outcomes, particularly in the context of immunotherapies. This review synthesized findings from 43 clinical trials to evaluate the current landscape of KDIs in cancer care, with a focus on the gut microbiota and immunotherapy. Although 47% of identified trials are completed, none have yet published results combining KDIs with immunotherapy. Since 2020, however, there has been a significant increase in ongoing studies investigating this combination and incorporating microbiome endpoints. While KDIs may help shape an immunotherapy-permissive environment, further clinical evaluation is necessary to determine the full extent of KDIs on the microbiome. Future research should prioritize longitudinal microbiome profiling and standardized adherence reporting to clarify the therapeutic potential of KDIs as a metabolic adjuvant to immune checkpoint inhibitors.},
}

@article {pmid42077151,
year = {2026},
author = {Horner, KM and Corish, CA and Quinn, AM},
title = {Addressing Undernutrition in Older Adults with Plant-Based Products.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-31},
doi = {10.1017/S0029665126103000},
pmid = {42077151},
issn = {1475-2719},
abstract = {The aim of this review is to provide an overview of the evidence to date and several key considerations regarding addressing undernutrition in older adults with plant-based products. Undernutrition, resulting from inadequate protein and energy intake is common among older adults, and is associated with poor health and quality of life. Ensuring adequate protein and energy intake is a key component of strategies aiming to prevent and/or treat undernutrition. Increasing diversity of protein intake to include more sustainable plant-based sources is encouraged in the general population. However, to support healthy ageing, it is important to consider factors such as the impact of greater consumption of plant-based products on appetite and nutritional status, muscle protein synthesis and skeletal muscle mass. Although the literature in older adults is limited, the current evidence suggests no significant differences when comparing effects of plant to animal-based products/diets on a range of outcomes including appetite, nutritional status, longer-term muscle protein synthesis and muscle mass. Furthermore, there is evidence of improvements in nutritional status and muscle protein synthesis following plant protein supplementation compared to before supplementation or lower protein intakes. Therefore, greater intake of certain plant-based products could assist in enhancing sustainability of food systems and meeting nutritional requirements to prevent undernutrition. Among other factors, the plant protein source, the food matrix and presence of other nutrients need consideration. Further studies are needed in several areas, including investigating the effects of greater intake of plant-based products on the gut microbiome, and in the treatment of undernutrition.},
}

@article {pmid42077290,
year = {2026},
author = {Logan, AC and Mishra, P and Berryessa, CM and Caruso, GD and Hagenbeek, FA and Denson, TF and Robinson, JM and Prescott, SL},
title = {Challenging the prescientific frameworks of criminal justice: neurobiology and criminolytic interventions in the legalome era.},
journal = {Frontiers in psychology},
volume = {17},
number = {},
pages = {1791262},
pmid = {42077290},
issn = {1664-1078},
abstract = {Contemporary systems of criminal justice are rooted in prescientific folk psychology assumptions related to moral fiber, free will, agency, and near-universal levels of willpower. For instance, people often believe that morally "defective" people make voluntary choices, failing to utilize their own self-control capacities. Given the wide acceptance of such beliefs, they are considered "normative" within law, serving to underpin retributive punishment. However, rapid advances in biological sciences-aided by multi-omics technologies-have illuminated the ways in which brain architecture and current metabolic conditions can constrain agency and shape here-and-now decision-making. Here in this perspective article, we examine how these advances are placing the prescientific foundations of criminal justice systems under duress. Older single-gene and single neuroimage attempts at explaining criminal behavior are giving way to the legalome era. This describes a more holistic epoch in which the simultaneous integration of mass biological data (e.g., polygenetic, metabolic, microbiome, metabolomic, lipidomic, and other omics-derived information) can provide explanatory power to criminal behavior and vulnerability, and guide personalized approaches to prevention and treatment. Advances in behavioral epigenetics are revealing how genetic predispositions interact with the exposome to shape human behavior through dynamic, potentially modifiable mechanisms. Moreover, evidence suggests that the human microbiome acts as a dynamic interface between environment and brain, influencing behavior in ways that are relevant to vulnerability, impulse control, and decision-making. Promising criminolytic interventions range from nutritional and pharmaceutical approaches to cognitive-behavioral therapy and contemplative practices. The integration of biological evidence and science education, along with ethically guided neurointerventions, will be critical to more humane systems of judgement.},
}

@article {pmid42077435,
year = {2026},
author = {DiTulio, M and Navarro-Torres, CA},
title = {Clearance of multiple antibiotic-resistant coagulase-negative staphylococci is selectively associated with higher circulating α-melanocyte stimulating hormone in patients evaluated for chronic inflammatory response syndrome.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1728408},
pmid = {42077435},
issn = {1664-2392},
mesh = {Humans ; *alpha-MSH/blood ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Staphylococcus/drug effects/isolation & purification ; Adult ; Biomarkers/blood ; *Staphylococcal Infections/blood/microbiology ; Coagulase/metabolism ; Aged ; Matrix Metalloproteinase 9/blood ; Anti-Bacterial Agents/therapeutic use ; Vasoactive Intestinal Peptide/blood ; Chronic Disease ; Drug Resistance, Bacterial ; },
abstract = {INTRODUCTION: Neuroimmune regulatory peptides play central roles in coordinating inflammatory, metabolic, and mucosal immune processes in humans. Among these, α-melanocyte stimulating hormone (α-MSH), a proopiomelanocortin-derived peptide, has been implicated in modulation of cytokine signaling, epithelial barrier function, and pain processing. However, determinants of circulating α-MSH levels in chronic inflammatory states remain incompletely characterized in human clinical populations. Persistent sinonasal colonization with multiple antibiotic-resistant coagulase-negative staphylococci (MARCoNS) has been reported in some cohorts presenting with environmentally associated multisystem illness, described in some clinical settings as Chronic Inflammatory Response Syndrome (CIRS). Yet its relationship to systemic neuroendocrine biomarkers has not been quantitatively examined.

METHODS: This retrospective observational cohort study examined whether follow-up MARCoNS culture status was associated with longitudinal trajectories of α-MSH, compared with two additional biomarkers commonly assessed in this population: matrix metallopeptidase-9 (MMP-9) and vasoactive intestinal polypeptide (VIP). A total of 188 adult patients evaluated within a CIRS-informed clinical framework at a single clinical site were included. Each participant contributed two timepoints of laboratory data for α-MSH, MMP-9, and VIP, along with MARCoNS culture results.

RESULTS: Across the full cohort, α-MSH increased by an estimated 10 pg/mL, MMP-9 decreased by 398 ng/mL, and VIP increased by 20 pg/mL between baseline and follow-up. Mixed-effects modeling revealed a significant timepoint-by-MARCoNS interaction for α-MSH, such that patients who were MARCoNS-negative at follow-up exhibited higher circulating α-MSH levels compared with those who remained positive. In contrast, no corresponding MARCoNS interaction was observed for VIP or MMP-9.

DISCUSSION: These findings provide quantitative evidence that follow-up MARCoNS culture status is selectively associated with α-MSH trajectories in this retrospective cohort, supporting further prospective investigation into potential links between persistent bacterial nasal colonization and neuroendocrine-immune biomarkers in multisystem chronic illness.},
}

Humans
*alpha-MSH/blood
Male
Female
Retrospective Studies
Middle Aged
*Staphylococcus/drug effects/isolation & purification
Adult
Biomarkers/blood
*Staphylococcal Infections/blood/microbiology
Coagulase/metabolism
Aged
Matrix Metalloproteinase 9/blood
Anti-Bacterial Agents/therapeutic use
Vasoactive Intestinal Peptide/blood
Chronic Disease
Drug Resistance, Bacterial

@article {pmid42077489,
year = {2026},
author = {Islam, MZ and Pitta, DW and Niu, M},
title = {Breed-specific microbiomes drive differential responses to 3-nitrooxypropanol and Acacia mearnsii in dairy cows.},
journal = {JDS communications},
volume = {7},
number = {3},
pages = {332-338},
pmid = {42077489},
issn = {2666-9102},
abstract = {Methane (CH4) inhibitor 3-nitrooxypropanol (3-NOP) shows variable efficacy in Brown Swiss (BS) and Holstein (HF) cows, but the underlying mechanisms remain unclear. Rumination bolus, a proxy for rumen microbiota, combined with exhalomics (analysis of exhaled volatiles), offered a noninvasive approach to differentiate breed responses to CH4 mitigation strategies. We investigated whether differences in rumination bolus microbiota and exhaled VFA (eVFA) between BS and HF cows contribute to their responses to 3-NOP. Sixteen multiparous cows (8 BS, 8 HF) were studied in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of 3-NOP (0 or 60 mg/kg of DM) and Acacia mearnsii tannin extract (TAN; 0% or 3% of DM). Rumination bolus samples collected 6 h postfeeding during the fourth period of the experiment were sequenced for full-length 16S rRNA sequences (PacBio Revio platform) to assess bacterial diversity, while exhaled samples from all 4 periods were analyzed for VFA using secondary electrospray ionization-MS. Microbial community shifts were analyzed using Bray-Curtis, unweighted, and weighted unique fraction metric (UniFrac) distances. Spearman correlations were performed between genus-level information and eVFA, CH4, hydrogen (H2), carbon dioxide (CO2), DMI, and milk yield between breeds. Supplementation of 3-NOP induced a modest but consistent shift in microbial composition, whereas TAN effects were minimal and inconsistent. Breed-specific differences were evident: BS harbored more Prevotella and Rikenellaceae, and HF were enriched in Succinivibrionaceae and Acetitomaculum. Under 3-NOP, HF genera aligned more strongly with propionate-producing pathways and showed stronger negative correlations with CH4, and BS genera remained more associated with acetate and butyrate proportions. Correlations with feed intake and milk yield were generally weak and inconsistent across genera. Overall, our results indicate that HF cows are more responsive to 3-NOP, likely redirecting spared H2 toward propionate-producing bacteria, and BS are more resilient to H2 fluxes and consequently less responsive to 3-NOP. Findings from this pilot study highlight the importance of host-microbiome interactions in evaluating and implementing enteric CH4 mitigation strategies in dairy cattle.},
}

@article {pmid42077491,
year = {2026},
author = {Navarro Marcos, C and de Evan, T and Gonzalez Recio, Ó and Gutiérrez Rivas, M and Dolores Carro, M},
title = {Effects of feeding agroindustrial byproducts on rumen fermentation and microbiome of sheep.},
journal = {JDS communications},
volume = {7},
number = {3},
pages = {315-320},
pmid = {42077491},
issn = {2666-9102},
abstract = {The use of agroindustrial byproducts in ruminant nutrition is gaining increased attention because of economic and environmental benefits and their potential to enhance ruminal function and animal performance. However, the effect of these byproducts on ruminal microbiome and fermentation has been scarcely investigated. This study aimed to evaluate the effects of replacing conventional feeds with agroindustrial byproducts (18:18:8 mixture of corn dried distillers grains with solubles, dry citrus pulp, and exhausted olive cake) on the ruminal microbiome and fermentation parameters of sheep. Four rumen-fistulated Lacaune sheep were used in 2 experimental periods, receiving mixed diets composed of 50% alfalfa hay and 50% of either a control concentrate (CON diet) or a concentrate with agroindustrial byproducts (BYP diet). Ruminal samples were collected at 0, 3, and 6 h postfeeding to assess microbial composition and fermentation parameters. Diet significantly influenced the ruminal microbiome, but the effect of individual sheep was more pronounced than that of the diet. Sampling time also influenced the ruminal microbiome. The inclusion of agroindustrial byproducts in the concentrate did not significantly alter ruminal fermentation parameters. However, the BYP diet led to more steady ruminal fermentation, preventing large fluctuations in total VFA and ammonia concentrations, likely the result of a broader range of fermentable substrates present in the BYP concentrate and changes in ruminal microbiome. These results may indicate improved synchronization of nutrient availability for ruminal microorganisms. Overall, replacing conventional feed ingredients with agroindustrial byproducts promoted microbial diversity and improved ruminal fermentation, potentially leading to increased dairy ruminant performance.},
}

@article {pmid42077790,
year = {2026},
author = {Fan, X and Zhou, X and Wang, L and Zhang, X and Shen, Y and Xiao, Y and Wang, H and Deng, L and Xie, Y},
title = {Comparative Analysis of Gut Microbiomes in Parasitic Roundworms Reveals Phylogeny-Associated Community Structure and Functional Adaptation.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {},
pages = {2764696},
pmid = {42077790},
issn = {1865-1682},
mesh = {Animals ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Toxocara/microbiology ; Female ; Male ; *Ascaris/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Roundworm nematodes are globally distributed zoonotic parasites that inhabit the intestinal tract of various mammals. Although these parasites reside in the host's guts, their own intestinal ecosystems remain poorly understood. Recent evidence suggests that helminths may harbor distinct gut microbiomes that contribute to their physiology and host interactions, yet cross-species comparisons are lacking. Here, we performed full-length 16S rRNA sequencing to characterize and compare the gut microbiomes of four major roundworm species-Ascaris suum (As), Baylisascaris schroederi (Bs), Toxocara cati (Tc), and Toxocara vitulorum (Tv). Across 38 individual worms, we identified 359 bacterial taxa dominated by Enterobacteriaceae, with Escherichia coli, Salmonella enterica, and Klebsiella pneumoniae forming a conserved core community. Despite this compositional similarity, beta-diversity and hierarchical clustering analyses revealed that microbial community structure was primarily determined by parasite phylogeny and roundworm sex, not host diet. Functional prediction using PICRUSt2 indicated clear species-specific enrichment in metabolic pathways, such as carbohydrate metabolism in Bs and xenobiotic metabolism in As, reflecting adaptive divergence of microbial functions. Collectively, these findings demonstrated that roundworm gut microbiomes exhibited taxonomic conservation but functional specialization, shaped by the evolutionary history of the parasites themselves. This study established a conceptual framework viewing the parasite as the primary host of its microbiome and provided new insights into the co-evolutionary relationships between helminths and their symbiotic bacteria.},
}

Animals
*Gastrointestinal Microbiome
Phylogeny
RNA, Ribosomal, 16S/genetics
*Toxocara/microbiology
Female
Male
*Ascaris/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid42077846,
year = {2026},
author = {Pinheiro, GL and Lin, NJ and Parratt, KH and Hines, I and Hack, HR and Servetas, SL and Iyer, H and Da Silva, SM},
title = {The Integration of Focused Ultrasonication, ddPCR, and Flow Cytometry Effectively Estimates Genome Copies per Cell and Enhances DNA Extraction Efficiency in Escherichia coli Samples.},
journal = {ACS omega},
volume = {11},
number = {16},
pages = {23885-23899},
pmid = {42077846},
issn = {2470-1343},
abstract = {Microbiology researchers rely on nucleic acid measurement techniques, such as the quantitative polymerase chain reaction (qPCR) and DNA sequencing, to address diverse scientific and practical challenges. These applications range from detecting microbial contaminants in regenerative medicine and biotherapeutic products to advancing waste remediation, pathogen detection, biosurveillance, and microbiome studies. A critical step in these techniques is DNA extraction, which involves breaking cells to release their DNA as the required input for downstream analyses. The efficiency of this process, known as DNA extraction efficiency (DEE), directly impacts the accuracy of quantitative measurements and, therefore, the interpretation of results. Unfortunately, most DNA extraction methods suffer from suboptimal efficiency that varies across microbial strains, potentially leading to inaccurate results. In this paper, we present a highly efficient DNA extraction protocol leveraging adaptive focused acoustics (AFA) technology to achieve a balance between cell lysis and DNA integrity. Using Escherichia coli as the model organism, the protocol delivers nearly 100% DEE, setting a benchmark for performance. A key innovation in this protocol is the integration of focused ultrasonication, droplet digital polymerase chain reaction (ddPCR), and flow cytometry to estimate genome copies and the corrected DNA extraction efficiency (cDEE), which accounts for the number of genome copies. The proposed protocol addresses the need for an accurate assessment of DEE and DNA quantification, as demonstrated here with E. coli, for various DNA-based techniques, including metagenomic analysis of complex microbial communities and the development of new DNA extraction protocols. This novel protocol addresses a longstanding limitation in microbiological research and has the potential to significantly enhance accuracy and reproducibility across various applications. While there is significant potential for applying this approach, the authors acknowledge that further studies using microorganisms with thicker cell walls will enhance the utility of this framework. However, the knowledge generated in this study can be readily applied and tailored to the specific objectives of individual research groups.},
}

@article {pmid42077904,
year = {2026},
author = {Nigam, AK and Falah, K and Momper, JD and Nigam, SK},
title = {Selectivity of OATs and OATPs for Endogenous Metabolites and Signaling Molecules In Vivo.},
journal = {ACS omega},
volume = {11},
number = {16},
pages = {24714-24724},
pmid = {42077904},
issn = {2470-1343},
abstract = {Organic anion transporters (OATs, SLC22) in the kidney and organic anion-transporting polypeptides (OATPs, SLCO) in the liver play crucial roles in the disposition of small molecule drugs that are organic anions. According to the Remote Sensing and Signaling Theory, these multispecific "drug" transporters are also central to crosstalk between the liver, kidney, and other organs via endogenous small molecules (e.g., metabolites, signaling molecules, gut microbiome products). These multispecific drug transporters govern access of small molecules with high informational content across multiple scales (organism to organelle). Previous chemoinformatic and machine learning methods have proven useful for identifying molecular properties of organic anion drugs that predispose them to handling by the OAT (renal) and the OATP (hepatic) transporters. This is important for understanding pharmacokinetics (ADME) in the context of chronic kidney disease (CKD) and liver disease. Given that OATs and OATPs are involved in many metabolic diseases, we sought to determine whether molecular properties could be identified for distinguishing OAT- versus OATP-interacting endogenous metabolites in vivo. This is essential for understanding endogenous small molecule communication between the kidney proximal tubule and hepatocytes in a larger Remote Sensing and Signaling System. We analyzed in vivo metabolomics data from OAT and OATP knockout mice, focusing on endogenous metabolites selective for OATs (e.g., OAT1 or SLC22A6; OAT3 or SLC22A8) vs OATPs (including the locus containing Oatp1b2, the closest homologue of human OATP1B1 or SLCO1B1 and OATP1B3 or SLCO1B3). Applying chemoinformatic methods to a data set of 210 metabolites based on knockout mouse metabolomics (92 OAT-selective, 118 OATP-selective), we identified a set of distinguishing molecular properties (e.g., MolLogP, RingCount, NumRotatableBonds). We then used machine learning approaches (e.g., Random Forest, Naive Bayes, Logistic Regression) to classify OAT vs OATP metabolites, achieving over 75% accuracy. These results support the view that transporter knockout mouse metabolomics can help define selectivity of SLC drug transporters for endogenous metabolites, signaling molecules, antioxidants, nutrients, and gut microbiome products. In the context of the Remote Sensing and Signaling Theory, we discuss the implications for understanding organ crosstalk and interorganismal communication as well as drug disposition, drug-metabolite interactions, and metabolite-based drug design.},
}

@article {pmid42077990,
year = {2026},
author = {Kijpornyongpan, T and Krasaesin, A and Chongcharoenkit, T and Rattanapornsompong, K and Truntipakorn, A and Bhuridej, P and Rodthongkum, N and Cho, SD and Porntaveetus, T},
title = {Microbial signatures of dental caries in the incarcerated elderly: a salivary microbiota study in a restricted environment.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2662787},
pmid = {42077990},
issn = {2000-2297},
abstract = {BACKGROUND: Dental caries is driven by microbial dysbiosis and influenced by diet and lifestyle. Incarcerated populations living under regulated regimens offer a unique model to study the oral microbiota in older adults by minimising environmental confounding variables.

OBJECTIVES: This study aimed to characterise the salivary microbiota of older incarcerated adults and identify bacterial taxa associated with caries status and severity.

