@article {pmid42692206,
year = {2026},
author = {Browning, BD and Kirkland, AE and Meredith, LR and Perica, MI and Engevik, MA and Barb, JJ and Ferguson, PL and Tomko, RL and Squeglia, LM},
title = {Within- and Between-Visit Variability and Reproducibility of the Oral Microbiome in Young Adults with Alcohol Use Disorder.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2026.09.001},
pmid = {42692206},
issn = {1873-6823},
abstract = {BACKGROUND: The oral microbiome has emerged as a potential biomarker and pharmacological target in alcohol use disorder (AUD) due to its associations with alcohol use and related biological processes. However, its temporal variability and reproducibility remain poorly understood, limiting its utility.

METHODS: Saliva samples were obtained from participants enrolled in a randomized controlled trial of young adults with AUD. Temporal variability and reproducibility were evaluated using within-visit samples (∼4 hours apart; before and after sesame oil placebo and standardized snack) and between visits (∼25 days; pre-treatment). Alpha diversity, beta diversity, differential abundance, and intraclass correlation coefficients (ICCs) were calculated at the genus and species levels.

RESULTS: Significant within-visit differences were observed in alpha diversity, beta diversity, and the abundance of several genera and species. Snack type and time since last alcohol use explained comparable or greater variance in microbial composition than within-visit timepoint (4-6%). Although reproducibility of alpha diversity within-visit was generally low, most genera (70.3%) and species (74.6%) demonstrated at least moderate reproducibility. In contrast, no detectable systematic between-visit differences were observed in diversity or taxon abundance, and reproducibility was generally moderate for alpha diversity measures and most genera (67.6%) and species (72.2%).

CONCLUSIONS: Despite group-level microbial shifts within-visit, individual-level microbial features were generally reproducible both within (∼4 hours) and between (∼25 days) visits. No systematic group-level differences were detected between-visits.These findings support the use of the oral microbiome in AUD research while emphasizing the importance of longitudinal designs and accounting for recent exposures.},
}

@article {pmid42692250,
year = {2026},
author = {Wang, L and Zhang, Y and Li, W and Zhang, X and Li, C and Liu, Y and Su, Z and Wang, Y and Sun, C and Huang, L},
title = {Mulberry-derived endophytic Bacillus velezensis suppresses gray mold and promotes mulberry growth via reshaping the root metabolism and microbiome.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.09.002},
pmid = {42692250},
issn = {2090-1224},
abstract = {INTRODUCTION: Gray mold is an important fungal disease caused by Botrytis cinerea which threatens global agriculture. As chemical control faces limitations, biological control using Bacillus has gained attention for its environmental friendliness and growth promotion. However, their ecological basis and application potential in mulberry gray mold control remain insufficiently understood.

OBJECTIVE: This study aimed to evaluate the biocontrol efficacy of the mulberry derived endophytic strain Bacillus velezensis ZJU_268 and to investigate its associated effects on plant growth, root-associated microbiomes, and metabolic profiles.

METHODS: Greenhouse assays were combined with genomic and comparative genomic analyses, amplicon sequencing, non-targeted metabolomics, and functional validation of isolated microbes and metabolites to assess the effects of ZJU_268 and its cell free supernatant (CFS) on mulberry seedlings.

RESULTS: This study isolated a mulberry derived endophytic bacterium, B. velezensis ZJU_268, which exhibits strong antifungal activity and reduces the incidence of gray mold in mulberry seedlings. Whole-genome sequencing and comparative genomic analyses revealed strain-specific regions and genes associated with root colonization, stress adaptation, and antimicrobial biosynthesis. Both live cells and CFS significantly promoted seed germination, seedling growth, and biomass accumulation in a dose dependent manner. Amplicon sequencing showed that ZJU_268 and its supernatant reshaped the mulberry root microbiome, enriching beneficial bacterial and fungal taxa while reducing potentially pathogenic members. Cultivable members of the enriched microbiota displayed strong antifungal activity against B. cinerea and promoted mulberry growth. Metabolomic profiling further showed that ZJU_268 and its supernatant were associated with marked metabolic shifts in mulberry roots, accompanied by the accumulation of selected metabolites that supported the growth of representative enriched isolates.

CONCLUSIONS: This study demonstrates that ZJU_268 suppresses gray mold and promotes mulberry growth in association with direct antagonistic activity, microbiome restructuring, and holobiont-level metabolic shifts, providing a promising biological strategy for sustainable mulberry disease management.},
}

@article {pmid42692351,
year = {2026},
author = {Liu, P and Li, J and Zhu, C and Mao, S and Xie, F and Jin, W},
title = {Dietary supplementation of resveratrol alters rumen microbiome and reduces urinary trimethylamine/trimethylamine N-oxide excretion in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28661},
pmid = {42692351},
issn = {1525-3198},
abstract = {Trimethylamine (TMA) is a major product of ruminal choline metabolism. Understanding the microbial pathways associated with TMA formation may provide opportunities to improve rumen fermentation efficiency and animal productivity; however, effective strategies to regulate rumen TMA production remain poorly understood. In this study, in vitro and in vivo experiments were combined to investigate the effects of resveratrol on rumen TMA production and urinary excretion in dairy cows. In vitro rumen fermentation was conducted with 4 resveratrol doses (0, 0.5, 5, and 50 mmol/L). Concentrations of TMA were significantly lower in the 5 and 50 mmol/L resveratrol treatments compared with the control (0 mmol/L). The in vivo experiment was conducted using 36 mid-lactation Holstein cows with an average days in milk (DIM) of 171 ± 7 d and an average parity of 3.2 ± 0.4. The experiment lasted for 5 weeks, consisting of a 1-week adaptation period followed by a 4-week experimental period. Cows were blocked according to parity, milk yield, and days in milk and then randomly assigned to CON (basal diet), RES2.4 (basal diet + 2.4 g resveratrol/cow/day), and RES4.8 (basal diet + 4.8 g resveratrol/cow/day). The total concentrations of TMA and trimethylamine N-oxide (TMAO) in plasma and urine were reduced in cows in the RES4.8 group. Resveratrol did not affect dry matter intake, apparent nutrient digestibility, and milk performance, but it altered rumen fermentation parameters. Resveratrol also increased serum globulin and glutathione peroxidase levels and reduced serum IL-6, malondialdehyde, and superoxide dismutase. Metagenomic analysis showed that resveratrol shifted the structure of bacterial and archaeal communities but did not affect those of protozoa and fungi. The relative abundance of Prevotella was significantly lower in the RES4.8 group, whereas Eubacterium_S and the archaeal orders Methanobacteriales, Methanomicrobiales, and Methanococcales were higher. Functional profiling showed that resveratrol did not affect the overall composition of carbohydrate-active enzymes but decreased the abundance of pathways related to oxidative phosphorylation, the tricarboxylic acid (TCA) cycle, terpenoid backbone biosynthesis, lipopolysaccharide synthesis, and phenylpropanoid biosynthesis. Collectively, these findings provide new insights into the mechanisms underlying resveratrol-mediated regulation of rumen function and host TMA/TMAO metabolism.},
}

@article {pmid42692433,
year = {2026},
author = {Ahamba, IS and Goswami, N and Kinkpe, L and Han, H and Ikele, CM and Duan, Q and Kadurumba, O and Dong, X and Ren, Z},
title = {Host genetic and gut microbiota interactions regulating intramuscular fat deposition in livestock: mechanistic insights and implications for meat quality.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.260478},
pmid = {42692433},
issn = {2765-0189},
abstract = {Intramuscular fat (IMF) is a major determinant of meat quality, influencing tenderness, juiciness, flavor, oxidative stability, and nutritional value in livestock products. Increasing evidence indicates that IMF deposition is regulated by complex interactions between host genetics and gut microbial metabolism. This review summarizes current advances in the molecular and metabolic mechanisms linking host genetics and gut microbiota to IMF accumulation and meat quality traits. At the host level, IMF deposition is regulated by coordinated adipogenic networks involving PPARγ-C/EBPα signaling, lipogenic regulators, nutrient-sensitive pathways, and epigenetic modifications that control adipocyte differentiation and lipid storage. In parallel, the gut microbiota acts as an important metabolic regulator by producing bioactive metabolites, including short-chain fatty acids and secondary bile acids, which influence adipogenesis, inflammation, nutrient partitioning, and metabolic flexibility. Emerging evidence further demonstrates that microbial metabolites can modulate host transcriptional and epigenetic programs, thereby linking microbial activity with tissue-specific lipid metabolism. Integrative multi-omics approaches are increasingly revealing the mechanistic basis of host-microbiome interactions underlying variation in carcass composition and meat quality across livestock species. This review further highlights the translational potential of precision nutrition, microbiome modulation, and microbiome-informed breeding strategies for sustainable meat production.},
}

@article {pmid42692679,
year = {2026},
author = {Feng, G and Bayinbate, B and Huang, D and Badar, IH and Xu, B and Hu, Y and Zhang, L},
title = {Unraveling the mechanisms of flavor improvement in salt-reduced dry fermented sausages: Insights from yeast-modulated microbial interactions.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120265},
doi = {10.1016/j.foodres.2026.120265},
pmid = {42692679},
issn = {1873-7145},
mesh = {*Meat Products/microbiology/analysis ; Fermentation ; *Food Microbiology ; *Taste ; *Sodium Chloride ; *Microbial Interactions ; Candida/metabolism ; *Debaryomyces/metabolism ; Animals ; Lactobacillales/metabolism ; *Fermented Foods/microbiology ; Odorants/analysis ; Microbiota ; Hydrogen-Ion Concentration ; Yeasts ; },
abstract = {The present study investigated the modulatory effects of Candida zeylanoides AKS6 and Debaryomyces hansenii AKS44 on the quality profile attributes of reduced-NaCl fermented sausages. Results indicated that yeast inoculation decreased pH, moisture content and water activity of reduced-NaCl fermented sausages, establishing a foundation for enhanced microbial safety. Microbiome analysis revealed that the inoculated strains dominated the fungal community, exerting competitive exclusion against endogenous undesirable fungi (e.g., Trichosporon), while synergistically promoting beneficial lactic acid bacteria such as Latilactobacillus and Weissella. Volatile profiling demonstrated that NaCl reduction induced severe flavor defects. Yeast inoculation reduced formic acid content and mitigated lipid oxidation. Furthermore, driven by enhanced microbial esterification, the synthesis of fruity esters was promoted. This microbial restructuring drove the flavor improvement: suppression of off-flavor fungi combined with lactic acid bacteria-mediated ester biosynthesis enriching the fruity ester profile. Specifically, the odor activity value of methyl hexanoate significantly increased, becoming the dominant aroma contributor. These findings highlight the remarkable potential of C. zeylanoides AKS6 and D. hansenii AKS44 as starter cultures to reconstruct the microbial metabolic network and rescue the flavor quality of low-sodium fermented meat products.},
}

*Meat Products/microbiology/analysis
Fermentation
*Food Microbiology
*Taste
*Sodium Chloride
*Microbial Interactions
Candida/metabolism
*Debaryomyces/metabolism
Animals
Lactobacillales/metabolism
*Fermented Foods/microbiology
Odorants/analysis
Microbiota
Hydrogen-Ion Concentration
Yeasts

@article {pmid42692700,
year = {2026},
author = {Li, Z and Guo, Y and Zhang, X and Xie, N and Zhang, F and Zhen, Z},
title = {Integrated microbiome and metabolome analysis reveals microbial and metabolic dynamics associated with goose foie gras spoilage during refrigerated storage.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120303},
doi = {10.1016/j.foodres.2026.120303},
pmid = {42692700},
issn = {1873-7145},
mesh = {Animals ; *Metabolome ; *Food Storage/methods ; *Refrigeration ; *Microbiota ; *Geese/microbiology ; Thiobarbituric Acid Reactive Substances/analysis ; *Food Microbiology ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Colony Count, Microbial ; Bacteria ; Chromatography, High Pressure Liquid ; },
abstract = {Goose foie gras spoils rapidly under refrigeration, yet its microbial and metabolite dynamics during storage are poorly described. Samples from a single Landes production batch were stored at 4 °C in air-sealed polyethylene pouches and analysed on days 0, 2, 4, 6, 8, 10 and 12. Three biological replicates per time point were processed for total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substances (TBARS), 16S ribosomal RNA (rRNA) amplicon sequencing, and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based untargeted metabolomics. TVC increased from 3.85 to 6.16 log CFU/g, TVB-N from 8.99 to 27.77 mg/100 g and TBARS from 0.18 to 0.72 mg MDA/kg between day 0 and day 12, with the steepest changes appearing after day 6. The maximum TVC reached 6.16 log CFU g[-1] on day 12, below the 7 log CFU g[-1] level cited for some meat products; no sensory evaluation was performed. The late storage period is therefore described as a phase of concurrent rises in TVC, TVB-N and TBARS rather than as a confirmed spoilage endpoint. The 14 most abundant genera were retained for multivariate analysis. Seven genera, including Brochothrix, Pseudomonas, Lactobacillus and Lactococcus, met the operational definition of candidate spoilage-associated taxa. Forty candidate metabolites were screened by random forest. Five (tyramine, 4-hydroxyphenylacetaldehyde, adenosine monophosphate, oxidized glutathione and γ-glutamylcysteine) were prioritized on the joint basis of random forest importance, Benjamini-Hochberg-adjusted Kruskal-Wallis p < 0.05, ROC AUC ≥ 0.85 and KEGG pathway interpretability. Microbe-metabolite co-variation was quantified through Benjamini-Hochberg-adjusted Spearman correlation, yielding 108 microbe-metabolite pairs at BH-adjusted P < 0.05 (|ρ| ≥ 0.6), and canonical correlation analysis explained 73.39% of the joint cross-covariance in the first two variates. This study establishes a quantitative microbial-metabolic deterioration signature for refrigerated goose foie gras under air-sealed storage, provides a set of biomarker candidates with defined ROC performance, and identifies shifts in specific tyrosine, glutathione, purine and phospholipid pathways. The concordance between microbial succession and these pathway changes is hypothesis-generating and requires metagenomic confirmation, and these findings are presented as preliminary biochemical anchors for future targeted validation and preservation research.},
}

Animals
*Metabolome
*Food Storage/methods
*Refrigeration
*Microbiota
*Geese/microbiology
Thiobarbituric Acid Reactive Substances/analysis
*Food Microbiology
Metabolomics
RNA, Ribosomal, 16S/genetics
Colony Count, Microbial
Bacteria
Chromatography, High Pressure Liquid

@article {pmid42692712,
year = {2026},
author = {Fu, C and Ye, K and Qiu, Z and Hu, X and Wang, X and Xiao, H},
title = {Agaricus bisporus polysaccharides alleviate high-fat diet-induced cognitive impairment via microbiota-gut-brain axis modulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120317},
doi = {10.1016/j.foodres.2026.120317},
pmid = {42692712},
issn = {1873-7145},
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Agaricus/chemistry ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Mice, Inbred C57BL ; *Cognitive Dysfunction/drug therapy/etiology/prevention & control ; *Brain/drug effects/metabolism ; *Polysaccharides/pharmacology ; Hippocampus/drug effects/metabolism ; *Brain-Gut Axis/drug effects ; Neuronal Plasticity/drug effects ; Microglia/drug effects ; *Fungal Polysaccharides/pharmacology ; Fatty Acids, Volatile/metabolism ; },
abstract = {This study aimed to explore the protective effect of Agaricus bisporus polysaccharide (ABP) against high-fat diet (HFD) induced cognitive impairment (CI), with a particular focus on gut-brain communication. ABP supplementation alleviated anxiety-like behavior and cognitive deficits in HFD-fed mice. These effects were associated with enhanced hippocampal synaptic plasticity and attenuated inflammatory responses, which were accompanied by the elevation of Bdnf levels and the upregulated expression of plasticity-related genes (e.g., Gria2, Grin2b, Tdp2, and Fxr1). Crucially, ABP supplementation was associated with alleviated HFD-induced morphological changes in microglia and reduced inflammatory factor mRNA levels (Tnf, Il1b). Meanwhile, ABP remodeled the gut microbiome, significantly enriching beneficial taxa including Akkermansia and Bacteroides and enhancing the production of short-chain fatty acids (SCFAs), mainly acetate and propionate. These findings suggest that ABP may serve as a promising nutritional component for alleviating diet-related CI with effect associated with modulation of the microbiota-gut-brain axis.},
}

Animals
*Diet, High-Fat/adverse effects
*Agaricus/chemistry
*Gastrointestinal Microbiome/drug effects
Male
Mice
Mice, Inbred C57BL
*Cognitive Dysfunction/drug therapy/etiology/prevention & control
*Brain/drug effects/metabolism
*Polysaccharides/pharmacology
Hippocampus/drug effects/metabolism
*Brain-Gut Axis/drug effects
Neuronal Plasticity/drug effects
Microglia/drug effects
*Fungal Polysaccharides/pharmacology
Fatty Acids, Volatile/metabolism

@article {pmid42692846,
year = {2026},
author = {Vykypělová, M and Khrapova, V and Adamovský, O},
title = {Microplastic in human body - a critical insight into current microplastic research.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {58-62},
doi = {10.48095/ccko2026S58},
pmid = {42692846},
issn = {1802-5307},
mesh = {Humans ; *Microplastics/analysis ; *Environmental Exposure/adverse effects/analysis ; Particle Size ; *Environmental Pollutants/analysis ; },
abstract = {BACKGROUND: Microplastics and nanoplastics are ubiquitous environmental contaminants, and human exposure via ingestion and inhalation is increasingly recognized. Numerous studies report microplastics in human tissues and biological fluids, yet the biological relevance and robustness of these findings remain uncertain. This critical work evaluates current evidence on microplastics in the human body, focusing on exposure pathways, particle size relevance, and analytical limitations. Mechanistic data indicate that translocation across intestinal and pulmonary barriers is likely restricted to small microplastics (< 10 µm) and nanoplastics, raising questions about reports of larger particles in human tissues. Key challenges include secondary contamination, size-dependent detection limits, and methodological artifacts associated with common analytical techniques. Experimental evidence for biological effects, including inflammation, microbiome disruption, and cancer-related pathways, is discussed in the context of physiological relevance.

AIM: Overall, our work highlights the need for standardized analytical methods, rigorous quality control, and mechanistic studies using realistic exposure scenarios to support sound microplastics related human health research.},
}

Humans
*Microplastics/analysis
*Environmental Exposure/adverse effects/analysis
Particle Size
*Environmental Pollutants/analysis

@article {pmid42692847,
year = {2026},
author = {Budinská, E},
title = {Microbiome in early cancer detection - biomarker potential and limitations.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {63-66},
doi = {10.48095/ccko2026S63},
pmid = {42692847},
issn = {1802-5307},
mesh = {Humans ; *Early Detection of Cancer/methods ; *Neoplasms/diagnosis/microbiology ; *Microbiota ; *Biomarkers, Tumor ; },
abstract = {BACKGROUND: Microbiome analysis in cancer research has experienced a surge in interest comparable to the introduction of microarrays for tumor gene expression profiling 25 years ago. Associative studies investigating the composition of the microbiome in stool, tumor tissue swabs and tumor biopsies of oncology patients have been conducted across most cancer types, and their number continues to grow. Screening approaches based on non-invasive or minimally invasive sampling, including the analysis of stool, saliva, urine, and buccal and rectal swabs, are from a clinical perspective among the most promising, owing in part to simpler logistics and the possibility of repeated sampling. These types of specimens are commonly used in microbiome studies, making the microbiome an attractive target for both screening and diagnostic applications.

AIM: This review aims to summarize current knowledge regarding the potential of the microbiome in the early detection of cancer, emphasizing its clinical applicability and limitations in the context of population-based prevention.},
}

Humans
*Early Detection of Cancer/methods
*Neoplasms/diagnosis/microbiology
*Microbiota
*Biomarkers, Tumor

@article {pmid42692848,
year = {2026},
author = {Bořilová Linhartová, P and Száraz, D},
title = {Probiotics, postbiotics, and synbiotics in the prevention of oncological diseases.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {67-71},
doi = {10.48095/ccko2026S67},
pmid = {42692848},
issn = {1802-5307},
mesh = {Humans ; *Probiotics/therapeutic use ; *Synbiotics/administration & dosage ; *Neoplasms/prevention & control/microbiology ; Animals ; Prebiotics ; Microbiota ; },
abstract = {BACKGROUND: In the context of oncological diseases of (not only) the gastrointestinal tract and the oral cavity, the role of microorganisms is being increasingly discussed and investigated. A growing body of evidence supports the significance of specific microbial strains and their products both in the etiopathogenesis of certain cancers and in their prevention and therapy.

AIM: This review summarizes recent findings on the targeted modulation of the human microbiota using probiotics (including Bifidobacteria, Lactobacilli, etc.), their products (postbiotics, e. g. butyrate), and formulations combining probiotics with prebiotics (synbiotics), in the context of cancer prevention and progression, adverse effects of anticancer therapy, and associated complications related to the disease and surgical treatment. The results of clinical studies demonstrate the benefits of these preparations, particularly in preventing and alleviating gastrointestinal symptoms and postoperative infectious complications, as well as inflammatory mucosal damage (including oral mucositis) in oncology patients, with multi-strain probiotic formulations demonstrating greater efficacy. Research is even underway in animal models to explore the use of probiotics in immunotherapy. Despite the promising results obtained from modulating the human microbiota to improve the quality of life of cancer patients, as well as for cancer prevention and potentially even therapy, broader clinical implementation is limited by interindividual variability of the microbiome, safety concerns in immunocompromised patients, and the insufficiently documented quality of some available products. Nevertheless, given the undeniable mechanistic and translational potential of probiotic, postbiotic, and synbiotic supplementation, continued clinical research in this field is highly warranted.},
}

Humans
*Probiotics/therapeutic use
*Synbiotics/administration & dosage
*Neoplasms/prevention & control/microbiology
Animals
Prebiotics
Microbiota

@article {pmid42692861,
year = {2026},
author = {Subrahmanian, A and Patel, A and Veerus, L and Dominguez-Bello, MG and Blaser, MJ},
title = {Methanogens: vital but threatened members of the human microbiome?.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.08.008},
pmid = {42692861},
issn = {1878-4380},
abstract = {Methanogens are an ancestral group of archaea that occupy a unique niche within the human gut microbiome by virtue of their methane production. In this process, they serve as hydrogen sinks, allowing continued bacterial fermentation and influencing short-chain fatty acid production. Available evidence suggests that methanogen abundance may be declining in parallel with the broader reduction in gut microbial diversity accompanying industrialization. We describe the evolution of methanogens, their ecological roles in the human microbiome, and evidence for their apparent decline. If confirmed, reductions in methanogen prevalence and abundance may have substantial metabolic consequences, reframing these archaea as keystone species in need of scientific attention and conservation efforts.},
}

@article {pmid42692903,
year = {2026},
author = {Hejndorf, S and Gulay, A and Zheng, C and Nielsen, RV and Rasmussen, SB and Grønlykke, L and Nørgaard, JC and Rasmussen, KK and Rafiq, S and Català-Moll, F and Ravn, HB and Lundgren, J and Murray, DD and Ilett, E},
title = {The Relationship Between the Preoperative Gut Microbiome and Systemic Inflammatory Response Syndrome After Cardiac Surgery: A Prospective Cohort Study.},
journal = {Journal of cardiothoracic and vascular anesthesia},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.jvca.2026.08.119},
pmid = {42692903},
issn = {1532-8422},
abstract = {OBJECTIVES: To determine whether preoperative intestinal microbiome characteristics are associated with the development of systemic inflammatory response syndrome (SIRS) after cardiac surgery.

DESIGN: Single-center prospective observational cohort study.

SETTING: Tertiary university hospital.

PARTICIPANTS: A total of 196 adults undergoing elective cardiac surgery with extracorporeal circulation between 2018 and 2019.

INTERVENTIONS: No microbiome-targeted intervention was performed.

MEASUREMENTS AND MAIN RESULTS: Shotgun metagenomic sequencing was used to assess microbial diversity (inverse Simpson index, gene richness, dominance), taxonomic composition, and functional potential. The primary outcome was development of SIRS within 24 hours postoperatively. Associations were evaluated using Wilcoxon rank-sum tests, χ[2] tests, and logistic regression adjusted for age and sex. Forty-four patients (22%) developed SIRS. Microbiome diversity did not differ significantly between patients with and without SIRS (median inverse Simpson index 20.4 v 19.3, p = 0.12; gene richness, p = 0.30; dominance, p = 0.61). In adjusted analyses, diversity was not associated with SIRS risk (odds ratio, 1.04; 95% confidence interval, 0.99-1.07). Descriptive analyses of taxonomic composition and functional potential similarly revealed no significant differences between SIRS and non-SIRS groups.

