@article {pmid42100955,
year = {2026},
author = {Alsheikh, ZSA and Qingsong, T and Qinjie, L and Youkun, C},
title = {Re-arming checkpoint blockade in MSS colorectal cancer: A precision-microbiome playbook from mechanisms to clinic.},
journal = {Turkish journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.47717/turkjsurg.2026.2025-8-3},
pmid = {42100955},
issn = {2564-6850},
abstract = {Immune checkpoint blockade transforms outcomes for the 15% of colorectal cancers (CRCs) with mismatch-repair deficiency; yet most tumours remain refractory. Beneficial gut microbes can change this. Akkermansia muciniphila, Bacteroides fragilis, and short-chain fatty acid producers prime dendritic cells to produce interleukin (IL)-12, polarise Th1 cells, and reinvigorate CD8[+] T-cells. Antibiotics, Western-style diets, and Fusobacterium nucleatum foster myeloid suppression and β-catenin- or IL-17-mediated signalling, which blunt checkpoint activity. Multi-omics analyses link biosynthetic genes for inosine, riboflavin, and folate to durable clinical benefit. Faecal microbiota transplantation from responders has produced objective regressions in otherwise refractory microsatellite-stable disease. This narrative review maps CRC-microbiota-immune crosstalk, evaluates biomarkers and interventions, and proposes a CRC-specific, three-tiered clinical algorithm. We outline standards for trial design and manufacturing processes to facilitate the translation of microbiota-guided therapy into routine practice.},
}

@article {pmid42101034,
year = {2026},
author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM},
title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70354},
pmid = {42101034},
issn = {1758-2229},
support = {NA19NOS4190106//Texas General Land Office/ ; },
mesh = {*Estuaries ; *Fresh Water/chemistry/microbiology/virology ; Salinity ; *Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; Temperature ; Metagenomics ; Ecosystem ; },
abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.},
}

*Estuaries
*Fresh Water/chemistry/microbiology/virology
Salinity
*Viruses/genetics/classification/isolation & purification
Bacteria/genetics/classification/isolation & purification
Temperature
Metagenomics
Ecosystem

@article {pmid42101085,
year = {2026},
author = {El Sehrawy, AAMA and Aljumaili, OI and Axmedov, U and Khasawneh, MAS and Alanazi, MA and Smerat, A and Basunduwah, TS},
title = {Personalized Medicine in Autism Spectrum Disorder: Integrating Epigenomics, Microbiome Research and Early Diagnostics.},
journal = {International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience},
volume = {86},
number = {3},
pages = {e70128},
doi = {10.1002/jdn.70128},
pmid = {42101085},
issn = {1873-474X},
mesh = {Humans ; *Autism Spectrum Disorder/diagnosis/genetics/therapy/microbiology ; *Precision Medicine/methods ; *Epigenomics/methods ; *Microbiota/physiology ; Early Diagnosis ; Biomarkers ; *Gastrointestinal Microbiome ; },
abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by persistent difficulties in social communication together with restricted, repetitive patterns of behaviour and sensory-processing differences. Growing evidence suggests that ASD is shaped by complex interactions among genetic susceptibility, epigenetic regulation, immune signalling, maternal and early-life exposures and gut microbiome-related pathways. However, many of these associations remain biologically plausible rather than definitively causal, particularly when findings from experimental models are considered alongside human clinical data. This narrative review examines recent advances across these interconnected domains, with particular emphasis on maternal immune activation, prenatal nutrition, gut microbial imbalance, epigenetic and molecular mechanisms, emerging therapeutic directions and developing biomarker platforms. We also discuss current diagnostic limitations and evaluate the potential of salivary microRNAs, perinatal metabolic and epigenetic markers, oxidative stress-related measures and microbiome-based profiles as early and biologically informative indicators of ASD risk. Special attention is given to the need for biologically informed stratification, although current subgrouping frameworks remain preliminary and not yet sufficiently validated for routine clinical use. Likewise, candidate biomarkers remain investigational and require stronger evidence for reproducibility, external validation, longitudinal performance and clinically meaningful sensitivity and specificity before they can be considered for screening or precision-guided care. Emerging therapeutic strategies targeting immune, epigenetic and microbiome-related pathways are also reviewed, but most remain preclinical or early-stage and face substantial translational barriers. The convergence of epigenomics, microbiome research and early diagnostic science may help advance a more personalized medicine framework for ASD, provided that future studies improve cross-cohort reproducibility, clarify brain relevance of peripheral signals and develop practical multiomics models that can support clinically meaningful integration.},
}

Humans
*Autism Spectrum Disorder/diagnosis/genetics/therapy/microbiology
*Precision Medicine/methods
*Epigenomics/methods
*Microbiota/physiology
Early Diagnosis
Biomarkers
*Gastrointestinal Microbiome

@article {pmid42101126,
year = {2026},
author = {Azarkan, SY and Ünal, HSA and Akçay, S},
title = {Pharmacomicrobiomics in Precision Pharmacotherapy: Bidirectional Microbial-Drug Interactions as a Key Determinant of Therapeutic Response.},
journal = {Drug metabolism reviews},
volume = {},
number = {},
pages = {1-31},
doi = {10.1080/03602532.2026.2671428},
pmid = {42101126},
issn = {1097-9883},
abstract = {Interindividual variability in drug efficacy and toxicity remains a major challenge in clinical pharmacotherapy. Although pharmacogenomics has substantially advanced personalized medicine, host genetic variation alone cannot fully explain differences in drug disposition, response, and adverse effects. Increasing evidence identifies the human gut microbiotaas an additional, functionally relevant metabolic layer that complements host drug-metabolizing enzymes, giving rise to the field of pharmacomicrobiomics. This discipline examines bidirectional interactions between drugs and microbial communities that influence absorption, metabolism, enterohepatic circulation, and pharmacodynamic outcomes. The gut microbiota can directly biotransform or sequester drugs through diverse enzymatic reactions, including deconjugation, reduction, and decarboxylation, thereby modifying systemic drug exposure and toxicity. In parallel, microbially derived metabolites and bile acid-mediated signaling pathways regulate host drug-metabolizing enzymes and transporters, including cytochrome P450 enzymes and ATP-binding cassette transporters. Conversely, many commonly used medications-such as antibiotics, chemotherapeutic agents, targeted therapies, immunotherapies, psychotropic drugs, and proton pump inhibitors-can substantially reshape microbial composition and function, resulting in dysbiosis that feeds back onto drug metabolism and therapeutic outcomes. This review summarizes the mechanistic basis and clinical relevance of microbiota-drug interactions across key therapeutic areas, including oncology (chemotherapy and immunotherapy), neuropsychiatric disorders, and metabolic diseases. Well-established examples, including microbial β-glucuronidase-mediated reactivation of irinotecan, microbiota-dependent modulation of levodopa and antidepressant pharmacokinetics, and microbiota-driven variability in immune checkpoint inhibitor efficacy, are discussed to illustrate causality. Emerging microbiome-informed strategies-such as selective inhibition of microbial enzymes, microbiota modulation, and microbial biomarker-based patient stratification-are highlighted. Finally, we examine integration of pharmacomicrobiomics with pharmacogenomics within multi-omic and systems pharmacology frameworks, emphasizing implications for predictive modeling and precision drug metabolism.},
}

@article {pmid42101202,
year = {2026},
author = {Yashar, M and Thigale, UY and Karakus, S},
title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICU.0000000000001228},
pmid = {42101202},
issn = {1531-7021},
abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.

RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced α-diversity and shifts in dominant taxa. Genera such as Staphylococcus, Corynebacterium, and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.

SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.},
}

@article {pmid42101281,
year = {2026},
author = {Wang, Z and Mao, J and Ma, L},
title = {A Tree-Based Model for Addressing Sparsity and Taxa Covariance in Microbiome Compositional Count Data.},
journal = {Statistics in medicine},
volume = {45},
number = {10-12},
pages = {e70584},
pmid = {42101281},
issn = {1097-0258},
support = {R01-GM135440/GM/NIGMS NIH HHS/United States ; DMS-2013930//National Science Foundation/ ; DMS-1749789//National Science Foundation/ ; },
mesh = {Humans ; Bayes Theorem ; *Microbiota ; *Models, Statistical ; Computer Simulation ; Logistic Models ; Infant ; Normal Distribution ; Multivariate Analysis ; },
abstract = {Microbiome compositional data are often high-dimensional, sparse, and exhibit pervasive cross-sample heterogeneity. We introduce the "logistic-tree normal" (LTN) model, a generative model that allows flexible covariance among the microbiome taxa, enables scalable computation, and effectively captures other key characteristics of microbiome compositional data such as the abundance of zeros. LTN incorporates a tree-based decomposition for effective aggregation over sparse taxa counts and models the relative abundance at the tree splits jointly using a (multivariate) logistic-normal distribution. The latent Gaussian structure allows a wide range of multivariate analysis and modeling tools for high-dimensional data-such as those enforcing sparsity or low-rank assumptions on the covariance structure-to be readily incorporated. As a general-purpose, fully generative model, LTN can be applied in a wide range of contexts, while at the same time, efficient computational recipes for Bayesian inference under LTN are available through conjugate blocked Gibbs sampling enabled by pólya-gamma augmentation. We demonstrate the use of LTN in a compositional mixed-effects model for differential abundance analysis through both numerical experiments and a reanalysis of the infant cohort in the DIABIMMUNE study. We explain and showcase through numerical experiments and the case study how LTN, through adequately accounting for the cross-sample heterogeneity, is capable of generating the appropriate proportion of zeros without incurring an explicit zero-inflation component. This confirms a recent viewpoint that "zero-inflation" in count-based sequencing data are often results of unaccounted cross-sample variation.},
}

Humans
Bayes Theorem
*Microbiota
*Models, Statistical
Computer Simulation
Logistic Models
Infant
Normal Distribution
Multivariate Analysis

@article {pmid42101372,
year = {2026},
author = {Zhang, H and Zhang, S and Zhu, J},
title = {Molecular-level host-microbe interactions: mechanisms, molecules, and modeling toward precision probiotics.},
journal = {Expert opinion on therapeutic targets},
volume = {},
number = {},
pages = {},
doi = {10.1080/14728222.2026.2671689},
pmid = {42101372},
issn = {1744-7631},
abstract = {INTRODUCTION: Advancing next-generation probiotics (NGPs) as precision therapeutics depends on a detailed understanding of host - microbe molecular interactions, as these organisms exert targeted effects through defined bioactive molecules rather than broad, nonspecific mechanisms. This review addresses the need to systematically organize emerging knowledge on microbe-derived molecules (MDMs) that underpin NGP efficacy.

AREAS COVERED: This narrative review summarizes recent discoveries of MDMs isolated from NGPs and classifies them based on three principal molecular interaction interfaces: protein - protein/peptide, protein - lipid or glycopeptide, and protein - metabolite interactions. We discuss how these molecules - encompassing proteins/peptides, lipids, glycoconjugates, and small metabolites - modulate host immune and metabolic pathways to maintain homeostasis. The literature was identified through targeted searches of recent peer-reviewed studies focusing on host - microbe molecular mechanisms and probiotic-derived bioactives. We also review the application of molecular docking, molecular dynamics simulations, and artificial intelligence - based tools in predicting host - microbe interactions and accelerating therapeutic discovery.

EXPERT OPINION: By integrating experimental insights with computational strategies, we propose a framework to guide the development of precision microbiome-based interventions tailored to specific diseases and individual microbiome profiles. These advances lay the foundation for rational design of targeted NGP therapies for metabolic, inflammatory, infectious, and neurodegenerative disorders.},
}

@article {pmid42101618,
year = {2026},
author = {Nguyen, PN and Rehan, SM},
title = {Microbial Communities Across Social Roles in Small Carpenter Bee Nests.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02787-2},
pmid = {42101618},
issn = {1432-184X},
abstract = {Bee microbiota form important symbiotic relationships with their hosts, but microbial communities vary across bee species, sociality, and environment. Comparing the microbiome of bees with different social roles and foraging behaviours may uncover the ways in which microbiota are environmentally acquired and subsequently introduced and spread into the nest environment. Here, we performed metabarcoding of the 16S rRNA, ITS, and ribulose biphosphate carboxylase large (rbcL) regions on mothers, dwarf eldest daughters, and regular daughters in nests of the facultatively social, small carpenter bee, Ceratina calcarata, contrasting bacteria, fungi, and plant associates. We also performed two different sampling types by characterizing the microbiome using whole-guts and whole-bodies. Social role in nest impacted the microbial community composition and mothers were found to demonstrate increased plant diversity compared to their daughters, more specifically in whole-bodies, highlighting the ability to determine plants that bees are visiting during foraging through DNA metabarcoding. We also found that metabarcoding of the whole-body recovered increased fungal and plant diversity compared to whole-guts, suggesting that including microbiota from beyond the gut offers an opportunity to characterize uncommon associates that bees encounter, particularly through plant-pollinator relationships. As the transmission of beneficial symbionts and pathogens between individuals are studied for its impact on bee health, microbial analyses of bees across different environments and levels of sociality provides unique biomonitoring that can indicate the health of the larger bee community.},
}

@article {pmid42101639,
year = {2026},
author = {Makkar, P and Singh, CK and V, N and Narang, PK and Sodhi, KK},
title = {Insect immunity unveiled: exploring the molecular and cellular defenses against microbial threats.},
journal = {Archives of microbiology},
volume = {208},
number = {8},
pages = {},
pmid = {42101639},
issn = {1432-072X},
mesh = {Animals ; *Immunity, Innate ; *Insecta/immunology/microbiology ; Receptors, Pattern Recognition/immunology ; Microbiota/immunology ; Hemocytes/immunology ; Symbiosis ; Drosophila melanogaster/immunology/microbiology ; Bombyx/immunology/microbiology ; },
abstract = {Insects, as diverse and ecologically dominant organisms, rely exclusively on innate immunity to defend against a wide array of microbial threats. This paper presents an integrative review of insect immune mechanisms, highlighting the molecular, cellular, and systemic components that underpin host defense. The immune response is orchestrated through physical barriers, cellular processes and humoral factors. Evolutionarily conserved pattern recognition receptors (PRRs) are essential to these processes. Emphasis is laid on pivotal functions of hemocytes, the significance of microbiome interactions in immune regulation, and the emerging influence of non-coding RNAs. Furthermore, the paper explores defensive symbiosis, environmental and evolutionary influences on immune dynamics, and applications in biotechnology and pest management. Model organisms, such as Drosophila melanogaster and Bombyx mori, serve as critical systems for unravelling innate immunity, with translational relevance to vertebrate immunology and vector control strategies. Understanding these mechanisms offers valuable insights into conserved immune pathways and holds promise for advancing strategies in human disease prevention, therapeutic innovation, and global health.},
}

Animals
*Immunity, Innate
*Insecta/immunology/microbiology
Receptors, Pattern Recognition/immunology
Microbiota/immunology
Hemocytes/immunology
Symbiosis
Drosophila melanogaster/immunology/microbiology
Bombyx/immunology/microbiology

@article {pmid42101655,
year = {2026},
author = {Miwa, T and Hsu, CL and Shimizu, M and Bloom, PP and Schnabl, B},
title = {Covert hepatic encephalopathy as a multi-organ syndrome: the gut-liver-muscle-brain axis, diagnosis, treatment, and multidisciplinary care.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42101655},
issn = {1435-5922},
support = {JP24K18908//Japan Society for the Promotion of Science/ ; },
abstract = {Covert hepatic encephalopathy (CHE) is a highly prevalent complication of liver cirrhosis. Despite the absence of overt symptoms, CHE is strongly associated with impaired quality-of-life, overt hepatic encephalopathy, and mortality. Over the past two decades, evidence regarding the pathophysiology, diagnosis, and treatment of CHE has accumulated considerably, and clinical guidelines recommend screening in patients with cirrhosis. Nevertheless, diagnostic and therapeutic algorithms have not been fully implemented in real-world practice, and many patients remain undiagnosed and untreated. Understanding the natural history of CHE is essential to improve cirrhosis care, as it provides a framework for appropriate screening, treatment decision-making, and patient counseling. CHE is a multi-organ syndrome with complex interactions between the liver, gut, skeletal muscle, kidneys, and brain, with impaired ammonia handling and systemic inflammation acting as central drivers of this organ crosstalk. Hyperammonemia induces astrocytic dysfunction, brain edema, and neuroinflammation, while systemic inflammation, oxidative stress, sarcopenia, gut dysbiosis, and altered microbial metabolites, including bile acids and short-chain fatty acids, further modulate disease expression. In this review, we summarize current understanding of CHE pathophysiology, diagnostic testing, including psychometric batteries and point-of-care tools, such as the Stroop test and animal naming test, and therapeutic options, ranging from lactulose and rifaximin to microbiome-targeted approaches, including fecal microbiota transplantation. We also highlight major challenges in CHE management, including limited implementation of testing, inadequate biomarkers, diagnostic difficulties in geriatric cirrhosis, and unmet needs in fall and driving risk management, and emphasize the importance of multidisciplinary team-based approaches to improve patient outcomes.},
}