DESIGN: Twenty-eight incarcerated men (aged ≥ 50 years) were stratified into caries-active (CA) and caries-free (CF) groups (n = 14 each). The salivary microbiota was profiled using 16S rRNA gene sequencing to assess diversity and differential taxonomic abundance.

RESULTS: CA subjects exhibited higher genus richness and beta-dispersion compared to CF controls. The CF group was enriched with Haemophilus parainfluenzae, Aggregatibacter sp. HMT-949 and Riemerella sp. HMT-322. Conversely, the CA group harboured elevated levels of Dialister invisus, Megasphaera micronuciformis, Prevotella intermedia, Selenomonas sputigena, Capnocytophaga ochracea and Gemella haemolysans. Furthermore, G. haemolysans, Solobacterium moorei and Streptococcus were positively correlated with caries severity, whereas Veillonella rogosae and Streptococcus koreensis and Peptostreptococcusexhibited negative correlation.

CONCLUSION: This study elucidates salivary dysbiotic signatures in older adults within a controlled environment. The identified bacterial profiles provide biomarkers for caries risk, underscoring the need for targeted oral health surveillance and preventative strategies in institutionalised populations.},
}

@article {pmid42078142,
year = {2026},
author = {Fu, M and Kang, Y and Zhou, J and Zhu, L and Wang, W and Lyu, T and Lin, L},
title = {Contrasting elevational patterns of soil and root-associated fungal communities highlight host-driven filtering in Quercus wutaishansea forests.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1825787},
pmid = {42078142},
issn = {1664-462X},
abstract = {The role of plant hosts in shaping root-associated microbial communities remains a central question in ecology, particularly in the face of changing environmental conditions. While considerable attention has been paid to soil microbial diversity, the interactive dynamics between plant individuals and soil microbial pool during root-associated fungi establishment across environmental gradients remain poorly understood. In this study, we explored the elevational variation in the diversity of soil and root-associated fungal communities of Quercus wutaishansea across ten elevational belts (1020 m-1770 m above sea level (asl)) on Dongling Mountain, Beijing, China. We found that root-associated fungal communities exhibited significantly increased alpha diversity with elevation (P < 0.05), whereas soil fungal communities showed no clear elevational trends (P > 0.05). Despite substantial variation in the soil fungal pool, the composition of root-associated fungal communities remained notably stable, suggesting a strong host filtering effect (P < 0.05). Compared with hump-shaped Sim and decreasing Morisita β-diversity of soil fungi as elevation increased (P < 0.05), the β-diversity of root-associated fungi did not exhibit a consistent elevational pattern nor mirror soil fungal β-diversity. These results suggest that, beyond environmental filtering, Q. wutaishansea plays an active role in shaping its root fungal community by selecting compatible fungal partners according to its physiological needs across altitudes. The findings reveal a significant and variable plant selectivity in the recruitment of microbiomes across different elevations, offering novel insights into plant-microbiome interactions within forest ecosystems in response to climate change.},
}

@article {pmid42078328,
year = {2026},
author = {Li, M and Wong, W and Xiong, H and Chen, K},
title = {16S rRNA gene sequencing-based preliminary study on the differences in the microbiota between children with rampant caries and those with arrested caries.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1693174},
pmid = {42078328},
issn = {2673-4842},
abstract = {OBJECTIVE: In clinical practice, arrested caries (AC) poses less harm to children than rampant caries (RC), as the development of caries is arrested. However, there is limited research on the microbiology of the two types of caries. This research study the differences in microbial profiles among AC, caries-free (CF)and RC patients.

METHODS: Thirty-six children aged 3-5 years were selected, grouped into AC, CF, and RC groups, with 12 children in each group. A total of 72 samples, including non-stimulated saliva and dental plaque, were collected. Microbial DNA was extracted, and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. Bioinformatics analysis was performed with QIIME2, and taxonomic classification was based on the SILVA database. Alpha and beta diversity were assessed, and the Kruskal-Wallis test (with Benjamini-Hochberg correction) was used to identify taxonomic abundance differences.

RESULTS: The α-diversity in plaque was significantly lower than in saliva. While the salivary microbiome showed minimal variation across different caries states, the plaque microbiome displayed distinct structural differences. At the taxonomic level, Bacteroidota and Prevotella were enriched in the RCP group, while Fusobacteriota and Leptotrichia were more abundant in the ACP and CFP groups, with Corynebacterium being most abundant in the arrested caries group. Differential abundance analysis identified five putative species-level biomarkers associated with specific clinical states in dental plaque.

CONCLUSION: This study suggests that different caries statuses are linked to distinct microbial profiles in dental plaque. The analysis revealed clear differences in microbial community structures across the three clinical groups, highlighting a potential connection between caries activity and plaque dysbiosis.},
}

@article {pmid42078366,
year = {2026},
author = {Sy, M and Ndiaye, T and Thakur, R and Gaye, A and Levine, ZC and Ngom, B and Bellavia, KL and Firer, D and Toure, M and Ndiaye, IM and Diedhiou, Y and Mbaye, AM and Gomis, JF and DeRuff, KC and Deme, AB and Ndiaye, M and Badiane, AS and Paye, MF and Sabeti, PC and Ndiaye, D and Siddle, KJ},
title = {Oral and plasma microbiome in the context of acute febrile illness.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.26351042},
pmid = {42078366},
abstract = {Emerging infectious diseases and antimicrobial resistance (AMR) have surfaced as two major public health threats over the past two decades. Consequently, integrative surveillance systems capable of detecting both emerging pathogens and resistance-carrying bacteria are crucial. With advances in next-generation sequencing, simultaneous detection of pathogens and AMR is increasingly feasible. In this study, we used short-read metatranscriptomics complemented by total 16S rRNA metagenomic long-read sequencing to analyze paired oral and plasma samples from a cohort of febrile individuals at two locations in Senegal. Oral microbiomes differed in community composition between locations, and reduced diversity and richness were significantly associated with high fever. We identified at least one known pathogen in 15.33 % (23/150) of samples, with Borrelia crocidurae as the most frequently detected pathogen. We detected both pathogenic and non-pathogenic viruses in oral (10/72) and plasma (09/78) samples. Finally, we observed a high frequency of genes associated with resistance and virulence: 10% of samples expressed at least one AMR gene (ARG), and 24% expressed virulence factor genes. Resistance to widely used beta-lactam antibiotics was the most prevalent. Our findings provide critical data on oral and plasma microbiomes in the context of acute febrile illness in Senegal while expanding understanding of circulating ARGs.},
}

@article {pmid42078518,
year = {2026},
author = {Batistel, F},
title = {Using gnotobiotic ruminants to dissect host-microbe interactions for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771182},
pmid = {42078518},
issn = {1664-302X},
abstract = {Ruminant animals host one of the most complex gut microbial ecosystems, enabling the conversion of fibrous plant biomass into nutrient-dense foods such as meat and milk, which are essential for global food security. Over time, successive waves of research-from the initial recognition of microbes in the rumen, through anaerobic cultivation, to more recent multi-omics approaches-have progressively expanded our understanding of rumen microbial composition and its links to animal production and greenhouse gas emissions. Despite these advances, most insights into rumen microbial composition and traits of interest are based on associative or correlative evidence, and the host-derived mechanisms that actively shape rumen microbial composition and function remain poorly defined. Early gnotobiotic studies in ruminants demonstrated the value of maintaining animals under defined microbial conditions to dissect host-microbe interactions; however, this experimental capability has largely been lost from contemporary rumen research. This Perspective argues that revisiting gnotobiotic ruminant models is both timely and necessary for establishing causal mechanisms that govern host-microbe interactions in the rumen. Integrating gnotobiotic ruminant models is essential for establishing causal relationships between host biology and rumen microbial composition, thereby providing a foundation for biologically informed strategies that can enhance the sustainability of ruminant production systems.},
}

@article {pmid42078524,
year = {2026},
author = {Najnine, F and Guo, X and Cai, J},
title = {Lactobacillus salivarius GZPH2 reshapes hepatopancreatic microbiome structure and enhances immunometabolism in Litopenaeus vannamei under farm conditions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762396},
pmid = {42078524},
issn = {1664-302X},
abstract = {INTRODUCTION: The hepatopancreas of Litopenaeus vannamei plays a central role in digestion, metabolism, mineral homeostasis, and immune defense; however, its strain-specific responsiveness to probiotics remains insufficiently characterized. This study aimed to elucidate the comparative effects of a single-strain probiotic (Lactobacillus salivarius GZPH2; HH) and a mixed-strain consortium (EM; TH) on hepatopancreatic function under tropical semi-intensive culture conditions.

METHODS: An integrated multi-omics approach, combining histology, mineral profiling, 16S/18S rRNA sequencing, and 4D data-independent acquisition (4D-DIA) proteomics, was applied to evaluate probiotic-induced changes after 90 days of feeding, with a non-supplemented group (WH) as control.

RESULTS: Both probiotics significantly improved growth, survival, and feed efficiency, increasing biomass by 26-27% relative to the control; however, distinct mechanistic responses were observed. HH enhanced hepatopancreatic regeneration by increasing embryonic (E) and fibrillar (F) cells while reducing blister-like (B) and resorptive (R) cells, alongside greater accumulation of Mg, Fe, Ca, and Se. It also promoted microbial evenness and enriched beneficial Alphaproteobacteria (e.g., Labrenzia, Tropicibacter) and fungal taxa (Candida-Lodderomyces clade). Proteomic analysis revealed upregulation of carbohydrate metabolism, calcium regulation, immune-related proteins, and antioxidant enzymes, including hemocyanin, crustin-like proteins, chitinase, and catalase. In contrast, TH maintained a storage-oriented morphology, exhibited lower mineral deposition and microbial diversity, was dominated by Bacillus, and preferentially enriched proteolytic enzymes and redox-related pathways.

DISCUSSION: These findings demonstrate that the single-strain probiotic GZPH2 induced a more regenerative, metabolically efficient, and immunologically robust hepatopancreatic state than the mixed consortium. These findings provide multi-omics evidence supporting strain-specific probiotic selection as a precision strategy to enhance shrimp health and sustainability in aquaculture.},
}

@article {pmid42078525,
year = {2026},
author = {Brahmbhatt, HD and Chavda, P and Vadee, D and Patel, AK and Bagatharia, S},
title = {Genome characterization and comparative genomics of Limosilactobacillus reuteri HDB isolated from the gut of an Indian infant.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780782},
pmid = {42078525},
issn = {1664-302X},
abstract = {Limosilactobacillus reuteri, formerly Lactobacillus reuteri, is a rod-shaped, Gram-positive, facultative anaerobe that colonizes the gastrointestinal tract of most vertebrates, including humans. We report the first isolation of L. reuteri strain HDB from the stool of a healthy Indian infant. Species assignment using the Type (Strain) Genome Server (TYGS) placed HDB within the L. reuteri clade, showing closest affinity to L. reuteri subspecies porcinus (dDDH 69.7%) yet clustering phylogenomically with L. reuteri DSM 17938. Hybrid de novo assembly (Illumina + Oxford Nanopore GridION MK1) generated a single circular 2,226,956 bp chromosome (GC 39.04%) encoding 2,160 CDS. Functional annotation identified genes involved in vitamin B12 biosynthesis, reuterin production, and probiotic functions, along with enriched carbohydrate and cofactor metabolic pathways. Comparative analysis with 59 L. reuteri genomes revealed a pangenome of 11,725 gene families, including 944 core gene families, 171 soft-core gene families, 1912 shell gene families, and 8698 cloud gene families, highlighting notable diversity. Core-genome phylogeny aligns HDB closely with the reference strain DSM 17938, confirming its identity as a human-associated lineage. dN/dS analysis indicated strong purifying selection across host niches, with no evidence of widespread positive selection. Genome-scale modeling predicts expanded carbohydrate flux in HDB against global references. The genetic background, along with its conserved metabolic features, suggests that HDB carries genomic characteristics commonly associated with human-derived L. reuteri strains. These observations support its consideration for further evaluation as a regionally sourced probiotic candidate. These conclusions are based on genomic and computational predictions and require experimental validation through adhesion, colonization, and safety studies.},
}

@article {pmid42078528,
year = {2026},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R and Han, Y},
title = {Identification of novel CRESS-DNA viruses in the human vaginal microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1790643},
pmid = {42078528},
issn = {1664-302X},
abstract = {INTRODUCTION: Circular replication-associated protein (Rep)-encoding single-stranded DNA (CRESS-DNA) viruses are widely distributed across diverse hosts and environments, yet their diversity within the human vaginal virome remains poorly characterized. This study aimed to investigate the presence, diversity, and evolutionary relationships of CRESS-DNA viruses in the human vaginal niche.

METHODS: Viral metagenomic sequencing was performed on 24 pooled vaginal swab libraries derived from women with and without vaginitis. After host sequence removal and quality control, de novo assembly and viral identification were conducted. Candidate viral genomes were curated based on genomic features, followed by functional annotation, phylogenetic analysis using Rep protein sequences, and genome-wide pairwise nucleotide identity comparisons.

RESULTS: A total of five CRESS-DNA viral genomes were identified, including four complete and one nearly complete circular genomes. All genomes exhibited canonical architectures, encoding Rep and Cap proteins and containing conserved HUH endonuclease and superfamily 3 helicase motifs. Phylogenetic analysis placed these viruses within the orders Rohanvirales, Ringavirales, Cirlivirales, and Cremevirales, representing multiple distinct evolutionary lineages. Genome-wide pairwise identity analysis showed that all identified viruses fell below established species- and genus-level thresholds, indicating that they represent novel taxa. Comparative analyses further revealed substantial divergence from known environmental and vertebrate-associated viruses.

DISCUSSION: These findings expand the known diversity of CRESS-DNA viruses in the human vaginal virome and highlight their broad evolutionary diversity. The detected viruses likely represent diverse ecological origins rather than stable host-specific infections, and no clear association with vaginitis was observed. This study provides new insights into the evolutionary landscape of CRESS-DNA viruses in the human reproductive tract and underscores the need for further investigation into their biological roles and potential health implications.},
}

@article {pmid42078532,
year = {2026},
author = {Padmanabhan, C and Puig, A},
title = {Editorial: Metagenomic insights into microbial communities in fruits and vegetable plants.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1844864},
pmid = {42078532},
issn = {1664-302X},
}

@article {pmid42078537,
year = {2026},
author = {Shen, T and Zhou, Y and Gao, J and Xiong, X and Chen, C},
title = {Gut microbiota regulates growth retardation in pigs through their metabolites of taurine and butyric acids.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1811659},
pmid = {42078537},
issn = {1664-302X},
abstract = {Growth retardation of piglets has always been observed in current pig production system. Here we defined these pigs as stunted pigs. Stunted pigs show normal feed intake, but exhibit extremely slow growth speed. This brings a big economic loss to pig industry. Many factors can lead to growth retardation, including gut microbiota which has been reported to play important roles in growth retardation of children. However, whether and which gut microbial taxa are associated with growth retardation of piglets are largely unknown. Here we used 16S rRNA gene and shotgun metagenomic sequencing to identify bacterial taxa associated with growth retardation in 126 pigs including stunted pigs and their pairwise littermates showing normal growth. We identified several Clostridium spp. significantly enriched in the gut of normal growing pigs, including Clostridium symbiosum which was the key biomarker distinguishing stunted pigs and normal growing pigs, while several Bacteroides spp. had higher abundances in stunted pigs. Clostridium spp. was significantly associated with the shifts of functional capacities of the gut microbiome between normal and stunted pigs, e.g., biosynthesis of unsaturated fatty acids. Untargeted serum metabolome analysis found that normal growing pigs had higher concentration of taurine in serum. Increased concentration of serum taurine was associated with increased abundance of Clostridium symbiosum. Furthermore, all metabolites having higher abundances in normal growing pigs were enriched in the pathway of taurine and hypotaurine metabolism. Short-chain fatty acids (SCFAs) analysis identified butyric acid having higher concentration in feces of normal growing pigs in both discovery and validation cohorts, and the changes in the abundances of Clostridium symbiosum was correlated with the shifts of the concentrations of fecal SCFAs. These results suggested that Clostridium spp., especially Clostridium symbiosum improved pig growth by increasing the concentrations of serum taurine and fecal butyric acid, and was an important biomarker associated with pig growth. This study provided important insights into the effect of the gut microbiome on pig growth retardation.},
}

@article {pmid42078551,
year = {2026},
author = {Yang, W and Ren, Q and Li, B},
title = {Case Report: Washed microbiota transplantation for the treatment of malnutrition with multidrug-resistant Klebsiella pneumoniae and Candida tropicalis coinfection in a child.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1809311},
pmid = {42078551},
issn = {2296-2360},
abstract = {BACKGROUND: Multidrug-resistant (MDR) Klebsiella pneumoniae and fungal coinfection in children with severe malnutrition are difficult to control with antibiotics alone. This report describes an 8-year-old boy whose pulmonary infection remained uncontrolled and whose nutritional status progressively deteriorated. Washed microbiota transplantation (WMT) was introduced as part of a multimodal salvage treatment strategy, after which the patient showed gradual improvement during continued antimicrobial therapy, respiratory support, and nutritional rehabilitation.

CASE PRESENTATION: We report the case of an 8-year-old boy with chronic malnutrition and recurrent severe pneumonia associated with an underlying central nervous system disorder. He developed recurrent respiratory failure and a persistent pulmonary infection caused by ESBL-producing MDR K. pneumoniae and Candida tropicalis. Despite broad-spectrum antimicrobial therapy, respiratory support, bronchoscopy/bronchoalveolar lavage, and enteral nutrition through a nasojejunal tube, infection control remained poor and nutritional status continued to deteriorate, complicated by sepsis and antibiotic-associated diarrhea. In this context, WMT was introduced through a nasojejunal tube as part of a multimodal salvage treatment strategy and was administered in two treatment courses. Thereafter, during continued antimicrobial treatment, respiratory support, and nutritional rehabilitation, the patient showed progressive clinical improvement, with subsequent negative sputum culture results, gradual radiographic resolution of pulmonary inflammation, weight gain from 14.0 to 22.5 kg, and marked functional recovery.

