@article {pmid42538110,
year = {2026},
author = {Zhang, S and Ren, Y and Zhang, Q and Fan, Y},
title = {Non-pharmacological interventions for lactational mastitis: a systematic review and meta-analysis protocol.},
journal = {BMJ open},
volume = {16},
number = {7},
pages = {e120579},
doi = {10.1136/bmjopen-2026-120579},
pmid = {42538110},
issn = {2044-6055},
mesh = {Humans ; Female ; *Mastitis/therapy ; Systematic Reviews as Topic ; *Lactation ; Meta-Analysis as Topic ; Breast Feeding ; Research Design ; Probiotics/therapeutic use ; Acupuncture Therapy ; },
abstract = {BACKGROUND: Lactational mastitis is a common inflammatory condition that can adversely affect maternal well-being and is associated with early cessation of breastfeeding. Although antibiotics and analgesics are widely used in clinical practice, concerns regarding antimicrobial resistance and potential effects on the infant microbiome have prompted increasing interest in non-pharmacological approaches. A range of physical and biological interventions, including probiotics, therapeutic ultrasound, acupuncture and manual therapies, have been investigated; however, the comparative effectiveness and safety of these interventions remain unclear. This study aims to systematically evaluate the efficacy and safety of non-pharmacological interventions for lactational mastitis.

METHODS AND ANALYSIS: This protocol is reported in accordance with the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P) guidelines. We will systematically search PubMed, Embase, Web of Science, the Cochrane Library, CNKI, Wanfang, VIP and SinoMed as well as relevant trial registries from database inception to March 2026.We will include randomised controlled trials enrolling adult lactating women diagnosed with mastitis. Eligible studies will compare non-pharmacological interventions with usual care, placebo or pharmacological treatments. Interventions involving pharmacologically active agents will be excluded.Two reviewers will independently perform study selection, data extraction and risk of bias assessment using the Cochrane RoB 2 tool. The primary outcome will be resolution of mastitis, defined as the return of body temperature to normal (<37°C) and resolution of localised breast symptoms (eg, pain, erythema and swelling). Secondary outcomes will include inflammatory markers (eg, C-reactive protein), pain intensity (measured using the Visual Analogue Scale or similar validated scales), incidence of adverse events, complete blood count parameters, time to symptom resolution or normalisation of body temperature, incidence of breast abscess and breastfeeding continuation rates.Meta-analysis will be conducted, where appropriate, using random-effects models. Continuous outcomes will be summarised using mean differences or standardised mean differences, and dichotomous outcomes using risk ratios, all with 95% CIs. Statistical heterogeneity will be assessed using the I² statistic. Subgroup and sensitivity analyses will be performed to explore potential sources of heterogeneity. Publication bias will be assessed using funnel plots and Egger's test when sufficient studies are available. The certainty of evidence will be evaluated using the Grading of Recommendations Assessment, Development and Evaluation（GRADE）approach.

ETHICS AND DISSEMINATION: Ethical approval is not required for this study as it is based on published data. The findings will be disseminated through peer-reviewed publications and conference presentations.

PROSPERO REGISTRATION NUMBER: CRD420261347640.},
}

Humans
Female
*Mastitis/therapy
Systematic Reviews as Topic
*Lactation
Meta-Analysis as Topic
Breast Feeding
Research Design
Probiotics/therapeutic use
Acupuncture Therapy

@article {pmid42538186,
year = {2026},
author = {Ma, B and Hu, H and Lin, Y and Wang, Z and Song, Q},
title = {Corrigendum to "Technology-enabled integration of single-cell transcriptomics and microbiome data identifies RNA-targetable host-microbiota networks in colorectal adenoma" [SLAS Technology (2025) 100365].},
journal = {SLAS technology},
volume = {},
number = {},
pages = {100453},
doi = {10.1016/j.slast.2026.100453},
pmid = {42538186},
issn = {2472-6311},
}

@article {pmid42538270,
year = {2026},
author = {Tsugaru, K and Suzuki, S and Miyamoto, K and Murakami, K and Chida, A and Kato, C and Fukasawa, N and Shigehara, A and Hasegawa, M and Yoshimatsu, Y and Sasabe, J and Mita, M and Barker, N and Harada, Y and Sukawa, Y and Teratani, T and Nakamoto, N and Kawakubo, H and Takabayashi, K and Kato, M and Yahagi, N and Kondo, T and Arai, E and Kitagawa, Y and Hirata, K and Hamamoto, Y and Kanai, T and Sujino, T},
title = {d-serine as a metabolic immune checkpoint in the tumour microenvironment.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {106402},
doi = {10.1016/j.ebiom.2026.106402},
pmid = {42538270},
issn = {2352-3964},
abstract = {BACKGROUND: d-amino acids (D-AAs), the enantiomers of proteinogenic l-amino acids, are detectable in mammals, yet their biological roles in cancer immunity remain largely unexplored. Whether specific D-AAs modulate tumour progression or influence responsiveness to immunotherapy in gastrointestinal cancer is unknown. We aimed to determine how D-AAs, particularly d-serine (D-ser), shape the tumour immune microenvironment and affect clinical outcomes in gastrointestinal cancers.

METHODS: Mechanistic studies were conducted using murine MC38 tumours and orthotopic gastric cancer (GC) organoid allografts with or without D-AAs supplementation. Immune landscape alterations were assessed using single-cell RNA sequencing of tumour-infiltrating immune cells, flow cytometry, ex vivo macrophage-T cell co-culture assays, and microbiome manipulation experiments. D-AAs concentrations in plasma, urine, and stool were quantified in healthy controls (HCs; n = 87) and patients with GC across three cohorts (Cohort 1, n = 14; Cohort 2, n = 108; Cohort 3, n = 28). Associations between plasma D-ser levels, disease stage, immune cell infiltration, and clinical outcomes following anti-PD-1 antibody therapy were analysed.

FINDINGS: D-ser promoted tumour progression by suppressing CD8[+] T cell immunity and enhancing SPP1-associated immunosuppressive macrophage signalling in murine model. Across all clinical cohorts, the plasma, urine, and stool levels of several D-AAs, most prominently D-ser, were significantly elevated in patients with GC compared to HCs. Plasma concentration of D-ser strongly correlated with disease stage (I-IV). Elevated plasma D-ser is associated with an immunosuppressive tumour microenvironment and poor response to anti-PD-1 monotherapy in patients with advanced gastric cancer.

INTERPRETATION: This study identifies D-ser as a previously unrecognised immunosuppressive metabolite that promotes tumour immune evasion by increased macrophages and reduced CD8[+] T cell effector function, thereby shifting the tumour microenvironment toward an immunosuppressive phenotype. Clinically, D-ser is a potential metabolite to predict cancer progression and immunotherapy resistance.

FUNDING: This work was supported by The Japan Science and Technology Agency (JST) Fusion Oriented Research for Disruptive Science and Technology (FOREST)[JPMJFR210P], Grants-in-Aid from the Japanese Society for the Promotion of Science (JSPS) (25K10430, 21K18272, 23H02899, 23K27590, 25K22627), KGRI challenge grant, Sakaguchi Memorial Foundation, Japan Agency for Medical Research and Development (CREST 21gm1510002h0001), and Miyarisan Pharmaceutical Grant.},
}

@article {pmid42538274,
year = {2026},
author = {Gallardo-Escárate, C and Valenzuela-Muñoz, V and Núñez-Acuña, G and Valenzuela-Miranda, D and Benaventel, BP and Sáez-Vera, C and Urrutia, H and Novoa, B and Figueras, A and Roberts, S and Assmann, P and Bravo, M},
title = {Retraction notice to "The wastewater microbiome: A novel insight for COVID-19 surveillance" [Sci. Total Environ. 764 (2021) 142867].},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {182116},
doi = {10.1016/j.scitotenv.2026.182116},
pmid = {42538274},
issn = {1879-1026},
}

@article {pmid42538321,
year = {2026},
author = {Iqbal, R and Mehmood, H and Hyder, S and Jabborova, D and Murtaza, G and Alotaibi, MS and Aloteeb, AS and Ullah, S and Ali, S},
title = {Foliar serotonin and allantoin mitigate tellurium toxicity in Quinoa (Chenopodium quinoa Willd.) through antioxidant activation and nutrient homeostasis to enhance yield and grain quality.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2710523},
doi = {10.1080/15592324.2026.2710523},
pmid = {42538321},
issn = {1559-2324},
mesh = {*Serotonin/pharmacology ; *Chenopodium quinoa/drug effects/metabolism/growth & development ; *Antioxidants/metabolism ; Homeostasis/drug effects ; *Allantoin/pharmacology ; *Tellurium/toxicity ; *Plant Leaves/drug effects/metabolism ; *Edible Grain/drug effects ; Photosynthesis/drug effects ; *Nutrients/metabolism ; },
abstract = {Tellurium toxicity severely impairs soil health, plant physiology and crop productivity, posing a critical threat to global food security, ecosystem sustainability and human health. The exogenous application of phytohormones and osmoprotectants offers a sustainable strategy for mitigating heavy metal-induced phytotoxicity and restoring agricultural viability. A comprehensive experiment was conducted to evaluate the synergistic efficacy of serotonin (5-HT) and allantoin (ALL) in ameliorating tellurite stress in quinoa plants. Plants subjected to 50 µM sodium tellurite soil drenching were treated with 50 µM 5-HT and 100 µM ALL via foliar spray under a randomized complete block design with a factorial arrangement and four replications. Tellurite stress alone drastically reduced morphological traits and overall yield, while simultaneously elevating oxidative damage. However, combined 5-HT and ALL application under stress increased grain yield by 90.41%, photosynthetic rate by 78.68%, stomatal conductance by 80.30%, relative water content by 33.52%, and antioxidant enzyme activities by up to 84.86%. Furthermore, it decreased malondialdehyde content by 58.20%, hydrogen peroxide by 61.16%, tellurium root accumulation by 52.48%, shoot translocation by 60.41%, and grain residue by 66.74% compared to stressed controls, while concurrently improving soil microbial biomass carbon by 63.71%, dehydrogenase activities by 88.49%, and available nitrogen by 39.48%. The integrated treatment significantly restored cellular ion homeostasis, enhanced complex root architectural traits, and effectively restricted heavy metal translocation to the edible harvested grains. Consequently, the co-application of 5-HT and ALL is highly recommended as a robust agronomic intervention to safeguard crop productivity, improve soil health, and ensure long-term food safety in severely Te-contaminated agricultural environments.},
}

*Serotonin/pharmacology
*Chenopodium quinoa/drug effects/metabolism/growth & development
*Antioxidants/metabolism
Homeostasis/drug effects
*Allantoin/pharmacology
*Tellurium/toxicity
*Plant Leaves/drug effects/metabolism
*Edible Grain/drug effects
Photosynthesis/drug effects
*Nutrients/metabolism

@article {pmid42538347,
year = {2026},
author = {Rath, C and Fursule, A and Wong, F and Rao, S and Patole, S},
title = {Influence of probiotics on faecal antibiotic resistome in neonates: a systematic review.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42538347},
issn = {1530-0447},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) and its associated complications represent a major global health threat. Probiotics, among the limited available preventive strategies, may play an important role in reducing the risk of AMR.

METHODS: A systematic review of studies assessing faecal antibiotic resistome in neonates who did versus did not receive probiotic supplementation. Databases were searched in October 2025.

RESULTS: Eighteen studies (n = 3496) were included, comprising eight randomized controlled trials (RCTs) and ten observational studies (non-RCTs). Ten of the eighteen studies (RCTs: 5, non-RCTs: 5) reported significant reduction in the prevalence of faecal antibiotic resistome among probiotic supplemented infants. Five of the eight studies that reported no reduction relied on culture or polymerase-chain reaction-based methods rather than metagenomic analyses. No consistent associations were observed between probiotic dose and strain, or type of milk feeding and resistome colonization. Most included studies were assessed as having a low risk of bias. The certainty of evidence was rated as low to very low.

CONCLUSION: Probiotic supplementation may reduce faecal AMR gene colonization in neonates. Future RCTs should employ standardized study designs and include quantitative assessment of AMR gene abundance, along with clinically relevant outcomes such as sepsis and its associated complications.

IMPACT: The first comprehensive systematic review focused on the effect of probiotics on neonatal fecal resistome and mobile genetic elements, incorporating evidence from 18 studies involving 3496 neonates. Suggests a potential role for targeted probiotic strategies as an intervention for reducing early neonatal antimicrobial resistance colonization, particularly in preterm infants at high risk of multi-drug resistance sepsis. Positions microbiome modulation as a strategy complementary to antibiotic stewardship in tackling global neonatal antimicrobial resistance.},
}

@article {pmid42538364,
year = {2026},
author = {Zhu, YG and Zhu, D and Chen, QL and Rillig, MC},
title = {Impacts of pollution on the soil microbiome.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42538364},
issn = {1740-1534},
abstract = {Soil microbiomes underpin terrestrial ecosystem functioning and drive nutrient cycling, plant productivity and ecological resilience. However, diverse pollutants, ranging from heavy metals and pesticides to plastics, perfluoroalkyl and polyfluoroalkyl substances and nanomaterials, are reshaping microbial communities in ways that threaten soil health and broader ecological stability. Thus, soils are hotspots of microbial evolution under chemical mixtures. Pollution alters microbial diversity, composition and functional capacity through mechanisms such as direct toxicity, shifts in soil chemistry and selective evolutionary pressures. These disruptions impair nutrient cycling, destabilize plant-microorganism interactions and accelerate the spread of antimicrobial resistance, with cascading effects on food webs and human health under a One Health framework. At the same time, soil microbiomes can serve as indicators of ecosystem stress and as tools for bioremediation and ecological restoration. This Review synthesizes current understanding of terrestrial pollution-microbiome interactions, highlights functional and health implications, and explores how microbiome-informed approaches can guide sustainable soil management and environmental protection under global change, while identifying key knowledge gaps and outlining future research directions for predictive and integrative microbiome-based solutions.},
}

@article {pmid42538494,
year = {2026},
author = {Cuba-Gutierrez, L and Invernón-Monedero, M and Osuna, E and Hernández-Romero, D},
title = {Application of artificial intelligence in the determination of the postmortem interval: Systematic review of the literature and metaanalysis.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {42538494},
issn = {1556-2891},
abstract = {Accurate estimation of the postmortem interval (PMI) is essential in forensic medicine for reconstructing the timeline and circumstances of death. Artificial intelligence (AI) has emerged in recent years as a promising tool to enhance this estimation through the analysis of complex biological data. This study aims to conduct a systematic review of recent advances in AI applied to PMI estimation, complemented by a meta-analysis assessing the predictive performance of commonly used AI models such as neural networks, ensemble models, and random forest, using the area under the curve (AUC) as the primary metric. A literature search was conducted across PubMed, Scopus, and Google Scholar for the period 2015-2025, identifying 16 eligible studies. The analyzed models integrated microbiological, proteomic, imaging, and spectroscopic data, achieving over 90% accuracy in several studies. The meta-analysis, based on five studies with comparable data, yielded a combined AUC of 0.94 (95% CI ((Confidence Interval): 0.81-1.08), with no significant heterogeneity or publication bias. These findings highlight the strong potential of AI-particularly when combined with multi-omics approaches-as a precise and robust method for PMI estimation. This approach addresses several limitations of traditional forensic methods, although certain technical and implementation challenges remain to be resolved.},
}

@article {pmid42538621,
year = {2026},
author = {Javid, FA and Golčić, M and Hrkać, AH and Belančić, A},
title = {The Relationship Between (Endo)cannabinoids, the Microbiome and Melanoma.},
journal = {Pharmacology research & perspectives},
volume = {14},
number = {4},
pages = {e70304},
doi = {10.1002/prp2.70304},
pmid = {42538621},
issn = {2052-1707},
mesh = {Humans ; *Melanoma/drug therapy/microbiology/immunology ; *Cannabinoids/pharmacology/therapeutic use ; Animals ; *Skin Neoplasms/drug therapy/microbiology/immunology ; *Microbiota/drug effects ; Immunotherapy/methods ; Cannabidiol/pharmacology/therapeutic use ; Skin Microbiome ; },
abstract = {Despite advances in targeted and immunotherapy for melanoma, resistance to treatment and severe adverse effects pose significant challenges. This necessitates the development of new treatment strategies, and cannabinoids, because of the extensive preclinical evidence for their cytotoxic action on carcinoma cells in a variety of cancers, can offer a novel therapeutic option when used appropriately. Indeed, the potential therapeutic benefits of cannabinoids were formally recognized in the world and much more recently in the United Kingdom when cannabis-based medicinal products were moved from Schedule 1 of the Misuse of Drugs Regulations 2001 to Schedule 2 in 2018. This move further encouraged scientists to look at more applications of cannabinoids in different disorders. Although the potential psychoactivity of cannabis as a Schedule 1 drug hinders research, more research could focus on non-psychoactive components such as cannabidiol (CBD) and cannabigerol (CBG). This review summarizes some past and current research on the relationship between the cannabinoid system and the microbiome in patients with metastatic melanoma who undergo immunotherapy. The review also provides a comprehensive background on the function of the cannabinoid system in normal and diseased skin, as well as future directions in using cannabinoids as an adjunct to chemotherapeutics in the treatment of the disease.},
}

Humans
*Melanoma/drug therapy/microbiology/immunology
*Cannabinoids/pharmacology/therapeutic use
Animals
*Skin Neoplasms/drug therapy/microbiology/immunology
*Microbiota/drug effects
Immunotherapy/methods
Cannabidiol/pharmacology/therapeutic use
Skin Microbiome

@article {pmid42538655,
year = {2026},
author = {Hasanova, Z},
title = {Literature Review: Literature Review: Nutritional Management in Hemodialysis Patients.},
journal = {Experimental and clinical transplantation : official journal of the Middle East Society for Organ Transplantation},
volume = {24},
number = {Suppl 2},
pages = {39-43},
doi = {10.6002/ect.MESOT2025.P189},
pmid = {42538655},
issn = {2146-8427},
mesh = {Humans ; *Renal Dialysis/adverse effects ; *Nutritional Status ; *Protein-Energy Malnutrition/physiopathology/therapy/diagnosis/epidemiology/etiology ; Nutrition Assessment ; Risk Factors ; Treatment Outcome ; Dietary Supplements ; Parenteral Nutrition ; },
abstract = {Protein energy wasting is a highly prevalent and clinically significant complication in patients receiving maintenance hemodialysis, affecting approximately 30 % to 50 % of this population worldwide. Protein energy wasting is associated with substantially increased risk of all -cause and cardiovascular mortality, reduced functional capacity, impaired immune function, and poor quality of life. The pathogenesis of protein energy wasting is multifactorial and involves reduced dietary intake, chronic inflammation, metabolic acidosis, dialysis -related nutrient losses, hormonal and metabolic disturbances, and comorbid disease burden. This narrative literature review synthesized contemporary evidence (2020 -2025) on the epidemiology, pathophysiology, assessment, and nutritional management of protein energy wasting in patients receiving hemodialysis. We highlighted limitations of traditional biochemical markers such as serum albumin and emphasized the importance of multidimensional nutritional assessment using validated clinical tools, including the Subjective Global Assessment and Malnutrition-Inflammation Score, complemented by objective body composition techniques. We also discussed current guideline -recommended targets for protein and energy intake, as well as real -world barriers to achieving these targets. We reviewed and examined evidence supporting oral nutritional supplementation as first -line therapy, along with indications for intradialytic parenteral nutrition in selected patients with severe or refractory protein energy wasting, and the role of micronutrient management, vitamin D repletion, and targeted trace element supplementation. Emerging adjunctive strategies, including omega -3 fatty acids, gut microbiome modulation, and exercise -nutrition synergy, were also addressed. Overall, effective management of protein energy wasting requires early identification, individualized dietary strategies, and integration within multidisciplinary dialysis care models. Future research should prioritize pragmatic trials focused on hard clinical outcomes and personalized approaches to nutritional therapy in this high -risk population.},
}

Humans
*Renal Dialysis/adverse effects
*Nutritional Status
*Protein-Energy Malnutrition/physiopathology/therapy/diagnosis/epidemiology/etiology
Nutrition Assessment
Risk Factors
Treatment Outcome
Dietary Supplements
Parenteral Nutrition

@article {pmid42538990,
year = {2026},
author = {Sadik, O},
title = {Enzymatic Defluorination of Perfluorooctanoic Acid by an Evolutionarily Distinct Haloacid Dehalogenase.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10043589/v1},
pmid = {42538990},
issn = {2693-5015},
abstract = {Here, we demonstrate the successful purification of haloacid dehalogenase type II (HAD-II) enzyme, validating its catalytic capacity to directly mediate the cell-free defluorination of long-chain perfluorooctanoic acid (PFOA) by systematically cleaving the resilient C-F bond. While conventional remediation strategies rely on energy-intensive chemical methods, biological alternatives are limited to sluggish whole-microbiome consortia. We discovered a novel HAD-II enzyme from Achromobacter mucicolens harvested from PFAS-contaminated lacustrine sediment. Within 24 hours, the recombinant enzyme achieved cell-free PFOA defluorination, releasing 0.55 ppm of free fluoride (17% yield). Structural and phylogenetic analyses reveal that this HAD-II belongs to a deeply divergent lineage sharing only 25% sequence identity with the previously characterized Delftia homologue while preserving the core HAD-like catalytic fold. Comparative molecular docking elucidated that PFOA adopts a productive binding orientation near the conserved catalytic Asp15 within the A. mucicolens active-site pocket. Together, our work establishes a clean mechanistic paradigm for targeted environmental biotechnology.},
}

@article {pmid42539130,
year = {2026},
author = {Kozlova, EV and Denys, ME and Bishay, AE and Do, EA and Lui, R and Luna, CN and Lam, A and Piamthai, V and Hsiao, A and Curras-Collazo, M},
title = {Social and neuroendocrine phenotypes reprogrammed by endocrine-disrupting chemicals can be mitigated by Limosilactobacillus reuteri modulation of the gut microbiome-thyroid-oxytocin axis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.18.739173},
pmid = {42539130},
issn = {2692-8205},
abstract = {INTRODUCTION: Environmental factors are increasingly implicated in the etiology of autism spectrum disorder (ASD). Polybrominated diphenyl ethers (PBDEs) are anthropogenic toxicants added as flame retardants to consumer products that have become ubiquitous environmental contaminants and disrupt thyroid hormone (TH) and neuroendocrine systems. We have previously shown that developmental PBDE exposure produces ASD-like traits with involvement of oxytocin (OXT)-thyroid hormone signaling. Limosilactobacillus reuteri (LR), a widely used probiotic bacterium, has been shown to improve social functioning and increase TH and OXT levels in murine models. Therefore, we tested the hypothesis that LR supplementation (LR) prevents PBDE-induced deficits in socioemotional behavior with concomitant modulation of TH signaling genes on hypothalamic OXT neurons.

METHODS: C57BL/6N mouse offspring were exposed to a commercial penta-mixture of PBDE congeners, DE-71, at an environmentally realistic concentration, 0.1 mg/kg/d (DE-71), or to corn oil vehicle (VEH/CON) via their mothers during gestation and lactation. Offspring received supplementation with LR ATCC PTA 6475 (10 [7] -10 [8] CFU/mL, po) indirectly via the dam or continuation directly through adulthood. Unsupplemented controls were given saline.

RESULTS: Fecal microbiome analysis in offspring confirmed colonization of LR at postnatal day (P) 40 and depletion by P104. LR treatment increased plasma total thyroxine in DE-71 and plasma OXT in VEH/CON dams. In DE-71 offspring of both sexes, LR normalized deficient scores on social novelty preference and emotional recognition in adult females and males and deficient long-term social recognition memory (SRM) in adult DE-71 females; DE-71 males were normal. Reduced olfactory dishabituation between two social odors may partly explain the compromised socioemotional behavior produced by DE-71 in an LR-dependent manner. Multiplex RNA in situ hybridization performed on immunoreactive OXT-ergic neurons in the paraventricular hypothalamic nucleus (PVH) revealed significant upregulation of TH transporter monocarboxylate transporter 8 (Mct8) and downregulation of iodothyronine deiodinase 3 (Dio3) in DE-71 relative to VEH/CON females. This toxicant-induced reprogramming was prevented by probiotic treatment. DE-71 males expressed reduction in Mct8 and Dio3 transcripts on OXT-ergic neurons with minimal LR protection. In the female supraoptic nucleus (SON), Mct8 and Dio3 were downregulated by DE-71 and normalized in DE-71+LR; there were no group effects on transcript levels in male SON. Results of fecal 16S rRNA sequencing indicated reduced α-diversity and altered β-diversity in the gut bacterial community of female but not male DE-71 exposed offspring; most changes were correctable by LR. Alterations in taxa-level abundance caused by DE-71 and reversed by LR were observed in both sexes. These involved Bifidobacterium, Coprococcus, Desulfovibrio, Oscillospira , and Peptococcaceae in females and Desulfovibrionaceae, Rikenella , and Turicibacter in males. Exposed dams showed no detriment in α- and β-diversity while showing reduced abundance of several Firmicutes and Proteobacteria taxa that could be rescued by LR. The relative abundance of Lactobacillus was upregulated in DE-71 males and DE-71+LR males and dams.