CONCLUSIONS: In this cohort of elective cardiac surgery patients, preoperative gut microbiome diversity, composition, and functional potential were not associated with the development of postoperative SIRS. These findings do not support a strong causal or predictive role of the presurgical gut microbiome in postoperative inflammatory responses after cardiac surgery.},
}

@article {pmid42692915,
year = {2026},
author = {Pushpakumara, BLDU and Coffey, MJ and Hudson, J and Halim, J and Chuang, S and Prentice, B and Jaffe, A and Edwards, R and Day, AS and Oliver, M and Ranganathan, S and Wainwright, C and Selvadurai, H and van Dorst, J and Ooi, CY},
title = {The cystic fibrosis gut microbial dysbiosis index (CF-GMDI): a quantitative measure of gut microbial imbalance in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.08.007},
pmid = {42692915},
issn = {1873-5010},
abstract = {BACKGROUND: Gut dysbiosis is a hallmark of cystic fibrosis (CF), typically characterised using non-specific diversity metrics and study-specific taxonomic lists, limiting comparability across studies. We aimed to develop a metagenomic, species-level CF Gut Microbial Dysbiosis Index (CF-GMDI) to standardise measurement of gut microbial imbalance in children with CF (cwCF) METHODS: CF-GMDI was derived using stool metagenomic data from the PEARL-CF study (70 cwCF; 67 healthy controls (HC); 0-6 years). Differentially abundant taxa were identified between cwCF and HC using MaAsLin2. The index was calculated as the log10 ratio of the summed relative abundances of taxa enriched in CF vs HC to those depleted in CF vs HC. Reproducibility was assessed in the independent EARTH cohort (56 cwCF; 56 HC; 0-18 years). Responsiveness to therapy was evaluated using publicly available metagenomic data from an Elexacaftor/Tezacaftor/Ivacaftor (ETI) study (39 cwCF; 6-18 years).

RESULTS: CF-GMDI was significantly higher in cwCF than HC (p < 0.001), inversely correlated with species richness (ρ = -0.74, p < 0.001), and higher in pancreatic-insufficient vs pancreatic-sufficient cwCF in the PEARL-CF cohort (p = 0.01). Key ecological and clinical associations were replicated in the EARTH cohort. In the ETI study, CF-GMDI decreased significantly at 6 and 12 months post-treatment, whereas alpha diversity remained unchanged.

CONCLUSIONS: CF-GMDI is a CF-associated metric that captures clinically relevant gut microbiome restructuring not detected by standard diversity measures in cwCF (0-18 years). It differentiates disease and pancreatic status and tracks therapeutic modulation, supporting its use as a novel endpoint in CF intervention studies.},
}

@article {pmid42693012,
year = {2026},
author = {Nan, YQ and Wei, LW and Chen, RN and Zheng, XX and Chai, S and You, M and Zhang, H and Qin, N},
title = {[Role of bidirectional interaction between TCM and gut microbiota in treatment of osteoporosis].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {16},
pages = {4581-4593},
doi = {10.19540/j.cnki.cjcmm.20260504.801},
pmid = {42693012},
issn = {1001-5302},
mesh = {Humans ; *Osteoporosis/drug therapy/microbiology/metabolism ; Animals ; *Drugs, Chinese Herbal/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Medicine, Chinese Traditional ; },
abstract = {With the progressive aging of the population in China, the incidence of osteoporosis(OP) is rising annually. This condition not only severely impacts patients' quality of life but also imposes a substantial economic burden on both families and the society. Although modern western medicine has achieved progress in inhibiting OP progression and alleviating associated clinical symptoms, its overall therapeutic efficacy remains suboptimal due to issues such as adverse drug reactions and patient tolerance. Consequently, developing efficient, safe, and cost-effective prevention and treatment strategies has become an urgent priority in current OP-related clinical and scientific research. In recent years, growing insights into the microbiome have revealed that the gut microbiota can regulate bone quantity and quality through multiple mechanisms, including immune modulation, calcium and phosphorus absorption, and the production of short-chain fatty acids, thereby improving the bone microenvironment. As an important component of traditional medicine, TCM is characterized by multi-component and multi-target effects, with therapeutic advantages in holistic regulation. Studies have shown that TCM can effectively improve bone mineral density, inhibit bone resorption, and promote bone formation, with a low incidence of adverse reactions and mild pharmacological effects, demonstrating its unique clinical value in the prevention and treatment of OP. Simultaneously, complex interactions exist between TCM and the gut microbiota. On the one hand, the active components of TCM can modulate the composition and structure of the gut microbiota, reduce systemic inflammation, and ultimately improve bone metabolism. On the other hand, the gut microbiota can metabolize and transform the active components of TCM, enhancing their bioavailability and promoting therapeutic efficacy. This article systematically reviews the roles of gut microbiota and TCM in OP, as well as the bidirectional interaction between TCM and gut microbiota in the prevention and treatment of OP, aiming to provide new insights and evidence for the clinical management of OP.},
}

Humans
*Osteoporosis/drug therapy/microbiology/metabolism
Animals
*Drugs, Chinese Herbal/administration & dosage
*Gastrointestinal Microbiome/drug effects
Medicine, Chinese Traditional

@article {pmid42693341,
year = {2026},
author = {Berto, LP and Ding, J and Sakae, LO and Niemeyer, SH and Wierichs, RJ and Ricomini-Filho, AP and Meyer-Lueckel, H and Baumann, T and Carvalho, TS},
title = {Effect of a sodium fluoride rinse on the composition of early oral biofilms formed in situ on enamel and dentine.},
journal = {Clinical oral investigations},
volume = {30},
number = {9},
pages = {},
pmid = {42693341},
issn = {1436-3771},
mesh = {Humans ; *Biofilms/drug effects ; *Sodium Fluoride/pharmacology ; Double-Blind Method ; *Dental Enamel/microbiology ; Cross-Over Studies ; *Dentin/microbiology ; *Mouthwashes/pharmacology ; Adult ; Male ; Female ; Fluoride Treatment ; *Cariostatic Agents/pharmacology ; },
abstract = {OBJECTIVES: Dental caries results from dysbiotic shifts in the microbial community, so modulating biofilm composition represents a valid preventive strategy. The aim of this double-blind randomized crossover in situ study was to investigate how a fluoride rinse can modify the composition of the early oral biofilm formed on enamel and dentine.

MATERIALS AND METHODS: Twelve volunteers wore mandibular appliances containing 3 enamel and 3 dentine specimens for 1 min, to allow basal pellicle formation, then rinsed (1 min) with a NaF solution (500 ppm F⁻) or deionized water (DW) and kept the appliance overnight (8 h). The composition of the biofilms was analysed using full-length 16 S rRNA gene sequencing.

RESULTS: Alpha and beta diversity did not differ between groups. Dominant genera were Streptococcus (61-71%), Haemophilus (15-24%), Gemella (4-6%), Veillonella (1-3%), and Rothia (1-2%), with no significant group differences. On both enamel and dentine, NaF rinse significantly increased the relative abundance of several Streptococcus spp., including S. salivarius and S. toyakuensis, while decreasing species of Streptococcus, Neisseria, and Prevotella. On enamel, NaF reduced S. gordonii and increased S. oralis and S. parasanguinis; on dentine, it increased species of Rothia and Haemophilus.

CONCLUSIONS: NaF rinse induces subtle species-level changes in early biofilms formed on enamel and dentine, while overall community diversity and dominant genera remain stable.

CLINICAL RELEVANCE: This exploratory study suggests that a 500 ppm NaF rinse is associated with subtle species-level shifts in early oral biofilms. Further studies are needed to determine whether these changes translate into functional benefits or improved oral health outcomes.

CLINICAL TRIAL REGISTRATION: The study protocol was registered at ClinicalTrials.gov (NCT04033263).},
}

Humans
*Biofilms/drug effects
*Sodium Fluoride/pharmacology
Double-Blind Method
*Dental Enamel/microbiology
Cross-Over Studies
*Dentin/microbiology
*Mouthwashes/pharmacology
Adult
Male
Female
Fluoride Treatment
*Cariostatic Agents/pharmacology

@article {pmid42693392,
year = {2026},
author = {Zhao, Q and Hu, X and Zeng, X and Zhang, D and Xiao, X and Wei, Y and Cao, X and Zhang, L and Xi, H and Zhao, S},
title = {Effects of Continuous Cropping on Chili Root Rot: Insights from Rhizosphere Microbial Communities and Synthetic Community Applications.},
journal = {Plant disease},
volume = {},
number = {},
pages = {PDIS06251298RE},
doi = {10.1094/PDIS-06-25-1298-RE},
pmid = {42693392},
issn = {0191-2917},
abstract = {Continuous cropping often results in stunted plant growth and a higher incidence of soil-borne diseases. Soil microbial communities play a crucial role in promoting plant growth, maintaining plant health, and enhancing plant resistance to various diseases. This study examines the impact of continuous cropping on chili root rot and explores the contribution of soil microbial communities to alleviating this issue. The results revealed that prolonged continuous cropping significantly altered the composition of the rhizosphere bacterial community. High-throughput sequencing analysis indicated a marked increase in the abundance of Fusarium pathogens, accompanied by a significant decline in antagonistic bacteria from the genera Bacillus and Pseudomonas. LEfSe analysis showed that Bacillus and Pseudomonas were the core bacterial biomarkers in chili continuous cropping soil, which were successfully isolated and demonstrated significant antagonistic effects against Fusarium solani. Utilizing these antagonistic bacteria, nine different synthetic communities (SynComs) were constructed. Among them, the T7 SynCom exhibited excellent biocontrol efficacy. It effectively suppressed the pathogen, reduced the incidence of root rot, and enhanced systemic induced resistance by activating the plant immune-associated pathways, including the MAPK signaling pathway, ethylene signaling pathway, and pathways mediated by jasmonic acid and salicylic acid. These findings offer new insights into using functional SynComs as a sustainable agricultural solution and open new avenues for overcoming the challenges posed by continuous cropping.[Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}

@article {pmid42693537,
year = {2026},
author = {Liu, C and Wang, J and Liaw, A and Ning, Y and Lai, A and Salomon, C and Seneviratne, CJ and Ivanovski, S and Han, P},
title = {Salivary Extracellular Vesicles from Host, Bacteria and Fungus as Nanomessengers Reflecting Host-Microbiome Interaction in Periodontal Inflammation.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.6c09503},
pmid = {42693537},
issn = {1944-8252},
support = {1195451//National Health and Medical Research Council/ ; 2034591//National Health and Medical Research Council/ ; PJ-0000042//Australian Dental Research Foundation/ ; },
abstract = {Extracellular vesicles (EVs) secreted by the host and polymicrobial oral community are natural endogenous biological nanoparticles that mediate host-microbe interactions. Given their abundance in biofluids, host, fungal and bacterial EVs circulating in saliva may reflect periodontitis-associated microbial dysbiosis and inflammation. In this study, salivary EVs from 20 healthy controls and 57 stages III/IV periodontitis were isolated using a dual strategy: immunoaffinity to isolate host EVs for cytokine profiling, followed by size-exclusion chromatography (SEC) to enrich non-host (microbial) EVs for 16S rRNA and fungal ITS sequencing. In periodontitis, we observed a significant increase in CD49e+ and CD105+ host EV subpopulations and elevated host EV-associated cytokines of tumor necrosis factor alpha (TNF-α), interleukin-6 (IL-6), and granulocyte-macrophage colony-stimulating factor (GM-CSF), indicating an enhanced inflammatory host-EV profile. 16s rRNA sequencing of non-host microbial EV-DNA profiling revealed enrichment of bacterial EVs (BEVs), including genera Porphyromonas, Treponema, Filifactor, and Tannerella, with species of Porphyromonas gingivalis, Filifactor alocis, Tannerella forsythia, Treponema denticola, and Treponema socranskii. In contrast, commensal genera BEVs (Neisseria, Haemophilus) and fungal EVs from Malassezia globosa were enriched in health. Fungal EVs from Candida albicans and M. arunalokeiwere also elevated in disease. Combined host-EVs-IL-9 and T. forsythia-BEVs achieved an AUC of 0.989, increasing to 0.992 with the addition of F. alocis-BEVs, outperforming individual markers (AUC = 0.85-0.91). Pooled periodontitis microbial EVs (10 µg/mL) induced a proinflammatory response in the oral keratinocytes (OKFs) after 24 h, with increased IL-6 and IL-8 cytokines, and upregulated mRNA expression of C-C motif chemokine ligand 2 (CCL2), IL-1β, and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) compared with the no-EV control. Our findings demonstrated that salivary host-, bacterial-, and fungal-derived salivary EVs act as natural nanomessengers reflecting host-microbiome interactions and represent promising non-invasive candidate biomarkers of periodontitis.},
}

@article {pmid42693757,
year = {2026},
author = {Lorefice, L and Fenu, G and Fantola, G and Zoledziewska, M},
title = {Ultra-processed foods and multiple sclerosis: Evidence, pitfalls and perspectives.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585261481479},
doi = {10.1177/13524585261481479},
pmid = {42693757},
issn = {1477-0970},
abstract = {Ultra-processed foods are increasingly recognised as drivers of adverse health outcomes, yet their implications for multiple sclerosis remain underexamined. Emerging evidence suggests that ultra-processed food-rich dietary patterns are associated with greater central adiposity, pro-inflammatory metabolic signatures, microbiota disruption and adverse neuroimmune profiles relevant to multiple sclerosis. Major conceptual pitfalls, including the heterogeneity of ultra-processed foods and the scarcity of longitudinal or interventional studies addressing neuroimmune outcomes, continue to limit interpretation. Ultra-processed food-driven comorbidities, such as obesity, hypertension, dyslipidaemia, insulin resistance and depression, may further accelerate disability accumulation and reduce treatment efficacy in multiple sclerosis, underscoring the need for integrated dietary-immune models. This review integrates evidence from epidemiology, mechanistic studies, microbiome research and exposome science to provide a coherent framework for interpreting ultra-processed food-multiple sclerosis interactions. Recognising ultra-processed food exposure as a potentially modifiable contributor to multiple sclerosis activity may inform future preventive and therapeutic strategies.},
}

@article {pmid42694203,
year = {2026},
author = {Sun, W and Wang, Y and Zhang, X and Yue, Y and Sun, X and Miao, J and Han, S and Zhou, Z and Wang, X and Zhu, W},
title = {Dietary tryptophan ameliorates metalaxyl-induced colitis by restoring microbial tryptophan metabolism and aryl hydrocarbon receptor activation.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1930000},
pmid = {42694203},
issn = {2296-861X},
abstract = {INTRODUCTION: The extensive production of environmental pollutants has heightened susceptibility to intestinal disorders, potentially through alterations in the gut microbiota. However, the precise role of the gut microbiota in environmental pollutant-induced inflammation remains incompletely understood.

METHODS: In this study, wild-type and IL-10[-/-] mice were employed to simulate the responses of healthy individuals and those genetically predisposed to inflammatory bowel disease (IBD) to environmental toxicants. Mice were exposed to metalaxyl, and an integrated multi-omics approach combining microbiome and metabolome profiling with machine learning was conducted to investigate the underlying mechanisms. Additionally, dietary tryptophan supplementation was administered to evaluate its protective effects.

RESULTS: Metalaxyl exposure induced low-grade colonic inflammation in wild-type mice and triggered severe colitis in IBD-susceptible mice. Multi-omics analysis revealed that metalaxyl significantly disrupted gut microbial composition, reduced the synthesis of endogenous tryptophan-derived metabolites, and inhibited aryl hydrocarbon receptor (AhR) signaling, ultimately initiating intestinal barrier dysfunction and inflammatory cascades. Notably, dietary tryptophan restored gut tryptophan metabolite levels, strengthened AhR signaling, mitigated intestinal inflammation, and repaired barrier defects.

DISCUSSION: This study identifies the gut microbiota as a central mediator of environmental pollutant-induced IBD and demonstrates that a high-tryptophan diet exerts beneficial effects against environmental colitis via the AhR axis. Furthermore, the stable phenotypes and high reproducibility of this dual-genotype mouse model underscore its utility as an ideal platform for investigating the enterotoxic effects of environmental pollutants.},
}

@article {pmid42694259,
year = {2026},
author = {Maslov, DE and Osipov, ID and Zabelina, DS and Demina, DS and Tomilova, YE and Berdieva, SB and Makukha, VV and Komissarova, TV and Agletdinov, EF and Netesov, SV},
title = {Molecular epidemiology of respiratory viral infections in hospitalized children in Novosibirsk, Russia, 2021-2023.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1882419},
pmid = {42694259},
issn = {2296-2360},
abstract = {BACKGROUND: Acute respiratory infections (ARIs) are among the leading global causes of morbidity and mortality in children. While viral agents of ARI are rigorously monitored, other pathogenic organisms and pathobionts - bacteria and fungi native to the host microbiome - remain largely neglected. Adenoviral types also warrant particular attention especially given the widespread use of adenoviral vector vaccines during the COVID-19 pandemic.

METHODS: Oro-nasal swabs collected from 1679 children under the age of 18 hospitalized in Novosibirsk, Russia between February 2021 and June 2023, were tested for the presence of nucleic acids by the diagnostic panel targeting 17 viruses, 12 bacteria and one yeast. Adenovirus-positive samples were additionally fine-typed by Sanger sequencing.

RESULTS: Overall, 79.15% of samples were positive for at least one of 17 viral pathogens, with RSV (22.87% positives) and RhV (24.54% positives) dominating the etiological structure. Oro-nasal presence for respiratory pathobionts and opportunistic pathogens was 67.96% and 11.49%, respectively. Generally, viral seasonality was typical for continental climate, with only two notable deviations: MpV absence in spring of 2022 followed by earlier December peaks in the same year; an earlier RSV maximum in October 2021 with extended circulation the next epidemic season. Overall, the epidemiology of the analyzed viruses was consistent with worldwide surveillance trends and largely stable between the two later epidemic seasons. In viral-bacterial association analysis we identified two significantly attracted pairs, in which virus is known to facilitate bacterial adherence to respiratory epithelium. Adenovirus fine-typing provided preliminary evidence that serotypes 1, 2, 3, and 7 are the most frequently detected among the typed samples, while vaccine serotype AdV-5 was identified in only two cases.

CONCLUSION: Broad target coverage allowed for a comprehensive analysis of epidemiological patterns, highlighting a trend toward stabilization of the etiological structure to pre-pandemic levels, and allowed for prioritization of clinically relevant viral-bacterial associations. Preliminary findings in adenoviral fine-typing are consistent with global trends in serotype prevalence and help address an important gap in regional adenoviral epidemiology.},
}

@article {pmid42694300,
year = {2026},
author = {Mojsak, P and Zmyslowska-Polakowska, E and Chmielewska, S and Sołowiej, K and Ploszaj, T and Skoczylas, S and Grzybowska-Adamowicz, J and Pienkowski, T and Kretowski, A and Zmyslowska, A and Ciborowski, M},
title = {Integrated Oral Microbiome and Metabolome Profiling Identifies Disease-Associated Multi-Omics Signatures in Alström and Bardet-Biedl Syndromes.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0211},
pmid = {42694300},
issn = {2001-0370},
abstract = {Background: Alström syndrome (ALMS) and Bardet-Biedl syndrome (BBS) are rare ciliopathies characterized by multisystem involvement, including obesity, insulin resistance, and type 2 diabetes. Systemic metabolic dysfunction may influence the oral microbiome; however, integrative analyses that combine microbial and metabolic profiles in these disorders remain limited. Methods: Saliva and gingival crevicular fluid (GCF) samples were collected from genetically confirmed ALMS and BBS patients, as well as from obesity and healthy control groups. Microbial communities were profiled using V3-V4 16S rRNA gene amplicon sequencing, and untargeted metabolomic profiling was performed by gas chromatography-mass spectrometry. Microbiome-metabolome associations were evaluated using Spearman's rank correlation analysis, followed by multi-omics integration using Multiple Co-Inertia Analysis (MCIA) and the supervised Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO) framework (mixOmics). Results: Integrated analysis identified distinct microbiome-metabolome association patterns in ALMS and BBS. Compared with controls, the ALMS+BBS group showed enrichment of Prevotella, Enterococcus, and Eikenella, alongside reduced Lactobacillus abundance. Metabolomic profiling revealed alterations in amino acid, fatty acid, and carbohydrate metabolism. GCF exhibited structured associations between metabolites and Firmicutes, Proteobacteria, and Actinobacteriota, whereas saliva showed broader interaction networks. These associations were absent or markedly weaker in obesity and healthy controls. MCIA demonstrated coordinated variation across the oral microbiome, salivary metabolome, and GCF metabolome, while DIABLO identified a shared multi-omics signature. Conclusions: Coordinated shifts in amino acid, lipid, and central carbon metabolism can be linked to oral microbial reorganization in ALMS and BBS. Integrative multi-omics analyses identified coordinated microbiome-metabolome signatures across the oral microbiome, saliva, and GCF. These findings warrant validation in larger longitudinal and functional studies.},
}

@article {pmid42694318,
year = {2026},
author = {Das, M and Thajuddin, N and Muralitharan, G and Pundeer, M and Ponnusamy, R and Mishra, A and Nayak, P},
title = {From Gut to Mind: Impact of Probiotics on Depression, Anxiety, Mood, Gut Microbiota, Sleep and Stress-A Systematic Review of RCTs.},
journal = {Annals of neurosciences},
volume = {},
number = {},
pages = {09727531261478458},
pmid = {42694318},
issn = {0972-7531},
abstract = {BACKGROUND: Probiotic supplementation may influence mental health through the gut-brain axis, with potential effects on depression, anxiety, sleep, cognition, stress hormones, and gut microbial composition. This systematic review aimed to evaluate the effects of probiotics on psychological, physiological, and gut microbiome-related outcomes across diverse populations.

SUMMARY: A comprehensive search of PubMed, MEDLINE, PsycINFO, and ScienceDirect identified randomized controlled trials evaluating probiotic supplementation. Twenty RCTs were included, of which 15 were assessed as having a low risk of bias and five as having a high risk of bias. Commonly assessed outcomes included depression (n = 17), anxiety (n = 10), sleep quality (n = 9), stress (n = 6), cortisol (n = 7), cognitive function (n = 5), quality of life (n = 5), gut microbial composition (n = 11), and other neuroendocrine and inflammatory markers. Overall, probiotics were associated with improvements in depression, anxiety, sleep quality, mood, cognition, quality of life, and beneficial gut microbial populations, although findings for cortisol and stress-related outcomes were inconsistent.

KEY MESSAGE: Probiotic supplementation may provide beneficial effects on psychological well-being and gut microbial composition. However, heterogeneity among interventions, populations, outcome measures, and study quality warrants further well-designed RCTs.},
}

@article {pmid42694357,
year = {2026},
author = {Chen, L and Ye, L and Li, X and Zhou, H},
title = {The relationship between C. psittaci infection and respiratory failure based on respiratory microbiota analysis: a retrospective cohort study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1899239},
pmid = {42694357},
issn = {2296-858X},
abstract = {OBJECTIVES: This study aimed to explore the impact of the pulmonary microbiota on the occurrence of respiratory failure in patients with psittacosis pneumonia.

METHODS: A total of 20 patients diagnosed with psittacosis pneumonia were enrolled in this study. Patients were divided into two groups according to the presence or absence of respiratory failure at admission. Clinical data, laboratory findings, and bronchoalveolar lavage fluid analyses were collected. Next-generation sequencing was employed to analyze the pulmonary microbiota.

RESULTS: In this cohort, patients with respiratory failure exhibited a significantly higher relative abundance sequences of C. psittaci compared with those without respiratory failure. Notably, Spearman correlation analysis indicated a significant negative correlation between C. psittaci relative abundance of sequences and CD4+ T-lymphocyte counts (r = -0.870, p = 0.002) and a positive correlation with the pulmonary arteriovenous oxygen partial pressure difference (r = 0.728, p = 0.017). Further analysis of the bacterial communities showed a negative association between Pseudomonas and C. psittaci (r = -0.509, p = 0.031), whereas Veillonella was positively correlated with C. psittaci (r = 0.533, p = 0.023).