CONCLUSION: This case suggests that, in severely malnourished children with refractory multidrug-resistant pulmonary bacterial and fungal infections, WMT may have potential adjunctive value as part of comprehensive management. However, because multiple interventions were implemented concurrently and no pre- and post-WMT microbiome sequencing was performed, the observed clinical improvement could not be attributed exclusively to WMT. Therefore, this case should be interpreted only as an exploratory clinical observation rather than confirmatory evidence, and future prospective studies under strict ethical oversight need to be conducted.},
}

@article {pmid42078569,
year = {2026},
author = {Oliveira, JS and Keim, KS and Evans, R and Kurasch, J and Jahansouz, C and Teigen, LM and Lin, AW},
title = {Capturing static and dynamic dietary patterns for human gut microbiome research: a conceptual framework.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2665578},
pmid = {42078569},
issn = {2993-3935},
abstract = {There is inconsistency in the evidence regarding the effects of food on the gut microbiome. These inconsistencies arise, in part, from substantial inter- and intraindividual variations in diet. The wide range of foods consumed directly influences substrate availability for the microbiota. By categorizing foods into broad groups and overlooking interactions among food constituents within individual foods, current dietary pattern approaches can obscure food-specific differences needed to understand dietary effects. Differences in habitual and occasional intake further complicate analyses since frequency of food consumption can produce different gut microbiota responses within the same individual. Flexible analytical approaches are needed to capture within-individual food intake frequency and food-specific effects. To address these challenges, this narrative review presents dietary pattern concepts that distinguish static (stable or consistent) and dynamic (fluctuating or episodic) intake of specific foods at the individual level. We performed a literature search in three databases, including Medline, CINAHL, and PsycINFO, to retrieve relevant articles that distinguish the concepts of "core foods" and "secondary foods" in population-level studies. We adapt these concepts to a microbiome context at the individual level and propose future directions for studies investigating the impact of diet on the gut microbiome.},
}

@article {pmid42078571,
year = {2026},
author = {Nakato, G and Inoue, H and Onawa, S and Furukawa, R and Obana, N and Tanaka, K and Agematu, H and Song, I and Inoue, J and Fukuda, S},
title = {Development of a monoclonal antibody-based approach for selective enrichment of target Bifidobacterium longum from a complex fecal community.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2663732},
pmid = {42078571},
issn = {2993-3935},
abstract = {Individual differences in gut microbiota composition highlight the need for methods capable of selectively enriching host-associated bacteria from complex microbial communities. Conventional cultivation approaches lack the precision required for targeted enrichment, limiting progress in personalized microbiome research. Here, we established a proof-of-concept monoclonal antibody-based strategy for the selective enrichment of a target gut bacterium. We generated a monoclonal antibody (8H2) exhibiting preferential reactivity toward the human-derived Bifidobacterium longum Jih1 and demonstrated that it selectively enriched viable Jih1 cells from a defined bacterial consortium and a human fecal sample. Proteomic and genetic analyses suggested that 8H2 recognizes glutamine synthetase (GS), an enzyme typically localized intracellularly, but detected on the surface of Jih1 cells. This surface association enables antibody binding and facilitates selective enrichment within complex microbial communities. These data support the feasibility of antibody-based, selective enrichment of viable bacteria and suggest potential applications for monitoring individual-associated bacteria in personalized nutrition and microbiome-based interventions.},
}

@article {pmid42064212,
year = {2026},
author = {Anshory, M and Strepis, N and Rosandy, MG and Pawestri, AR and Iskandar, A and Wulanda, IA and Setyowatie, L and David, NI and Malem, NR and Kalim, H and Nijsten, TEC and Nouwen, JL and Thio, HB},
title = {Skin microbiome variation in people living with HIV: associations with antiretroviral therapy and host factors.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1794878},
pmid = {42064212},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/drug therapy/microbiology ; *Skin/microbiology ; Male ; *Microbiota/drug effects ; Female ; Adult ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Indonesia ; *Anti-Retroviral Agents/therapeutic use ; DNA, Bacterial/genetics ; Skin Microbiome ; },
abstract = {INTRODUCTION: The skin microbiome plays a key role in cutaneous immunity and is shaped by host immune status. HIV infection is associated with immune dysfunction and dermatological disease, yet its impact on the skin microbiome and the modifying effect of antiretroviral therapy (ART) remain incompletely defined. This prospective observational study conducted in Indonesia aimed to characterize differences in skin microbiome composition across HIV status and ART exposure and relate these profiles to clinical parameters.

METHODS: Skin swabs were obtained from sebaceous (posterior neck) and dry (dorsal forearm) sites in HIV-ART-naïve individuals, people living with HIV on ART, and HIV-negative controls, and analyzed using 16S rRNA gene sequencing. Microbial diversity and community structure were assessed using Bray-Curtis dissimilarity, PERMANOVA, and differential abundance testing with ANCOM-BC2, with multivariable models adjusting for demographic, clinical, behavioral, and anatomical factors and subgroup analyses by body mass index, skincare habits, and sampling site.

RESULTS: In total, 488 samples from 244 participants were analyzed. Both HIV groups showed significantly reduced alpha diversity compared with controls, and overall community composition differed by HIV status, although sampling site explained a larger proportion of variation. Across groups, the microbiome was dominated by Corynebacterium, Cutibacterium, Staphylococcus, and Streptococcus. Differential abundance analyses indicated targeted genus-level shifts rather than global dysbiosis, with ART-naïve individuals showing the most consistent deviations, including increased Staphylococcus and reduced Streptococcus relative to controls, and partial attenuation among participants receiving ART. HIV-associated differences were observed within both sebaceous and dry sites, and HIV status remained independently associated with microbiome composition after adjustment.

CONCLUSIONS: These findings suggest that HIV infection is associated with subtle but consistent alterations in the skin microbiome within the context of strong site-specific skin microenvironments. Longitudinal studies integrating functional profiling and host markers of cutaneous barrier integrity and inflammation are needed to clarify their clinical implications.},
}

Humans
*HIV Infections/drug therapy/microbiology
*Skin/microbiology
Male
*Microbiota/drug effects
Female
Adult
Prospective Studies
RNA, Ribosomal, 16S/genetics
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Indonesia
*Anti-Retroviral Agents/therapeutic use
DNA, Bacterial/genetics
Skin Microbiome

@article {pmid42064216,
year = {2026},
author = {Pang, S and Zhang, Z and Ma, Q and Liu, Y and Wang, S and Wang, J and Bi, Y},
title = {The gut-kidney microbiome-oxalate axis in calcium oxalate nephrolithiasis: mechanisms and microbiome-based interventions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1804800},
pmid = {42064216},
issn = {2235-2988},
mesh = {Humans ; *Nephrolithiasis/microbiology/therapy/metabolism ; *Gastrointestinal Microbiome/physiology ; *Calcium Oxalate/metabolism ; *Kidney/microbiology/metabolism ; Dysbiosis ; *Oxalates/metabolism ; Animals ; Hyperoxaluria ; },
abstract = {INTRODUCTION: Calcium oxalate nephrolithiasis is increasingly recognized as a disorder influencednot only by diet and host oxalate handling, but also by the gut-kidneymicrobiome axis. Emerging multi-omics studies suggest that disturbances inintestinal and urinary microbiota, together with altered microbial metabolites,may contribute to disrupted oxalate homeostasis, inflammatory signaling, epithelialinjury, and crystal retention.

METHODS: We performed a narrative, semi-structuredreview of PubMed, Embase, and Web of Science (2010-2025), focusing onoxalate metabolism, gut and urinary microbiota, and microbiome-targeted interventionsin nephrolithiasis, with emphasis on calcium oxalate stones. Human andexperimental studies examining microbial composition, microbial metabolites,host transport and genetic determinants, and nutritional or microbial therapieswere qualitatively synthesized.

RESULTS: Current evidence indicates that loss of oxalatedegradinggut bacteria and broader dysbiosis are associated with hyperoxaluriaand increased calcium oxalate stone risk, whereas microbiome-supportive dietarypatterns may be protective. Multi-omics analyses reveal coordinated alterationsacross stool, urine, and stone-associated microbiota, implicating pathways involvingshort-chain fatty acids, bile acids, and unconjugated bilirubin in oxalatehandling, inflammation, and lithogenesis. Nutritional modulation may favorablyinfluence this axis, while probiotics, synbiotics, and engineered livebiotherapeutics show encouraging preclinical results.

DISCUSSION: Fecal microbiota transplantationremains highly preliminary in this field, and overall human data remainlimited and heterogeneous. The gut-kidney microbiome-oxalate axis providesan integrative framework linking diet, host pathways, microbial metabolites, andmulti-site microbial communities to calcium oxalate nephrolithiasis, and may helpinform future microbiome-based prevention and adjunctive managementstrategies.},
}

Humans
*Nephrolithiasis/microbiology/therapy/metabolism
*Gastrointestinal Microbiome/physiology
*Calcium Oxalate/metabolism
*Kidney/microbiology/metabolism
Dysbiosis
*Oxalates/metabolism
Animals
Hyperoxaluria

@article {pmid42064333,
year = {2026},
author = {Reider, KE and Fannin, C and Hannah, KA and Gelona, AR and Anderson, C and Barnard-Kubow, K and Enke, RA},
title = {16S rRNA amplicon metabarcoding dataset from a retreating glacier forefield in the high tropical andes.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112758},
pmid = {42064333},
issn = {2352-3409},
abstract = {Glaciers are retreating rapidly worldwide, particularly at high elevations, changing the environments and habitats of microorganisms, plants, and animals drastically and leaving behind nutrient-poor sediment. We sought to explore seasonal, elevational, and soil age differences in microbial community diversity found in moraine deposits exposed by recent deglaciation and previously exposed during the Little Ice Age in the Cordillera Vilcanota of southeastern Peru. In the wet and dry seasons of 2023, JMU students and other researchers collected soil samples from 35 sites across a 2.5 square kilometer range in the Andes mountains. Each sample was assigned to the season collected, elevation of collection, and age of exposure. Total DNA was extracted from samples and the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform. The data were then processed and analyzed using the QIIME2 bioinformatics pipeline. This dataset will be useful to the field for studying ecological community and ecosystem formation in glacier forefields emerging from climate change.},
}

@article {pmid42064368,
year = {2026},
author = {Berbudi, A and Riswari, SF and Kwarteng, A},
title = {Helminth Infection, Gut Microbiome Alterations, and Their Impact on Pulmonary Tuberculosis Susceptibility.},
journal = {Journal of tropical medicine},
volume = {2026},
number = {},
pages = {3767562},
pmid = {42064368},
issn = {1687-9686},
abstract = {BACKGROUND: Helminth infections and pulmonary tuberculosis (TB) frequently coexist in low- and middle-income countries and interact through immune-mediated mechanisms that influence host susceptibility to Mycobacterium tuberculosis (Mtb). Beyond direct immunomodulation, increasing evidence indicates that helminth infections alter gut microbiome composition and microbial metabolite production, thereby shaping systemic and pulmonary immune responses through the gut-lung axis. Given the central role of the gut microbiome in regulating T-cell polarization, macrophage function, and inflammatory balance, microbiome-mediated pathways have emerged as a potential link between helminth infection and impaired host defense against pulmonary TB.

OBJECTIVES: This narrative review examines current evidence on how helminth-induced immunological changes and gut microbiome alterations, within the context of the gut-lung axis, may influence susceptibility to pulmonary TB.

METHODS: A narrative review approach was used to synthesize findings from experimental, observational, and clinical studies addressing helminth infection, gut microbiome dynamics, immune regulation, and TB.

RESULTS: Helminth infections are associated with Th2-skewed immune responses characterized by increased regulatory T-cell activity and anti-inflammatory cytokine production, which may attenuate Th1-mediated immunity essential for Mtb control. Helminths also modulate gut microbiome composition, with effects ranging from increased microbial diversity to dysbiosis, depending on helminth species and host context. These microbiome alterations may influence systemic immunity through microbial metabolites such as short-chain fatty acids (SCFAs). Importantly, SCFAs exhibit context-dependent effects, potentially supporting immune homeostasis while, under certain conditions, promoting regulatory pathways that may dampen protective antimycobacterial responses.

CONCLUSIONS: Current evidence suggests that helminth-associated immune modulation and gut microbiome alterations may influence pulmonary TB susceptibility, although most findings remain associative rather than causal. Further mechanistic and clinical studies are needed to clarify the role of the gut-lung axis in helminth-TB coinfection and to inform integrated disease management strategies in endemic regions.},
}

@article {pmid42064411,
year = {2026},
author = {Weiss, G and Voroshilina, E and Koranda, M and Blauensteiner, J and Schenk, M},
title = {Microbial signatures in follicular fluid and their association with fertilization success.},
journal = {Frontiers in reproductive health},
volume = {8},
number = {},
pages = {1773092},
pmid = {42064411},
issn = {2673-3153},
abstract = {BACKGROUND: Emerging evidence suggests that the upper female reproductive tract is not sterile and that microbial signals within follicular fluid (FF) may influence oocyte competence. However, previous studies have largely relied on pooled FF samples or dominant follicles, limiting insight into follicle-specific associations with fertilization outcomes.

METHODS: In this exploratory paired study, follicular fluid samples were collected from 24 women undergoing IVF/ICSI treatment. For each patient, two FF samples were analyzed individually: one associated with a fertilized oocyte, and one associated with an oocyte that failed fertilization. Bacterial DNA and total bacterial load (TBL) were assessed using quantitative real-time PCR targeting predefined microbial taxa.

RESULTS: Bacterial DNA above the predefined detection threshold was identified in 39.6% of all FF samples. Notably, within this exploratory cohort, FF samples associated with fertilization failure were more frequently TBL-positive compared with FF samples linked to successful fertilization (70.8% vs. 8.3%). Follicles from the same patient often differed in bacterial DNA presence, indicating substantial intra-individual variability. Several bacterial taxa, including Fannyhessea vaginae, Ureaplasma spp., and Lactobacillus spp., were more frequently detected in FF samples associated with failed fertilization; however, no individual taxon showed a consistent association with outcome across all samples.

CONCLUSION: In this paired follicle-level analysis, the absence of detectable bacterial DNA in follicular fluid was associated with fertilization outcome. These findings highlight follicle-level heterogeneity in microbial DNA detection and underscore the importance of follicle-specific analyses in reproductive microbiome research. Larger prospective studies are required to validate these observations and to clarify the biological mechanisms underlying follicular microbial signals.},
}

@article {pmid42064742,
year = {2026},
author = {Gordon, S and Evans, S and Kirven, K and Whisonant, M},
title = {Increased dietary iron alters taxonomic composition and function of zebrafish gut microbiome.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {42064742},
issn = {2578-9430},
abstract = {Gut microbiota are crucial to both gastrointestinal tract health and host well-being. Oral iron supplementation is commonly used, but knowledge of iron's impact on the gut microbiome is limited. Using Zebrafish (Danio rerio) as a model organism, we tested effects of increased dietary iron on gut taxonomic composition and function. Increased dietary iron significantly altered the zebrafish microbiome taxonomic composition and enriched physiological conditions of aerobic respiration. Mass spectrometry (GCMS and LCMS), utilized to measure primary metabolite and lipid levels, pointed to significant increases in amino acids under increased iron supplementation, but no significant change in lipid metabolite levels.},
}

@article {pmid42064815,
year = {2026},
author = {Li, J and Zhang, S and Zhang, Y and Wang, X and Zhuge, Y and Wu, Q and Zhao, Y and Gao, Q and Chen, R and Wang, Y and Jin, Q and Zhang, Y},
title = {Harnessing the gut microbiome for precision therapeutics in heart failure.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1781470},
pmid = {42064815},
issn = {1663-9812},
abstract = {Heart failure (HF) management remains challenging because patients often show large differences in how well treatments work and in how often adverse drug reactions occur. Traditional pharmacogenomics cannot fully explain these differences. Emerging evidence from pharmacomicrobiomics shows that the gut microbiome represents a previously underappreciated factor influencing drug responses. This review summarizes the two-way interactions between the gut microbiota and key HF drugs, including digoxin, angiotensin receptor-neprilysin inhibitors (ARNIs), ACE inhibitors (ACEIs), angiotensin receptor blockers (ARBs), β-blockers, sodium-glucose cotransporter 2 (SGLT2) inhibitors, mineralocorticoid receptor antagonists (MRAs), and diuretics. On the one hand, gut microbes can change drug effects because they can metabolize drugs and affect host physiological pathways. On the other hand, HF drugs can change the structure and function of the gut microbial community. This review also discusses how microbiome-related features may serve as biomarkers to support personalized treatment and how strategies such as dietary changes and microbiota-targeted therapies may improve clinical outcomes. Although evidence remains limited, and certain methods require further refinement, integrating microbiome insights into HF treatment may support more precise and individualized treatment strategies and help address current therapeutic limitations.},
}

@article {pmid42064906,
year = {2026},
author = {Nguyen, T and Woods, C and Liu, J and Wang, C and Lin, AL and Cheng, J},
title = {A multimodal AI model for modeling the genetic risk factor of Alzheimer's disease.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.13.26350803},
pmid = {42064906},
abstract = {The apolipoprotein E ε 4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), the most common form of dementia. APOE4 carriers exhibit cerebrovascular and metabolic dysfunction, structural brain alterations, and gut microbiome changes decades before the onset of clinical symptoms. Better understanding of the early manifestion of these physiological changes is critical for development of timely AD interventions and risk reduction protocols. Multi-modal datasets encompassing a wide range of APOE ε 4 and AD associated biomarkers provide a valuable opportunity to gain insight into the APOE4 phenotype; however, these datasets often present analytical challenges due to small sample sizes and high heterogeneity. Here, we propose a two-stage multimodal AI model (APOEFormer) that integrates blood metabolites, brain vascular and structural MRI, microbiome profiles, and other clinical and demographic data to predict APOE4 allele status. In the first stage, modality-specific encoders are used to generate initial representa-tions of input data modalities, which are aligned in a shared latent space via self-supervised contrastive learning during pretraining. The contrastive learning objective encourages learning of informative and consistent representations across modalities through leveraging cross-modality relationships. In the second stage, the pretrained representations are used as inputs to a multimodal transformer that integrates information across modalities to predict a key AD-risk genetic variant (APOE4). Across 10 independent experimental runs with different train-validation-test splits, APOEFormer predicts whether an individual carries an APOE4 allele with an average prediction accuracy of 75%, demonstrating robust performance under limited sample sizes. Post hoc perturbation analysis of the predictive model revealed valuable insights into the driving components of the APOE4 phenotype- including key blood biomarkers and brain regions strongly associated with APOE4.},
}

@article {pmid42065024,
year = {2026},
author = {Bharat, AA and Ali, O and Sahadeo, UM and Ramsubhag, A and Jayaraman, J},
title = {Preparation of a fermented Sargassum extract, microbial dynamics involved, and its effect on Capsicum annuum.},
journal = {3 Biotech},
volume = {16},
number = {5},
pages = {170},
pmid = {42065024},
issn = {2190-572X},
abstract = {UNLABELLED: The study explored Sargassum valorization through the production of a fermented extract for its application as a crop biostimulant. The dried and ground Sargassum (S. natans and S. fluitans) was subjected to anaerobic fermentation utilizing the endogenous microorganisms already present in the seaweed. During the fermentation process, samples were periodically taken (5, 15, 20, 27, 30, and 35) for 16S rRNA and ITS paired-end amplicon metataxonomics. Microbiome profiling revealed distinct temporal microbiome shifts over the 35 days of fermentation, with Firmicutes, Bacteroidota, and Nectriaceae emerging as the core microbiome. Furthermore, microbial network analysis identified Clostridiaceae, Sporolactobacillaceae, and Pirellulaceae as dominant bacterial families, while Gibberella and Aspergillus showed up as prevalent fungal genera. Beta-diversity analyses showed a significant shift in microbial composition on Day 35. Extracts were screened for their antimicrobial properties against plant pathogens (Xanthomonas campestris pv. vesicatoria and Alternaria solani), however results indicated no antimicrobial effect. Plant growth trials were conducted using Capsicum annuum L. plants and the extracts were applied as foliar application sprays at 0.5-1% v/v concentrations under greenhouse conditions. All parameters measured (chlorophyll content, root and shoot length, and root and shoot weights were all significantly greater than Control-treated plants. Chlorophyll content, root length, shoot length, fresh root and shoot weight, and dry root and shoot weight all had significant increases of up to 28.82%, 60.13%, 15.95%, 67.95%, 53.90%, 82.05%, and 95.86% respectively. The result of the study promotes the usage of fermented Sargassum extracts as an organic biostimulant and aligns with sustainable agricultural practices.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04811-1.},
}

@article {pmid42065141,
year = {2026},
author = {Talbott, S and Stephens, B and Talbott, J and Oddou, M and Fumiki, A},
title = {Effects of Lactiplantibacillus Plantarum KABP051 Probiotic on Body Composition, Microbiome and Mood in Healthy Overweight Adults.},
journal = {Journal of medicinal food},
volume = {},
number = {},
pages = {1096620X261448041},
doi = {10.1177/1096620X261448041},
pmid = {42065141},
issn = {1557-7600},
abstract = {Obesity and mental health disorders are among the greatest public health challenges of the 21st century. Interestingly, an altered microbiome profile has been associated with both conditions. The aim of this randomized, double-blind, placebo-controlled clinical trial was to evaluate the effects of dietary supplementation with a specific probiotic strain (Lactiplantibacillus plantarum KABP051) on body composition and gut microbiome balance, together with measures of mood state, in a population of healthy overweight subjects. Sixty healthy, moderately stressed, nondepressed and overweight or obese volunteers were supplemented for 12 weeks with probiotic (L. plantarum KABP051; 1 billion colony forming units/day) or placebo (microcrystalline cellulose). The KABP051 group experienced significantly greater improvements compared with placebo on body composition measurements, including a reduction in body weight and waist circumference, which decreased in 1.97 ± 0.77 (mean ± SE) kg and 2.15 ± 0.81 (mean ± SE) cm versus placebo at the end of the intervention (both P < .05, mixed model for repeated measures [MMRM] and post-hoc analysis). Microbiome composition improved in KABP051 group, with significant increase in the relative abundance of Lactiplantibacillus spp. versus placebo. Body fat percentage, profile of mood states fatigue, and confusion sub-scores showed a global trend toward improvement compared with placebo, with the change at 12 weeks being significant in the three measurements in post-hoc analysis (P = .015, P = .014, and P = .016, respectively). No serious adverse events were registered during the intervention period. These results suggest that a specific strain of probiotic bacteria (L. plantarum KABP051) may have both metabolic and psychobiotic effects and may be beneficial for enhancing weight loss and body composition, improving energy (less fatigue) and mood levels while embarking on a healthy lifestyle regimen. ClinicalTrials.gov identifier: NCT06808061.},
}

@article {pmid42065212,
year = {2026},
author = {Shen, Y and Wang, Z and Cheng, X and Tang, F and Rao, S and Zhang, D},
title = {Cluster analysis of research hotspots and trends in probiotics for constipation: A comprehensive bibliometric analysis (1977-2024).},
journal = {Medicine},
volume = {105},
number = {18},
pages = {e48338},
doi = {10.1097/MD.0000000000048338},
pmid = {42065212},
issn = {1536-5964},
support = {KS2201//Kunshan key R & D program/ ; },
mesh = {*Probiotics/therapeutic use ; *Bibliometrics ; *Constipation/therapy/microbiology ; Humans ; Cluster Analysis ; *Biomedical Research/trends ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Probiotics are increasingly recognized as a promising therapeutic approach for managing constipation, sparking widespread interest in their effects on gastrointestinal health. This study conducts a cluster analysis to systematically map global research trends and hotspots in probiotics for constipation from 1977 to 2024.