CONCLUSIONS: These results indicate that developmental probiotic supplementation effectively mitigated organohalogen-induced ASD-like deficits in socioemotional behavior and partially corrected dysbiosis of gut bacterial communities in exposed offspring of both sexes. Concomitantly, PBDEs altered the expression of TH regulatory genes Mct8 and Dio3 in PVH OXT neurons in a sex-dependent manner, suggesting that TH regulation of OXT neuroendocrine cells may modulate the emergence of toxicant-induced ASD-relevant behavior. While LR reinstated normal behavioral outcomes in PBDE-exposed offspring of both sexes, coincident normalization of hypothalamic TH signaling transcripts occurred more broadly in females, indicating the existence of unique parallel processes influencing the preventive effects of LR on ASD-relevant behavioral deficits in both sexes.},
}

@article {pmid42539242,
year = {2026},
author = {De Santiago, A and Bik, H},
title = {MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.23.740139},
pmid = {42539242},
issn = {2692-8205},
abstract = {Microbes closely interact with every living organism, including meiofauna (i.e., microbial eukaryotes 38 μm - 1 mm in length), and influence the development, life cycle, and evolution of diverse metazoans. Together, meiofauna and their microbiomes, collectively referred to as the holobiont, underpin biogeochemical cycles and drive decomposition of organic matter. However, our understanding of the ecological and evolutionary dynamics of meiofauna microbiomes are limited, typically owed to low-resolution 16S rRNA surveys, which cannot accurately delineate bacterial taxa. Single-specimen holobiont sequencing can help overcome the limitations of metabarcoding approaches by 1) generating metagenome-assembled genomes (MAGs) of the host microbiome and 2) recovering host single-copy genes (SCGs) to phylogenetically confirm the identity of the host organism. However, most bioinformatics pipelines for the assembly of metagenomic datasets have been developed for the assembly of high-complexity microbial communities of bulk sediment or soil samples (and cannot be used for the assembly of host genomes), rely on co-assembly approaches (which collapses strain-level genomic information of bacterial taxa), and focus on binning either prokaryotic or eukaryotic taxa. Therefore, there is a tremendous need for a computational workflow for the dual analysis of host genomes and their microbiomes. Here, we developed MeioBIOME, a modular Snakemake pipeline for the reproducible analysis of holobiont metagenomes obtained from individually sequenced microbial metazoa. We analyze publicly available single-specimen metagenomics datasets to show the utility of MeioBIOME and recover host-associated symbiont MAGs and host SCGs. Additionally, we integrate state-of-the-art binning algorithms which generate more MAGs than the DOE Joint Genome Institute metagenomic pipeline. We anticipate that MeioBIOME will facilitate studies of phylosymbiosis by generating high-quality host genome skims (to build well-supported host phylogenetic trees) and host-associated prokaryotic MAGs obtained from single specimens.},
}

@article {pmid42539467,
year = {2026},
author = {Dera, N and Żeber-Lubecka, N and Ziemska-Legiecka, J and Piątkowska, M and Balabas, A and Ciebiera, M and Massalska, D and Kosińska-Kaczyńska, K and Ostrowski, J and Bubień, K and Kozera, T and Dera, K and Szymusik, I},
title = {Niche-driven microbial architecture in mothers and newborns with minimal cohort influence across anatomically distinct sites.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1896420},
doi = {10.3389/fimmu.2026.1896420},
pmid = {42539467},
issn = {1664-3224},
mesh = {Humans ; Female ; Infant, Newborn ; Pregnancy ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Adult ; Vagina/microbiology ; Amniotic Fluid/microbiology ; Placenta/microbiology ; *Bacteria/genetics/classification ; Mothers ; },
abstract = {UNLABELLED: The microbiota plays a crucial role in the functioning of the human body. Several theories have been proposed regarding the origin of the uterine microbiota, including both ascending pathways from the vagina and translocation from the gastrointestinal tract. Numerous studies suggest that, in preterm births, amniotic fluid may contain microbial DNA or signals associated with microorganisms ascending from the vagina, even in the presence of intact fetal membranes, as well as by microbes originating from the placental microbiome.

BACKGROUND: The aim of this study was to comprehensively characterize the maternal and neonatal microbiome across multiple anatomically and biologically distinct niches and to determine the extent to which the structure of microbial communities reflects (i) anatomical location, (ii) maternal-infant relationships, and (iii) cohort-related perinatal factors.

METHODS: The study included eight women who delivered between 34 + 0 and 36 + 6 weeks of gestation, along with their neonates. The control group consisted of eight women who delivered at ≥37 + 0 weeks of gestation and their neonates. Prior to delivery, a cervical swab, an oral (buccal) swab, and a stool sample were collected. After delivery, the following samples were obtained from the neonate: a skin swab, a sample of amniotic fluid aspirated from the stomach, a rectal swab, and placental tissue. To assess microbiota composition, microbiome profiling based on 16S rRNA gene sequencing was performed.

RESULTS: The analysis did not demonstrate significant differences in microbiota composition between late preterm and term pregnancies, in either mothers or neonates.

CONCLUSION: Comparative analysis of maternal and neonatal microbiota suggests a possible association with microbial signals consistent with an ascending vaginal contribution; however, without a detectable influence on neonatal microbiota. Conversely, the findings may indicate a potential association with maternal microbiota consistent with a hematogenous contribution, however, no direct evidence of microbial colonization or transmission can be inferred.},
}

Humans
Female
Infant, Newborn
Pregnancy
*Microbiota
RNA, Ribosomal, 16S/genetics
Adult
Vagina/microbiology
Amniotic Fluid/microbiology
Placenta/microbiology
*Bacteria/genetics/classification
Mothers

@article {pmid42539514,
year = {2026},
author = {Li, Y and Zhu, J and Huang, M and Liu, X and Wang, L},
title = {Microbiota-innate immune crosstalk drives atherosclerosis: mechanisms, disease progression, and emerging therapeutic strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1900899},
doi = {10.3389/fimmu.2026.1900899},
pmid = {42539514},
issn = {1664-3224},
mesh = {Humans ; *Atherosclerosis/immunology/metabolism/therapy/microbiology/etiology ; *Immunity, Innate ; Animals ; Disease Progression ; *Gastrointestinal Microbiome/immunology ; Signal Transduction ; },
abstract = {Atherosclerosis (AS) is a complex cardiovascular disease driven by the interplay of dysregulated lipid metabolism, chronic inflammation, and immune dysfunction. Increasing evidence has revealed that the gut microbiota not only regulates host metabolic homeostasis but also actively contributes to the initiation and progression of AS through intricate interactions with the innate immune system. Microbial-derived signaling molecules, including lipopolysaccharides, outer membrane vesicles, extracellular nucleic acids, and TMAO, can activate Toll-like receptors, the NLRP3 inflammasome, and nucleic acid-sensing pathways, thereby promoting inflammatory cytokine production, endothelial dysfunction, and foam cell formation. In contrast, beneficial microbial metabolites such as short-chain fatty acids, bile acids, and tryptophan-derived metabolites exert immunomodulatory and vasculoprotective effects through signaling pathways involving FFAR2/3, the AhR, the FXR, and TGR5. Conversely, the innate immune system shapes microbial composition and function through barrier defense, phagocytic clearance, and antimicrobial factor production, establishing a dynamic and reciprocal microbiota-immune interaction network. This review systematically summarizes alterations in microbial ecology and innate immune homeostasis associated with atherosclerosis, elucidates the key molecular mechanisms underlying microbiota-innate immune crosstalk, and examines its dynamic involvement across four critical stages of disease evolution: endothelial dysfunction, foam cell formation, plaque progression, and plaque destabilization and rupture. In addition, emerging therapeutic approaches, including microbiota remodeling, modulation of microbial metabolic pathways, and precision microbiome-based interventions, are comprehensively discussed. The microbiota-innate immune axis provides a novel conceptual framework for understanding atherosclerosis pathogenesis and represents a promising target for future disease prevention, risk stratification, and precision therapeutics.},
}

Humans
*Atherosclerosis/immunology/metabolism/therapy/microbiology/etiology
*Immunity, Innate
Animals
Disease Progression
*Gastrointestinal Microbiome/immunology
Signal Transduction

@article {pmid42539524,
year = {2026},
author = {Fletcher, AA and Koberssy, Z and Daher, J and Moussallem, N and McComsey, GA},
title = {Feeding the gut-immune axis: dietary, prebiotic, and probiotic strategies to target persistent inflammation in ART-treated HIV: a narrative review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1877822},
doi = {10.3389/fimmu.2026.1877822},
pmid = {42539524},
issn = {1664-3224},
mesh = {Humans ; *HIV Infections/immunology/drug therapy ; *Probiotics/therapeutic use/administration & dosage ; *Prebiotics/administration & dosage ; *Inflammation/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; Dysbiosis ; Intestinal Barrier Function ; },
abstract = {People living with HIV (PWH) experience ongoing systemic inflammation driven by gut dysbiosis, epithelial barrier disruption, and microbial translocation, despite antiretroviral therapy (ART). This review examines evidence from randomized controlled trials, mechanistic studies, systematic reviews, and meta-analyses evaluating nutritional and microbiome-based interventions to reduce inflammation in PWH. Reduced production of short-chain fatty acids (SCFAs) by the gut microbiota has been observed to precede morbidity and mortality in PWH, with SCFAs, mainly butyrate, exerting immunomodulatory effects through promoting regulatory T-cell differentiation via histone deacetylase inhibition and G protein-coupled receptor 43 (GPR43) and GPR109A signaling, suppressing nuclear factor kappa B (NF-κB)-mediated pro-inflammatory cytokine production, and enhancing epithelial tight junction integrity. Probiotics, prebiotics, synbiotics, and fecal microbiota transplantation have demonstrated reductions in inflammatory biomarkers including soluble CD14 (sCD14), lipopolysaccharide-binding protein (LBP), and high-sensitivity C-reactive protein (hsCRP). The Mediterranean diet, omega-3 fatty acids, and polyphenol-rich foods represent an underexplored area as modulators of gut microbiota composition and SCFA production. Existing gaps in the literature include a lack of trials with clinically meaningful endpoints, optimal probiotic strains and doses, and lack of randomized trials evaluating anti-inflammatory dietary patterns in PWH. We propose a research agenda prioritizing Mediterranean diet intervention trials, precision microbiome interventions, and combination approaches integrating dietary modification with microbiome-targeted therapies. Lastly, we provide practical nutritional recommendations for clinicians managing PWH.},
}

Humans
*HIV Infections/immunology/drug therapy
*Probiotics/therapeutic use/administration & dosage
*Prebiotics/administration & dosage
*Inflammation/immunology/therapy
*Gastrointestinal Microbiome/immunology
Dysbiosis
Intestinal Barrier Function

@article {pmid42539536,
year = {2026},
author = {Leeanansaksiri, W and Dechsukhum, C},
title = {Berry-derived Bioactive Compounds as Chemopreventive Agents in Colorectal Cancer: Molecular Mechanisms and Gut Microbiota Interactions.},
journal = {Journal of cancer prevention},
volume = {31},
number = {3},
pages = {127-139},
doi = {10.15430/JCP.26.020},
pmid = {42539536},
issn = {2288-3649},
abstract = {Berry-derived bioactive compounds are increasingly recognized as promising chemopreventive agents for colorectal cancer (CRC). CRC develops through a multistep process involving genetic, epigenetic, inflammatory, and microbiota-related alterations. Polyphenol-rich berries are abundant in anthocyanins, ellagitannins, ellagic acid, quercetin, and related phytochemicals. These compounds target multiple hallmarks of colorectal carcinogenesis. Experimental studies have shown that berry-derived compounds exert anti-proliferative effects by inducing cell-cycle arrest at the G0/G1, S, or G2/M phase. These effects are associated with modulation of cyclin-dependent kinases (CDK), and CDK inhibitors such as p21 and p27. In addition, they inhibit key oncogenic signaling pathways, including Wnt/β-catenin, NF-κB, PI3K/Akt, and ERK/MAPK. Berry phytochemicals also promote programmed cell death. Thus, they activate both intrinsic and extrinsic apoptotic pathways, alter the balance of Bcl-2 family proteins, disrupt mitochondrial integrity, and induce caspase activation. Moreover, berry compounds attenuate chronic inflammation by downregulating expression/production of COX-2, inducible nitric oxide synthase, and pro-inflammatory cytokines through suppression of NF-κB- and STAT3-dependent signaling. Further, they also enhance Nrf2-mediated antioxidant responses. Although parent polyphenols have limited bioavailability, they are extensively metabolized by gut microbiota into bioactive compounds such as protocatechuic acid and urolithins. These metabolites often exhibit comparable or greater anticancer activity and reach physiologically relevant concentrations in the colorectum. Berry polyphenols further modulate gut microbiota composition, promoting beneficial microbes and reinforcing anti-carcinogenic signaling. Altogether, these mechanisms highlight berry-derived compounds as strong candidates for CRC chemoprevention, which merits further clinical investigation.},
}

@article {pmid42539542,
year = {2026},
author = {Cui, M and Zhao, Y and Wang, Y},
title = {Molecular Mechanisms of the Anticancer Activity of the Flavonoid Kaempferol: A Comprehensive Review.},
journal = {Journal of cancer prevention},
volume = {31},
number = {3},
pages = {116-126},
doi = {10.15430/JCP.26.014},
pmid = {42539542},
issn = {2288-3649},
abstract = {Kaempferol (KAE), a natural flavonoid, has emerged as a promising multi-target antineoplastic agent characterized by high efficacy and minimal systemic toxicity. Moving beyond fragmented descriptive summaries, this comprehensive review provides a highly integrated conceptual framework of KAE's anticancer mechanisms. Specifically, KAE orchestrates tumor eradication by enforcing cell cycle arrest across multiple phases and triggering a complex, interconnected network of programmed cell death. We highlight how reactive oxygen species and endoplasmic reticulum stress serve as central upstream nodes driving the mechanistic crosstalk among apoptosis, lethal autophagy, gasdermin E-mediated pyroptosis, and ferroptosis. Furthermore, KAE actively remodels the tumor microenvironment by inhibiting angiogenesis and repolarizing tumor-associated macrophages, thereby converting immunosuppressive "cold" tumors into immune-active "hot" tumors. Notably, this review introduces the emerging prebiotic-like crosstalk between KAE and the gut microbiome, providing a strong mechanistic rationale for its synergistic application with immune checkpoint inhibitors. As a potent chemosensitizer, KAE also overcomes multidrug resistance and mitigates chemotherapy-induced toxicities. Finally, we critically evaluate current translational bottlenecks-including the disparity between supraphysiological in vitro concentrations and clinical pharmacokinetics, the lack of robust in vivo validations, and the long-term biosafety of emerging nano-delivery systems. By addressing these critical limitations, this review offers strategic perspectives to bridge the gap from preliminary bench research to future precision oncological practice.},
}

@article {pmid42539550,
year = {2026},
author = {Spanoghe, L and Quaaden, A and Lannoo, J and Banchi, P and Domain, G and Posastiuc, FP and Opsomer, G and Van Soom, A},
title = {Practices and perceptions of antibiotic use in canine breeding: a survey among breeders and veterinarians.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1879574},
doi = {10.3389/fvets.2026.1879574},
pmid = {42539550},
issn = {2297-1769},
abstract = {Antibiotic use in canine breeding, particularly prior to mating, is frequently discussed in practice despite increasing awareness of antimicrobial stewardship and the recognition that the canine vaginal tract naturally harbors a microbiome. Diagnostic uncertainty, especially regarding bacterial culture findings and Mycoplasma spp. detection, may contribute to antimicrobial use in this setting. This study aimed to investigate antibiotic use, bacteriological testing practices, and underlying beliefs among dog breeders and veterinarians involved in canine reproduction. Two anonymous online questionnaires targeting breeders and veterinarians were distributed in Belgium and the Netherlands between October 2025 and February 2026. The surveys collected data on antibiotic use, diagnostic practices, and perceptions regarding vaginal bacteriology and the detection of Mycoplasma spp. Descriptive statistics and logistic regression analyses were performed to identify factors associated with antibiotic use. A total of 426 breeders and 94 veterinarians participated. Thirty-two percent of breeders reported ever administering antibiotics around the time of breeding, most commonly prior to mating. Forty-nine percent of breeders had ever had vaginal bacteriology performed in their breeding bitches, which was strongly associated with consequent antibiotic use (OR = 4.93, 95% CI 3.14-7.90, p < 0.001). In contrast, most veterinarians reported never prescribing antibiotics to clinically healthy bitches, whereas 27% had done so occasionally. Breeder request, duration of professional experience and use of genital bacteriology were positively associated with antibiotic prescribing in univariable analyses. Lack of knowledge regarding the clinical relevance of Mycoplasma spp. was observed among both breeders and veterinarians, despite frequent testing for it and a tendency toward antibiotic treatment following detection. Antibiotic use in canine breeding is influenced by bacteriological testing, diagnostic uncertainty, and precautionary decision-making. Discrepancies between breeder-reported practices and veterinarian prescribing behavior highlight the complexity of antimicrobial use in this field. Targeted education and improved communication are essential to promote evidence-based reproductive management and responsible antimicrobial use.},
}

@article {pmid42539556,
year = {2026},
author = {Kim, EJ and Hwang, SY and No, K and Lee, MH},
title = {Insights into the Relevance of the Interaction between Colorectal Cancer and Gut Microbiota-Derived Metabolites.},
journal = {Journal of cancer prevention},
volume = {31},
number = {3},
pages = {140-152},
doi = {10.15430/JCP.25.057},
pmid = {42539556},
issn = {2288-3649},
abstract = {Colorectal cancer (CRC) is strongly associated with gut microbial dysbiosis, characterized by increases in Escherichia coli, Enterococcus faecalis, and Bacteroides spp., and reduction in short chain fatty acid producing taxa such as Akkermansia muciniphila, Faecalibacterium prausnitzii, and Roseburia. These shifts parallel metabolomic disturbances, including decreased butyrate and immune dysregulation. Several microbial and metabolic markers such as Akkermansia, Faecalibacterium, butyrate, tryptophan metabolites, and sarcosine have demonstrated strong diagnostic performance, with area under the receiver operating characteristic curve (AUC) values commonly ranging from 0.80 to 0.93 in CRC prediction models. This review integrates current evidence for microbes and metabolite interactions that drive CRC progression and summarizes biomarker studies employing high AUC microbial and metabolite signatures for early detection and patient stratification. We further highlight phytochemicals, including resveratrol, curcumin, and quercetin which mitigate CRC by modulating cyclooxygenase-2 activity, macrophage polarization, inflammatory cytokine signaling, and metabolic pathways, as well as the restoration of beneficial gut microbial communities. These insights support the advancement of microbiome targeted and metabolite informed approaches for CRC risk assessment, diagnosis, and therapeutic development.},
}

@article {pmid42539585,
year = {2026},
author = {Van Damme, KFA and Hertens, P and Sichien, D and Van der Borght, K and Van Moorleghem, J and De Prijck, S and Klarenbeek, A and Louagie, E and Lammens, I and Vanhee, S and Vanhove, C and De Bleser, P and Van Laecke, S and Dendooven, A and Hammad, H and Vereecke, L and Elewaut, D and van Loo, G and Lambrecht, BN},
title = {TNFAIP3/A20 dysfunction drives innate and sterile hyperinflammation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1856810},
doi = {10.3389/fimmu.2026.1856810},
pmid = {42539585},
issn = {1664-3224},
mesh = {Animals ; *Tumor Necrosis Factor alpha-Induced Protein 3/genetics/immunology/metabolism ; *Immunity, Innate ; *Inflammation/immunology/genetics/metabolism ; Mice ; Mice, Transgenic ; Mice, Knockout ; Humans ; Autoantibodies/immunology ; B-Lymphocytes/immunology ; Disease Models, Animal ; },
abstract = {Feedback mechanisms regulate immune activation and prevent excessive tissue damage. TNFAIP3, also known as A20, serves as a crucial brake on inflammation, and mutations or haploinsufficiency of this gene are linked to diseases characterized by inappropriate inflammation. In this study, we document highly conserved patterns of cell type-specific gene expression, regulation, and induction of TNFAIP3, and employ transgenic and gnotobiotic mouse models to investigate how adaptive immunity and the gut microbiome contribute to pathology arising from impaired A20 function. Contrary to our expectations, systemic inflammation resulting from Tnfaip3 deficiency in CD11c (Itgax)-expressing cells developed independently of autoreactive antibodies, B cells, and T cells. The microbiome also proved dispensable for disease manifestations in these models. These findings suggest that in diseases caused by insufficient TNFAIP3/A20 activity, autoantibodies may reflect a downstream consequence of disease rather than a causative driver, suggesting autoinflammatory rather than autoimmune pathology. These insights carry therapeutic implications for the treatment of TNFAIP3-associated diseases.},
}

Animals
*Tumor Necrosis Factor alpha-Induced Protein 3/genetics/immunology/metabolism
*Immunity, Innate
*Inflammation/immunology/genetics/metabolism
Mice
Mice, Transgenic
Mice, Knockout
Humans
Autoantibodies/immunology
B-Lymphocytes/immunology
Disease Models, Animal

@article {pmid42539620,
year = {2026},
author = {Leclercq, L and Kientz, G and Lloret, E and Palaric, C and Taminiau, B and Daube, G and Molinié, R and Fontaine, JX and Mathiron, D and Drider, D and Siah, A and Desprez, B and Cordonnier, M and Hilbert, JL and Lucau-Danila, A},
title = {Root metabolite profiles support a chemical-trophic filtering hypothesis for genotype- and stage-specific rhizosphere assembly in chicory.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1855632},
doi = {10.3389/fmicb.2026.1855632},
pmid = {42539620},
issn = {1664-302X},
abstract = {The rhizosphere is a dynamic interface where plant- and soil-derived factors jointly influence microbial community assembly. In chicory (Cichorium intybus L.), the respective roles of genotype, developmental stage, and root metabolites in structuring rhizosphere communities remain insufficiently understood. This study aimed to characterize patterns of microbial assembly and to assess their associations with root metabolite profiles. Rhizosphere and bulk soil from three chicory genotypes were sampled at two developmental stages and analyzed using bacterial and fungal metabarcoding. Diversity metrics, differential abundance analyses, and literature-based functional annotation were integrated with root metabolite profiling to explore associations between microbial taxa and metabolite profiles. Rhizosphere microbial communities associated with chicory differed from bulk soil and were structured by plant genotype and developmental stage. Lower α-diversity at early stages may reflect the selective enrichment of specific taxa, suggesting non-random assembly. Community variation was associated with root metabolite profiles, including primary metabolites and sesquiterpene lactones (STLs). Across development, the microbiome shifted from taxa linked to nutrient transformation and microbial interactions including Nitratireductor, Sphingomonas, and Serratia, toward communities dominated by saprotrophic and organic matter-degrading taxa such as Streptomyces, Pseudarthrobacter, and Lecanicillium. Genotype-dependent differences further suggested that plant genetic background contributed to rhizosphere assembly patterns. However, these relationships are correlative, and the underlying mechanisms require validation through targeted experimental approaches. The observed correlations led us to propose a hypothesis of temporally structured chemical-trophic filtering, meaning that plant metabolites and soil nutrient conditions jointly contribute to shaping microbial communities in a genotype-dependent manner.},
}

@article {pmid42539659,
year = {2026},
author = {He, Q and Zhang, P and Chen, Z and Wen, C and Wang, M},
title = {Frontier research and clinical application prospects of microbiome biomarkers in autoimmune diseases.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1752840},
doi = {10.3389/fimmu.2026.1752840},
pmid = {42539659},
issn = {1664-3224},
mesh = {Humans ; *Autoimmune Diseases/microbiology/therapy/diagnosis/immunology/etiology ; Biomarkers ; *Microbiota/immunology ; Dysbiosis/immunology ; Animals ; Multiomics ; Precision Medicine ; },
abstract = {The microbiome is increasingly recognized as a master regulator of immune homeostasis and a key environmental factor associated with the pathogenesis of autoimmune diseases (ADs). This review comprehensively synthesizes current knowledge on how microbial communities and their metabolites may contribute to ADs' development through microbial-immune interactions, dysbiosis, and the involvement of viral and fungal components within an integrated inter-kingdom ecosystem. We propose an operational definition of microbiome biomarkers as measurable microbiome-associated features reflecting disease susceptibility, activity, prognosis, or therapeutic response and categorize them into three classes: taxonomic, functional/metabolic, and host-microbiome interaction-derived biomarkers. We critically evaluate the evidence for specific microbial signatures as biomarkers for early diagnosis, disease monitoring, and prediction of therapeutic responses, incorporating evidence grading that distinguishes validated biomarkers from those that remain exploratory and discussing shared versus disease-specific signatures across ADs. The translational potential of microbiome-targeted interventions, including probiotics, prebiotics, and fecal microbiota transplantation, is examined within a personalized medicine framework, with barriers to clinical implementation explicitly addressed. Key confounding factors such as diet, geographic origin, and medication use are highlighted as critical variables shaping microbiome signatures independently of disease. Looking forward, the convergence of multi-omics technologies and artificial intelligence for biomarker discovery, multi-omics integration, and clinical validation promises to unravel the complex microbiome-immune crosstalk, enabling more accurate diagnosis, prognostic stratification, and ultimately, individualized microbiota-informed therapy.},
}

Humans
*Autoimmune Diseases/microbiology/therapy/diagnosis/immunology/etiology
Biomarkers
*Microbiota/immunology
Dysbiosis/immunology
Animals
Multiomics
Precision Medicine

@article {pmid42539707,
year = {2026},
author = {Selvaraj, H and Jayaprakash, V and Kumar, JS and Mathew, GG and Sundaram, K and Prabhu, V},
title = {Altered tryptophan metabolism as a contributor to cognitive impairment in chronic kidney disease: a narrative review.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1872778},
doi = {10.3389/fnins.2026.1872778},
pmid = {42539707},
issn = {1662-4548},
abstract = {Approximately 40% of patients with chronic kidney disease (CKD) experience cognitive impairment (CI), which is strongly associated with increased mortality. CI is driven by multiple factors, including vascular injury, accumulation of uremic toxins, disruption of the blood-brain barrier, and chronic inflammation. Recent evidence suggests that kidney disease and neurocognitive decline are mechanistically linked through dysregulated tryptophan metabolism. Tryptophan is metabolised through three main pathways: the kynurenine, indole, and serotonin pathways, each producing bioactive metabolites with distinct neurophysiological effects. The hallmarks of CKD include chronic inflammation, gut microbial dysbiosis, and impaired renal clearance, all of which alter tryptophan metabolism. Inflammation drives tryptophan metabolism towards the kynurenine pathway, increasing the formation of neurotoxic compounds that promote oxidative stress, excitotoxicity, and neuronal injury. However, reduced availability of tryptophan for serotonin synthesis impairs serotonergic signalling and neurotransmission, as well as melatonin biosynthesis, thereby contributing to circadian rhythm disturbances and impaired glymphatic clearance. Concurrently, gut dysbiosis and reduced renal clearance promote the accumulation of indole-derived uremic toxins, leading to endothelial dysfunction, neuroinflammation, and disruption of the blood-brain barrier. This review highlights the current evidence of dysregulated tryptophan metabolism in CKD and its impact on the pathogenesis of neurocognitive complications. The review also discusses potential biomarkers and therapeutic strategies, including kynurenine pathway inhibitors, gut microbiota modulation, uremic toxin adsorption, melatonin supplementation and personalised medicine to mitigate cognitive impairment in CKD.},
}

@article {pmid42539849,
year = {2026},
author = {Malmin, A and Olsen, MVT and Thomseth, VM and Kjellevold Haugen, IB and Utheim, TP and Forsaa, VA},
title = {Long-term Impact of Intravitreal Injections on the ocular surface; a 2-year follow-up study.},
journal = {Frontiers in ophthalmology},
volume = {6},
number = {},
pages = {1829818},
doi = {10.3389/fopht.2026.1829818},
pmid = {42539849},
issn = {2674-0826},
abstract = {BACKGROUND: Intravitreal injection (IVI) therapy is the most frequently performed intraocular procedure worldwide, with topical povidone-iodine (PVP-I) as the standard pre-injection antiseptic. However, PVP-I has been shown to exert cytotoxic effects on the ocular surface. The purpose of this study was to evaluate the impact of two years of serial anti-vascular endothelial growth factor (VEGF) IVI on ocular surface parameters.