@article {pmid42101775,
year = {2026},
author = {Szpytma, M and Dobrzyński, J},
title = {Interactions of PGPR from the phylum bacillota with native rhizosphere microbiota: current insights and future perspectives.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42101775},
issn = {1573-0972},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics ; Crops, Agricultural/microbiology/growth & development ; Plant Development ; Soil/chemistry ; Plant Roots/microbiology ; Agriculture ; },
abstract = {The intensive use of synthetic fertilizers and pesticides has increased crop productivity but also contributed to soil degradation and biodiversity loss, highlighting the need for more sustainable agricultural strategies. Among emerging solutions, plant growth-promoting rhizobacteria (PGPR), particularly members of the Bacillota phylum, are gaining attention as effective bioinoculants that enhance plant growth and tolerance to biotic and abiotic stresses. However, introduced strains do not function in isolation. They enter complex microbial communities, shaped by plant type and developmental stage, influenced by soil properties and environmental conditions. While the positive effects of PGPR on plant performance are well documented, their impact on indigenous rhizosphere microbiota remains less studied. This review synthesizes current knowledge on how Bacillota-based inoculants influence native microbial communities in cereals, vegetables, orchard crops, and fiber plants. Most studies report shifts toward plant-beneficial taxa and reduced abundance of potential pathogens following Bacillota application. Frequently enriched genera include Bacillus, Pseudomonas, Lysobacter, Sphingomonas, Streptomyces, Azotobacter, Arthrobacter, Pseudarthrobacter, Bradyrhizobium, Devosia, Flavobacterium, Klebsiella, Herbaspirillum, and Rhodanobacter. These changes are often associated with improved plant growth and yield, and stress resilience. However, responses strongly depend on strain, plant and methodological approach. We summarize commonly applied approaches used to assess these interactions. Despite technological advances, limitations remain, such as single time-point sampling, simplified experimental systems, and insufficient integration of inoculant persistence with community analyses. Standardized, multi-site experimental frameworks, with multiple sampling terms are needed to improve predictability and ensure the safe implementation of PGPR-based solutions in sustainable agriculture.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
*Bacteria/classification/genetics
Crops, Agricultural/microbiology/growth & development
Plant Development
Soil/chemistry
Plant Roots/microbiology
Agriculture

@article {pmid42101879,
year = {2026},
author = {Theys, C and Decaestecker, E and Stoks, R},
title = {Extending space-for-time substitutions: the missing role of the gut microbiome.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voag032},
pmid = {42101879},
issn = {1420-9101},
abstract = {The space-for-time substitution (SFTS) approach is widely used to predict evolutionary trait responses to global warming. The current approach ignores the explicit role of the gut microbiome in shaping the future host phenotype, despite its strong influence on thermal adaptation and its ability to show more rapid adaptation than the host. We propose integrating reciprocal gut microbiome transplants into SFTS and identify a set of contrasts between treatment combinations to disentangle host and gut microbiome contributions to thermal adaptation under future warming. To illustrate our approach, we apply the proposed contrasts between treatment groups to re-interpret data on immune functioning of Ischnura elegans damselfly nymphs of which the gut microbiome was reciprocally transplanted between nymphs from warm-adapted low-latitude and cold-adapted high-latitude populations reared at both the cold (high-latitude) and warm (low-latitude) thermal regime. By disentangling the contributions of the host and its gut microbiome, our conceptual approach shows that gut microbiome adaptation can buffer against immune suppression in the high-latitude populations under future warming, while adaptation of the host will not. Incorporating the gut microbiome into SFTS may enhance realism in predicting species resilience to climate change and better inform conservation strategies under future climates.},
}

@article {pmid42102024,
year = {2026},
author = {Abu, BAZ and Zhang, L and Beblavy, R and Wu, Y and Lu, X and Fiscella, K and Sohn, MB and Xiao, J},
title = {Effects of pica practice on oral bacteriome and mycobiome profiles among pregnant women: A comparative study.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0328198},
pmid = {42102024},
issn = {1932-6203},
mesh = {Humans ; Female ; Pregnancy ; Adult ; *Pica/microbiology ; Cross-Sectional Studies ; *Mycobiome ; *Microbiota ; *Mouth/microbiology ; Saliva/microbiology ; Young Adult ; Bacteria/genetics/classification ; },
abstract = {INTRODUCTION: Pica, the excessive craving and consumption of non-food substances such as clay, and ice, is common among pregnant women but may pose risks for oral and systemic infections.

OBJECTIVE: Assessed the comparative effect of pica practice on the oral microbiome (bacteriome and mycobiome) profiles of pregnant women.

METHODS: A cross-sectional study was conducted in Upstate New York among pregnant women. Demographic, socioeconomic, pica practices (current and past), and oral hygiene practices were collected via questionnaires. The medical history of anemia was self-reported and verified using electronic records. A calibrated dentist assessed dental caries, periodontal status, and a comprehensive oral examination (plaque index, bleeding on probing). Oral samples (saliva and supragingival plaque) and pica samples were collected for the microbiome for Genomic DNA using I6S rRNA and ITS DNA sequencing and analyzed using linear regression with and without anemia as a covariate.

RESULTS: Of the 20 pregnant women in the study, 17 were minority women (75% non-white). The mean age of participants was 29 years, and 29 weeks of gestational age. Eight participants (40.0%) reported practicing pica, and six provided samples, namely ice (and popsicles), and chalk. Streptococcus, Actinomyces, and Prevotella dominated in both saliva and plaque samples, but the microbial compositions differed. Between the pica and the non-pica groups, two differentially abundant (DA) bacterial taxa were identified in saliva samples with and without anemia namelyOribacterium sinus (p < 0.05). In plaqueseven identical DA bacterial taxa including Prevotella nigrescens were seen except for Leptotrichia goodfellowii, which was unique to when anemia was controlled for (p < 0.05). Network analysis showed the co-occurrence of Candida albicans and Lactobacillus in the pica group.

CONCLUSION: Pica practice was associated with specific oral taxa abundance change in saliva and supragingival plaque, reflecting distinct microbiome distributions. In the regression model, including anemia as a covariate had almost no impact on the overall DA results. These findings are preliminary, indicating that future large prospective cohort studies are warranted to thoroughly assess the impact of pica practice on oral flora.},
}

Humans
Female
Pregnancy
Adult
*Pica/microbiology
Cross-Sectional Studies
*Mycobiome
*Microbiota
*Mouth/microbiology
Saliva/microbiology
Young Adult
Bacteria/genetics/classification

@article {pmid42102421,
year = {2026},
author = {Li, X and Liu, J and Yue, W and Yang, W and Zhang, L and Guo, C and Qing, W},
title = {Chronic endometritis and reproductive failure: The paradigm shift from microbial eradication to ecological restoration.},
journal = {Journal of reproductive immunology},
volume = {175},
number = {},
pages = {104906},
doi = {10.1016/j.jri.2026.104906},
pmid = {42102421},
issn = {1872-7603},
abstract = {Despite advancements in assisted reproductive technologies, such as preimplantation genetic testing, clinical success rates have plateaued, thereby increasing the clinical focus on the endometrial factor. Chronic endometritis (CE), a persistent and often asymptomatic mucosal inflammation, is an underdiagnosed condition associated with reproductive failure, particularly in cohorts with repeated implantation failure (RIF) and recurrent pregnancy loss (RPL). This review examines the evolving understanding of CE pathophysiology, transitioning from a traditional infection model toward a framework involving endometrial dysbiosis and potential bacterial biofilm formation. These microbial alterations are hypothesized to trigger maladaptive immune activation and may induce persistent epigenetic modifications that desynchronize endometrial receptivity. We critically evaluate current diagnostic modalities, addressing controversies regarding CD138 immunohistochemistry thresholds and the interpretive limitations of molecular microbiome screening associated with relic DNA. Therapeutically, while antibiotic regimens remain the standard of care, there is conflicting evidence regarding their universal clinical efficacy. Consequently, we review the rationale for transitioning from generalized broad-spectrum microbial eradication toward antibiotic stewardship and targeted ecological restoration using biotherapeutics. Synthesis of current evidence, including data from euploid embryo transfers, suggests that resolving histopathological inflammation improves live birth rates in specific high-risk cohorts. The future management of CE necessitates the implementation of risk-stratified algorithms and therapeutic strategies that focus on functional endometrial recovery rather than isolated histological clearance.},
}

@article {pmid42102504,
year = {2026},
author = {IJdema, F and Broeckx, L and Deruytter, D and Frooninckx, L and van Miert, S and De Smet, J},
title = {Short communication: The persistent influence of host lineage on the gut microbiomes of black soldier fly and yellow mealworm.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {5},
pages = {101828},
doi = {10.1016/j.animal.2026.101828},
pmid = {42102504},
issn = {1751-732X},
abstract = {Production insects such as the black soldier fly (BSF) and yellow mealworm (YM) are increasingly recognised as sustainable protein sources, and selective breeding of genetically distinct lines offers opportunities to improve production efficiency. However, insect performance is also influenced by the gut microbiome, which provides essential metabolic and protective functions. Despite this, current breeding programmes typically focus on host genetics and phenotypes, assuming that microbiome composition remains stable under consistent rearing conditions. However, this hypothesis remains largely untested. We examined gut bacterial communities in ten distinct BSF and YM populations reared for multiple generations under identical conditions. Each species shared a distinct set of ten zero-radius operational taxonomic units (zOTUs) across all populations, but their relative abundances varied, indicating host-specific effects on microbiome composition. Strain-specific zOTUs also persisted despite uniform environments. These findings suggest that host genetic background exerts a more persistent influence on gut microbiome composition than previously assumed.},
}

@article {pmid42102652,
year = {2026},
author = {Al-Salihy, AAS},
title = {Toward an immunological classification of autism spectrum disorder: A PRISMA-ScR-compliant scoping review.},
journal = {Journal of neuroimmunology},
volume = {417},
number = {},
pages = {578962},
doi = {10.1016/j.jneuroim.2026.578962},
pmid = {42102652},
issn = {1872-8421},
abstract = {Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental condition increasingly linked to disturbances in immune signaling and neuroimmune cross-talk. This PRISMA-ScR-guided scoping review synthesizes contemporary evidence to propose a structured immunological classification of ASD comprising six immune-related subtypes: immune overactivation, immune deficiency, autoimmunity-linked ASD, gut-immune axis dysregulation, post-infectious or immune-triggered onset patterns, and maternal immune activation. Each subtype is defined by characteristic neuroimmune features - including cytokine imbalances, aberrant microglial activation, altered microbiome-immune communication, and prenatal immune priming - reflecting distinct biological pathways through which immune dysfunction may influence neurodevelopment. Based on 42 mapped sources identified through a search strategy that primarily emphasized literature published between 2020 and 2025, while incorporating selected foundational earlier studies through citation chaining when necessary for conceptual and mechanistic context, and spanning human clinical and epidemiological studies, animal models, and integrative neuroimmune reviews, this synthesis identifies candidate biomarkers and immune signatures relevant to each subtype, including systemic and CNS-localized inflammation, autoantibodies, disrupted gut-immune-brain pathways, and maternal cytokine profiles. The framework also clarifies ongoing debates by distinguishing immune-mediated vulnerability and timing-dependent unmasking of susceptibility from assumptions of direct causation regarding environmental or infectious exposures. Conceptualizing ASD along immune-related subtypes provides a foundation for precision-based diagnostic and therapeutic approaches, highlighting opportunities for targeted immunomodulation, microbiome-informed interventions, and biomarker-driven stratification, thereby advancing translational efforts at the interface of immunology, neuroscience, and developmental psychopathology.},
}

@article {pmid42102900,
year = {2026},
author = {Hamerlinck, H and Boelens, J and De Looze, D and Messiaen, AS and Vandendriessche, S and Holvoet, T and Verhasselt, B},
title = {Seven years of stool banking: clinical and microbiological insights from the Ghent Stool Bank.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108744},
doi = {10.1016/j.ijid.2026.108744},
pmid = {42102900},
issn = {1878-3511},
abstract = {OBJECTIVES: The Ghent Stool Bank (GSB) was founded in 2018 at Ghent University Hospital to provide safe, ready-to-use faecal suspensions for faecal microbiota transplantation (FMT), primarily targeting recurrent Clostridioides difficile infection (rCDI) and supporting clinical trials.

METHODS: This retrospective cohort study explores the relationship between donor characteristics and rCDI treatment outcomes following FMT.

RESULTS: Between 2018 and 2024, 12.0% of screened candidates qualified as donors after rigorous evaluation, resulting in 159 approved donations. Forty-four FMT procedures were carried out in forty rCDI patients, achieving a primary cure rate of 77.1%, which increased to 85.7% following a second treatment. Donor microbiome diversity did not show association with treatment outcomes, and no statistically significant differences in taxa abundance were observed. Notably, faecal suspensions stored for up to five years were as effective as those stored for shorter periods. Additionally higher donor age did not appear to negatively impact treatment success in rCDI patients.

CONCLUSION: These findings support the role of stool banks like the GSB in ensuring safe FMT procedures. Allowing higher donor age and longer storage periods may help sustain sufficient high‑quality donor availability. Future efforts should focus on improving safety, enhancing donor-recipient compatibility through microbiome profiling and increasing public awareness.},
}

@article {pmid42103091,
year = {2026},
author = {Todua, I},
title = {Management of salt-sensitive hypertension in clinical settings: how should we approach it?.},
journal = {The American journal of medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjmed.2026.05.003},
pmid = {42103091},
issn = {1555-7162},
abstract = {Salt sensitivity is a major component of highly prevalent uncontrolled hypertensive disease. Multiple disease determinants, such as age, sex, genetic predisposition, pro-inflammatory factors, renal and vascular dysfunction, disrupted blood-brain barrier integrity, as well as gut microbiome health, effectively regulate sodium turnover and associated adverse outcomes. Salt sensitive blood pressure can be commonly observed in patients with both primary and secondary hypertension. Furthermore, patients suffering from obesity and insulin-resistant states, heart failure, chronic kidney disease, as well post-menopausal females and senior citizens, may be particularly sensitive to excessive salt exposure. Despite paramount importance, diagnosis or treatment of salt sensitive blood pressure remain challenging, often pushing clinicians into complicated management labyrinths. Significant discordance between objective findings, such as degree of thirst and edema on presentation, and results of laboratory testing, such as serum sodium, potassium, NT-proBNP, or RAAS essay, is often observed delaying the provision of appropriate care. This review offers detailed description of underlying pathophysiology, diagnosis and treatment of salt sensitive blood pressure in clinical settings, intending to ameliorate the burden of uncontrolled hypertension.},
}

@article {pmid42103112,
year = {2026},
author = {Kumwan, B and Meachasompop, P and Adisornprasert, Y and Rajitdumrong, C and Chaemlek, P and Srisapoome, P and Phaksopa, J and Buncharoen, W and Thangsunan, P and Thangsunan, P and Rodkhum, C and Paankhao, N and Kingwascharapong, P and Uchuwittayakul, A},
title = {Sequential nanoimmersion and hydrogel-based multivalent vaccination induce durable multilayered immunity against four bacterial pathogens in Nile tilapia (Oreochromis niloticus).},
journal = {Fish & shellfish immunology},
volume = {175},
number = {},
pages = {111398},
doi = {10.1016/j.fsi.2026.111398},
pmid = {42103112},
issn = {1095-9947},
abstract = {Bacterial infections caused by Flavobacterium oreochromis, Aeromonas veronii, Streptococcus agalactiae, and Edwardsiella tarda represent major threats to Nile tilapia aquaculture. This study evaluated a multistage mucosal vaccination strategy combining sequential nanoemulsion immersion priming with oral hydrogel-based boosters against these four pathogens in Oreochromis niloticus. Vaccination was associated with significant enhancement of both mucosal and systemic humoral immunity, as evidenced by elevated pathogen-specific IgM levels in gills, skin mucus, intestine, and serum across three successive challenge rounds. Immune-related gene expression analysis revealed significant upregulation of ighm, ighd, and ight in key immune tissues, consistent with broad activation of B cell-mediated responses. Label-free quantitative proteomic profiling demonstrated extensive immune remodeling in vaccinated fish, characterized by increased abundance of antigen-presentation molecules, complement factors, lysozyme, serpins, and mucosal defense-associated enzymes. Intestinal microbiome analysis revealed that vaccination reshaped microbial community composition toward a more stable and pathogen-resistant structure, with markedly reduced colonization by all four target pathogens. These immunological and microbial changes were associated with significantly higher survival rates under both immersion and intraperitoneal challenge conditions. Taken together, these findings suggest that multistage sequential vaccination may induce broad-spectrum, durable, multilayered protection in Nile tilapia through synergistic enhancement of humoral immunity, immunoglobulin gene expression, proteomic remodeling, and microbiome stabilization, providing a promising framework for sustainable disease management in intensive aquaculture.},
}