METHODS: Relevant publications were retrieved from the Web of Science Core Collection. Bibliometric tools, including VOSviewer, CiteSpace, and R, were applied for cluster analysis, network visualization, and trend mapping.

RESULTS: A total of 519 publications were included in the analysis. China led in publication volume, while the United States demonstrated the highest academic influence. Key institutions, such as the University of California System and Harvard University, were identified as major contributors. High-impact journals, including Nutrients, World Journal of Gastroenterology, and Digestive Diseases and Sciences, played central roles in disseminating research. Quigley Eamonn M. M. indicated significant influence in the field. Cluster analysis of keywords revealed 6 principal research hotspots: microbial diversity and mechanisms, gut microbiota-host interaction and pathophysiology, dietary factors and microbiome analysis techniques, epidemiology, prevalence, and population health, clinical management and therapeutic efficacy, and clinical trials and study design. Citation burst analysis indicated a recent research focus shift toward mechanisms, personalized interventions, and gut microbiome modulation.

CONCLUSION: This bibliometric study based on cluster analysis identified 6 major research hotspots in probiotics for constipation, reflecting the evolving trends and collaborative networks of the field. These findings provide a comprehensive perspective on current research priorities and can guide future studies toward innovative and evidence-based clinical applications.},
}

*Probiotics/therapeutic use
*Bibliometrics
*Constipation/therapy/microbiology
Humans
Cluster Analysis
*Biomedical Research/trends
Gastrointestinal Microbiome

@article {pmid42065376,
year = {2026},
author = {Bullard, BM and VanderVeen, BN and Cardaci, TD and McDonald, SJ and Bastian, AV and Willis, NB and Xu, M and Li, J and Pierre, JF and Hofseth, LJ and Fan, D and Murphy, EA},
title = {Panaxynol mitigates chemotherapy-induced intestinal mucositis by improving the colonic microenvironment in murine models.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00035.2026},
pmid = {42065376},
issn = {1522-1547},
support = {R01CA246809//HHS | NIH | National Cancer Institute (NCI)/ ; U01CA272977//HHS | NIH | National Cancer Institute (NCI)/ ; F31AT012589//HHS | NIH | National Center for Complementary and Integrative Health (OAM)/ ; R00CA27689//HHS | NIH | National Cancer Institute (NCI)/ ; F99CA294251//HHS | NIH | National Cancer Institute (NCI)/ ; P20GM155896//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32DK007665//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; T32CA244125//HHS | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Chemotherapy-induced mucositis (CIM) is a debilitating side-effect impacting as many as 90% of cancer patients undergoing treatment. Patients receiving 5-Fluorouracil (5FU), a first-line chemotherapeutic in colorectal cancer, experience significant gastrointestinal distress that perpetuates poor patient quality of life and reduces treatment tolerance, efficacy, and survival. Natural compounds have shown promise in improving CIM through their pleiotropic actions, including immune and mucosal regulation. We examined whether panaxynol, a bioactive compound isolated from American ginseng, can alleviate murine CIM symptomology and severity. Intestinal mucositis was induced in C57BL/6J male and female mice by 5 consecutive intraperitoneal injections of 5FU (35 mg/kg/day); PBS was used as the control. Vehicle or panaxynol (2.5 mg/kg/day) was administered via oral gavage every other day, starting on Day -1, for a total of 4 treatments. Panaxynol significantly improved overall mucositis symptomology, attenuated 5FU-induced cytopenia and anemia, ameliorated the 5FU-induced loss of goblet cells per crypt, suppressed pro-inflammatory immune cells in the colonic lamina propria, and altered microbial diversity and taxonomy. Sex differences were observed, with panaxynol exerting a stronger effect in males, significantly reducing the relative percentage of colonic macrophages and neutrophils. Panaxynol treatment was associated with sex-dependent alterations in gut microbial community structure and modulation of specific taxa, including Dubosiella and Bifidobacterium, alongside male-specific increases in Romboutsia and Alistipes; Akkermansia abundance was primarily influenced by 5FU treatment. These preclinical findings support the potential of panaxynol as a therapeutic candidate for the treatment of CIM and highlight the importance of considering sex as a biological variable.},
}

@article {pmid42065459,
year = {2026},
author = {Liu, M and Yang, Z and Liu, B and Cheng, H and Qin, J and Zhang, P and Tang, T and Peng, F and Yang, J and Wei, P and Su, H},
title = {Correction: Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo90033j},
pmid = {42065459},
issn = {2042-650X},
abstract = {Correction for 'Multi-omics reveals gut microbiome- and metabolome-specific responses to sugar alcohols' by Mengling Liu et al., Food Funct., 2026, https://doi.org/10.1039/D6FO00282J.},
}

@article {pmid42065740,
year = {2026},
author = {Mohsenzadeh, A and Mohammadi, A and Mohsenzadeh, H and Kamali, K and Moradi, M and Ebrahimi, N and Sheikhy, M and Zabet, AH and Mirheidari, H and Bavari, S and Elahi, R},
title = {The gut microbiota and kawasaki disease: exploring the role of microbial dysbiosis and metabolites in pathogenesis and therapeutics.},
journal = {European journal of pediatrics},
volume = {185},
number = {5},
pages = {},
pmid = {42065740},
issn = {1432-1076},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/complications/therapy/microbiology ; Child ; },
abstract = {Kawasaki disease (KD) is an acute, immune-mediated medium-vessel vasculitis and the leading cause of acquired heart disease in children, yet its underlying etiology remains only partially defined. Emerging evidence implicates the gut microbiota as a key modulator of KD susceptibility, immune dysregulation, and therapeutic response. This narrative review aims to synthesise current insights linking gut microbial dysbiosis and microbial metabolites to the pathogenesis, clinical expression, and treatment of KD, and to explore microbiome-informed strategies with diagnostic and therapeutic potential. We conducted a comprehensive search of PubMed, Embase, Web of Science, and Google Scholar from database inception to April 2025 for English-language studies on Kawasaki disease and the gut microbiota, including terms related to microbiome, microbial dysbiosis, metabolites, pathogenesis, immunity, inflammation, and therapy. Reference lists of relevant articles and key reviews were also screened. Children with acute KD exhibit characteristic alterations in gut microbial composition, including an overrepresentation of Streptococcus species, depletion of short-chain fatty acid (SCFA)-producing taxa such as Faecalibacterium, Ruminococcus, and Roseburia, and a significant reduction in fecal butyrate. These changes have been associated with impaired intestinal barrier integrity, heightened NLRP3 inflammasome activation, and dysregulated cytokine signalling, contributing to systemic inflammation and vascular injury. Additional factors, such as antibiotic exposure and concurrent respiratory or oropharyngeal infections, can intensify dysbiosis and have been linked to resistance to intravenous immunoglobulin (IVIG) and an increased risk of coronary artery aneurysms. Conclusions: Gut microbial imbalance and metabolite disruption are likely associated with KD, potentially through interaction with host genetics and immune pathways. Microbiome-targeted approaches, including probiotics, dietary modulation, and metabolite-based therapies, hold promise for improving diagnostic precision, predicting treatment response, and guiding the development of targeted interventions in KD.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/microbiology/therapy
*Gastrointestinal Microbiome
*Dysbiosis/complications/therapy/microbiology
Child

@article {pmid42065823,
year = {2026},
author = {Esteban, DJ and Feeley, M and Goud, M and Abban-Demitrus, AM and Mishalani, L and Touchon, J and Czesak, ME},
title = {Alteration of the Microbiome is Associated with Changes in Mating and Locomotion in Callosobruchus Maculatus.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02783-6},
pmid = {42065823},
issn = {1432-184X},
abstract = {The seed beetle Callosobruchus maculatus is a model organism used to study environmental and genetic factors in the evolution of mating behaviors and life history traits. We sought to address the hypothesis that the microbiome of C. maculatus is associated with host life history traits and mating. To manipulate the microbiome, we developed a chemical treatment protocol to surface sterilize C. maculatus eggs and the food source on which they develop and examined the effect on microbial community structure, beetle life history traits, and mating behaviors including mate choice, and locomotion. Treatment eliminated culturable bacteria from the surface and altered the emerged adult beetle microbiome such that diversity was reduced and the community structure was altered. Treatment reduced survival of small male and female beetles; among the adults that did survive and emerge, females had higher fecundity compared to controls. We found that the treatment also affected mating behavior. Treated beetle pairs had a higher percentage of successful matings and a shorter mating latency period than control beetles. In mate choice tests in which a female was presented with either a treated or control male, females were more likely to mate with treated males. Finally, treated beetles exhibited increased locomotion. Treatment caused selective mortality of smaller individuals and reduced the diversity and altered the structure of the whole-body microbiome of the surviving adults. The treatment was also associated with enhanced mating behavior, increased fecundity and increased locomotion. These experiments revealed that treatment-induced perturbations in larvae result in altered adult behavior and life history traits that are associated with shifts in the beetle microbiome.},
}

@article {pmid42066053,
year = {2026},
author = {Rezaei, A and Habibabad, FS and Bina, S and Khoshnoud, MJ and Haghshenas, M and Rashedinia, M},
title = {Beyond antimicrobial efficacy: Complex interactions of sodium benzoate, potassium sorbate, and citrate alter the rat gut microbiome.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70703},
pmid = {42066053},
issn = {1097-0010},
support = {29466//Shiraz University of Medical Sciences/ ; },
abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a target of dietary food additives. Sodium benzoate (SB), potassium sorbate (PS), and citric acid (Cit) are widely used preservatives, yet their combined effects on the intestinal microbiota remain poorly understood. This study investigated the individual and combinatorial impacts of these three compounds on key bacterial populations in the rat gut.

METHODS AND RESULTS: Thirty-five adult male Sprague-Dawley rats received SB (500 mg kg[-1] BW d[-1]), PS (300 mg kg[-1] BW d[-1]), Cit (1200 mg kg[-1] BW d[-1]), or their binary combinations in drinking water for 8 weeks. Fecal samples were analysed by selective culture and quantitative real-time polymerase chain reaction (PCR). All treatments significantly reduced Lactobacillus abundance (P < 0.05). Citrate alone and in combination with SB markedly increased Enterobacteriaceae (P < 0.01), with the Cit + SB group showing the highest levels. Enterococcus populations were elevated in most treatment groups, particularly after Cit + SB exposure. Staphylococcus responses were context-dependent: increased by SB or PS alone, but suppressed by citrate-containing combinations. Combination effects were often non-additive, with citrate frequently overriding the antimicrobial action of benzoate or sorbate.

CONCLUSION: Chronic exposure to common preservatives at no-observed-adverse-effect level (NOAEL) induces significant, synergistic shifts in the gut microbiota, characterized by loss of beneficial Lactobacillus and expansion of potentially pro-inflammatory Enterobacteriaceae and Enterococcus. The unexpected promotion of Enterobacteriaceae by citrate reveals its role as an active ecological modulator. Our findings challenge the adequacy of single-additive safety assessments and support the inclusion of microbiome endpoints in regulatory toxicology. © 2026 Society of Chemical Industry.},
}

@article {pmid42066227,
year = {2026},
author = {Ponte, AT and Liu, A and Acquah, KS and Balunas, MJ},
title = {The Complex Interplay between Botanical Supplements and the Human Gut Microbiome.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c01493},
pmid = {42066227},
issn = {1520-6025},
abstract = {Botanical supplements have been used for the prevention and treatment of human diseases since ancient times and remain important, widely consumed therapeutics. While they display promising efficacy across a broad spectrum of biological activities, poor oral bioavailability often limits their utility. Upon ingestion, these compounds may remain in the gastrointestinal tract prior to absorption, during which time they interact with gut microbiota. These interactions can significantly alter their bioavailability since microbial enzymes, known for their wide substrate specificity, are capable of readily transforming xenobiotics, often changing their biological activity as well as their bioavailability. Herein, we summarize the chemistry of microbial biotransformations of botanical supplements, highlighting key enzymatic transformations. The reciprocal interactions between four widely used botanical supplements and the human gut microbiome are outlined including green tea, açai, red wine, and mangosteen. Their microbial metabolism and modulation of human gut microbiota is discussed, highlighting the various enzymes and metabolites reported from relevant literature. Although the direct effect of microbiome bioconversion of botanical supplements is largely unexplored due to the complexity of both systems, this review provides a framework for research to determine the bidirectional effects of botanicals and gut microbiota on human health.},
}

@article {pmid42066401,
year = {2026},
author = {Wälchli, DL and Rathinavelu, S and Ackeret, J and Aquino, NJ and Beck, K and Janssen, DJ and Bürgmann, H},
title = {Ripples of resistance: Unveiling antimicrobial resistance dynamics along Switzerland's Aare river.},
journal = {Water research},
volume = {301},
number = {},
pages = {126005},
doi = {10.1016/j.watres.2026.126005},
pmid = {42066401},
issn = {1879-2448},
abstract = {The global spread of antimicrobial resistance (AMR) is a serious public health concern, driven by widespread antibiotic use and the global environmental circulation of antibiotic-resistant bacteria and resistance genes (ARGs). Wastewater treatment plants (WWTPs) are important sources of anthropogenic AMR entering large rivers, which serve as vital water resources but facilitate downstream dissemination. The drivers and dynamics of AMR propagation along river systems remain poorly understood. As Switzerland's longest and one of its largest rivers, the Aare, situated in the upper Rhine watershed, plays a central role in the 'water castle of Europe'. This study examines the impact of WWTP discharges, some receiving high loads of hospital effluent, on ARG distribution along the 288 km Aare river-continuum. Using quantitative PCR targeting 14 ARGs conferring resistance to eight antibiotic classes, combined with 16S rRNA gene amplicon sequencing, we conducted a high-resolution spatial survey to assess shifts in the riverine ARG content and microbiome. Concentrations of trace metals and nutrients were analyzed as tracers of anthropogenic inputs. Results revealed a progressive increase in ARG abundance downstream, driven by WWTP effluents enriched in ARGs. Effluents had 70-fold higher mean ARG concentrations than upstream waters, raising downstream levels up to 141-fold. Major tributaries such as the Reuss and Limmat sustained elevated ARG levels, while passage through lakes markedly reduced concentrations. This study provides the first detailed baseline for ARG prevalence along a large swiss river system, from pristine headwaters to pollution-affected lower reaches and insights into aquatic AMR dynamics and guidance for future monitoring.},
}

@article {pmid42066404,
year = {2026},
author = {Sitinjak, MC and Chen, JK and Lee, HJ and Chen, CM and Wang, CY},
title = {Antiviral effect of lactoferrin against infectious bronchitis virus (IBV) are associated with alterations in the gastrointestinal microbiome.},
journal = {Poultry science},
volume = {105},
number = {7},
pages = {106995},
doi = {10.1016/j.psj.2026.106995},
pmid = {42066404},
issn = {1525-3171},
abstract = {Coronaviruses (CoVs) are an enveloped, polymorphic, positive-sense single-stranded RNA viruses. Currently, both humans and animals are threatened by CoVs, making them a major public health concern. Among the four genera of the family Coronaviridae, infectious bronchitis virus (IBV), which belongs to the genus Gammacoronavirus, continues to cause substantial economic losses in the poultry industry. Nephropathogenic IBV strains, including the Taiwan-I (TW-I) and Taiwan-II (TW-II) serotypes, are the most prevalent IBVs in Taiwan and China and have continued to spread and generate variants through mutation and genetic recombination. Because IBV can replicate in the epithelial cells of the trachea, lung, kidney, and intestine, this study investigated the dysbiosis of the ileal microbiota caused by IBV TW-I and TW-II serotypes. The reduced weight gain of chickens infected with IBV TW-I or TW-II was improved by lactoferrin (LF). The antiviral effects of LF included a significant reduction in viral loads in the ileum of infected chickens. Furthermore, the villus shedding, decreased villus height, increased crypt depth, and reduced number of goblet cells induced by IBV infection were markedly attenuated by LF. Alterations in the ileal microbiome were also observed following LF treatment. Regarding cytokine responses, the IBV-induced upregulation of TGF-β and IL-10 and the elevated infiltration of CD3[+] T cells in the ileum were reduced by LF, whereas the mRNA expression levels of IFN-γ, IL-2, and IL-4 were upregulated by LF. Moreover, the IBV-induced downregulation of MUC2, occludin, and ZO-1 in the ileum was reversed by LF. LF shifted the ileal microbiota toward homeostasis, regulated the immune response to facilitate viral clearance, and restored the intestinal barrier damaged by IBV TW-I and TW-II infection.},
}