METHODS: Patients with neovascular age-related macular degeneration (nAMD) receiving unilateral intravitreal anti-VEGF injections were examined at two time points, separated by a two-year interval. An aseptic protocol with PVP-I was applied prior to each injection. Tear meniscus height (TMH), bulbar redness (BR), and meibomian gland (MG) loss were assessed using the Oculus Keratograph 5M, with the fellow eye serving as control. For statistical analysis, the related-samples Wilcoxon signed-rank test was applied to non-normally distributed data, and the paired-sample Student's t-test to normally distributed data.

RESULTS: Sixty patients (mean age, 78.6 ± 8.5 years; range, 55-96) were included. Between examinations, patients received a mean of 15.5 ± 6.5 IVI (range, 5-30). A significant increase in mean BR was observed in untreated fellow eyes compared with baseline measurements (1.68 ± 0.47 vs. 1.41 ± 0.46; p < 0.001). At follow-up, BR was significantly higher in fellow eyes than in treated eyes (p < 0.001), and this difference had increased over the study period. Median TMH increased significantly in untreated eyes (0.42 mm [IQR, 0.28-0.57] vs. 0.31 mm [IQR, 0.23-0.47]; p = 0.003), whereas the increase in treated eyes was not significant (p = 0.74). At follow-up, mean TMH did not differ significantly between treated and fellow eyes (p = 0.15). Both treated and untreated eyes showed significant MG loss after two years of serial IVI; however, no significant differences in mean MG loss were detected between eyes in either the upper or lower eyelid at follow-up.

CONCLUSIONS: Eyes receiving repeated intravitreal anti-VEGF injections with preoperative PVP-I antisepsis were significantly less hyperemic than fellow untreated eyes, and this difference increased over two years of continued treatment. Potential mechanisms include a beneficial alteration of the ocular surface microbiome by PVP-I or an antiangiogenic effect of anti-VEGF therapy.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT04458012, identifier NCT04458012.},
}

@article {pmid42539876,
year = {2026},
author = {Singh, R and Asthana, S and Arya, A and Kaushik, M and Khan, M},
title = {The Oral-Brain Axis: Mechanistic Insights Linking Periodontitis With Alzheimer's and Parkinson's Diseases.},
journal = {Cureus},
volume = {18},
number = {6},
pages = {e111856},
doi = {10.7759/cureus.111856},
pmid = {42539876},
issn = {2168-8184},
abstract = {Neurodegenerative diseases, including Alzheimer's disease (AD) and Parkinson's disease (PD), are major causes of disability and mortality worldwide. Emerging evidence suggests that chronic peripheral inflammation and microbial dysbiosis may contribute to neurodegenerative processes. The oral-brain axis has recently gained attention as a biological framework linking oral microbial communities, systemic inflammatory responses, immune regulation, and central nervous system function. Within this context, periodontitis, a prevalent chronic inflammatory disease driven by oral dysbiosis, has been proposed as a potential modifiable risk factor for neurodegeneration. This narrative review examines current evidence supporting the oral-brain axis and its role in the relationship between periodontitis and neurodegenerative disorders. Key mechanisms include systemic dissemination of periodontal pathogens and their virulence factors, persistent inflammatory signaling, blood-brain barrier dysfunction, neuroimmune activation, oxidative stress, and protein aggregation. Particular attention is given to the contribution of Porphyromonas gingivalis and associated virulence factors to neuroinflammation, amyloidogenesis, and neuronal injury. Epidemiological, clinical, and experimental studies linking periodontal disease with cognitive decline, Alzheimer's disease, and Parkinson's disease are also discussed. Current evidence supports a biologically plausible association between periodontal disease and neurodegeneration through interconnected microbial, inflammatory, and vascular pathways. Although causality remains to be established, the oral-brain axis provides valuable insight into potential mechanisms underlying this relationship. Improved understanding of these interactions may facilitate the development of preventive and therapeutic strategies that integrate oral healthcare with approaches aimed at preserving neurological health and reducing the burden of neurodegenerative diseases.},
}

@article {pmid42540270,
year = {2026},
author = {Wu, Q and Li, H and Niu, Y and Li, H and Liu, J and Pan, Y and Li, C and Zhang, S},
title = {Porphyromonas gingivalis sialidase reshapes gut microbiota to affect serum metabolism and splenic immunity: insights from a murine study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2710456},
doi = {10.1080/20002297.2026.2710456},
pmid = {42540270},
issn = {2000-2297},
abstract = {BACKGROUND: Porphyromonas gingivalis (P. gingivalis), a major periodontal pathogen can alter the gut microbial composition, serum metabolites and systemic immune status in mice. However, the role of its sialidase in modulating these parameters remains unexplored.

OBJECTIVE: This study aims to investigate the effects of P. gingivalis sialidase on gut microbiota, serum metabolites and their correlations with systemic immune responses.

DESIGN: C57BL/6 mice were orally inoculated with P. gingivalis W83, its sialidase-deficient ΔPG0352 mutant or PBS twice weekly following antibiotic pretreatment. After 40 days, spleen samples were collected for histological examination and cytokine analysis. Faecal samples were collected for 16S rRNA sequencing, and the serum samples were analysed by untargeted metabolomics.

RESULTS: P. gingivalis W83 group exhibited severe splenic inflammation and higher inflammatory cytokine levels than the other two groups. 16S rRNA gene analysis identified 19 differential bacterial genera (including Staphylococcus and Prevotellaceae_UCG-001) between the P. gingivalis W83 and ∆PG0352 groups. Metabolomics detected 12 key differential metabolites mainly involved in energy metabolism and amino acid biosynthesis pathways. Correlation analysis revealed phosphatidylcholine as a central metabolite, positively correlated with Staphylococcus, Prevotellaceae_UCG-001 and IL-1β, confirming its hub role linking metabolic shifts to immune activation.

CONCLUSIONS: P. gingivalis sialidase exacerbated systemic inflammation by reshaping gut microbiota, driving phosphatidylcholine-centred metabolic reprogramming and amplifying splenic immunity.},
}

@article {pmid42540406,
year = {2026},
author = {Ross, PA and de Jonge, N and Yang, Q and Paris, V and Kristensen, TN and Hoffmann, AA},
title = {Interactions Between Inbreeding, Fitness and the Bacterial Microbiome in Aedes aegypti Mosquitoes.},
journal = {Evolutionary applications},
volume = {19},
number = {8},
pages = {e70308},
doi = {10.1111/eva.70308},
pmid = {42540406},
issn = {1752-4571},
abstract = {Laboratory and field populations of insects can experience a decline in fitness and loss of genetic diversity due to inbreeding depression and genetic drift, respectively. Matings among related individuals and small population size may also influence insect host microbiomes with consequences for fitness. In the dengue vector mosquito, Aedes aegypti, the bacterial microbiome is largely environmentally determined, but recent studies have also revealed host genetic components. We generated a panel of 55 inbred lines from either of two founding outbred populations of Ae. aegypti to test for associations between life history traits, inbreeding, allelic diversity, and microbiome composition using ddRADseq and bacterial 16S rRNA gene sequencing on pools of mosquitoes. Effects of inbreeding were diverse, with severe composite fitness costs in many lines but minimal costs in others despite similar low levels of genetic diversity. We found no strong relationship between major life history traits across inbred lines, suggesting that any costs due to inbreeding were trait specific. Bacterial microbiome analysis of pooled samples from a subset of lines revealed common microbes across lines, with Elizabethkingia, Aeromonas, and Ralstonia being the most abundant. Despite bacterial composition varying widely, there was no clear relationship between microbiome composition and fitness or population origin. However, there were several significant positive correlations between the relative abundance of different microbial taxa across lines. Our results demonstrate diverse impacts of inbreeding on the fitness of mosquito populations but with limited impacts on the microbiome.},
}

@article {pmid42540493,
year = {2026},
author = {Peters, Y and Ferrando, ML and Zhou, C and Morsche, RT and van der Leeden, B and Cremers, R and Le, PD and van Dijk, L and Schrauwen, RWM and Tan, AC and van der Post, RS and van Baarlen, P and Siersema, PD and Boleij, A},
title = {A fermented milk drink containing Lactobacillus casei strain Shirota modulates the esophageal microbiome composition in Barrett's esophagus.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116910},
doi = {10.1016/j.isci.2026.116910},
pmid = {42540493},
issn = {2589-0042},
abstract = {Esophageal adenocarcinoma and its precursor, Barrett's esophagus (BE), are associated with a pro-inflammatory, Gram-negative-dominated esophageal microbiome. In a single-arm pilot study, 23 patients with BE consumed a fermented milk drink containing Lactobacillus casei strain Shirota (LcS) twice daily for 4 weeks, based on the hypothesis that this intervention could shift the microbiome toward a more beneficial Gram-positive profile. Post-intervention, metaplastic columnar epithelium showed a significant increase in Gram-positive Firmicutes (p < 0.01) without changes in overall Eubacterial abundance. DNA-based analyses demonstrated a higher Gram-positive to Gram-negative ratio, with Proteobacteria decreasing from 74% to 52% and Firmicutes increasing from 20% to 31%, including enrichment of Lactobacillus. Microbial diversity increased markedly (p = 9.98 × 10[-7]) in squamous and metaplastic epithelium. Notably, BE-associated taxa Prevotella and Haemophilus also increased in both tissue types. Overall, the intervention shifted the esophageal microbiome toward a more Gram-positive and diverse composition, while highlighting complex ecological effects warranting further investigation.},
}

@article {pmid42540510,
year = {2026},
author = {Solazzo, G and Rovelli, S and Iodice, S and Spinazzé, A and Cavallo, DM and Bollati, V and Ghedin, E and Ferrari, L},
title = {Effects of Seasonality and Air Pollution on the Nasal Microbiota in Healthy Italian Adults.},
journal = {Hygiene and environmental health advances},
volume = {19},
number = {},
pages = {},
doi = {10.1016/j.heha.2026.100189},
pmid = {42540510},
issn = {2773-0492},
abstract = {Air pollution is a major environmental risk factor for respiratory health, yet its interaction with seasonality in shaping the upper airway microbiota remains poorly understood. We conducted a longitudinal repeated-measures study to investigate whether seasonality modulates the effects of indoor and outdoor air pollution on the nasal microbiota of healthy adults. Twenty-six participants were sampled weekly for three weeks in winter and three weeks in summer. Microbial composition was characterized using 16S rRNA gene sequencing (124 samples) and whole-genome shotgun sequencing (141 samples). Weekly exposure to indoor total suspended particles (TSP) and outdoor pollutants (particulate matter, black carbon, benzene, and carbon monoxide) was assessed using environmental monitoring data. The nasal microbiota was stable within seasons but differed significantly between seasons, with winter enrichment of Moraxella species, particularly among women with children. Across seasons, higher pollutant levels were negatively associated with relative abundance of commensal taxa, particularly Corynebacterium species. In addition, this study identified significant season-pollutant interactions. For example, in summer, commensal bacteria (e.g., Staphylococcus epidermidis and Cutibacterium granulosum) were found to be negatively associated with particulate matter exposure. Among host factors, sex explained the largest proportion of variance in microbial diversity, while household characteristics contributed additional compositional variability. These findings indicate that the respiratory microbiome varies across seasons and is associated with air pollution, suggesting that both seasonality and environmental exposures can contribute to differences in respiratory microbial communities.},
}

@article {pmid42540515,
year = {2026},
author = {Azarbad, H and Alizadeh, M},
title = {Seed bacterial microbiota: transmission, community assembly, and prospects for engineering heritable functions in crops.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100647},
doi = {10.1016/j.crmicr.2026.100647},
pmid = {42540515},
issn = {2666-5174},
abstract = {Seeds represent specialized, low-biomass microbial niches that facilitate the transmission of the plant-associated microbiota from one generation to another. Residing as both epiphytes and endophytes, seed-associated bacteria contribute to microbial community assembly during the seed-to-seedling transition. Recent integration of single-seed omics and synthetic bacterial communities has moved the field beyond descriptive surveys to identify the microbial drivers of plant germination success and early-life resilience. Despite this potential, the establishment and persistence of seed-borne bacteria are often constrained by competition with soil-derived microbiota. Seedling bacterial community assembly is further shaped by host genotype, domestication history, and maternal environmental conditions. In this review, we synthesize the mechanisms of bacterial transmission from flowering through seedling emergence and evaluate the functional capacity of the seed holobiont. We define the ecological parameters for the successful recruitment of engineered seed-based consortia into the soil-plant continuum, providing an experimental roadmap to move seed-based technologies from the laboratory to the field. Ensuring the functional stability of these heritable microbial traits will be essential for stabilizing agricultural productivity under increasing climatic volatility.},
}

@article {pmid42540841,
year = {2026},
author = {Wang, J and Bai, L and Leng, N and Yang, Y and Cao, X and Peng, W and Xu, J and Xie, E},
title = {Neuraminidase-Associated Vaginal Dysbiosis Correlates with HPV Infection Across Oncogenic Risk Subtypes.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {614023},
doi = {10.2147/IDR.S614023},
pmid = {42540841},
issn = {1178-6973},
abstract = {BACKGROUND: Human papillomavirus (HPV) infection is a major cause of cervical cancer, and increasing evidence suggests that cervicovaginal microbial dysbiosis may influence HPV susceptibility. This study evaluated the association between microbial enzymatic markers and HPV infection across different risk subtypes.

METHODS: A cross-sectional analysis was conducted in 43,426 women undergoing HPV screening. HPV status and subtype classification (high-, possible-, and low-risk) were determined using standardized genotyping. Clinical and laboratory parameters including age, white blood cells (WBC), red blood cells (RBC), vaginal pH, leukocyte esterase, fungal infection, Trichomonas vaginalis, and microbial enzymatic markers (neuraminidase [NEU], N-acetylglucosaminidase [NAG], β-glucuronidase [GUS], and H2O2), were analysed.

RESULTS: HPV positivity was identified in 20.6% of participants. Neuraminidase emerged as the most consistent independent predictor across all HPV categories (adjusted OR range: 1.437-1.828; p<0.001), indicating a strong association between anaerobic bacterial activity and HPV infection. Age was uniformly associated with increased HPV risk across all models (adjusted OR ≈ 1.014-1.018 per year; p < 0.001). Fungal infection demonstrated a significant protective association (adjusted OR range: 0.636-0.778). Leukocyte esterase and WBC showed selective associations, particularly with high-risk HPV. In contrast, vaginal pH, T. vaginalis, and NAG lost significance after adjustment, suggesting confounding effects. Model explanatory power was modest (pseudo-R[2]: 0.010-0.016).

DISCUSSION: Neuraminidase-associated vaginal dysbiosis is strongly associated with HPV infection across multiple risk subtypes. These findings highlight the potential role of microbial functional biomarkers in understanding cervicovaginal dysbiosis and HPV susceptibility, particularly in populations vulnerable to microbial imbalance and secondary infections.},
}

@article {pmid41430052,
year = {2026},
author = {Kim, SS and Cheong, JY and Eun, JW},
title = {Correspondence to editorial on "Bacteroides eggerthii ameliorates metabolic dysfunction-associated steatotic liver disease through host-microbe signaling and highlights 2-hydroxyisocaproate as a potential effector".},
journal = {Clinical and molecular hepatology},
volume = {32},
number = {3},
pages = {e361-e364},
doi = {10.3350/cmh.2025.1416},
pmid = {41430052},
issn = {2287-285X},
support = {//Korea Health Industry Development Institute/ ; HR21C1003//Ministry of Health and Welfare/ ; RS-2022-NR070489//Ministry of Science and ICT/ ; RS-2024-00422549//Ministry of Science and ICT/ ; RS-2025-00521818//Ministry of Science and ICT/ ; RS-2025-00562556//Ministry of Science and ICT/ ; },
}

@article {pmid42532253,
year = {2026},
author = {Ha, GD and Li, Y and Liu, Q and Shi, H and Zhang, Z and Tian, Z and Wang, Y and Bian, X and Wan, G and Meng, Y and Huang, M and Sankoh, MA and Qiu, T and Li, J and Li, H and Ge, H and Wei, J and Ma, J and Tang, Q and Wu, W},
title = {Gut microbiome associations in male reproductive endocrine-skeletal physiology: a taxonomic-resolution Mendelian randomization study.},
journal = {Molecular and cellular endocrinology},
volume = {},
number = {},
pages = {112878},
doi = {10.1016/j.mce.2026.112878},
pmid = {42532253},
issn = {1872-8057},
abstract = {The gut microbiome is increasingly linked to endocrine physiology, but human evidence that individual microbial traits contribute to male reproductive and skeletal phenotypes remains largely observational. We integrated MiBioGen genus-level and Dutch Microbiome Project species-level microbiome genome-wide association studies with sex-stratified steroid traits, sex hormone-binding globulin (SHBG), and heel estimated bone mineral density (eBMD) in a two-sample Mendelian randomization (MR) screen of 1,204 microbe-outcome tests. The leading male endocrine association linked genetically proxied abundance of the MiBioGen-defined Eubacterium rectale group to greater odds of detectable male estradiol (odds ratio = 1.36; 95% CI, 1.12-1.65; P = 0.00246; eight instruments). This binary endpoint denotes assay detectability above 175 pmol/L, not circulating estradiol concentration. Independent GTEx V10/SuSiE fine-mapping of CYP19A1 expression in subcutaneous adipose provided aromatase-relevant tissue context but did not localize or mediate the microbial association. Complementary associations linked Roseburia hominis with SHBG and Alistipes finegoldii with heel eBMD; the latter was the only study-wide Bonferroni-significant result (P = 6.55 × 10[-8]). A Bifidobacterium longum-female testosterone association attenuated after exclusion of the LCT/MCM6 region, indicating substantial host-diet genetic influence. Across 172 matched genus-species pairs, effect estimates showed little correlation, directional agreement was no better than chance, and no pair shared clumped instruments. These findings nominate the E. rectale group for targeted male endocrine follow-up and show that taxonomic resolution is part of the exposure definition in microbiome MR.},
}

@article {pmid42532353,
year = {2026},
author = {Li, T and Chang, Y and Tang, S and Chen, Y and Li, X and Wang, Y},
title = {The Microbiota-Gut-Brain Axis in Neuropsychiatric Disorders: Mechanisms, Advances, and Clinical Applications.},
journal = {Brain research bulletin},
volume = {},
number = {},
pages = {112062},
doi = {10.1016/j.brainresbull.2026.112062},
pmid = {42532353},
issn = {1873-2747},
abstract = {Neuropsychiatric disorders are increasingly recognized as systemic conditions arising from dynamic interactions within the gut-brain-immune network. The Microbiota-Gut-Brain Axis (MGBA) serves as a central regulatory system orchestrating neurodevelopment, neural homeostasis, and immune-metabolic balance. This review summarizes evidence across seven major neuropsychiatric disorders, Depression, Autism Spectrum Disorder, Attention-Deficit/Hyperactivity Disorder, Alzheimer's disease, Schizophrenia, Anxiety and Obsessive Compulsive Disorder, demonstrating that dysregulation of the MGBA constitutes a shared pathological mechanism. On this common basis, we delineate disorder specific neurochemical and immunological features and highlight the clinical potential of microbiota-targeted interventions. Moreover, psychotropic medications profoundly alter microbial physiology, influencing bacterial growth and metabolism, thereby complicating interpretation of MGBA-disease relationships. Future research should define strain-specific therapeutic actions and integrate multi-omics approaches to unravel causal pathways, ultimately enabling precision microbiome modulation in neuropsychiatric medicine.},
}

@article {pmid42532542,
year = {2026},
author = {Yang, JM and Yuan, ML and Zhang, YY and Chen, Y and Qu, X},
title = {[Research progress on the bidirectional relationship between oral infectious diseases and mental health issues].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {8},
pages = {1243-1250},
doi = {10.3760/cma.j.cn112144-20251031-00437},
pmid = {42532542},
issn = {1002-0098},
support = {72374146//National Natural Science Foundation of China/ ; },
abstract = {Infectious oral diseases represent the most prevalent categories of oral conditions, including dental caries, periodontitis, periapical lesions, and pericoronitis. Their bidirectional relationship with mental health has emerged as a critical interdisciplinary research frontier. This paper integrates epidemiological findings and molecular mechanism evidence to analyze the significant comorbidity and correlation characteristics between infectious oral diseases such as caries and periodontitis, and psychological disorders including depression and anxiety. Oral diseases not only directly impair mental well-being through pain, functional impairment, and social anxiety, but also induce systemic inflammatory responses that disrupt the blood-brain barrier, activate microglia, and alter neurotransmitter metabolism, thereby contributing to functional dysregulation within emotional regulatory centers. The dysbiosis of the oral microbiota caused by infectious oral diseases plays a central role in the vicious cycle of "oral infection-mental health disorders" through the"oral-gut-brain axis", inflammation-mediated neuroimmune cascades, and hypothalamic-pituitary-adrenal axis dysregulation. Meanwhile, mental disorders exacerbate oral microbial imbalance and tissue destruction through poor oral hygiene behaviors, xerostomia induced by psychotropic medications, and stress-related neuroendocrine alterations. This paper advocates for synergistically integrate oral clinical interventions with mental health improvement strategies, and for the development of microbiome-targeted precision modulation approaches. It further proposes an integrated health management paradigm that bridges dentistry and psychiatry, providing both theoretical foundations and practical pathways to transcend traditional disciplinary boundaries and achieve holistic oral-mental co-management.},
}

@article {pmid42532766,
year = {2026},
author = {Wang, L and Zhang, L and Rillig, MC and van der Heijden, MGA and Johnson, NC and Feng, G},
title = {Arbuscular mycorrhizal fungi orchestrate belowground microbiomes in plant holobionts.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.07.003},
pmid = {42532766},
issn = {1878-4372},
abstract = {The traditional model of plant-arbuscular mycorrhizal (AM) fungal coevolution, based solely on interactions between plants and AM fungi, became obsolete with the discovery of the critical roles that belowground microbiomes play in the function of mycorrhizal symbiosis. Based on insights into hyphosphere microbiota, we expand the plant-AM fungus-bacterium continuum into a multipartite AM fungal-orchestrated holobiont (H-AMF) framework, where AM fungi integrate plant roots with soil microbiota into a cross-kingdom ecological unit. A division of labor exists among plants, AM fungi, and hyphosphere microbes in the mycocentric H-AMF perspective. We summarize mechanisms by which AM fungi sustain cooperative relationships with plants and hyphosphere microbiota and propose holobiont-scale methodologies to advance understanding of plant-fungal-microbial interactions and their ecological functions.},
}

@article {pmid42532775,
year = {2026},
author = {Nealon, NJ},
title = {Next-Generation Sequencing in Companion Animal Practice for Infectious Disease Diagnostics and Characterizing Normal Microbiomes.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cvsm.2026.06.005},
pmid = {42532775},
issn = {1878-1306},
abstract = {The purpose of this article is to review and compare the most common and emergent next-generation sequencing methodologies used in small animal veterinary practice, with a focus on their applications to bacterial diagnostics and assessment of the healthy gut microbiome. These methodologies include whole genome sequencing, amplicon sequencing, shotgun metagenomic sequencing, and transcriptomics. Understanding the benefits and limitations of each methodology will help small animal practitioners to make informed decisions for their patients and maximize the utility of each test as part of a complete patient health assessment.},
}