@article {pmid42103122,
year = {2026},
author = {Dhayalan, A and Manoharan, S and Waheeb, MQ and Rabbee, MF and Govindasamy, B and Selvan, ST and Pachiappan, P},
title = {An examination of the microbiome of Bacillus cereus (PS5) isolated from Puntius sarana (Olive barb) for α-amylase production, optimization, macromolecule extraction, and structural characterization with industrial and agricultural applications.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152420},
doi = {10.1016/j.ijbiomac.2026.152420},
pmid = {42103122},
issn = {1879-0003},
abstract = {The α-amylase enzyme plays a vital role in enzyme therapy and the intestinal digestive system, and is widely utilized in the food and pharmaceutical industries. Thus, this study aimed to isolate intestinal bacterial strains that produce α-amylase, optimize enzyme production, and characterize the molecular properties of the produced proteins. A total of 11 strains were isolated from the fish gut; 9 strains were positive for α-amylase production. The PS5 strain exhibited the highest enzymatic activity and was confirmed as Bacillus cereus. Optimization of B. cereus culture conditions revealed parameters of pH 7.0, temperature 35 °C, incubation time 40 h, and starch and yeast extracts of 1.5% and 2.53%, respectively. The bacterial protein was extracted, purified, and shown to have a molecular weight of 55 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. FTIR spectroscopy confirmed the presence of functional groups, such as phenols, alkanes, amides, and aromatic and aliphatic amines. Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)-tandem mass spectrometry (MS/MS) analysis identified 12 peptides, with the major peptide sequence being SVGLLLVLLLPMLGAAAPLTTQMLDSGWQFR (m/z 2383.97; S/N 69.3). The α-amylase protein sequence (513 amino acids) was used for structural prediction, while protein-protein interaction analysis revealed a significant interaction with pullulanase (interaction score 0.945). Molecular docking analysis showed strong binding energy of propoxur (-7.2 kcal/mol) and the hormone indole-3-acetic acid (-6.9 kcal/mol) with α-amylase protein. These findings indicate that Bacillus cereus (PS5) is a promising source of α-amylase for diverse industrial and agricultural applications. Further investigation into the activity and stability of these enzymes in natural environments could enhance the associated potential biotechnological applications.},
}

@article {pmid42103208,
year = {2026},
author = {Abdelhalim, KA and Wang, Y and Amirkhani Namagerdi, A and Alfuraiji, N and Mburu, D and Hassan, HA},
title = {Gut Oxalate Transport and Gut Microbiome as Potential Therapeutic Targets for Hyperoxaluria and Hyperoxalemia: Implications for Related Human Disease.},
journal = {Mayo Clinic proceedings},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mayocp.2026.04.020},
pmid = {42103208},
issn = {1942-5546},
abstract = {Besides kidney stones (KS), oxalate potentially contributes to chronic kidney disease (CKD) and its progression, CKD- and end stage kidney disease (ESKD)-associated cardiovascular diseases, and poor kidney transplant survival. KS affect about 1 in 5 men and 1 in 11 women and the recurrence rate remains high (50% in 5 years and up to 80% in 10-20 years), reflecting that current interventions are inadequate, and novel therapies are needed. 70-80% of KS are composed of calcium oxalate and small increases in urine oxalate enhance the KS risk. The gastrointestinal tract (gut) plays a major role in oxalate homeostasis by acting as a site for oxalate absorption and secretion. Therefore, the gut potentially represents a novel therapeutic pathway for body oxalate elimination. Strategies aiming at reducing the gut's ability to absorb oxalate and/or enhancing its ability to secrete oxalate can lead to decreased plasma and urinary oxalate levels and therefore can serve as novel approaches for the prevention and/or treatment of hyperoxalemia and hyperoxaluria. Humans lack oxalate metabolizing enzymes, and they rely on gut bacteria referred to as oxalate-degrading bacteria (oxalobiome) for gut oxalate degradation. This limits net gut oxalate absorption, thereby helping with maintaining normal oxalate homeostasis. This review focuses on the role of gut oxalate transport and gut microbiome in overall oxalate homeostasis and how they can be therapeutically targeted. Importantly, the majority of evidence for gut oxalate transport is derived from animal studies, but the relevance of these findings to human gut oxalate transport remains to be established.},
}

@article {pmid42103277,
year = {2026},
author = {Yan, J and Jin, N and Xu, C and Wu, H and Jiang, Q and Liu, H and Yuan, J and Yin, D and Lin, F and Wang, R and Liang, Y and Feng, Y and Lan, Y and Lin, X and Wang, Y and Zhang, N and Dai, L and Li, T and Dong, S and Cheng, L and Sun, X},
title = {Multi-omics landscape and machine learning predictors of acute and chronic coronary syndrome diagnosis in young patients.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.05.015},
pmid = {42103277},
issn = {2090-1224},
abstract = {BACKGROUND: Acute coronary syndrome (ACS) is a leading global cause of death, and its incidence is increasingly rising in young adults, who exhibit distinct clinical characteristics from elderly patients. However, multi-omics studies focusing specifically on young coronary heart disease (CHD) patients remain scarce, hindering precise diagnosis and mechanism exploration.

METHODS: Here, we enrolled 206 young chest pain patients (18-45 years old), including 122 ACS patients, 38 chronic coronary syndrome (CCS) patients, and 46 individuals with healthy coronary arteries (NC). We performed integrated analyses of peripheral blood mononuclear cell transcriptomics, serum metabolomics, stool metabolomics, and gut microbiome metagenomics to characterize CHD subtypes and develop targeted diagnostic tools.

RESULTS: Our results showed that single omics layers had limited ability to distinguish CHD subtypes, while multi-omics integration significantly improved diagnostic efficacy. We identified unique molecular signatures for different subtypes: STEMI was associated with abnormal amino acid and carbohydrate metabolism, CCS was dominated by amino acid metabolism disturbances, and both STEMI and ACS showed enriched inflammation-related pathways. Novel biomarkers including p-chlorobenzene sulfonamide, cotinine, and the gut bacterium Streptococcus parasanguinis were identified, with Streptococcus parasanguinis validated as an atherogenic pathogen in a murine model. We constructed three multi-omics fusion diagnostic models (ACS vs. NACS, CCS vs. NC, STEMI vs. NSTE-ACS) with AUC values of 0.99, 0.95, and 0.96, respectively, and integrated them into a comprehensive diagnostic pipeline. Furthermore, multi-omics functional analysis unraveled a synergistic "microbiota-metabolism-immunity" regulatory network underlying CHD subtypes, linked to disordered amino acid and carbohydrate metabolism and aberrant inflammatory activation.

CONCLUSION: This study provides a systematic molecular landscape of young CHD, a high-precision diagnostic strategy, and novel targets for mechanism research and targeted intervention, addressing the unmet clinical need for precise management of young CHD patients.},
}

@article {pmid42103586,
year = {2026},
author = {Liu, WC and Chang, TT},
title = {From intratumoral microbiome association to spatial microbiome biology in primary liver cancer: a response and perspective.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.05.021},
pmid = {42103586},
issn = {0929-6646},
}

@article {pmid42103590,
year = {2026},
author = {Fukuda, K and Hozaka, Y and Ohtsuka, T},
title = {Reply to the Letter to the Editor regarding microbiome-genetic interplay in intraductal papillary mucinous neoplasms of the pancreas.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pan.2026.04.016},
pmid = {42103590},
issn = {1424-3911},
}

@article {pmid42103597,
year = {2026},
author = {Fan, Z and Shahgaleh, H and Ding, S},
title = {Nitrous oxide mitigation in hybrid maize mediated by Massilia.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.04.015},
pmid = {42103597},
issn = {1878-4372},
abstract = {Massilia presents a functional paradox in maize heterosis: its enrichment correlates with lower nitrous oxide (N2O) emissions, yet it lacks reduction genes. We propose that Massilia functions as an ecological hub, coordinating the rhizosphere microbiome and engineering the microenvironment to suppress N2O emissions. This paradigm guides new strategies for breeding climate-smart crops.},
}

@article {pmid42103701,
year = {2026},
author = {Wu, H and Wang, M and Ouyang, Q and Zhang, X and Liao, L and Wang, Y and Tang, N and Wang, Z},
title = {Comprehensive analysis of microbiome and transcriptome revealed the mechanisms of Flammulina velutipes stem-base enhance intestinal health in Gymnocypris eckloni.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70490},
pmid = {42103701},
issn = {1095-8649},
support = {23ZR102//Chengdu Agricultural College/ ; 23BS03//Chengdu Agricultural College/ ; },
abstract = {Although Flammulina velutipes residues are increasingly used in fish feeds, their mode of action in the gut is poorly defined. Here, we show that feeding Gymnocypris eckloni diets supplemented with F. velutipes stem-base (FVS) or its polysaccharides (FVP) selectively enhance foregut morphology-increasing both villus height and muscle layer thickness-without affecting mid- or hindgut regions. Transcriptome profiling revealed that 1831 differentially expressed genes (DEGs) were generated by FVS diet in the foregut mainly enriched in the signalling pathways related to DNA replication, fat digestion and absorption and HIF-1 signalling pathway. In addition, the differential genes between the FVP group and the control group were enriched in cell adhesion molecules, MAPK signalling pathway and cytokine-cytokine receptor interaction. Consistent with this, KEGG enrichment highlighted HIF-1α and MAPK as key pathways activated by FVS and FVP, respectively. Importantly, FVP also shifted the gut microbiota composition, boosting Weissella and other putative beneficial bacteria. These findings imply that F. velutipes has the potential to strengthen the intestinal barrier and improve intestinal health, offering valuable insights for the aquaculture of G. eckloni.},
}

@article {pmid42103708,
year = {2026},
author = {Basler, N and De Smet, L and Bouras, G and Swinnen, J and Pranga, K and Brussaard, CPD and Vandamme, P and de Graaf, DC and Matthijnssens, J},
title = {The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72757-2},
pmid = {42103708},
issn = {2041-1723},
support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 817622//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; H2020//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Honey bees (Apis mellifera) contribute to crop production and floral biodiversity via pollination, but their health is increasingly challenged by stressors including pathogens, parasites and agricultural practices. Although the honey bee gut microbiome is relatively simple, its phages are not well studied. Here, we conducted a metagenomic study, providing a comprehensive catalogue of honey bee gut phages from 450 virus-enriched samples from 63 hives, across eight European countries, three seasons and three gut sections. We describe a diverse phageome including many phages that appear to belong to novel taxa, as well as a core set of 97 highly prevalent phages. In addition, we identify potential auxiliary metabolic genes, such as a sulfur metabolism gene carried by phages that are predominantly temperate and likely infect mutualistic honey bee core bacteria. This gene is associated with land use around the sampled hives, indicating complex ecological interactions in the tripartite system of the honey bee, its microbiota and the phages therein.},
}

@article {pmid42103720,
year = {2026},
author = {Easter, QT and Huynh, KLA and Stolf, CS and Xie, J and Matuck, BF and Hasuike, A and Alvarado-Martinez, Z and Kim, WS and Chen, Z and Ribeiro, AA and Pareek, N and Azcarate-Peril, AM and Wu, D and Casarin, R and Ko, KI and Liu, J and Byrd, KM},
title = {CD38[+] endothelial remodeling marks spatially patterned vasculopathy in rapidly advancing periodontitis and peri-implantitis.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72452-2},
pmid = {42103720},
issn = {2041-1723},
support = {Volpe Research Scholar Award//ADA Foundation (American Dental Association Foundation)/ ; Large Research Grant//American Academy of Implant Dentistry (AAID)/ ; #1RM1DE035338-01//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; #1R03DE034507-01//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; #5R01DE030415-05//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; startup funds//Virginia Commonwealth University (VCU)/ ; #2021/11082-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (São Paulo Research Foundation)/ ; Overseas Researcher Grant//Nihon University/ ; Schoenleber Grant//University of Pennsylvania (Penn)/ ; #P30CA016059//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; #UM1TR004360//U.S. Department of Health & Human Services | NIH | National Center for Advancing Translational Sciences (NCATS)/ ; },
abstract = {Oral inflammatory diseases affect nearly half of all humans, yet mechanisms underlying rapidly-destructive inflammation remain poorly understood. We compared peri-implantitis with moderate- and high-grade periodontitis using integrated microbial and single-cell sequencing (>967,169-cells; single-cell RNA-seq, spatial proteotranscriptomics). Laser capture microdissection with compartmental microbiome analysis revealed reduced bacterial load and diversity in peri-implantitis. Expansion of the Human Periodontal Atlas with peri-implantitis single-cell RNA-seq data (36-samples; 121,395 cells) identified CD34[+] vascular endothelial cell (VEC) rarefaction and oxidative stress, hypoxia, and NAD[+] metabolism-associated transcriptional programs enriched in a TNFRSF6B[+]/ICAM1[+] post-capillary venule (PC-VEC) subpopulation. NAD[+]-consuming ectoenzyme CD38 was selectively enriched and orthogonally confirmed by spatial transcriptomics (6-samples; 283,377-cells) and proteomics (23-samples; 562,397-cells). Spatial neighborhood analyses demonstrated CD38[+]-high PC-VEC expansion, closer proximity, and higher IL16-CD4 T cell signaling in peri-implantitis. Matched high-grade periodontitis biopsies confirmed spatially restricted CD38[+]-VECs despite similar microbial burden, identifying endothelial vasculopathy underlying rapidly advancing oral inflammation and a potential therapeutic axis.},
}

@article {pmid42103800,
year = {2026},
author = {Bahuguna, M and Diwan, P and Wahlang, J and Gupta, RK},
title = {Comparative microbiome profiling of betel quid chewers and non-chewers to identify dysbiotic microbial signatures.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-46533-7},
pmid = {42103800},
issn = {2045-2322},
support = {2019-3072//Indian Council of Medical Research/ ; 2019-3072//Indian Council of Medical Research/ ; 2019-3072//Indian Council of Medical Research/ ; },
abstract = {Recent studies are showing an association between oral microbiome community changes and oral diseases, including oral cancer. The prevalence of betel quid chewing has been linked to the incidence of oral cancer, particularly in the Northeast region of India. Hence, the study to understand the bacterial community shifts induced by betel quid to identify dysbiotic microbial signatures will not only aid in early diagnosis of oral cancers but also facilitate the development of strategies to restore microbial balance and potentially prevent disease progression. The present cross-sectional study evaluated the oral microbiome of 92 adults in Meghalaya, India, using a 16 S rRNA sequencing approach. Significant differences were observed in the bacterial community in betel quid chewers and non-chewers. Alpha diversity, assessed using Chao1 and observed genera metrics, was significantly higher in betel quid chewers as compared to non-chewers, especially among long-term users and male individuals. Beta diversity analysis revealed significant community compositional differences between Betel quid chewers and non-chewers, more notably in males and individuals aged 40-60 years. Betel quid chewers demonstrated a higher number of unique taxa (63 Overall; 102 Male; 123 in 40-60 years old) compared to non-chewer samples. Linear discriminant analysis identified Haemophilus, Fusobacterium, and Lautropia enriched in non-chewers, while Lachnoclostridium, Ottowia, and Prevotella were enriched in chewers. Additionally, Pediococcus pentosaceus and Leuconostoc citrenum were found exclusively in older, long-term chewers; Lactobacillus reuteri and Lactobacillus salivarius in non-chewers. These findings highlight profound BQ-associated oral microbiome dysbiosis.},
}

@article {pmid42103814,
year = {2026},
author = {Petrás, S and Szabó, BV and Kiss, T and Bahar, MA and Csupor, D and Tóth, B},
title = {Prenatal maternal antibiotic use increases the risk of childhood eczema: a systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51441-x},
pmid = {42103814},
issn = {2045-2322},
abstract = {Early-life disruption of microbiome development is known to impair health; however, the long-term effects of pregnancy-related pharmacological alterations to the maternal gut microbiota on offspring health remain unclear. This meta-analysis aimed to evaluate the impact of maternal antibiotic use (either prenatal or intrapartum) on the risk of childhood atopic dermatitis, based on cohort and case-control studies. Literature searches were conducted in EMBASE, PubMed, Cochrane, and Web of Science databases using predefined PICO (patients, intervention, comparison, outcome) criteria. Overall, our meta-analysis included 30 studies with a total of 4,125,143 mothers and 4,346,050 children. Using the random effects model, our study found that prenatal antibiotic use was associated with higher odds of atopic dermatitis in childhood (aOR: 1.32; 95% CI: 1.12; 1.56). This result remained significant after adjusting publication bias by the trim-and-fill method (aOR: 1.22; 95% CI: 1.03; 1.44), highlighting the potential relevance of antibiotic prescribing practices during pregnancy in relation to childhood atopic disease risk. Intrapartum antibiotic use was not associated with elevated risk for atopic dermatitis in the children (OR: 1.64; 95% CI: 0.84; 3.17). Prenatal antibiotic use appears to have a modest effect on atopic dermatitis in offspring.},
}

@article {pmid42103910,
year = {2026},
author = {Lyu, WN and Shen, CY and Tsai, YJ and Chen, LH and Lee, YH and Chen, SK and Lee, JM and Lou, PJ and Chuang, EY and Tsai, MH},
title = {Intratumoral microbial networks as biomarkers for second primary oral cancer risk in esophageal squamous cell carcinoma.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52247-7},
pmid = {42103910},
issn = {2045-2322},
support = {PL-202208034-V//Fu Jen Catholic University Hospital/ ; 115KKZA3T1//Development Center for Medical Devices, National Taiwan University/ ; },
abstract = {Esophageal squamous cell carcinoma (ESCC) survivors remain at elevated risk of developing second primary oral cancer (SPOC), yet the role of intratumoral microbiomes in SPOC emergence is not fully understood. We performed 16 S rRNA V3-V4 sequencing on tumor brushings from 28 ESCC patients (20 SPOC-negative, 8 SPOC-positive) to profile microbial diversity, taxonomic composition, functional potential, and interaction networks. Alpha diversity metrics (Chao1, Shannon) did not differ significantly between groups (p > 0.05), whereas sparse partial least squares-discriminant analysis of beta diversity robustly separated SPOC-positive from SPOC-negative tumors (p < 0.001), identifying 32 discriminant amplicon sequence variants (ASVs) linked to 41 differential KEGG pathways. Intratumoral Spearman correlation networks (|r| > 0.3, p < 0.05) between the ten most abundant genera and these pathways revealed two distinct modules: a SPOC-associated network centered on Prevotella pallens and P. scopos, enriched in carbohydrate metabolism, PI3K-Akt signaling, and glycosaminoglycan degradation; and a non-SPOC network anchored by Alcaligenaceae, Cyanobiaceae, Rhodobacteraceae, and Prevotella oris, associated with macrolide biosynthesis and aminobenzoate degradation. These findings demonstrate that specific intratumoral microbial interaction networks distinguish ESCC patients who develop SPOC, and highlight network-based microbial signatures as promising biomarkers for SPOC risk stratification.},
}