@article {pmid42066496,
year = {2026},
author = {Río-López, R and Vourlaki, IT and Clavell-Sansalvador, A and Valdés, A and Padilla, L and García-Gil, LJ and Xifró, X and Ballester, M and Quintanilla, R and Ochoteco-Asensio, J and Prenafeta-Boldú, FX and Dalmau, A and Ramayo-Caldas, Y},
title = {Integrative metagenomic and metabolomic profiling identifies faecal biomarkers of prolonged social stress in pigs.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {5},
pages = {101823},
doi = {10.1016/j.animal.2026.101823},
pmid = {42066496},
issn = {1751-732X},
abstract = {Stressors significantly impact human and animal health, increasing the risk of physical and mental disorders, in part by affecting the gut-brain axis. Although a link between stress, alterations in gut microbial composition, and the serum metabolite profile has already been established in humans, multiomics studies integrating the faecal microbiome and untargeted metabolomics remain unavailable. The objectives of the present study were twofold: first, to identify microbial and metabolic signatures associated with prolonged stress, and second, to evaluate the potential of integrative multiomics approaches to predict key metabolites and discover non-invasive faecal biomarkers of stress in pigs (n = 60). Gut microbial profiles were obtained by shotgun metagenomic sequencing, while faecal metabolites were analysed by untargeted reverse-phase liquid chromatography quadrupole time of flight mass spectrometry, followed by partial least squares discriminant analysis. Metabolite prediction from microbial features was performed using the machine learning method based on neural ordinary differential equations. Eleven discriminant metabolites were identified. In the control group, neurotransmitters such as serotonin and metabolites such as 2-acetamidophenol and sinapine (which possess anti-inflammatory and antioxidant properties) were the most prominent. Conversely, the stressed group exhibited elevated levels of xanthosine, pyrimidine bases (thymine and uracil), n-octadecylamine, and N-α-acetyl-L-lysine. N-octadecylamine (r = 0.37) showed a positive, and serotonin (r = -0.32) a negative correlation with hair cortisol. The results revealed interspecific interactions that modulated microbial and metabolic shifts between the control and stressed pig groups. Feature selection further identified 64 microbial genes that improved classification accuracy between control and stressed pigs to 91.06% and enhanced the prediction of key metabolites, including serotonin and xanthosine. Overall, this integrative multiomics framework elucidates complex microbiome-metabolite interactions and identifies non-invasive biomarkers of prolonged stress-induced metabolic dysregulation, providing valuable insights for animal welfare and translational human health research.},
}

@article {pmid42066508,
year = {2026},
author = {Papadopoulos, GA and Giannenas, I and Lioliopoulou, S and Tassis, P and Papageorgiou, K and di Benedetto, M and van Hoeck, V},
title = {Effects of xylanase supplementation in low- and high-fiber diets on performance and fecal microbiota of lactating sows and their piglets.},
journal = {Research in veterinary science},
volume = {207},
number = {},
pages = {106216},
doi = {10.1016/j.rvsc.2026.106216},
pmid = {42066508},
issn = {1532-2661},
abstract = {The objective of this study was to evaluate the effect of xylanase supplementation in high- and low-fiber diets on the performance of lactating sows and their offspring. At d108 of gestation, 48 sows were assigned to four treatments in a 2 × 2 factorial design: a low-fiber control diet (LF; LF-Con; 12.43% NDF), LF supplemented with 45,000 U/kg xylanase (LF + XYL), a high-fiber control diet (HF; HF-Con; 13.93% NDF), and HF supplemented with xylanase (HF + XYL). Sow body weight (BW) and P2 backfat thickness were recorded at d108 of gestation and weaning. Average daily feed intake (ADFI) was recorded throughout lactation, and piglet BW was measured 24 h post-farrowing and at weaning. Results indicated that sows fed HF diets consumed more feed compared to LF sows (P = 0.003). Furthermore, xylanase supplementation significantly increased ADFI (P = 0.002), reduced lactation weight loss (P = 0.001), and attenuated backfat mobilization (P = 0.003) compared to unsupplemented controls. Regarding the fecal microbiota, HF diets increased the relative abundance of Prevotellaceae and Rikenellaceae. Notably, an increase in the butyrate-producing genus Roseburia (family Lachnospiraceae) was observed, likely driven by cross-feeding mechanisms. Xylanase supplementation reduced the relative abundance of Prevotellaceae, potentially by altering the availability of their preferred carbohydrate substrates. In conclusion, supplementing lactating sows with an endo-1,4-β-xylanase in both LF + XYL and HF + XYL diets, influenced sow energy balance, by elevating feed intake and reducing tissue mobilization, while simultaneously altering the fecal microbiome to a more beneficial, butyrate-producing composition, particularly when using fibrous feedstuffs.},
}

@article {pmid42066511,
year = {2026},
author = {Cha, HE and Seo, J and Cho, HS and Lee, JW and Jeon, AJ and Lim, SK},
title = {Temporal dynamics and stability of the human microbiome for forensic individual identification.},
journal = {Forensic science international. Genetics},
volume = {84},
number = {},
pages = {103519},
doi = {10.1016/j.fsigen.2026.103519},
pmid = {42066511},
issn = {1878-0326},
abstract = {The human microbiome is ubiquitous across nearly all body sites and exhibits biological characteristics that enable stable detection under diverse environmental conditions. Microbial DNA can be analyzed even when human DNA is present in trace amounts or is severely degraded, supporting its potential as a complementary approach to conventional DNA-based identification. However, systematic validation of whether the microbiome simultaneously maintains individual specificity and long-term stability remains limited. In this study, we conducted a longitudinal analysis of the microbiome from the scalp, cheek, hand, and saliva of five healthy Korean participants over a period of up to three years. Intra-individual temporal stability and inter-individual variability were evaluated across multiple temporal scales, ranging from daily to annual intervals. Microbial community dynamics were assessed using relative abundance analysis, beta diversity metrics, and the theta-YC similarity index. Individual identification performance was evaluated for each sampling source using an XGBoost-based machine learning approach. Skin sites and saliva represented distinct ecological niches, with intra-individual similarity exceeding inter-individual similarity across sampling sites and temporal intervals. Although transient community shifts were observed in frequently exposed sites such as the scalp and hand under the four-season climate of the Republic of Korea, individual-specific microbial signatures were maintained over time. The XGBoost-based identification models achieved high accuracy, particularly for saliva (93.3%) and cheek (92.9%) samples. These findings support the potential of the skin and saliva microbiome as complementary tools for individual identification, particularly in forensic contexts where conventional human DNA analysis is limited.},
}

@article {pmid42066541,
year = {2026},
author = {Li, L and Chi, Y and Kong, Y and Zheng, D and Shi, Z and Kang, X},
title = {Rapid species-level discrimination of pulmonary TB and NTM by metagenomic next-generation sequencing with concurrent respiratory microbiome profiling.},
journal = {Diagnostic microbiology and infectious disease},
volume = {116},
number = {1},
pages = {117442},
doi = {10.1016/j.diagmicrobio.2026.117442},
pmid = {42066541},
issn = {1879-0070},
abstract = {INTRODUCTION: Rapid discrimination between Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) remains clinically challenging, especially when conventional microbiological evidence is limited. Whether metagenomic next-generation sequencing (mNGS) can provide rapid species-level identification while simultaneously characterizing the respiratory microbiome remains to be systematically evaluated.

METHODS: Bronchoalveolar lavage fluid from 74 retrospectively enrolled patients with clinically diagnosed pulmonary mycobacterial disease (62 TB, 12 NTM-pulmonary disease (NTM-PD)) was analyzed by mNGS. Conventional test results were extracted from medical records. A supplementary assessment excluding mNGS from diagnostic review was additionally performed to reduce potential incorporation bias. Microbial diversity and between-group differences in the respiratory microbiota were evaluated.

RESULTS: In the clinically diagnosed cohort, mNGS was positive in 61/62 TB cases (98.4%) and 12/12 NTM-PD cases (100%). Mycobacterial cultures were negative in all tested patients in routine clinical practice. By comparison, AFB (8.82%, 3/34), T-SPOT.TB (71.43%, 10/14), and Xpert MTB/RIF (69.23%, 9/13) showed lower positivity among tested patients. In the supplementary assessment, 45/46 independently classified TB cases were mNGS-positive (97.8%). mNGS additionally detected non-mycobacterial pathogens in 62.16% (46/74) of patients, facilitating recognition of polymicrobial infection. Microbiome analysis revealed that the TB group showed relatively higher abundance of Streptococcus parasanguinis besides MTB, whereas NTM group was relatively enriched in opportunistic pathogens including Pseudomonas aeruginosa and Stenotrophomonas maltophilia.

CONCLUSION: In this retrospective real-world cohort, mNGS achieved rapid species-level discrimination of MTB and NTM with high positive detection rates, and simultaneously provided clinically relevant microbiome information, supporting its value as an adjunctive diagnostic tool for pulmonary mycobacterial infection.},
}

@article {pmid42066584,
year = {2026},
author = {Xu, Q and Wang, Q and Hou, D and Zhang, F and Zhang, C and Qi, B and Wei, M and Chen, J and Zha, Q and Qin, H and Song, Y and Wu, X},
title = {Cryptococcal pneumonia susceptibility in immunocompetent patients: Role of pseudomonas aeruginosa via IL-2/IL-12/IL-17 pathways.},
journal = {Journal of infection and public health},
volume = {19},
number = {6},
pages = {103230},
doi = {10.1016/j.jiph.2026.103230},
pmid = {42066584},
issn = {1876-035X},
abstract = {BACKGROUND: While pulmonary cryptococcosis affects immunocompromised patients, it also occurs in immunocompetent individuals. However, underlying mechanisms contributing to susceptibility in immunocompetent patients remain poorly understood.

METHODS: We enrolled 43 patients with pulmonary cryptococcosis, including 19 apparently immunocompetent patients (ICPC) and 24 immunocompromised patients (IMCPC), compared with community-acquired pneumonia (CAP) controls. Bronchoalveolar lavage fluid (BLAF) microbiota composition was analyzed using metagenomic next-generation sequencing. Peripheral blood immune parameters were measured, and correlation analyses were performed to identify potential associations. Publicly available single-cell transcriptomic datasets were analyzed to explore immune pathway alterations associated with chronic Pseudomonas infection.

RESULTS: ICPC patients were predominantly male, less likely to present with fever, and showed normal inflammatory markers compared to CAP controls. Despite normal reference ranges, ICPC patients demonstrated significantly reduced CD4⁺ T lymphocyte percentages，accompanied by elevated IL-2 and reduced IL-12p70 and IL-17A levels. BALF analysis revealed a significant enrichment of nonfermenting gram-negative bacteria: Ralstonia, Sphingomonas, Acinetobacter, Stenotrophomonas, Burkholderi and Pseudomonas, in ICPC patients，whereas no such alterations were observed in the IMCPC group. Correlation analyses demonstrated inverse relationships between the relative abundances of Stenotrophomonas and Pseudomonas abundance and CD4 + T lymphocyte percentages and CD4 + /CD8 + ratios. Furthermore, single-cell transcriptomic analysis of chronic Pseudomonas infection showed enrichment of IL-2 signaling genes and suppression of IL-12 and IL-17A signaling pathways.

CONCLUSIONS: ICPC patients exhibit decreased peripheral CD4 + T lymphocyte percentage with elevated IL-2 and reduced IL-12p70/IL-17A levels. The observed enrichment of specific bacterial taxa, particularly Pseudomonas species, and its inverse correlation with immune parameters suggest potential microbiome-immune interactions that may contribute to cryptococcal susceptibility.},
}

@article {pmid42066608,
year = {2026},
author = {Liao, X and Xie, C and Wang, L},
title = {Differential regulation of cadmium accumulation by root microbiomes in high- and low-Cd accumulating rice cultivars.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142256},
doi = {10.1016/j.jhazmat.2026.142256},
pmid = {42066608},
issn = {1873-3336},
abstract = {Cadmium (Cd) contamination threatens rice safety, and while low Cd-accumulating cultivars (LACs) offer a promising strategy, the mechanisms mediated by their root microbiome remain unclear. To address this gap, this study aimed to compare the rhizosphere and root endosphere bacterial communities of LACs and high Cd-accumulating cultivars (HACs) and to elucidate their roles in regulating Cd accumulation. A field experiment was conducted in Hengyang, China, to comparatively analyze the rhizosphere and root endosphere bacterial communities of LACs (CLiangYou755, ShenLiangYou5814, XiangWanXian-12) and HACs (MeiXiangZhan-2, YangDao-6, Changxianggu). Results confirmed that grain Cd content of LACs (0.14 ± 0.018 mg/kg) was significantly lower than that of HACs (0.23 ± 0.061 mg/kg). Critically, LACs rhizosphere exhibited significantly lower soil available Cd and higher pH compared to HACs, correlating with reduced Cd uptake. Physiological analysis indicated that LACs minimized Cd accumulation primarily by restricting root uptake and hindering root-to-shoot translocation. Microbiome profiling revealed that LACs assembled a potentially protective root microbial community. Specifically, their rhizosphere exhibited higher bacterial α-diversity and was enriched with taxa possessing potential Cd-immobilizing capabilities, such as Caldilinea and norank_f__norank_o__SJA-15, which were negatively correlated with soil available Cd and positively with pH. Within root endosphere, LACs specifically enriched key Cd translocation‑limiting taxa like Sideroxydans and specific operational taxonomic units (OTUs, e.g., OTU1619), collectively forming a microbial niche that further inhibits grains Cd accumulation. In contrast, HACs enriched taxa that may activate Cd, such as Bacillus and Geobacter in the rhizosphere, and were dominated by Anaerovorax in the root endosphere, exhibiting functional redundancy and assembly imbalance. In conclusion, this study elucidates that LACs mitigate grain Cd through a coordinated "rhizosphere co-shaping and root endosphere specific assembly" microbial strategy. These findings provide a crucial theoretical foundation for developing innovative, microbiome-based green technologies aimed at ensuring food security in contaminated regions.},
}

@article {pmid42066637,
year = {2026},
author = {Ioannou, S and Stern, E and Damas, OM},
title = {Personalizing nutrition therapy in inflammatory bowel disease: Practical applications and review of the latest studies.},
journal = {Current opinion in pharmacology},
volume = {88},
number = {},
pages = {102627},
doi = {10.1016/j.coph.2026.102627},
pmid = {42066637},
issn = {1471-4973},
abstract = {Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a chronic condition influenced by genetic and environmental factors, including diet. Dietary interventions modulate IBD pathophysiology through microbiome reshaping, short-chain fatty acid production, and immune regulation. While pharmacologic therapies remain central, dietary interventions have emerged as evidence-based adjunctive strategies for inducing and maintaining remission. In UC, the Mediterranean diet (MED) demonstrates consistent improvements in clinical symptoms and inflammatory markers in mild-to-moderate disease, with emerging evidence supporting benefit in moderate-to-severe UC when combined with pharmacotherapy. The ulcerative colitis exclusion diet (UCED) shows preliminary promise, though larger trials are needed. For maintenance, anti-inflammatory whole-food patterns reduce fecal calprotectin and promote favorable microbiota shifts. In CD, exclusive enteral nutrition (EEN) remains the gold standard for induction, primarily in pediatric Crohn's disease, while the Crohn's disease exclusion diet (CDED) with partial enteral nutrition offers a well-tolerated food-based alternative. Notably, enteral nutrition combined with biologics enhances drug bioavailability and clinical outcomes. Across interventions, microbiome modulation, including increased SCFA-producing bacteria and enhanced microbial diversity, represents a unifying therapeutic mechanism. Future research priorities include trials with endoscopic endpoints, identification of predictive biomarkers, and development of precision nutrition approaches tailored to individual disease characteristics.},
}

@article {pmid42066640,
year = {2026},
author = {Sim, M and Hwang, GS and Shin, DM and Jeong, Y},
title = {Associations of solute carrier family 23 member 1 (SLC23A1) rs6596473 genetic variant with serum vitamin C status and gut microbial profiles in healthy adults: A cross-sectional study.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106669},
doi = {10.1016/j.clnu.2026.106669},
pmid = {42066640},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Solute carrier family 23 member 1 (SLC23A1) encodes sodium-dependent vitamin C transporter 1, which mediates intestinal vitamin C absorption. Although SLC23A1 variants are associated with vitamin C bioavailability, their relationship with gut microbiome remains unexplored. We aimed to investigate the associations of SLC23A1 polymorphism with serum vitamin C status and gut microbial profiles in healthy Korean adults.

METHODS: We genotyped the SLC23A1 rs6596473 polymorphism in 257 healthy individuals (20-39 years) and measured their serum vitamin C concentrations, which were categorized as optimal (≥50 μM) or suboptimal (<50 μM). Logistic regression analysis was used to evaluate the association between genotypes and suboptimal serum vitamin C status after adjusting for covariates. A subset of 43 participants with suboptimal serum vitamin C status underwent gut microbiota analysis and serum short-chain fatty acid (SCFA) measurements. Microbial profiles and SCFA concentrations were compared across the genotypes.

RESULTS: The genotype distributions were 92 CC, 131 CG, and 34 GG, with G as the minor allele. After covariate adjustment, GG carriers had higher odds of suboptimal serum vitamin C status than CC carriers (odds ratio = 2.65; p = 0.03). Among individuals with suboptimal serum vitamin C status, GG carriers (n = 7) exhibited distinct microbial community structures compared with CC (n = 13) and CG (n = 23) carriers, with elevated richness and evenness. GG carriers had higher abundances of Bifidobacterium (vs. CC, p < 0.01; vs. CG, p = 0.054) and Ruminococcaceae incertae sedis (all p < 0.05) compared with CC and CG carriers. In line with these microbial findings, GG carriers had higher propionate and butyrate concentrations than CC and CG carriers (all p < 0.05).

CONCLUSIONS: The SLC23A1 rs6596473 variant was associated with reduced vitamin C absorption into systemic circulation in the overall population; however, among individuals with suboptimal serum vitamin C status, it was associated with beneficial gut microbial profiles. Our findings suggest that this genetic variant in the vitamin C transporter has complex health effects that extend beyond circulating vitamin C levels to gut microbial ecology, supporting the use of genotype-informed nutritional approaches.

CLINICAL TRIAL REGISTRY: Clinical Research Information Services KCT0005074 (https://cris.nih.go.kr/cris/search/detailSearch.do?seq=16832&status=5&seq_group=16832&search_page=M) and KCT0004276 (https://cris.nih.go.kr/cris/search/detailSearch.do?seq=14590&status=5&seq_group=14590&search_page=M).},
}

@article {pmid42066682,
year = {2026},
author = {Su, C and Dong, B},
title = {A mendelian randomization study investigates the causal relationship between oral microbiome and cerebral aneurysm in East Asian population.},
journal = {Clinical neurology and neurosurgery},
volume = {267},
number = {},
pages = {109453},
doi = {10.1016/j.clineuro.2026.109453},
pmid = {42066682},
issn = {1872-6968},
abstract = {BACKGROUND: Growing evidence supports that oral microbiome play an essential role in the etiology of cerebral aneurysm.This study aimed to investigate the causal relationships between the oral microbiome and cerebral aneurysm in the East Asian population using Mendelian randomization (MR).

METHODS: Genetic summary data related to oral microbiota and cerebral aneurysm were collected from genome-wide association studies involving participants of East Asian descent. MR estimates were generated by conducting various analyses.Two-sample Mendelian randomization (MR) was utilized to compute the causal effects between the oral microbiome and cerebral aneurysm.

RESULTS: In the saliva group, we found causal relationships between 11 oral microbiotas and cerebral aneurysm,9 negative causal associations and 2 positive. In the tongue group, we found causal relationships between 15 oral microbiotas and cerebral aneurysm,9 negative causal associations and 6 positive.We found a causal relationship between cerebral aneurysm and Firmicutes (p = 0.024, IVW), suggesting a bidirectional causal relationship between cerebral aneurysm and Firmicutes.

CONCLUSION: There may exist a potential correlation between oral microbiome and cerebral aneurysm within the East Asian population. The present study offers novel insights into the correlation between oral microbiome and cerebral aneurysms. Additional research is required to clarify the underlying mechanisms and validate our discoveries in diverse populations.},
}

@article {pmid42066822,
year = {2026},
author = {McMahan, RH and Evans, MR and Najarro, KM and Frank, DN and Basak, JM and Kovacs, EJ},
title = {Ethanol exacerbates post-burn neuroinflammation and gut-brain barrier dysfunction which are associated with microbiome changes.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2026.04.007},
pmid = {42066822},
issn = {1873-6823},
abstract = {BACKGROUND: Acute alcohol intoxication at the time of burn injury is associated with increased morbidity and worsened systemic inflammation. While the detrimental effects of ethanol on peripheral organs after burn injury are well established, its impact on neuroinflammation and the blood-brain barrier (BBB) integrity remains to be defined. We hypothesized that ethanol exposure prior to burn injury heightens neuroinflammation through disruption of intestinal and cerebrovascular barriers and alterations in the gut microbiome.