@article {pmid42533020,
year = {2026},
author = {Cho, MY and Eom, JH and Kim, JW and Kim, YW and Hwang, J and Lee, D and Kim, YY and Kim, HS and Hwang, I},
title = {Site-specific oral microbiome profiles in healthy young Korean women.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42533020},
issn = {2045-2322},
support = {2024ER050700//Korea National Institute of Health/ ; },
mesh = {Humans ; Female ; *Microbiota/genetics ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; *Bacteria/genetics/classification ; Dental Plaque/microbiology ; Tongue/microbiology ; Adult ; Young Adult ; },
abstract = {We characterized site-specific organization of the oral microbiome in 59 healthy, non-smoking women in their twenties using 16S rRNA (V3-V4) sequencing of dental plaque (DQ), mouthwash (MW), and tongue coating (TC) samples (177 libraries; rarefied to 29,853 reads). The order of alpha diversity was DQ > MW > TC (p < 0.001), with mean Observed Features of 227.6, 208.7, and 142.4, respectively, consistent with differences in local niche structure within the oral cavity. Beta diversity (Bray-Curtis; weighted/unweighted UniFrac) showed clear separation by site (PERMANOVA overall p < 0.001), with DQ most distinct from MW and TC. At the phylum level, DQ was enriched for Actinobacteriota and Proteobacteria, whereas Firmicutes predominated in MW and TC, indicating compositional shifts across oral microenvironments. Dominant genera included Streptococcus (20.6%), Neisseria (11.7%), Haemophilus (10.1%), Prevotella (7.1%), Veillonella (6.0%), Rothia (5.1%), and Lactobacillus (4.4%). Site-associated taxa included Cardiobacterium, Corynebacterium, and Campylobacter in DQ; Actinobacillus in MW; and Absconditabacteriales (SR1) and Lactobacillus in TC. TC exhibited the lowest alpha diversity but the highest genus richness (n = 340), indicating an uneven community with many low-abundance taxa. LEfSe identified discriminant taxa, including Rothia, Actinomyces, Fusobacterium (DQ), Streptococcus, and Gemella (MW); and Lactobacillus, Prevotella, Veillonella, and Haemophilus (TC). These results demonstrate pronounced site specificity within the oral cavity of a well-defined healthy cohort and indicate that multi-site resolution is essential for advancing mechanistic and translational oral microbiome research.},
}

Humans
Female
*Microbiota/genetics
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Republic of Korea
*Bacteria/genetics/classification
Dental Plaque/microbiology
Tongue/microbiology
Adult
Young Adult

@article {pmid42533069,
year = {2026},
author = {Kramer, D and Santos Rocha, C and Gaulke, CA and Nearing, M and Sankaran-Walters, S and Loque, I and Kidigannappa, A and Pham, E and Hu, S and Wanakumjorn, P and Abbattista, R and Dandekar, A and Faller, R and Dandekar, S},
title = {Microbiota-derived 10-hydroxystearic acid activates PPARα to restore gut epithelial barrier integrity and enhance anti-retroviral therapy.},
journal = {Nature microbiology},
volume = {11},
number = {8},
pages = {2365-2383},
pmid = {42533069},
issn = {2058-5276},
support = {R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI123105//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32 AI060555/AI/NIAID NIH HHS/United States ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R37 AI 153025//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P51 OD011107/CD/ODCDC CDC HHS/United States ; },
mesh = {Animals ; *PPAR alpha/metabolism/genetics ; Humans ; Intestinal Barrier Function ; *Intestinal Mucosa/drug effects/metabolism ; Epithelial Cells/drug effects/metabolism ; HIV Infections/drug therapy ; *Gastrointestinal Microbiome ; Lipid Metabolism/drug effects ; *Anti-Retroviral Agents/therapeutic use/pharmacology ; Macaca mulatta ; Simian Immunodeficiency Virus/drug effects ; Disease Models, Animal ; },
abstract = {HIV infection disrupts gut epithelial barrier integrity and mucosal immunity, driving chronic inflammation and disease progression which are not fully resolved despite anti-retroviral therapy. Here we identify the microbiota-derived octadecanoid-hydroxy-fatty-acid metabolite 10-hydroxystearic acid (10-HSA), produced by Lactiplantibacillus plantarum, as a key mediator of gut epithelial barrier repair in human intestinal epithelial cells in vitro, ex vivo and in the non-human primate model of HIV/AIDS. X-ray crystallography and transcriptomics combined with functional analyses revealed that 10-HSA directly binds PPARα, inducing lipid metabolism, mitochondrial regeneration and subsequent epigenetic histone crotonylation, thereby promoting gut epithelial renewal. Co-administration of 10-HSA with anti-retroviral therapy in SIV-infected macaques accelerated viral suppression, resolved systemic inflammation, repaired gut epithelial integrity and recovered the gut microbiota. These findings identify a microbiota-derived lipid metabolite-PPARα-histone crotonylation axis that activates gut epithelial regeneration. This study defines a host-microbiome metabolic pathway that restores epithelial-immune homeostasis and enhances the efficacy of anti-retroviral therapy.},
}

Animals
*PPAR alpha/metabolism/genetics
Humans
Intestinal Barrier Function
*Intestinal Mucosa/drug effects/metabolism
Epithelial Cells/drug effects/metabolism
HIV Infections/drug therapy
*Gastrointestinal Microbiome
Lipid Metabolism/drug effects
*Anti-Retroviral Agents/therapeutic use/pharmacology
Macaca mulatta
Simian Immunodeficiency Virus/drug effects
Disease Models, Animal

@article {pmid42533119,
year = {2026},
author = {Lalhmunsangi, J and Sudharsan, R and Laldinmawii, G and Lalngaihzuali, R and Das, M and Das, S and Mukherjee, S and Bhattacharyya, S and Ramamurthy, T and Roychoudhury, P and Akter, F and Mukhopadhyay, A and Roy, A and Kesavan, M and Senthil Kumar, N and Roy, S and Dutta, T},
title = {Comparative microbiome profiling of plant- and animal-derived traditional fermented foods from Mizoram, India using full-length 16S rRNA sequencing.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {8},
pages = {},
pmid = {42533119},
issn = {1572-9699},
support = {Order No. ER/FBS/Phase-II/2023/DR/MD(Part-C) [e-177060]//Indian Council of Medical Research/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; India ; Animals ; *Fermented Foods/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Fermentation ; Phylogeny ; Food Microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Plants/microbiology ; },
abstract = {Traditional fermented foods represent complex microbial ecosystems shaped by substrate composition, indigenous processing practices, and local environmental conditions. However, the microbiomes of many traditional fermented foods from Northeast India remain poorly characterized. In this study, the bacterial communities associated with thirteen traditional fermented foods from Mizoram, India, representing both plant- and animal-derived fermentations, were characterized using full-length 16S rRNA gene sequencing on the Oxford Nanopore platform. Sequencing generated approximately 1.94 million high-quality reads, enabling high-resolution taxonomic profiling of the fermented food microbiomes. The microbial communities were predominantly composed of Bacillota, Pseudomonadota, and Cyanobacteriota, although their relative abundances varied considerably among fermented food types. Plant-derived fermented foods were enriched with fermentative bacterial genera, including Bacillus, Lactobacillus, Lacticaseibacillus, Pediococcus, and Weissella, whereas animal-derived fermented foods showed a greater abundance of anaerobic taxa, particularly Clostridium. Alpha diversity analyses demonstrated higher microbial richness in plant-derived fermented foods, while beta diversity revealed clear substrate-dependent clustering of microbial communities. Functional prediction indicated that metabolism-related pathways, particularly carbohydrate and amino acid metabolism, predominated across the fermented food microbiomes, and LEfSe analysis identified distinct microbial biomarkers associated with plant- and animal-derived fermentations. Collectively, these findings provide the first comprehensive microbiome characterization of traditional fermented foods from Mizoram and demonstrate that fermentation substrate is a major determinant of microbial community composition and predicted functional potential. Although full-length 16S rRNA gene sequencing improved taxonomic resolution, taxonomic interpretations were made cautiously at the genus level where appropriate because of the inherent limitations of 16S rRNA gene-based classification.},
}

*RNA, Ribosomal, 16S/genetics
India
Animals
*Fermented Foods/microbiology
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Fermentation
Phylogeny
Food Microbiology
DNA, Bacterial/genetics
Sequence Analysis, DNA
Plants/microbiology

@article {pmid42533345,
year = {2026},
author = {Devasahayam, BRF and McNeil, T and Wubet, T and Schmutzer, T},
title = {Nanopore sequencing reveals coordinated host and microbiome responses across barley genotypes.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {},
pmid = {42533345},
issn = {1741-7007},
mesh = {*Hordeum/genetics/microbiology ; *Microbiota/genetics ; *Genotype ; Nanopore Sequencing ; Rhizosphere ; Plant Roots/microbiology/genetics ; Metagenome ; Metagenomics ; Transcriptome ; },
abstract = {BACKGROUND: Barley (Hordeum vulgare L.) provides a suitable model for studying domestication-driven plant-microbiome interactions. Although wild, landrace, and modern genotypes host distinct rhizosphere communities, the extent to which roots and microbes reciprocally influence each other remains unclear. Here, we applied an integrated multi-omics approach combining long-read metagenomics, root transcriptomics, and plant genomics to understand genotype-specific host-microbiome coordination.

RESULTS: Oxford Nanopore whole metagenome sequencing (WMS) revealed genotype-associated shifts in rhizosphere communities across seasons. Functional profiling showed a conserved metabolic backbone including amino acid metabolism, energy production, and secondary metabolite biosynthesis, alongside genotype-dependent variation in carbohydrate metabolism and transport-associated pathways. Genome-resolved analysis through metagenome-assembled genomes (MAGs) further detailed the taxonomic and functional architecture of key rhizosphere lineages. Root transcriptome profiling identified extensive differential expression associated with microbial perception, signaling, defense, and metabolic processes. Integration of host and microbiome data revealed coordinated molecular patterns, indicating that barley genotypes are associated with distinct microbial assemblages and corresponding transcriptional responses.

CONCLUSIONS: These findings indicate that domestication has shaped coordinated associations between barley genotypes and their rhizosphere microbiomes, reflected in both microbial community composition and host transcriptional regulation. This work provides new insights into the evolutionary tuning of plant-microbiome relationships and highlights opportunities for microbiome-informed strategies in barley improvement.},
}

*Hordeum/genetics/microbiology
*Microbiota/genetics
*Genotype
Nanopore Sequencing
Rhizosphere
Plant Roots/microbiology/genetics
Metagenome
Metagenomics
Transcriptome

@article {pmid42533363,
year = {2026},
author = {Weingarden, AR and Dahlberg, FS and Broude, CN and Meng, X and Jain, S and Weakley, AM and Cabrera, AV and Dileepan, T and Fischbach, MA and Jenkins, MK},
title = {Gut microbial composition modulates endogenous food-specific CD4+ T cells in food allergy.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {215},
number = {7},
pages = {},
doi = {10.1093/jimmun/vkag172},
pmid = {42533363},
issn = {1550-6606},
support = {R01AI187164//National Institute of Allergy and Infectious Diseases (NIAID)/ ; //Life Science Research Foundation postdoctoral fellowship and Open Philanthropy/ ; },
mesh = {Animals ; *Food Hypersensitivity/immunology/microbiology ; Mice ; *Gastrointestinal Microbiome/immunology ; Allergens/immunology ; *T-Lymphocytes, Regulatory/immunology ; *CD4-Positive T-Lymphocytes/immunology ; Female ; Th2 Cells/immunology ; Disease Models, Animal ; },
abstract = {The growing food allergy epidemic is thought to be related to changing environmental factors, particularly changes in the gut microbiome. While prior work has demonstrated that food allergy can be modulated by gut microbes, little is known about how food allergen-specific CD4+ T cells are affected by gut microbial composition. Here, we report that food allergy severity differs between mice obtained from 2 different specific pathogen-free mouse vendors (Jackson Labs [Jax] and Taconic Biosciences [Tac]). Mice from Tac develop diarrhea and anaphylaxis after fewer allergen exposures than mice from Jax. Using food allergen peptide: MHCII tetramers, we also find that Tac mice have fewer allergen-specific regulatory T cells in the small intestine compared to mice from Jax with concomitant increase in allergen-specific Th2 cells. In addition, Tac mice have increased intestinal permeability. Increased food allergy severity, phenotype of allergen-specific T cells, and increased gut permeability were transferable to Jax animals via co-housing, which corresponded to a shift in Jax microbial communities towards those found in Tac mice. Our findings demonstrate that food allergen-specific Treg cells can be modulated by gut microbial community composition, which in turn is correlated to food allergy severity.},
}

Animals
*Food Hypersensitivity/immunology/microbiology
Mice
*Gastrointestinal Microbiome/immunology
Allergens/immunology
*T-Lymphocytes, Regulatory/immunology
*CD4-Positive T-Lymphocytes/immunology
Female
Th2 Cells/immunology
Disease Models, Animal

@article {pmid42533399,
year = {2026},
author = {Simeoni, S and Ponziani, FR and Gasbarrini, G and Gasbarrini, A and Ianiro, G},
title = {Letter: The Microbiome-Mediated Impact of Proton Pump Inhibitors on Spontaneous Bacterial Peritonitis.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70883},
pmid = {42533399},
issn = {1365-2036},
}

@article {pmid42533584,
year = {2026},
author = {He, LW and Tang, RX and Liu, SY and Zhang, ZJ and Li, Y and Wang, XM and Yue, BS and Fan, ZX},
title = {Host phylogeny and diet shape gut microbiome and virome in wild small mammals of Gongga Mountain, China.},
journal = {Zoological research},
volume = {47},
number = {4},
pages = {1332-1352},
doi = {10.24272/j.issn.2095-8137.2025.448},
pmid = {42533584},
issn = {2095-8137},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; *Virome ; *Diet/veterinary ; China ; *Rodentia ; *Mammals/virology ; },
abstract = {Gut microbiotas play pivotal roles in host adaptation, yet their composition and function in high-altitude small mammals remain poorly characterized. This study investigated how host phylogeny (order-level) and dietary habits shape the gut microbiome and virome of three mammalian orders (Eulipotyphla, Rodentia, Lagomorpha) in Gongga Mountain, a biodiversity hotspot on the Qinghai-Xizang Plateau. Metagenomic sequencing of 219 samples from 22 species revealed order-specific microbial signatures: Eulipotyphla (carnivorous) harbored higher abundances of potential pathogens (e.g., Helicobacter, Hafnia) and Retroviridae; Lagomorpha (herbivorous) was enriched in cellulolytic bacteria (e.g., Lachnospiraceae, Prevotella) and carbohydrate-active enzymes (CAZymes); Rodentia (omnivorous) showed intermediate traits. We reconstructed 1 385 high-quality metagenome-assembled genomes (MAGs), 1 328 representing novel species, and identified 749 viral operational taxonomic units (vOTUs), >80% being Caudoviricetes. Crucially, Retroviridae abundance in Eulipotyphla suggests zoonotic risk. Phage-host network analysis indicated Caudoviricetes regulates cellulolytic bacteria in Lagomorpha. Host phylogeny and diet jointly drive gut microbiome divergence in small mammals. We establish the first gut microbiome and virome resource of small mammals in the high-altitude area of Gongga Mountain, highlighting Eulipotyphla as a potential vector for zoonotic pathogens.},
}

Animals
*Gastrointestinal Microbiome
*Phylogeny
*Virome
*Diet/veterinary
China
*Rodentia
*Mammals/virology

@article {pmid42533623,
year = {2026},
author = {Kerns, KA and Naumann, AA and Soon, LY and Hendrickson, EL and Barbour, A and Chen, D and Trivedi, HM and Glogauer, M and McLean, JS},
title = {Zinc-stabilized stannous fluoride modulates the periodontal microbiome, reducing Fusobacteria, key Gram-negative species, and overall inflammation within an experimental gingivitis clinical trial.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70168},
pmid = {42533623},
issn = {1943-3670},
abstract = {BACKGROUND: This study aimed to evaluate the effects of a dentifrice containing stannous fluoride stabilized with zinc phosphate on subgingival microbiome composition and clinical inflammation during experimental gingivitis, compared with a sodium fluoride control.

METHODS: This investigation was conducted as a secondary analysis of a randomized, parallel-arm, double-blind, controlled clinical trial. Clinical resolution of experimental gingivitis was assessed using bleeding on probing, gingival index, and plaque index. Deeply sequenced subgingival plaque metagenomic data were analyzed to compare microbial composition and functional potential between a stannous fluoride stabilized with zinc phosphate dentifrice (test) and a sodium fluoride dentifrice (control) over a 21-day experimental gingivitis period.

RESULTS: Use of the stannous fluoride stabilized with zinc phosphate dentifrice was associated with depletion of periodontal disease-associated Gram-negative bacteria, including Fusobacterium nucleatum and multiple Porphyromonas and Prevotella species. This reduction in Gram-negative taxa corresponded with shifts in microbial community metabolic functions and was associated with significantly reduced clinical inflammation compared with the control over the 21-day period.

CONCLUSIONS: Short-term use of stannous fluoride stabilized with zinc phosphate may provide additional protection against gingival inflammation by limiting the outgrowth of key periodontal pathogens, including the bridging organism Fusobacterium nucleatum, and by altering plaque functional capacity. These effects were associated with improved periodontal health outcomes compared with a standard sodium fluoride dentifrice.

PLAIN LANGUAGE SUMMARY: In this study, we analyzed bacteria within the periodontal pocket using deep metagenomic sequencing to better resolve bacterial species and their functions. Results from this study show that using a toothpaste containing stannous fluoride stabilized with zinc phosphate was associated with the reduction of several important Gram-negative bacteria associated with periodontal disease, including Fusobacterium nucleatum and species of Porphyromonas and Prevotella compared with a control toothpaste. These bacteria are well‑known contributors to gingival inflammation and biofilm maturation. When levels of these specific bacteria decreased within the stannous fluoride treatment group, the overall subgingival microbiome shifted which notably persisted during the subsequent 21-day oral hygiene abstention period in this experimental gingivitis model - resulting in significantly lower clinical inflammation. Our findings suggest that even short‑term use of stannous fluoride stabilized with zinc phosphate may provide added protection against early gingival inflammation. Notably, stannous fluoride stabilized with zinc phosphate appears to limit the growth of key periodontal pathogens-particularly Fusobacterium nucleatum, an important bridging organism in subgingival biofilms-and may alter the functional activity of dental plaque in ways that support improved periodontal health when compared with a standard sodium fluoride toothpaste.},
}

@article {pmid42534264,
year = {2026},
author = {Adam, A and Khan, R and Lu, B and Lin, T and Liao, H and Peng, L},
title = {Bacillus thuringiensis and nucleopolyhedrovirus combination against Spodoptera litura alters the cigar tobacco leaves microbiome during air curing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1855531},
pmid = {42534264},
issn = {1664-302X},
abstract = {INTRODUCTION: Spodoptera litura continues feeding on cigar tobacco leaves during air curing, causing substantial economic losses. This study evaluated the synergistic efficacy of a Bacillus thuringiensis (Bt) and nucleopolyhedrovirus (NPV) combination for controlling Spodoptera litura and investigated its effects on the bacterial and fungal microbiomes of cigar tobacco leaves during air curing.

METHODS: Laboratory bioassays were conducted to determine the optimal Bt:NPV ratio and evaluate the synergistic toxicity. The selected formulation was subsequently validated under field conditions. Cigar tobacco leaves treated with the optimal Bt-NPV mixture were air-cured for 23 days, after which bacterial (16s rRNA) and fungal (ITS) communities were characterized using Illumina NovaSeq high-throughput sequencing.

RESULTS: The Bt:NPV mixture at a 4:1 ratio exhibited the strongest synergistic activity against second-instar Spodoptera litura, with an LC50 of 0.64 ml L[-1] and a co-toxicity coefficient of 153.8. Bt-NPV treatment significantly altered the leaf microbiomes by reducing microbial richness while increasing microbial diversity and evenness. Compared with the control, treated leaves showed increased relative abundances of Pantoea, Pseudomonas, and Eurotiales, together with reduced abundances of Staphylococcus and Cladosporiales. These findings demonstrate that Bt-NPV treatment effectively controlled Spodoptera litura while reshaping bacterial and fungal community composition during air curing.

DISCUSSION: The synergistic Bt-NPV formulation represents an effective and environmentally friendly strategy for controlling Spodoptera litura during air curing while promoting an ecological framework that may support leaf preservation. However, the direct effects of Bt-NPV-induced microbiome changes on cigar tobacco quality, aroma development, and chemical maturation were not evaluated and should be investigated through integrated chemical, metabolomic, and sensory analyses in future studies.},
}

@article {pmid42534357,
year = {2026},
author = {Tania, MNT and Sabrin, MS and Mannan, MA and Islam, MM and Hossain, MT and Rahman, MH and Islam, MR and Sultana, S and Hossain, MS and Islam, M},
title = {Comparative 16S rRNA Gene Amplicon Sequencing of the Fecal Microbiome in Pet Dogs and Cats of Different Breeds in Dhaka City, Bangladesh: With Preliminary Insights Into Zoonotic Relevance.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {8738439},
pmid = {42534357},
issn = {1687-918X},
abstract = {Dogs and cats are the most commonly kept pets, and the popularity of different breeds of them continues to increase in Dhaka City, Bangladesh. Pets naturally harbor a diverse gut microbiome that plays a significant role in digestion, immunity, and overall health. Although pets provide valuable companionship, their feces may occasionally harbor bacteria with zoonotic potential. However, little is known about the fecal microbial diversity and its zoonotic relevance in Bangladesh. This study investigated the diversity of pets' fecal microbiome using 16S rRNA metagenomics and explored the zoonotic bacterial taxa. Fecal samples were collected from 24 apparently healthy pets, including 12 dogs and 12 cats, from randomly selected households in Dhaka City. High-throughput sequencing revealed a diverse microbial community comprising 1,148 amplicon sequence variants (ASVs) distributed across 20 phyla and 258 genera. Although cats showed slightly higher microbial richness and diversity, both species shared common bacterial phyla such as Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Relative abundance of bacterial taxa varied between pet species and among breeds rather than the presence of distinct microbial groups. Furthermore, Enterococcus cecorum, Schaalia canis, Campylobacter helveticus, and Sutterella wadsworthensis were the explored bacterial taxa with zoonotic relevance rather than a direct assessment of zoonotic risk; however, they were very low in number than the dominating bacteria. This study provides the first 16S rRNA-based metagenomic snapshot of the fecal microbiome of 24 urban pets in Bangladesh and highlights the need for routine microbial surveillance and public awareness about zoonoses.},
}

@article {pmid42534410,
year = {2026},
author = {Menon, A and Morelli, MK and Hulec, H},
title = {Wohlfahrtiimonas chitiniclastica Bacteremia Associated With Maggot-Infested Ulcers and Tumor Lysis Syndrome in Ohio, USA: A Case Report.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {6760136},
pmid = {42534410},
issn = {2090-6625},
abstract = {BACKGROUND: Wohlfahrtiimonas chitiniclastica is an emerging Gram-negative bacillus historically linked to larvae of the parasitic fly Wohlfahrtia magnifica. Although most human infections have been reported in Europe and Asia, cases are increasingly recognized in North America.

CASE SUMMARY: A 74-year-old man from Ohio presented with sepsis and maggot-infested decubitus ulcers. Blood cultures grew Gram-negative, oxidase-positive rods that could not be identified at the home institution. The isolate was referred to an outside hospital, where it was initially misidentified as Edwardsiella species before definitive identification as W. chitiniclastica by MALDI-TOF MS (Bruker MALDI Biotyper), confirmed by supplementary biochemical testing, 6 days after the initial culture draw. Additional testing identified the rare anaerobe Tissierella praeacuta. Blood cultures at the home institution also identified Proteus mirabilis and Staphylococcus aureus. The clinical course was complicated by metastatic cancer and spontaneous tumor lysis syndrome (uric acid 14.6 mg/dL, LDH 2157 U/L) that improved following rasburicase therapy. The patient received empiric intravenous piperacillin-tazobactam for approximately 24 days, followed by de-escalation to ceftriaxone. Follow-up blood cultures were sterile. Goals of care were transitioned to palliation, and the patient died on hospital day 30.