@article {pmid42103925,
year = {2026},
author = {Anil, and Ramesh, KB and Gouda, MNR and Subramanian, S},
title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52250-y},
pmid = {42103925},
issn = {2045-2322},
abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.},
}

@article {pmid42104127,
year = {2026},
author = {Byrne, D},
title = {How a passion for baking fermented a fresh career move.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-026-01390-2},
pmid = {42104127},
issn = {1476-4687},
}

@article {pmid42104135,
year = {2026},
author = {Cheong, KL and Pan, T and Wang, M and Wang, D and Zhong, S},
title = {Impact of prebiotics, probiotics, and postbiotics on maternal and fetal health: mechanisms, efficacy, and safety across pregnancy.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42104135},
issn = {1530-0447},
abstract = {Microbiome-directed biotics are gaining attention in obstetrics. This review clarifies terminology, mechanisms, clinical effects, and safety for prebiotics, probiotics, and postbiotics. Prebiotics are nondigestible substrates that are selectively used by host microbes to confer health benefits. Probiotics are defined as live microorganisms that improve health when given in adequate amounts. Postbiotics are preparations of nonviable microbes or their components that trigger beneficial responses. We summarize how these agents may influence maternal and fetal physiology across gut, immune, metabolic, vaginal, placental, and human milk contexts. In the gut, they reshape short-chain fatty acid and bile acid pools, modulate enteroendocrine hormones, and recalibrate basal immunity. They also tighten epithelial junctions and stimulate goblet cell mucin, which reduces microbial translocation, endotoxemia, and vascular strain. In the vaginal and urogenital niches, lactobacilli maintain acidity, suppress pathobionts, and may lower colonization risk. At the placenta and in milk, microbial metabolites and immune mediators, including human milk oligosaccharides and secretory IgA, carry maternal cues that shape fetal and neonatal development. Safety profiles differ by class. Prebiotics are generally well tolerated, with dose-dependent gastrointestinal symptoms most common. Probiotics require strain-level validation, viability control, and contaminant-free production. Postbiotics need to be verified inactivation and structural characterization. IMPACT: Provides a comprehensive, mechanism-based overview of how prebiotics, probiotics, and postbiotics influence maternal and fetal health across multiple physiological systems. Clarifies definitions, safety profiles, and quality standards for biotics in pregnancy, addressing current inconsistencies in research and commercial products. Integrates emerging evidence on postbiotics and vertical microbial transmission, offering a timely framework for future clinical applications and regulatory guidance.},
}

@article {pmid42104237,
year = {2026},
author = {An, L and Liu, X and Li, X and Chu, Y and Sun, X and Chu, J and Nie, Y},
title = {Contact-mediated bacterial transmission and infection risk dynamics in a newly opened hospital ward.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05030-7},
pmid = {42104237},
issn = {1471-2180},
support = {32500094//National Natural Science Foundation of China/ ; },
abstract = {The hospital microbiome significantly influences patient recovery and clinical outcomes. However, the dynamics of microbial colonization and transmission following initial patient occupancy remain poorly understood. Here, we employed 16 S rRNA gene amplicon sequencing of the V3-V4 region (Illumina platform) to investigate bacterial community dynamics on surfaces within neurosurgery ward and patients as a new hospital became operational. Our results showed that bacterial colonization in hospital wards follows distinct site-specific patterns, after hospital opening, alpha diversity was significantly increased on floors and drawer handles but decreased on bedrails and faucet handles compared to preopening. Beta diversity analysis showed that surfaces frequently contacted by patients exhibited the greatest compositional turnover, such as bedrails, drawer handles, and faucet handles, bacterial communities in after-opening were more homogeneous across sites than preopening, indicating potential bacterial transmission. Moreover, we found that following patient admission, patient hand-derived microbiomes exert a significant influence on the bacterial communities in hospital wards, with a particularly pronounced impact on bedrails. Additionally, the potential pathogenic potential of the microbial community at the taxonomic level of bedrails in post-opening was significantly higher than preopening, which does not reflect direct clinical infection risk. Taken together, these findings underscore the critical role of human contact in shaping hospital microbiomes and highlight the importance of targeted infection control strategies to mitigate potential pathogen transfer.},
}

@article {pmid42104530,
year = {2026},
author = {Bibinger, S and Nosenko, T and Sivaprakasam Padmanaban, PB and Schulz, S and Schroeder, H and Kersten, B and Zimmer, I and Buegger, F and Schloter, M and Schnitzler, JP},
title = {Provenance legacies override species effects in shaping oak rhizosphere microbiomes and metabolomes.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71213},
pmid = {42104530},
issn = {1469-8137},
support = {457330647//Deutsche Forschungsgemeinschaft/ ; 2220WK09A4//German Federal Ministry of Food and Agriculture (BMEL), Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU)/ ; 2220WK09B4//German Federal Ministry of Food and Agriculture (BMEL), Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU)/ ; },
abstract = {As climate change drives more frequent drought-heat extremes, selecting drought-tolerant trees is crucial for future forest resilience. However, the role of tree-microbial associations remains largely unclear. We investigated how geographic origin, species identity, and intrinsic water use efficiency (iWUE) shape the rhizosphere microbiome and root-rhizosphere metabolome of Quercus robur L. and Q. petraea (Matt.) Liebl. In a 6-yr common garden experiment, we analyzed trees from two distinct geographic origins (upper Rhine basin and north German lowland) using 16S/ITS metabarcoding and untargeted metabolomics. We found a consistent legacy effect of seed origin on the prokaryotic rhizosphere microbiome and metabolome, whereas tree species had no significant impact. The bacterial family Pseudonocardiaceae was enriched for trees from the drier origin (NGL), while Blastocatellaceae and Micromonosporaceae were associated with iWUE. Higher iWUE also correlated with lower prokaryotic diversity. Ellagic acid, a polyphenol associated with drought tolerance, was enriched in the drier origin. The rhizosphere fungal community, however, was largely unaffected by origin or species. Our findings suggest that ecotypic adaptation linked to origin can outweigh species-level traits in shaping the oak rhizosphere. These findings emphasize that provenance-driven adaptation influences plant-microbe interactions and underscore the need for provenance-aware selection to strengthen forest drought resilience.},
}

@article {pmid42104576,
year = {2026},
author = {Ii C, JF and Vidal, MJS and Dela Cruz, FSE and Tantengco, OAG and Menon, R},
title = {The Microbiome Signature of the Placenta and its Role in Spontaneous Preterm Birth: A Systematic Review and 16S rRNA Re-Analysis.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {5},
pages = {e70246},
doi = {10.1111/aji.70246},
pmid = {42104576},
issn = {1600-0897},
mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Premature Birth/microbiology/immunology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; },
abstract = {PROBLEM: The advent of high-throughput 16S rRNA sequencing has enabled deeper insights into microbial communities associated with adverse pregnancy outcomes, including spontaneous preterm birth (sPTB). While microbial dysbiosis in the cervicovaginal and oral-gut microbiomes has been implicated in sPTB, the existence of a placental microbiome remains contentious. Traditional paradigms of a "sterile womb" have been challenged by studies suggesting a low-biomass microbial community in the placenta, though recent evidence disputes this claim, attributing findings to contamination or transient microbial DNA signals.

METHOD: This study systematically reviewed placental microbiome studies employing 16S rRNA sequencing and re-analyzed publicly available datasets to determine microbial signatures in term and preterm placentas. Following a comprehensive search of three databases and stringent inclusion criteria, seven studies were included. The risk of bias was assessed using a modified Joanna-Briggs tool, revealing moderate-to-low risk across studies. Methodological heterogeneity, including differences in contamination controls, sequencing regions, and analytical platforms, was a significant limitation.

RESULTS: A re-analysis of sequencing data showed no consistent microbiome signature distinguishing the term from preterm placentas. Beta diversity analysis revealed no group clustering, while alpha diversity indices showed comparable species richness. Bacterial DNA in placental tissues was primarily attributed to contamination from the urogenital tract or laboratory processes.

CONCLUSION: Findings underscore the importance of robust contamination control and standardized protocols in low-biomass microbiome research. Future studies should employ advanced techniques, such as metagenomics and fluorescence in situ hybridization, to evaluate the functional relevance of microbial communities in the placenta, as well as rule out microbial DNA deposited in the placenta through circulating bacterial extracellular vesicles (EVs).},
}

Humans
Female
Pregnancy
*Placenta/microbiology
*Premature Birth/microbiology/immunology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics

@article {pmid42104937,
year = {2026},
author = {Kang, X and Hu, L and Song, J and Zhang, Z and Li, Y and Zhang, Q and Luo, C and Pang, Y and Guo, P and Yue, B and Li, P and Fan, Z},
title = {Snake Gut Microbiota as a Source of Anti-Inflammatory Probiotics: Isolation and Functional Characterization of Two Novel Strains.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70118},
pmid = {42104937},
issn = {1749-4877},
support = {2023NSFSC1935//Sichuan Science and Technology Program/ ; },
abstract = {The intestinal microbiome is fundamental to host physiological homeostasis, while deviations from its balanced state have been linked to inflammatory bowel diseases (IBD). To address the limitations of conventional antibiotic therapies, this study explored snake gut microbiota as a novel source of anti-inflammatory probiotics. We explored the gut microbiota of five snake species (Deinagkistrodon acutus, Trimerodytes annularis, Trimerodytes percarinatus, Lycodon rufozonatus, and Trimeresurus stejnegeri) through metagenomic sequencing. Community composition analysis revealed that the phylum-level composition was mainly Proteobacteria, Bacteroidetes, Actinomycetota, and Firmicutes. We further detected some potential probiotic species, such as Enterococcus, Lactobacillus, and Limosilactobacillus. From 196 isolated strains, Lactobacillus johnsonii DA0116 and Limosilactobacillus reuteri DA0218 were selected through rigorous safety and functional assessments, including acid/bile tolerance, pathogen inhibition, and adhesion capacity. In a DSS-induced murine colitis model, both strains significantly reduced disease activity index (DAI), pro-inflammatory cytokines (TNF-α, IL-6, and IL-8), and restored gut microbiota diversity. Additionally, whole-genome analysis identified bacteriocin synthesis clusters (gassericin-S/T) and carbohydrate metabolism genes, explaining their antimicrobial and immunomodulatory properties. This study not only emphasizes the untapped latent value of reptilian gut microbiota for probiotic discovery but also provides two candidate strains with therapeutic promise for IBD and functional food applications.},
}

@article {pmid42105032,
year = {2026},
author = {Saeed, T and Grover, M and Singh, AK and Prasanna, R and Kaushik, R and Meena, MC and Mandal, PK and Kumar, P},
title = {Hydrophyte root microbiome: a novel reservoir of plant growth-promoting bacteria for enhancing lettuce (Lactuca sativa L.) growth and nutritional quality under soilless cultivation.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {6},
pages = {},
pmid = {42105032},
issn = {1573-0972},
mesh = {*Lactuca/growth & development/microbiology ; *Plant Roots/microbiology/growth & development ; *Microbiota ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Biomass ; Plant Growth Regulators/metabolism ; Nutritive Value ; Soil/chemistry ; Germination ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Soilless cultivation is a major component of modern protected agriculture; however, often lack the beneficial microbial communities that support plant health in natural soils. This study explored hydrophyte root microbiomes as an eco-friendly and novel source of plant growth-promoting bacteria (PGPB) for engineering beneficial microbial communities in soilless systems. Bacteria associated with the roots of Eichhornia crassipes, Pistia stratiotes, and Alternanthera philoxeroides, expressing PGP traits were assessed for their growth-promoting potential on lettuce (Lactuca sativa L. cv. 'Lolo Red') using cocopeat-based soilless media and soil under polyhouse conditions. Hydrophyte associated rhizobacteria exhibited diverse PGP functions, including nutrient solubilization and phytohormone production, similar to those exhibited by rhizobacteria associated with terrestrial plants. Under soil and soilless conditions, lettuce crop inoculated with hydrophyte associated rhizobacteria significantly enhanced germination, plant biomass, root architecture, photosynthetic pigments and leaf quality traits, including TSS (total soluble solids), total phenolics, vitamin C, anthocyanins, antioxidant enzyme activities, DPPH (2,2-Diphenyl-1-picrylhydrazyl) radical scavenging and FRAP (Ferric Reducing Antioxidant Power) responses in both the cultivation systems. Two strains viz. Bacillus aerius Aq35 and Pseudomonas protegens Aq45 were particularly very promising. Under soilless cultivation, Aq35 enhanced root fresh weight and surface area by 90.0% and 83.5%, respectively, while Aq35 and Aq45 increased lettuce yield by 39.62% and 28.70%, respectively. Bacterial inoculation significantly enhanced the availability of soil and plant macro (N, P, and K) and micronutrients (Fe, Mn, Zn, and Cu) along with a marked increase in enzymatic activities and microbial biomass carbon (MBC). Under soilless substrate, dehydrogenase activity increased from 43.40 to 64.65 µg TPF g[-1] day[-1], while alkaline phosphatase activity increased from 261.53 to 380.87 µg PNP g[-1]h[-1] inoculated (Aq35) treatment over uninoculated treatment indicating enhanced substrate biological quality. These results demonstrate that hydrophytes as rich, pre-adapted reservoirs of potent PGPB, and strains such as B. aerius Aq35 and P. protegens Aq45 hold strong potential as biostimulants for sustainable soilless agriculture.},
}

*Lactuca/growth & development/microbiology
*Plant Roots/microbiology/growth & development
*Microbiota
Soil Microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
Biomass
Plant Growth Regulators/metabolism
Nutritive Value
Soil/chemistry
Germination
RNA, Ribosomal, 16S/genetics

@article {pmid42105271,
year = {2026},
author = {Meijer, GW and Fogliano, V and Lähteenmäki, L and Ahrné, LM and Labbe, D and Forde, CG},
title = {From fiction to facts: on the safety, rules, perception, and role of food additives.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-26},
doi = {10.1080/10408398.2026.2669055},
pmid = {42105271},
issn = {1549-7852},
abstract = {Consumer perceptions of food additives are often negative, driven by unfamiliar terminology, associations with "ultra‑processed food," and concerns about reduced naturalness. Despite this, additives play essential roles in food preservation, sensory quality, and safety, and undergo rigorous safety evaluation in jurisdictions worldwide by authoritative bodies such as JECFA, EFSA, and the (US-)FDA. While some studies suggest possible effects of specific emulsifiers or sweeteners on the microbiome or metabolism, evidence is limited and often not reflective of real dietary exposure. Broader claims-such as additives causing "hyper‑palatability" or "food addiction"-lack scientific support, with research showing that overeating is more closely linked to energy density and food availability than additives themselves. Reducing additives use, without sound scientific justification, may inadvertently worsen nutrient profiles of foods, and increase food waste and health risks. Improving public understanding of additives safety and function is essential to counter misconceptions and avoid counterproductive reformulation decisions.},
}

@article {pmid42105460,
year = {2026},
author = {Ma, C and Chang, M and Zang, S and Shi, K and Sha, Z},
title = {Dual-omics links host genomic variation to gut microbiome restructuring under Mycobacterium marinum challenge in Cynoglossus semilaevis.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101838},
doi = {10.1016/j.cbd.2026.101838},
pmid = {42105460},
issn = {1878-0407},
abstract = {Disease outbreaks caused by Mycobacterium marinum pose a major challenge to marine aquaculture and threaten the sustainable production of Cynoglossus semilaevis. Increasing evidence suggests that host genetic variation and gut microbial communities may jointly influence disease-related phenotypes, yet their interaction under mycobacterial challenge remains poorly understood. In this study, we combined host whole-genome resequencing and gut 16S rRNA sequencing to explore host-microbiome associations in C. semilaevis following M. marinum challenge. Gut microbiota analysis revealed significant differences in community structure and composition between the experimental and control groups, with marked shifts in dominant taxa and differential enrichment of several bacterial genera. Genome-wide association analysis identified nine significant SNPs (λ = 1.02) associated with infection status, distributed across chromosomes 5, 10, 13, 18, and 19. Functional annotation showed that most of these loci were located in non-coding or regulatory regions, including six intronic SNPs, one ncRNA_exonic SNP, one ncRNA_intronic SNP, and one intergenic SNP. Correlation network analysis further linked host genetic variants with changes in gut microbial taxa, suggesting a potential association between host genomic variation and microbiome restructuring under challenge conditions. Overall, these results provide preliminary evidence that host genomic variation may be associated with gut microbiome dynamics during M. marinum infection in C. semilaevis. Although limited by sample size, this dual-omics framework offers a useful basis for future validation of host-microbiome markers relevant to disease-resilience breeding in aquaculture. CONCLUSION: Host genomic variation in C. semilaevis may be associated with gut microbiome restructuring under M. marinum challenge, particularly involving Acinetobacter dynamics. Although limited by sample size, this dual-omics framework provides a preliminary basis for future disease-resilience breeding in aquaculture.},
}