METHODS: Using a clinically relevant murine model, mice received acute ethanol exposure 30 minutes prior to burn injury. Brains were analyzed 24 hours later for inflammatory gene and protein expression. Microglial activation was determined by IBA-1 immunofluorescence and quantitative PCR of isolated microglia. Intestinal barrier dysfunction was evaluated by bacterial translocation to mesenteric lymph nodes (MLN) and serum lipopolysaccharide (LPS) levels. BBB permeability was assessed in brain tissue by albumin accumulation. Fecal microbiome composition was characterized by 16S rRNA gene sequencing.

RESULTS: Burn injury alone induced morphological evidence of reactivity, yet did not significantly increase brain pro-inflammatory cytokine transcription. In contrast, ethanol exposure prior to the burn injury elevated brain expression of Ccl2, Tnfa, and S100a8. Isolated microglia from the brains of mice given ethanol and burn injury exhibited enhanced expression of Ccl2 compared to burn alone. Ethanol exposure also resulted in an 8-fold increase in bacterial translocation to MLNs and a 5-fold increase in brain albumin levels, indicating exacerbated intestinal and BBB permeability. Microbiome analysis revealed expansion of Escherichia species in mice subjected to ethanol and burn injury, which positively correlated with brain S100a8 expression.

CONCLUSIONS: Ethanol exposure prior to burn injury potentiates neuroinflammation, enhances microglial pro-inflammatory reactivity, disrupts BBB integrity, and is associated with gut microbial dysbiosis. These findings implicate dysregulation of the gut-brain axis as a mechanistic contributor to worsened neuroinflammation in intoxicated burn injury and identify potential therapeutic targets to mitigate neurologic complications in this high-risk population.},
}

@article {pmid42066826,
year = {2026},
author = {Zhang, J and Li, H and Tan, J and Wu, J and Liu, Y and Huang, H and Jiang, J and Zeng, D and Xu, J},
title = {Polygonatum sibiricum polysaccharide alleviates irritable bowel syndrome via multidimensional phenotypic improvement and sex-specific gut microbiota modulation in mice.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121789},
doi = {10.1016/j.jep.2026.121789},
pmid = {42066826},
issn = {1872-7573},
abstract = {Polygonatum sibiricum polysaccharide (PSP), as a major bioactive component of P. sibiricum Delar. ex Redoute (Liliaceae, PS), holds great potential for treating irritable bowel syndrome (IBS). However, its therapeutic effects and mechanisms remain unknown.

AIM OF THIS STUDY: IBS is a prevalent functional gastrointestinal disorder. The limitation and adverse effects of current therapies highlight the need for novel strategies. This study aimed to optimize PSP extraction and evaluate the therapeutic effects of PSP on IBS model mice.

MATERIALS AND METHODS: Water-extraction and ethanol-precipitation were optimized via orthogonal experimental design to obtain PSP, which was purified via molecular sieve chromatography. PSP composition was characterized using 1-phenyl-3-methyl-5-pyrazolone precolumn-derivatization HPLC. PSP was administered to IBS model mice, which were evaluated via routine monitoring, blood tests, histopathology, microbiome analysis, network pharmacology and molecular docking.

RESULTS: Under optimal extraction conditions of a 1:15 g/ml solid-to-liquid ratio, 80°C, and 150 W ultrasonic power for 120 min, 228.68 mg/g of PSP was obtained, which was mainly composed of six monosaccharides. PSP administration (200-600 mg/kg) significantly alleviated IBS symptoms by normalizing the faecal moisture content and blood indices, decreasing oxidative stress, reversing intestinal mucosal damage and microbiota homeostasis in a sex-based manner. Multiple targets, including DRD1, TRPV1 and HTR2, which theoretically had favourable binding energies with PSP and associated with PLA/PLC-ERK1/2-PKC signalling pathway, were predicted to involve in the therapeutic effects.

CONCLUSION: Subchronic PSP intervention promotes mouse recovery from IBS in a sex-specific manner. Putative targets and molecular pathways provide a theoretical direction for future validation.},
}

@article {pmid42066862,
year = {2026},
author = {Verdugo-Meza, A and Gill, SK and Godovannyi, A and Chiang, HM and Bosetti, S and Barnett, JA and Estaki, M and Ishida, R and Ye, J and Quin, C and Haskey, N and Mehain, H and Jafaripour, S and Josephson, JK and Ghesquiere, C and Copp, A and Usakiewicz, J and Adur, MK and Ghosh, S and Bergstrom, K and Sly, LM and Gibson, DL},
title = {Bioengineering a probiotic to bloom during colonic inflammation promotes reliable efficacy in translational models of colitis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.04.007},
pmid = {42066862},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Emerging insights into the gut microbiome have sparked interest in exploring microbial therapeutics for treating inflammatory bowel diseases (IBD). However, no microbial therapeutics have yet shown clinical efficacy for IBD. E. coli Nissle 1917 (EcN) while effective for maintenance of remission, is only marginally effective for treating active colitis. We postulated that EcN effectiveness is hindered by the inflamed intestine, which prevents colonization since EcN lacks stress-resistance mechanisms necessary to persist during colitis. To address this, we introduced a fitness advantage, the ttr operon, to EcN (EcN::ttr), enabling tetrathionate, a byproduct of intestinal inflammation, to be used as fuel. We hypothesized that EcN::ttr bioengineered to bloom during colitis would effectively treat colitis.

METHODS: We evaluated the efficacy of EcN::ttr in murine colitis: acute DSS and a chronic mucin 2-deficient model. To determine the role of IL-10 in EcN::ttr protection, we tested its efficacy in IL-10-deficient mice. Finally, we co-incubated EcN::ttr with human colonoids to understand its effect on barrier proteins.

RESULTS: EcN::ttr ameliorated colitis more effectively than EcN and 5-aminosalicylate. EcN::ttr bloomed during inflammation and promoted immunoregulatory responses reliant on IL-10 that limited leukocyte infiltration and decreased TNF-α[+] myeloid resident cells. EcN::ttr induced functional changes in the gut microbiome related to mucosal healing, increased butyric acid, reduced bacterial translocation, and improved ZO-1 organization.

CONCLUSIONS: We provide a proof-of concept study that bioengineering ttr into EcN unlocks a robust therapeutic effect during colitis. EcN::ttr may be a novel microbiome therapeutic for IBD due to its enhanced ability to successfully colonize the inflamed gut.},
}

@article {pmid42066875,
year = {2026},
author = {Liu, E and Huang, Y and Zhao, Z and Teng, T and Zhou, H and Liu, C and Liu, F},
title = {2-Hydroxyfluorene triggers a vicious cycle of oxidative stress and gut dysbiosis, leading to intestinal injury in the polychaete Perinereis aibuhitensis.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110556},
doi = {10.1016/j.cbpc.2026.110556},
pmid = {42066875},
issn = {1532-0456},
abstract = {Fluorene is biotransformed into the more toxic 2-hydroxyfluorene in the Perinereis aibuhitensis. However, the underlying toxicological mechanisms remain poorly defined. This study aims to decipher the mechanisms of intestinal injury in P. aibuhitensis under 2-hydroxyfluorene exposure. This study employed an integrated multi-endpoint approach to evaluate the dose-dependent effects of 2-hydroxyfluorene (0, 5, 50, and 500 μg/L) on P. aibuhitensis over a 28-day period. Results demonstrated that escalating concentrations triggered pronounced metabolic stress, indicating a shift in energy allocation toward detoxification and repair. Histopathological analysis identified the intestine as the primary target, showing mucosal necrosis and fragmented muscle fibers. These structural aberrations were mechanistically linked to sustained oxidative stress, which compromised intestinal permeability and paralyzed digestive and neurological functions. 16S rRNA sequencing further revealed that 2-hydroxyfluorene exposure reduced gut microbial diversity and the abundance of the beneficial genus, while promoting the abundance of the harmful genus. In conclusion, 2-hydroxyfluoreneinduces severe intestinal injury and metabolic dysfunction in P. aibuhitensis by initiating a vicious cycle: direct oxidative damage compromises gut barrier integrity, which in turn fosters dysbiosis microbiota. This dysbiosis characterized then likely exacerbates the initial host injury. This host-microbe interplay likely exacerbated the initial intestinal injury. These findings highlight the significant ecological risks posed by hydroxylated polycyclic aromatic hydrocarbon (PAH) metabolites to marine benthic invertebrates and underscore the crucial contribution of the gut microbiome in mediating environmental toxicity.},
}

@article {pmid42067083,
year = {2026},
author = {Yadav, AK and Naz, F and Singh, A and Sharma, S and Deka, J and Madhuri, M and Saini, C and Kumar, M and Kaur, P and Singh, TP and Ethayathulla, AS},
title = {Crystal structure of FtsZ from Acinetobacter baumannii and identification of a potential inhibitor targeting its GTPase domain.},
journal = {International journal of biological macromolecules},
volume = {364},
number = {},
pages = {152295},
doi = {10.1016/j.ijbiomac.2026.152295},
pmid = {42067083},
issn = {1879-0003},
abstract = {Acinetobacter baumannii is an opportunistic pathogen known for its extensive antibiotic resistance, posing a significant concern in healthcare settings. Given global concern over broad-spectrum antibiotic use and its impact on the human microbiome, targeting the bacterial cell-division protein Filamenting temperature-sensitive Z (FtsZ) is a promising strategy for developing new antibiotics, as this protein is essential for bacterial cell division. FtsZ polymerizes into filaments to form the Z-ring at the cell division site. This Z-ring orchestrates the recruitment of other crucial proteins in cytokinesis and cell wall synthesis, making it critical for bacterial viability. To target FtsZ from Acinetobacter baumannii (abFtsZ), we have elucidated the first crystal structures in the apo and GDP-bound state. The structural analysis revealed that the abFtsZ-GDP complex exists in a relaxed state conformation with weak inter-subunit interactions. The GTPase activity of abFtsZ showed a Vmax of 3.3 ± 0.4 nmolP/nmolFtsZ/min, and a Km of 2.3 mM. By virtual screening using the crystal structure of abFtsZ, we identified six potential inhibitors: Gossypin, Stafib-1, Tryphostin A51, Sangivamycin, Scutellarin, and Ellagic acid that target the GTP-binding pocket. These inhibitors exhibited high docking scores ranging from -10.2 to -8.4 kcal/mol and remained stable throughout the 500 ns MD simulation. These inhibitors can serve as lead molecules for the development of a new antibacterial agent.},
}

@article {pmid42067149,
year = {2026},
author = {Harlow, C and Mohamad, M and Bajaj, JS and Nibali, L and Banerjee, A and Patel, VC},
title = {Harnessing the oral microbiome in chronic liver disease: mechanisms, therapeutic modulation and translational frontiers.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2026.04.023},
pmid = {42067149},
issn = {1600-0641},
abstract = {Advanced chronic liver disease (ACLD) with cirrhosis is increasingly recognised as a condition shaped by the 'oral-gut-liver axis', in which dysbiosis within the oral microbiome contributes to systemic inflammation, infection, decompensation, and acute-on-chronic liver failure. Periodontal disease is highly prevalent in ACLD and is associated with endotoxaemia, immune dysfunction, and hepatic complications. The protected dental biofilm and keystone pathogens are key to the development of local and systemic inflammatory processes. The concept of "oralisation" of the gut microbiome further links oral dysbiosis to microbial translocation and hepatic injury. Recent advances in multi-omics, resistome profiling, and spatially resolved imaging have deepened insights into community function and host-microbial crosstalk, while salivary biomarker panels and microbial signatures across different aetiologies suggest potential tools for non-invasive diagnosis and risk stratification. Clinical priorities now lie along two paths which complement each other. The first is immediate implementation: embedding routine periodontal assessment and professional plaque removal within hepatology care; consistent advice on oral hygiene, fluoride use, diet, and smoking and alcohol cessation; careful review of proton-pump inhibitor use; and much closer coordination between hepatologists and dentists to facilitate indicated procedures. The second is innovation: development of precision microbiome-based interventional trials powered for hepatic outcomes, including targeted probiotics and postbiotics, biofilm-disrupting and quorum-quenching strategies, and phage or narrow-spectrum antimicrobial therapies supported by rapid diagnostics and robust antimicrobial stewardship. Integrating oral health into hepatology practice may represent a practical opportunity to reduce infection risk, delay decompensation, and improve survival and quality of life in people living with ACLD. This review aims to synthesise concepts around current understanding of the patho-biological mechanisms, analytical innovations, and therapeutic opportunities that define this evolving connection, as well as identify gaps in the knowledge base and propose avenues to harness and exploit the oral-gut-liver axis.},
}

@article {pmid42067484,
year = {2026},
author = {Roviello, G and Catalano, M and Gambale, E and Aquino, IG and Lai, E and Messina, C and Vascotto, IA and Rossi, V and Bimbatti, D and Erbetta, E and Messina, M and Mennitto, A and Rebuzzi, SE and Nasso, C and Mercinelli, C and Maiorano, BA and Fanelli, M and Sorarù, M and Scolari, F and Mela, MM and Galli, L and Salfi, A and Rizzo, M and Puglisi, S and Orlando, V and Fornarini, G and Rametta, A and Giannatempo, P and Cerbone, L and Buti, S and Doni, L and Pillozzi, S and Antonuzzo, L},
title = {Concomitant medications and survival outcomes in patients receiving avelumab maintenance for advanced urothelial carcinoma: sub analysis of Meet-URO 25 study.},
journal = {Clinical genitourinary cancer},
volume = {},
number = {},
pages = {102550},
doi = {10.1016/j.clgc.2026.102550},
pmid = {42067484},
issn = {1938-0682},
abstract = {BACKGROUND: Concomitant medications may impair immune checkpoint inhibitor (ICI) activity through modulation of the gut microbiome and systemic immunity. While a medication-based risk model (drug score) has been validated in pan-cancer cohorts, evidence in advanced urothelial carcinoma (aUC) remains limited. This study assessed the association between concomitant medications and survival in patients receiving avelumab maintenance in the Meet-URO 25 cohort.

METHODS: We retrospectively analyzed patients with aUC treated with avelumab maintenance in several Italian centers. The drug score assigned 1 point each for antibiotics and PPIs, and 2 points for corticosteroids ≥ 10 mg prednisone equivalent. Patients were classified as good (0), intermediate (1-2), or poor (3-4) risk. Progression-free survival (PFS) and overall survival (OS) were evaluated using Kaplan-Meier and Cox models.

RESULTS: Among 251 patients (median age 72; 82% male), use of interfering medications was low. Drug score distribution was 76.5% good, 21.9% intermediate, and 1.6% poor risk. Median PFS was 8.0, 3.9, and 2.9 months, respectively; median OS was 27.6, 14.0, and 3.4 months. Drug score, ECOG performance status, and bone metastases were independent prognostic factors.

CONCLUSIONS: The drug score showed significant prognostic value in aUC patients receiving avelumab maintenance, supporting its integration into risk stratification for ICI-treated UC.},
}

@article {pmid42067720,
year = {2026},
author = {Bindal, N and Mohanty, S},
title = {Neuroprotective role of Curcuma amada evidenced from pesticide-induced stressed Drosophila melanogaster: insights from RNAseq and gut microbiome analyses.},
journal = {Molecular genetics and genomics : MGG},
volume = {301},
number = {1},
pages = {},
pmid = {42067720},
issn = {1617-4623},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Drosophila melanogaster/drug effects/genetics ; *Curcuma/chemistry ; *Neuroprotective Agents/pharmacology ; *Pesticides/toxicity ; *Plant Extracts/pharmacology ; Oxidative Stress/drug effects ; RNA-Seq ; },
abstract = {Prolonged exposure to pesticides is linked to neurodegenerative disorders through mechanisms involving oxidative stress, inflammation, and neuronal signaling. Therapeutic plants may offer a promising and natural alternative for protecting against such damage. Hence, the present study aims to understand the role of Curcuma amada in mitigating pesticide-induced neurotoxicity and its molecular mechanism in Drosophila. The pesticidal stress was induced in Drosophila through oral feed of ethion and its action was confirmed through behavioural assay. The stressed flies were treated with C. amada rhizome and the effect of both ethion and ethion + C. amada was assessed through RNA profiling and gut microbiome analysis. Decrease in locomotory activity on exposure to ethion represents the induced neuronal stress and an increase was seen after C. amada was fed to the stressed flies. Many DEGs were identified through RNAseq results of stressed and C. amada treated which were further analysed using Cytoscape. In ethion and ethion + C. amada treated flies, the upregulated and downregulated genes were found to be associated with neuronal signal processing and mitochondrial function [MRPs, Dop2R, 5-HT1A, aminoacyl-tRNA synthetase (AARs), ND-B17]. A significant change in the gut microbial population (especially decrease in Lactiplantibacillus species) was observed in stressed flies. But the restoration of healthy bacterial population such as Lactiplantibacillus in C. amada treated flies evidencing the crucial role of gut microbiome in neuronal health. This study highlights the beneficial effects of C. amada from pesticidal stress which needs to be further researched to understand the underlying molecular mechanisms.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Drosophila melanogaster/drug effects/genetics
*Curcuma/chemistry
*Neuroprotective Agents/pharmacology
*Pesticides/toxicity
*Plant Extracts/pharmacology
Oxidative Stress/drug effects
RNA-Seq

@article {pmid42067885,
year = {2026},
author = {Cai, B and Zhang, L and Wu, Z and Wang, J and Wei, Y and Waseem, R and Zhang, M and Qi, D and Zhou, D and Zhao, Y and Li, K and Hu, H and Xie, J and Wang, W},
title = {Streptomyces-induced Glycerol-3-Phosphate enriches beneficial microbiota to enhance resistance against banana Fusarium wilt.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02409-6},
pmid = {42067885},
issn = {2049-2618},
support = {325RC849//Hainan Provincial Natural Science Foundation of China/ ; 322RC660//Hainan Provincial Natural Science Foundation of China/ ; 2024YFD1401101//Bingyu Cai, National Key Research and Development Program of China/ ; CARS-31//China Agriculture Research System/ ; NKLTCBCXTD27//the National Key Laboratory for Tropical Crop Breeding/ ; 1630052022006//Central Public-interest Scientific Institution Basal Research Fund/ ; 32202437//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4) is the causal agent of banana Fusarium wilt, a destructive soil-borne disease. Using antagonistic microorganisms, such as Streptomyces species, offers a promising strategy for controlling fungal diseases. However, their field application is limited by an incomplete understanding of microbe-plant-pathogen interactions.

RESULTS: This study shows that the marine-derived Streptomyces malaysiensis WHL7 exhibits strong antagonistic activity against multiple phytopathogenic fungi in vitro, particularly Foc TR4. In pot experiments using natural soil, WHL7 treatment significantly reduced the incidence of Fusarium wilt from 55% in the Foc TR4-inoculated control to 15%. No protective effect was observed in sterilized soil, indicating that its biocontrol efficacy depends on the indigenous microbial community. Integrated metabolomic analysis reveals that WHL7 stimulates the key root secretion of glycerol-3-phosphate (G3P). The compound enriches beneficial Bacillus and Pseudomonas species in the rhizosphere. Compared to the Foc TR4-treated group, exogenous application of G3P reduced Foc TR4 abundance by 73%, inhibited pathogenic infection, and consistently increased the populations of Bacillus and Pseudomonas. These enriched microbes were directly linked with reduced disease severity by inducing systemic ACQUIRED RESISTANCE OF plant.