CONCLUSION: This case illustrates W. chitiniclastica bacteremia in Ohio, USA, and highlights diagnostic challenges including initial misidentification by conventional methods, the importance of MALDI-TOF MS for definitive identification, and possible vector adaptation to regional muscid fly species. The coisolation of T. praeacuta underscores the complex wound microbiome associated with chronic neglected ulcers.},
}

@article {pmid42534443,
year = {2026},
author = {Niu, D and Pang, H and Wang, X and Song, L and Zhang, J and Terry, A and Li, J and Cao, J and Liu, Q and Han, D and Wang, J and Kim, JG and Ataku, K and Bureenok, S and Tan, Z and Bai, F and Shao, T and Huhe, T and Wang, L and Han, P and Xu, C and Yang, F and Cai, Y},
title = {Beyond omics: From descriptive profiling to causal and scalable design of fermentation microbiomes.},
journal = {iMeta},
volume = {},
number = {},
pages = {e70161},
pmid = {42534443},
issn = {2770-596X},
abstract = {Fermentation microbiomes play essential roles in food production, feed preservation, waste valorization, and diverse sustainable industrial processes. Although multi-omics and systems biology have substantially advanced our understanding of their assembly, interactions, and functional dynamics, industrial translation remains constrained by fragmented datasets, limited causal validation, and transport constraints during scale-up. Large language models act as upper-level knowledge and workflow orchestrators, accelerating data integration, hybrid AI-mechanistic modeling, hypothesis generation, and perturbation-guided learning. Collectively, these advances enable fermentation microbiome research to move beyond descriptive omics toward mechanism-guided synthetic microbial community design, causal validation, and scalable biomanufacturing.},
}

@article {pmid42534462,
year = {2026},
author = {Ren, G and Feng, Z and Wang, X and He, J and Yu, Z and Cao, L},
title = {Knowledge mapping and bibliometric analysis of metabolic phenotypes in childhood and adolescent obesity: research hotspots and emerging trends from 2000 to 2026.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1907434},
pmid = {42534462},
issn = {2296-2565},
mesh = {Humans ; *Bibliometrics ; Phenotype ; Adolescent ; *Pediatric Obesity/epidemiology/metabolism ; Child ; },
abstract = {BACKGROUND: Childhood and adolescent obesity is increasingly understood as a heterogeneous condition in which excess adiposity may be accompanied by distinct cardiometabolic phenotypes. Metabolically healthy obesity and metabolically unhealthy obesity have become important concepts for risk stratification, but the overall knowledge structure and emerging research directions in this field remain insufficiently mapped.

METHODS: Records on metabolic phenotypes in childhood and adolescent obesity published between 1 January 2000 and 20 February 2026 were retrieved from the Web of Science Core Collection and PubMed on 20 February 2026. English-language articles and reviews were independently screened by two researchers. After database merging, deduplication and data cleaning, 4,963 records were retained for bibliometric analysis, including 4,384 WoSCC-retained records and 579 PubMed-only records. CiteSpace 6.4. R1, VOSviewer 1.6.20, R 4.5.2 and bibliometrix 5.4.1 were used to analyze annual publication trends, country and institutional collaboration, author and reference co-citation, keyword co-occurrence, clustering and burst terms. Citation-dependent analyses were based on WoSCC-retained records with complete cited-reference metadata.

RESULTS: Publication output increased overall and showed three broad phases: an initial phase centered on BMI criteria, obesity prevalence and metabolic syndrome recognition; a rapid growth phase associated with insulin resistance, glucose-lipid abnormalities and metabolic heterogeneity; and a recent consolidation phase emphasizing phenotype transition, gut microbiota, non-alcoholic fatty liver disease, physical activity, cardiometabolic health and precision intervention. The United States, Spain, China and England were leading contributors, although cross-regional collaboration remained uneven. Co-cited references, author networks and keyword clusters indicated that the field has moved from weight-based classification toward integrated cardiometabolic risk identification, with emerging attention to central adiposity, visceral fat, microbiome-related mechanisms and phenotype-guided management.

CONCLUSION: Research on metabolic phenotypes in childhood and adolescent obesity is shifting from BMI-centered description toward risk-stratified interpretation of metabolic heterogeneity. Future studies should harmonize pediatric phenotype definitions, strengthen multicenter longitudinal cohorts and integrate body composition, fat distribution, insulin sensitivity, liver fat, inflammatory markers, lifestyle exposure and gut microbiota to support early identification and precision prevention of cardiometabolic risk.},
}

Humans
*Bibliometrics
Phenotype
Adolescent
*Pediatric Obesity/epidemiology/metabolism
Child

@article {pmid42534689,
year = {2026},
author = {Li, Z and Wang, J and Hong, Z and Li, M and Liu, T and Wang, Y and Men, L},
title = {Mechanistic and clinical investigation of Jiajiang Xuming decoction in multi-modal programmed cell death in stroke-associated pneumonia.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1889833},
pmid = {42534689},
issn = {2296-634X},
abstract = {BACKGROUND: Stroke-Associated Pneumonia (SAP) is one of the leading causes of sepsis and ICU mortality among stroke patients, attributed to dysregulated immune responses as well as multiple MODES of cell death. Jiajiang Xuming Decoction (JXD) is a traditional Chinese medicine (TCM) formula to treat the symptoms of Wind-Phlegm-Stasis Obstruction Syndrome, blamed for all SAP-related sepsis.

METHODS: A single-centre retrospective cohort study was conducted in 100 ICU patients with microbiologically confirmed sepsis (Sepsis-3 criteria): 58 Stroke-Associated Pneumonia (SAP) and 42 non-SAP sepsis, compared to thirty healthy controls. On admission, Day 3 and Day 7, serial inflammatory markers (IL-6, IL-1β, TNF-α PCT CRP) and organ-function indicators were measured (hepatic: ALT AST; renal: creatinine (BUN); cardiac: cTnI† NT-proBNP). Therapeutic efficacy of JXD was evaluated in a propensity-score-matched (JXD n = 29; conventional treatment n = 29) sub-cohort. Mechanistic evidence were derived from scRNA-seq and an in vitro LPS + OGD cell model as well as ferroptosis characterisation (GEO: GSM5319987).

RESULTS: Compared to non-SAP sepsis, SAP patients had significantly higher levels of inflammatory cytokines, markers of hepatic injury (ALT, AST), renal impairment (creatinine, BUN), and cardiac injury (cTnI, NT-proBNP) all P < 0.001; FDR q < 0.001). An AUC = 0.872 for SAP diagnosis with a combination of four markers (PCT + IL-6 + ALT + creatinine) was established. Supplemental JXD therapy provided a significant advantage over conventional treatment in Day-7 clinical improvement rate (72.4% vs. 48.3%, P = 0.048) and shortened ICU stay (12.1 vs. 16.3 days, P = 0.002), along with markers of mode microbiome-related inflammation and injury reduction in this population of patients with acute disturbances post-septic organs (Galluzzi et al., Cell Death Differ, 2018, 25(3), 486-541). JXD basically inhibited apoptosis (CASP3), pyroptosis (NLRP3), necroptosis (RIPK3) in vitro, and reversed ferroptotic death by restoring GPX4, downregulating MDA, as well as inhibiting ACSL4.

CONCLUSION: Multi-organ dysfunction biomarkers independently predicts sepsis sequelae post-SAP (AUC = 0.872)) and track treatments response Conclusions: JXD modulates a number of cellular death pathways in vitro, and markedly improves clinical outcomes in SAP-associated sepsis.},
}

@article {pmid42534735,
year = {2026},
author = {Berríos-Farías, V and Guajardo-Leiva, S and Gallardo-Cerda, J and Galbán-Malagón, C and Egas, C and Molina-Montenegro, MA and Castro-Nallar, E},
title = {Metagenomic insights into potential PET hydrolases from Antarctic soils and rhizospheres.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1749101},
pmid = {42534735},
issn = {1664-302X},
abstract = {Polyethylene terephthalate (PET) is a persistent synthetic polymer that is increasingly detected in terrestrial environments, where it influences soil microbial activity and carbon cycling. Microorganisms capable of hydrolyzing PET and related polyesters constitute a valuable enzymatic resource for developing low-temperature biocatalysts and for advancing the understanding of soil functional adaptation to plastic pollution. Here, we conducted a metagenomic analysis of soil and rhizosphere samples from the Antarctic vascular plants Deschampsia antarctica and Colobanthus quitensis, as sources of microbial enzymes with potential PET-hydrolytic activity. Hidden Markov Models constructed from experimentally validated PET hydrolases identified 152 putative PET hydrolases (pPETHs) spanning multiple protein families. Four candidates exhibited amino acid motifs characteristic of Ideonella sakaiensis PETase, including the conserved alpha/beta hydrolase fold and the Ser-His-Asp catalytic triad. One candidate from a Duganella genome also contained a tryptophan residue associated with efficient product release during PET hydrolysis. Molecular docking and molecular dynamics analyses revealed that candidates retain the core catalytic architecture of established PET hydrolases, while simultaneously displaying structural signatures of cold adaptation. These findings demonstrate the diversity of PET-hydrolase-like genes within Antarctic rhizosphere and soil microbiomes, broadening the current understanding of microbial enzymatic potential under cold, oligotrophic conditions. The identified sequences highlight the rhizosphere as a reservoir of functional diversity relevant to soil biotechnology, cold-adapted catalysis, and microbial strategies for transforming recalcitrant carbon substrates.},
}

@article {pmid42534803,
year = {2026},
author = {Stø, K and Skagen, K and Bjerkeli, V and Ueland, PM and Hov, JR and Trøseid, M and Aukrust, P and Ueland, T and Halvorsen, B and Skjelland, M},
title = {Gut microbiota derived indoles are altered and associate with immune activation in moderate and severe carotid stenosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1796312},
pmid = {42534803},
issn = {1664-3224},
mesh = {Humans ; Male ; *Indoles/blood/metabolism ; *Carotid Stenosis/immunology/microbiology/metabolism/surgery ; Female ; *Gastrointestinal Microbiome/immunology ; Aged ; Biomarkers/blood ; Cross-Sectional Studies ; Middle Aged ; Methylamines/blood ; Severity of Illness Index ; },
abstract = {BACKGROUND: An imbalance of gut microbiota, their metabolites as well as inflammatory mediators have been increasingly linked to both atherosclerosis and stroke. However, data on microbiota derived tryptophan and histidine metabolites in carotid atherosclerosis are scarce.

PURPOSE: We investigated serum microbiota derived indoles, imidazole propionate (ImP) and trimethylamine N-oxide (TMAO), representing three distinct gut bacterial-related metabolites, in patients with carotid atherosclerosis compared with healthy controls with normal findings on carotid ultrasound. We aimed to examine their relation to plaque characteristics, immune activation markers and traditional cardiovascular risk factors.

METHODS: Thirty patients scheduled for carotid endarterectomy and 18 control subjects were included in this cross-sectional study. Carotid arteries were investigated with ultrasound. Indoles, ImP and TMAO were analyzed by liquid chromatography-tandem mass spectrometry, and Lipopolysaccharide (LPS) by a Limulus Amebocyte Lysate chromogenic assay.

RESULTS: Compared to controls, patients exhibited lower levels of indole-3-propionic acid (IPA) (p=0.004) and indole-3-acetic acid (IAA) (p = 0.030). In patients, higher levels of indole metabolites were associated with lower C-reactive protein. ImP and TMAO did not differ between patients and controls.

CONCLUSION: Patients with carotid atherosclerosis exhibited reduced serum concentrations of IPA and IAA, thought to have anti-inflammatory effects, and increased inflammatory markers, possibly suggesting disruptions in the gut-vascular-immune axis.},
}

Humans
Male
*Indoles/blood/metabolism
*Carotid Stenosis/immunology/microbiology/metabolism/surgery
Female
*Gastrointestinal Microbiome/immunology
Aged
Biomarkers/blood
Cross-Sectional Studies
Middle Aged
Methylamines/blood
Severity of Illness Index

@article {pmid42534899,
year = {2026},
author = {Guitart-Matas, J and Bravo, M and Tort-Miró, C and Giler-Baquerizo, N and Fraile, L and Caldas-Ramayo, Y and Ballester, M and Migura-Garcia, L},
title = {Dynamics of archaeal diversity and functionality in the piglet gut microbiome under common antimicrobial treatments.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1833734},
pmid = {42534899},
issn = {2235-2988},
mesh = {Animals ; *Archaea/classification/genetics/drug effects ; Swine ; Metagenomics ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Metagenome ; Weaning ; *Biodiversity ; *Anti-Infective Agents/administration & dosage/pharmacology ; Gene Expression Profiling ; Phylogeny ; Diarrhea/drug therapy/veterinary ; Anti-Bacterial Agents ; },
abstract = {INTRODUCTION: The gut microbiota comprises a diverse and dynamic community of microorganisms that collectively enhance host metabolism, physiology, and overall functionality. In this context, the swine archaeome remains largely underexplored despite growing evidence that archaea may greatly influence host health. Advances in high-throughput approaches provide new opportunities to reveal the dynamics and composition of archaea. Herein, we uncover the taxonomic and functional landscape of the piglet archaeome during the weaning transition under multiple experimental conditions, integrating shotgun metagenomic and metatranscriptomic analyses to elucidate its contribution to gut microbial ecology.

METHODS: The seven experimental conditions included four antibiotic treatments for post-weaning diarrhoea (trimethoprim/sulfamethoxazole, colistin, gentamicin, amoxicillin), an oral vaccine, acidifiers in drinking water, and a no-intervention group. A total of 280 faecal samples were collected longitudinally one day before weaning (ST1), three days (ST2), two weeks (ST3), and four weeks (ST4) after the start of the treatment. Treatment was initiated eleven days after arrival at the experimental farm following the onset of clinical signs. Shotgun metagenomics was used to assess archaeal taxonomic diversity and recover archaeal metagenome-assembled genomes (aMAGs), while metatranscriptomics was integrated to assess differentially expressed genes at ST1, ST2, and ST4.

RESULTS: The results revealed archaea as the second most abundant microorganism, exhibiting a longitudinal increase in diversity over the experimental time. The most predominant genus was Methanobrevibacter, including Methanobrevibacter smithii. Eleven high-quality aMAGs were recovered, belonging to the Methanobacteriota and Thermoplasmatota phyla. Genome-inferred functional analyses revealed that the predominant metabolic processes included the biosynthesis of nucleic acids, amino acids, organic anions, and vitamins. Additional functional traits suggested potential roles in the degradation of sugars, amino acids, and antibiotics were also observed. Moreover, significant differences were detected on the archaeal metatranscriptome between the experimental groups treated with antibiotics and the rest of the groups, underscoring their response to changes in microbial interactions, substrate availability and, in some cases, direct effect of the antimicrobials on metabolic pathways.

DISCUSSION: Altogether, this study highlights the biological significance of archaeal dynamics during initial life stages and demonstrates how combining metagenomics and metatranscriptomics uncovers their functional potential and the pathways actively expressed in the piglets' gut.},
}

Animals
*Archaea/classification/genetics/drug effects
Swine
Metagenomics
*Gastrointestinal Microbiome/drug effects
Feces/microbiology
Metagenome
Weaning
*Biodiversity
*Anti-Infective Agents/administration & dosage/pharmacology
Gene Expression Profiling
Phylogeny
Diarrhea/drug therapy/veterinary
Anti-Bacterial Agents

@article {pmid42534910,
year = {2026},
author = {Mao, L and Yang, Z and Jiang, F},
title = {Reappraising traumatic brain injury and ventilator-associated pneumonia through the brain-lung-immune-microbiome axis.},
journal = {Frontiers in neurology},
volume = {17},
number = {},
pages = {1844556},
pmid = {42534910},
issn = {1664-2295},
abstract = {Ventilator-associated pneumonia (VAP) remains the most prevalent and lethal infectious complication among patients with severe traumatic brain injury (TBI) requiring invasive mechanical ventilation. Historically, the pathogenesis of VAP within neurocritical care settings has been attributed to mechanical and physical factors. This traditional paradigm posits that the endotracheal tube bypasses natural upper airway defenses, impairs glottic reflexes, and allows for the continuous micro-aspiration of pathogen-laden oropharyngeal secretions into the lower respiratory tract. However, this biomechanical model fails to adequately explain the disproportionately high incidence of VAP in TBI patients compared to other critically ill populations. A profound conceptual paradigm shift is transitioning the focus from isolated airway mechanics toward multidimensional biological construct: the Brain-Lung-Immune-Microbiome Axis. The fundamental catalyst for respiratory vulnerability following neurotrauma is central nervous system injury-induced immunodepression syndrome (CIDS), a profound systemic immune remodeling driven by acute neuroendocrine and autonomic dysregulation, as well as the translocation of pathogenic gut microbiota to the lungs. By synthesizing evidence from neuroimmunology, microbiology, and critical care medicine, this narrative review details the tripartite interplay of neurological trauma, immune exhaustion, and microbiome evolution. Ultimately, this review evaluates emerging host-directed immunomodulatory therapies and microbiome-targeted interventions, advocating for a critical transition from simple mechanical airway hygiene to precision immuno-microbiome therapeutics in the neuro-intensive care unit.},
}

@article {pmid42534989,
year = {2026},
author = {Abdigulov, B and Ordabayeva, A and Kuibagarov, M and Suminov, A and Ilderbayev, O and Dauletov, A and Kadyrova, M and Abdrakhmanov, S and Vergnaud, G and Shevtsov, A},
title = {Stage-associated enrichment of Dietzia in the conjunctival microbiome of calves with infectious bovine keratoconjunctivitis: a cross-sectional microbiome and genomic characterization study.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1890304},
pmid = {42534989},
issn = {2297-1769},
abstract = {BACKGROUND: Infectious bovine keratoconjunctivitis (IBK) is a major ocular disease of cattle. Although the bovine conjunctival microbiome has been studied in IBK-affected and healthy animals, microbiome patterns across clinically defined lesion stages remain poorly understood, and the occurrence of Dietzia on the diseased bovine ocular surface has not been systematically investigated.

METHODS: This cross-sectional study enrolled 57 calves from two commercial farms in Kazakhstan, stratified across six clinical stages of IBK severity (0-5). Conjunctival swabs were analyzed by culture-based Dietzia recovery and 16S rRNA gene amplicon sequencing. Alpha and beta diversity were assessed using standard ecological metrics, and stage-associated Dietzia abundance was evaluated using Kruskal-Wallis testing and quadratic regression. Two representative Dietzia isolates were subjected to whole-genome sequencing, phylogenomic placement and homology-based screening against resistance and virulence-factor databases.

RESULTS: IBK stage was not associated with significant global restructuring of the conjunctival microbiome. Alpha-diversity indices did not differ significantly across stages, and PERMANOVA showed no stage-specific beta-diversity separation (R [2] = 0.098, p = 0.323). In contrast, Dietzia showed a non-linear stage-associated abundance pattern in a quadratic model, with the highest reads-per-million (RPM) abundance in samples classified at stages 2-3, which are clinically characterized by active corneal ulceration. Culture-based recovery of Dietzia was frequent overall (42/57 samples; 73.7%) but showed no monotonic relationship with lesion severity. Whole-genome analysis of two isolates revealed phylogenomic heterogeneity: one isolate clustered within phylogenomic Group A, whereas the second was positioned outside the four major Dietzia groups, adjacent to the divergent animal isolate Dietzia sp. B32. Both genomes contained conserved stress-response, regulatory and metabolic homologues, without clear evidence of specialized virulence systems.

CONCLUSION: IBK lesion stage was not associated with major alpha- or beta-diversity restructuring, but Dietzia displayed stage-associated enrichment during the active ulcerative phase. These findings support interpretation of bovine ocular Dietzia as a surface-accessible opportunistic colonizer rather than a confirmed primary aetiological agent of IBK.},
}

@article {pmid42535026,
year = {2026},
author = {Jia, Z and Peng, Y and Jiang, S and Tang, Y and Yin, H and Huang, L and Li, P and Mo, C and Wu, R},
title = {Multi-habitat microbiome profiling identifies habitat-dependent alterations and complementary discriminatory information in urolithiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1853826},
pmid = {42535026},
issn = {2235-2988},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Urolithiasis/microbiology ; *Microbiota/genetics ; Female ; Feces/microbiology ; Saliva/microbiology ; Male ; *Ecosystem ; Middle Aged ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Urine/microbiology ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: Urolithiasis has been associated with microbial alterations in individual anatomical niches; however, whether microbial signatures across urinary, intestinal, and oral habitats represent shared, site-specific, or complementary disease-associated information remains unclear. This study aimed to characterize multi-habitat microbiome alterations associated with urolithiasis and to evaluate whether integrated multi-site profiling captures internally cross-validated disease-associated microbial information.

METHODS: Salivary, clean-catch midstream urinary, and fecal samples were collected from 80 stone formers (SF) and 40 healthy controls (HC) and profiled using 16S rRNA gene sequencing. After quality control, the final analytical dataset comprised 101 urinary, 117 fecal, and 120 salivary samples, with 98 participants contributing complete three-habitat profiles. Habitat-specific alpha- and beta-diversity, taxonomic alterations, and exploratory inferred-network and predicted-functional profiles were evaluated. Random forest models were assessed using repeated nested stratified cross-validation to examine internal discriminatory information from single- and multi-habitat microbial features.

RESULTS: Urolithiasis was associated with statistically detectable but modest differences in microbial community structure across all three habitats, with small PERMANOVA effect sizes and significant dispersion differences. Fecal samples from SF showed significantly reduced richness, including lower Sobs, Chao1, and ACE indices than HC after false discovery rate correction (all q = 0.022), whereas urinary and salivary alpha-diversity did not show broad loss. Taxonomic alterations were habitat dependent: saliva yielded the broadest covariate-robust genus-level candidate set, feces showed fewer stable HC-enriched genera alongside reduced richness, and urinary candidate associations were identified but require prospective contamination-controlled validation because of the low-biomass nature of urine and the absence of negative controls. In matched participants, the combined multi-habitat microbiome model achieved an area under the receiver operating characteristic curve of 0.865 (95% CI, 0.839-0.886), exceeding the limited clinical-only model based on age, sex, and body mass index (AUC, 0.738; delta-AUC, 0.128; 95% CI, 0.026-0.229). Improvement over the best single-habitat microbiome model was not statistically conclusive. External contextual analyses provided partial urinary community-level support in KiSMi and an inverse but FDR-non-significant NHANES oral-richness association after extensive covariate adjustment, supporting harmonized prospective validation.

CONCLUSIONS: These findings identify habitat-dependent microbiome alterations in urolithiasis and show that integrated multi-habitat profiling captures disease-associated microbial information beyond a limited clinical baseline. The combination of reduced fecal richness, broad salivary covariate-robust candidates, biologically proximal urinary candidates, and external contextual signals supports simultaneous multi-site profiling as a valuable framework for future mechanistic and translational studies. Prospective studies with rigorous low-biomass controls, comprehensive exposure metadata, direct functional measurements, and prespecified independent validation are warranted.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Urolithiasis/microbiology
*Microbiota/genetics
Female
Feces/microbiology
Saliva/microbiology
Male
*Ecosystem
Middle Aged
Adult
*Bacteria/classification/genetics/isolation & purification
Urine/microbiology
DNA, Bacterial/genetics

@article {pmid42535369,
year = {2026},
author = {Zhang, L and Yang, S and Wu, H and Zhou, H},
title = {Integrating gut‑brain axis insights into bundled nutrition care for critically ill patients: From mechanisms to implementation (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {4},
pages = {},
doi = {10.3892/mmr.2026.13978},
pmid = {42535369},
issn = {1791-3004},
mesh = {Humans ; *Critical Illness/therapy ; Gastrointestinal Microbiome ; *Brain/metabolism ; Intestinal Barrier Function ; Dysbiosis ; *Brain-Gut Axis ; Enteral Nutrition/methods ; Critical Care/methods ; *Nutrition Therapy/methods ; },
abstract = {Critical illness induces a marked disruption of the gut‑brain axis, which is characterized by systemic inflammation and the rapid collapse of intestinal barrier integrity. These pathological shifts facilitate the translocation of pathogen‑associated molecular patterns, thereby driving neuroinflammation and exacerbating intensive care unit‑acquired syndromes such as delirium and muscular wasting. Although conventional nutritional strategies emphasize caloric and protein goals, emerging evidence has highlighted the necessity of modulating the host‑microbiome interface to preserve neurological and systemic homeostasis. The integration of fermentable fibers, probiotics and specialized lipid mediators into a standardized framework may effectively interrupt the self‑perpetuating cycle of dysbiosis and organ failure. The present review uniquely contributes to the field by integrating an implementation science framework for clinical bundle application and discussing artificial intelligence driven precision nutrition advances, which are topics that have not been comprehensively covered in the majority of previous reviews. Therefore, the present review bridges mechanistic insights with practical, scalable strategies to optimize nutritional care and improve recovery trajectories in patients with critical illness.},
}

Humans
*Critical Illness/therapy
Gastrointestinal Microbiome
*Brain/metabolism
Intestinal Barrier Function
Dysbiosis
*Brain-Gut Axis
Enteral Nutrition/methods
Critical Care/methods
*Nutrition Therapy/methods

@article {pmid42535384,
year = {2026},
author = {Zhang, X and An, X},
title = {Association between periodontitis and heart failure: Mechanisms and clinical implications (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {4},
pages = {},
doi = {10.3892/mmr.2026.13974},
pmid = {42535384},
issn = {1791-3004},
mesh = {Humans ; *Heart Failure/etiology/epidemiology/complications ; *Periodontitis/complications/microbiology/epidemiology/therapy ; Microbiota ; Inflammation ; Animals ; },
abstract = {Periodontitis, a common oral disease, is increasingly recognized for its potential impact on systemic health, particularly its association with heart failure (HF). HF is a complex clinical syndrome with a multifactorial pathogenesis. Emerging evidence suggests that periodontitis may influence the cardiovascular system and contribute to the onset and progression of HF through mechanisms such as systemic inflammation, microbial shifts, and immune dysregulation. However, current research still faces limitations in establishing causality and elucidating the precise underlying mechanisms. Furthermore, clinical intervention strategies require further investigation. Relevant literature was identified from PubMed, Web of Science, and Scopus using keywords related to periodontitis and heart failure, and screened for relevance to epidemiological evidence, mechanistic insights, and clinical implications. The present review aimed to summarize the mechanisms linking periodontitis and HF, analyze their shared pathophysiological basis, and discuss the potential role of periodontal treatment in improving outcomes for patients with HF. Clinically, periodontal assessment may be considered in patients with heart failure as part of multidisciplinary care, but current evidence remains insufficient to support definitive recommendations that such evaluation or treatment improves HF outcomes.},
}