@article {pmid42105533,
year = {2026},
author = {Nizam, A and Shireen, N and Hasan, MR and Singh, S and Farooqui, M and Naithani, D and Farooqi, H},
title = {Artificial intelligence, omics, and biomarkers: Redefining lung cancer early detection.},
journal = {Current problems in cancer},
volume = {63},
number = {},
pages = {101312},
doi = {10.1016/j.currproblcancer.2026.101312},
pmid = {42105533},
issn = {1535-6345},
abstract = {Lung cancer, the leading cause of death worldwide, claims millions of lives yearly, largely due to limited early interventions. Currently used lung cancer screening methods are still limited in their reach and accuracy due to invasiveness, radiation exposure, and low sensitivity, especially in early stages, necessitating the need for innovative technologies. This review examines emerging tools for the early detection of lung cancer, utilizing biomarkers in conjunction with omics approaches and AI technology, which could significantly impact its clinical landscape. Tumor cells release specific biological indicators called biomarkers, which can be cellular components, nucleic acid fragments, protein fragments, or metabolites, detected from bodily fluids through non-invasive methods. The integration of biomarkers with omics technologies (such as proteomics and genomics) or multi-omics provides a comprehensive insight into the molecular profiles of various cancer subtypes and stages. Artificial intelligence, including machine learning and deep learning tools, further increases the accuracy and precision of these techniques. However, challenges still persist in its clinical translation, including technical limitations, regulatory hurdles and ethical concerns. Overcoming these limitations requires standardised protocols, interdisciplinary collaborations, and strategies for equitable access to innovative technologies. Novel, cutting-edge technological interventions, such as advanced imaging techniques, sensor technology, nanotechnology, breathomics, and microbiome analysis, have the potential to enhance early lung cancer diagnosis, ultimately improving patient outcomes and reducing the global burden of this disease.},
}

@article {pmid42105545,
year = {2026},
author = {Shan, X and Wang, H and Liu, X and Li, P and Zhang, F and Wang, R and Xue, M and Li, F},
title = {Remodeling distinct rhizosphere interactions of plant-microbiome by legacy and alternative PFASs: A multi-omics insight and biphasic role of iron plaque.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142313},
doi = {10.1016/j.jhazmat.2026.142313},
pmid = {42105545},
issn = {1873-3336},
abstract = {Rhizosphere microhabitat as a dominant sink for per(poly)fluoroalkyl substances (PFASs) and hotspot for redox reactions and root iron plaque (IP) forming is largely affected by the interactions between plants and bacteria. However, whether PFOA and its substitute (HFPO-DA) modulated distinct rhizosphere symbiotic patterns and what roles IP played remain unclear. This study integrated plant physiology, metabolism and rhizosphere microbiome to systematically elucidate their differences in remodulating plant-microbiome interactions and IP roles. Results showed that PFOA preferred to accumulate in roots and induced serious oxidative stress, while HFPO-DA was more easily transported to shoots directly affecting photosynthesis. Molecular docking suggested higher proteinic affinity of HFPO-DA, inhibiting superoxide dismutase activity. PFOA and HFPO-DA increased organic acids and sugars in root exudates recruiting differential beneficial bacteria. However, HFPO-DA downregulated the glycerophospholipid metabolism, shaped a more vulnerable and simpler bacterial network. Remarkably, PFASs concentration determined the double-edged roles of IP. At environmental levels, IP promoted glycerophospholipids and small peptides release facilitating azotobacter recruitment and photosynthesis. But under high-dose stress, it induced accelerated pollutant migration especially HFPO-DA, thereby exacerbating phytotoxicity. Partial least squares path modeling revealed that PFOA indirectly influenced plant phenotypes via shaping bacterial community, while HFPO-DA not only modified that but also altered root exudates. This work unveils distinct rhizosphere symbiotic patterns and IP biphasic role remodulated by legacy and alternative PFASs, and provides a reference for their risk assessment and control through nature-based solutions.},
}

@article {pmid42105760,
year = {2026},
author = {Fitzpatrick, CR and Allen Smith, R and Hige, J and Law, TF and Russ, D and Ajayi, OE and Eida, AA and Jacob, P and Jowers, M and Kumar, N and Lai, CTU and Anguita-Maeso, M and Peterson, SB and Saha, C and Skelly, T and Zhao, Q and Zhou, W and Grant, SR and Mougous, JD and Jones, CD and Dangl, JL},
title = {Streptomyces enrichment in roots during drought is uncoupled from plant benefit and is driven by host suppression of iron uptake and immunity.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.04.027},
pmid = {42105760},
issn = {1097-4172},
abstract = {Drought reshapes the plant root microbiota, yet the mechanistic drivers and consequences of this observation remain unclear. We discovered that suppression of host immunity and iron homeostasis is required for Streptomyces enrichment in roots during drought across diverse soils. Genetic and physiological manipulation of these host pathways confirmed their requirement in modulating Streptomyces root enrichment. Drought-induced suppression of iron uptake was conserved across the ∼160 mya monocot-eudicot divergence. Some Streptomyces strains enhanced plant growth and rescued iron uptake under drought. These benefits were uncoupled from Streptomyces root enrichment. They were instead shaped by intra-Streptomyces antagonism. We propose a two-step model: drought-driven downregulation of host iron and immune pathways enriches Streptomyces, while intra-genus dynamics fine-tune strain-level assembly and functional outcomes. Our data refine the idea that Streptomyces are enriched in roots during drought in response to a plant "cry for help" and consequently contribute to the alleviation of this abiotic stress.},
}

@article {pmid42105814,
year = {2026},
author = {Khan, YA and Anas, M and Khan, F and Ali, M and Al-Zharani, M and Nasr, FA and Qamar, W and Rahman, S},
title = {Cannabinoids in autoimmune diseases: mechanistic insights and translational challenges.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {118032},
doi = {10.1016/j.bcp.2026.118032},
pmid = {42105814},
issn = {1873-2968},
abstract = {Cannabinoids are traditionally recognized for their effect on the nervous system. Emerging evidence suggests that cannabinoids mitigate inflammation driven by Th1/Th17 responses, which are linked to autoimmune diseases. In addition to their symptomatic, and analgesic effects, cannabinoids suppress the immune response by modulating regulatory T-cell activity, reducing microglial activation, and help in maintaining the integrity of the epithelial barrier. These findings suggest that cannabinoids may be involved in immune, and metabolic regulatory pathways. Despite the promising preclinical data, translating these findings into effective treatments for autoimmune disorders has proven challenging. Current human studies have primarily focused on symptomatic relief such as reducing spasticity, managing pain, improving sleep quality, and boosting appetite. However, few trials have included immune profiling, i.e., assessed cytokine panels, performed immune cell phenotyping, tracked relapses, or utilized inflammation-focused imaging endpoints. Consequently, documented benefits are primarily symptomatic, while potential disease-modifying effects are not yet adequately studied. Cannabinoids interact with CB1, CB2, TRP, and PPAR-γ receptor proteins, suggesting that they may offer targeted immune modulation rather than broad immunosuppression, potentially overcoming limitations of conventional therapies. Moreover, new compounds like cannabigerol (CBG), cannabidivarin (CBV), and CB2-selective agonists with minimal psychoactivity offer expanded therapeutic options. However, challenges persist due to variability in formulations, bioavailability issues, regulatory hurdles, and a lack of long-term safety data. Future clinical development will require standardised GMP-grade preparations, robust pharmacokinetic evaluation, and trials that include immune-related endpoints such as T-cell polarisation, inflammasome markers, oxidative stress profiles, microbiome signatures, and longitudinal imaging, to clarify their therapeutic potential in autoimmune diseases.},
}

@article {pmid42105827,
year = {2026},
author = {Bottaro, F and Enrico, P and Ratti, G and Brambilla, P and Delvecchio, G},
title = {Gut Microbiome Variability and Brain Alterations in Schizophrenia: A Scoping Review of Structural and Functional MRI Studies.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {106739},
doi = {10.1016/j.neubiorev.2026.106739},
pmid = {42105827},
issn = {1873-7528},
abstract = {INTRODUCTION: Schizophrenia (SCZ) is increasingly considered a multifactorial disorder involving gut-brain interactions. Current evidence supports gut microbiome alterations in SCZ, along with well-established structural and functional brain abnormalities. However, findings linking gut microbiome variability to neuroimaging alterations in SCZ have not yet been comprehensively integrated.

METHODS: Following the Joanna Briggs Institute methodology for scoping reviews and the PRISMA-ScR checklist, a literature search was performed in PubMed, Scopus, and Web of Science, selecting structural magnetic resonance imaging (sMRI) and resting-state functional MRI (fMRI) studies examining the associations between gut microbiome variability and brain alterations in first-episode and chronic SCZ.

RESULTS: Eight studies (one sMRI-only, one fMRI-only, and six combining sMRI and fMRI) met the inclusion criteria. The sMRI studies primarily showed associations between gut microbiome composition and gray matter volume in frontal, temporal, and limbic regions, while the fMRI studies found microbial variations associated with resting-state activity and functional connectivity across cortico-subcortical and large-scale brain networks. Notably, gut microbiome-neuroimaging associations differed between early and chronic stages of the disorder, suggesting stage-dependent gut-brain relationships.

CONCLUSIONS: Available evidence supports an association between gut microbiome variability and neuroimaging alterations in SCZ, with emerging differences between first-episode and chronic patients. Despite methodological heterogeneity and predominantly cross-sectional designs, these findings highlight the relevance of a multimodal gut-brain framework. Future longitudinal, multimodal studies integrating gut microbiome, neuroimaging, and clinical features may help disentangle biological heterogeneity and improve patient stratification in SCZ.},
}

@article {pmid42105950,
year = {2026},
author = {Kuna, A and Killi, K and Mettu, TR},
title = {Quantum-Enabled Approaches to Precision Nutrition: Linking Molecular Interactions with Metabolic Prediction.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101584},
doi = {10.1016/j.tjnut.2026.101584},
pmid = {42105950},
issn = {1541-6100},
abstract = {Precision nutrition aims to tailor dietary guidance to individual biology, yet current methods struggle to integrate complex molecular and multi-omic data into clinical care. Emerging quantum-driven technologies encompassing quantum computing, quantum chemistry and quantum-enhanced sensors link detailed molecular modelling with real-time metabolic forecasting. Quantum chemical simulations and machine learning model nutrient protein interactions at the atomic level, while quantum algorithms and echo state networks have been applied to create digital metabolic avatars that predict weight and metabolic trajectories from daily diet and activity data. Quantum computing enables rapid integration of genomic, metabolomic and microbiome datasets and supports optimization of personalised diet plans. Advances in computational molecular modelling now allow prediction of molecular structures and properties relevant to food components, and prototype quantum metabolic twins have demonstrated the capacity to forecast weight trends from incomplete real-world data. The clinical implications include proactive dietary interventions, noninvasive nutrient deficiency screening and improved prediction of disease risk from metabolic profiles, all of which can enhance patient outcomes and clinical decision making. This perspective synthesizes recent advances and delineates research directions at the intersection of quantum science, medical diagnostics, metabolism and clinical nutrition, with implications for clinicians, physicians, dietitians and clinical decision support in patient care.},
}

@article {pmid42105976,
year = {2026},
author = {Gomes, J and Rodrigues, ES and Carvalhinho-Lopes, PS and Comis-Neto, AA and Pujol Arena, RV and Birmann, PT and Fidelis, EM and Meus, SS and Rodrigues, BG and Alves de Jesus, GF and Ávila, DS and Pesarico, AP and Ribeiro, AM and Rosa, SG and Pinton, S},
title = {Paraprobiotics attenuate oxidative stress, dopaminergic neuron loss, and gut microbiome imbalance in an intranasal MPTP rat model of Parkinson's disease.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {111011},
doi = {10.1016/j.neuropharm.2026.111011},
pmid = {42105976},
issn = {1873-7064},
abstract = {Intestinal dysbiosis may contribute to the progression of Parkinson's disease (PD) by promoting inflammation and oxidative stress. Paraprobiotics, defined as non-viable microbial cells, have emerged as a promising therapeutic strategy. This study evaluated the neuroprotective, gastroprotective, and microbiota-modulating effects of a paraprobiotic blend comprising Lactobacillus casei CCT 7859, Bifidobacterium lactis CCT 7858, and Streptococcus thermophilus ATCC 19258 in a murine PD model induced via intranasal administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Seventy female Wistar rats received either intranasal MPTP or saline, followed 24 hours later by 14 days of paraprobiotic treatment (100 mg/kg/day, intragastrically). Fecal and tissue samples were collected for microbiota, oxidative stress, dopaminergic neurodegeneration, and physiological parameter analyses. Antioxidant enzymes (superoxide dismutase and catalase), oxidative damage markers (malondialdehyde, reactive oxygen and nitrogen species), gut microbiota composition, immunohistochemistry for tyrosine hydroxylase, and physiological variables such as body weight, intestinal length, fecal water content, and ash levels were assessed. Paraprobiotic administration enhanced antioxidant defenses, reduced oxidative damage in brain and intestinal tissues, preserved dopaminergic neurons within the nigrostriatal pathway, improved fecal hydration (indicating constipation relief), and decreased fecal mineral content, suggesting improved nutrient absorption. Notably, modulation of gut microbiota, including an increased abundance of beneficial families (Lactobacillaceae and Sutterellaceae) and a reduced abundance of potentially harmful families (Clostridiaceae and Peptostreptococcaceae), may have contributed to oxidative stress attenuation, preservation of gut health, and prevention of dopaminergic neuron loss. Collectively, these findings suggest that paraprobiotics may modulate microbiota composition and oxidative stress in both intestinal and brain tissues, and may attenuate dopaminergic neurodegeneration in an experimental model of PD.},
}

@article {pmid42106160,
year = {2026},
author = {Wang, Y and Liu, J and Verbeke, K and Retamal, NG and Akkerman, R and de Vos, P},
title = {Dietary fiber and GLP-1 receptor agonists in obesity management: converging mechanisms, interactions, and strategies for durable weight control.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100647},
doi = {10.1016/j.advnut.2026.100647},
pmid = {42106160},
issn = {2156-5376},
abstract = {Glucagon-like peptide-1 receptor agonists (GLP-1RAs) have transformed the management of obesity by producing substantial and durable weight loss. However, gastrointestinal adverse effects, including nausea, vomiting, and constipation, are a common, dose-dependent, and frequent cause of discontinuation. Furthermore, weight regain is typical after drug withdrawal, reflecting the chronic and relapsing nature of obesity. Long-term adherence is essential but often constrained by high cost, injection burden, and patient preference. Moreover, the consequences of chronic GLP-1 receptor activation on gut physiology, microbiota composition, and immune tolerance remain incompletely defined. In parallel, dietary fibers offer a physiological means of engaging the same gut-brain axis through microbial fermentation and the stimulation of endogenous GLP-1. Fibers deliver broad benefits as they strengthen gut barrier function, enrich short chain fatty acid, and recalibrate immunity toward an anti-inflammatory state. Nevertheless, weight loss with fiber alone is typically more modest than with GLP-1RAs and depends on the type, dose, and duration of use. Tolerability can be limited by bloating or gas, particularly if intake is increased too rapidly. This review critically examines the convergence and divergence between GLP-1RAs and dietary fibers. We discuss their mechanistic overlaps in appetite control, metabolism and immune modulation, and highlight potential interactions, such as altered fermentation dynamics during pharmacological slowing of gastric emptying and the potential for GLP-1R desensitization. We explore opportunities for fibers to mitigate GLP-1RA-related adverse effects, support bowel regularity, and stabilize the microbiota during treatment or after discontinuation. A pragmatic framework is raised to place dietary fiber and lifestyle measures as the foundation of care, reserves GLP-1RA therapy for highest-risk individuals, and plans for fiber supplements once pharmacotherapy is reduced. Well-designed trials that combine GLP-1RAs with well-characterized fibers, include microbiome end points, and assess long-term outcomes are needed to optimize efficacy and reduce dependence on costly pharmacotherapy.},
}

@article {pmid42106331,
year = {2026},
author = {Davin, ME and Ortís Sunyer, J and Delgado, LF and Tavis, SL and Lowndes, T and Zafar, Z and Caussin, J and Halder, R and Hickl, O and Laczny, CC and Hanslian, E and Koppold, DA and Rajput-Khokhar, A and Steckhan, N and Schade, S and Schneider, J and Mollenhauer, B and Michalsen, A and May, P and Hettich, RL and Wilmes, P},
title = {High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72762-5},
pmid = {42106331},
issn = {2041-1723},
support = {863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Graduate Research Fellowship Program//National Science Foundation (NSF)/ ; },
abstract = {Small open reading frames (smORFs), which encode proteins under 100 amino acids, represent an underexplored dimension of the human gut microbiome, despite growing evidence of their essential biological roles. Due to small size and poor annotation, smORFs are typically excluded from metagenomic/metaproteomic analyses. Here, we present a high-resolution multi-omic workflow that integrates smORF prediction into metaproteome searches and enables ultra-deep detection of smORF-encoded proteins (SEPs), without experimental size-based enrichment, utilizing state-of-the-art mass spectrometry instrumentation. Applied to human gut microbiomes, this approach resulted in the largest number of detected SEPs to date, allowing identification of over 25,000 SEPs in the metaproteome, alongside the measurements of the larger proteins. Our multi-omics integrative strategy is critical for advancing human metaproteome research. It also provides a generalizable strategy for comprehensive SEP discovery across diverse microbial ecosystems greatly expanding the previously hidden proteomic landscape.},
}