CONCLUSIONS: The relative abundance sequences of C. psittaci was significantly higher in patients with respiratory failure than in those without respiratory failure, suggesting an association between C. psittaci load and disease severity. The significant negative correlation between relative abundance sequences of C. psittaci and CD4+ T-lymphocyte count suggests that C. psittaci may exacerbate disease progression by compromising the host immune response, but direction of this relationship cannot be determined. Furthermore, the negative correlation between the relative abundance sequences of Pseudomonas and C. psittaci suggests a possible competitive or protective interaction between these two organisms. In contrast, the positive correlation between Veillonella and C. psittaci may indicate a shared ecological niche. These findings provide preliminary evidence of a relationship between lung microbiota composition and the severity of psittacosis pneumonia, while the causal mechanisms remain to be elucidated in future studies.},
}

@article {pmid42694431,
year = {2026},
author = {Putignani, L and Marsiglia, R and Turco, L and Russo, A and Pane, S and Fusco, A and Lopetuso, L and Trecarichi, EM},
title = {The gut reservoir of carbapenem-resistant Enterobacterales: from dysbiosis and colonization to infection and decolonization, with a focus on patients with hematologic malignancies - a narrative review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1939690},
pmid = {42694431},
issn = {2235-2988},
mesh = {Humans ; *Hematologic Neoplasms/complications/microbiology ; *Dysbiosis/microbiology ; *Enterobacteriaceae Infections/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Probiotics ; },
abstract = {Carbapenem-resistant Enterobacterales (CRE) remain among the highest-priority antimicrobial-resistant pathogens worldwide, and intestinal colonization is increasingly recognized as the key precursor of invasive infections, particularly in patients with hematological malignancies. Increasing evidence indicates that disruption of the gut microbial ecosystem, reflected in reduced diversity, depletion of beneficial anaerobic taxa, intestinal barrier dysfunction, immune dysregulation, and expansion of Enterobacterales, plays a central role in the transition from colonization to infection. Consequently, restoring colonization resistance through microbiome-targeted interventions has emerged as a promising preventive strategy. This narrative review summarizes the current evidence on the epidemiology and clinical impact of CRE colonization and infection, with particular emphasis on the ecological alterations of the gut microbiome linking gut dysbiosis to epithelial barrier dysfunction, immune dysregulation, and loss of colonization resistance to CRE persistence and invasive infection. We critically discuss both conventional and emerging decolonization approaches, including selective digestive decontamination, probiotics, prebiotics and synbiotics, fecal microbiota transplantation (FMT), bacteriophage therapy, and CRISPR-Cas-based technologies, highlighting their mechanisms of action, available clinical evidence, and current limitations. Particular attention is given to patients with hematological malignancies, in whom the clinical need for effective decolonization strategies is greatest. Although FMT currently represents the most promising microbiome-based intervention, the available evidence remains heterogeneous and largely derived from small studies. Overall, durable and standardized decolonization strategies have yet to be established, underscoring the need for well-designed multicenter randomized clinical trials to define effective microbiome-directed approaches for preventing CRE-related infections in high-risk populations.},
}

Humans
*Hematologic Neoplasms/complications/microbiology
*Dysbiosis/microbiology
*Enterobacteriaceae Infections/microbiology/therapy
*Carbapenem-Resistant Enterobacteriaceae/drug effects
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation
Anti-Bacterial Agents/pharmacology/therapeutic use
Probiotics

@article {pmid42694482,
year = {2026},
author = {Ma, K and Thairu, M and Sankaran, K},
title = {Design, processing, and modeling for longitudinal multiomics microbiome data.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1837109},
pmid = {42694482},
issn = {2235-2988},
mesh = {*Multiomics/methods ; *Microbiota ; Humans ; Longitudinal Studies ; Research Design ; Machine Learning ; },
abstract = {Longitudinal multiomics studies can reveal mechanisms underlying microbiome dynamics. Though gathering such data has become increasingly accessible, challenges remain in experimental design, data processing, and interaction modeling. This mini-review surveys practical approaches for analyzing longitudinal multiomics microbiome data. We provide an overview of fundamental questions these experimental designs can address, discuss concepts for reducing confounding, review tools for data management, and describe statistical and machine learning methods for identifying interactions across time and biological layers. We conclude with emerging trends and open problems.},
}

*Multiomics/methods
*Microbiota
Humans
Longitudinal Studies
Research Design
Machine Learning

@article {pmid42694486,
year = {2026},
author = {Niu, Q and Mu, T and Zhang, J and Chen, Y and Guo, Z and Zhu, Y and Li, L},
title = {Gastrointestinal motility in microgravity: a critical review of multi-level mechanisms and model-dependent effects.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1930628},
pmid = {42694486},
issn = {1664-042X},
abstract = {BACKGROUND: Gastrointestinal motility disturbances rank among the most frequently reported medical complications of spaceflight. Astronauts experience delayed gastric emptying, erratic small intestinal transit and reduced colonic propulsion. The underlying mechanisms are multifactorial. Microgravity alters intra-abdominal physical mechanics, disrupts autonomic and enteric neural circuits, shifts gastrointestinal hormone secretion profiles, inflicts oxidative stress upon effector cells, and perturbs gut microbial communities. Cross-model comparisons reveal substantial disagreement, suggesting that no single ground-based analog fully captures the pathophysiology of orbital flight.

AIM: To critically review how weightlessness affects gastric emptying, small intestinal transit and colonic motility; to critically evaluate contradictory findings across simulation platforms; and to delineate the neural, humoral, cellular and microbiological mechanisms involved.

METHODS: We searched PubMed, Web of Science and the NASA Technical Reports Server for articles published between January 1990 and June 2026 (last search 30 June 2026). Search terms included: "microgravity", "weightlessness", "spaceflight", "gastrointestinal motility", "gastric emptying", "intestinal transit", "gut microbiome", "interstitial cells of Cajal" and "oxidative stress". Studies using head-down bed rest, hindlimb unloading, clinorotation, parabolic flight and actual spaceflight were included. The review follows a critical narrative design; the full search strategy and the framework used to appraise the evidence are described in Section 1.1.

RESULTS: Altered-gravity studies suggest that gastrointestinal dysmotility may involve neurohumoral dysregulation, oxidative injury to interstitial cells of Cajal and smooth muscle, barrier dysfunction and altered enteric signaling; however, most mechanistic evidence derives from simulated models and has not been directly validated during human spaceflight. Direct human motility measurements remain sparse, and the evidence comprises a mixture of direct observations, model-dependent inferences and testable hypotheses. Cross-study agreement is poor: some head-down bed rest trials report accelerated small-bowel transit, whereas tail-suspension models and limited flight observations suggest motor suppression. These divergences may reflect model-specific confounding rather than a uniform effect of microgravity.

CONCLUSION: Current ground-based models each capture only partial aspects of orbital GI pathophysiology. Future work should combine multi-omics profiling with next-generation simulation platforms to develop evidence-based countermeasures for long-duration missions.},
}

@article {pmid42694531,
year = {2026},
author = {Carvalho, A and Gschwendtner, S and Schloter, M and Gil, AM and Marques, CR},
title = {Stool microbiota variations along the adenoma-colorectal carcinoma sequence - robustness of disease-associated microbial features.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1822941},
pmid = {42694531},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) has been linked with gut microbiota dysbiosis, thereby fostering the discovery of disease-associated microbial signatures. However, the use of covariate-adjusted methods accounting for confounders effects on microbiome shifts is far from being a gold standard approach, leading to spurious microbial-disease associations. This study aimed to characterize stool microbiota alterations along the adenoma-carcinoma sequence in a Portuguese cohort, and assess the robustness of candidate microbial features.

METHODS: Stool samples from healthy individuals (HC), adenoma patients (AP), and CRC patients at early (SI/II) and advanced (SIII/IV) stages, were analyzed using 16S rRNA gene amplicon sequencing. Microbial features' profiles were compared with publicly available datasets from France, Ireland, Italy, and USA/Canada. Differential abundance (DA) analysis was conducted through multiple DA models (ANCOM-BC2, fastANCOM, MaAsLin2, limma voom, and LEfSe) and statistical approaches, including covariate (age, sex, and body mass index (BMI)) adjustment, prevalence filtering, and analysis of matched subsets.

RESULTS AND DISCUSSION: Among the altered taxa along de adenoma-carcinoma sequence, Sutterella and Desulfovibrio were generally enriched across different DA tools and matched subset analyses, while Parasutterella and Adlercreutzia were depleted. Sutterella, Parasutterella, and Adlercreutzia, were already altered in adenoma and early-stage CRC samples, maintaining or increasing their effect sizes towards advanced CRC stages. This pattern highlights the potential of these taxa as early microbial signatures of colorectal cancer progression. In contrast, Fusobacterium, which is a widely accepted CRC biomarker, was not detected after covariate adjustment. Cross-cohort comparison revealed a limited reproducibility of microbial features (i.e., Dialister was enriched in the Portuguese and French cohorts; Parasutterella and Terrisporobacter were depleted in the Portuguese and USA/Canada datasets), being most of them cohort-specific.

CONCLUSION: Overall, our results strengthen the importance of covariate control towards the identification of potentially robust and reproducible microbial markers of CRC onset and progression.},
}

@article {pmid42694632,
year = {2026},
author = {Ma, J and Li, S and Qiao, Y and Gao, Z and Liu, J and Song, Y and Liu, Y and Ji, X and Li, J and Zhang, J and Chang, L and Huo, B},
title = {Context-dependent functions of the aryl hydrocarbon receptor in gastrointestinal cancers: from microenvironmental regulation to precision targeted therapy.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1886657},
pmid = {42694632},
issn = {2296-634X},
abstract = {The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor with context-dependent roles in gastrointestinal (GI) tumor development. Depending on cellular context and microenvironment, AhR can preserve epithelial integrity, suppress inflammation, and inhibit tumor growth, but it can also promote immune evasion and metabolic reprogramming to drive tumor progression. Most existing reviews have focused on a single GI tumor type or functional dimension, and the concept of AhR as a context-dependent signaling hub has not been effectively linked to therapeutic stratification across the full spectrum of GI malignancies. No prior review has systematically compared AhR across five GI cancer types-esophageal, gastric, colorectal, hepatocellular, and pancreatic-or addressed the translational gap between preclinical data and clinical application. This review addresses these gaps in three key ways. First, it provides the first head-to-head comparative analysis of AhR functions across these five cancer types. Second, it adopts a functional stratification framework integrating five core mechanistic dimensions-tumor stemness, epithelial-mesenchymal transition, immune remodeling, metabolic reprogramming, and drug resistance-and proposes a three-dimensional AhR stratification model. Third, it systematically discusses emerging AhR-targeted therapeutic strategies-including antagonists, selective AhR modulators (SAhRMs), PROTACs, combination therapies, and microbiome-based interventions-while critically evaluating translational challenges. By establishing this context-informed framework, we aim to provide a conceptual basis for biomarker-guided evaluation of AhR-targeted strategies in GI cancers.},
}

@article {pmid42694728,
year = {2026},
author = {Bautista, J and Iñiguez-Ramírez, A and Villegas-Chávez, JA and Bunces-Larco, D and López-Cortés, A},
title = {Skin microbiome and cutaneous aging mechanisms and clinical implications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1917816},
pmid = {42694728},
issn = {1664-302X},
abstract = {The skin microbiome is an integral component of the cutaneous ecosystem and contributes to barrier, immune, and metabolic homeostasis. Available evidence is examined across three distinct levels: microbial community structure, functional activity, and host biological response. This ecological-functional distinction is necessary because taxonomic abundance alone does not establish microbial activity, biological effects, or causality. Age-associated microbial variation is considered within the physiological context of cutaneous aging, including reduced sebaceous activity, altered hydration and surface pH, impaired barrier recovery, chronic low-grade inflammation, oxidative stress, and extracellular matrix deterioration. Microbial alterations reported in acne, atopic dermatitis, and rosacea further illustrate how changes in the cutaneous environment can modify host-microbiome interactions and contribute to clinically relevant phenotypes. Translational developments in dermatology and aesthetic medicine include microbiome-compatible skincare, prebiotic and postbiotic formulations, live biotherapeutic approaches, and strategies intended to preserve microbial and barrier recovery after dermatological procedures. Interpretation of the available literature remains limited by low microbial biomass, anatomical and interpersonal heterogeneity, contamination risk, differences in sampling and sequencing methods, and limited functional and longitudinal resolution. Observed microbial remodeling should be interpreted within a bidirectional host-microbiome relationship. Physiological changes that accompany aging can reshape microbial ecology, whereas microbial products may modify barrier and immune responses. Current evidence does not establish whether these microbial alterations are causes, consequences, or correlates of cutaneous aging. Integration of strain-resolved microbiome data with microbial gene expression, metabolite measurements, host molecular responses, and clinical phenotypes will be required to identify biologically relevant microbial functions and determine their value in dermatological practice.},
}

@article {pmid42694733,
year = {2026},
author = {Zhao, X and Liu, Z and Yang, J and Xie, Q and Mao, T and Zhou, H and Wang, H and Zheng, P and Jiang, K and Gao, F},
title = {Causal AI for cancer immunotherapy: a narrative framework review of target trial emulation, treatment-effect learning and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1896755},
pmid = {42694733},
issn = {1664-3224},
mesh = {Humans ; *Neoplasms/therapy/immunology ; *Immunotherapy/methods ; *Artificial Intelligence ; Translational Research, Biomedical ; Treatment Outcome ; Clinical Trials as Topic ; },
abstract = {This narrative framework Review examines how artificial intelligence (AI) can move cancer immunotherapy research from outcome prediction toward target-trial-based treatment-effect learning. AI has produced increasingly accurate models for predicting response, survival and immune-related toxicity during cancer immunotherapy. Yet most models estimate outcome risk under observed care rather than the causal effect of choosing one strategy over another. We therefore frame immunotherapy AI as a causal digital-medicine problem: clinically useful AI should begin with a target-trial question that specifies eligibility, time zero, treatment strategies, comparators, outcomes, estimands and bias-control plans before model development. Within this framework, multimodal AI outputs from imaging, digital pathology, omics, microbiome data, electronic health records and clinical text can function as baseline confounders, candidate effect modifiers, longitudinal state variables or outcome-ascertainment tools. We distinguish established causal-inference approaches, such as target trial emulation, propensity-score weighting, g-methods, TMLE, DML and heterogeneous-treatment-effect estimation, from exploratory technologies such as reinforcement learning and digital twins that require prospective safety validation. We close by outlining validation, reporting, workflow, regulatory and lifecycle-monitoring requirements for moving from predictive biomarkers to trustworthy causal learning systems in immuno-oncology.},
}

Humans
*Neoplasms/therapy/immunology
*Immunotherapy/methods
*Artificial Intelligence
Translational Research, Biomedical
Treatment Outcome
Clinical Trials as Topic

@article {pmid42694775,
year = {2026},
author = {Shouq, MI and Saleem, HGM and Wang, Y and Sohail, M and Hussain, A and Zhang, H and Zheng, H},
title = {Lesion-specific oral microbiome signatures and predicted carcinogenic pathways in oral squamous cell carcinoma: a paired-site study in Pakistan.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2721025},
pmid = {42694775},
issn = {2000-2297},
abstract = {BACKGROUND: Oral squamous cell carcinoma accounts for over 90% of oral neoplasms. Despite therapeutic advances, the lack of reliable, non-invasive biomarkers and delayed diagnosis continues to impede effective clinical management. By combining paired lesion and non-lesion sampling with predictive metagenomics analysis, our study addresses this gap and advances the current understanding of microbiome‒tumor interactions.

METHODS: We analyzed 92 buccal swab samples from 39 OSCC patients and 14 healthy controls using 16S rRNA gene (V3-V4) sequencing. Taxonomic profiling was conducted using QIIME2 and SILVA/eHOMD databases, functional pathways were predicted using PICRUSt2, and hub taxa were identified through co-abundance network analysis.

RESULTS: Microbial community structure differed significantly across lesion, non-lesion, and healthy sites (PERMANOVA, p = 0.001). Lesions were enriched with Selenomonas infelix and Treponema vincentii, while healthy controls harbored Streptococcus oralis and Gemella haemolysans. Co-abundance network analysis revealed lesion-specific hub species, notably T. vincentii, strongly correlated with predicted activation of pyrimidine biosynthesis pathways (r = 0.69, q < 1E-6), suggesting predicted metabolic alterations in the tumor microenvironment. Non-lesion sites were also characterized by two hub species, Prevotella melaninogenica and Segatella oulorum.

CONCLUSION: Our findings define a lesion-specific microbial signature of OSCC characterized by the depletion of health-associated taxa, enrichment of pro-inflammatory pathobionts, and predicted associations with metabolic pathways implicated in carcinogenesis. These alterations reflect a predicted functionally altered tumor microenvironment.},
}

@article {pmid42694794,
year = {2026},
author = {Huang, TY and Chen, LL and Peng, FS and Chu, FY and Gau, ML},
title = {Effects of two different perineal preparations before vaginal birth on maternal and neonatal infections and hospital resources: A randomized controlled trial.},
journal = {European journal of midwifery},
volume = {10},
number = {},
pages = {},
pmid = {42694794},
issn = {2585-2906},
abstract = {INTRODUCTION: Perineal preparation during the second stage of labor may influence maternal and neonatal infection risk and healthcare resource utilization. Although povidone-iodine sterilization is traditionally used, microbial flora theory suggests that water cleansing may preserve normal flora without increasing infection while reducing workload and cost. This study compared water cleansing with povidone-iodine sterilization for perineal preparation at Far East Memorial Hospital, Taiwan, from 26 November 2024 to 5 June 2025.

METHODS: A randomized controlled trial design was employed, including 143 mothers randomly assigned to either the water cleansing group (n=72) or the povidone-iodine sterilization group (n=71). Outcome measures included maternal and neonatal infection parameters (maternal postpartum temperature, C-reactive protein, REEDA scores, neonatal temperature, and neonatal oral flora colonization), along with cleansing time and medical costs. Data were analyzed using t-tests, chi-squared tests, and generalized estimating equation (GEE).

RESULTS: GEE analysis revealed no significant differences between the two groups in maternal and neonatal infection indicators (REEDA, 95% CI: -0.53-0.18, p=0.337; maternal temperature, 95% CI: -0.06-0.21, p=0.278; neonate temperature, 95% CI: -0.12-0.19, p=0.636). The water group had significantly lower average medical costs than the povidone-iodine group (7.49 vs 110.92 TWD, t= -50.22, p<0.001), as well as a shorter cleansing time. Regarding neonatal flora colonization, the water group showed higher rates of normal flora (33.8% vs 15.5%) and lower rates of pathogenic bacteria (5.6% vs 12.7%, χ[2]=10.88, p=0.028).

CONCLUSIONS: Perineal preparation with water was not associated with an increased risk of maternal or neonatal infection or adverse neonatal oral microbial colonization at birth and was associated with lower medical costs. These findings suggest that water may be a safe and cost-effective alternative to povidone-iodine for perineal preparation among women with low-risk pregnancies in hospitals with high episiotomy rates. Further longitudinal studies are needed to determine the effects of intrapartum povidone-iodine exposure on neonatal microbiome development and its potential long-term health consequences.

CLINICAL TRIAL REGISTRATION: The study is registered on the official website of ClinicalTrials.gov.

IDENTIFIER: NCT06880445.},
}

@article {pmid42694997,
year = {2026},
author = {Abboud, E and Rossi, P and Crouzy, B and Evangeliou, N and Nenes, A and Violaki, K},
title = {Characterization of the atmospheric microbiome in a semi-rural area of Central Europe using flow cytometry.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag167},
pmid = {42694997},
issn = {2730-6151},
abstract = {Characterizing bioaerosols is important for understanding their potential impacts on the environment and public health. In this study, we developed a novel flow cytometry-based approach to determine the low nucleic acid (LNA), high nucleic acid (HNA), dead, and intact bioaerosol populations in samples collected with a wet cyclone at Payerne, Switzerland, during spring and summer 2024. We found that the average bioaerosol number concentration reached (2.47 ± 3.35)×10[4] m[-3]. The HNA and intact populations were the most abundant populations, representing the largest fraction of total bioaerosols within 65% and 97% of the samples, respectively. Our results show that the LNA can be composed of dead bioaerosols, which correlated strongly with atmospheric particulate mass. Quantitative Polymerase Chain Reaction (qPCR) and metagenomic analysis reveal significant correlations and associations (Spearman, PERMANOVA, and Mantel) between the different kingdoms analyzed, reflecting complex ecological interactions in the atmosphere among the communities. Despite this complexity, LNA was mainly associated with the archaea Nitrososphaerota and bacteria Actinomycetota, whereas HNA was enriched by fungal classes such as Pichiomycetes and Ustilaginomycetes. Pollen abundance was positively correlated with temperature and negatively correlated with relative humidity and pollution (NOx and NO2), as these conditions promote the formation of sub-pollen particles (pollen fragments) through osmotic (bursting) and oxidative stress. Factor analysis indicates a seasonal dynamics transition from plant-associated bioaerosols in the spring season, to other bioaerosol types to be co-emitted during summer. Overall, the integration of flow cytometry with molecular analysis provides a framework to characterize and quantify bioaerosols and provides new insights into the ecological structure, variability, and sources of the atmospheric microbiome.},
}

@article {pmid42695007,
year = {2026},
author = {Pan, Q and Tsompanidou, E and Hu, W and Khan, MT and van Dijl, JM},
title = {Faecalibacterium harmsenii sp. nov., an abundant but previously overlooked Faecalibacterium in the human gut.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag221},
pmid = {42695007},
issn = {2730-6151},
abstract = {Faecalibacterium is one of the most abundant anaerobes in the human colon. At the genus level, this bacterium shows a strong positive association with human health. Expanding collections of isolates and metagenome-assembled genomes have revealed its species diversity, yet species-level functions remain so far underexplored. Here, we describe a novel species, Faecalibacterium harmsenii. In addition, we reclassify another isolate as a member of the recently reported Faecalibacterium langellae species. Despite close genomic relatedness, these isolates exhibit distinct physiological and biochemical traits, including differences in carbohydrate utilization, stress tolerance, enzymatic activity, Gram-staining and fatty acid composition. Our present comparative genomics analyses further uncover extensive functional diversity and plasticity across type strains, with F. harmsenii being distinguished by an expanded carbohydrate gene repertoire and reduced defense systems, mobile genetic elements and antibiotic resistance genes. Extending to the species, we identify species-specific ecological niches across hosts and differential sensitivities to human diseases, highlighting certain species as reliable biomarkers of gut health. Together, these findings refine our understanding of Faecalibacterium diversity and provide a framework for its use in microbiome-based diagnostics and therapeutic development.},
}

@article {pmid42695179,
year = {2026},
author = {Nett, N and Dumack, K},
title = {A Pan-European Whole-Microbiome Study of Wastewater Influent: Prokaryotes, Protists, Fungi, and Metazoa.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {5},
pages = {e70112},
doi = {10.1111/jeu.70112},
pmid = {42695179},
issn = {1550-7408},
support = {556896378//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; },
mesh = {*Wastewater/microbiology/parasitology ; *Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Europe ; *Microbiota ; *Eukaryota/classification/genetics/isolation & purification ; Seasons ; Animals ; },
abstract = {Microbial communities entering wastewater treatment plants (WWTPs) through untreated sewage represent an important interface between human, environmental, and treatment-associated microbiomes, yet our understanding of their biogeography remains poorly resolved, particularly for microbial eukaryotes. Using shotgun metagenomic time-series data from influent samples of seven WWTPs across a European latitudinal gradient, we analyzed the taxonomic composition and dynamics of bacteria, protists, fungi, and microscopic metazoa. Influent community composition varied with geographic location and season, with a pronounced north-south divergence driven by dominant taxa and stronger seasonal shifts observed at higher latitudes. Cross-domain associations were pervasive, suggesting that co-varying bacterial and eukaryotic components structure the incoming microbial pool. Our findings provide a pan-European baseline for whole-microbiome wastewater surveillance and highlight that influent communities differ regionally and seasonally. These patterns may be relevant for downstream treatment-stage microbiomes, but direct effects on reactor community assembly and treatment performance require targeted sampling across treatment stages.},
}

*Wastewater/microbiology/parasitology
*Fungi/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Europe
*Microbiota
*Eukaryota/classification/genetics/isolation & purification
Seasons
Animals

@article {pmid42695265,
year = {2026},
author = {Zhao, L and Long, Y and Zeng, K and Chen, S and Qiu, T and Fu, O},
title = {Chronic CeA[CRH] Activation Disrupts Colonic IL-22/Reg3g Signaling and Induces Depression-Associated Microbiome Shifts in Male Mice.},
journal = {Journal of integrative neuroscience},
volume = {25},
number = {8},
pages = {48170},
doi = {10.31083/JIN48170},
pmid = {42695265},
issn = {0219-6352},
support = {32400838//Natural Science Foundation of China/ ; 32571190//Natural Science Foundation of China/ ; BK20231046//Basic Research Program of Jiangsu/ ; },
mesh = {Animals ; Male ; *Interleukins/metabolism/immunology ; *Gastrointestinal Microbiome/physiology ; *Stress, Psychological/immunology/metabolism/microbiology ; Interleukin-22 ; *Corticotropin-Releasing Hormone/metabolism ; *Depression/immunology/metabolism/microbiology ; Mice ; *Pancreatitis-Associated Proteins/metabolism/immunology ; *Colon/metabolism/immunology ; Signal Transduction/physiology ; Mice, Inbred C57BL ; Disease Models, Animal ; *Anxiety/metabolism/immunology ; },
abstract = {BACKGROUND: Psychological stress shapes brain-body interactions through bidirectionally signaling between central neural circuits and peripheral systems. Central amygdala corticotropin-releasing hormone (CeA[CRH]) neurons are key regulators of stress response and immune function. However, their chronic impact on the brain-gut-immune axis and gut microbiota remains poorly understood.

METHODS: We established a chronic stress model in mice by 14-day chemogenetic activating CRH neurons in the CeA. Behavioral assays were conducted to evaluate anxiety and depressive-like phenotypes. mRNA expression level of cytokines, tight junction proteins and antimicrobial peptide were compared in spleen or colon using qPCR between CeA[CRH] activated group and control. In addition, 16S rRNA sequencing was performed to characterize changes in the microbial composition.

RESULTS: Chronic activation of CeA[CRH] neurons showed a tendency toward anxiety-like behavior and significantly disrupts splenic and colonic immune homeostasis. Notably, the colonic interleukin-22 (IL-22)/regenerating islet‑derived protein 3 gamma (Reg3g) mucosal defense axis was suppressed. Microbiota analysis revealed a shift toward a depression-associated profile, characterized by an increase in potentially pathogenic taxa (e.g., Eggerthella and Actinomycetota) and a reduction in short-chain fatty acid producers (e.g., Ruminococcaceae and Roseburia). These microbial alterations are consistent with clinical observations in patients with depression, supporting the translational relevance of mental disorders and gut microbiota.