Humans
*Heart Failure/etiology/epidemiology/complications
*Periodontitis/complications/microbiology/epidemiology/therapy
Microbiota
Inflammation
Animals

@article {pmid42535839,
year = {2026},
author = {Bolino, MJ and Frese, SA},
title = {CAMEO: a CAZyme mapping engine optimized for HUMAnN.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0070726},
doi = {10.1128/mra.00707-26},
pmid = {42535839},
issn = {2576-098X},
abstract = {There are technical barriers to creating functional mapping databases and a dearth of validated databases that can be easily implemented by users. We present CAMEO, a precomputed and validated mapping file for carbohydrate-active enzymes, as well as an approach to building new CAZyme mapping files, for use with HUMAnN.},
}

@article {pmid42535843,
year = {2026},
author = {Luan, L and Song, X and Zeng, Y and Xie, Y and Hong, Y and Tang, J and Ma, C and Gu, B and Wang, L},
title = {Differential pro-tumorigenic effects of Helicobacter pylori and Streptococcus anginosus on AGS cells: contact-dependent versus metabolite-driven mechanisms.},
journal = {mBio},
volume = {},
number = {},
pages = {e0158926},
doi = {10.1128/mbio.01589-26},
pmid = {42535843},
issn = {2150-7511},
abstract = {Gastric cancer remains a major global health burden, ranking fifth worldwide in both incidence and mortality. While Helicobacter pylori is a well-established Group I carcinogen, increasing evidence suggests that non-H. pylori bacteria, including Streptococcus anginosus, may also contribute to gastric carcinogenesis. However, their comparative pathogenic roles and interactions remain poorly defined. In this study, public databases showed stage-dependent abundance changes of H. pylori and S. anginosus but no significant correlation during gastric cancer progression. We further quantified both bacteria in gastric fluid samples collected from 500 individuals using a non-invasive gastric string test and in fecal samples from an independent cohort of 500 individuals by qPCR. In the two cohorts, no significant correlations were observed between the two bacterial pathogens, suggesting distinct colonization and pathogenic patterns. To evaluate functional differences, AGS cell co-culture models were established to explore their pro-tumorigenic effects. H. pylori predominantly exerted tumor-promoting effects through bacterial cell-associated mechanisms, whereas S. anginosus exerted stronger pro-tumorigenic effects via its metabolites. In particular, transcriptomic analysis revealed that proliferation-associated genes, including DEK and RTF1, were significantly upregulated by 21.9-fold and 19.2-fold, respectively, in cells treated with Streptococcus anginosus metabolite (SAM). Metabolomic profiling of SAM identified increased levels of spermidine and polyamine-related metabolites. Among these, N-acetylcadaverine, N-acetyltyrosine, N-acetyltryptophan, and urocanic acid were experimentally validated to significantly promote AGS cell proliferation. Collectively, these findings demonstrate that H. pylori and S. anginosus drive gastric tumorigenesis through contact-dependent and metabolite-mediated mechanisms, respectively, highlighting bacterial metabolites as emerging contributors to gastric cancer progression.IMPORTANCEThe gastric microbiota plays a critical role in gastrointestinal health and disease. However, the ecological interactions between Helicobacter pylori and non-H. pylori bacteria remain poorly understood. Among established bacterial pathogens linked to gastric carcinogenesis, H. pylori and Streptococcus anginosus are recognized as major contributors. In this study, we systematically evaluated infection patterns and potential associations between these two pathogens using public metagenomic data sets and qPCR analysis of clinical samples (feces and gastric fluid) from multicenter cohorts. We found no significant association between their infection statuses (P > 0.05), indicating independent colonization patterns and likely differences in their pathogenic mechanisms within the human host. Complementary in vitro and cellular analyses further showed that H. pylori primarily acts through direct mucosal colonization and virulence factors, whereas S. anginosus influences host responses mainly via its metabolic products. These findings demonstrate that H. pylori and S. anginosus operate through distinct colonization strategies and pathogenic pathways. They underscore the importance of accounting for mechanistic heterogeneity in gastric microbiome research and provide a conceptual framework for future investigations into microbe-driven pathogenesis of gastric disease.},
}

@article {pmid42535857,
year = {2026},
author = {Szafrański, SP and Joshi, AA and Steglich, M and Yang, I and Qu, T and Behrens, W and Muthukumarasamy, U and Melidis, D and Schaefer-Dreyer, P and Grischke, J and Hegermann, J and Nejdl, W and Häussler, S and Stiesch, M},
title = {High-resolution taxonomic profiling and metatranscriptomics identify microbial, biochemical, host, and ecological factors in peri-implant disease.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0075425},
doi = {10.1128/msystems.00754-25},
pmid = {42535857},
issn = {2379-5077},
abstract = {UNLABELLED: Biofilm-associated diseases like peri-implant mucositis (PIM) and peri-implantitis (PI) are significant clinical challenges affecting millions of dental implant patients globally. Although studies have described the role of microbial, host, or environmental factors in disease development, their complex interplay, particularly during dysbiosis, remains poorly understood. This cross-sectional study characterized the microbiome composition and metatranscriptomes of 125 peri-implant biofilms from 48 individuals, uncovering molecular signatures linked to peri-implant health (PIH), PIM, and PI. Distinct variations were observed in biofilm amount, microbial composition and activity, phage populations, and host response. Biofilms were categorized into four community types (CTs) based on the bacterial transcriptional activity: one linked to PIH, one to PI, and two to PIM. PIH and PIM were primarily characterized by aerotolerant taxa with increased anabolic processes, while PI was dominated by obligate anaerobes with complex biofilm morphology. PIM samples, relative to PIH, were characterized by biofilm expansion with minimal functional changes, except for the Neisseria-rich PIM subtype showing higher pyruvate and lipoic acid metabolism. The phagome mirrored the bacterial compositional variations across disease states. Furthermore, human transcriptome responses varied, indicating increased keratinization in PIH, enhanced expression of ribosome components in PIM, and inflammatory signaling and hypoxia in PI. Additionally, we identified complex species-enzyme, phage-bacterium, and host-microbe associations within the peri-implant ecosystem. Our integrative multi-omics approach provides a comprehensive view of microbial, biochemical, host, and ecological factors associated with dysbiosis, offering novel insights into peri-implant disease dynamics.

IMPORTANCE: Peri-implant mucositis and peri-implantitis are highly prevalent inflammatory conditions that compromise the long-term survival and success of dental implants, yet their underlying biological mechanisms are largely unresolved. The full-length 16S rRNA gene amplicon sequencing (full-16S) allows for high-resolution taxonomic profiling of peri-implant biofilms, thereby advancing our understanding of microbial composition across health and peri-implant diseases. The integration of metatranscriptomics, furthermore, captures actively transcribed genes within the biofilm and offers direct insights into microbial community functions and the broader molecular context of peri-implant dysbiosis. DNA- and RNA-derived abundances were strongly correlated, with only a few microbial classes showing moderate diagnosis-related differences after DNA-based normalization of transcriptional activity. In this study, we integrated full-16S with metatranscriptomic profiling to simultaneously assess microbial taxonomy, functional activity, phage dynamics, and host gene expression in peri-implant biofilms. Importantly, we provide a systems-level view and report previously undescribed associations between different molecular signatures in the peri-implant ecosystem.},
}

@article {pmid42535886,
year = {2026},
author = {Eckles, AE and Poelstra, JW and Toth, HN and McKenzie, ZA and Jacobs, JM and Peduto Hand, F},
title = {Transmission of Xanthomonas campestris pv. incanae and Associated Microbiome in Matthiola incana Seed.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-03-26-0074-FI},
pmid = {42535886},
issn = {0031-949X},
abstract = {Xanthomonas campestris pv. incanae (Xci) is known to cause systemic infections in the stem of Matthiola incana. Prior research observed that the pathogen can invade the vascular system and extend into the seed peduncles of infected plants, suggesting a likely mean for internal contamination of the seeds. However, this and other potential pathways of seed infection and seed-to-seed transmission, have not been sufficiently investigated. Using both culture-based and metagenomic approaches, we evaluated the potential for and efficiency of seed infection by Xci after vascular and floral inoculation of the mother plants, as well as the possibility for seed-to-seed transmission. We also explored the diversity of the M. incana seed microbiome in response to inoculation with Xci. Results showed that the vascular system was a viable and highly efficient pathway of seed infection by Xci, unlike the floral organs, and that seed infection by the vascular pathway negatively impacted seed germination. We also demonstrated that seed-to-seed transmission of Xci occurred at an epidemiologically significant degree. The primary difference among microbiomes of seeds harvested from inoculated and non-inoculated plants was the presence of Xci, which had extremely high relative and absolute abundance in infested seeds. Additionally, minor effects of inoculation treatment, seed infection pathway, and the interaction between the two were observed for overall seed microbial community composition and diversity. These findings pave the way to future exploration of the seed microbiome in M. incana.},
}

@article {pmid42535945,
year = {2026},
author = {Zhong, W and Zhu, Z and Zeng, Z and Wu, J and Xie, X and Li, X and Lv, Q and Li, D and Liu, M and Ward, G and Knol, J and Wopereis, H and Guyard, C and Xia, J and Han, L and Wang, B and Li, Y and Roeselers, G and Gong, S},
title = {Correction: Early-life gut microbiome-metabolome development trajectories in Chinese infants: a decentralized real-world evidence study.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo90062c},
pmid = {42535945},
issn = {2042-650X},
abstract = {Correction for 'Early-life gut microbiome-metabolome development trajectories in Chinese infants: a decentralized real-world evidence study' by Wanying Zhong et al., Food Funct., 2026, 17, 6596-6607, https://doi.org/10.1039/D6FO02082H.},
}

@article {pmid42535965,
year = {2026},
author = {Usandizaga, S and Beltrán, J and Rodríguez-Valdecantos, G and Parada-Pozo, G and Guillemin, ML and Faugeron, S and Trefault, N and Camus, C},
title = {Experimental evidence for early bacterial inheritance in the giant kelp, Macrocystis pyrifera.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag089},
pmid = {42535965},
issn = {1574-6941},
abstract = {Bacteria associated with macroalgae influence the development, health, and ecological interactions of their hosts. Although vertical transmission of bacterial symbionts has been proposed in some algal species, evidence remains limited. In this study, we combined 16S rRNA gene amplicon sequencing, fluorescence in situ hybridization (FISH), and transmission electron microscopy (TEM) to assess bacterial presence and localization throughout early developmental stages of the brown macroalga Macrocystis pyrifera. Amplicon sequencing detected bacterial taxa in reproductive sori, released spores, and gametophytes, even under sterile conditions and using pasteurized, filtered seawater. Certain bacterial taxa, including Balneola alkaliphila and Marinoscillum luteum, were recurrently detected across multiple developmental stages. FISH imaging showed bacterial signal associated with host tissues across life stages, distinguishable from algal autofluorescence, while TEM observations revealed structures consistent with intracellular bacterial cells within the cytoplasm of gametophyte cells and embedded in sporangial cuticles. Together, these observations suggest that bacteria are associated with both internal and external reproductive tissues, pointing to multiple potential transmission routes. Altogether, our findings provide evidence consistent with early-stage bacterial inheritance in M. pyrifera, contributing to the growing evidence that macroalgal holobionts are assembled, at least in part, through vertical transmission of symbionts.},
}

@article {pmid42536059,
year = {2026},
author = {Inoue, M and Sakanaka, A and Katakami, N and Nishizawa, H and Omori, K and Taya, N and Ishikawa, A and Mayumi, S and Takeuchi, H and Amano, A and Takeshita, T and Fukusaki, E and Shimomura, I and Kuboniwa, M},
title = {Alteration of subgingival microbiome in patients with type 2 diabetes induced by diabetes treatment.},
journal = {Journal of diabetes investigation},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdi.70408},
pmid = {42536059},
issn = {2040-1124},
support = {JP22ym0126809//Japan Agency for Medical Research and Development/ ; 22H03300//Japan Society for the Promotion of Science/ ; 22K19622//Japan Society for the Promotion of Science/ ; 21K18281//Japan Society for the Promotion of Science/ ; 20K18827//Japan Society for the Promotion of Science/ ; JP23KJ15250//Japan Society for the Promotion of Science/ ; 25K02837//Japan Society for the Promotion of Science/ ; },
abstract = {AIMS/INTRODUCTION: Diabetes and periodontal disease, a bacterial infection involving the oral microbiome, have a bidirectional relationship. However, the relationship between poor glycemic control and the oral microbiome remains unclear. The aim of this study was to assess the direct effect of intensive glycemic control on the oral microbiome in patients with type 2 diabetes mellitus (T2DM).

MATERIALS AND METHODS: Twenty-nine patients with T2DM and 29 controls were enrolled in this study. Patients underwent a 2-week intensive glycemic control regimen. We collected subgingival dental plaque and conducted full-length 16S ribosomal RNA gene sequencing to identify bacterial species. The focus was on the subgingival microbiome, particularly 29 species of oral bacteria related to periodontal disease, and the characteristics of the diabetic cohort. Periodontal inflammation was quantified using the periodontal inflamed surface area (PISA).

RESULTS: Prior to diabetes treatment, the relative abundance of Porphyromonas gingivalis (P = 0.018), Tannerella forsythia (P < 0.001), Fusobacterium nucleatum (P = 0.041), and Prevotella intermedia (P < 0.001), known for their high pathogenicity in periodontal disease, was higher in the diabetes group than in the control group. The bacterial species whose relative abundance changed significantly before and after treatment differed between the PISA improved and non-improved groups in patients with diabetes.

CONCLUSIONS: Oral bacteria changed pre- and post-diabetes treatment, correlating with improvements in PISA.},
}

@article {pmid42536076,
year = {2026},
author = {Cady, N and Meyer, SR and Kim, K and Lo, BC and So, N and Chen, GY and Rosshart, SP and Shah, YM and Núñez, G and Sexton, JZ and Schmidt, TM},
title = {An innovative organoid model to screen for bacteria and their metabolites that protect against inflammation-induced colonic barrier disruption.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0092625},
doi = {10.1128/msphere.00926-25},
pmid = {42536076},
issn = {2379-5042},
abstract = {Organoids provide a useful model system to study interactions between gut microbes and the activity of host tissues, including gastrointestinal (GI) barrier function. However, most organoid models have limited capacity to mimic the physiological hypoxia experienced by the colonic epithelium in vivo. While oxygen is required to support respiration in the host cells, many gut microbes are anaerobes that require anoxic conditions to grow. Using an innovative anaerobe co-culture system that maintains constant oxygen concentrations on the basolateral side of colonic epithelial monolayers and anoxic conditions on the luminal side, we demonstrate that colonic monolayers derived from a primary human cell line behaved more like in vivo epithelia when cultivated in the co-culture system than when cultured under ambient oxygen concentrations. We then identified interactions between the colonic epithelium and a strain of Bifidobacterium adolescentis-an oxygen-sensitive species that is prevalent and abundant in the adult gut microbiome. Co-culturing colonic monolayers with Bifidobacterium adolescentis U269-1 in the anoxic apical chamber mitigated loss of the barrier function in monolayers exposed to inflammatory cytokines. We identified indole lactic acid (ILA) as one metabolite from B. adolescentis that provides dose-dependent protection against inflammatory cytokines. Oral administration of ILA was well tolerated in mice and provided protection against immunotherapy-induced (anti-CTLA4) colitis in female, but not male mice. Together, we demonstrated the utility of the co-culture system for screening microbes and their metabolites for interactions with the colonic epithelium, as well as advancing our understanding of interactions between bifidobacteria and host barrier function.IMPORTANCEThe present study yielded strong evidence for the beneficial effects of B. adolescentis on the maintenance of colonic barrier function in an asymmetric oxygen system that mimics the colonic environment. The bifidobacterial metabolite indole lactic acid was implicated in this protection both in vitro and in a mouse model. We also refined and scaled the co-culture system to a 96-well plate format to provide the capacity for higher-throughput screening of microbes and microbial metabolites under physiologically relevant conditions.},
}

@article {pmid42536162,
year = {2026},
author = {Chegeni, SA and Yalameha, B and Rashidi, S and Javani, G and Seddighi, N and Bagheri, HS and Khalifezadeh, M and Roozbahani, G and Molaaghaee-Rouzbahani, S and Rahbarghazi, R},
title = {Effect of gut bacterial extracellular vesicles on angiogenic potential and vascular integrity: positive and negative aspects.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {75},
number = {1},
pages = {},
pmid = {42536162},
issn = {1420-908X},
support = {IR.TBZMED.VCR.REC.1404.100//Tabriz University of Medical Sciences/ ; },
mesh = {Humans ; Animals ; *Extracellular Vesicles/physiology ; *Gastrointestinal Microbiome ; *Angiogenesis ; *Bacteria ; Endothelial Cells/physiology ; Endothelium, Vascular ; Neovascularization, Physiologic ; },
abstract = {Extracellular vesicles (EVs) are intercellular mediators in prokaryotic and eukaryotic systems that have the potential to regulate various physiological and pathological processes in recipient cells. Among them, bacterial extracellular vesicles (BEVs), including Gram-negative outer membrane vesicles (OMVs) and Gram-positive membrane vesicles (MVs) produced by the gut microbiota, have special roles in humans and animals. Due to their nanoscale dimensions and distinct molecular payloads, BEVs can cross biological barriers, including the vascular endothelium, to reach distant target tissues and affect various pathophysiological processes. Dysbiosis and compromised epithelial barriers facilitate the systemic dissemination of gut microbiota-derived BEVs, increasing the risk of diseases such as atherosclerosis and cardiovascular disease. Importantly, while this review emphasizes symbiotic intestinal BEVs, evidence from oral and pathogenic bacteria has also been integrated as indirect mechanistic sources to shed more light on BEV-induced endothelial dysfunction and altered angiogenesis. Here, we aimed to highlight the impact of BEVs on the vascular compartment, focusing on endothelial cells (ECs) in terms of molecular and cellular events. Understanding the underlying mechanisms will enable us to develop sophisticated engineered BEVs to control and inhibit certain pathological conditions.},
}

Humans
Animals
*Extracellular Vesicles/physiology
*Gastrointestinal Microbiome
*Angiogenesis
*Bacteria
Endothelial Cells/physiology
Endothelium, Vascular
Neovascularization, Physiologic

@article {pmid42536199,
year = {2026},
author = {Chávez-Tinoco, M and Senés-Guerrero, C and Verduzco Garibay, M and Carrillo-González, R and González-Chávez, MDCA},
title = {Cover trees associations shape bacterial diversity in coffee production systems.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {9},
pages = {},
pmid = {42536199},
issn = {1572-9699},
mesh = {*Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; *Trees/microbiology ; *Musa/microbiology ; Soil/chemistry ; *Coffee ; Plant Roots/microbiology ; *Mangifera/microbiology ; Phylogeny ; Coffea ; DNA, Bacterial/genetics ; Agriculture/methods ; Microbiota ; },
abstract = {Traditional coffee agroforestry systems often involve shade trees, which play a crucial role in maintaining soil fertility and biodiversity. In contrast, monoculture systems negatively influence soil chemistry, microbial diversity, and overall soil health over time. Although the use of cover trees such as mango (Mangifera indica L.) and banana (Musa paradisiaca, var. Cavendish.) has been shown to have beneficial effects on the soil chemical properties, little is known about their influence on microbial communities associated with coffee production systems. The main objective of this study was to identify the bacteria inhabiting roots and soil of three coffee management systems via partial 16S rRNA sequencing, and to assess how coffee-shade tree associations, with different soil and plant parameters, influence the bacterial ecosystem. Results revealed that the association between coffee and shade trees increased alpha diversity, with the highest diversity found in the agroforestry systems. The dominant bacterial genera found in most of the samples, i.e., Kribbella, Nonomuraea, Nitrospira, Sphingobium and Neobacillus were strongly correlated with key soil chemical properties, including nitrogen content, organic matter, and available phosphorus. These correlations suggest that tree cover strategies exert beneficial effects on the bacterial microbiome. Moreover, the overall bacterial community structure was different when comparing coffee monoculture system and shade-associated systems. Our findings highlight that traditional coffee agroforestry practices involving shade trees foster more diverse bacterial communities, thereby contributing to healthier soils and more sustainable coffee production.},
}

*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Biodiversity
*Trees/microbiology
*Musa/microbiology
Soil/chemistry
*Coffee
Plant Roots/microbiology
*Mangifera/microbiology
Phylogeny
Coffea
DNA, Bacterial/genetics
Agriculture/methods
Microbiota

@article {pmid42536708,
year = {2026},
author = {Molinero-Domingo, L and S Pascual, L and Rivero, RM and Mittler, R and I Zandalinas, S},
title = {Decoding multifactorial stress responses in plants: lessons from omics integration.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag389},
pmid = {42536708},
issn = {1460-2431},
abstract = {Plants in natural and agricultural environments are continuously exposed to multiple simultaneous abiotic stresses whose combined effects markedly differ from those of individual stresses. Despite this, our mechanistic understanding of plant stress biology still largely relies on reductionist frameworks based on single or pairwise interactions. Here, we argue that plant responses to increasing stress complexity are fundamentally non-additive and involve emergent molecular, metabolic, and physiological states that require a shift towards integrative and predictive approaches. We synthesize recent advances showing how signaling and metabolic networks are rewired under multifactorial stress combination (MFSC), leading to nonlinear behaviors and context-dependent regulation. We highlight the central role of multi-omics integration in uncovering system-level responses and discuss how emerging computational frameworks, including machine learning, can transform high-dimensional datasets into predictive models linking molecular states to plant performance. We further evaluate the limitations of current experimental systems, emphasizing the gap between controlled-environment studies and field conditions, where stress dynamics, microbiome interactions, and genotype × environment complexity shape plant responses. Together, we propose a roadmap towards a predictive science of plant resilience under MFSC, with direct implications for crop improvement in the context of climate change.},
}

@article {pmid42537292,
year = {2026},
author = {Han, S and Mo, Q and Wen, X and Wang, X and Wang, X and Yu, Y and Yang, Y and Yang, C and Cai, Z and Zhou, J},
title = {AI-2 type quorum-sensing signal enhances mercury resistance and adsorption in thermotolerant Bacillus subtilis.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143148},
doi = {10.1016/j.jhazmat.2026.143148},
pmid = {42537292},
issn = {1873-3336},
abstract = {Heavy metal contamination in coastal sediments threatens marine microbes and ecological health. Elucidating microbial community synergistic resistance mechanisms is essential for developing novel bioremediation strategies. Microorganisms are known to regulate population-level adaptation to environmental stress through quorum-sensing signals, yet the role of autoinducer-2 (AI-2) in mercury (Hg) resistance and immobilization remains poorly understood. Here, we isolated a thermotolerant Bacillus subtilis strain from coastal sediments and demonstrated that Hg stress selectively activated luxS-associated AI-2 production. AI-2 addition enhanced bacterial survival under combined Hg and heat stress by reducing intracellular reactive oxygen species, increasing antioxidant enzyme activities, promoting biofilm formation, and strengthening Hg adsorption. Sediment microcosm validation further showed that the B. subtilis + AI-2 treatment reduced soluble Hg by 29.6% after 24 h and increased the biomass-associated Hg fraction. These results reveal an AI-2-associated microbial strategy that links intracellular detoxification with extracellular Hg immobilization. While further genetic validation is needed to establish its causal role, this mechanism provides mechanistic insight for microbiome-assisted mercury remediation in thermally dynamic coastal sediments.},
}

@article {pmid42537413,
year = {2026},
author = {Lee, S and Miyamoto, H and Takai, Y and Suda, W and Ohno, H and Shimasaki, Y and Oshima, Y},
title = {Changes in dysbiosis and gene expression in the gut of wharf roach (Ligia spp.) fed with expanded polystyrene.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 1},
pages = {120200},
doi = {10.1016/j.marpolbul.2026.120200},
pmid = {42537413},
issn = {1879-3363},
abstract = {The East Asian region, with its intensive human and fishery activity, suffers from serious marine plastic pollution along its coastlines. Wharf roaches (Ligia spp.) on the coast of western Japan frequently ingest expanded polystyrene (EPS) and excrete it as microplastic in their feces, yet the effects on their gut remain unclear. Under controlled laboratory exposure, we examined both the host gut transcriptome, and the gut microbiome of wharf roaches fed EPS versus a fasted control group. DESeq2 and PyDESeq2 yielded a high-confidence set of 25 differentially expressed genes, among which xenobiotic-metabolism enzymes-a cytochrome P450, a UDP-glucuronosyltransferase, and a sulfotransferase-were up-regulated in the EPS-fed group. In contrast, the overall gut microbial community structure was unchanged: neither alpha nor beta diversity differed significantly between groups in any domain. At the taxon level, a few low-abundance archaeal and viral taxa, including the archaea Methanospirillum, Halalkalicoccus, and Desulfurococcus, and T4-like viruses, were detected in all EPS samples but were below the detection limit in all controls. Because the comparison used a fasted control, the extent to which these responses are specific to EPS exposure remains to be established. Building on previous field studies identifying wharf roaches as bioindicators of coastal EPS pollution, this study highlights the wharf roach as a tractable model for investigating the gut-level effects of plastic ingestion.},
}

@article {pmid42537619,
year = {2026},
author = {da Silva Figueiredo Vidal, I and de Souza, ATB and Silva, LG and de Andrade Santana, LH and de Morais Filho, JR and Câmara, ABF and Cobucci, RN and de Lima, KMG and de Oliveira Crispim, JC},
title = {Near-infrared spectroscopy with chemometric analysis distinguishes genitourinary syndrome of menopause in vaginal samples.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {325},
number = {},
pages = {115336},
doi = {10.1016/j.ejogrb.2026.115336},
pmid = {42537619},
issn = {1872-7654},
abstract = {BACKGROUND: Genitourinary syndrome of menopause (GSM) is a prevalent condition characterized by estrogen deficiency-induced vulvovaginal and urinary symptoms, yet lacks objective diagnostic biomarkers.