@article {pmid42106335,
year = {2026},
author = {Xue, H and Godneva, A and Tang, F and Li, H and Li, Y and Hu, M and Li, R and Su, J and Segal, E and Razzak, I},
title = {Population-scale characterization of the oral microbiome and associations with metabolic health.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-72748-3},
pmid = {42106335},
issn = {2041-1723},
abstract = {The oral microbiome may capture system-specific information about host metabolic health, yet large-scale, multi-system evidence remains scarce. We analyzed 9,431 participants in the Human Phenotype Project (HPP), integrating buccal-swab oral whole metagenome profiles with 44 metabolic measures spanning liver ultrasound, continuous glucose monitoring (CGM), and dual energy X ray absorptiometry (DXA). Here we show that using a microbiome-wide association study (MWAS) framework, we constructed a multilayer map across strains, gene families and pathways, revealing widespread associations: 213 strains, 124,603 gene families and 299 pathways were significantly associated with metabolic measures. Prioritizing the strongest and cross-phenotype signals, we identified multiple oral features with most significant associations to metabolic health. For example, acyl carrier protein (ACP) was associated with lower liver inflammation and reduced adiposity, whereas polyamine biosynthesis and ceramide α oxidation tracked higher glucose variability and adverse liver and adiposity phenotypes. Leveraging these MWAS-derived signals, we trained disease classification models using phenotype-selected oral features, which outperformed full-feature oral models across six metabolic diseases. These association signals were also robust in oral-health sensitivity analyses in HPP, and key BMI and waist-circumference associations directionally replicated at the genus level in an independent cohort (n = 20, 293). Together, these findings provide a population-scale oral-metabolic association map and highlight the potential of oral microbial markers as non-invasive tools for metabolic risk stratification.},
}

@article {pmid42106361,
year = {2026},
author = {Sun, Y and Wu, S and Wu, Z and Zhu, W and Gao, H and Xing, J and Zhao, J and Fan, X and Su, X},
title = {Instance-based transfer learning enables cross-cohort early detection of colorectal cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01001-y},
pmid = {42106361},
issn = {2055-5008},
support = {2021YFF0704500//National Key Research and Development Program of China/ ; 20251ZDYF020482//Innovation Yongjiang 2035 Key R&D Programme/ ; },
abstract = {Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent differences between groups in microbial signatures provide the fundamental basis for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability and advances the application of non-invasive approaches for the early screening and prevention of CRC.},
}

@article {pmid42106371,
year = {2026},
author = {Shi, X and Hu, Y and Wang, C and Hua, G and Liu, S},
title = {Gut microbiota and their role in male reproductive health.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00845-0},
pmid = {42106371},
issn = {2396-8370},
support = {No. 2023YFD1300604)//the National Key R&D Program of China/ ; },
abstract = {The gut microbiota, as the "second genome" of the human body, plays a central regulatory role in maintaining host physiological homeostasis; conversely, its dysbiosis can impair male reproductive function via the "gut-testis axis", leading to a series of pathological manifestations such as abnormal semen quality, sexual dysfunction, and reproductive organ damage. Gut microbiota exerts multidirectional effects on host metabolism, immunity, endocrinology, and the neural system, collectively forming a complex regulatory network for male reproduction. Among these, microbiota-derived metabolites such as short-chain fatty acids (SCFAs), serotonin (5-HT), and secondary bile acids, function as systemic signaling molecules that exert direct and indirect effects on the testis through blood circulation and modulation of gut barrier integrity, regulation of systemic inflammation, epigenetic reprogramming, respectively. The potential and limitations of microbiota-targeted intervention strategies, including probiotics, prebiotics, synbiotics, traditional natural herbal extracts, and fecal microbiota transplantation (FMT), are also discussed. Finally, we propose that future interventions should be tailored to individual gut microbiota profiles to achieve precise regulation of male reproductive function. This review aims to provide a new systems biology perspective for understanding the complex etiology of male infertility and to lay a theoretical foundation for the development of innovative microbiome-based diagnostic tools and therapeutic strategies.},
}

@article {pmid42106412,
year = {2026},
author = {Guo, L and Holyoak, GR and DeSilva, U},
title = {Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49532-w},
pmid = {42106412},
issn = {2045-2322},
abstract = {The Earth's estimated 10[31] virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.},
}

@article {pmid42106741,
year = {2026},
author = {Chopra, S and Madokoro, N and Bal, M and McNagny, KM},
title = {Prenatal training grounds: the developmental origins of chronic immune disease.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08213-y},
pmid = {42106741},
issn = {1479-5876},
support = {PJT-518208//Institute of Infection and Immunity/ ; PJT-4488212//Institute of Infection and Immunity/ ; MRT-168048/CAPMC/CIHR/Canada ; MRT168044/CAPMC/CIHR/Canada ; Vanier Canada Graduate Scholarships/CAPMC/CIHR/Canada ; },
abstract = {BACKGROUND: Immune cells seed tissues in orchestrated waves beginning in utero. While the impact of prenatal environmental exposures is well-documented in neuroimmunology, the influence of maternal-fetal interactions on systemic immune development and its contribution to lifelong chronic inflammatory disease remains underappreciated.

MAIN BODY: This narrative review synthesizes recent ontogeny data to demonstrate how diverse prenatal cues, ranging from maternal infection to microbial-derived metabolites, function as a "prenatal training ground" for the developing fetal immune system. These maternal signals interact with specific waves of hematopoiesis to shape long-lived tissue-resident immune cells. In many tissues, these prenatally programmed populations persist into adulthood, acting as lifelong immunological rheostats that dictate the type and intensity of local inflammatory responses. Furthermore, we critically evaluate the translational gaps in the field, highlighting fundamental species-specific differences in developmental timelines that necessitate careful alignment between preclinical animal models and human biology.

CONCLUSIONS: We propose that many chronic immune conditions are not strictly adult-onset in their etiology, but rather adult-manifesting, making prenatal immune seeding a critical, yet overlooked, determinant of long-term health. Current interventions largely focus postnatally, but reorienting research and clinical focus toward prenatal factors provides new insights into the developmental origins of chronic inflammation and offers a novel therapeutic window to optimize the health trajectory of the next generation.},
}

@article {pmid42106848,
year = {2026},
author = {Knapp, DG and Nagy, A and Badalzadehe, E and Molnár, A and Kroon, J and Romeralo, C and Diez, JJ and Witzell, J},
title = {Microbiome legacy influences necrosis formation in Diplodia sapinea-infected Scots pine shoots.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00904-9},
pmid = {42106848},
issn = {2524-6372},
abstract = {BACKGROUND: Fungal endophytes are important members of the holobiont of all plants, including that of Scots pine (Pinus sylvestris), potentially affecting host performance. One of the most important pathogens of Scots pine in Europe is Diplodia sapinea, which causes necrotic lesions and is becoming increasingly prevalent in northern regions. Although endophytes are known to affect plant performance, it remains unclear whether naturally established fungal communities in Scots pine shoots can modulate D. sapinea-induced necrosis. Using a field experiment, we tested the hypothesis that exclusion of airborne fungal inoculum shapes the endophytic community in shoots of pine seedlings, and that such alterations in this community influence the necrosis-inducing capacity of D. sapinea.

RESULTS: In the field site, airborne fungal inoculum was reduced in half of the saplings by covering shoots with mesh bags. Covered (bagged) and free (unbagged) shoots were transported to the laboratory and inoculated with D. sapinea. The morphology and physiological status of the shoots were monitored using a multispectral 3D scanner, and the necrotic lesion development was assessed. The propagule exclusion resulted in endophytic communities with slightly lower richness, while shoots showed no detectable morphological or physiological differences prior to inoculation. Shoots inoculated with D. sapinea developed clear necrotic lesions, which were significantly larger in covered shoots than in the free ones. Long-read Oxford Nanopore metabarcoding revealed that community shifts following inoculation were more pronounced in covered shoots. Community composition clearly separated necrotic and healthy tissues.

CONCLUSIONS: Our findings suggest that the structure of the resident fungal endophytic community may influence the extent of necrotic lesions caused by D. sapinea in Scots pine shoots. A more established, diverse fungal community was associated with smaller lesion sizes, whereas shoots exposed to lower propagule pressure developed larger lesions following inoculation. These results highlight the functional role of fungal community assembly in shaping disease outcomes and suggest that endophyte-based approaches may provide new opportunities for improving disease resistance in forest tree species. The results also suggest that endophytic status may need to be considered when lesion size is used to evaluate resistance to pathogens in tree breeding programs.},
}

@article {pmid42106858,
year = {2026},
author = {Turnlund, AC and O'Brien, PA and Rix, L and Ferguson, S and Webster, NS and Diaz-Pulido, G and Wahab, MA and Lurgi, M and Vanwonterghem, I},
title = {Insights into the role of crustose coralline algae microbiomes on coral larval settlement in the Great Barrier Reef.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00907-6},
pmid = {42106858},
issn = {2524-6372},
abstract = {BACKGROUND: Crustose coralline algae (CCA) enhance coral recruitment, but the response of coral larval settlement to CCA varies between CCA species. Furthermore, it is unclear whether coral larvae respond to settlement cues from the algal host itself or its associated microorganisms. To determine whether CCA-derived settlement cues have a microbial origin, we interrogated the microbiome of 14 coralline algal species and a calcareous non-coralline alga eliciting varying levels of settlement across 14 coral species from a wide diversity of families found in the Great Barrier Reef.

RESULTS: Linear regression, differential abundance, indicator species, and random forest analyses were used to identify microbial taxa associated with high or low coral settlement. We found that the relative abundance of specific microbial amplicon sequence variants (ASVs) correlated with settlement and that these responses were largely coral species-specific. A select few microbial taxa associated with high or low settlement were shared across the corals Dipsastrea favus, Echinophyllia aspera, Lobophyllia corymbosa, Mycedium elephantotus, and Platygrya sinensis, suggesting potential shared settlement or inhibition cues. While shared ASVs associated with high coral settlement were found across multiple CCA species, low settlement ASVs were confined to few low settlement CCA species. Candidatus Nitrosopumilus and Filomicrobium microbes were found as potential shared microbial inducers, and members of Pirellulaceae and Flavobacteriaceae were identified as potential settlement inhibitors.

CONCLUSIONS: These findings contribute to our growing knowledge of potential coral larval settlement cues and provide deeper insights into the link between the CCA microbiomes and coral recruitment.},
}

@article {pmid42107197,
year = {2026},
author = {Soleimani, RA and Abdoli, A and Milani, PG and Khani, N and Homayouni-Rad, A},
title = {Antiviral activity of postbiotics from Bifidobacterium animalis subsp. lactis BB-12 and Lacticaseibacillus rhamnosus GG against SARS-CoV-2: In-vitro and food model evaluation.},
journal = {Enzyme and microbial technology},
volume = {199},
number = {},
pages = {110899},
doi = {10.1016/j.enzmictec.2026.110899},
pmid = {42107197},
issn = {1879-0909},
abstract = {The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has presented ongoing global health, economic, and societal challenges. In addition to respiratory complications, increasing evidence suggests that disruptions to the gut microbiota may influence disease susceptibility and severity, highlighting the importance of microbiome-based interventions in supporting host immunity. While probiotics have been widely explored for their immunomodulatory and antiviral effects, limitations regarding their stability and safety under certain conditions remain a concern. Postbiotics, defined as non-viable microbial metabolites, secreted factors, and ultrasonicated bacterial lysate components, represent a promising alternative due to their enhanced safety profile, stability, and emerging antiviral properties. This study investigated the antiviral efficacy of postbiotics derived from Lacticaseibacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB-12 against SARS-CoV-2 using Vero E6 cells cultures. Furthermore, a novel food-based antiviral model was developed by incorporating postbiotic supernatants and ultrasonicated bacterial lysate at a concentration of 1500 μg/mL into a yogurt matrix. The postbiotic-enriched yogurt achieved a 1.87-2.48 log10 reduction in viral titer against the Wuhan strain of SARS-CoV-2 in vitro. These findings support the potential of postbiotics as functional food ingredients for viral risk reduction and contribute to the advancement of microbiome-derived antiviral strategies.},
}

@article {pmid42107297,
year = {2026},
author = {Petrović, M and Bez, C and Janakiev, T and Kruščić, K and Bertani, I and Ćurčić, Ž and Duduk, N and Duduk, B and Venturi, V and Dimkić, I},
title = {Development of bioformulations for sugar beet growth promotion and resilience using tailored microbial consortia.},
journal = {Microbiological research},
volume = {310},
number = {},
pages = {128540},
doi = {10.1016/j.micres.2026.128540},
pmid = {42107297},
issn = {1618-0623},
abstract = {Sugar beet production in Serbia is increasingly threatened by the combined effects of 'Candidatus Phytoplasma solani' and Macrophomina phaseolina, a pathogen pair known to interact synergistically and cause severe root rot. To evaluate whether tailored microbial consortia can improve plant performance and stabilize the microbiome under these pressures, we tested three multi-strain inoculants (Mix1, Mix2, and Mix3) in pot and semi-field conditions. In pot experiments, Mix2 enhanced above-ground biomass, while Mix3 maintained or increased microbial diversity over time. Colonization assays and metabarcoding revealed clear differences in strain persistence, with P. polymyxa C3-36, C. pusillum ED2-6 and several Bacillus spp. establishing most consistently. Phytoplasma infection markedly reduced the native root microbiota of sugar beet, indicating a strong disruption of the natural root-associated microbial community. In response, Skermanella and Blastococcus were enriched in root tissues, while Mix3 treatment notably altered the root microbial profile by enriching oligotrophic and soil-stable taxa such as 'Candidatus Udaeobacter', 'Candidatus Solibacter', Gemmatimonas, and Acidobacteria-associated lineages (e.g., RB41, Vicinamibacterales). In the rhizosphere, sugar beet actively recruited Arthrobacter and Blastococcus, whereas bacterial inoculation with Mix3 led to the enrichment of Pseudarthrobacter, Kozakia, and Streptomyces in response to phytoplasma infection. Collectively, these results highlight a stress-responsive and compartment-specific modulation of microbiome assembly driven by both phytoplasma infection and bacterial treatment, although further optimization is required to counteract phytoplasma-M. phaseolina-driven decline.},
}

@article {pmid42107405,
year = {2026},
author = {Guo, Y and Zhou, W and Dong, M and Qiu, W and Gao, X and Ahmad, T and Farid, B and Lyu, W and Sun, L},
title = {Root-secreted aminosalicylic acid and 4,6-dioxoheptanoic acid: Dual roles in enhancing 4-nonylphenol bioavailability and regulating rhizospheric microbiota community.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142282},
doi = {10.1016/j.jhazmat.2026.142282},
pmid = {42107405},
issn = {1873-3336},
abstract = {Root exudates and rhizospheric microorganisms are key drivers of organic pollutant degradation in soil. However, the mechanisms underlying their coordinated effects are not yet fully understood. This paper analyzes the changes in the composition of Astragalus sinicus root exudates induced by 4-nonylphenol (4-NP) exposure and investigates the effects of key exudate components on 4-NP sorption-desorption, rhizospheric degradation, and soil microbial community. Metabolomic analysis indicated significant alterations in profile composition induced by 4-NP exposure, with organic acids representing the major responsive category. Specifically, aminosalicylic acid and 4,6-dioxoheptanoic acid-two pivotal organic acids-markedly enhanced 4-NP desorption from soil at a concentration of 50 μmol/L. Their addition reduced the desorption coefficient by 6.4-fold and 3.2-fold, respectively, compared to the control. A pot experiment further validated that application of the two organic acids significantly increased rhizospheric dissipation of 4-NP by 20.0-23.0% compared to soils planted with A. sinicus alone. Metagenomic analysis demonstrated that the key root exudates selectively enriched pollutant-degrading microorganisms (Pseudoxanthomonas sp. A, Cupriavidus, Rhodococcus, and Penicillium), and increased the abundance of functional genes (Cox1, ligB, ligI, and pcaF) and pathways associated with xenobiotic biodegradation. These findings indicate that specific root exudates enhance microbial degradation capacity by improving 4-NP bioavailability, providing a mechanistic basis for the targeted optimization of phytoremediation strategies for 4-NP-contaminated soils.},
}