CONCLUSIONS: Chronic activation of CeA[CRH] neurons drives coordinated immune, gut barrier, and microbiota alterations, including Claudin-2 upregulation and suppression of the IL-22/Reg3g axis, with IL-22 significantly reduced and Reg3g showing only a decreasing trend. These findings suggest a neuro-immune-microbiota pathway linking central stress circuits to peripheral dysfunction. Targeting IL-22 signaling, epithelial barrier integrity, or microbiota composition may represent promising therapeutic strategies for chronic stress-related disorders.},
}

Animals
Male
*Interleukins/metabolism/immunology
*Gastrointestinal Microbiome/physiology
*Stress, Psychological/immunology/metabolism/microbiology
Interleukin-22
*Corticotropin-Releasing Hormone/metabolism
*Depression/immunology/metabolism/microbiology
Mice
*Pancreatitis-Associated Proteins/metabolism/immunology
*Colon/metabolism/immunology
Signal Transduction/physiology
Mice, Inbred C57BL
Disease Models, Animal
*Anxiety/metabolism/immunology

@article {pmid42695484,
year = {2026},
author = {Zhang, T and Niu, J and Hu, X and Hu, Z and Gao, Y and Liu, J and Chen, N and Hu, Y},
title = {Akkermansia muciniphila and Its Bioactive Derivatives: Emerging Regulators of Healthy Aging.},
journal = {Aging cell},
volume = {25},
number = {9},
pages = {e70702},
doi = {10.1111/acel.70702},
pmid = {42695484},
issn = {1474-9726},
support = {82300622//National Natural Science Foundation of China/ ; U22A20287//National Natural Science Foundation of China/ ; 23YF1423100//Shanghai Sailing Program/ ; },
mesh = {Humans ; *Healthy Aging ; Animals ; *Akkermansia ; Aging ; },
abstract = {The global aging trend underscores the urgent need for innovative interventions against aging-related decline. Accumulating evidence identifies Akkermansia muciniphila (A. muciniphila) as a key gut microbiota regulator of aging, with its depletion associated with age-related diseases (ARDs), whereas its abundance is enriched in healthy centenarians. This review summarized current evidence linking A. muciniphila to aging, examining their causal relationship, the roles of its bioactive derivatives, underlying mechanisms in aging and ARDs, findings from human clinical trials, and challenges in therapeutic translation. Clinically, A. muciniphila depletion correlated with aging and various ARDs, while its supplementation effectively ameliorated neurodegenerative disorders, metabolic dysfunction, musculoskeletal decline, intestinal barrier dysfunction, and atherosclerosis. Mechanistically, A. muciniphila and its derivatives (Amuc_1100, Amuc_1409, extracellular vesicles, and metabolites such as SCFAs) exerted anti-aging effects by enhancing intestinal barrier function, maintaining metabolic homeostasis, suppressing chronic inflammation, and modulating immune function, ultimately improving glucolipid metabolism, insulin sensitivity, cognitive function, musculoskeletal health, and vascular health. Emerging clinical trials further demonstrated its translational potential in ameliorating age-related sarcopenia, metabolic dysfunction, and respiratory symptoms. Despite promising preclinical and clinical results, translational applications reserve challenges related to strain heterogeneity, antimicrobial resistance gene transfer risk, biosafety, production stability, and limited clinical validation in elderly populations. Future research should prioritize large-scale clinical trials to establish optimal dosage, safety, and long-term efficacy, while exploring combined microbiota-targeted therapies. Harnessing the diverse benefits of A. muciniphila may enable novel strategies for promoting healthy aging.},
}

Humans
*Healthy Aging
Animals
*Akkermansia
Aging

@article {pmid42695691,
year = {2026},
author = {Carella, A and Carroll, KC and Munson, E},
title = {Update on novel, validly published, and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2025.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0097326},
doi = {10.1128/jcm.00973-26},
pmid = {42695691},
issn = {1098-660X},
abstract = {This review summarizes novel taxon designations ascribed to prokaryotes derived from human primary clinical material during calendar year 2025, as well as proposed revisions to existing taxonomy. Major activity took place in the Streptococcus genus, as more than one dozen novel species were validly and effectively published, with two of these later classified as synonyms of Streptococcus thalassemiae. Moreover, whole genome sequencing and phylogenetic investigation of Streptococcus mitis group organisms resulted in a proposal to designate five species-level Streptococcus spp. taxa as Streptococcus mitis and an additional taxon as Streptococcus oralis subsp. dentisani. More than one dozen taxa were newly included in order Enterobacterales in 2025. Select novel taxa within genera Providencia and Enterobacter commonly possessed genotypes that conferred resistance to carbapenem and/or higher-generation cephem agents. Stenotrophomonas muris sp. nov. and Terrisporobacter muris sp. nov., initially characterized in gnotobiotic murine systems within the past 4 years, had clinical significance in human infection that was demonstrated in primary literature. The vast majority of the more than 70 novel obligate anaerobic taxa were derived from microbiome studies and had little ascribed clinical significance. Four novel obligate anaerobic Gram-negative taxa were shown to be of greater abundance in persons with Parkinson's disease than in those without. Updates to taxa previously published in the Journal of Clinical Microbiology compendia reveal that several could serve as reservoirs for multiple antimicrobial resistance determinants. One example is the non-glucose fermentative Gram-negative bacillus Pseudomonas juntendi.},
}

@article {pmid42695693,
year = {2026},
author = {Claiborne, C and Lyu, Z},
title = {Meta-CD: a metagenomic sequencing coverage and depth calculator for target species.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0081126},
doi = {10.1128/mra.00811-26},
pmid = {42695693},
issn = {2576-098X},
abstract = {Metagenomic Coverage and Depth Calculator (Meta-CD) is a convenient, biologist-friendly tool for determining coverage and depth to enhance taxonomic detection, functional profiling, and metagenome-assembled genome (MAG) recovery in metagenomics. It supports experimental design and post-sequencing analysis, modeling how genome size, relative abundance, sequencing depth, and DNA quantity influence detection of target species.},
}

@article {pmid42695882,
year = {2026},
author = {Tamanna, I and Salonen, K and Mannochio-Russo, H and Kråkström, M and Gomes, PWP and Charron-Lamoureux, V and Mohanty, I and Forssten, SD and Ouwehand, AC and Hyötyläinen, T and Dickens, AM and Dorrestein, PC and Orešič, M and Lamichhane, S},
title = {Emerging Microbial Lipid Shifts in a Multistage Simulated Gut Inoculated with Human Fecal Microbiota.},
journal = {Journal of proteome research},
volume = {25},
number = {9},
pages = {4577-4588},
doi = {10.1021/acs.jproteome.6c00050},
pmid = {42695882},
issn = {1535-3907},
mesh = {Humans ; *Feces/microbiology ; *Colon/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Lipids/analysis ; Bile Acids and Salts/metabolism ; *Lipid Metabolism ; Putrescine/metabolism ; Histamine/metabolism ; },
abstract = {Food residues that bypass human digestion are further digested by gut microbes, leading to the production of diverse metabolites, including lipids. To investigate how lipids in our intestine are affected during this transition, we used a colon simulator with four distinct vessels (V1-V4) that mimic the proximal to distal part of the human colon. In total, 44 samples were collected from the colon simulator vessels (V1-V4). We observed dynamic shifts in a diverse array of microbially linked lipid molecules in the simulated intestinal chyme, including bile acids and N-acyl amides with short- and odd-chain lipids. Histamine-linked N-acyl lipids (histamine-C5) increased from the proximal to the distal colon vessels (pH 5.5-7.0), whereas putrescine-linked ones (putrescine-C19:2), initially abundant in the media, decreased across the colon vessels. We uncovered dynamic associations between in vitro-derived short-chain N-acyl lipids (C4:0, C5, C6, and C7 conjugates) and major lipid species such as cholesterol esters, phosphatidylethanolamines, ceramides, and sphingomyelins. To determine the broader relevance of these findings, we applied a reverse metabolomics approach and examined N-acyl lipid profiles in human small intestine and fecal samples from public data sets. Our results validate the colon simulator as a dynamic model for studying microbially transformed metabolites and suggest its potential utility as a platform for discovering novel microbial metabolites with relevance to human and animal health.},
}

Humans
*Feces/microbiology
*Colon/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
*Lipids/analysis
Bile Acids and Salts/metabolism
*Lipid Metabolism
Putrescine/metabolism
Histamine/metabolism

@article {pmid42695976,
year = {2026},
author = {de Kreek, F and Hertzberger, R and van Eeden, F and Illidge, S and Teunis, EJ and Hanemaaijer, M and Lievens, E and Rienstra, F and Wiedhaup, DE and Lisotto, P and Butler, D and Molenaar, D and Kort, R},
title = {Intra-individual genetic diversity of vaginal Lactobacillus crispatus revealed through citizen science-driven isolation and pangenome analysis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag218},
pmid = {42695976},
issn = {1365-2672},
abstract = {AIMS: A vaginal microbiome dominated by Lactobacillus crispatus is associated with positive reproductive and sexual health outcomes, yet intra-individual genetic diversity within this species remains largely unexplored. This study characterised inter- and intra-individual genomic variation in L. crispatus strains isolated through a citizen science initiative and assessed implications for multi-strain probiotic development.

METHODS AND RESULTS: Fifty-three women participated in this citizen science project. Self-sampling resulted in 48 shotgun metagenomes. Twenty-two participants isolated their own L. crispatus strains using selective enrichment and LAMP-based species confirmation, resulting in 53 whole-genome-sequenced isolates. L. crispatus dominated 20 of 48 metagenomes (50.1-99.6% relative abundance). Pangenome analysis revealed 3 456 gene families, of which 43.7% were core and 56.3% accessory. A 14-kb plasmid harbouring a Fic-domain toxin-antitoxin protein, but devoid of antimicrobial resistance genes, was present in 44 of 53 strains. Strains from the same individual clustered closely together yet harboured 1-123 gene differences. Intra-individual variation was observed in the pullulanase type I gene required for glycogen degradation: 40 strains were predicted to grow on glycogen, six showed genetic disruptions with unknown consequences, and seven were predicted to lack this ability entirely. Variation within individuals was also found for bacteriocin classes and CRISPR-Cas genes.

CONCLUSIONS: Substantial functional diversity exists within L. crispatus, even among strains from the same individual, supporting the rationale for multi-strain vaginal probiotics. This citizen science approach enabled discovery of host-specific adaptations while ensuring participant ownership of their strains.},
}

@article {pmid42696087,
year = {2026},
author = {Yan, J and Ding, S},
title = {Integrative multi-omics analyses suggest a candidate microbial metabolite-associated host gene network in ulcerative colitis.},
journal = {Immunologic research},
volume = {74},
number = {1},
pages = {},
pmid = {42696087},
issn = {1559-0755},
mesh = {Humans ; *Colitis, Ulcerative/genetics/microbiology/metabolism ; Multiomics ; *Gene Regulatory Networks ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Gene Expression Profiling ; Transcriptome ; Dysbiosis ; },
abstract = {Ulcerative colitis (UC) is associated with gut microbial dysbiosis, but the host molecular alterations potentially linked to microbially derived metabolites remain incompletely understood. We integrated Mendelian randomization (MR), microbial metabolite annotation, computational target prediction, colonic transcriptomics, network analysis, and machine learning. MiBioGen microbiome GWAS data were used as exposures and FinnGen Release 12 ULCERENTER as the outcome. Metabolites linked to MR-prioritized taxa were retrieved from GutMGene, and human targets were predicted using SwissTargetPrediction and SEA. UC-related genes were defined by integrating differential expression analysis and WGCNA and then intersected with predicted metabolite targets. MR prioritized one family and eight genera showing nominal genetically supported associations with UC, but none remained significant after Benjamini-Hochberg FDR correction. Three prioritized genera were linked to 15 microbe-metabolite records, corresponding to 13 unique metabolites; nine were retained for target prediction, yielding 277 unique predicted human targets. Transcriptomic analysis identified 1,530 DEGs and a 312-gene MEgrey60 module, with 273 overlapping genes, producing 1,569 unique UC-related genes. Their intersection with the 277 predicted targets yielded 47 candidate genes. Enrichment analyses highlighted mainly metabolic and lipid-related processes. Random Forest showed the highest mean AUC across the two independent external benchmarking cohorts, and SHAP prioritized EPHX1, HSD17B2, IGFBP5, and MMP10. IBDome analysis showed inflammation-associated expression differences in these genes. This study provides a genomics-informed, hypothesis-generating framework that prioritizes candidate microbe-metabolite-host relationships in UC for future experimental validation.},
}

Humans
*Colitis, Ulcerative/genetics/microbiology/metabolism
Multiomics
*Gene Regulatory Networks
*Gastrointestinal Microbiome
Genome-Wide Association Study
Gene Expression Profiling
Transcriptome
Dysbiosis

@article {pmid42696146,
year = {2026},
author = {Zhou, Y and Del Toro, S and Zeng, MY},
title = {Nutritional regulation of gut-brain immune crosstalk across the lifespan.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2725371},
doi = {10.1080/19490976.2026.2725371},
pmid = {42696146},
issn = {1949-0984},
mesh = {Humans ; *Brain/immunology ; Animals ; *Gastrointestinal Microbiome ; Aging/immunology ; *Gastrointestinal Tract/immunology ; *Brain-Gut Axis ; },
abstract = {The gut-brain immune axis integrates microbial, immune, and neural signals to regulate neurodevelopment, homeostasis, and disease susceptibility. Early-life nutrition, particularly human milk oligosaccharides, shapes beneficial microbiota composition, enhances hippocampal plasticity, promotes anti-inflammatory microglia polarization, and fosters immune tolerance. Gut microbiota-derived metabolites, including short-chain fatty acids, tryptophan derivatives and secondary bile acids, regulate microglia maturation, astrocyte function, T cell differentiation, neurotransmitter production, and vagus nerve signaling. These processes influence synaptic pruning, neurogenesis, and neuroinflammation. Adaptive immune cells in the central nervous system, notably meningeal and infiltrating CD4 T cells, further connect peripheral immunity to neuronal responses through cytokines, such as IL-4, IFNγ, and IL-17A. Nutritional imbalances may exacerbate disease-associated microglia and pathogenic T cell activity in Multiple Sclerosis, Alzheimer's disease, and autism spectrum disorders. In aging, diet helps mitigate "inflammaging" by countering metabolic shifts in microglia and lymphocytes. This review examines how nutrition modulates bidirectional gut-brain immune crosstalk across the lifespan.},
}

Humans
*Brain/immunology
Animals
*Gastrointestinal Microbiome
Aging/immunology
*Gastrointestinal Tract/immunology
*Brain-Gut Axis

@article {pmid42696197,
year = {2026},
author = {Alperstein, L and Nappi, J and Egan, S},
title = {Mariculture Probiotics: A Scoping Review of Research Trends, Knowledge Gaps and Opportunities.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {28},
number = {5},
pages = {},
pmid = {42696197},
issn = {1436-2236},
mesh = {*Probiotics ; Animals ; *Aquaculture/methods ; *Aquatic Organisms/microbiology ; Crustacea/microbiology ; Fishes ; Mollusca/microbiology ; },
abstract = {The use of probiotics - live microorganisms - to enhance growth and prevent disease in mariculture species is an emerging alternative to conventional methods including antibiotics, vaccines and chemical intervention. While others have reviewed specific host organisms and probiotic genera, this review synthesises the scientific literature on the use of probiotics across a range of marine organisms to identify knowledge gaps and research opportunities. We identified widespread methodological heterogeneity, making direct inter-study comparisons difficult. Despite this limitation, 86% of in vivo studies documented positive outcomes following probiotic administration. Crustacean and finfish research dominates the field, encompassing 77% of the current literature, while molluscs, macroalgae and other invertebrates remain relatively understudied despite their significant ecosystem services and contribution to aquaculture. Probiotics provide multiple reported benefits to marine hosts, including increased growth and survival, and protection against pathogens. Bacillus and Lactobacillus from terrestrial environments are the dominant probiotics used across all studies, while marine-derived probiotic genera including Pseudoalteromonas, Vibrio, Phaeobacter, Shewanella, and Halomonas showed benefits across several hosts but remain relatively underutilised. Approximately 34% of publications evaluated the use of microorganisms isolated from the same host species in which the probiotics were tested. This review highlights the opportunity for further research into underutilised autochthonous probiotic genera and development of standardised research guidelines. We propose that future research should prioritise understanding probiotic mechanisms of action, and their use in rapidly expanding and understudied systems including macroalgae and molluscs, to ensure continued productivity with minimal impact on marine ecosystems.},
}

*Probiotics
Animals
*Aquaculture/methods
*Aquatic Organisms/microbiology
Crustacea/microbiology
Fishes
Mollusca/microbiology

@article {pmid42696228,
year = {2026},
author = {Souza, N and Andaló, V and Indjai, LR and Martins, GD and de Faria, LS and de Assis, GA},
title = {Spatial distribution of entomopathogenic nematodes and their relationship with soil chemical attributes in tropical agroecosystems.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {9},
pages = {},
pmid = {42696228},
issn = {1573-2959},
mesh = {Animals ; *Soil/chemistry ; *Nematoda/growth & development/physiology ; Brazil ; *Environmental Monitoring ; Tropical Climate ; Agroecology ; Ecosystem ; Agriculture ; Pest Control, Biological ; Crops, Agricultural ; Soil Microbiology ; },
abstract = {The distribution of entomopathogenic nematodes (EPNs) in agricultural soils is influenced by complex interactions between edaphic factors and crop management practices, yet these relationships remain poorly understood under tropical conditions. This study evaluated the spatial distribution of EPNs and their association with soil chemical attributes in five crop systems in southeastern Brazil. A total of 82 soil samples were collected and analyzed using insect-baiting techniques and geospatial tools, including kernel density and interpolation methods. EPN occurrence varied across crops and was positively associated with higher concentrations of potassium and iron, while an inverse pattern was observed for copper. These results suggest that micronutrients may indirectly influence EPN distribution by modulating soil microbial communities and plant-soil interactions. Although causal relationships cannot be definitively established, the spatial patterns identified highlight the importance of soil chemical composition in structuring beneficial soil fauna. The integration of geospatial analysis provides a valuable framework for optimizing the application of biological control agents in Integrated Pest Management (IPM) programs. These findings contribute to a better understanding of soil ecological dynamics and support the development of more sustainable agricultural practices.},
}

Animals
*Soil/chemistry
*Nematoda/growth & development/physiology
Brazil
*Environmental Monitoring
Tropical Climate
Agroecology
Ecosystem
Agriculture
Pest Control, Biological
Crops, Agricultural
Soil Microbiology

@article {pmid42696299,
year = {2026},
author = {Román, R and Maestre, FT and Couradeau, E},
title = {Rainfall-induced microbial resuscitation reveals functional decoupling across biocrust succession.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag231},
pmid = {42696299},
issn = {1751-7370},
abstract = {Dryland ecosystems rely on infrequent rainfall pulses to activate soil microbial communities, yet the fraction and identity of microbes resuscitating after hydration remain unclear. We applied bioorthogonal non-canonical amino acid tagging coupled with fluorescence-activated cell sorting (BONCAT-FACS) and 16S rRNA gene sequencing to identify translationally active bacteria in early (L-BSC) and late (D-BSC) successional cyanobacteria-dominated biocrusts subjected to 3 mm simulated rainfall under light and dark conditions. Our results reveal that only a small subset of the microbial community resumes activity within six hours, with higher active cell abundances in mature crusts. Microbial activity patterns were largely independent of light exposure and showed partial decoupling from total community composition, indicating that presence does not predict short-term function. These findings suggest that biocrust maturity shapes microbial activation dynamics and that functional responses to precipitation pulses are governed by a conserved pool of fast responders, informing predictions of dryland soil microbiome resilience under changing precipitation regimes.},
}

@article {pmid42696306,
year = {2026},
author = {Sempert, T and Budzinski, L and Kempkens, R and Kang, GU and Maier, R and Chang, HD},
title = {A Step-by-Step Guide to Successful Multiparametric Microbiota Flow Cytometry.},
journal = {Current protocols},
volume = {6},
number = {9},
pages = {e70460},
doi = {10.1002/cpz1.70460},
pmid = {42696306},
issn = {2691-1299},
support = {//Rolf M. Schwiete Foundation/ ; 1.6./01"BacFlow-AnalysebakteriellerGemeinschaftendurchMikrobiota-Zytometrie"//EFRE-Project grant/ ; 375876048//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; 491069896//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; 565743763//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; 831434//Innovative Medicines Initiative 2 Joint Undertaking/ ; },
mesh = {*Flow Cytometry/methods ; Humans ; Feces/microbiology ; *Bacteria/isolation & purification ; *Microbiota ; Single-Cell Analysis/methods ; },
abstract = {The role of the human microbiota in host health is an important area of research. Conventional characterization of the complex microbial communities colonizing the human body is primarily performed using culture-based or high-throughput sequencing approaches, which have improved general understanding yet lack cellular features relevant for interaction and function at the single-cell level. Flow cytometry is an established tool for single-cell analysis, and recent improvements, such as increased resolution of small cells and particles, offer possibilities for characterizing complex microbial communities. Here, we describe an updated protocol to characterize complex microbial communities derived from human stool samples at the single-cell level by multiparametric microbiota flow cytometry. Our protocol covers the process from the isolation of bacteria from stool, preparation of cryo-stocks, staining procedure for phenotypic features of the bacteria, and flow cytometric analysis. Our phenotypic characterization includes light scattering properties, quantitative DNA staining, isotype-specific staining of host-antibody coating, and profiling of bacterial cell surface sugar moieties. In addition, we highlight the importance of determining the bacterial load for improved biological interpretation. External staining controls ensure reproducibility and quality controls. Additionally, we suggest a downstream analysis pipeline involving segmentation of multivariate data by a self-organized map (SOM) and machine learning to generate specific microbiota fingerprints. Optionally, bacteria with specific phenotypic characteristics can be isolated by fluorescence-activated cell sorting (FACS) for further investigation. Our protocol can be applied to any microbial community or sample source and offers the flexibility to be expanded with additional phenotypic markers. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of cryo-preserved bacterial stocks from a single-cell microbiota suspension derived from native human stool sample Basic Protocol 2: Staining protocol for cryo-preserved microbiota stocks and acquisition using a flow cytometer.},
}

*Flow Cytometry/methods
Humans
Feces/microbiology
*Bacteria/isolation & purification
*Microbiota
Single-Cell Analysis/methods

@article {pmid42696379,
year = {2026},
author = {Li, T and Zhang, S and Wang, Z and Huang, W and Zhang, Z and Wang, F and Liu, D and Cui, X and Che, R},
title = {Soil extracellular DNA fragments show variable degradation rates among sequences and environmental conditions.},
journal = {eLife},
volume = {15},
number = {},
pages = {},
doi = {10.7554/eLife.110251},
pmid = {42696379},
issn = {2050-084X},
support = {42007035//National Natural Science Foundation of China/ ; 42261012//National Natural Science Foundation of China/ ; 32560035//National Natural Science Foundation of China/ ; 202301AW070004//Yunnan Fundamental Research Projects/ ; 202301BF070001-006//Yunnan Fundamental Research Projects/ ; 202301AT070211//Yunnan Fundamental Research Projects/ ; YNQR-QNRC-2018-024//Xingdian Youth Talent Support Program of Yunnan Province/ ; YNQR-QNRC-2020-087//Xingdian Youth Talent Support Program of Yunnan Province/ ; YDFWDF202509//Science and Technology Project of Yunnan University for Serving Local Development/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Extrachromosomal DNA ; China ; *DNA, Environmental/genetics ; *DNA, Bacterial/genetics ; Bacteria/genetics ; },
abstract = {While extracellular DNA (eDNA) persistence substantially influences soil microbiome investigations, its degradation kinetics remain poorly quantified. Here, we developed a primer-labeled DNA approach coupled with microcosm incubation to determine the overall and sequence-specific degradation rates of eDNA amplicon fragments across China. We observed substantial variations in the overall degradation rates of extracellular 16S rRNA gene amplicon fragments among the study sites, with degradation rate constants ranging from 0.05 to 0.16 day[-1]. The overall degradation rate constants showed significant correlations with soil moisture content, prokaryotic abundance, prokaryotic community profiles, and mean annual precipitation. The significant influences of moisture content on the overall degradation rates were further verified by a moisture gradient microcosm experiment. The sequence-specific degradation rate constant profiles were additionally correlated with pH, nitrogen content, and mean annual temperature. Furthermore, propidium monoazide-based exclusion of eDNA signals significantly altered soil prokaryotic abundance, richness, and prokaryotic community profiles, and the pool sizes of sequence-specific extracellular 16S rRNA gene amplicon fragments were significantly correlated with their respective degradation rates. This study developed a methodology for determining the overall and sequence-specific degradation rates of eDNA amplicon fragments, highlighting the profound influences of eDNA on soil microbial research and informing the optimization of environmental DNA technologies.},
}

*Soil Microbiology
*Soil/chemistry
RNA, Ribosomal, 16S/genetics
Extrachromosomal DNA
China
*DNA, Environmental/genetics
*DNA, Bacterial/genetics
Bacteria/genetics

@article {pmid42696406,
year = {2026},
author = {},
title = {Correction to: Pseudomonas aeruginosa adaptation and persistence in the aspergilloma microbiome revealed by integrated multi-omics.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkag236},
pmid = {42696406},
issn = {2160-1836},
}

@article {pmid42696414,
year = {2026},
author = {Kimura, S and Nishi, K and Kawamoto, K and Mihashi, Y and Nishi, T and Sakata, T and Matsumoto, N and Yamano, T and Nakano, Y and Suzuki, N},
title = {Nasal irrigation increases upper-airway microbial diversity: a prospective pilot study.},
journal = {Acta oto-laryngologica},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/00016489.2026.2721206},
pmid = {42696414},
issn = {1651-2251},
abstract = {BACKGROUND: Nasal irrigation is widely recommended for chronic rhinosinusitis and allergic rhinitis, but its effects on the upper-airway microbiome remain unclear.