OBJECTIVE: This study aimed to investigate whether near-infrared (NIR) spectroscopy combined with multivariate chemometrics analysis of vaginal samples could serve as a quantitative diagnostic tool for GSM.

DESIGN: We applied NIR spectroscopy combined with multivariate chemometric analysis to vaginal samples from 81 postmenopausal women (50 GSM cases, 31 controls), assessing vaginal health via the Vaginal Health Index (VHI).

RESULTS: Women with GSM had significantly lower total VHI scores. GSM samples exhibited distinct spectral signatures related to tissue hydration, lipids, and proteins. Classification models using genetic and successive projections algorithms coupled with linear discriminant analysis achieved 100% accuracy in independent validation.

CONCLUSION: For the first time, this study demonstrated that NIR spectroscopy with chemometrics enables non-invasive, objective discrimination of GSM, supporting a shift from subjective symptom assessment toward quantitative molecular phenotyping. This study offers a novel perspective on the spectral differences associated with GSM. This approach holds promise for point-of-care diagnostics and monitoring therapeutic response, pending further validation. These findings should be regarded as hypothesis-generating, derived from a single-center pilot cohort, and require confirmation in larger, multicenter, prospective studies incorporating microbiome analysis before clinical implementation.},
}

@article {pmid42537648,
year = {2026},
author = {Rashid, RB and Chung, CK and Namubiru, P and Ahmed, T and , and Howard, DR and Sebina, I and Wilkins, T and Rana, MS and Morrow, JP and Creek, DJ and Moll, JM and Vidal, K and Fumero, C and Lavalle, L and Maes, D and Hays, NP and Silva-Zolezzi, I and Forbes-Blom, E and Sprenger, N and Picaud, JC and Phipps, S and Noti, M},
title = {Early-life immune imprinting by a B. infantis-HMO synbiotic shapes infant immune signatures and protects against experimental respiratory disease.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102935},
doi = {10.1016/j.xcrm.2026.102935},
pmid = {42537648},
issn = {2666-3791},
abstract = {Early microbial colonization influences immune development, with lower abundance of human milk oligosaccharide (HMO)-utilizing bifidobacteria linked to immune-related disorder risk. Here, we demonstrate that synbiotic supplementation with Bifidobacterium infantis (LMG 11588) and a blend of six structurally diverse HMOs plus Bifidobacterium lactis (CNCM I-3446) altered gut microbiome composition, changed systemic immune cell-networks, and reduced persistence of a T helper 2 (Th2) bias in formula-fed infants, following a pattern observed in breastfed infants. In preclinical models, synbiotic reduces lower respiratory tract infection (LRI) severity and aberrant type-2 immune responses and confers lasting immune benefits into adulthood. These effects are associated with changes in the circulating metabolome, including increased 12(S)-hydroxyheptadecatrienoic acid (12-HHT), which correlates with improved infection outcomes and phenocopies synbiotic-mediated protection when administered orally. Together, these findings indicate that infant-type synbiotic supplementation during a critical early-life window can imprint immune function and promote disease tolerance.},
}

@article {pmid42537713,
year = {2026},
author = {Li, M and Kablan, A and Toktau, G and Ahmad, A and Meng, L and Li, Z and Zuo, Z and Gemingbai, S and Otebay, A and Satiyeva, A and Xie, Y},
title = {Industrial additive and dietary fiber inulin induces tumor-selective necrotic death via mitochondrial lipid peroxidation involving MYC and YAP.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {116309},
doi = {10.1016/j.fct.2026.116309},
pmid = {42537713},
issn = {1873-6351},
abstract = {Inulin as a prebiotic fiber and an industrial additive, has been shown to regulate gut and small intestinal microbiome for health, but non-microbiota-dependent cellular pathways remain unclear. Here we aim to determine how the natural polysaccharide inulin reshapes metabolic stress responses especially in colon cancer cells. In tumor cells treated by inulin, oxidized lipids accumulated in the perimitochondrial region and were accompanied by mitochondrial fragmentation, Golgi dispersion, endoplasmic reticulum (ER) disorganization, lysosomal remodeling, increased mitochondrially encoded cytochrome c oxidase II (MTCO2), and nuclear p21, indicating organelle stress coupled to metabolic reprogramming. Non-malignant cells showed elevated lipid peroxidation but limited necrotic death, consistent with greater metabolic tolerance. YAP/MYC inhibition increased inulin sensitivity. Importantly, ataxia telangiectasia and Rad3-related (ATR) supported stress adaptation, particularly in normal cells. Additionally, inulin decreased nuclear active MYC and YAP and enhanced nuclear androgen receptor (AR). Network pharmacology identified inulin against colon cancer by AR-related hub gene PTGS2 (prostaglandin G/H synthase-2) and validated by a synergistic combination with progesterone. Thus, inulin triggers tumor-selective metabolic stress and disrupts adaptive MYC/YAP, providing a rationale for metabolism-based precision cancer therapy.},
}

@article {pmid42537823,
year = {2026},
author = {Laetitia Huët, MA and Bhaw-Luximon, A},
title = {Beyond the parasite: reframing cutaneous leishmaniasis as a host-microbiome-vector ecosystem.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {127250},
doi = {10.1016/j.ijpharm.2026.127250},
pmid = {42537823},
issn = {1873-3476},
abstract = {Disease outcomes of cutaneous leishmaniasis (CL) result from dynamic interactions between host immunity, Leishmania parasites and the host-sandfly microbiomes. Current treatments focus on parasite elimination but are limited by toxicity, drug resistance, side effects and poor wound healing. These challenges highlight the need for multi-targeted interventions by transforming CL treatment from a single-infection model to an integrated host-microbe-parasite model. This review features advances in host-microbe-parasite-vector-based strategies for CL treatment, including emerging engineering and synthetic biology approaches. We also discuss the growing role of computational and artificial intelligence (AI)-driven frameworks in guiding the design of novel therapeutics and enhancing the efficacy of existing treatments. Climate change through rising temperatures, altered precipitation, and extended suitable habitats, is likely to increase the risk and geographic range of CL in many parts of the world. By integrating these engineering platforms with AI-guided approaches, this review outlines a systems-level strategy for developing next-generation therapies aimed at reducing the global burden of CL.},
}

@article {pmid42538087,
year = {2026},
author = {Kaiser-Powers, T and Weingarden, AR},
title = {Probiotics for Primary or Secondary Prevention of Clostridioides difficile Infection.},
journal = {Gastroenterology clinics of North America},
volume = {55},
number = {3},
pages = {433-445},
doi = {10.1016/j.gtc.2026.05.004},
pmid = {42538087},
issn = {1558-1942},
mesh = {Humans ; *Probiotics/therapeutic use ; *Clostridium Infections/prevention & control ; *Secondary Prevention/methods ; Clostridioides difficile ; Primary Prevention/methods ; Prebiotics ; Anti-Bacterial Agents/therapeutic use ; Synbiotics ; },
abstract = {Clostridioides difficile infection (CDI) is a leading cause of hospital-acquired infectious diarrhea, often triggered by disruption of the gut microbiota. Recurrence is common after antibiotic treatment, prompting interest in microbial therapies such as probiotics. While some studies suggest probiotics may help prevent initial or recurrent CDI episodes, overall evidence remains inconsistent. Data on prebiotics and synbiotics are even more limited. Although generally safe, probiotics may delay restoration of the normal microbiome, which is key to preventing recurrence. Current guidelines vary from cautious support to discouragement of their use, leaving the role of these therapies in CDI management uncertain and investigational.},
}

Humans
*Probiotics/therapeutic use
*Clostridium Infections/prevention & control
*Secondary Prevention/methods
Clostridioides difficile
Primary Prevention/methods
Prebiotics
Anti-Bacterial Agents/therapeutic use
Synbiotics

@article {pmid42538092,
year = {2026},
author = {Adamopoulos, A and Stollman, N},
title = {Non-Fecal Microbiota Transplantation Strategies for Treatment of Recurrent Clostridioides difficile Infection.},
journal = {Gastroenterology clinics of North America},
volume = {55},
number = {3},
pages = {493-501},
doi = {10.1016/j.gtc.2026.05.009},
pmid = {42538092},
issn = {1558-1942},
mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; Recurrence ; Clostridioides difficile ; Fidaxomicin/therapeutic use ; Vancomycin/therapeutic use ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Secondary Prevention ; Microbiota ; },
abstract = {Clostridioides difficile infection (CDI) is a leading healthcare-associated illness with significant recurrence rates and clinical burden. Recurrent CDI (rCDI) arises from microbiota disruption, often exacerbated by antibiotic therapy. Current treatment strategies include fidaxomicin and vancomycin taper regimens, with adjunctive options such as rifaximin in select cases. Preventive approaches focus on environmental decontamination and microbiome preservation. Emerging therapies, including live biotherapeutics, non-toxigenic strains, and microbiome-protective agents, show promise in reducing recurrence. Dietary interventions that enhance microbial diversity may also support recovery. Together, these strategies highlight a shift toward microbiome-centered management of rCDI.},
}

Humans
*Clostridium Infections/therapy/microbiology
Anti-Bacterial Agents/therapeutic use
Recurrence
Clostridioides difficile
Fidaxomicin/therapeutic use
Vancomycin/therapeutic use
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation
Secondary Prevention
Microbiota

@article {pmid42538093,
year = {2026},
author = {Berry, P and Allegretti, JR and Khanna, S},
title = {Food and Drug Administration-Approved Fecal Microbiota-Based Therapies for Recurrent Clostridioides difficile Infection.},
journal = {Gastroenterology clinics of North America},
volume = {55},
number = {3},
pages = {503-516},
doi = {10.1016/j.gtc.2026.05.010},
pmid = {42538093},
issn = {1558-1942},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Clostridium Infections/therapy ; Recurrence ; United States ; Clostridioides difficile ; Anti-Bacterial Agents/therapeutic use ; United States Food and Drug Administration ; Secondary Prevention/methods ; },
abstract = {Recurrent Clostridioides difficile infection remains common despite optimized antibiotic therapy. Two Food and Drug Administration-approved donor-derived fecal microbiota-based products, fecal microbiota, live-jslm (Rebyota / RBL) and fecal microbiota spores, live-brpk (Vowst / VOS) reduce recurrence when administered after completion of standard antibiotics. This review summarizes the clinical development programs supporting these products, including pivotal randomized trials, open-label extensions, durability data, safety outcomes, and emerging real-world evidence. We also discuss patient selection, timing after antibiotics, diagnostic considerations, and practical implementation. These therapies represent standardized, evidence-based approaches to restoring colonization resistance and preventing recurrent infection in appropriately selected adults.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Clostridium Infections/therapy
Recurrence
United States
Clostridioides difficile
Anti-Bacterial Agents/therapeutic use
United States Food and Drug Administration
Secondary Prevention/methods

@article {pmid42527298,
year = {2026},
author = {Pluta, DH and Gilbertie, JM},
title = {The Methicillin-Resistant S pseudintermedius Crisis: Are We Out of Options to Treat the Most Common Canine Pathogen?.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cvsm.2026.06.004},
pmid = {42527298},
issn = {1878-1306},
abstract = {S pseudintermedius is a leading cause of canine pyoderma and an important pathogen in small animal skin, soft tissue, otic, wound, and postoperative infections. The emergence of methicillin-resistant S pseudintermedius (MRSP) has made recurrent infections more difficult to manage by combining multidrug resistance, biofilm-associated persistence, treatment failure, and repeated antimicrobial exposure. This article reviews MRSP emergence and epidemiology, mechanisms of resistance and recurrence, and the limitations of current treatment options. It discusses emerging therapeutic strategies, including phage-based therapies, microbiome-directed interventions, immune modulation, nanomaterials, photodynamic therapy, and antimicrobial peptides, that serve as adjuncts to standard care and reduce reliance on systemic antimicrobials.},
}

@article {pmid42527363,
year = {2026},
author = {de Matos-Konrad, C and Chima, N and Huntington, MK},
title = {Clostridium innocuum Bacteremia: Case Report and Systematic Review.},
journal = {South Dakota medicine : the journal of the South Dakota State Medical Association},
volume = {79},
number = {6},
pages = {271-273},
pmid = {42527363},
issn = {0038-3317},
mesh = {Humans ; *Clostridium Infections/diagnosis/drug therapy/microbiology ; *Bacteremia/microbiology/drug therapy/diagnosis ; *Clostridium/isolation & purification ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Diabetic Foot/complications ; Male ; Kidney Failure, Chronic/complications ; },
abstract = {Clostridium innocuum is an anaerobic gram-positive spore-forming bacteria, a commensal member of the human gut microbiome. We encountered a case of bacteremia with this organism as a complication of a foot ulcer in a middle-aged patient with diabetes, end-stage renal disease, and malnutrition. A systematic review of the limited number of previously reported cases of C. innocuum bacteremia is presented, along with a brief narrative review the organism's association with other diseases, ranging from diarrhea and local infections to modulating inflammatory bowel disease and kidney disease.},
}

Humans
*Clostridium Infections/diagnosis/drug therapy/microbiology
*Bacteremia/microbiology/drug therapy/diagnosis
*Clostridium/isolation & purification
Middle Aged
Anti-Bacterial Agents/therapeutic use
*Diabetic Foot/complications
Male
Kidney Failure, Chronic/complications

@article {pmid42527537,
year = {2026},
author = {Zaman, A and Cook, T and Mabou, DB and Schexnayder, M and Xiao, R and Perveen, Z and Penn, AL and Noël, A},
title = {Sex-specific modulation of lung function and transcriptome in neonate mice exposed to thirdhand electronic-cigarette aerosols.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42527537},
issn = {1530-0447},
abstract = {BACKGROUND: Vaping is increasingly prevalent among young adults at age for starting families. Thirdhand e-cigarette aerosols (THEA) are persistent residues that adhere to indoor surfaces and can resuspend in air. Since lung development continues after birth, infants from homes with adults who vape, are vulnerable to THEA exposures.

METHODS: Neonate mice were exposed to THEA with nicotine or nicotine + tobacco-flavoring from terrycloth and carpet for the first 21 days of life. We assessed broncho-alveolar lavage cytology, lung morphometry, gene expression, and intestinal microbiomes at 21 days. At 10 weeks, we evaluated lung function.

RESULTS: We showed that exposures to THEA during alveologenesis, a critical window of lung development, induced sex-specific alterations in pulmonary inflammatory and developmental trajectories. Females exhibited acute pulmonary neutrophilic inflammation with a resolving cytokine profile. In contrast, males exhibited upregulation of genes associated with pulmonary inflammation and epithelial mesenchymal transition, plus delayed lung development, leading to lung dysfunction in adulthood. Male gut microbiomes showed reduced abundance of taxa associated with xenobiotic biotransformation, suggesting host-microbial detoxification capacity as a target of THEA exposure.

CONCLUSION: Low-level of THEA exposures in early life can alter lung inflammation, structure, and function, increasing susceptibility to respiratory dysfunction later in life.

IMPACT: Early-life exposures to nicotine and carbonyls from thirdhand e-cigarette aerosols (THEA) may induce alterations in lung alveologenesis and augment susceptibility to lung conditions later in life. Using a preclinical model of pediatric airways, we showed that THEA exposures caused neutrophilic inflammation in neonate female mice. In neonate male mice, THEA exposures led to alterations in lung structure, gene expression, and gut microbiome dysbiosis. Adult male mice exposed to THEA as neonates exhibited decline in lung function characteristic of obstructive pulmonary physiology.},
}

@article {pmid42527633,
year = {2026},
author = {Brunner, S and Plagge, J and Zimmermann-Kogadeeva, M and Höring, M and Liebisch, G and Basic, M and Bolsega, S and Janssen, KP and Slack, E and von Gamm, S and Viehof-Beckmann, A and Clavel, T and Zimmermann, M and Heeren, J and Giansanti, P and Weiss, AS and Hermeling, S and Dupont, A and Ullrich, AL and Jokisch, F and Seeliger, C and Bleich, A and Hidrobo, M and Stecher, B and Coleman, OI and Moresi, C and Greter, G and Arnoldini, M and Scheiber, J and Matysik, S and Klingenspor, M and Küster, B and Haller, D and Burkhardt, R and Kuipers, F and Ecker, J},
title = {Gut microbiota restricts intestinal lipid uptake via modulation of bile phosphatidylcholine metabolism in mice.},
journal = {Nature microbiology},
volume = {11},
number = {8},
pages = {2349-2364},
pmid = {42527633},
issn = {2058-5276},
support = {395357507-SFB 1371, P13//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 446175916//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; INST 95/1650-1 FUGG//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 395357507-SFB 1371//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 279971426//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Phosphatidylcholines/metabolism ; Mice ; *Bile/metabolism ; *Lipid Metabolism ; *Gastrointestinal Microbiome/physiology ; Germ-Free Life ; Taurocholic Acid/metabolism ; Mice, Inbred C57BL ; Liver/metabolism ; Male ; Intestinal Absorption ; Intestinal Mucosa/metabolism ; },
abstract = {The gut microbiota influences host metabolism, but the mechanisms of lipid uptake from food remain mysterious. Here we used stable isotope-labelled tracers in gnotobiotic mouse models, which revealed that host uptake of dietary lipids depends on microbial colonization. Systemic lipid metabolism modelling predicted that the gut microbiota restricts intestinal lipid absorption, and labelled lipid administration verified that the gut contents of microbiota-colonized mice contained up to 12-fold more lipids than those of germ-free animals. A combination of lipidomics and proteomics showed that gut microbes trigger Myd88 signalling, leading to a downregulation of hepatic Cyp7b1 activity and increased taurocholate production. Taurocholate stimulates phospholipase A1 activity in bile, causing the degradation of phosphatidylcholine that is essential for luminal micelle formation and lipid uptake. A diverse microbiome was associated with lower phosphatidylcholine content. This previously unrecognized host-gut microbiota interplay via enzymes in bile could provide future targets to modulate dietary lipid absorption.},
}

Animals
*Phosphatidylcholines/metabolism
Mice
*Bile/metabolism
*Lipid Metabolism
*Gastrointestinal Microbiome/physiology
Germ-Free Life
Taurocholic Acid/metabolism
Mice, Inbred C57BL
Liver/metabolism
Male
Intestinal Absorption
Intestinal Mucosa/metabolism

@article {pmid42527661,
year = {2026},
author = {Dagbasi, A and Cai, M and Hirdaramani, A and Hanyaloglu, A and Morrison, DJ and Frost, G},
title = {Short-chain fatty acids.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {42527661},
issn = {2522-5812},
support = {BB/N016947/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Short-chain fatty acids (SCFAs), principally acetate, propionate and butyrate, are produced by the gut microbiota through the fermentation of non-digestible carbohydrates. Beyond serving as energy substrates, SCFAs act as signalling molecules that influence metabolism, immune function and physiological homeostasis across multiple organ systems. This Review consolidates the fragmented literature on SCFAs and provides an overview of their production, metabolism and physiological actions. We discuss the microbial and dietary determinants of SCFA production, including the roles of the gut microbiome, cross-feeding interactions and dietary carbohydrates. We then examine the mechanisms through which SCFAs exert their effects, focusing on receptor-mediated signalling, epigenetic regulation and tissue-specific physiological functions. Finally, we evaluate the current evidence linking SCFAs to metabolic health and disease and consider the translational potential of targeting SCFA pathways through dietary and therapeutic approaches. At a time when inadequate dietary fibre intake is a growing public health concern, this Review highlights the physiological importance of SCFAs and their potential role in metabolic health and disease prevention.},
}

@article {pmid42527892,
year = {2026},
author = {Dhawan, N and Yasrebi, S and Hagan, J and Brasher, MI and Patil, MS},
title = {Impact of labor before delivery on necrotizing enterocolitis in very low birth weight infants.},
journal = {Journal of neonatal-perinatal medicine},
volume = {},
number = {},
pages = {19345798261475330},
doi = {10.1177/19345798261475330},
pmid = {42527892},
issn = {1878-4429},
abstract = {BackgroundNecrotizing Enterocolitis (NEC) is multifactorial, and the gut microbiome may contribute. Neonatal gut colonization differs by delivery mode; while delivery mode has not been linked to NEC in prior studies, the impact of labor prior to delivery is unknown. Our objective was to investigate the impact of labor prior to delivery on NEC incidence in very low birth weight (VLBW, <1500 g) infants.MethodsWe performed a single-center retrospective cohort study of VLBW infants 23 0/7-34 6/7 weeks gestation born at our center between 03/25/2012 and 12/31/2023. Infants with congenital anomalies or who died prior to admission were excluded. Labor was defined as uterine contractions with cervical dilation or effacement. When cervical exam was undocumented, labor was determined by presence of regular contractions >1 h before delivery. Multivariable logistic regression evaluated the association between labor before delivery and NEC after adjusting for baseline differences.ResultsAmong 1,951 infants, 1,175 (60.2%) were exposed to labor before delivery. Groups differed by gestational age, birth weight, chorioamnionitis, maternal diabetes, multiple gestation, and small for gestational age. Exposure to labor had lower odds of NEC (odds ratio [OR] = 0.606, 95% confidence interval [CI]: 0.407-0.902, p = 0.01), compared to those unexposed. This association remained significant after adjustment (adjusted OR = 0.614, 95% CI: 0.384-0.983, p = 0.04). There was no difference in surgical NEC.ConclusionsLabor prior to delivery was associated with lower odds of NEC in this VLBW cohort, highlighting the potential importance of perinatal microbial exposures and suggesting new avenues for NEC risk stratification and prevention.},
}

@article {pmid42527911,
year = {2026},
author = {Brändel, SD and Melville, DW and Wilhelm, K and Corman, VM and Page, R and Drosten, C and Tschapka, M and Sommer, S and Wasimuddin, },
title = {Astrovirus infection alters gut microbial communities in a widespread neotropical bat across human-modified landscapes.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42527911},
issn = {1471-2180},
mesh = {Animals ; *Chiroptera/microbiology/virology ; *Astroviridae Infections/veterinary/virology/epidemiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Panama ; *Astroviridae/isolation & purification ; Humans ; RNA, Ribosomal, 16S/genetics ; Forests ; Sequence Analysis, DNA ; Feces/microbiology/virology ; Phylogeny ; Biodiversity ; },
abstract = {Astroviruses are becoming a growing concern in public and veterinary health. In humans, astrovirus infections can cause severe diarrhea and may lead to neuropathological encephalitis, whereas in wildlife, these enteropathogenic viral infections often lack overt symptoms and thus remain unnoticed. Yet their close interaction with the host's gastrointestinal microbiome might drive cascading effects with disadvantages for host health. Bats harbor many zoonotic viruses without showing signs of disease, and many species move freely along the gradient from pristine to agricultural landscapes. To better understand the impact of astrovirus (AstV) infection under a One Health framework, we investigated the gut microbiome of naturally AstV-infected Seba's short-tailed bats (Carollia perspicillata, n = 234) inhabiting old-growth lowland forests or forest fragments embedded in an agricultural matrix in Panama. AstV prevalence was higher in forest fragments. We observed that AstV infection is associated with a shift in microbial beta but not alpha diversity, which points towards the replacement of common gut microbial taxa when infected. Indeed, potentially beneficial bacteria, such as Lactococcus, decreased in abundance, whereas potentially pathogenic bacteria from the Helicobacter genus increased in AstV-positive bats. Two Helicobacter haplotypes closely related to avian Helicobacter species were identified. We conclude that even though the impact of infection on the microbiome was not amplified in forest fragments, the higher infection likelihood in landscapes altered by humans implies more frequent or prolonged health repercussions for bats.},
}

Animals
*Chiroptera/microbiology/virology
*Astroviridae Infections/veterinary/virology/epidemiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
Panama
*Astroviridae/isolation & purification
Humans
RNA, Ribosomal, 16S/genetics
Forests
Sequence Analysis, DNA
Feces/microbiology/virology
Phylogeny
Biodiversity