@article {pmid42107605,
year = {2026},
author = {Pinzerato, M and Dieni, C and Giacomini, I and Cocetta, V and Bertin, W and Ghirardello, L and Amadio, E and Perin, S and Frison, C and Brun, P and Agostino, E and Trombetta, D and Smeriglio, A and Montopoli, M},
title = {From phytochemical complexity to biological function: A comparative study of Capparis spinosa fruit extracts.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {107270},
doi = {10.1016/j.fitote.2026.107270},
pmid = {42107605},
issn = {1873-6971},
abstract = {Capparis spinosa L. is a Mediterranean species traditionally used for the treatment of inflammatory and skin-related disorders and increasingly explored as a source of multifunctional ingredients for dermocosmetic applications. In this study, three commercially available C. spinosa fruit extracts obtained through different extraction strategies (two aqueous extracts, CAP1 and CAP2, and one hydroalcoholic extract, CAP3) were comparatively investigated using an integrated phytochemical and biological approach. Phytochemical profiling by LC-DAD-ESI-MS/MS. revealed a complex composition dominated by flavonol glycosides (mainly quercetin- and kaempferol-based derivatives), phenylpropanoid esters, and glucosinolates, which define the core chemical signature of caper fruits. While the extracts shared a largely overlapping qualitative profile, marked differences in relative metabolite abundance were related to the extraction solvent, the drug-to-extract ratio, and formulation parameters. The biological relevance of the extracts was evaluated using skin-related cellular models and antimicrobial assays. All extracts showed good cytocompatibility in human keratinocytes and preserved epithelial barrier integrity. Distinct, concentration-dependent effects were observed on intracellular ROS modulation, UVB-induced cellular senescence, collagen type I production in dermal fibroblasts, and antimicrobial activity. CAP1 exhibited the most pronounced antioxidant and antimicrobial effects, CAP2 showed intermediate and balanced activity, whereas CAP3 displayed a more complex redox behaviour combined with marked anti-senescent activity. Overall, these findings demonstrate that extraction strategy critically influences the biological performance of C. spinosa fruit extracts and support their potential as multifunctional dermocosmetic ingredients targeting skin homeostasis, photoaging, and the balance of the skin microbiome (including bacterial and fungal components).},
}

@article {pmid42107800,
year = {2026},
author = {Wu, R and Ma, Y and Wang, Y and Liang, Q and Gao, L and Hou, L},
title = {Polymer-environment interplay drives microplastic degradation in a surface-flow wetland: New insights into bacterial assembly, network structure, and function across aquatic and sedimentary habitats.},
journal = {Bioresource technology},
volume = {455},
number = {},
pages = {134839},
doi = {10.1016/j.biortech.2026.134839},
pmid = {42107800},
issn = {1873-2976},
abstract = {It remains unclear how polymer types (petroleum- vs. bio-based) and environmental media interact to affect microplastic (MP) biodegradation in wetlands. We conducted a 120-day in situ experiment, incubating five MPs (polylactic acid [PLA], polyurethane [PU], polyethylene terephthalate [PET], polyethylene [PE], and polypropylene [PP]) in a surface-flow wetland. A distinct degradation order was observed: PU (15.2 ± 3.2% in sediment; 12.0% ± 3.9% in water) > PE (11.9% ± 2.9%; 8.2% ± 4.0%) > PLA (4.4% ± 2.2%; 5.0% ± 3.1%) ≈ PET (2.4% ± 1.5%; 7.1% ± 3.5%) ≫ PP (0.0-0.3%), showing faster degradation of most petroleum-based MPs than bio-based PLA. Integrating 16S rRNA sequencing, co-occurrence network analysis, neutral and null model analyses, we demonstrated plastisphere community assembly was governed by deterministic habitat filtering (>85% contribution) over polymer type. Functional specialization diverged between habitats, with aquatic plastispheres being enriched in nitrate reducers and aromatic hydrocarbon degraders (Nitrospira, Methyloversatilis, and Hydrogenophaga), whereas sedimentary ones were dominated by plastic/polysaccharide degraders (Psychrobacter and Microbulbifer). Co-occurrence networks contrasted sharply, being high-modularity/low-connectivity structures in water but low-modularity/high-connectivity ones in sediment. Structural equation modeling identified the plastisphere microbiome as the direct degradation driver. This degradation is enhanced by light irradiation (loadings: 0.888) in water and but is inhibited by the contents of organic matter (-0.738), DGT-labile Fe (-0.876) and S (-0.876) in sediment. These findings underscore the critical interplay between habitat and polymer type in controlling MP fate in wetlands.},
}

@article {pmid42107801,
year = {2026},
author = {Walt, HK and Smith, MB and Harris, E and McPeek, S and Meyer, F and Behmer, ST and Hoffmann, FG and Tomberlin, JK and Picard, CJ and Jordan, HR},
title = {Dietary shifts illuminate host-microbiome-diet interplay in black soldier fly larvae.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134821},
doi = {10.1016/j.biortech.2026.134821},
pmid = {42107801},
issn = {1873-2976},
abstract = {Understanding the tripartite interaction between diet, the microbiome, and host physiology is essential for optimizing the bioconversion efficiency of black soldier fly larvae (Hermetia illucens). These interactions were investigated by analyzing life-history traits and metatranscriptomes of larvae fed carbohydrate-rich (1P:5C), protein-rich (5P:1C), and balanced ratio macronutrient (1P:1C) diets. The results showed that dietary macronutrients correlated with shifts in the microbial community and gene expression. In particular, optimal larval performance, characterized by the highest weight and survivorship, was achieved on the balanced ratio diet. While the carbohydrate-rich diet increased microbial alpha diversity and enriched microbial transcripts for carbohydrate metabolism and transport, it significantly delayed pupation, reduced larval weight, and induced host immune genes related to pathogen recognition. Larval guts were predominantly composed of the fungal genus Magnusiomyces, no matter the diet, whereas the frass microbiome was primarily bacterial. In the frass, Klebsiella dominated the carbohydrate-rich diet, while Streptococcus, Lactobacillus, and Klebsiella were the most prevalent taxa in the balanced and protein-rich treatments. Significant correlations were identified between host gene expression and microbial alpha diversity and transcript expression, suggesting host-microbe crosstalk in response to nutritional stress. Ultimately, these findings demonstrate that balanced macronutrient ratios are required to synchronize host-microbiota metabolic synergy and mitigate physiological stress, providing a definitive mechanistic framework for optimizing industrial black soldier fly rearing outcomes.},
}

@article {pmid42107897,
year = {2026},
author = {Lu, W and Liu, Y and Hao, H and Li, X and Hou, G and Zhang, J and Li, W and Wang, Q and Huang, Q},
title = {Lacticaseibacillus paracasei 18 effectively ameliorates dextran sodium sulfate-induced colitis in mice through regulating gut microbiota metabolite-mediated PI3K/AKT/NF-κB signaling pathway.},
journal = {International immunopharmacology},
volume = {182},
number = {},
pages = {116807},
doi = {10.1016/j.intimp.2026.116807},
pmid = {42107897},
issn = {1878-1705},
abstract = {Ulcerative colitis (UC) is a persistent inflammatory bowel disorder marked by mucosal inflammation and dysbiosis of the gut microbiome. Lacticaseibacillus paracasei 18 (LP18) is a versatile carbohydrate-degrading bacteria that may work as a probiotic to improve gut health by modulating gut microbiota. However, its exact function and mechanisms in UC remain ambiguous. This research employed integrated microbiome, metabolome, and transcriptome analysis to investigate the therapeutic benefits and underlying mechanisms of Lacticaseibacillus paracasei on dextran sulfate sodium (DSS)-induced colitis in murine models. After the intervention of LP18, colitis mice demonstrated an improvement in body weight loss and a mitigation of colonic shortening, accompanied by a moderate increase of expressions in colonic tight junction-related genes (Claudin-1, Claudin-2, Claudin-5, ZO-1, and Occludin). Additionally, LP18 improved the structure and diversity of the gut microbiota in these DSS-induced mice. Metabolomic study suggested that LP18 substantially influenced the intestinal metabolic profile, particularly compounds associated with tryptophan metabolism. The metabolic alterations were closely linked to the enhancement of the microbial community makeup. The analysis of colon RNA sequencing indicated that, in comparison to the DSS group, LP18 significantly downregulated various immune-related signaling pathways, especially the PI3K/AKT/NF-κB pathways. Correlation analysis of microbiota, metabolism, and genes uncovered a substantial association between the taxa enhanced by LP18 and the critical genes in the NF-κB signaling pathways. Overall, the integrated analysis of multiple omics approaches revealed that LP18 may function as a probiotic therapeutic agent for UC. It represents novel dietary and therapeutic strategies for controlling UC through the regulation of gut microbiota, modification of metabolic profiles, reinforcement of the intestinal barrier, and downregulation of the PI3K/AKT/NF-κB signaling pathway.},
}

@article {pmid42108103,
year = {2026},
author = {Funatsu, O and Ishii, H and Shimatsu, R and Shimokawa, Y and Asahina, A and Dekio, I},
title = {Polyamines induce prolonged maintenance of stationary phase turbidity in coagulase-negative Staphylococcus.},
journal = {The Journal of general and applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2323/jgam.2026.04.002},
pmid = {42108103},
issn = {1349-8037},
abstract = {Microorganisms on the human skin and host form a close and complex community. Abnormal proliferation of certain commensal microorganisms can disrupt this balanced interaction, resulting in the development of skin diseases. Cosmetics is a significant factor affecting the balance of the skin microbiome. We focused a major commensal coagulase-negative Staphylococcus and evaluated the growth effect by five cosmetic ingredients including polyamines. Two polyamines showed notable effects, although others showed no impact effects. They significantly reduced the turbidity during the active growth phase and recovered in the stationary phase. During the death phase, they prolonged the stationary phase turbidity in a concentration-dependent manner, continued by the end of experiments. Our findings could be a previously uncharacterized effect under these experimental conditions.},
}

@article {pmid42108149,
year = {2026},
author = {Wang, WT and Lee, CY and Hsieh, YC and Huang, PH and Hsu, PF and Leu, HB and Lu, TM and Wang, YP and Wang, CT and Chiou, SH and Huang, SS and Luo, JC and Hou, MC and Wu, TC},
title = {Distinct gut microbiota signatures and predicted lipid metabolism pathways in Taiwanese patients with acute versus chronic coronary syndromes.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.04.127},
pmid = {42108149},
issn = {0929-6646},
abstract = {BACKGROUND: The gut microbiota plays a pivotal role in host lipid metabolism and cardiovascular health. However, comparative profiling of microbial composition and predicted metabolic functions between acute coronary syndrome (ACS) and chronic coronary artery disease (CAD) remains limited, especially in Asian populations.

METHODS: This study employed a cross-sectional microbiome analysis of prospectively enrolled patients, including 20 ACS and 22 CAD patients whose paired stool and serum samples were collected. Fecal bacterial DNA was analyzed using 16S rRNA gene sequencing. Microbial diversity and taxonomic composition were assessed using QIIME2-based pipelines. Functional predictions were performed via PICRUSt2, Tax4Fun, and BugBase, with KEGG and Clusters of Orthologous Groups (COG) annotations. Correlations with serum lipid parameters were also evaluated.

RESULTS: Distinct microbial signatures were observed between the ACS and CAD groups. In ACS, Bacteroides plebeius, Tyzzerella, and Sutterella were enriched, whereas Parasutterella and Actinobacteriota were more abundant in CAD. Several taxa were correlated with serum triglyceride, LDL, and HDL levels. Although most lipid metabolism-related pathways were comparable between the groups, nominal differences were noted in linoleic acid metabolism and the biosynthesis of unsaturated fatty acids (p < 0.05; all q > 0.05). BugBase analysis revealed a significantly greater abundance of potentially pathogenic bacteria in ACS patients (q = 0.027). The NSTI scores (mean ± SD = 0.073 ± 0.03) supported the reliability of the functional predictions.

CONCLUSIONS: Patients with ACS and CAD demonstrated distinct gut microbiota profiles, with ACS showing enrichment of pro-inflammatory and potentially pathogenic taxa. Although the predicted lipid metabolic functions are largely similar, subtle pathway differences and phenotypic traits suggest that a potential microbiota-lipid axis is associated with cardiovascular disease severity. These findings warrant further investigation in larger cohorts.},
}

@article {pmid42108153,
year = {2026},
author = {Marsh, R and Tricker, JM and Delhaes, L and Bomberger, JM and van der Gast, C},
title = {The gut microbiome: Recent findings and future opportunities in cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.05.003},
pmid = {42108153},
issn = {1873-5010},
abstract = {The gut microbiome is a key modulator of human health throughout life, from infancy to old age. Within this relatively young field, microbiome characteristics are being utilized as useful clinical endpoints and indicators of health. Moreover, microbiome-based interventions have been developed to modulate the gut microbiome to ameliorate a range of disorders, including inflammatory bowel disease, obesity, and diabetes. Conversely, there is a paucity of knowledge on the cystic fibrosis (CF) gut microbiome, despite its obvious importance in gastrointestinal (GI) symptoms in this disorder. In this short review we focus on recent findings in CF gut microbiome research and draw upon advances and knowledge from the wider field of gut microbiome research. We recommend increased efforts to improve our understanding of the CF gut microbiome, with knowledge transfer from the field of gut microbiome research being a pragmatic approach to both guiding and providing novel interventions to manage and improve CF GI pathophysiology and associated comorbidities.},
}

@article {pmid42098757,
year = {2026},
author = {Jiang, X and Zhang, C and Zhang, Y and Li, J and Ren, J and Wang, J and Hou, X and Zhang, Z and Wu, S and Yao, J},
title = {Multi-omics analysis of soy isoflavone-induced responses in rumen fermentation, endocrine status and milk production in cows with varying milk yields.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42098757},
issn = {1674-9782},
support = {2024-KFKT-011//the National Center of Technology Innovation for Dairy/ ; 32272829//National Natural Science Foundation of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; },
abstract = {BACKGROUND: Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.

RESULTS: Fifty‑six lactating Holstein cows (28 high‑yield cows, HY; 28 low‑yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2 × 2 factorial design with four experimental groups (n = 14 per group): high‑yield control (HCON), high‑yield SIF (HSIF), low‑yield control (LCON), and low‑yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+ 7.20%), dry matter intake (+ 3.20%), and feed efficiency (+ 3.26%), with larger gains in HY cows (milk yield + 8.89%; feed efficiency + 4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (- 2.70%), higher propionate (+ 4.55%), and a reduced acetate-to-propionate ratio (- 7.02%), accompanied by increased microbial crude protein (+ 21.53%) without changes in pH or NH3-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.

CONCLUSIONS: In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.},
}

@article {pmid42098796,
year = {2026},
author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V},
title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42098796},
issn = {2049-2618},
support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Università e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; },
mesh = {Humans ; Female ; *Microbiota/genetics ; *Vulva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; *RNA, Messenger/genetics ; Vagina/microbiology ; *Host Microbial Interactions/genetics ; *RNA-Seq/methods ; Transcriptome ; },
abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.

RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.

CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.},
}

Humans
Female
*Microbiota/genetics
*Vulva/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
*RNA, Messenger/genetics
Vagina/microbiology
*Host Microbial Interactions/genetics
*RNA-Seq/methods
Transcriptome

@article {pmid42098798,
year = {2026},
author = {Evens, KC and Bakke, I and Bohannan, BJM},
title = {Aquaculture facility-specific microbiota shape the zebrafish gut microbiome.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00573-6},
pmid = {42098798},
issn = {2524-4671},
abstract = {BACKGROUND: Environmental microbiomes, such as those in recirculating aquaculture systems (RAS), can play a key role in shaping host-associated microbial communities. In zebrafish (Danio rerio) research, these interactions can introduce uncontrolled sources of variation, potentially confounding experimental outcomes across multiple facilities. Despite widespread zebrafish use in microbiome studies, few have characterized the microbial composition of both tank water and fish across multiple independent facilities to evaluate the consequences of environmental microbiome variation on the host microbiome.

RESULTS: We compared water and zebrafish gut microbiomes across five aquaculture facilities two in the United States and three in Norway- using a nested sampling design and 16S rRNA gene sequencing. Alpha diversity was consistently higher in tank water than in fish guts, and beta diversity analyses revealed significant clustering by sample type, facility, and geographic location, with facility identity explaining the largest proportion of compositional variance. Multivariate dispersion also differed significantly across facilities, indicating that observed compositional differences reflect both shifts in community composition and differences in within-facility variability. Each facility harbored a distinct microbial community in both water and fish gut samples, with geographic location further structuring community composition between Oregon and Norwegian facilities. Similarity Percentage analysis identified key taxa driving facility differences, including Cetobacterium, Vibrio, and Aeromonas in fish gut microbiomes and Pseudomonas and Rheinheimera in tank water. Microbial source tracking using FEAST revealed that facility-level tank water contributed measurably to fish gut microbiome composition in most facilities, though unknown sources dominated estimates across all facilities (71-99%) and the strength of fish-water microbiome association varied substantially across facilities.