OBJECTIVE: To determine whether 30 days of buffered isotonic saline nasal irrigation alters bacterial diversity in the nasal cavity, nasopharynx, and oral cavity.

MATERIAL AND METHODS: Ten volunteers performed twice-daily irrigation for 30 days. Swabs from the nasal cavity, nasopharynx, and posterior tongue were collected at baseline and day 30. Bacterial communities were analysed by 16S rRNA gene sequencing. The primary endpoint was change in nasal Shannon diversity; other microbiome, endoscopic, and correlation analyses were exploratory.

RESULTS: Nasal Shannon diversity increased significantly (median [IQR], 1.02 [0.80-1.48] vs 1.50 [1.37-1.66]; p = 0.040), whereas nasopharyngeal and oral diversity did not. Micrococcaceae, Lactobacillus, and Corynebacterium showed directional increases but did not survive FDR correction. Nasal mucosal erythema decreased (p = 0.039). No participant developed acute sinusitis or severe complications; transient mild discomfort occurred in three.

CONCLUSIONS AND SIGNIFICANCE: Thirty-day saline nasal irrigation was associated with increased nasal bacterial diversity and reduced mucosal erythema. These single-arm pilot findings are exploratory and warrant validation in larger controlled studies.},
}

@article {pmid42696444,
year = {2026},
author = {Yin, Y and Pommier, T and Zhang, X and Chi, F and Zhang, Z and Hendrich, CG and Sheriff, EK and Ruan, C and Xu, Y and Friman, VP and Wei, Z},
title = {Competition between resident rhizosphere bacteria enhances phytopathogen suppression via emergent antagonism.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag229},
pmid = {42696444},
issn = {1751-7370},
abstract = {Resident bacterial interactions can shape the invasion resistance of rhizosphere microbiomes, but whether interactions between weakly antagonistic resident bacteria can generate emergent antagonism against invading pathogens remains poorly understood. Here, we used a systematic pairwise interaction screening to identify Ralstonia pickettii RAL5 and Acinetobacter oleivorans ACI4 bacterial pair, that together provided a strong suppression of the phytopathogenic R. solanacearum Rs1115 strain. Although RAL5 and ACI4 monocultures only weakly inhibited pathogen growth, the RAL5-ACI4 co-cultures strongly suppressed the Rs1115, which was associated with asymmetric competition where the RAL5 dominated the ACI4 species. In line with this competitive asymmetry, broad transcriptional reprogramming was detected in RAL5 and only limited stress- and catabolism-associated responses in ACI4. The increased suppressiveness of co-cultures was associated with clear shifts in the extracellular metabolite profile, including the accumulation of candidate antimicrobial metabolites (e.g., a novobiocin-like feature and 4-aminophenol), and with the release of intracellular contents from ACI4 following RAL5-mediated lysis. The observed emergent antagonism also held in greenhouse experiments with tomato, where the RAL5-ACI4 consortium reduced R. solanacearum abundance and bacterial wilt severity relatively much more compared to when either strain was applied alone. Together, these results suggest that competitive interactions between resident bacteria can activate latent biocontrol potential in rhizosphere microbiomes, providing a new approach to harness resident bacterial interactions for enhanced pathogen suppression and biocontrol.},
}

@article {pmid42696749,
year = {2026},
author = {Cisneros-Martínez, AM and Varela, MÁF and González-Serrano, F and Rebollar, EA},
title = {Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag103},
pmid = {42696749},
issn = {1574-6941},
abstract = {Bacteriophages play important roles in shaping microbial community dynamics across diverse environments. In the amphibian skin, most microbiome studies have focused on bacteria and their interactions with the fungus Batrachochytrium dendrobatidis (Bd), leaving other microbial components, including viruses, largely unexplored. Here, we present the first characterization of the viral community in the amphibian skin microbiome, focusing on ecological drivers of bacteriophage diversity and functional potential in the axolotl Ambystoma altamirani. Using public shotgun metagenomes, we found that the viral fraction was dominated by bacteriophages of the class Caudoviricetes. Bacteriophage diversity was significantly associated with local physicochemical parameters at the time of sampling, and showed a strong positive correlation with bacterial diversity, whereas no significant associations were detected with the presence of Bd. In addition, seasonality influenced the composition and properties of bacteria-bacteriophage co-abundance networks. Functional annotation of assembled bacteriophage sequences revealed a diverse functional potential, including putative auxiliary metabolic genes, superinfection exclusion, toxin-antitoxin, and virulence factors. Overall, these findings highlight the ecological relevance of bacteriophages in amphibian skin microbiomes and underscore the need for further studies on their role in the amphibian host's health.},
}

@article {pmid42696758,
year = {2026},
author = {Royle, JWL and Applebaum, I and Wasan, JP and Asselin, SR and Bennett, JA},
title = {Host-specific soil oomycete communities are spatially repeatable across natural grasslands.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2026-0106},
pmid = {42696758},
issn = {1480-3275},
abstract = {Soil oomycetes contain some of the most devastating plant pathogens, and are widespread within the soil microbiome, yet how individual plant species structure oomycete communities in natural soils, and whether any such structuring is consistent across space, remains poorly resolved. Because host-specific pathogen accumulation is a central prediction of plant-soil feedback theory but is rarely tested outside greenhouse conditions, we focused on whether the host-specific fraction of these communities is preferentially pathogenic. Using oomycete-specific ITS amplicons, we sequenced rhizosphere-associated and paired bulk soils from four grassland species across 25 sites on the Canadian Prairies spanning more than 200,000 km[2], totalling 1800 samples. Each host supported a distinctive core of taxa, with two species more likely to host pathogenic taxa unique to their rhizosphere. This enrichment was decoupled from richness of oomycete taxa in the rhizosphere, indicating selective accumulation rather than a by-product of resource-rich environments. Community composition also differed among hosts after accounting for site level edaphic variation. Host plant identity therefore leaves a detectable, spatially repeatable imprint on soil oomycete communities, one expressed most strongly through the selective accumulation of pathogenic taxa.},
}

@article {pmid42696789,
year = {2026},
author = {Kan, Y and Fu, Y and Yang, W and Harindintwali, JD and Liu, Q and Jiang, X and Wang, C and Hu, J and Chen, L and Wang, C and Tian, D and Ye, M and Jiang, X},
title = {Rhizosphere microbiome assembly and functional enrichment drive salt tolerance in wheat.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130869},
doi = {10.1016/j.jenvman.2026.130869},
pmid = {42696789},
issn = {1095-8630},
abstract = {Soil salinization is a major constraint on wheat production, as seedling-stage stress strongly constrains early growth and potential yield. However, the mechanisms by which the rhizosphere microbiome mediates varietal differences in salt tolerance remain poorly understood. Here, we compared a salt-tolerant wheat cultivar (Jimai60, JM60) and a salt-sensitive cultivar (Guomai301, GM301) grown in saline-alkali soil. Integrating soil physicochemical, enzymatic analyses and 16S rRNA gene and shotgun metagenomic sequencing, we investigated rhizosphere microbiome assembly, network structure, and functional potential at the seedling stage. JM60 assembled a distinct rhizosphere microbiome enriched in Bacteroidota, with Sphingobacterium acting as a keystone taxon in a more stable co-occurrence network. In contrast, GM301 was dominated by Zobellella and exhibited increased negative microbial interactions, indicating a reduced network that is structurally more cooperative. Metagenomic analyses showed enrichment in JM60-associated microbiomes of genes linked to oxidative stress resistance (katE), central carbon metabolism (pdhD), and nitrogen utilization (hutF), suggesting enhanced redox homeostasis, nutrient cycling, and ion balance regulation. These functional traits aligned with higher leaf antioxidant enzyme activity and altered rhizosphere nutrient profiles in JM60. Our findings demonstrate that wheat salt tolerance is linked to assembly of a functionally enriched rhizosphere microbiome, highlighting microbiome-driven mechanisms for improving crop resilience in saline soils.},
}

@article {pmid42696924,
year = {2026},
author = {Bhowmik, M and Jaiswal, S and Haldar, S},
title = {Metabolic fingerprint establishes ecological linkage between polychaete gut microbes with surrounding benthic ecosystem.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108388},
doi = {10.1016/j.marenvres.2026.108388},
pmid = {42696924},
issn = {1879-0291},
abstract = {In gut-associated symbiosis, microbes play a pivotal role in shaping the habitat and diet preferences of the host. In intertidal deposit-feeding polychaetes, gut microbial assemblages are influenced by both water and sediment biota. In the present study, the metabolic profiling of gut microbial communities of Perinereis sp. was compared with its surrounding environmental microbiome. Effective utilization of amine, amino acids, and carbohydrate substrates by gut microbes was noticed within 48 h of incubation. Moreover, it reached an average well colour development of 0.54 at 120[th] hour of incubation. Low Gini coefficient (0.332) revealed a substrate-generalized communities with diverse metabolism pathways persist in the gut. The multi-level pattern analysis indicated some important substrates that were commonly utilized by gut as well as sediment microbes. Similarity percentage revealed maximum resemblance (64.1%) of gut microbes with its sediment which possibly explained by their deposit-feeding trait and diet preferences. Further, a generalized additive model was applied to study the non-linear trend in time-dependent utilization of carbon guilds by different microbial communities. The results overall indicate the functional overlaps in utilization pattern and possibly explain how polychaete gut microbiome share functional similarity with environmental microbiome with maintaining a distinct community structure. The capacity of utilizing wide varieties of substrate denote high metabolic plasticity of gut microbes which may help in host's survival in the organically enriched mudflat. Furthermore, overlaps in substrate utilization reveal that common environmental factors drive the ecological similarity between gut and sediment microbes.},
}

@article {pmid42697029,
year = {2026},
author = {Mollica, L and Tassi, E and Copaloni, A and De Simone, I and Barouni, RM and De Giorgi, S and Pagano, A and Lampertico, G and Noviello, M and Ferrara, M and Garavaglia, B and Guarnieri, S and Bulotta, A and Viganò, MG and Ogliari, FR and Oresti, S and Damiano, G and Russo, V and Riva, ST and Nuccio, A and Salomone, F and Venanzi, FM and Passaretti, F and Papotto, L and Zotti, D and Di Lello, A and Carbone, C and Bria, E and Sistigu, A and Musella, M and Verlicchi, A and Ulivi, P and Genova, C and Tagliamento, M and Ferlazzo, G and Russo, GL and Brambilla, M and Pasello, G and Mandruzzato, S and Corbo, V and Pilotto, S and De Sanctis, F and Gelibter, A and Piconese, S and Tiseo, M and Mazzaschi, G and Pluchino, M and Cappuzzo, F and Minuti, G and Landi, L and Nisticò, P and Arasanz, H and Labiano, I and Mezquita, L and Pascal, M and Lavaud, P and Chaput, N and Grisanti, S and Bettini, AC and Cortinovis, DL and Galli, G and La Verde, N and Panni, S and Liguigli, W and Petrelli, F and Santo, A and Signorelli, D and Tomasello, G and Toschi, L and Catania, C and Fazio, GRD and Anselmi, E and De Giglio, A and Ardizzoni, A and Bennati, C and Indraccolo, S and Genua, M and Ostuni, R and Bellone, M and Clementi, N and Esposito, A and De Cobelli, F and Palumbo, D and Damascelli, A and Prato, F and De Pretis, S and Lazarević, D and Ruggiero, E and Ponzoni, M and Arrigoni, G and Pedica, F and Veronesi, G and Colombo, MP and Rulli, E and Torri, V and Sacco, M and Garassino, MC and Besse, B and Reni, M and Cascinu, S and Ciceri, F and Bonini, C and Sangaletti, S and Ferrara, R},
title = {Hyperprogression Upon Cemiplimab Alone or With Short Course Chemotherapy in PD-L1 ≥ 50% Non-small Cell Lung Cancer: A Biomarker Guided Multicenter International Phase 2 Trial-HYPERBOLIC Study.},
journal = {Clinical lung cancer},
volume = {27},
number = {8},
pages = {14-21},
doi = {10.1016/j.cllc.2026.08.005},
pmid = {42697029},
issn = {1938-0690},
abstract = {BACKGROUND: Immune checkpoint inhibitor (ICI) monotherapy is the standard first-line treatment for advanced non-small cell lung cancer (NSCLC) with PD-L1 ≥ 50%; however, up to 30% of patients experience early progression or death, including cases of hyperprogressive disease (HPD). High baseline levels (≥ 30.5%) of circulating CD10[-] low-density neutrophils (LDNs) have been associated with increased HPD occurrence. Emerging evidence suggests that combining ICI with platinum-based chemotherapy (PCT) may mitigate the risk of HPD. Currently, no prospective studies have addressed HPD prevention in this context.

PATIENTS AND METHODS: HYPERBOLIC (NCT07274384) is a phase 2, randomized, open-label, multicenter, international trial evaluating whether adding 3 cycles of PCT to first-line cemiplimab reduces HPD rate in stage IV NSCLC with PD-L1 ≥ 50% and CD10[-] LDNs (identified by flow cytometry as CD15⁺CD11b⁺ within the PBMC fraction, with immature cells defined by loss of CD10) ≥ 30.5%. Seventy-four patients will be randomized (1:1 ratio) to receive cemiplimab alone or cemiplimab plus 3 PCT cycles, followed by cemiplimab maintenance. Randomization will be stratified by Lung Immune Prognostic Index. The first computed tomography scan at week 7 after treatment start will assess HPD occurrence, defined as RECIST v 1.1. disease progression with a delta tumor growth rate (ΔTGR) ≥ 50% and/or TGR ratio ≥ 2. The primary endpoint will be the combined rate of HPD and early death (death within 12 weeks with no radiological evaluation). Secondary endpoints will be HPD rate according to alternative definitions, overall survival, progression free survival, objective response rate, and safety. An extensive translational research platform will include spatial transcriptomics of tumor tissue, single-cell RNA sequencing of PBMCs, circulating-free DNA and plasma factors profiling, and saliva/stool microbiome genomics and metabolomics, to longitudinally explore tumor-host dynamic interactions during treatment.

CONCLUSION: to our knowledge, HYPERBOLIC is the first prospective, biomarker-driven trial investigating early treatment escalation based on HPD risk in PD-L1-high NSCLC.},
}

@article {pmid42697040,
year = {2026},
author = {Frangieh, MR and Saad, M and Fattouh, N and Sawan, S},
title = {Antibiotics and nanoparticles in Parkinson's disease: From gut microbiota dysbiosis to neuroprotection and targeted nanotherapies.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {203},
number = {},
pages = {119903},
doi = {10.1016/j.biopha.2026.119903},
pmid = {42697040},
issn = {1950-6007},
abstract = {Parkinson's disease (PD) is increasingly linked to gut-brain axis dysfunction. While broad-spectrum antibiotics may contribute to gut dysbiosis, which has been associated with an increased abundance of curli-producing Enterobacteriaceae and processes implicated in α-synuclein aggregation, certain antibiotic classes, particularly tetracyclines and β-lactams, have demonstrated neuroprotective properties in pre-clinical models of PD. This creates a therapeutic paradox: antibiotics may exert either beneficial or detrimental effects depending on many factors including host microbiome composition. Importantly, much of the current evidence remains observational or pre-clinical, and a direct causal relationship between antibiotic exposure and PD has not yet been established. This review synthesizes current epidemiological, mechanistic, and pre-clinical evidence regarding this paradox and explores the emerging role of nanotechnology in resolving it. Preclinical studies suggest that nanoparticle-based drug delivery systems may enhance BBB penetration and enable more targeted drug release. Such approaches have been proposed as a means to reduce systemic exposure and potentially limit microbiota disruption, although these benefits have not yet been demonstrated in clinical PD populations. We further discuss the translational hurdles, including nanotoxicity and regulatory requirements, and propose a roadmap for future research that integrates metagenomics with precision nanomedicine. Collectively, these findings provide a framework for future investigation of targeted therapeutic strategies for PD. However, substantial mechanistic, clinical, and translational validation is required before their therapeutic potential can be established.},
}

@article {pmid42684938,
year = {2026},
author = {Petry, B and Boggiatto, PM and Buckley, A and Cassmann, ED and Sarlo Davila, K and Olsen, SC and Fernandes, LGV and Tibbs-Cortes, B and Rahic-Seggerman, FM and Palmer, MV and Putz, EJ},
title = {Temporal transcriptomic and microbiome changes in American bison during experimental SARS-CoV-2 challenge.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkag231},
pmid = {42684938},
issn = {2160-1836},
support = {//U.S. Department of Agriculture/ ; //American Rescue Plan (ARP)/ ; #3625-32000-232-00D//Agricultural Research Service (ARS)/ ; //Animal and Plant Health Inspection Service (APHIS)/ ; //Wildlife Services (WS)/ ; //ARS Research Participation Program/ ; //Oak Ridge Institute for Science and Education (ORISE)/ ; //U.S. Department of Energy (DOE)/ ; //ORAU/ ; DE-SC0014664//DOE/ ; },
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to pose a threat to humans as well as domestic and wild animals. The variability in severity of clinical signs, the zoonotic potential, and the host-specific response to infection contribute to the persistence of circulation of disease. In wildlife species, white-tailed deer have been shown to be more permissive to infection than bovids. However, among bovids, American bison have shown a greater susceptibility than cattle. In this study, we investigate the transcriptomic response to experimental SARS-CoV-2 infection in bison over time. Substantial numbers of differentially expressed genes were identified between pre- and 2, 5, 7, 14, and 21 days post-inoculation. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology term analysis identified associations with immune response, inflammatory response, and viral infection including COVID-19. Ingenuity Pathway Analysis of the coronavirus pathway highlighted differences in signaling at days 2 versus 21 post-inoculation. We additionally examined changes in the nasal microbiome of bison over the course of experimental infection, which suggested an increase in opportunity for secondary infection causing pathogens such as Mannheimia. Collectively, this study presents a profile of bison transcriptomic response to SARS-CoV-2 infection and continues to expand our understanding of variation in host response.},
}

@article {pmid42685157,
year = {2026},
author = {Abedi, AA and Pourbozorg, G and Abdou, M and Hoveidaei, AH and Parvizi, J and Citak, M},
title = {Changes in the Management of Periprosthetic Joint Infection Over the Past 50 Years.},
journal = {The Journal of bone and joint surgery. American volume},
volume = {},
number = {},
pages = {},
doi = {10.2106/JBJS.26.00650},
pmid = {42685157},
issn = {1535-1386},
abstract = {➢ Periprosthetic joint infection (PJI) remains a major complication of joint arthroplasty, associated with morbidity and health-care burden. Although room for progress remains, the management of PJI has evolved over the past 50 years from empiric, procedure-centered approaches to structured, evidence-based, and biologically informed strategies.➢ This article summarizes key developments in the prevention, diagnosis, and treatment of PJI, driven by advances across multiple clinical and scientific subspecialties.➢ Diagnostic approaches have advanced from reliance on clinical findings and culture to a multimodal framework integrating validated criteria, serological and synovial biomarkers, and molecular techniques. Surgical management has similarly evolved toward individualized strategies, including debridement with implant retention, 1-stage or 2-stage revision, and salvage surgery tailored to host, pathogen, and disease characteristics.➢ Advances in microbiology, particularly the recognition of biofilm and the emerging role of the human microbiome, have further reshaped the understanding of PJI. Overall, this article examines how developments in prevention, diagnosis, surgical treatment, and microbiology have driven a transition toward precision-based, biology-informed, and individualized management of PJI.},
}

@article {pmid42685222,
year = {2026},
author = {Feng, C and Gao, G and He, Q and Kwok, LY and Liu, C and Li, C and Dong, L and Sun, Z and Zhang, H},
title = {Bifidobacterium animalis subsp. lactis V9 overcomes CYFRA 21-1-linked immunochemotherapy resistance in NSCLC via microbial metabolites.},
journal = {Science advances},
volume = {12},
number = {36},
pages = {eaeg8202},
pmid = {42685222},
issn = {2375-2548},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology/metabolism/drug therapy ; Animals ; *Lung Neoplasms/therapy/immunology/metabolism/drug therapy/microbiology ; *Bifidobacterium animalis/metabolism ; *Antigens, Neoplasm/blood/metabolism ; Mice ; *Keratin-19/blood/metabolism ; *Drug Resistance, Neoplasm ; Female ; Immunotherapy ; Male ; },
abstract = {Gut dysbiosis drives therapeutic resistance, yet the relationships among typical tumor markers, gut microbiota, and treatment efficacy remain poorly defined. Here, elevated serum CYFRA 21-1 in advanced non-small cell lung cancer (NSCLC) correlates with gut dysbiosis, including Bifidobacterium animalis depletion and reduced immunomodulatory metabolites. Fecal supernatant from patients with high-CYFRA attenuated immunochemotherapy efficacy in tumor-bearing mice, linked to disrupted tryptophan and phenylalanine metabolism. Adjuvant B. animalis subsp. lactis V9 enhanced tumor control and antitumor immunity, coinciding with elevated quinaldic acid and catechol, metabolites associated with caspase-dependent apoptosis and ferroptosis. Cell-free fecal supernatant transferred antitumor effects, independent of bacterial colonization. In a randomized, double-blind, placebo-controlled pilot trial (n = 30), adjunctive B. lactis V9 associated with a higher objective response rate (47% versus 33%), disease control rate (87% versus 67%), and prolonged progression-free survival in responders, who exhibited enriched B. animalis and elevated quinaldic acid/catechol (area under the curve = 0.73/0.82). These findings suggest CYFRA 21-1 may identify a modifiable, microbiome-linked state of treatment resistance.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/therapy/immunology/metabolism/drug therapy
Animals
*Lung Neoplasms/therapy/immunology/metabolism/drug therapy/microbiology
*Bifidobacterium animalis/metabolism
*Antigens, Neoplasm/blood/metabolism
Mice
*Keratin-19/blood/metabolism
*Drug Resistance, Neoplasm
Female
Immunotherapy
Male

@article {pmid42685246,
year = {2026},
author = {Lei, S and Qiu, X and Wang, Z and Zhang, Z and Zha, A and Zhou, Y and Chen, H and Huang, J and Yu, Z},
title = {Gut microbial H2S promotes metabolic dysfunction in mice via hepatic PPARα suppression.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag226},
pmid = {42685246},
issn = {1751-7370},
abstract = {This study investigates the role of gut microbiota-derived hydrogen sulfide (H2S) in obesity and glucose metabolism disorders. By integrating human gut metagenomic data, intervention experiments in mouse models, and in vitro cellular assays, we identified a signature of microbial sulfur metabolism in human cohorts and provided experimental evidence for its causal role and underlying metabolic mechanisms in mice. In clinical cohorts with obesity and glucose metabolism disorders, we observed a notable enrichment of genes involved in sulfur transport and H2S production. In mouse models, administration of H2S-producing Desulfovibrio desulfuricans, engineered Escherichia coli expressing phsABC, and the H2S donor NaHS consistently induced body weight gain and impaired glucose tolerance. Transcriptome analysis and cellular experiments indicated that H2S was associated with downregulation of the PPAR signaling pathway and lipid metabolism pathways in the liver, which may contribute to the abnormal accumulation of lipids and glycogen. Furthermore, rescue experiments using a PPAR agonist and an H2S adsorbent partially reversed these metabolic abnormalities. Collectively, our work provides experimental evidence in mouse models demonstrating that gut microbial H2S promotes metabolic dysfunction through hepatic PPARα suppression, providing potential targets for microbiome-based therapeutic interventions.},
}

@article {pmid42685265,
year = {2026},
author = {Ren, J and Yang, Z and Liu, W and Tat Alexander Ng, M},
title = {AResKGLM: a graph-grounded language-model framework for interpretable multi-hop antimicrobial resistance reasoning.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag456},
pmid = {42685265},
issn = {1477-4054},
support = {//Tencent AI for Life Sciences Lab/ ; },
mesh = {*Computational Biology/methods ; Large Language Models ; *Drug Resistance, Microbial ; Humans ; },
abstract = {Antimicrobial resistance (AMR) threatens microbiology and microbiome bioinformatics because resistance phenotypes are shaped by interactions among genes, mobile genetic elements, and functional environments across microbial communities. Prioritizing resistance determinants requires models that reason across knowledge graphs (KGs) linking genes, proteins, pathways, drugs, and microbial phenotypes. Existing graph-based methods compress this evidence into scalar scores, whereas large language models can produce explanations not grounded in structured evidence. We developed AResKGLM (Antimicrobial Resistance Knowledge Graph Language Model), a graph-grounded language-model framework for interpretable microbial AMR bioinformatics that serializes breadth-first-search-retrieved multi-hop paths and per-entity biomedical descriptions into a structured Context-Path-Question prompt. Llama-3-8B and DeepSeek-R1-7B are adapted with QLoRA to produce binary link predictions and concise reasoning traces. On the KIDs benchmark, AResKGLM (Llama-3-8B) achieved F1 = 0.8482, outperforming KG-BERT (0.7213), NBFNet (0.5260), and ULTRA (0.2541) (paired Wilcoxon $p = 1.2 \times 10^{-7}$
). Its advantage increased with reasoning depth: F1 decreased from 0.9197 at 2 hops to 0.8148 at 6 hops, whereas KG-BERT dropped from 0.8110 to 0.6716. Counterfactual path corruption produced an apparent F1 of 0.000, mechanically forced by the probe label assignment; the operative diagnostic is the per-sample flip rate (0.04-0.16), consistent with sensitivity to supplied biological evidence rather than reliance on pretrained priors alone. Cross-species evaluation yielded F1 = 0.81-0.88 with Matthews correlation coefficient (MCC) = 0.35-0.54 on Mycobacterium tuberculosis, Pseudomonas aeruginosa, and Staphylococcus aureus. Temporal ranking of 81 post-2022 gene-drug associations achieved Precision@20 = 100% and AUC-PR = 0.855. AResKGLM offers an interpretable, reproducible framework for multi-hop AMR reasoning, linking candidate prioritization with mechanism-oriented hypothesis generation.},
}