CONCLUSIONS: While S. malaysiensis WHL7 directly suppresses Foc TR4 via antagonistic compounds in vitro, it controls disease in pot experiments indirectly by reshaping the rhizosphere microbiome. This restructuring induces host resistance through a g3p-mediated signaling pathway. the study highlights g3p-mediated priming as a sustainable strategy for managing soil-borne diseases. Video Abstract.},
}

@article {pmid42067956,
year = {2026},
author = {Shah, AH and Liu, Y and Armstrong, HK and Han, J and Goodlett, DR and Ravandi, A and Dhingra, S},
title = {Association of Fontan Circulation With Gut Microbiome Derived Straight and Branched Short Chain Fatty Acids.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70405},
pmid = {42067956},
issn = {1440-1746},
support = {//Department of Internal Medicine, University of Manitoba/ ; },
abstract = {BACKGROUND: Fontan circulation is associated with progressive multisystem dysfunction, yet its biochemical mechanisms are poorly understood. Gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs) and bile acids, shape cardiovascular health. We previously reported elevated secondary bile acids in Fontan patients, but their SCFA profile remains uncharacterized.

MATERIALS AND METHODS: Fontan patients and matched healthy subjects were evaluated by body composition, frailty, cardiopulmonary exercise testing, hemodynamics, and plasma SCFA quantification.

RESULTS: Twenty Fontan patients (25.5 years [IQR: 22.8-30.3]; 35% women) and 20 healthy controls (30.0 years [25.8-34.3]; 30% women) were enrolled. Compared to controls, Fontan patients exhibited elevated plasma levels of several SCFAs: propionic acid (1.84 [1.45-2.68] vs. 1.19 [1.07-1.49] μM; p = 0.002), butyric acid (1.27 [0.90-1.71] vs. 0.75 [0.52-0.94] μM; p = 0.002), valeric acid (0.25 [0.15-0.36] vs. 0.13 [0.11-0.16] μM; p < 0.001), and caproic acid (0.44 [0.35-0.67] vs. 0.25 [0.21-0.39] μM; p < 0.001). Acetic acid levels did not differ significantly between groups. Additionally, branched-chain SCFAs were elevated in Fontan patients: isobutyric acid (0.44 [0.32-0.68] vs. 0.26 [0.23-0.30] μM; p < 0.001) and 2-methylbutyric acid (0.38 [0.27-0.58] vs. 0.19 [0.15-0.25] μM; p < 0.001). Notably, caproic, isobutyric, and 2-methylbutyric acids showed strong correlations with key clinical and hemodynamic parameters. Furthermore, isobutyric and 2-methylbutyric acids were significantly correlated with dehydrolithocholic acid levels (R = 0.67 and 0.54, respectively) and other bile acid components.

CONCLUSION: Fontan patients have elevated plasma straight and branched SCFAs linked to adverse clinical and hemodynamic profiles; further evaluation is warranted.},
}

@article {pmid42068031,
year = {2026},
author = {Chen, S and Feng, H and Wang, Y and Huang, J and Xu, S and Gong, Y and Liu, X and Ouyang, Y and Ye, Q and Zheng, D and Sun, K and Wang, A and Chen, Y},
title = {Intestinal epithelial Syndecan-1 maintains mucosal homeostasis in inflammatory bowel disease by enhancing Faecalibacterium prausnitzii biofilm formation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2665870},
doi = {10.1080/19490976.2026.2665870},
pmid = {42068031},
issn = {1949-0984},
mesh = {Animals ; *Syndecan-1/genetics/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Mice ; *Intestinal Mucosa/microbiology/metabolism ; Gastrointestinal Microbiome ; *Biofilms/growth & development ; Mice, Knockout ; Humans ; *Faecalibacterium prausnitzii/physiology/genetics/growth & development ; Mice, Inbred C57BL ; Homeostasis ; Disease Models, Animal ; Dextran Sulfate ; Colitis/microbiology/chemically induced ; Male ; Fecal Microbiota Transplantation ; },
abstract = {Despite the rising global incidence of inflammatory bowel disease (IBD), curative therapies remain unavailable. While our previous work implicated the intestinal proteoglycan Syndecan-1 (SDC1) in IBD-associated barrier dysfunction and inflammation, the underlying mechanism was unclear. This study aimed to elucidate how SDC1 maintains intestinal barrier integrity through interactions with the gut microbiome. In DSS-induced colitis, global knockout of Sdc1 (Sdc1[-/-]) exhibited exacerbated inflammatory infiltration and greater impairment of barrier structure and function than wild-type (WT). Formation of intestinal organoids was independent of genotype, indicating that Sdc1[-/-] does not impair barrier function via disrupting epithelial development. The heightened colitis susceptibility in Sdc1[-/-] mice was abolished in the antibiotic-treated pseudo-germ-free models, and transmissible to WT mice via fecal microbiota transplantation. Similar results were reproduced in a germ-free mouse model. Metagenomic sequencing identified Faecalibacterium prausnitzii as the most significantly depleted species upon Sdc1 knockout. In vitro, SDC1-attached glycosaminoglycans (heparan sulfate (HS) and chondroitin sulfate (CS)) but not the SDC1 core protein promoted F. prausnitzii growth. Prokaryotic transcriptome profiling indicated that HS/CS induces cobalamin biosynthesis in F. prausnitzii. The critical role of cobalamin as a mediator was confirmed, as its synthetic inhibition significantly diminished the growth-promoting effect of HS/CS. Mechanism studies showed that HS/CS enhanced biofilm formation in F. prausnitzii, thereby facilitating cobalamin biosynthesis. Oral administration of HS ameliorated DSS-induced colitis and promoted mucosal colonization of F. prausnitzii, independent of the host genotype. Finally, human IBD biopsies revealed a positive correlation between epithelial SDC1 and mucosal F. prausnitzii, as well as an inverse correlation with bacterial translocation and the number of LPS‑positive cells. Our study elucidates a novel mechanism in which the glycosaminoglycan chains of SDC1 promote F. prausnitzii colonization and growth through enhanced biofilm formation and cobalamin synthesis, thereby highlighting the therapeutic potential of HS for IBD and offering a new basis for host-directed microbiota regulation.},
}

Animals
*Syndecan-1/genetics/metabolism
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Mice
*Intestinal Mucosa/microbiology/metabolism
Gastrointestinal Microbiome
*Biofilms/growth & development
Mice, Knockout
Humans
*Faecalibacterium prausnitzii/physiology/genetics/growth & development
Mice, Inbred C57BL
Homeostasis
Disease Models, Animal
Dextran Sulfate
Colitis/microbiology/chemically induced
Male
Fecal Microbiota Transplantation

@article {pmid42068047,
year = {2026},
author = {Shou, J and Fu, T},
title = {The gut microbiome-bile acid-FXR interplay: a pivotal axis in metabolic and gastrointestinal diseases.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2665890},
doi = {10.1080/19490976.2026.2665890},
pmid = {42068047},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bile Acids and Salts/metabolism ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Signal Transduction ; Animals ; *Gastrointestinal Diseases/metabolism/microbiology ; Receptors, G-Protein-Coupled/metabolism/genetics ; *Metabolic Diseases/metabolism/microbiology ; Bacteria/metabolism/genetics/classification ; Gastrointestinal Tract/microbiology/metabolism ; },
abstract = {The gut microbiota is increasingly recognized as an essential metabolic "organ", involved not only in nutrient extraction and energy metabolism but also in generating diverse bioactive metabolites. Among these metabolites, bile acids (BAs) - initially synthesized in the liver - are substantially modified by bacterial enzymes in the gut, enabling them to engage various host signaling pathways. Notably, these BAs interact with critical host receptors, such as nuclear farnesoid X receptor (FXR) and G protein-coupled BA receptor 1 (TGR5), influencing numerous metabolic processes. Given the complexity and significance of BAs signaling between microbiota-host interactions, a comprehensive review of this interplay is essential. Here, we systematically explore the molecular mechanisms underlying the BA-microbiota axis, emphasizing its role in metabolic, gastrointestinal, and immune-related diseases, with a focus on the roles of FXR signaling pathways.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Bile Acids and Salts/metabolism
*Receptors, Cytoplasmic and Nuclear/metabolism/genetics
Signal Transduction
Animals
*Gastrointestinal Diseases/metabolism/microbiology
Receptors, G-Protein-Coupled/metabolism/genetics
*Metabolic Diseases/metabolism/microbiology
Bacteria/metabolism/genetics/classification
Gastrointestinal Tract/microbiology/metabolism

@article {pmid42068399,
year = {2026},
author = {Allegrini, M and Villamil, MB and Zabaloy, MC},
title = {Anaerobic digestate fertilization reshapes the rhizosphere bacterial communities of Lolium perenne L. at compositional and predicted functional potential levels.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42068399},
issn = {1573-0972},
support = {PICT-2021-I-INVI-00467//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (Argentina)/ ; PICT-2020-02289//Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (Argentina)/ ; award ILLU-802-978//United States Department of Agriculture, USDA-NIFA/ ; },
mesh = {*Rhizosphere ; *Lolium/microbiology ; *Fertilizers ; *Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; Anaerobiosis ; *Microbiota/genetics ; Soil/chemistry ; Integrons/genetics ; Manure/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The effects of anaerobic digestates on soil microbial communities have received increasing attention due to their potential impacts on soil health and antibiotic resistance. To date, no integrated analysis of rhizosphere bacterial community structure, antibiotic resistance genes (ARGs), and mobile genetic elements has been conducted in digestate-treated perennial ryegrass (Lolium perenne L.). We analyzed rhizosphere bacterial communities of this pasture using metabarcoding to study the effects of a manure-derived digestate on community structure and predicted functions. We also explored the association between digestate-enriched taxa and explanatory variables, including the abundance of two ARGs, class 1 integrons, and IncP-1ε plasmids. The greenhouse study included an unfertilized control and three fertilization treatments: digestate, inorganic fertilizer, and combined fertilizer (digestate + inorganic fertilizer). The results indicated a significant effect of the fertilizer type on bacterial communities and a stimulation of predicted functions related to genetic information processing by digestate and its combination. Digestate application resulted in the greatest differentiation in bacterial community structure relative to the unfertilized control and shifted communities toward amplicon sequence variants (ASVs) positively associated with class 1 integrons. Differential abundance analysis identified three ASVs and three genera (Arenimonas, Algoriphagus and Novosphingobium) that were significantly enriched under digestate treatment, relative to both urea and the unfertilized control. Our results demonstrate that anaerobic digestate application alters bacterial community structure and highlight the need for further studies to elucidate the potential adaptive role of class 1 integrons in rhizosphere microbiomes following digestate fertilization, including their contribution to antibiotic resistance.},
}

*Rhizosphere
*Lolium/microbiology
*Fertilizers
*Soil Microbiology
*Bacteria/genetics/classification/isolation & purification
Anaerobiosis
*Microbiota/genetics
Soil/chemistry
Integrons/genetics
Manure/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid42068426,
year = {2026},
author = {Wang, RQ and Elshafey, AE and Liu, ZT and Wen, B and Gao, JZ and Chen, ZZ},
title = {Gut microbiota and growth differentiation in koi carp with identification of a growth promoting Exiguobacterium sp. strain WY(Y)3.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42068426},
issn = {1573-0972},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Carps/growth & development/microbiology ; *Probiotics/administration & dosage ; Animal Feed/analysis/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Phylogeny ; },
abstract = {Discovering specific microbial markers and probiotics related to rapid growth offers a route for developing targeted feed solutions. This study was conducted in two phases: Phase I: Using 16 S rRNA sequencing to characterize the intestinal landscape and to discover a significant taxonomic shift in koi (Cyprinus carpio) that grow fast (FG) and grow slow (SG). Phase II: A dietary intervention trial was implemented across four experimental cohorts: a negative control (NC) fed a basal diet and three treatment groups (C1, C2, and C3) supplemented with Exiguobacterium sp. strain WY(Y)3 at escalating concentrations of 1 × 10[6], 1 × 10[7], and 1 × 10[8] CFU/g, respectively. The FG fish (11.44 ± 0.61 cm; 20.81 ± 1.33 g) harbored markedly higher proportions of Cyanobacteriota, Actinobacteriota, Chloroflexota, and notably Exiguobacterium sp., alongside enhanced metabolic pathways related to secondary metabolite biosynthesis compared with the SG fish. A piscine-derived strain, Exiguobacterium sp. WY(Y)3, isolated from the FG, significantly improved growth performance when supplemented in feed, with the 1 × 10[6] CFU/g producing the best overall outcomes (WGR = 186.26 ± 1.07 and FCR = 1.437 ± 0.08), including higher gut microbial diversity and stability. Integrated microbiome and metabolomic analyses revealed that supplementation with Exiguobacterium enhances growth performance by reshaping gut microbial composition and regulating host energy metabolism. This includes the downregulation of fatty acid β-oxidation and pyruvate metabolism pathways, alongside the upregulation of bile acid synthesis and vitamin-associated pathways (p < 0.05). Collectively, dietary inclusion of 1 × 10[6] CFU/g of Exiguobacterium sp. WY(Y)3 effectively promotes growth through microbiota restructuring and metabolic optimization, supporting its potential as a probiotic in aquaculture nutrition.},
}

Animals
*Gastrointestinal Microbiome
*Carps/growth & development/microbiology
*Probiotics/administration & dosage
Animal Feed/analysis/microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Phylogeny

@article {pmid42068598,
year = {2026},
author = {Xu, M and Cheng, K and Cai, Z and Chen, G and Zhou, J},
title = {Metagenomic and metatranscriptomic insights into Ruegeria profundi-driven protective responses in coral holobionts against Vibrio coralliilyticus infection.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128530},
doi = {10.1016/j.micres.2026.128530},
pmid = {42068598},
issn = {1618-0623},
abstract = {In the context of climate-driven coral reef degradation, opportunistic pathogens such as Vibrio coralliilyticus are emerging as significant secondary threats, acting in synergy with thermal stress to accelerate coral bleaching and mortality. In this study, we investigated the role of Ruegeria profundi in mitigating V. coralliilyticus-induced bleaching. Specifically, the responses of coral holobiont members to pathogenic and probiotic influences were evaluated using metagenomics and metatranscriptomics. We found that the presence of V. coralliilyticus enhanced the metabolic potential of the coral-associated bacterial community, particularly regarding carbohydrate utilization and virulence. Conversely, R. profundi reduced the relative abundance of pathogenic Vibrio species by over 50% and broadly suppressed the expression of virulence genes within the coral-associated bacterial community, including a > 2-fold downregulation of genes involved in quorum sensing and flagellar assembly. Transcriptomic data indicated that immune-related genes in the host were upregulated, whereas photosynthesis-related genes in photosymbiotic microalgae were downregulated in response to V. coralliilyticus infection. R. profundi significantly promoted apoptosis resistance and antimicrobial peptide activity in the host and enhanced photosynthesis in photosymbiotic microalgae (p < 0.05). Furthermore, R. profundi significantly suppressed virulence gene expression in the coral-associated bacterial community (p < 0.05). Collectively, our results indicated that R. profundi orchestrates a tripartite defense mechanism involving the coral host, its associated bacterial community, and symbiotic microalgae, effectively mitigating pathogen-induced dysbiosis and bleaching. These findings have promising implications for microbiome-based strategies in coral reef restoration.},
}

@article {pmid42068622,
year = {2026},
author = {Ogbanga, N and Mickleburgh, HL and Nelson, A and Smith, D and Gocha, TP and Wescott, DJ and Procopio, N},
title = {Microbial decomposition in experimental single and mass graves: New insights on post-burial interval estimation.},
journal = {Forensic science international. Genetics},
volume = {84},
number = {},
pages = {103517},
doi = {10.1016/j.fsigen.2026.103517},
pmid = {42068622},
issn = {1878-0326},
abstract = {Soil microbiomes are increasingly recognized as valuable indicators in forensic investigations, but microbial dynamics in mass graves remain poorly understood. This study investigates differences in microbial succession between individual graves (IG) and mass graves (MG) with human body donors and evaluates the potential of soil microbiome data to predict post-burial interval (PBI). Using ASV-level assessment, we analysed soil samples collected over time from both grave types in a controlled decomposition experiment. At the final timepoint (M18), MG and IG soils exhibited significantly different microbial compositions, with specific taxa, some associated with specific decomposition stages, enriched in each context. A regression model trained on IG samples predicted PBI with a mean error of 2.68 months when adjusted for seasonal variation but performed poorly on MG samples (RMSE = 7.12 months), highlighting ecological complexity and reduced generalisability. These findings underscore the importance of studying MG-specific microbial processes and caution against applying models developed from single-body burials to mass grave contexts. As mass graves are encountered in humanitarian and criminal investigations and establishing the duration of burial can be an important component of forensic reconstruction, our findings highlight the value of further research into context-specific microbiome models and their integration alongside existing methods for detection and time estimation in complex burial environments.},
}

@article {pmid42068645,
year = {2026},
author = {Liu, J and Liu, M and Xu, Y and Wang, Z and Zhou, X and Sun, Q},
title = {Genetically predicted TTK inhibition and its association with reduced breast cancer risk: a two-step Mendelian randomization study of potential gut microbiome mediation.},
journal = {Clinics (Sao Paulo, Brazil)},
volume = {81},
number = {},
pages = {100961},
doi = {10.1016/j.clinsp.2026.100961},
pmid = {42068645},
issn = {1980-5322},
abstract = {BACKGROUND: BOS172722, a selective TTK inhibitor, shows promise for Breast Cancer (BC) treatment. The role of gut microbiota as a potential mediator in this process has not been established. This Mendelian Randomization (MR) study investigated the causal effect of TTK inhibition on BC and conducted an exploratory analysis of potential mediation by gut microbiota.

METHODS: A two-step, two-sample drug target MR analysis used IEU Open GWAS project datasets. The inverse-variance-weighted method estimated causal effects, with sensitivity tests confirming robustness. False Discovery Rate (FDR) correction was applied to analyses for all microbial taxa.

RESULTS: Genetically predicted TTK inhibition significantly reduced BC risk (OR = 0.667, 95 % CI 0.543-0.819; FDR-adjusted p < 0.001). In secondary analyses, initial uncorrected results indicated nominal associations between TTK inhibition and 20 gut microbial taxa, and between 6 taxa and BC risk. However, none of these microbiota-related associations remained statistically significant after FDR correction (all q-values >0.1). An exploratory mediation analysis on Genus Anaerostipes id.1991, which showed the strongest nominal signals (TTK inhibition on Anaerostipes: uncorrected p = 0.003; Anaerostipes on BC: uncorrected p = 0.025), was performed for hypothesis generation only; no statistically significant mediation was observed.