@article {pmid42528084,
year = {2026},
author = {Sun, Y and Wei, K and Yang, K and Hui, J and Xia, D and Wang, X and Cartmill, AD and López, IF and Ma, C and Zhang, Q},
title = {Rhizosphere Engineering by Root Exudates: High-Yielding Alfalfa Recruits Functional PGPR to Sustain Soil Nutrient Availability Under Long-Term Cultivation.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70631},
pmid = {42528084},
issn = {1365-3040},
support = {2023B02031//Xinjiang Uygur Autonomous Region Key R&D Task Special Project/ ; 2026DB001//Science and Technology Program of XPCC/ ; 32260347//National Natural Science Foundation of China/ ; //T. R. Ellett Agricultural Research Trust/ ; },
abstract = {Soil nutrient transformation capacity is a critical determinant of sustainable productivity in perennial cropping systems; however, the extent to which high-yielding crops actively regulate rhizosphere microbial assembly to maintain nutrient availability remains poorly understood. We investigated whether root exudates from high-yielding alfalfa (Medicago sativa L.) selectively recruit plant growth-promoting rhizobacteria (PGPR) to enhance nutrient transformation. In an 8-year continuous alfalfa system (2018-2025), high-yielding cultivars increased soil organic carbon by 8.64%, total nitrogen by 6.01%, and moderately labile phosphorus fractions by 1.62%. Rhizobox experiments demonstrated that root exudates enhanced growth only with an active microbiome. High-yielding alfalfa enriched PGPR communities, specifically Ensifer, Pseudomonas, and Bacillus. Isolated strains exhibited N fixation, P solubilisation, and IAA production. Metabolomic profiling revealed that exudates were enriched in specific sugars and amino acids. Maltopentaose, maltotetraose, taurine, N-acetyl-L-leucine, and asparagine functioned as chemoattractants, stimulating PGPR proliferation and biofilm formation. These findings demonstrate that root exudate-mediated, targeted recruitment of functional PGPR enhances N fixation and P transformation, thereby supporting sustained high alfalfa productivity. This study demonstrates a key rhizosphere mechanism underlying the long-term sustainability of high-yielding perennial legume systems and provides a mechanistic basis for microbiome-informed sustainable alfalfa production and management.},
}

@article {pmid42528237,
year = {2026},
author = {Komiya, T and Koyama, K and Akiyama, R and Oda, H and Gokita, K and Sako, T and Mori, A},
title = {Comparison of the effects of four commercially available prescription diet regimens on the fecal microbiome in healthy cats.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.24-0494},
pmid = {42528237},
issn = {1347-7439},
abstract = {Diet significantly influences the gut microbiota, with variations in macronutrient content (proteins, fats, and carbohydrates) and the presence of non-digestible carbohydrates, such as fiber, playing crucial roles in shaping microbial composition. This study investigated the effects of four commercial prescription diets (low-carbohydrate, weight-loss, high soluble fiber, and renal) on the fecal microbiome of five healthy domestic cats using a 4×4 Latin square design. Fecal samples were analyzed using Illumina sequencing of the bacterial 16S rRNA gene to assess bacterial community structure and diversity. Results showed that cats fed the renal diet (low protein, high carbohydrate, high fat) were associated with higher relative abundances of the phylum Actinobacteria, particularly Bifidobacterium. The low-carbohydrate diet was associated with higher relative abundances of Adlercreutzia, Collinsella, and Slackia. The high-soluble fiber diet was associated with a higher relative proportion of Streptococcaceae. In contrast, the renal diet was associated with lower relative abundances of Blautia and Erysipelotrichaceae. No significant differences were observed in alpha-diversity indices among diets, whereas beta-diversity analysis showed significant differences in microbial community composition among dietary groups. These findings suggest that dietary composition may influence the fecal microbiome in healthy cats. However, given the exploratory design and compositional nature of the sequencing data, these findings should be interpreted cautiously and considered hypothesis-generating.},
}

@article {pmid42528288,
year = {2026},
author = {Mishra, S and Solanki, H and Mandal, P},
title = {Biomarkers From the Microbiome to Predict ALD Progression and Its Severity: A Comprehensive Review.},
journal = {Mediators of inflammation},
volume = {2026},
number = {1},
pages = {e7244952},
pmid = {42528288},
issn = {1466-1861},
mesh = {Humans ; *Biomarkers/metabolism ; Disease Progression ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Liver Diseases, Alcoholic/metabolism/microbiology ; Animals ; },
abstract = {Alcohol use is a major global health issue, causing about 3.3 million deaths each year, or roughly 5.9% of all deaths worldwide. Alcohol-related liver disease develops in stages: steatosis, steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. If alcohol consumption is discontinued at early stages, alcohol-related fatty liver disease can be reversed; however, continued exposure leads to progressive liver injury and increased mortality risk. Current diagnostic tools lack sufficient sensitivity and specificity to detect early-stage disease or accurately assess disease progression. This highlights the need for reliable and mechanistically relevant biomarkers for early diagnosis and staging. This review examines alterations in gut microbiota across different stages of alcohol-associated liver disease and evaluates gut microbiota-associated biomarkers, including microbial metabolites, in the context of their potential diagnostic and prognostic utility. In addition, the review discusses the limitations of existing biomarkers and highlights the emerging role of microbiome-derived signals in reflecting disease mechanisms. These findings suggest that gut microbiota-related biomarkers may provide a promising but still evolving approach for improving early detection and understanding disease progression in alcohol-associated liver disease.},
}

Humans
*Biomarkers/metabolism
Disease Progression
*Gastrointestinal Microbiome/physiology
*Microbiota
*Liver Diseases, Alcoholic/metabolism/microbiology
Animals

@article {pmid42528381,
year = {2026},
author = {Liu, L and Wang, G and Safo, SE},
title = {Multivariate functional linear discriminant analysis with feature selection: an application to inflammatory bowel disease classification.},
journal = {Biostatistics (Oxford, England)},
volume = {27},
number = {1},
pages = {},
pmid = {42528381},
issn = {1468-4357},
support = {/NH/NIH HHS/United States ; },
mesh = {Humans ; Discriminant Analysis ; *Inflammatory Bowel Diseases/classification/microbiology ; Multivariate Analysis ; Colitis, Ulcerative/microbiology/classification ; },
abstract = {Inflammatory Bowel Disease (IBD), including Crohn's Disease (CD) and Ulcerative Colitis (UC), presents significant public health challenges due to its complex etiology. Motivated by the IBD study of the Integrative Human Microbiome Project, our objective is to identify microbial pathways that distinguish between CD, UC, and non-IBD over time. Most current research relies on simplistic analyses that examine 1 variable or time point at a time, or address binary classification problems, limiting our understanding of the dynamic interactions within the microbiome over time. To address these limitations, we develop a novel functional data analysis approach for discriminant analysis of multivariate functional data that can effectively handle multiple high-dimensional predictors, sparse time points, and categorical outcomes. Our method seeks linear combinations of functions (ie discriminant functions) that maximize separation between 2 or more classes over time. We impose a sparsity-inducing penalty when estimating the discriminant functions, allowing us to identify relevant discriminating variables over time. Applications of our method to the motivating data identified microbial features related to mucin degradation, amino acid metabolism, and peptidoglycan recognition, which are implicated in the progression and development of IBD. Furthermore, our method highlighted the role of multiple vitamin B deficiencies in the context of IBD. By moving beyond traditional analytical frameworks, our innovative approach holds the potential for uncovering clinically meaningful discoveries in IBD research.},
}

Humans
Discriminant Analysis
*Inflammatory Bowel Diseases/classification/microbiology
Multivariate Analysis
Colitis, Ulcerative/microbiology/classification

@article {pmid42528616,
year = {2026},
author = {El-Kafrawy, SA and Abbas, AT and El-Kafrawy, AS and El-Daly, MM and Azhar, EI},
title = {Coexist or eliminate? Antibody-based functional silencing versus eradication in gut microbiome- targeted therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1903103},
pmid = {42528616},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology/drug effects ; *Antibodies, Monoclonal/therapeutic use ; Clostridioides difficile/immunology ; Immunoglobulins/immunology/therapeutic use ; *Clostridium Infections/immunology/microbiology/therapy ; },
abstract = {BACKGROUND: Dominant anti-infective strategies equate therapeutic success with pathogen eradication, yet in the gut most clinically relevant "pathogens" are pathobionts that cause disease only under specific ecological conditions. Antibiotics resolve infection but decimate commensal communities and select for resistance.

SCOPE AND APPROACH: We review antibody-based interventions, native mucosal antibodies (IgA, IgM), monoclonal antibodies, and immunoglobulin Y (IgY), as mechanistic test cases for a functional silencing paradigm, in which pathobiont virulence is attenuated through non-bactericidal mechanisms while preserving community architecture.

KEY FINDINGS: Drawing on randomized trial data (bezlotoxumab in Clostridioides difficile recurrence prevention, MODIFY I/II, n = 2,655), preclinical and early clinical IgY studies in enteric infections, and long-term IgY deployment in aquaculture, we find that functional silencing delivers durable benefit when disease is driven by discrete virulence factors. However, evolutionary risks, including phase variation, conformational switching, and the theoretical framework of "imperfect immunity", identify conditions under which retained pathobionts may re-emerge as threats.

CONCLUSIONS: Eradication and functional silencing are best understood as complementary strategies whose optimal deployment depends on host immune status, barrier integrity, and the nature of pathobiont virulence. Defining the boundary between safe coexistence and evolutionary rebound constitutes the field's central unresolved challenge.},
}

Humans
Animals
*Gastrointestinal Microbiome/immunology/drug effects
*Antibodies, Monoclonal/therapeutic use
Clostridioides difficile/immunology
Immunoglobulins/immunology/therapeutic use
*Clostridium Infections/immunology/microbiology/therapy

@article {pmid42528685,
year = {2026},
author = {Yu, X and Liu, Q and Huang, Y and Wang, Q and Wang, Y and Zhao, G},
title = {Microbial dysbiosis and wound healing in diabetic foot ulcers: a mini review with a note on the role of artificial intelligence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1891884},
pmid = {42528685},
issn = {2235-2988},
mesh = {Humans ; *Diabetic Foot/microbiology/therapy ; *Dysbiosis/microbiology/therapy ; *Wound Healing ; *Artificial Intelligence ; Biofilms/growth & development ; Probiotics/therapeutic use ; Gastrointestinal Microbiome ; Animals ; Skin Microbiome ; },
abstract = {Diabetic foot ulcers (DFUs) are a serious diabetes-related complication characterized by high rates of amputation and mortality. Emerging evidence suggests that DFUs are not simply the result of infection, but also involve microbiome dysbiosis, which impairs healing. Systemically, disturbances to the gut microbiota via the gut-skin axis promote systemic inflammation and metabolic dysfunction. Locally, skin microbial diversity is significantly reduced, allowing opportunistic pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa to form resilient biofilms. These biofilms resist antibiotics and host immunity, while microbial virulence factors exacerbate tissue damage and disrupt the healing cascade. This synergy between host pathology and dysbiosis perpetuates chronic ulceration. Novel therapeutic strategies therefore aim to modulate this aberrant ecology by shifting from broad-spectrum eradication to targeted restoration. Promising approaches include probiotics, phage therapy, traditional Chinese medicine, and faecal microbiota transplantation, which seek to recalibrate the microbiome and promote healing. However, translation into clinical practice requires more robust evidence from large-scale trials. Future perspectives point towards personalized microbial medicine, integrating multi-omics data and artificial intelligence to match interventions with specific microbial ecotypes, which may reduce the global burden of DFUs.},
}

Humans
*Diabetic Foot/microbiology/therapy
*Dysbiosis/microbiology/therapy
*Wound Healing
*Artificial Intelligence
Biofilms/growth & development
Probiotics/therapeutic use
Gastrointestinal Microbiome
Animals
Skin Microbiome

@article {pmid42528698,
year = {2026},
author = {Selim, S and Adhikary, K and Sarkar, R and Ganguly, K and Misra, A and Kashmiry, AA and Alshareef, SA and Alkhatib, SN and Hagagy, N and Maiti, R},
title = {Ecological and functional roles of plant microbiomes in environmental detoxification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1883316},
pmid = {42528698},
issn = {1664-302X},
abstract = {Plant-associated microbiomes play a crucial role in environmental detoxification by influencing the degradation, immobilization, and resistance to toxins in polluted settings. The ecological and functional activity of endogenous microbial communities, such as rhizobacteria and endophytic microorganisms, is not well studied when examining contaminants and their environments, despite the fact that plant-mediated bioremediation has garnered a lot of research attention. The majority of previously published research focuses on a single biodegradation route or solitary plant-microbe interactions. Our knowledge of how the microbiome's composition, functional diversity, and ecological stability of microbial communities work together to produce detoxifying results in practical applications is currently lacking. To advance understanding of how plant microbiomes cooperatively mediate environmental detoxification through metabolic interactions, adaptive responses, and host-microbiome communication, this review integrates insights from microbial ecology and functional microbiology. Its primary objective is to synthesize current knowledge on key microbial functions, including metal sequestration, xenobiotic degradation, redox regulation, and modulation of plant responses to biotic stress, while linking these functions to ecological processes such as host specificity, niche specialization, and community assembly. A distinctive aspect of this review is its ecosystem-level perspective, which shifts the focus from individual microbial taxa to the functional resilience of microbial communities in determining detoxification efficiency. The information provided in this review has a scope to provide framework to develop ecologically-sustaining, microbiome-based strategies for the detoxification of the environment and for conducting future bioremediation research.},
}

@article {pmid42528754,
year = {2026},
author = {Guo, L and Lu, J and Liu, L and Zhang, M and Yu, N and Lu, L and Yang, T and Zhou, J and Hou, B and Chen, Y and Geng, Y},
title = {Decoding the gut-adipose-ovary axis in polycystic ovary syndrome: from metabolic dysregulation to oncological risk modulation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1882127},
pmid = {42528754},
issn = {1664-302X},
abstract = {Polycystic ovary syndrome (PCOS) is traditionally managed as a localized reproductive disorder, but emerging evidence redefines it as a systemic metabolic-endocrine continuum with profound long-term health implications. This review comprehensively synthesizes the pathogenic role of the nutrition-mediated "gut-adipose-ovary axis" in bridging PCOS-associated metabolic dysfunction with an elevated risk of gynecological malignancies. Aberrant nutritional intake acts as the primary environmental catalyst, driving gut microbiota dysbiosis and metabolic endotoxemia. These gut-derived signals provoke visceral adipose tissue dysfunction, initiating a self-reinforcing cascade of systemic insulin resistance, hyperandrogenism, and chronic low-grade inflammation. Crucially, the convergence of these systemic insults continuously remodels the localized ovarian microenvironment. By sustaining proliferative signaling, forcing metabolic reprogramming, and fostering immune evasion, these convergent insults may contribute to a permissive pre-neoplastic microenvironment in susceptible patients with PCOS. To dismantle this pathogenic network, we outline a multi-dimensional therapeutic framework that integrates precision nutrition, microbiome modulation, and targeted pharmacological agents. Ultimately, this systems-biology perspective mandates a paradigm shift in clinical practice: moving beyond empirical symptom palliation toward proactive, risk-stratified interventions that interrupt the disease continuum and reduce long-term oncological risk in appropriately stratified women with PCOS.},
}

@article {pmid42528773,
year = {2026},
author = {Huang, GJ and Li, LJ and Li, PS and Fan, ZJ and Lu, BQ},
title = {Trained immunity in chronic rhinosinusitis: epigenetic reprogramming of innate immune memory as a driver of mucosal inflammation and recurrence.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1822395},
pmid = {42528773},
issn = {1664-3224},
mesh = {Humans ; *Rhinosinusitis/immunology/genetics ; *Trained Immunity ; *Immunity, Innate ; Chronic Disease ; *Immunologic Memory ; *Epigenesis, Genetic ; Animals ; Recurrence ; Inflammation/immunology ; *Nasal Mucosa/immunology ; Immunity, Mucosal ; },
abstract = {Chronic rhinosinusitis (CRS) is a highly prevalent and debilitating inflammatory condition of the upper airway, affecting 5-28% of the global population and imposing a substantial socioeconomic burden. Despite major advances in endoscopic sinus surgery, pharmacological management, and targeted biologic therapies, long-term disease recurrence following treatment remains an unresolved clinical challenge. Current pathophysiological frameworks centered on adaptive type 2 immunity, eosinophilic inflammation, and pathogen persistence fail to fully account for the chronification and therapy resistance of CRS. Emerging evidence positions trained immunity (the epigenetic and metabolic reprogramming of innate immune cells enabling non-antigen-specific functional memory) as a fundamental and previously underappreciated mechanism driving CRS recurrence. Persistent sinonasal microbial colonizers, including Staphylococcus aureus biofilms and fungal components, along with viral pathogens and dysbiotic microbiome communities, function as potent epigenetic training stimuli that reprogram sinonasal macrophages, group 2 innate lymphoid cells (ILC2s), and epithelial progenitor cells. The recent identification of a TLR4+ trained ILC2 subset in nasal polyp tissue, sustained by AP-1-driven chromatin remodeling at the Tlr4 locus, exemplifies the cellular specificity of this phenomenon. Concurrently, nasal basal stem cells acquire heritable pro-inflammatory chromatin states following type 2 cytokine exposure, encoding an epithelial inflammatory memory that perpetuates mucosal dysfunction independent of ongoing stimulation. This review systematically examines the microbial triggers, epigenetic mechanisms, key cellular mediators, and therapeutic implications of trained immunity in CRS, proposing a new framework for disease-modifying strategies targeting the sinonasal epigenetic inflammatory landscape.},
}

Humans
*Rhinosinusitis/immunology/genetics
*Trained Immunity
*Immunity, Innate
Chronic Disease
*Immunologic Memory
*Epigenesis, Genetic
Animals
Recurrence
Inflammation/immunology
*Nasal Mucosa/immunology
Immunity, Mucosal

@article {pmid42528838,
year = {2026},
author = {Kossenas, K and Damaskos, C and Garmpis, N},
title = {The diet-microbiota-inflammation axis and colorectal cancer.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1895753},
pmid = {42528838},
issn = {2234-943X},
abstract = {BACKGROUND: Colorectal cancer (CRC) is still one of the leading causes of cancer morbidity and mortality worldwide. There is increasing evidence that diet, gut microbiota, microbial metabolites and chronic inflammation are important factors in colorectal carcinogenesis and may provide novel opportunities for prevention, diagnosis and treatment.

AIM: To provide a comprehensive review of the current evidence on the role of diet, nutrition, microbial metabolism and chronic inflammation in CRC, with emphasis on emerging translational applications including microbiome-based biomarkers and microbiota-targeted therapeutic strategies.

METHODS: A literature search was performed with PubMed, Scopus and the Cochrane Library. Relevant studies on diet-microbiota interactions, microbial metabolites, inflammatory mechanisms, colorectal carcinogenesis, microbiome-derived biomarkers, and microbiota-targeted interventions were identified and reviewed. Preclinical and clinical studies and high quality reviews and meta-analyses were considered.

RESULTS: Dietary patterns have been shown to have a major impact on the composition and function of the gut microbiota. Rich-fiber diets and short-chain fatty acids (SCFAs) production seem protective against CRC, while western dietary patterns, ultra-processed foods and dysbiosis-associated metabolites promote a pro-inflammatory environment associated with carcinogenesis. Some microorganisms such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis and pks-positive Escherichia coli have been associated with CRC by inflammatory, genotoxic and immune-modulatory mechanisms. Recent advances in sequencing technologies and multi-omics approaches have enabled the identification of microbial signatures with potential diagnostic and prognostic value. Moreover, microbiota-targeted interventions such as probiotics, prebiotics, postbiotics, faecal microbiota transplantation, and next-generation microbial therapies have yielded promising preclinical and early clinical results.

CONCLUSIONS: The diet-microbiota-inflammation axis is a key player in colorectal carcinogenesis and a promising target for translational research. Microbiome-based biomarkers and microbiota-targeted therapies may have a role in future precision prevention and personalised management strategies of colorectal cancer despite significant challenges in terms of causation, standardisation and translation into clinical practice.},
}

@article {pmid42528952,
year = {2026},
author = {Liu, X and Cheng, W and Li, C and Dessie, W and Qi, C and Ayaz, M and Xu, X},
title = {Integrated metagenomic and metabolomic insights into microbial metabolic reprogramming in the rhizosphere of the invasive plant Praxelis clematidea under low-temperature stress.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852122},
pmid = {42528952},
issn = {1664-302X},
abstract = {A primary factor preventing the spread of the invasive plant Praxelis clematidea to higher latitudes and altitudes is the low-temperature stress induced by global climate change. The present study investigated the impact of low-temperature stress on the rhizosphere soil micro-ecosystem of P. clematidea, with the aim of examining its adaptive micro-ecological mechanisms via a comprehensive multi-omics approach. The rhizosphere soils of plants were compared under low-temperature (LT, 5 °C) or normal-temperature (HT, 25 °C) treatments. Using soil physicochemical analysis, enzyme activity assay, metagenomics, and non-targeted metabolomics, we observed that LT stress did not significantly alter microbial alpha diversity but strongly shifted the community structure. This change enriched cold-tolerant bacterial taxa, including Nocardiopsis, Sphingobium and Azoarcus. The LT stress was associated with altered carbon and nitrogen cycling, as indicated by increased soil urease activity but decreased alkaline phosphatase and catalase activities. The nitrate-N and ammonium-N levels increased, but total nitrogen, total organic carbon, and organic matter were reduced. Additionally, metagenomic study revealed overexpression of major microbial carbon metabolism genes (e.g., TCA cycle and glycolysis) and downregulation of nitrogen assimilation genes (e.g., glnA and NasA). Furthermore, metabolomics indicated a rise in carbohydrates and vitamins, along with a notable accumulation of stress-resistant secondary metabolites such as phenolic acids, flavonoids, and terpenes in the rhizosphere soils under LT stress. Correlation analysis indicated strong positive associations between the enriched cold-tolerant genera and these stress-resistant metabolites (e.g., costunolide and choline sulfate). Functional enrichment analysis suggested a metabolic reprogramming signature coupled with low-temperature treatment. Finally, this integrated multi-omics study reveals that P. clematidea is associated with an altered rhizosphere microbiome, differential functional gene abundance, and reorganized metabolic networks under low-temperature conditions. These findings offer a vital micro-ecological elucidation for P. clematidea effective colonization and propagation in novel, colder habitats.},
}

@article {pmid42529037,
year = {2026},
author = {Zhao, Y and Gao, Q and Li, G and Zhou, Q and Yang, F and Zhu, X},
title = {Microbiota-directed therapies for atopic dermatitis: a three-tier framework for inflammation control, immune modulation, and microbiome restoration.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1873455},
pmid = {42529037},
issn = {1664-3224},
mesh = {Humans ; *Dermatitis, Atopic/therapy/immunology/microbiology ; Skin Microbiome ; Animals ; *Immunomodulation ; Inflammation/therapy/immunology ; Probiotics/therapeutic use ; *Microbiota/immunology ; Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; Skin/microbiology/immunology ; },
abstract = {The pathogenesis of atopic dermatitis (AD) involves cutaneous barrier dysfunction, immune dysregulation, and microbiota imbalance. Although microbiota-directed therapeutic approaches have garnered increasing attention, current evidence is heterogeneous, encompassing probiotics, postbiotics, microbial metabolites, local microbial interventions, antimicrobials and ecological modulation strategies. This narrative review does not aim to provide clinical guidelines, but rather seeks to synthesise existing evidence within a three-tier conceptual framework. This framework classifies interventions into three categories: those primarily addressing local inflammation and barrier-associated microbiota dysbiosis; those exerting systemic immunomodulation via gut-derived microbial signals; and those modulating the skin microbiota ecology. It should be noted that human clinical data are still limited and heterogeneous, and much mechanistic insight is derived from preclinical research. By clarifying mechanistic layers and evidentiary gaps, this framework may facilitate future research to evaluate the sequencing or combination of anti-inflammatory therapy, barrier restoration, and microbiota ecological modulation.},
}

Humans
*Dermatitis, Atopic/therapy/immunology/microbiology
Skin Microbiome
Animals
*Immunomodulation
Inflammation/therapy/immunology
Probiotics/therapeutic use
*Microbiota/immunology
Dysbiosis/immunology/therapy
*Gastrointestinal Microbiome/immunology
Skin/microbiology/immunology

@article {pmid42529077,
year = {2026},
author = {Zhao, X and McCarter, SJ and Gupta, VK and Grant, KM and St Louis, EK and Kantarci, K and Savica, R and Hill, M and Vuong, HE and Staley, C and Boeve, BF and Ross, OA and Teigen, LM and Sung, J},
title = {Shotgun metagenomic analysis reveals taxonomic and functional alterations in the gut microbiome across prodromal and symptomatic Lewy body disease.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1834726},
pmid = {42529077},
issn = {2813-4338},
abstract = {BACKGROUND: Lewy body disease (LBD) is a progressive neurodegenerative a-synucleinopathy, whereas isolated REM sleep behavior disorder (iRBD) is recognized as a prodromal stage of LBD. Although growing evidence implicates the gut-brain axis in neurodegeneration, the taxonomic and functional roles of the gut microbiome across the prodromal-to-symptomatic LBD continuum remain poorly defined.

METHODS: Here, we performed shotgun metagenomic sequencing on stool samples from 25 patients with LBD (10 mild cognitive impairment due to LBD [MCI-LB] and 15 dementia with Lewy bodies [DLB]), 10 individuals with iRBD, and their household matched cohabitant controls to characterize disease-associated microbial alterations while minimizing environmental confounding.

RESULTS: Despite no significant differences in global microbial diversity, we identified convergent shifts in microbial taxa, metabolic pathways, and gene families across disease stages. Both LBD and iRBD showed increased abundance of microbial taxa potentially associated with gut barrier disruption, as well as higher abundance of functional pathways related to lipopolysaccharide biosynthesis. LBD showed lower abundance of pathways related to complex carbohydrate fermentation, and both groups showed lower abundance of pathways associated with neurotransmitter-related metabolism. In particular, pathways and gene families associated with starch degradation were reduced in LBD, and those associated with histidine-to-glutamate/ GABA metabolism were reduced in both groups.

DISCUSSION: These exploratory findings represent the first high-resolution, shotgun metagenomic characterization of gut microbiome alterations across the LBD continuum, highlighting functional patterns that may serve as candidate markers of disease progression in future longitudinal and mechanistic studies.},
}