*Computational Biology/methods
Large Language Models
*Drug Resistance, Microbial
Humans

@article {pmid42685266,
year = {2026},
author = {Colajanni, A and Uricaru, R and Darko, S and Subramanian, R and Douek, DC and Thiébaut, R and Thebault, P},
title = {Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag454},
pmid = {42685266},
issn = {1477-4054},
mesh = {Humans ; *Microbiota/genetics ; Benchmarking ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; *Computational Biology/methods ; },
abstract = {Human RNA sequencing (RNA-seq) data originally generated for human transcriptome profiling are overwhelmingly dominated by host sequences, yet they often contain a small fraction of non-human reads that can be exploited for microbial detection. When such datasets are repurposed for secondary microbiome-oriented analyses, extracting and accurately classifying this weak microbial signal becomes technically challenging, and no ready-to-use pipeline currently exists. In this study, we evaluate computational strategies for filtering host reads and classifying microbial transcripts in host-dominated RNA sequencing data. We compare assembly-based approaches similar to those used in a previous study focusing on microbial translocation with state-of-the-art assembly-free methods, and assess their respective strengths and limitations using simulated datasets reflecting low microbial abundance. Our results show that assembly-based methods yield accurate taxonomic predictions but struggle at low read depth, whereas assembly-free methods are more robust in sparse settings at the cost of reduced precision. To leverage the complementarity of both approaches, we propose a hybrid pipeline that integrates assembly-based and assembly-free classification. On simulated data, this hybrid strategy improves microbial classification performance compared with either approach alone. Application to a real human metatranscriptomic dataset analyzed in a microbial translocation context illustrates the broader microbial signal captured by the hybrid approach, despite intrinsic challenges related to the absence of reliable ground truth and the risk of host read misclassification. Our work provides a framework for extracting microbial signals from host-dominated human metatranscriptomes, enabling the reuse of existing transcriptomic datasets for microbiome-related analyses, including but not limited to microbial translocation studies.},
}

Humans
*Microbiota/genetics
Benchmarking
*Transcriptome
*Gene Expression Profiling/methods
Sequence Analysis, RNA/methods
*Computational Biology/methods

@article {pmid42685372,
year = {2026},
author = {Kim, C and Kim, C and Choi, IG and Kalčíková, G and Laforsch, C and Jung, J},
title = {Contrasting effects of conventional PET and biodegradable PHB microplastics on population dynamics and gut microbiome responses in Daphnia magna.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {300},
number = {},
pages = {107982},
doi = {10.1016/j.aquatox.2026.107982},
pmid = {42685372},
issn = {1879-1514},
abstract = {Research on the ecotoxicity of biodegradable microplastics (MPs) in Daphnia magna is rapidly growing, while their population-level effects remain unclear. This study compared the population-level effects of conventional MPs (polyethylene terephthalate, PET) and biodegradable MPs (polyhydroxybutyrate, PHB) on D. magna over 45 days. Gut microbiome and transcriptomic analyses were also conducted to elucidate the underlying mechanisms of the observed responses. PET MPs significantly (p < 0.05) decreased D. magna population biomass relative to control, whereas PHB MPs showed no significant effects. Both types of MPs altered the gut microbial community structure of D. magna, with PHB inducing a selective increase in potential degraders. Transcriptomic data showed that PET MPs significantly (p < 0.05) increased the expression of genes related to stress and defense responses. In contrast, PHB MPs significantly (p < 0.05) upregulated genes associated with metabolic processes. Further research incorporating direct assessment of PHB degradation, host energy assimilation, and wider range of exposure concentrations is required to clarify the mechanisms underlying the distinct responses to biodegradable and conventional MPs. This study highlights the importance of considering polymer types in MP environmental risk assessments and underscores the need of integrating multiple endpoints for a comprehensive evaluation.},
}

@article {pmid42685478,
year = {2026},
author = {Wang, Y and Zhang, Y and Gao, F and Liu, J and He, Y and He, J and Xu, G},
title = {Self-sustaining microbial reductive debromination of brominated flame retardants driven by sewage sludge-derived endogenous organics amid competing electron acceptors.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143412},
doi = {10.1016/j.jhazmat.2026.143412},
pmid = {42685478},
issn = {1873-3336},
abstract = {Polybrominated diphenyl ethers (PBDEs) and tetrabromobisphenol A (TBBPA) are prevalent brominated flame retardants in wastewater and sewage sludge, yet the sustainability and robustness of their microbial reductive debromination remain poorly understood, particularly in the presence of co-existing electron acceptors (e.g., nitrate and sulfate). Here we revealed that sewage sludge-derived endogenous organic matter sustained efficient microbial reductive debromination of both TBBPA and PBDEs without external organics amendment. Over 99% TBBPA was transformed to bisphenol A within 30 days, whereas PBDE debromination occurred sequentially after TBBPA depletion, producing lower-brominated congeners (33.9%) and diphenyl ether (17.9%) after 120 days. Unexpectedly, amendment of external organic carbons (formate, acetate, pyruvate, and lactate) did not enhance debromination and instead stimulated methanogenesis, indicating diversion of electron flow towards competing reduction pathways. Reductive debromination remained highly active in the presence of 0.5-10 mM nitrate and sulfate, and similar debromination extent of both pollutants was achieved as the controls, although high nitrate and sulfate concentrations decreased TBBPA debromination rates by 42.8-67.4%. Notably, active debromination persisted even at sulfide concentrations exceeding 6 mM generated from sulfate reduction, revealing exceptional sulfide tolerance of sludge-associated organohalide-respiring bacteria (OHRB). Dehalococcoides and Dehalobacter were identified as obligate OHRB involved in debromination, with Dehalococcoides exhibiting high tolerance to nitrate-, sulfate-, and sulfide-associated stress. Moreover, the sludge microbiome was resilient and metabolically integrated despite redox perturbations. Collectively, these findings reveal sewage sludge as a self-sustaining and resilient platform for reductive debromination and provide a low-cost strategy for remediation of brominated pollutants in wastewater, sludge and other anaerobic environments.},
}

@article {pmid42685797,
year = {2026},
author = {Spencer, S and Valenzuela, KN and Cheng, Z and Leung, B},
title = {Spatially controlled polymicrobial human airway model recapitulates complex interactions between Pseudomonas aeruginosa and lung commensals.},
journal = {Biomedical materials (Bristol, England)},
volume = {},
number = {},
pages = {},
doi = {10.1088/1748-605X/aea1cc},
pmid = {42685797},
issn = {1748-605X},
abstract = {Airway barrier dysfunction is a hallmark of chronic lung diseases including cystic fibrosis, asthma, and chronic obstructive pulmonary disease, and is often shaped by polymicrobial rather than single-species interactions with the host tissue. However, extended host-microbe co-culture with rapid-colonizing airway pathogens such as Pseudomonas aeruginosa is difficult to sustain in accessible in vitro systems, limiting mechanistic study of polymicrobial barrier and inflammatory dynamics. Here we developed and validated an aqueous two-phase system (ATPS) that spatially confines bacterial communities over a human bronchial epithelial-endothelial transwell co-culture, extending the stable co-culture window to 24 h while preserving assayable barrier and cytokine readouts. Using a validation-by-recapitulation approach, the platform reproduced established in vivo phenomena: P. aeruginosa-driven barrier disruption, attenuation of pathogenic effects by the commensals R. mucilaginosa and L. casei with preserved junctional architecture, and S. pneumoniae exacerbation of barrier permeability accompanied by elevated IL-8 despite apparent junctional preservation. This accessible ATPS-based biomaterials platform requires no microfluidic or iPSC-derived components and provides a tractable foundation for mechanistic studies of polymicrobial interactions at the airway epithelial barrier.},
}

@article {pmid42685805,
year = {2026},
author = {Arena, L and Prescott, MP},
title = {Parental Factors Associated with US Youth Ultra-Processed Food Outcomes: A Systematic Review.},
journal = {Appetite},
volume = {},
number = {},
pages = {108774},
doi = {10.1016/j.appet.2026.108774},
pmid = {42685805},
issn = {1095-8304},
abstract = {Ultra-processed food (UPF) comprises 67% of the average US youth diet, among the highest rates globally. Health burdens associated with youth UPF intake include overweight/obesity, glucose dysregulation, poor cardiovascular health, liver disease, microbiome disruption, dental problems, DNA damage, mental health concerns, and lower cognitive and academic performance. This systematic review investigates parental factors associated with US youth UPF intake, preference, selection, or access. A comprehensive literature review was conducted using PRISMA guidelines. PubMed, CINAHL, Scopus, and Web of Science databases were searched. Inclusion criteria required studies to examine youth (aged 0-19) UPF outcomes and parental factors. The Mixed Methods Appraisal Tool assessed study bias and quality. PROSPERO registration number: CRD420251248701. The search yielded 1727 articles, 888 after duplicates removed. Full text review resulted in 11 extracted articles: 9 quantitative and 2 qualitative. Parental factors associated with child UPF outcomes included education level, gender (female), UPF intake, more frequent soda and fast-food intake, belief in food advertising, reward-based eating drive, allowing youth to watch greater hours of TV, and the home food environment. Mixed findings were found with parental substance use, depending on prenatal, maternal, and paternal use, cigarette, alcohol, or illicit drugs, and child age. Notable null findings included parent age, living with a partner, household income, shared family meals, human milk exposure, and parent motivation, attitude, and self-efficacy to limit junk food and eat more fruits/vegetables. Further research around parental factors and US youth UPF intake is warranted. Intervening in identified target areas may help mitigate youth UPF outcomes.},
}

@article {pmid42685867,
year = {2026},
author = {Zhang, L and Chun, Y and Valeiron, S and Grishina, G and Lo, T and Wang, J and Sicherer, S and Bunyavanich, S},
title = {Coordinated changes in oral propionate, oral microbiota, and peripheral blood inflammatory processes during peanut oral immunotherapy.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.08.015},
pmid = {42685867},
issn = {1097-6825},
abstract = {BACKGROUND: Peanut allergy is an increasingly prevalent condition without curative treatment. Oral immunotherapy (OIT) can induce desensitization, but its mechanisms are not fully understood. Administration of oral short-chain fatty acids (SCFAs) in murine models induces favorable immunomodulation that overlaps with processes observed in OIT. We hypothesized that in human populations, oral SCFA levels change during OIT and are associated with systemic downregulation of Type 2 processes.

METHODS: Within a clinical trial of children age 4-14 years with high-threshold peanut allergy randomized to OIT or avoidance, we profiled oral SCFA levels, the oral microbiome, and peripheral blood transcriptome over the course of OIT or avoidance. Statistical and network analyses were carried out to test our hypotheses.

RESULTS: Among the 56 children in the clinical trial with complete multi-omic profiles over the trial duration, 29 were randomized to OIT and 27 to avoidance. 100% of the participants in the OIT group achieved desensitization compared to 18.5% in the avoidance group. Oral levels of the SCFA propionate increased with OIT but not avoidance (FDR=0.042) and remained elevated with sustained unresponsiveness. Oral propionate levels positively correlated with the relative abundances of several oral microbes, including known propionate producers Prevotella spp. (r=0.47, FDR 3.75x 10-3) and Veillonella (r=0.39, FDR 1.45x10-2). Oral propionate levels negatively correlated with peripheral blood transcript expression of OIT-associated Fcγ receptors (FDR≤ 0.05), IL-4 & IL-13 signaling (FDR≤ 0.05), and neutrophil degranulation pathways (FDR≤ 0.05).

CONCLUSIONS: This study raises the intriguing possibility of oral propionate serving as an important immunoregulatory bridge between local and systemic processes in peanut OIT.

TRIAL REGISTRATION: ClinicalTrials.gov NCT03907397.},
}

@article {pmid42685930,
year = {2026},
author = {Babenkova, PI and Golovina, NA and Reprintseva, VN and Karaulova, SO and Vostrikova, AD and Burakova, IY and Pogorelova, SV and Smirnova, YD and Morozova, PD and Shutikov, VA and Mikhailov, EV and Kozin, SV and Dzhimak, SS and Gureev, AP and Syromyatnikov, MY},
title = {Comenic acid as a modulator of the gut-testis axis in pyridaben-induced toxicity.},
journal = {Reproductive toxicology (Elmsford, N.Y.)},
volume = {},
number = {},
pages = {109342},
doi = {10.1016/j.reprotox.2026.109342},
pmid = {42685930},
issn = {1873-1708},
abstract = {Pyridaben is an acaricide that inhibits mitochondrial complex I, which disrupts mitochondrial viability and causes oxidative stress. Pyridaben administration was associated with significant damage to mitochondrial DNA (mtDNA) in mice. The oxidative stress related to pyridaben exposure also co-occurred with alterations in the morphology of the testes and intestines, leading to the activation of the Nrf2-dependent protective pathway in testicular tissue, reduction of the seminiferous tubule lumen accompanied by interstitial tissue swelling, and adaptive changes in the intestinal epithelial tissue. Comenic acid (CA) exhibits active antioxidant properties; in the group receiving CA, the mtDNA copy number increased. Functionally, pyridaben considerably reduced the alpha diversity of the intestinal microbiome, while CA administration appeared to normalize this indicator, also mitigating shifts in beta diversity. Taxonomic analysis revealed that pyridaben elevated the abundance of the families Bacteroidaceae and Muribaculaceae, which aligned with a functional upregulation of endotoxic dTDP-β-L-rhamnose and L-lysine biosynthesis pathways. Conversely, CA treatment attenuated these shifts, reducing opportunistic taxa while concurrently upregulating protective pathways, including folate transformations and CDP-diacylglycerol biosynthesis. These findings suggest that CA, potentially due to its antioxidant properties and modulation of the intestinal microbial and functional profiles, may exert a compensatory effect against pyridaben-induced toxicity via the gut-testis axis.},
}

@article {pmid42686068,
year = {2026},
author = {Zhou, J and Gu, T and Li, S},
title = {A bioinformatics framework using public 16S rRNA gene amplicon data to assess the presence of target bacteria in bat and rodent samples.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107684},
doi = {10.1016/j.mimet.2026.107684},
pmid = {42686068},
issn = {1872-8359},
abstract = {Validating the ecological distribution of a newly isolated bacterial species in natural hosts remains challenging due to the lack of specific detection assays and the cost of large-scale screening. Here, we describe a dual-strategy bioinformatics pipeline that leverages publicly available 16S rRNA gene amplicon sequencing data to reliably and inexpensively confirm target bacterial presence. The method first extracts hypervariable regions from the target bacterium's full-length 16S rRNA gene and evaluates their specificity by calculating an A-value-defined as the highest sequence similarity to any non-target strain in reference databases. Regions with an A-value below the 98.7% species threshold are selected. These are then aligned against Amplicon Sequence Variants (ASVs) from public datasets to compute a B-value (highest similarity to ASVs within a sample). A novel classification logic (B > A) is applied to designate samples as positive or negative, reducing false positives. The pipeline incorporates multi-level controls, including process/biological negatives and positives. Testing with novel species (Clostridium sp. nov.) and a formally described species (Streptococcus lishijunsis), along with common commensal species demonstrated that region-specific performance varies, highlighting the need for pre-validation. The framework successfully distinguished target-positive from negative samples, with phylogenetic support for specificity. This approach provides a rigorous, cost-effective, and accessible workflow that links in vitro isolation to in vivo ecological validation using existing public data.},
}

@article {pmid42686295,
year = {2026},
author = {Schouten, D and Wiersinga, WJ and van Vught, L},
title = {Post-Sepsis Syndrome: From Pathogenesis Toward Novel Management Strategies.},
journal = {Critical care clinics},
volume = {42},
number = {4},
pages = {745-761},
doi = {10.1016/j.ccc.2026.05.003},
pmid = {42686295},
issn = {1557-8232},
mesh = {Humans ; *Sepsis/complications/therapy/physiopathology ; Post-Infectious Disorders ; Patient Readmission/statistics & numerical data ; },
abstract = {Sepsis survivorship is increasing, but many survivors develop post-sepsis syndrome, marked by high early readmission rates and new-onset conditions, notably recurrent infections, cardiovascular, psychiatric, and kidney disease. Persistent physical, cognitive, and psychological sequelae may further impair daily functioning. Emerging evidence suggests lasting immune dysregulation, likely interacting with mitochondrial dysfunction, immunosuppression, endothelial injury, low-grade inflammation, and microbiome disruption. While evidence for targeted postdischarge interventions remains limited and yields mixed results, much can still be done. Several strategies can begin during hospitalization, and after discharge a primary-care-centered, risk-stratified follow-up pathway may support recovery and reduce readmissions and complications.},
}

Humans
*Sepsis/complications/therapy/physiopathology
Post-Infectious Disorders
Patient Readmission/statistics & numerical data

@article {pmid42686665,
year = {2026},
author = {Morris, MJ and Jaggernath, KC and Martin, AD and Ramdass, RS},
title = {The Puerperium in the Modern Dairy Cow: A Review.},
journal = {Reproduction in domestic animals = Zuchthygiene},
volume = {61 Suppl 2},
number = {},
pages = {e70303},
doi = {10.1111/rda.70303},
pmid = {42686665},
issn = {1439-0531},
mesh = {Animals ; Female ; Cattle/physiology ; *Postpartum Period/physiology ; Uterus/physiology ; Pregnancy ; Cattle Diseases/physiopathology ; Uterine Diseases/veterinary ; Fertility/physiology ; },
abstract = {The puerperium represents a critical physiological period during which the bovine reproductive tract transitions from pregnancy to renewed fertility. In the modern high-producing dairy cow, this transition is challenged by profound metabolic, endocrine, immunological, and structural demands that collectively influence uterine health, ovarian function, and subsequent reproductive performance. This review examines current understanding of the physiology of the puerperium in dairy cattle, with particular emphasis on uterine involution, immune clearance of postpartum contamination, endocrine regulation, and resumption of ovarian cyclicity. Further, it contrasts high-yielding Holsteins with fertility selected dairy populations. Normal uterine involution involves coordinated myometrial contraction, tissue remodelling, endometrial regeneration, and tightly regulated inflammatory responses. Failure of these processes predisposes cows to postpartum uterine disorders, including retained fetal membranes, metritis, endometritis (purulent vaginal discharge with cytological confirmation), and pyometra, which remain major contributors to subfertility and economic loss. Central to the pathophysiology of puerperal disease is negative energy balance, which disrupts immune competence, alters hepatic steroid metabolism, impairs ovarian signalling, and compromises oocyte and embryo quality. Emerging evidence highlights the complex interplay between metabolism, immunity, and the uterine microbiome, shifting current perspectives away from pathogen-centric models toward host resilience. Advances in biomarkers, genomic selection, and precision monitoring offer new opportunities for targeted reproductive management. Ultimately, optimisation of transition period management remains the cornerstone of supporting physiological puerperal recovery and sustaining reproductive efficiency in modern dairy systems.},
}

Animals
Female
Cattle/physiology
*Postpartum Period/physiology
Uterus/physiology
Pregnancy
Cattle Diseases/physiopathology
Uterine Diseases/veterinary
Fertility/physiology

@article {pmid42686848,
year = {2026},
author = {Wu, Y and Liu, F and Liu, Y and Zheng, M and Sun, J and Shi, X and Wu, J and Du, Y and Deng, H and Zhou, X},
title = {Dynamic biomass micro-nanofibre framework for entrapment and clearance of gastrointestinal microplastics.},
journal = {Nature nanotechnology},
volume = {},
number = {},
pages = {},
pmid = {42686848},
issn = {1748-3395},
support = {52373062//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52173061//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52573122//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52203069//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microplastics (MPs) are infiltrating global food systems, where they disseminate systemically, posing unmet health risks as current strategies fail to prevent bioaccumulation. We have engineered an oral alginate-chitin micro-nanofibre framework (Alg-Ch) as a pH-responsive scavenger, which was formed via lyophilization-induced hydrogen bonding and physical entanglement between alginate microfibres and chitin nanofibrous sheets (1:10 ratio). Alg-Ch captured MPs predominantly through two mechanisms: electrostatic adsorption onto a protonated chitin nanonetwork in gastric acid, and physical entrapment by swollen alginate at intestinal pH. It captured 500-nm spherical MPs of varying surface chemistry (polystyrene (PS), PS-COOH, PS-NH2) and composition (polyethylene terephthalate, polymethyl methacrylate), and irregular fragments including PS fibres, polypropylene, and polyethylene, achieving capacities of 816.6 mg g[-1] (stomach) and 1114.5 mg g[-1] (intestine), and retained >47% efficacy with food. In mice, Alg-Ch reduced colonic MP fluorescence by ∼50% within 2 h and accelerated faecal elimination. A 13-week Alg-Ch intervention restored tight-junction proteins ZO-1, occludin and claudin-5, decreased serum levels of interleukin-6, lipopolysaccharide, tumour necrosis factor and interleukin-1β, and promoted recovery of short-chain fatty acid-producing genera, with no evidence of body-weight loss, organ toxicity or histopathological lesions. This biocompatible platform unifies mechanical sequestration, barrier repair and microbiome rehabilitation, offering a scalable strategy to mitigate the risks of ingested MPs and the global health burden of plastic pollution.},
}

@article {pmid42687109,
year = {2026},
author = {Capparotto, A and Ciampanelli, A and Salvucci, P and Chesneau, G and Herpell, J and Sello, S and Sudiro, C and Clauw, P and Altissimo, A and Hacquard, S and Vuolo, F and Giovannetti, M},
title = {Plant genetic and root-associated microbial diversity modulate Lactuca sativa responsiveness to a soil inoculum under phosphate deficiency.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71529},
pmid = {42687109},
issn = {1469-8137},
support = {//NextGenerationEU/ ; //Ministero dell'Università e della Ricerca/ ; //Università degli Studi di Torino - Dipartimento di Scienze della Vita e Biologia dei Sistemi/ ; },
abstract = {Microbial-based approaches offer a promising strategy to decrease the use of chemical fertilizers in agriculture. Among them, arbuscular mycorrhizal fungi (AMF), which extend root surface area and enhance phosphate uptake, and phosphate-solubilizing bacteria (PSB) are particularly relevant. However, their effectiveness depends strongly on plant genetic diversity. To identify genetic markers underlying plant responses to beneficial soil microbes, we studied a panel of 128 fully sequenced Lactuca sativa varieties under controlled phosphate-starvation conditions and treated with AMF and PSB. Lettuce genetic variation showed a strong effect on physiological and morphological responses to microbial inoculation. Genome-wide association studies identified specific genomic regions associated with changes in leaf phosphate content and shoot biomass following treatment. Beyond genetic factors, we observed shifts in fungal β-diversity and increased bacterial α-diversity associated with phenotypic variation. We also identified 44 amplicon sequence variants associated with agriculturally relevant traits. Among these, six bacterial strains were experimentally validated through in vitro and pot experiments for their effects on leaf phosphate concentration and shoot biomass. Overall, we highlighted key genetic, microbial, and physiological mechanisms that may enhance microbial treatments for improved plant phosphate management in lettuce.},
}

@article {pmid42687557,
year = {2026},
author = {Vorobev V, A and Gadzhieva Z, K and Malov S, I and Syrova A, I and Su-Yanz K, M and Syrova A, I},
title = {[Microbiome as a Novel Player in the Development and Treatment of Renal Cancer: A Systematic Review and Meta-Analysis].},
journal = {Urologiia (Moscow, Russia : 1999)},
volume = {},
number = {1},
pages = {143-153},
pmid = {42687557},
issn = {1728-2985},
mesh = {Humans ; *Kidney Neoplasms/microbiology/therapy ; *Carcinoma, Renal Cell/microbiology/therapy ; *Microbiota ; Gastrointestinal Microbiome ; },
abstract = {RELEVANCE: Growing evidence highlights the significant role of the human microbiota and microbiome in the pathogenesis of malignant tumors, including renal cell carcinoma (RCC). This systematic review evaluates studies addressing the associations between the microbiota/microbiome and the development and progression of RCC, as well as the influence of the microbiota on therapeutic efficacy in this malignancy.

MATERIALS AND METHODS: The review was conducted in accordance with PRISMA guidelines. A systematic search of bibliographic databases (PubMed, Scopus, etc.) using the keywords ("renal cell carcinoma"/"kidney cancer"/"renal cancer" and "microbiota"/"microbiome") identified 12,547 publications. After removal of duplicates and screening for eligibility, 33 studies directly examining the relationship between the microbiota and RCC were included in the analysis. Studies not relevant to the topic or focusing on tumor growth without specific reference to kidney cancer were excluded.