CONCLUSION: This study provides robust genetic evidence that TTK inhibition is causally associated with a decreased risk of breast cancer. The exploratory analysis of gut microbiota as a mediator did not yield statistically significant results after correction for multiple testing. The potential role of specific microbes, such as Genus Anaerostipes, remains inconclusive and requires further dedicated investigation.},
}

@article {pmid42068651,
year = {2026},
author = {Jia, J and Wang, S and Chen, Y and Li, H and Zheng, C and Deng, J and Zhao, F},
title = {Heavy metals, gastrointestinal polymer-related materials, and gut microbiome in an Indo-Pacific bottlenose dolphin (Tursiops aduncus) recovered from a fisheries bycatch-related event in the East China Sea.},
journal = {Ecotoxicology and environmental safety},
volume = {317},
number = {},
pages = {120191},
doi = {10.1016/j.ecoenv.2026.120191},
pmid = {42068651},
issn = {1090-2414},
abstract = {Incidental cetacean bycatch provides irreplaceable opportunities to investigate population dynamics, mortality, and health. This multidisciplinary study examined morphology, age, gut microbiome, heavy metals, and gastrointestinal polymer-related materials in an immature male Indo-Pacific bottlenose dolphin (Tursiops aduncus, 248 cm, 114 kg, 5 years) accidentally captured in the East China Sea. Morphometrics indicated excellent body condition (BCI = 0.506) and superior dorsal fin shape compared to captive individuals, highlighting the role of natural environments in development. The gut microbiome was dominated by Proteobacteria and Firmicutes, showing segment-specific variation. Heavy metals accumulated mainly as Cd in kidneys and Cu and Zn in liver, with overall levels lower than those in other Chinese marine regions. LDIR analysis indicated the presence of polymer-related materials in the gastrointestinal tract, including reported matches to polyamide and chlorinated polyethylene, which may be associated with fisheries activities. These findings provide critical baseline ecotoxicological data for the East China Sea and underscore the importance of standardized passive biomonitoring networks that transform bycatch events into valuable scientific and conservation resources.},
}

@article {pmid42068814,
year = {2026},
author = {Kanannejad, Z and Taylor, WR and Ghatee, MA and Mohkam, M},
title = {Microbial regulation of immune tolerance during embryonic implantation and pregnancy.},
journal = {Journal of reproductive immunology},
volume = {175},
number = {},
pages = {104898},
doi = {10.1016/j.jri.2026.104898},
pmid = {42068814},
issn = {1872-7603},
abstract = {Maternal immune tolerance is essential for successful embryo implantation and maintenance of pregnancy. The maternal microbiome, particularly in the gut, vagina, and possibly the placenta, has emerged as an important regulator of immune adaptation during gestation. Through continuous interaction with the maternal immune system, the microbiota influence key immune cell populations such as regulatory T cells, uterine natural killer cells, and dendritic cells. These cells promote a tolerogenic environment necessary for embryo acceptance and proper placental development. Microbial-derived metabolites, including short-chain fatty acids and tryptophan derivatives, play important roles in modulating cytokine production and immune cell differentiation. Disruption of microbial balance, or dysbiosis, has been associated with a range of pregnancy complications, including implantation failure, preeclampsia, gestational diabetes, and preterm birth. Additionally, the maternal microbiome may influence fetal immune development, with implications for the offspring's long-term health. Emerging translational research suggests that interventions targeting the maternal microbiota, such as probiotics, prebiotics, and fecal microbiota transplantation, may beneficially modulate immune responses during pregnancy. While these approaches are promising, variability in individual microbiome composition and immune responses underscores the need for personalized strategies. In summary, the maternal microbiome is a dynamic and influential factor in shaping immune tolerance during pregnancy. A deeper understanding of microbiota-immune interactions may pave the way for novel, microbiome-based therapies to enhance reproductive outcomes and promote maternal-fetal health.},
}

@article {pmid42068861,
year = {2026},
author = {Zhang, J and Wang, X and Wang, W and Cao, Y and Wang, G},
title = {Altered Salivary Microbiome and Increased Immune Markers in Mouth-Breathing Children: Implications for Oral Health.},
journal = {International dental journal},
volume = {76},
number = {4},
pages = {109580},
doi = {10.1016/j.identj.2026.109580},
pmid = {42068861},
issn = {1875-595X},
abstract = {OBJECTIVE: To investigate the impact of mouth breathing (MB) on the salivary microbiome in children by comparing the differences in biochemical indicators, immune proteins and microbial community structure between mouth-breathing children and nose-breathing children, as well as among mouth-breathing children with different malocclusion types.

METHODS: Saliva samples were collected from 30 mouth-breathing children (MB group) and 10 nose-breathing children (control group), aged 8 to 12, between August 2023 and August 2024. The MB group was further subdivided into Angle Class I, II and III malocclusion subgroups, with 10 cases each. Ion concentrations were measured using an automatic biochemical analyser, pH was determined using a pH metre, immune protein levels were assayed by enzyme-linked immunosorbent assay and the structure and diversity of the salivary microbiota were analysed using 16S rRNA high-throughput sequencing.

RESULTS: Compared with the control group, the MB group showed no significant difference in salivary pH (P > .05), but a significantly lower chloride ion (Cl⁻) concentration (P < .05). Conversely, the concentrations of secretory immunoglobulin A (SIgA) and peroxiredoxin-5 (PRDX5) were significantly higher in the MB group (P < .05). No statistically significant differences in these indicators were observed among the different malocclusion subgroups. Spearman correlation analysis revealed a positive correlation between PRDX5 and SIgA concentrations (rs = 0.808, P < .001) and negative correlations between both PRDX5 and SIgA concentrations and Cl⁻ concentration (rs = -0.588 and -.600, respectively; P < .001) in the MB group. Microbiota analysis indicated that the species richness (Chao1 index) of the salivary microbiota was significantly higher in the MB group. At the genus level, the relative abundances of Dialister, Streptobacillus, Anaeroglobus and Scardovia were significantly increased in the MB group (P < .05).

CONCLUSION: MB alters the physicochemical properties of children's saliva, triggering an enhanced local immune response and a state of oxidative stress. This leads to dysbiosis of the salivary microbial community, characterised by a higher abundance of pathogenic bacteria associated with dental caries and periodontal disease and shows a correlation with pathogens linked to upper respiratory tract inflammation. These findings suggest that MB may impact oral and potentially systemic health by disrupting the oral microenvironment.},
}

@article {pmid42068873,
year = {2026},
author = {Luo, L and Wang, P and Xu, Y and Li, Z and Liu, Y and Liu, J and Cheng, YX},
title = {The paradox of potency: Insights into emergent mechanisms of Ganoderma lucidum's antitumor effects.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {156},
number = {},
pages = {158203},
doi = {10.1016/j.phymed.2026.158203},
pmid = {42068873},
issn = {1618-095X},
abstract = {BACKGROUND: An arms race between cancer cells and therapeutic pressure fuels drug resistance, immune evasion, and tumor heterogeneity, hindering therapy. Ganoderma lucidum (G. lucidum), a traditional Chinese medicine (TCM) with multitarget pharmacology, offers potential to address this complexity. However, the mechanistic basis of the emergent effects of its meroterpenoids remains unexplored.

PURPOSE: This study used G. lucidum meroterpenoids as a model to elucidate the mechanisms underlying emergent effects in TCM and to evaluate their therapeutic potential for overcoming tumor resistance and heterogeneity.

STUDY DESIGN: This study employed an integrative design combining phenotypic screening, in vitro cell-based assays, in vivo tumor xenograft models, and multiomics analyses to investigate the emergent antitumor mechanisms of G. lucidum meroterpenoids.

METHODS: Meroterpenoid and polysaccharide extracts were evaluated in vitro and in vivo for their effects on TNBC growth. Transcriptomic, metabolomic, and microbiome analyses were performed to explore systemic mechanisms. Phenotypic screening and transcriptome analyses were performed to characterize the synergistic (0 + 0 + 0…>0) and potentiation (0 + 0 + 0…+1 > 1) effects of the meroterpenoid combinations and to elucidate the underlying molecular mechanisms.

RESULTS: In MDA-MB-231 cells, the meroterpenoid extracts inhibited proliferation and migration by inducing ferroptosis and reprogramming inflammatory signaling. In a mouse tumor model, total meroterpenoid extracts suppressed tumor growth, enriched beneficial gut microbiota, and partially restored tumor-depleted serum lipids and amino acids. Cotreatment with G. lucidum polysaccharides accelerated the restoration of the microbiota and achieved more extensive metabolomic correction. Notably, a set of inert meroterpenoids, defined as those lacking phenotypic effects, exhibited emergent anticancer activity when combined with one another or with active compounds. These combinations acted through 0 + 0 + 0…>0 synergy or 0 + 0 + 0…+1 > 1 potentiation to inhibit proliferation and migration by overcoming drug resistance, reprogramming metabolism, and inducing ferroptosis. They also triggered cell cycle collapse and necroptosis.

CONCLUSION: This case study provides insights into how meroterpenoids, particularly combinations of inert meroterpenoids, drive the emergent pharmacological effects of G. lucidum and suggests a strategy to overcome drug resistance and tumor heterogeneity.},
}

@article {pmid42068885,
year = {2026},
author = {Ke, H and Zhang, X and Xamxidin, M and Zhang, C and Fei, M and Li, J and Zhan, L and Lan, J and Chen, Y},
title = {Microbial community divergence and environmental responses across multi-phase landfill environments.},
journal = {Waste management (New York, N.Y.)},
volume = {219},
number = {},
pages = {115578},
doi = {10.1016/j.wasman.2026.115578},
pmid = {42068885},
issn = {1879-2456},
abstract = {Municipal solid waste landfills are highly heterogeneous ecosystems comprising solid waste, leachate, and subsoils wherein complex microbial consortia regulate organic matter degradation and contaminant transformation. However, comprehensive insights into their microbiome structure across multi-phase and depth profiles and responses to environmental gradients remain scarce. This study presents a rare, multidimensional characterization of landfill microbiomes that integrates deep drilling (to 50 m), 16S rRNA gene sequencing, and biogeochemical pathway analysis. To quantify the extent of waste stabilization, a solid-phase stabilization index (β) is proposed to link degradation stages with microbial succession. This index indicates a clear transition from a Firmicutes-dominated rapid degradation phase (β < 0.58) to a Proteobacteria-dominated stabilization phase (β > 0.83). Spatially, the microbiomes exhibit distinct solid-liquid niche partitioning, as evidenced by the prevalence of biofilm formers (Advenella and Brevundimonas) on solid waste surfaces and specific enrichment of the thermophilic planktonic Defluviitoga in the surrounding leachate. At the critical waste-soil interface, leachate infiltration exerts strong environmental filtering that drives a pronounced enrichment of the dual-tolerant Ralstonia, which constitutes up to 46.49% of the community. Cu, Be, and Cd emerge as the key heavy metals driving the evolution of subsoil microorganisms. These findings collectively provide an integrated framework that advances the mechanistic understanding of waste stabilization and leachate-soil interactions, offering new insights for assessing landfill maturity and understanding pollution fronts.},
}

@article {pmid42068931,
year = {2026},
author = {Tsai, W and Zhu, F and Bar-Or, A and Bernstein, CN and Bonner, C and Graham, M and Marrie, RA and Mirza, AI and O'Mahony, J and Yeh, EA and Banwell, B and Waubant, E and Tremlett, H and , },
title = {The gut microbiome in pediatric-onset acquired demyelinating syndromes by myelin oligodendrocyte glycoprotein antibody status.},
journal = {Multiple sclerosis and related disorders},
volume = {110},
number = {},
pages = {107216},
doi = {10.1016/j.msard.2026.107216},
pmid = {42068931},
issn = {2211-0356},
abstract = {BACKGROUND: Alterations of the gut microbiome have been reported in central nervous system demyelinating diseases. While the gut microbiome in pediatric multiple sclerosis (MS) has been studied, the role of the gut microbiome in other pediatric-onset acquired demyelinating syndromes (ADS) remains unknown. We compared the gut microbiome composition between myelin oligodendrocyte glycoprotein antibody-positive (MOG+) and antibody-negative (MOG-) participants with pediatric-onset ADS.

METHODS: Participants aged ≤21 years enrolled in the Canadian Pediatric Demyelinating Disease Network microbiome study (2015-2018) with a single episode or relapsing non-MS, non-neuromyelitis optica spectrum disease attacks of demyelination with symptom onset <18 years were included. Stool sample-derived DNA underwent 16S rRNA (V4) sequencing. Serum MOG-IgG antibodies were tested within 30 days of first attack onset. Alpha-diversity (Shannon, Margalef's index, Chao1) and beta-diversity (weighted UniFrac) were analysed. Phylum/genus-level taxa were assessed using negative binomial models with false discovery rate correction. Rate ratios were sex- and age-adjusted (aRR).

RESULTS: Forty-six participants (18 MOG+/28 MOG-) were included. Mean age at stool sample collection (MOG+/MOG-) was 14.7/17.2 years. Alpha-/beta-diversities did not differ between MOG+/MOG- participants (p > 0.3). At the phylum level, the relative abundance of Proteobacteria was lower in MOG+ than MOG- participants (aRR:0.22;95%CI:0.07-0.69;q = 0.03). At the genus level, the relative abundance of Escherichia/Shigella was lower in MOG+ than MOG- participants (aRR:0.01;95%CI:0.001-0.07;q = 0.001), CONCLUSIONS: While alpha/beta-diversities did not differ between MOG+/MOG- participants, taxa-level differences were observed. Our findings suggest that the gut microbiome composition may differ by MOG serostatus among pediatric-onset ADS participants. Future work is warranted, utilizing larger cohorts and longitudinal follow-up.},
}

@article {pmid42069117,
year = {2026},
author = {Makowska-Zawierucha, N and Trzebny, A and Mokracka, J and Bradley, JA},
title = {The high Arctic resistome: stress-response genes, virulence determinants, and microbial populations in human-impacted environments of Spitsbergen.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128242},
doi = {10.1016/j.envpol.2026.128242},
pmid = {42069117},
issn = {1873-6424},
abstract = {The high Arctic, particularly Spitsbergen, faces the combined challenges of climate change and other anthropogenic pressures - including waste and contaminant release from human activity - that influence microbial populations and the spread of antimicrobial resistance (AMR). This study presents a snapshot analysis of metagenomes from various environments across Spitsbergen, including untreated and treated wastewater outflows, fjords, and glacial ice cores, to explore the abundance of stress-response genes, including antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs), and virulence genes (VGs), alongside the compositions of the associated bacterial populations. We reveal varying levels of stress-response genes and VGs in environments exposed to differing levels of human influence. ARGs and MRGs dominate in raw sewage, while VGs are more prevalent in fjord waters receiving both raw sewage and effluent, indicating that specific environmental conditions favor different resistance and virulence traits. We detect high abundance of ARGs and VGs downstream of both untreated and treated wastewater. Our analyses indicate the presence of bacterial populations with resistance and virulence traits - including Enterobacteriaceae, Enterococcaceae, Bacillaceae, and Staphylococcaceae - in downstream ecosystems. While we do not directly assess effects on human health or ecosystem function, these observations point to potential ecological impacts in Arctic environments and highlight the importance of continued monitoring to understand and manage the possible effects of human activities and climate change.},
}

@article {pmid42069481,
year = {2026},
author = {Faherty-McGrath, LB and van Sinderen, D and Browne, HP},
title = {Developing spore-forming gut bacteria as model organisms.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.006},
pmid = {42069481},
issn = {1878-4380},
abstract = {Anaerobic gut bacteria have highly evolved functions that promote transmission between human hosts. These include resilient spores produced by many Bacillota (formerly Firmicutes) bacteria, which are tolerant to extended ambient oxygen exposure. Recent culturing and genomic studies have revealed the taxonomic diversity of gut spore-formers and their prevalence in human populations. However, due to a reliance on spore-forming model organisms that are not representative of commensal gut bacteria, we still have a limited understanding of gut microbiome-specific sporulation processes and their underlying genetics. In this opinion article, we outline a rational path for development of new model organisms derived from commensal spore-forming gut bacteria in order to obtain fundamental insights into sporulation and to provide a discovery platform for novel probiotic or microbiome-based therapeutic development.},
}

@article {pmid42069521,
year = {2026},
author = {Harriman, D and Ng, A and Bronowski, M and Yang, R and Dang, T and Sherwood, K and Nguan, C and Miller, A and Lange, D},
title = {Urobiome composition after renal transplantation: an exploratory study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05106-4},
pmid = {42069521},
issn = {1471-2180},
abstract = {BACKGROUND: The urobiome of renal transplant recipients is poorly defined. The purpose of this study was to investigate whether there are characteristic changes in the urobiome between pre- to post-transplant states, at varying degrees of post-transplant allograft function, and between those with acute T-cell mediated rejection (TCMR) versus a non-rejector cohort.

PATIENTS AND METHODS: 41 patients who consented to have urine stored in our transplant biobank were included in this study: 1) Rejectors (n = 10 pts: 6 borderline, 1 Banff IA, 3 Banff IIA TCMR, mean age: 47.4 ± 12.4 yrs); 2) Women (n = 16 pts; mean age: 49.3 ± 17.3 yrs); 3) Men (n = 15 pts, mean age: 47.5 ± 17.2 yrs). Urine was collected via mid-stream clean-catch technique prior to transplant (n = 21), at the time of TCMR (n = 9; within 1 month of transplant), 1-month (n = 15), and 3-months post-transplant (n = 38). Samples were processed and stored at -80 [Formula: see text] until 16S rRNA sequencing. Alpha diversity, beta diversity, and differential abundance analysis was performed.

RESULTS: The urobiome was altered post-transplant, with rejectors gaining Corynebacterium and Pseudomonas at time of rejection, and non-rejectors gaining Lactobacillus among other taxa. Within individuals, post-transplant urobiome composition was ~ 75% dissimilar from pre-transplant (p < 0.001). Urobiome composition differed by sex (p = 0.002), but not by age. Differential abundance analysis based on 3-month post-transplant eGFR revealed consistent loss of Lactobacillus with decreased renal function.

CONCLUSIONS: Our results suggest that renal transplantation has a strong impact on individual urobiome composition, but not diversity, and microbial imbalance may be associated with acute rejection and post-transplant renal function. Our findings indicate a need for further research into the urobiome during renal transplantation to elucidate its potential as a biomarker of and/or contributor to post-transplant allograft health.},
}

@article {pmid42069543,
year = {2026},
author = {Tang, W and Wang, P and Jiang, T and Chen, N and Xue, M and Chen, Y and Pang, R and Zhang, J and Wang, R and Wang, Q and Chen, J and Ren, C and Huang, Y and Zhang, Z and Cheng, X},
title = {Multi-omics analysis reveals circadian disruption of rumen microbiota and serum metabolites in Tibetan sheep under transport stress.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05109-1},
pmid = {42069543},
issn = {1471-2180},
support = {CARS-38//the National Modern Meat Sheep Industry Technology System/ ; 32402701//Young Scientists Fund of the National Natural Science Foundation of China/ ; 2022-NK-134//the Science and Technology Program of Qinghai Province/ ; GXXT-2022-073//Anhui Provincial University Synergistic Innovation Project/ ; },
abstract = {BACKGROUND: Off-site fattening of Tibetan sheep is a key strategy to mitigate the effects of high-altitude grassland degradation and winter forage scarcity, promoting sustainable development in plateau animal husbandry. However, transport stress (TS) presents a significant challenge to realizing its benefits. The mechanism by which TS affects the health of Tibetan sheep by regulating rumen microbial and serum metabolite rhythmic changes remains unclear.

METHODS: This study selected six healthy male Tibetan sheep, aged seven months and of comparable body weight, for the transport experiment. Blood and rumen fluid samples were collected at four-hour intervals during 24-hour periods pre-transport (CON) and post-transport (TS) for serum indicators, serum metabolome, and rumen microbiome analyses.

RESULT: The results showed that TS significantly increased serum concentrations of cortisol (COR), melatonin (MT), lipopolysaccharide-binding protein (LBP), serum amyloid A (SAA), and non-esterified fatty acid (NEFA), while significantly decreasing glucose (GLU), total antioxidant capacity (T-AOC), and glutathione peroxidase (GPx) (P < 0.05). Furthermore, the circadian rhythms of COR, MT, LBP, SAA, NEFA, and GPx were significantly disrupted (ADJ.P < 0.05). TS reduced the proportion of rumen microbial circadian rhythms from 3.46% to 1.99%, with Prevotella, Butyrivibrio, and Ruminococcus losing their circadian rhythmicity in the TS phase (ADJ.P < 0.05). Additionally, TS decreased the proportion of circadian rhythm-regulated serum metabolites from 51.74% to 29.51%. In the TS phase, rhythmically regulated metabolites, including 3',5'-cyclic AMP, fumarate, dopamine, glutathione, and angiotensin (1-7), were enriched in pathways such as oxidative phosphorylation, retinol metabolism, and tryptophan metabolism. Multi-omics analyses demonstrated significant correlations between Ruminococcus and energy metabolites (malic acid, 3',5'-cyclic AMP, fumarate, NEFA), and between Butyrivibrio, Anaeroplasma, and inflammatory/antioxidant markers (glutathione, SAA, LBP). In conclusion, this study reveals that TS induces a homeostatic imbalance in Tibetan sheep by disrupting the circadian rhythms of both the rumen microbiota and host metabolism. These findings provide a theoretical basis and molecular targets for developing interventions to alleviate TS in livestock.},
}