RESULTS: The review summarizes the composition and alterations of the microbiota in RCC: (1) the intratumoral microbiota of renal tumors differs from that of adjacent healthy kidney tissue, showing reduced diversity and distinct bacterial profiles; (2) the gut microbiota of RCC patients is dysbiotic compared with healthy controls, characterized by enrichment of potentially pro-carcinogenic taxa and depletion of protective bacteria; (3) the urinary microbiome also undergoes changes in RCC, though data remain limited. Potential mechanisms have been proposed: microbiota-derived metabolites (e.g., tryptophan-kynurenine pathway intermediates, short-chain fatty acids, trimethylamine N-oxide [TMAO]) may influence the tumor microenvironment, immune response, and metastatic potential. Importantly, gut microbiota composition has been shown to modulate response to immunotherapy in RCC: higher microbial diversity and the presence of specific taxa (e.g., Akkermansia muciniphila) are associated with improved response to immune checkpoint inhibitors, whereas dysbiosis and antibiotic exposure correlate with diminished efficacy. Several studies have demonstrated that modulation of the microbiome (via probiotics, prebiotics, or fecal microbiota transplantation) can enhance antitumor immunity and improve treatment outcomes in RCC, although clinical data specifically addressing RCC onset and progression remain limited.

CONCLUSIONS: The microbiota and microbiome are increasingly recognized as key factors in the development and progression of renal cell carcinoma, also influencing the effectiveness of contemporary therapeutic strategies. Further research is required to establish causal relationships and to develop microbiome-oriented approaches for the prevention and treatment of RCC.},
}

Humans
*Kidney Neoplasms/microbiology/therapy
*Carcinoma, Renal Cell/microbiology/therapy
*Microbiota
Gastrointestinal Microbiome

@article {pmid42687641,
year = {2026},
author = {Lee, M},
title = {From resistance mechanisms to therapy: Antimicrobial resistance in Gram-negative bacteria.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {8},
pages = {e2604017},
doi = {10.71150/jm.2604017},
pmid = {42687641},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; RS-2023-00210754//Ministry of Science and ICT/ ; },
mesh = {*Gram-Negative Bacteria/drug effects/genetics ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gram-Negative Bacterial Infections/microbiology/drug therapy ; *Drug Resistance, Multiple, Bacterial ; beta-Lactamases/metabolism/genetics ; *Drug Resistance, Bacterial ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Antimicrobial resistance poses a major global health challenge, and infections caused by multidrug-resistant Gram-negative bacteria are associated with substantial morbidity and mortality. In contrast to many Gram-positive pathogens, Gram-negative bacteria combine intrinsic barriers with acquired determinants, including enzymatic drug inactivation, reduced outer membrane permeability, active efflux, and target modifications, which collectively compromise the efficacy of multiple antibiotic classes. Previous reviews have largely catalogued resistant pathogens or antimicrobial agents. This review provides a mechanism-focused overview of antimicrobial resistance in clinically important Gram-negative bacteria and explains how dominant resistance determinants translate into clinically relevant failure modes, such as delayed effective therapy, limited treatment options, and increased reliance on toxic last-line agents. Current and emerging therapeutic strategies are discussed through a mechanism-based lens, emphasizing newer β-lactam/β-lactamase inhibitor combinations and nontraditional approaches, including phages, antivirulence, and microbiome-based interventions. This review highlights the conceptual links between resistance mechanisms, clinical impact, and rational therapeutic choices and identifies priorities for future research aimed at mitigating antimicrobial-resistant Gram-negative infections.},
}

*Gram-Negative Bacteria/drug effects/genetics
Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
*Gram-Negative Bacterial Infections/microbiology/drug therapy
*Drug Resistance, Multiple, Bacterial
beta-Lactamases/metabolism/genetics
*Drug Resistance, Bacterial
Bacterial Proteins/metabolism/genetics

@article {pmid42687714,
year = {2026},
author = {Velsko, IM and Hübner, A and Fagernäs, Z and Yates, JAF and Mann, AE and Hofman, CA and Ozga, AT and Lewis, CM and Speller, C and Fiddyment, S and Francken, M and Wahl, J and Krause, J and Radini, A and King, T and Warinner, C},
title = {The Oral Microbiome of King Richard III of England.},
journal = {American journal of biological anthropology},
volume = {191},
number = {1},
pages = {e70350},
pmid = {42687714},
issn = {2692-7691},
support = {//Werner Siemens Stiftung/ ; //Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy/ ; //Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM)/ ; //Max Planck Society/ ; },
mesh = {Humans ; *Microbiota/genetics ; England ; *Dental Calculus/microbiology/history ; DNA, Ancient/analysis ; History, 15th Century ; *Mouth/microbiology ; History, Medieval ; History, Ancient ; Phylogeny ; Metagenome/genetics ; },
abstract = {OBJECTIVES: Metagenomic investigations of ancient dental calculus provide insights into oral health, disease, and diet. Here, we analyze the dental calculus metagenome of King Richard III of England (1452-1485).

MATERIALS AND METHODS: Dental calculus DNA was extracted from three teeth of King Richard III and shotgun sequenced to a depth of nearly 400 million reads. The metagenomic data were taxonomically profiled and compared to new and previously published dental calculus metagenomes from England, Ireland, the Netherlands, and Germany spanning the Neolithic to the present. Sequencing data were de novo assembled, and metagenome-assembled genomes assigned to the genus Tannerella were investigated for phylogenetic relatedness and virulence. Putative dietary DNA was assessed for authenticity.

RESULTS: The dental calculus of King Richard III was well-preserved and yielded an exceptionally high quantity of DNA. Oral microbiome species diversity fell within the range previously observed among other northern European populations, suggesting that a royal lifestyle and a rich diet did not substantially impact his oral microbiota. The reconstructed Tannerella genomes contained many virulence factors found today among oral Tannerella species. No putative dietary DNA could be authenticated.

DISCUSSION: The dental calculus of King Richard III produced one of the richest ancient oral metagenomes published to date, yet the species diversity was indistinguishable from that of commoners living in northern Europe over the last 7000 years. Insufficient plant and animal DNA were recovered to investigate diet, suggesting that dental calculus may not be a sufficient source of dietary DNA even when exceptionally well-preserved.},
}

Humans
*Microbiota/genetics
England
*Dental Calculus/microbiology/history
DNA, Ancient/analysis
History, 15th Century
*Mouth/microbiology
History, Medieval
History, Ancient
Phylogeny
Metagenome/genetics

@article {pmid42687847,
year = {2026},
author = {Dichter, J},
title = {Bile Acid Metabolism as a Unifying Readout for Diet, Microbiome Function, and Gastrointestinal Disease.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {17},
pages = {e72273},
pmid = {42687847},
issn = {1530-6860},
mesh = {Humans ; *Bile Acids and Salts/metabolism ; Animals ; *Gastrointestinal Diseases/metabolism/microbiology ; *Diet ; *Gastrointestinal Microbiome/physiology ; Receptors, Cytoplasmic and Nuclear/metabolism ; },
abstract = {Bile acid biology has advanced through significant conceptual shifts. Once understood primarily as biological detergents, bile acids are now recognized as signaling molecules and, more recently, as a chemically diverse set of host- and microbe-derived metabolites. The 2020 discovery of microbially conjugated bile acids (MCBAs) and the expansion of the recognized catalog from approximately 20 species to more than 200 mark a new phase in this trajectory. Clinical translation has not kept up. Direct farnesoid X receptor (FXR) agonism failed twice in trials for non-alcoholic steatohepatitis, later received a serious liver injury safety communication from the U.S. Food and Drug Administration, and was voluntarily withdrawn from the United States market. The standard of care for bile acid diarrhea and post-cholecystectomy diarrhea still relies largely on chemical binding with drugs introduced in the 1960s and 1970s. This Perspective argues that the gap between bile acid biology and bile acid medicine persists in part because the field has not been organized around the bile acid pool as a shared measurable output. Researchers studying dietary modulators of the gut microbiome have worked in separate communities around fiber, fermented foods, polyphenols, protein, and dietary fat. Each of these inputs can shape bile acid metabolism, yet many intervention studies do not measure it. The most immediately implementable bile acid-targeted strategy is specified dietary intervention designed with measurable bile acid outcomes and evaluated with the precision of pharmacological therapy. Four recommendations follow: intervention studies should routinely measure bile acid outcomes; clinicians should test bile acid metabolism in conditions involving dysregulation; regulators should develop a framework for multicomponent dietary therapies; and researchers should build infrastructure for population-scale longitudinal monitoring.},
}

Humans
*Bile Acids and Salts/metabolism
Animals
*Gastrointestinal Diseases/metabolism/microbiology
*Diet
*Gastrointestinal Microbiome/physiology
Receptors, Cytoplasmic and Nuclear/metabolism

@article {pmid42687886,
year = {2026},
author = {Youngblood, V and Armstrong, TD and Nguyen-Alley, K and Green, AE and Kelly, ME and Johnson, B and Stanley, A and Gilbreth, P and Cook, M and Coxe, T and Bradshaw, JL and Azad, RK and Cunningham, RL and Lund, AK},
title = {Sex-specific gut microbial and metabolic responses to inhaled diesel exhaust particle exposure are modified by probiotic treatment in C57BL/6 mice.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10713368/v1},
pmid = {42687886},
issn = {2693-5015},
abstract = {Background Epidemiological and experimental studies indicate that susceptibility to traffic-generated particulate matter (PM)-induced metabolic dysfunction varies by sex, with females frequently exhibiting greater vulnerability. Recent evidence suggests that disruption of the lung-gut axis and subsequent gut-derived inflammatory signaling may contribute to these outcomes. However, the effects of inhaled PM on gut microbiome signaling and the metabolic milieu across sexes remain inadequately characterized. This study examined whether diesel exhaust particulate (DEP) exposure induces sex-specific metabolic and inflammatory responses and whether probiotic supplementation differentially modifies these effects in males and females. Methods Male and female C57BL/6 mice were exposed to 35 µg DEP (1 mg/mL, SRM-2975) or saline control via oropharyngeal aspiration twice weekly for 50 days, with or without probiotic supplementation (Winclove Ecologic® Barrier probiotics). Systemic metabolic outcomes in plasma were assessed using a multiplex hormone panel. Gut microbiome composition was characterized using 16S rRNA sequencing, and gut-derived signaling was evaluated through plasma lipopolysaccharide (LPS) quantification and short-chain fatty acid (SCFA) analysis. Three-way ANOVAs with sex as a biological variable were conducted to determine differential responses to DEP exposure and probiotic intervention. Results DEP exposure induced sex-dependent alterations in gut microbial composition, circulating metabolites, and endotoxemia. In females, DEP exposure resulted in taxonomic shifts and reduced microbial diversity, whereas probiotic treatment produced the most pronounced community-level expansion in DEP-exposed males. Beta-diversity analyses confirmed significant treatment-associated differences in community composition, identifying probiotic treatment as the primary driver, with stronger community-level effects in females and more limited effects in males. These changes corresponded with alterations in circulating SCFA and LPS levels, with more pronounced effects observed in females. Conclusions Biological sex is a major determinant of susceptibility to DEP-induced metabolic and inflammatory dysregulation. Females demonstrated heightened systemic and gut-derived responses to DEP exposure. Probiotic supplementation modified several of these functions, with effects varying by sex. Notably, probiotic supplementation produced opposing effects on glucagon in DEP-exposed animals depending on sex, underscoring the importance of biological sex in determining both the direction and magnitude of microbiome-targeted intervention outcomes. These findings support the inclusion of sex as a biological variable in environmental health research and suggest that microbiome-targeted interventions may provide sex-specific protective effects against PM-induced metabolic dysfunction.},
}

@article {pmid42687904,
year = {2026},
author = {Sharma, S and Zhang, T and McElderry, J and Lee, O and Hoang, P and Zeng, L and Webster, N and Alexandrov, L and Raz, E and Landi, MT and Bertin, S},
title = {Detection of House Dust Mite-derived DNA in Human Lung Tumors by Whole-Genome Sequencing.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10438367/v1},
pmid = {42687904},
issn = {2693-5015},
abstract = {Lung cancer in never-smokers (LCINS) accounts for an increasing proportion of lung cancer cases, yet its risk factors remain poorly understood. House dust mites (HDM) are common aeroallergens that induce airway inflammation, but their potential contribution to lung cancer is unknown. We analyzed unmapped whole-genome sequencing reads from 783 lung cancers from the Sherlock- Lung (n = 621 never-smokers) and EAGLE (n = 162 smokers) cohorts, including 328 matched adjacent normal lung tissues. After removal of human sequences, reads were aligned to reference genomes from the two major HDM species and confirmed by BLAST. Samples with top BLAST matches were classified as HDM-detected. Associations between HDM detection and genomic, microbiome, and bulk RNA-seq-derived immune features were evaluated. HDM-derived DNA was detected at low abundance in a subset of tumors and adjacent normal tissues, with higher detection frequencies in tumors than matched normal tissues and in smokers than never-smokers. In LCINS tumors, HDM detection was not associated with tumor mutational burden or recurrent driver alterations but was associated with modest differences in immune cell composition and a limited but reproducible bacterial co-detection pattern. These findings provide a foundation for investigating aeroallergen-derived DNA signatures and their potential relationship to the lung tumor microenvironment.},
}

@article {pmid42688031,
year = {2026},
author = {Lu, L and Li, J and Yao, X},
title = {Probiotic mediated modulation of neonatal health: a meta-analysis of prematurity-related morbidity, jaundice, and respiratory distress.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1866590},
pmid = {42688031},
issn = {2235-2988},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Infant, Newborn ; *Respiratory Distress Syndrome, Newborn/prevention & control/epidemiology ; Infant, Premature ; *Jaundice, Neonatal/prevention & control/epidemiology ; *Infant Health ; Gastrointestinal Microbiome ; Dietary Supplements ; },
abstract = {INTRODUCTION: Prematurity remains a major contributor to neonatal morbidity and mortality worldwide, with neonatal jaundice and respiratory distress syndrome (RDS) representing two of the most common complications associated with immature hepatic and pulmonary development. Increasing evidence suggests that probiotic supplementation may improve neonatal outcomes through modulation of the gut microbiome, gut-liver axis, and gut-lung axis; however, published findings remain inconsistent. The meta-analysis evaluated the effects of probiotic supplementation on prematurity-related morbidity, with particular emphasis on neonatal jaundice and RDS.

METHODS: The study was conducted according to PRISMA 2020 guidelines, and a comprehensive literature search of PubMed, Scopus, Web of Science, and the Cochrane Library identified 18 eligible studies comprising 2,587 preterm infants. Methodological quality was assessed using the Cochrane Risk of Bias 2 tool and Newcastle-Ottawa Scale, and pooled effect estimates were calculated using random-effects models.

RESULTS: Probiotic supplementation significantly reduced the incidence of neonatal jaundice (RR = 0.72, 95% CI: 0.61-0.84; p < 0.001), peak total serum bilirubin levels (MD = -1.84 mg/dL, 95% CI: -2.47 to -1.21), and phototherapy requirements (RR = 0.68, 95% CI: 0.55-0.82; p < 0.001). The incidence of RDS was significantly reduced (RR = 0.79, 95% CI: 0.66-0.95; p = 0.012), accompanied by a shorter duration of respiratory support (MD = -1.9 days, 95% CI: -2.8 to -1.0). Moderate heterogeneity was observed across pooled analyses (I² = 42-57%). Exploratory meta-regression suggested that probiotic formulation, early initiation (<72 h), and gestational age contributed to between-study variability.

DISCUSSION: Probiotic supplementation was associated with favorable clinical outcomes in preterm infants. The moderate between-study heterogeneity, variability in probiotic strains, formulations, dosages, and treatment protocols, together with limited long-term safety data, warrant cautious interpretation. Future adequately powered multicenter randomized controlled trials, standardized probiotic interventions, individual-patient-data meta-analyses, and long-term follow-up studies are required before routine clinical implementation and standardized probiotic treatment recommendations can be established.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Infant, Newborn
*Respiratory Distress Syndrome, Newborn/prevention & control/epidemiology
Infant, Premature
*Jaundice, Neonatal/prevention & control/epidemiology
*Infant Health
Gastrointestinal Microbiome
Dietary Supplements

@article {pmid42688076,
year = {2026},
author = {Gao, G and Zhao, X and Lu, X and Yu, S and Chen, L},
title = {IBD-related inflammatory memory and colorectal cancer: epigenetic mechanisms and microbiome interventions.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1912351},
pmid = {42688076},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Epigenesis, Genetic ; *Colorectal Neoplasms/immunology/genetics/etiology/microbiology ; *Gastrointestinal Microbiome/immunology ; Trained Immunity ; *Inflammatory Bowel Diseases/immunology/microbiology/genetics/complications ; Epigenetic Memory ; *Colitis-Associated Neoplasms/immunology/microbiology/genetics ; Intestinal Mucosa/immunology/microbiology ; DNA Methylation ; *Immunologic Memory ; },
abstract = {Colitis-associated cancer (CAC) develops within chronically inflamed mucosa and differs from sporadic colorectal cancer in its field effects, multifocality, and sequence of molecular events. In addition to ongoing inflammation and mutation, experimental studies indicate that epithelial, immune, and stromal compartments can retain altered states after an initiating inflammatory stimulus has subsided. In this review, inflammatory memory is used operationally for a persistent molecular, cellular, tissue, or microbial state that changes the response to a later challenge. This definition distinguishes epithelial epigenetic memory from trained innate immunity, adaptive lymphocyte memory or exhaustion, and chronic signaling that depends on continued stimulation. We synthesize evidence for persistent chromatin accessibility, histone modification, DNA methylation, enhancer activity and three-dimensional organization, epithelial plasticity, immune-stromal circuits, and microbiota-derived metabolites. These responses can support mucosal repair, but repeated activation within a genetically altered field may facilitate clonal expansion and tumor development. We also assess emerging methylation, circulating tumor DNA, stool DNA, single-cell, and spatial biomarkers and grade proposed interventions according to evidence from cell culture, organoids, animal models, human tissues, and clinical studies. Because chromatin- and microbiome-directed interventions remain largely preclinical, selective modulation of pathological persistence-not complete "memory erasure"-is the appropriate translational objective.},
}

Humans
Animals
*Epigenesis, Genetic
*Colorectal Neoplasms/immunology/genetics/etiology/microbiology
*Gastrointestinal Microbiome/immunology
Trained Immunity
*Inflammatory Bowel Diseases/immunology/microbiology/genetics/complications
Epigenetic Memory
*Colitis-Associated Neoplasms/immunology/microbiology/genetics
Intestinal Mucosa/immunology/microbiology
DNA Methylation
*Immunologic Memory

@article {pmid42688171,
year = {2026},
author = {Zhang, J and Zhou, H and Zhang, G and Wang, HM},
title = {When the carcinogenic window opens before the screening window: the age-threshold blind spot in early-onset colorectal cancer.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1912787},
pmid = {42688171},
issn = {2234-943X},
abstract = {Early-onset colorectal cancer (EOCRC) screening is constrained by a structural blind spot concealed by age-threshold-based eligibility. This limitation does not primarily reflect insufficient screening resources, but rather a fundamental temporal mismatch between screening logic and carcinogenic exposure. High-risk states may be established decades earlier through accumulated early-life "exposure memory," whereas screening triggered by chronological age can intervene only after risk has already been formed. Consequently, individuals younger than 45 years-the population with one of the fastest increases in EOCRC incidence-remain systematically overlooked even after the initiation age for average-risk screening has been lowered to 45 years. This article outlines two parallel pathways: the metabolic-inflammatory axis, including hyperinsulinemia, IGF-1 signaling, and chronic low-grade inflammation; and the gut microbiome axis, including microbial genotoxicity and mucosal immune dysregulation. We clarify how these pathways may encode risk early in life and jointly shift the carcinogenic window forward, making further reductions in age thresholds insufficient for timely identification of truly high-risk young individuals. Accordingly, we argue that EOCRC screening should move from "age-triggered detection" toward "risk-memory recognition." We propose three strategies stratified by clinical readiness: symptom-triggered colonoscopy triage as diagnostic evaluation rather than screening, earlier assessment of exposure memory, and microbiome-informed risk stratification as a research direction. These approaches may help identify high-risk individuals before the conventional screening age and reduce missed diagnoses and diagnostic delays.},
}

@article {pmid42688227,
year = {2026},
author = {Sclabassi, E and Hur, J and Ling, J and Gao, Y},
title = {The gut microbiome as a modifiable contributor to autism spectrum disorder: a precision gut-immune-brain perspective.},
journal = {Frontiers in child and adolescent psychiatry},
volume = {5},
number = {},
pages = {1900538},
pmid = {42688227},
issn = {2813-4540},
}

@article {pmid42688244,
year = {2026},
author = {Cerckel, K and Frooninckx, L and Van Miert, S and De Smet, J and IJdema, F},
title = {Impact of nursery-to-fattening dietary transitions on gut microbiome composition and growth performance in black soldier fly larvae.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1901348},
pmid = {42688244},
issn = {1664-302X},
abstract = {Black soldier fly (BSF) (Hermetia illucens) larvae are used in large-scale bioconversion due to their capacity to convert diverse organic substrates into high-quality biomass. To improve circularity, rearing practices must be optimized, especially when nutritionally poor, low-cost substrates are used. Production systems often adopt a two-phase feeding strategy in which larvae first receive a nutrient-rich nursery diet before transitioning to a fattening diet. The effects of such a diet shift on the gut microbiome and larval performance remain unclear. This study explores how a diet shift between the nursery stage (0-7 days after egg harvest; DAH) and the fattening stage (DAH 8-15) influences larval performance and microbiome composition. Chicken feed (CF) and artificial supermarket food waste (SFW) were used as contrasting diets across four conditions: continuous feeding (CF to CF and SFW to SFW) and diet shifts (CF to SFW and SFW to CF). At the end of the nursery phase, there was no significant difference in larval weight between the two diets. Immediately after the diet shift (DAH 8-9), CF-nursed larvae were heavier than SFW-nursed larvae, but SFW-nursed larvae gradually reached comparable weights over time. This convergence occurred more rapidly when larvae were maintained on SFW. Notably, survival within both fattening diets was lower for SFW-nursed larvae than for CF-nursed larvae, which may have reduced larval density and feed competition during the fattening phase. Microbiome profiling through 16S rRNA gene amplicon sequencing revealed distinct bacterial communities associated with CF- and SFW-based rearing: CF-reared larvae maintained a consistently diverse community, whereas SFW-reared larvae exhibited low diversity. Following a diet transition, microbial composition shifted toward a fattening-driven profile. However, the rate and extent of this shift depended on the fattening substrate. Under SFW fattening, microbiome differences between nursery treatments disappeared by the end of the experiment, whereas several biomarkers persisted under CF fattening, suggesting a stronger legacy effect of the nursery diet. Overall, these findings demonstrate that interactions between diet, microbiome, and larval physiology shape performance in two-phase rearing systems, highlighting that early-life nutrition can influence microbiome trajectories and affect responses to subsequent feeds, an important consideration for optimizing BSFL production.},
}

@article {pmid42688450,
year = {2026},
author = {Chandrakar, R and Sarkar, S and Panchaxarimath, AV and Paikra, V and Pandey, AK and Rajwade, S},
title = {Ayurveda in Contemporary Clinical Practice: Integrating Traditional Principles With Preventive, Metabolic, and Mind-Body Medicine.},
journal = {Cureus},
volume = {18},
number = {8},
pages = {e113836},
pmid = {42688450},
issn = {2168-8184},
abstract = {The increasing burden of chronic, metabolic, and stress-related disorders has created a need for clinical models that emphasize prevention, lifestyle modification, individualized care, and long-term risk reduction. Ayurveda offers a structured framework for diet, behavior, metabolic regulation, constitutional assessment, and mind-body balance; however, its integration into contemporary clinical practice remains constrained by fragmented evidence, heterogeneous interventions, and variable methodological quality. This review examines the relevance of Ayurveda in preventive, metabolic, and mind-body medicine and evaluates how traditional principles may be aligned with evidence-based clinical care. A structured narrative review was conducted using PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar to identify primarily English-language literature published between January 2015 and June 2026. Original clinical studies, randomized trials, observational and translational studies, systematic reviews, methodological studies, and relevant policy documents were selected according to their relevance to preventive, metabolic, mind-body, personalized, safety, and regulatory aspects of Ayurveda. The review was intended as an illustrative narrative synthesis rather than a comprehensive systematic review. The evidence suggests that Ayurveda is most appropriately positioned as an adjunctive framework for cardiometabolic risk reduction, diabetes and metabolic syndrome management, mood and sleep regulation, chronic pain care, and personalized prevention. Emerging fields such as Ayurgenomics, Ayurinformatics, microbiome research, and systems biology may support the translation of traditional constructs such as Prakriti into testable biomedical models. Responsible integration requires rigorous trial design, standardized formulations, transparent reporting, pharmacovigilance, and regulatory oversight. Overall, Ayurveda may contribute to patient-centered preventive and integrative care when applied through evidence-informed, safety-conscious, and clinically accountable models.},
}

@article {pmid42688480,
year = {2026},
author = {Feng, H and Huang, X and Zhuang, Y and Pu, L and Dong, R and Ren, P},
title = {Enterococcus and cancer: from mechanistic insights to clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1882184},
pmid = {42688480},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Enterococcus/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Immunotherapy/methods ; Tumor Microenvironment/immunology ; Host-Pathogen Interactions/immunology ; },
abstract = {Despite advances in traditional therapies, the global burden of malignant tumors remains substantial. Although immunotherapy has achieved remarkable breakthroughs by activating the host immune system, its clinical benefits are limited to a subset of patientsowing to low response rates and drug resistance. Emerging evidence highlights the pivotal role of the gut microbiota in determining immunotherapy outcomes. Within this ecosystem, the genus Enterococcus acts as a "double-edged sword": whereas certain strains can enhance antitumor immunity, other species notably Enterococcus faecalis, drive tumor progression by inducing DNA damage and inflammatory cascades. Therefore, elucidating the intricate interactions between Enterococcus and the host immune system is imperative for optimizing immunotherapeutic strategies and developing novel microbiome-based therapies.},
}

Humans
Animals
*Enterococcus/immunology
*Neoplasms/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Immunotherapy/methods
Tumor Microenvironment/immunology
Host-Pathogen Interactions/immunology

@article {pmid42688507,
year = {2026},
author = {Qixiu, C and Chen, H and Hu, S and Dai, Y and Cui, Y and Zhang, Y and Ping, M and Li, X and Chen, J},
title = {Phenology-dependent assembly and functional potential of the Artemisia lavandulifolia rhizosphere microbiome.},
journal = {3 Biotech},
volume = {16},
number = {9},
pages = {402},
pmid = {42688507},
issn = {2190-572X},
abstract = {UNLABELLED: Plant developmental stages represent important endogenous drivers shaping rhizosphere microbiome assembly and functional potential. However, how rhizosphere microbial communities of Artemisia lavandulifolia shift across distinct phenological stages remains largely unexplored. To address this knowledge gap, we employed high-throughput sequencing to comprehensively characterize the rhizosphere bacterial and fungal communities of A. lavandulifolia during the early vegetative stage (EVS) and late vegetative stage (LVS). Additionally, quantitative PCR was used to determine the absolute abundance of bacterial 16S rRNA, fungal ITS genes, and key functional genes related to carbon, nitrogen, and phosphorus cycling. The results revealed significantly higher α-diversity in both bacterial and fungal communities at LVS compared to EVS (p < 0.05). Co-occurrence network analysis revealed that microbial co-occurrence patterns became increasingly complex with plant development, as evidenced by greater numbers of nodes and edges in both bacterial (1189 vs. 1049 nodes; 98,550 vs. 76,390 edges) and fungal (373 vs. 230 nodes; 6932 vs. 4509 edges) networks during LVS. Notably, absolute abundances of functional genes mediating carbon fixation (cbbLR), nitrogen cycling (amoA), and phosphorus mineralization (phoD) were significantly elevated at LVS relative to EVS (p < 0.05). Collectively, these findings demonstrate that plant ontogeny is associated with stage-dependent shifts in the functional potential of the A. lavandulifolia rhizosphere microbiome, suggesting adaptive adjustments in microbially mediated nutrient cycling to meet heightened host metabolic demands during late vegetative growth.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13205-026-05024-2.},
}

@article {pmid42688516,
year = {2026},
author = {Belenichev, I and Popazova, O and Dmytriieva, O and Chertov, S and Bukhtiyarova, N and Ryzhenko, V and Oliynyk, S and Lee, S and Yi, KH},
title = {Molecular cytokine-dependent mechanisms of periodontitis pathogenesis and the potential for pharmacological IL-1 modulation in disease treatment.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1849807},
pmid = {42688516},
issn = {2673-4915},
abstract = {Periodontitis (P) is one of the most common human dental diseases, with significant medical and social implications. According to the World Health Organization, more than 45% of the adult population worldwide exhibits clinical signs of periodontitis, with 10%-15% of cases becoming generalized with destruction of the alveolar bone. This review presents the results of modern research demonstrating that the etiopathogenesis of periodontitis is not limited to local microbial factors; systemic, social, and behavioral factors can play a significant role, determining the body's susceptibility to chronic inflammation. In this study, we focus on the role of cytokines in the athogenesis of periodontitis. Based on modern research, we demonstratethe general biological significance of cytokines and their role in initiating periodontal inflammation and systemic diseases associated with periodontitis. The molecular and biochemical cytokine-dependent mechanisms of initiation and progression of oxidative stress in periodontitis are covered in detail. The role of individual cytokines in the pathogenesis of periodontitis is shown: interleukin-1 (IL-1), IL-6, tumor necrosis factor (TNF-α), interferon-gamma, IL-10, IL-23, IL-17, and Th17 cells. The review presents a modern approach to complex drug therapy of periodontitis. The arsenal of antiseptics, antibiotics, and synthetic antimicrobial agents available to dentists is presented. A new approach is demonstrated in the use of probiotics-live microorganisms (probiotics, symbiotics, and bacteriophages) that maintain the balance of the oral microbiome. Beyond standard antimicrobial and anti-inflammatory therapies, host modulators, antioxidants, and bioregulatory agents play a vital role in treating P. They effectively suppress proinflammatory cytokines, mitigate oxidative stress, and improve metabolic activity in affected tissues. We present data on the development of individual regenerative structures using bioactive polymers and 3D printing for the future treatment of chronic periodontitis, as well as the potential use of biomaterials with nanostructured components, collagen matrices with nanoparticles, hydrogels with functional peptides, synthetic polymers with a modest antibacterial effect, and transplantation of mesenchymal stem cells, as well as bioactive scaffolds with stem cells. The most important section of the review is devoted to the clinical and pharmacological properties of cytokine modulators-TNF-α blockers, IL-6 blockers, and IL-1 blockers. Using current research results, including our own, we demonstrate the potential of using an IL-1 receptor antagonist and its new dosage form, such as a dental gel.},
}

@article {pmid42688521,
year = {2026},
author = {Zhou, J and Ye, X and Zou, J and Zou, L and Cheng, L and Zhu, Z and Liao, G and Zhou, X and Ren, B},
title = {[Age-Related Changes in the Oral Microbiota].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {4},
pages = {941-952},
pmid = {42688521},
issn = {1672-173X},
mesh = {Humans ; *Microbiota/physiology ; *Mouth/microbiology ; *Aging/physiology ; Age Factors ; Infant ; Child ; },
abstract = {The human microbiome consists of microbial communities inhabiting different body sites and their genetic information, and plays an important role in maintaining host health. As an important component of the human microbiome, the oral microbiota contributes to maintaining oral microbial homeostasis, regulating local immune responses, participating in nutrient metabolism, and modulating systemic health. Initial colonization of the oral microbiota in early life lays the foundation for subsequent microbial development and lifelong oral health, and alterations in the oral microbiota are closely associated with various oral and systemic diseases. This review systematically summarizes the age-related succession of the oral microbiota across infancy, childhood and adolescence, adulthood, and old age; analyzes oral diseases associated with microbial dysbiosis at different life stages; discusses host-related, microenvironmental, and exogenous factors influencing age-related changes in the oral microbiota; and summarizes intervention strategies based on microbial ecological regulation. This review aims to provide new insights into age-related changes in the oral microbiota and to support the development of a life-course oral microbial health management model.},
}

Humans
*Microbiota/physiology
*Mouth/microbiology
*Aging/physiology
Age Factors
Infant
Child

@article {pmid42688585,
year = {2026},
author = {Liu, S and Huang, L and Xiao, S and Li, Y and Luo, S and Hou, E and Zhang, Y and Jin, M and Wang, Y and Zong, X},
title = {Astaxanthin Alleviates Intestinal Ferroptosis through Gut Commensal Lepagella muris-Mediated Retinoic Acid Production and SLC7A11 Activation.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1421},
pmid = {42688585},
issn = {2639-5274},
abstract = {Intestinal epithelial injury is increasingly linked to ferroptosis, yet how dietary bioactives engage the gut microbiota to restrain this process remains largely unresolved. Here, astaxanthin (ASTA) was identified as a microbiota-engaged regulator of intestinal ferroptosis and lipid peroxidation. ASTA markedly ameliorated dexamethasone-induced intestinal injury, and this protection was closely associated with the attenuation of epithelial ferroptosis. Depletion of the gut microbiota largely abolished the protective effect of ASTA, establishing the gut microbiota as an essential mediator of its intestinal bioactivity. Microbiome and metabolome profiling further revealed that ASTA reshaped the microbial metabolic landscape, with retinol metabolism emerging as a dominant pathway linked to ferroptosis resistance. Among the altered metabolites, retinoic acid was identified as a pivotal ASTA-associated metabolite that connected microbial remodeling with the restoration of epithelial anti-ferroptosis capacity. Metagenomics combined with in vitro bacterial metabolic assays identified Lepagella muris as a candidate ASTA-responsive bacterium capable of contributing to retinoic acid production. Mechanistically, retinoic acid protected intestinal epithelial cells from ferroptosis and barrier disruption through activation of SLC7A11, thereby reinforcing the anti-ferroptosis defense system. This study moves beyond the conventional view of ASTA as a direct antioxidant and reveals a microbiota-enabled redox metabolic mechanism that may be therapeutically exploited for ferroptosis-associated diseases.},
}

@article {pmid42688768,
year = {2026},
author = {Gao, Y and Liu, C and He, X},
title = {The impact of gut microbiota on insulin resistance in polycystic ovary syndrome: mechanisms and therapeutic prospects.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1840605},
pmid = {42688768},
issn = {2235-2988},
mesh = {*Polycystic Ovary Syndrome/microbiology/therapy/physiopathology ; Humans ; *Insulin Resistance ; Female ; *Gastrointestinal Microbiome/physiology ; Dysbiosis ; Animals ; },
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine and metabolic disorder, with insulin resistance (IR) serving as its core pathophysiological feature and a key driver of long-term metabolic complications. Recent studies have revealed that the gut microbiota, as a critical environmental factor, plays a significant role in the pathogenesis of PCOS. The gut microbiota profoundly engages in the pathophysiology of PCOS-IR through multiple pathways and networked interactions. This review provides a comprehensive narrative synthesis of the latest evidence on gut microbiota dysbiosis in PCOS-IR, with a particular focus on its molecular mechanisms, and evaluates therapeutic strategies based on gut microbiota modulation. It seeks to provide theoretical foundations and forward-looking perspectives for precision microbiome therapies. Importantly, this is a narrative review with a mechanistic focus, rather than a formal systematic review or meta-analysis.},
}

*Polycystic Ovary Syndrome/microbiology/therapy/physiopathology
Humans
*Insulin Resistance
Female
*Gastrointestinal Microbiome/physiology
Dysbiosis
Animals

@article {pmid42688815,
year = {2026},
author = {Chen, Z and Liu, W and Guo, Z and Guo, Y and Hou, J and Rong, M and Zheng, H and Cui, Z},
title = {Research progress and application prospects of multi-omics integration strategies in precision risk stratification of type 1 diabetes mellitus.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1891938},
pmid = {42688815},
issn = {1664-3224},
mesh = {Humans ; *Diabetes Mellitus, Type 1/diagnosis/metabolism/genetics/etiology ; *Multiomics ; Biomarkers ; Risk Assessment ; *Precision Medicine/methods ; Metabolomics ; Genomics/methods ; Genetic Predisposition to Disease ; Proteomics/methods ; Animals ; },
abstract = {Type 1 diabetes (T1D) is a chronic metabolic disease mediated by autoimmunity. Its pathogenesis involves complex interactions between genetic susceptibility and environmental factors. Conventional T1D risk stratification primarily relies on genetic markers, islet autoantibodies, and glycemic indicators. Although these biomarkers remain indispensable in current clinical practice, they are often insufficient when used alone to accurately identify ultra-early high-risk individuals, predict disease progression rates, or support individualized preventive strategies. Consequently, more comprehensive molecular approaches are needed to improve precision risk stratification. In recent years, the rapid development of multi-omics technologies has provided new strategies for precise risk stratification of T1D. This narrative review critically evaluates how multi-omics integration strategies can improve precision risk stratification throughout the T1D disease continuum by integrating complementary molecular information from genomics, transcriptomics, proteomics, metabolomics, epigenomics, and the microbiome. Particular emphasis is placed on stage-specific biomarker discovery, multi-omics data integration frameworks, artificial intelligence-assisted prediction models, biomarker validation, and the opportunities and challenges associated with clinical translation. Current evidence suggests that integrated multi-omics approaches have the potential to improve risk prediction accuracy, distinguish heterogeneous disease trajectories, identify individuals at imminent risk of progression, and provide biologically informed targets for precision intervention. However, important challenges remain, including data harmonization, external validation, model interpretability, cost-effectiveness, and integration into routine clinical screening programs. Future research should prioritize prospective multicenter cohorts, standardized analytical pipelines, externally validated prediction models, and clinically interpretable multi-omics frameworks to facilitate the translation of precision risk stratification into routine T1D prevention and management.},
}

Humans
*Diabetes Mellitus, Type 1/diagnosis/metabolism/genetics/etiology
*Multiomics
Biomarkers
Risk Assessment
*Precision Medicine/methods
Metabolomics
Genomics/methods
Genetic Predisposition to Disease
Proteomics/methods
Animals

@article {pmid42688840,
year = {2026},
author = {Li, J and Liu, Y and Gao, T and Ding, H and Hu, R and Wang, Y and Wu, B},
title = {Progress in interventions for vaginal microecology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1888581},
pmid = {42688840},
issn = {2235-2988},
mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota ; *Probiotics/administration & dosage/therapeutic use ; *Dysbiosis/therapy/microbiology ; Prebiotics/administration & dosage ; Synbiotics/administration & dosage ; },
abstract = {A balanced vaginal microbiome is fundamental to reproductive and gynecologic health, yet dysbiosis is common and clinically consequential. This narrative review synthesizes recent advances in microecological interventions, including probiotic, prebiotic, and synbiotic regimens; combination therapies; and vaginal microbiota transplantation. We place a particular focus on emerging delivery platforms like hydrogel-based carriers, which improve probiotic viability, mucosal adhesion, and controlled release. The review also explores how metagenomic analysis is refining community state typing, identifying pathogenic consortia, and enabling data-driven patient stratification and response monitoring. Despite these advances, key challenges remain, such as strain selection, functional validation, colonization durability, heterogeneous clinical endpoints, and clear regulatory pathways for live biotherapeutics. Future priorities must include developing functionally defined strain consortia, standardizing clinical outcomes, integrating multi-omics with biomaterials engineering, and conducting rigorous multicenter trials to deliver durable, safe, and truly individualized therapies.},
}

Humans
*Vagina/microbiology
Female
*Microbiota
*Probiotics/administration & dosage/therapeutic use
*Dysbiosis/therapy/microbiology
Prebiotics/administration & dosage
Synbiotics/administration & dosage

@article {pmid42688927,
year = {2026},
author = {Dong, J and Lv, J and Sun, G and Xiao, Z},
title = {Phenotype-Aware Biomarker Discovery in Childhood Asthma: Microbiome-Metabolome Signatures and Translational Readiness.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {615244},
pmid = {42688927},
issn = {1178-7074},
abstract = {Childhood asthma is a common but biologically heterogeneous disease, and this heterogeneity limits the performance of one-size-fits-all biomarkers for diagnosis, risk stratification, and disease monitoring. Microbiome and metabolome profiling are attractive in pediatric asthma because they reflect host-environment interactions at mucosal surfaces and may capture clinically relevant variation not fully explained by conventional markers. However, their translational value in children remains uncertain. This review critically examines the current evidence on microbiome- and metabolome-based biomarkers in childhood asthma from a clinically oriented perspective, with emphasis on four settings of practical relevance: early-life risk and disease development, allergic and non-allergic asthma, severe, uncontrolled, or exacerbation-prone disease, and lung-function or inflammatory phenotypes. Current data suggest that composite and phenotype-linked signatures are more informative than isolated taxa or single metabolites. The most convincing signals arise in early-life microbial maturation trajectories and in unstable disease, where upper-airway microbial patterns and integrated metabolic profiles show the greatest potential for clinical stratification. Allergic burden appears to be reflected more consistently by metabolomic than microbiome findings, whereas lung-function and inflammatory phenotypes currently show stronger metabolite-trait associations than reproducible airway microbial correlates. Across phenotypes, pathway-level convergence is more robust than single-marker reproducibility, with recurring signals involving microbial fermentation and short-chain fatty acid biology, bile acid metabolism, tryptophan and histamine pathways, and lipid remodeling. Nevertheless, most pediatric studies remain cross-sectional, modest in size, and heterogeneous in phenotype definitions, sampling matrices, and analytical platforms. No microbiome- or metabolome-based signature is currently ready for routine pediatric clinical use. The most realistic near-term translational direction is the development of age-contextualized, phenotype-oriented reduced panels that are prospectively validated in multicenter cohorts and shown to provide clinical value beyond existing tools for childhood asthma diagnosis, risk stratification, and monitoring.},
}

@article {pmid42688943,
year = {2026},
author = {Rukonge, PA and Kawuribi, V and Lu, Z and Oluwaseun, AF and Sheng, Y and Yan, K and Zheng, Z and Liu, X and Chu, L and Yu, G},
title = {From granulomas to tumors: post-tuberculosis immune and structural lung remodeling as a driver of carcinogenesis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1889276},
pmid = {42688943},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/immunology/pathology/etiology ; Animals ; *Tuberculosis, Pulmonary/immunology/complications/pathology ; *Granuloma/immunology/pathology ; *Carcinogenesis/immunology ; T-Cell Exhaustion ; Tumor Microenvironment/immunology ; *Lung/immunology/pathology/microbiology ; },
abstract = {Although antibiotic therapy effectively cures active tuberculosis (TB), many survivors are left with permanent lung damage and long-lasting immune alterations. Growing epidemiological evidence indicates that individuals with prior pulmonary TB have a two- to three-fold increased risk of lung cancer, independent of smoking, suggesting mechanisms beyond shared risk factors. This review advances the concept that TB imprints a durable "memory" within the lung, characterized by persistent structural remodeling and immune reprogramming that together create a tumor-permissive microenvironment. We synthesize evidence showing that TB granulomas act as dynamic immune niches that induce hypoxia, fibrosis, and immune exhaustion, features that frequently persist after microbiological cure. Post-TB sequelae including fibrotic scarring, cavitation, bronchiectasis, and vascular remodeling, promote chronic inflammation, oxidative DNA damage, and mechanotransduction pathways linked to oncogenesis. Concurrently, sustained T-cell exhaustion, macrophage polarization toward tumor-associated phenotypes, and impaired antigen presentation weaken tumor surveillance. We further discuss emerging roles for lung microbiome dysbiosis in sustaining inflammation. Collectively, these processes provide a mechanistic framework linking healed TB to lung carcinogenesis and highlight TB survivors as a distinct population for targeted surveillance and preventive strategies.},
}

Humans
*Lung Neoplasms/immunology/pathology/etiology
Animals
*Tuberculosis, Pulmonary/immunology/complications/pathology
*Granuloma/immunology/pathology
*Carcinogenesis/immunology
T-Cell Exhaustion
Tumor Microenvironment/immunology
*Lung/immunology/pathology/microbiology

@article {pmid42689139,
year = {2026},
author = {Shuixing, Z and Jing, Z and Alshehri, D and Al-Amrah, H and Manzoor, I and Aiying, Y},
title = {Hormone priming and metabolic engineering of phytohormone crosstalk in rice under combined biotic and abiotic stresses: a multi-omics perspective for climate-resilient crop development.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1924558},
pmid = {42689139},
issn = {1664-462X},
abstract = {Rice (Oryza sativa L.) is the caloric backbone for more than half of humanity, yet it remains one of the most vulnerable crops to the simultaneous biotic and abiotic stresses exacerbated by climate change. Phytohormone priming and the complex crosstalk networks governed by transcription factor hubs like WRKY, MYB, and NAC serve as the central adaptive mechanism for stress resilience. This review synthesizes how multi-omics integration, including spatial and single-cell transcriptomics, is resolving the molecular architecture of hormonal priming and epigenetic stress memory. We critically evaluate advanced metabolic engineering and genome-editing strategies such as CRISPR-Cas9, base/prime editing, and synthetic gene circuits that enable precision modifications to decouple stress tolerance from historical yield penalties. Furthermore, we discuss the emerging roles of microbiome-assisted priming via synthetic consortia and the application of artificial intelligence and digital twins (continuously updated computational models of crop physiology) for predictive stress management. By integrating these diverse technological pillars, we propose a systems-level roadmap for developing climate-resilient rice cultivars capable of maintaining yield stability across a volatile combinatorial stress landscape. This synthesis provides a framework for translating mechanistic hormonal insights into field-applicable cultivars to ensure global food security.},
}

@article {pmid42689141,
year = {2026},
author = {Moser, B and Saxby, SM and Lebby, S and Letendre, JD and Lange, S and Mendez, MA and Trus, TL and Honigsberg, E and Billmeier, SE and Gilbert-Diamond, D and Dao, MC and Meijer, JL},
title = {Daily fiber supplementation after bariatric surgery demonstrates tolerability and influence on the fecal gut microbiome.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1912097},
pmid = {42689141},
issn = {2296-861X},
abstract = {INTRODUCTION: This study assessed the feasibility and tolerance of a 30-day resistant potato starch (RPS) supplement in patients who recently underwent bariatric surgery and its effect on microbial production of fecal short-chain fatty acids (SCFA).

METHODS: This clinical trial (ClinicalTrials.gov, identifier: NCT05653648), conducted at Dartmouth Hitchcock Medical Center, provided 30-days of RPS supplement (titration: 24 g for 15 days; 48 g for 15 days) starting 90-days post-op and assessed gastrointestinal symptoms, dietary intake (24 h recall), fecal SCFAs, and fecal gut microbiome (n = 30).

RESULTS: The RPS supplement was well tolerated by participants (77% achieving consumption goal), with modest, but significant increases in self-reported gas (p = 0.004) and abdominal rumbling (p = 0.047). It was associated with an increase in the Bifidobacterium genus (LDA score >4, p < 0.001) and specifically, an enrichment of B. faecale/adolescentis (p = 0.006), one of two known primary degraders of RPS. No changes were observed in the abundance of cross-feeders or in SCFA concentrations. Alpha diversity measures were significantly lower post-RPS, and there was no change in species richness.

DISCUSSION: This study demonstrated that a RPS supplement is tolerable in post-op bariatric patients and that the gut microbiome is responsive to fiber interventions. RPS increased the abundance of SCFA-producing bacteria but did not alter fecal SCFAs, likely due to competition among cross-feeders.},
}

@article {pmid42689286,
year = {2026},
author = {Liu, H and Li, J and Wei, Z and Li, N and Yao, K},
title = {Engineered Nanozymes for Colorectal Cancer Therapy: Catalytic Reprogramming of the Tumor Microenvironment.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {640248},
pmid = {42689286},
issn = {1178-2013},
mesh = {*Colorectal Neoplasms/drug therapy/therapy/metabolism ; Humans ; *Tumor Microenvironment/drug effects ; Animals ; Catalysis ; *Nanostructures/chemistry ; Antineoplastic Agents/chemistry ; Nanomedicine ; },
abstract = {Colorectal cancer (CRC) remains difficult to treat because redox adaptation, metabolic plasticity, mucin-associated delivery barriers, immune exclusion, and microbiota-dependent signaling jointly limit conventional therapy. Engineered nanozymes provide a reaction-centered strategy for exploiting these CRC-specific vulnerabilities. This review critically compares metal, metal-oxide, carbon-based, porous-framework, and single-atom nanozymes with respect to catalytic mechanism, enzyme-mimicking activity, substrate dependence, controllability, biosafety, and translational suitability. We examine how acidity, hydrogen peroxide, hypoxia, glutathione enrichment, metabolic dysregulation, mucin barriers, and the gut microbiota influence catalytic performance. We further evaluate evidence for chemotherapy sensitization, chemodynamic, photothermal, photodynamic, sonodynamic, immunotherapeutic, and multimodal treatment, emphasizing both mechanistic synergy and limitations of the available preclinical models. Major translational barriers include non-standardized catalytic assays, heterogeneous intratumoral substrates, off-target reactive oxygen species toxicity, uncertain degradation and long-term fate, microbiome disruption, manufacturing reproducibility, and limited validation in orthotopic, immunocompetent, organoid, and patient-derived systems. We therefore position CRC nanozyme therapy as a disease-oriented catalytic medicine platform whose clinical value will depend on biomarker-guided selection, programmable activation, and degradable, locally controllable designs.},
}

*Colorectal Neoplasms/drug therapy/therapy/metabolism
Humans
*Tumor Microenvironment/drug effects
Animals
Catalysis
*Nanostructures/chemistry
Antineoplastic Agents/chemistry
Nanomedicine

@article {pmid42689363,
year = {2026},
author = {Monika, P and Sadanandan, B and Tejashree, HR and Darbha, M and Gupta, K and Reneeka, S},
title = {Catechins and Their Effect on the Gut Microbiome in Health and Cancer.},
journal = {Phytotherapy research : PTR},
volume = {},
number = {},
pages = {},
doi = {10.1002/ptr.70435},
pmid = {42689363},
issn = {1099-1573},
abstract = {Catechins are a group of flavonoids found primarily in green tea, fruits, and berries; they play a significant role in the modulation of the gut microbiota, thereby having an impact on gut health and cancer prevention. Owing to their low bioavailability, catechins are transformed by the gut microbiota into various bioactive metabolites such as valerolactones and glucuronides, which support the growth of several beneficial bacterial species including Bifidobacterium and Lactobacillus while inhibiting harmful strains like Clostridium difficile and Escherichia coli. These interactions enhance metabolic balance, reduce inflammation, and help maintain gut homeostasis, which is critical for preventing gut dysbiosis. Dysbiosis is characterized by a shift from symbiotic to pathogenic microbial populations and is closely associated with cancer development, especially in the gut. This review explores how catechins, particularly epigallocatechin gallate (EGCG), contribute to cancer prevention by promoting a symbiotic microbial environment, supporting immune modulation, and inhibiting inflammatory pathways. By examining the role of catechins in both health and cancer, this paper aims to emphasize their therapeutic potential as dietary supplements in maintaining gut health and reducing cancer risk.},
}