CONCLUSIONS: This study demonstrates that zebrafish aquaculture facilities harbor unique microbial communities shaped by both environmental and geographic factors. While tank water microbiomes show associations with zebrafish gut microbiome composition, the dominant contribution of unknown sources to gut microbiome composition suggests that factors beyond the immediate tank water environment- including diet, host physiology, and other facility-specific conditions- are primary drivers of gut microbiome variation. The strength of this association varied considerably across facilities and appeared related to fish domestication history, a pattern that warrants direct experimental investigation. These findings underscore the importance of incorporating environmental microbiome assessments into zebrafish experimental design, particularly for studies focused on host-microbe interactions. Without such consideration, unaccounted variation in environmental microbiota may affect microbiome composition and reduce cross-study reproducibility. Moving forward, standardized reporting of environmental conditions and microbial composition across facilities will be critical for strengthening reproducibility and interpretation in zebrafish microbiome research.},
}

@article {pmid42098855,
year = {2026},
author = {Sattayawat, P and Promubon, K and Sripinta, K and Chunguaongsuk, W and Juntama, C and Noirungsee, N and Panya, A and Disayathanoowat, T},
title = {Proof-of-concept engineering of Escherichia coli expressing a bee-derived cytochrome P450 monooxygenase for thiamethoxam detoxification.},
journal = {Journal of biological engineering},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13036-026-00686-1},
pmid = {42098855},
issn = {1754-1611},
abstract = {Bees are unintentionally exposed to pesticides applied to control other insect pests. Although bees possess endogenous detoxification mechanisms, their efficiency may not always be sufficient. To this end, the use of probiotics that can assist in pesticide detoxification may offer an additional layer of protection. In this study, we engineered Escherichia coli BL21(DE3) to heterologously express the bee-derived cytochrome P450 monooxygenase (CYP450), CYP9Q1, from Apis mellifera as a proof-of-concept microbial platform for thiamethoxam biotransformation and future microbiome-assisted pesticide detoxification strategies. We first assessed the toxicity of thiamethoxam, a systemic insecticide, on E. coli, which showed obvious impaired growth at relatively high concentrations (5 and 10 g/L). Subsequently, we computationally modeled the 3D structure and modified the CYP450 to improve its solubility when expressed in E. coli. Molecular docking of the CYP450 and thiamethoxam was also performed to confirm their potential interaction. pRSFDuet-1 plasmid was used to carry the modified CYP450 gene for expression in E. coli and the induction condition was optimized, with 0.5 mM isopropyl 𝛽-D-1-thiogalactopyranoside (IPTG) yielding the most favorable expression level. A whole-cell detoxification assay subsequently showed reduced concentrations of thiamethoxam after 46 h of biocatalytic activity, as monitored by High-Performance Liquid Chromatography (HPLC). Liquid Chromatography-Mass Spectrometry (LC-MS) analysis further revealed the presence of desnitro thiamethoxam corresponding to m/z 247.04105 confirming enzymatic transformation of thiamethoxam. To our knowledge, this study provides the first demonstration of bee CYP9Q1 heterologous expression in E. coli for whole-cell thiamethoxam biotransformation, highlighting its potential as a platform for developing probiotic or gut microbiome-based detoxification strategies to support bee pesticide tolerance.},
}

@article {pmid42098876,
year = {2026},
author = {Liu, Z and Guo, Y and Xiao, L and Guo, J and Chen, Y and Wang, H and Nan, X and Zhou, M and Zhang, F and He, Y and Yu, Z and Wang, R and Ren, Z and Wu, J and Wang, M and Tang, X and Xiong, B},
title = {Proanthocyanidins inhibit methane emissions by interacting with methyl-coenzyme M reductase and reshaping rumen microbiome function.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02406-9},
pmid = {42098876},
issn = {2049-2618},
support = {2023YFD2000703//National Key R&D Program of China/ ; 2023YFD2000701//National Key R&D Program of China/ ; 32525054//National Natural Science Foundation of China/ ; CAAS-CSSAE-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; },
abstract = {BACKGROUND: Enteric methane (CH4) emissions from ruminants are a major source of agricultural greenhouse gases and represent an energy loss to the host. Methyl-coenzyme M reductase (MCR) is the terminal enzyme in methanogenesis and represents a key target for CH4 mitigation. This study integrated computational screening, in vitro fermentation, and in vivo experiments to identify plant-derived compounds capable of reducing enteric CH4.

RESULTS: Molecular docking of 3,900 phytochemicals identified proanthocyanidins (PAC) as top candidate, exhibiting strong predicted affinity to the MCR active site (-8.150 kcal/mol). In vitro rumen fermentation assays showed that PAC supplementation reduced CH4 production by 22% while increasing dry matter degradability. In lactating dairy cows, dietary PAC supplementation (10 or 20 g/kg dry matter) decreased daily CH4 emissions by ~ 8%, and improved ruminal nitrogen utilization without affecting milk yield or ruminal volatile fatty acid production. Amplicon sequencing and metagenomic analyses revealed PAC supplementation shifts in rumen microbial community, characterized by increased relative abundance of Bacteroidota taxa and a decreased relative abundance of methanogenesis-related genes. Functional genes associated with carbohydrate, lipid, and nitrogen turnover were more abundant, indicating potential improvements in nutrient utilization. Consistent with these changes, untargeted metabolomics likewise identified shifts in metabolite profiles that may associated with alternative routes for utilizing reducing equivalents.

CONCLUSIONS: This study provides integrated computational, microbial, and physiological evidence that PAC supplementation can reduce enteric CH4 emissions in lactating dairy cows, inducing rumen microbial and functional shifts and improving nitrogen utilization. These findings support the potential of PAC as a natural approach to lowering CH4 emissions and advancing sustainable dairy production. Video Abstract.},
}

@article {pmid42098920,
year = {2026},
author = {Zhang, H and Ni, T and Zha, X and Elsabagh, M and Wang, M},
title = {The Involvement of Gut Microbiota and Their Key Metabolites in Regulating Fetal Development via the Gut-Placental Axis.},
journal = {Cellular reprogramming},
volume = {},
number = {},
pages = {21524971261450000},
doi = {10.1177/21524971261450000},
pmid = {42098920},
issn = {2152-4998},
abstract = {The gut is the organ with the largest number of microorganisms in the organism, and host-microbe interactions allow the host to shape the composition of the microbiome and thus its numbers and diversity. The gut microbiome is integral to the facilitation of vital host functions that have a direct impact on the overall health of the host. This paper aims to present a thorough overview of the composition and function of the gut microbiome and its main metabolites (such as lipopolysaccharides, short-chain fatty acids, and bile acids), as well as their key roles and mechanisms in fetal development. The theme highlights the significance of the gut microbiome in fetal development, and the paper aims to establish their relationship and importance in a systematic manner. In the latter portion of the article, an analysis is presented regarding the proposed mechanism of the gut-placental axis, with an effort to outline strategies for regulating maternal gut microbiology in order to enhance fetal growth and development. By delving into this subject matter extensively, we aim to enhance comprehension of the correlation between maternal gut microbes and fetal development. This can contribute to safeguarding the mother's health, enhancing the survival and well-being of the fetus, and carrying significance for both human and animal reproduction. Furthermore, it can provide valuable insights for future research and clinical practices.},
}

@article {pmid42099162,
year = {2026},
author = {Kurmi, S and Shirodkar, S and Parab, SB and Doshi, G},
title = {A Multimodal Framework for Alzheimer's Prevention: Diet, Exercise, Fasting, Sleep, and Gut Microbiota.},
journal = {Current Alzheimer research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672050467997260323164241},
pmid = {42099162},
issn = {1875-5828},
abstract = {Alzheimer's Disease (AD) and related dementias arise from a multifactorial interplay of genetic susceptibility, metabolic dysfunction, neuroinflammation, and lifestyle determinants. With limited disease-modifying pharmacotherapies, lifestyle interventions have emerged as compelling, evidence-based avenues for prevention and early management. This review integrates mechanistic, translational, and clinical insights on major modifiable behaviours, physical activity, diet, intermittent fasting, sleep regulation, and gut-microbiome-based approaches that collectively shape cognitive ageing. Aerobic, anaerobic, and resistance exercises exert neuroprotective effects by activating BDNF-TrkB signalling, enhancing hippocampal neurogenesis, improving synaptic plasticity, and stimulating peripheral myokines (CTSB, IGF-1, GPLD1) that cross the blood-brain barrier to support neuronal resilience. Dietary interventions such as the Mediterranean, Mediterranean- DASH Intervention for Neurodegenerative Delay (MIND), and ketogenic diets mitigate AD pathology by reducing oxidative stress, inhibiting Aβ deposition, improving mitochondrial efficiency, and modulating APOE4-linked metabolic vulnerability. Intermittent fasting induces a metabolic shift toward ketone utilisation, activates autophagy pathways (AMPK, SIRT3, Nrf2), remodels the gut microbiome, and promotes angiogenesis through GDF11 signalling. The gut-brain axis contributes to cognitive health through microbial metabolites, such as Short-Chain Fatty Acids (SCFAs), tryptophan derivatives, modulation of neuroinflammation, and enhanced neuronal survival. Meanwhile, sleep quality, particularly slow-wave sleep, optimises glymphatic clearance and prevents the pathological accumulation of Aβ and tau. Collectively, the evidence suggests that multidomain lifestyle approaches offer synergistic benefits that exceed those of individual interventions, representing promising strategies for delaying cognitive decline. However, gaps remain regarding dose-response relationships, personalised protocols for APOE4 carriers, and long-term validation in diverse populations. Strengthening these research directions is crucial for integrating lifestyle medicine into preventive neurology and public health frameworks.},
}

@article {pmid42099164,
year = {2026},
author = {Nayak, RK and Mohapatra, SR and Sahoo, SK and Sahu, SK and Chowdhury, B and Banu, Z and Das, NR},
title = {Gut Microbiota Dysbiosis in Alzheimer's Disease and Possible Therapeutic Options.},
journal = {Current Alzheimer research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672050448298260303052535},
pmid = {42099164},
issn = {1875-5828},
abstract = {Human microbiota consists of trillions of microbial cells dominated by bacteria, which live in the human body, while the term microbiome refers to the collective genetic material of microorganisms. Among them, the gut microbiota has emerged as pivotal, producing its own metabolites, neurotransmitter precursors, and immune mediators that affect brain development and function. These signals function via the complex, bidirectional Gut-Brain Axis (GBA). This is a communication network that connects the gastrointestinal tract to the central nervous system. This axis plays an important role in the regulation of gastrointestinal homeostasis, neurodevelopment, emotional regulation, and cognitive processes. Increasing evidence suggests that microbial dysbiosis within the gastrointestinal tract is involved in the pathogenesis and progression of several neurological and neurodegenerative disorders, including mood disorders, schizophrenia, autism spectrum disorder, Alzheimer's Disease (AD), Parkinson's Disease (PD), and Huntington's Disease. These insights have opened new therapeutic possibilities, and multiple microbiota-targeted interventions, such as dietary modification, prebiotics, probiotics, postbiotics, psychobiotics, antibiotics, and Fecal Microbiota Transplantation (FMT), are now being explored for their therapeutic value, especially in Alzheimer's disease.},
}

@article {pmid42099232,
year = {2026},
author = {Song, J and Cui, H and Yang, P and Xu, Y and Liu, Y and Zhang, G and Liu, Y and Tian, A and Che, J and Sun, H and Zhang, Z},
title = {Gut microbiota and its metabolites: Key factors of drug resistance in the treatment of advanced prostate cancer (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {1},
pages = {},
doi = {10.3892/mmr.2026.13900},
pmid = {42099232},
issn = {1791-3004},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; *Prostatic Neoplasms/metabolism/drug therapy/microbiology/pathology/therapy ; *Drug Resistance, Neoplasm ; Antineoplastic Agents/therapeutic use/pharmacology ; Animals ; },
abstract = {Prostate cancer (PCa) is a leading cause of cancer‑related deaths among men, and its incidence is increasing worldwide. Current treatments include androgen deprivation therapy, surgery, radiotherapy, chemotherapy and immunotherapy, among others. Surgical treatment has a less effective therapeutic effect in patients with advanced PCa. However, drug‑based treatments often lead to the development of drug resistance, highlighting the need to adopt new treatment strategies. The present review summarizes the role of gut microbiota and its metabolites in the treatment resistance of advanced PCa, potential microbiome‑targeted therapies and future research directions, for developing novel therapeutic approaches to overcome drug resistance and improve prognosis.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Male
*Prostatic Neoplasms/metabolism/drug therapy/microbiology/pathology/therapy
*Drug Resistance, Neoplasm
Antineoplastic Agents/therapeutic use/pharmacology
Animals

@article {pmid42099457,
year = {2026},
author = {Liu, Y and Zhang, Z and Wu, G and Li, B and Wang, L and Wang, J and Wei, Z and Wang, Z and Yang, J and Zhang, K and Zhang, T and Tao, X and Chen, T and Fan, J and Zhou, J and Yang, X and Zhao, L and Wei, Y},
title = {Two stable gut microbiome guilds predict liver tumor class and treatment responses.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70123},
pmid = {42099457},
issn = {2770-596X},
abstract = {Gut microbiome alterations are increasingly associated with hepatocellular carcinoma (HCC), highlighting the gut-liver axis as a key contributor to tumor progression and prognosis. Taxon-based HCC microbiome studies have shown limited reproducibility because they are affected by database dependency, taxonomic ambiguity, and overlooked ecological interactions. The Two Competing Guilds (TCG) model, based on stable gut microbiome interactions, provides a structurally grounded framework for robust, generalizable biomarkers. Using shotgun metagenomic data from a newly recruited cohort of 120 surgically resectable HCC cases and 76 benign liver tumor controls, we constructed co-abundance networks to identify stably correlated genome pairs and assembled a hepatic cancer-TCG (HCC-TCG) model composed of 142 genomes. Functionally, one Guild had more genes for butyrate production from carbohydrate fermentation while the other Guild was enriched in genes for virulence factors and antibiotic resistance, highlighting its potential proinflammatory roles. Classifiers trained on the abundance profiles of HCC-TCG genomes successfully distinguished HCC from benign liver tumors (area under the receiver operating characteristic, AUROC = 0.70) and from colorectal liver metastases (CRLM) (AUROC = 0.78). In an external validation cohort, the model further discriminated against HCC from intrahepatic cholangiocarcinoma (iCCA) (AUROC = 0.72), and from healthy controls (AUROC = 0.79-0.85), demonstrating its broad applicability for tumor stratification across clinical contexts. Moreover, HCC-TCG profiles predicted post-resection recurrence risk and response to adjuvant therapies (AUROC up to 0.83). Importantly, external validation in two independent cohorts of advanced HCC patients treated with PD-1/PD-L1 inhibitors demonstrated consistent predictive performance (AUROC = 0.64-0.73), confirming the model's generalizability in nonsurgical and immunotherapy contexts. This genome-specific, ecologically structured, and database-independent framework identifies a conserved Guild-based microbiome signature for HCC. Our findings demonstrate that a fixed genome-resolved ecological structure retains transferable discriminatory signal across clinical contexts. The HCC-TCG framework provides a genome-specific, interaction-based foundation for future development of non-invasive microbiome stratification strategies requiring prospective validation.},
}

@article {pmid42099459,
year = {2026},
author = {Bai, D and Fang, O and Li, C and Cai, B and Tan, X and Jiang, M and Gan, B and Fu, J and Gao, Y and Wang, Y and Liu, YX},
title = {Accu16S/AccuITS: Accurate and broadly applicable amplicon sequencing for absolute microbiome quantification.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70116},
pmid = {42099459},
issn = {2770-596X},
abstract = {Traditional 16S rRNA gene and Internal Transcribed Spacer region amplicon sequencing provides only relative abundance, often leading to biased ecological interpretations. To overcome this limitation, we developed Accu16S/AccuITS, an absolute quantification method for bacterial and fungal amplicons based on synthetic internal spike-in DNA with known copy numbers. By adding internal standards prior to Polymerase Chain Reaction and sequencing, absolute microbial abundances can be calculated using standard curve regression. Accu16S/AccuITS exhibits sensitivity and consistency comparable to quantitative Polymerase Chain Reaction and is applicable to diverse sample types. A single sequencing run simultaneously yields relative abundance, total absolute abundance, and taxon-specific absolute abundance. Case studies across diverse ecosystems demonstrate that absolute quantification provides ecologically and functionally meaningful insights beyond those obtained from relative abundance analyses.},
}

@article {pmid42099462,
year = {2026},
author = {Zhang, C and Du, Y and Wu, M and Li, C and Jiang, R and Qi, E and Li, S and Yi, X and Chu, B and Feng, S and Zhou, H},
title = {Spinal cord injury induces acute microbiome shock and system-wide transcriptomic reprogramming.},
journal = {iMeta},
volume = {5},
number = {2},
pages = {e70128},
pmid = {42099462},
issn = {2770-596X},
abstract = {This study investigates the systemic consequences of spinal cord injury (SCI), with a particular focus on alterations in the gut microbiome and multi-organ transcriptomic responses. We identify a rapid and severe disruption of the gut microbiota-termed "microbiome shock"-that emerges within 12 h post-SCI and persists before gradually resolving by 5 days post-injury. To support further research in this field, we established an open-access resource, the Spinal Cord Injury Gut Microbiome and Multi-Organ Gene Expression Atlas (SCIGAMA).},
}

@article {pmid42099557,
year = {2026},
author = {Cui, G and Wang, X and Hong, W and Chen, Z and Kang, Y},
title = {Beyond antibiotics: Multidimensional interventions and coordinated governance against ESKAPE resistance.},
journal = {Biosafety and health},
volume = {8},
number = {2},
pages = {81-85},
pmid = {42099557},
issn = {2590-0536},
abstract = {ESKAPE, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. pose a significant global health threat due to their extensive drug resistance and rapid evolutionary capacity. This article advocates a paradigm shift from conventional antibiotic warfare to "ecological co-management", integrating four innovative strategies plus an overarching framework: (1) microbiome-based interventions using probiotics, phages, and niche modulation; (2) a One Health 2.0 framework that incorporates wastewater surveillance and artificial intelligence (AI)-driven stewardship; (3) evolutionary constraint methods including anti-virulence agents and clustered regularly interspaced short palindromic repeats (CRISPR)-based targeting; (4) metabolic pathway intervention and antimetabolite therapy such as biotin biosynthesis inhibition; and (5) the establishment of a clinical translation and risk management system for innovative antimicrobial strategies. These multidimensional efforts aim to disrupt resistance transmission, restore antibiotic susceptibility, and promote sustainable pathogen control through ecological and systems-level integration.},
}

@article {pmid42099577,
year = {2026},
author = {Penton, CR and Vadakattu, G},
title = {The root rhizosphere as a functional analog to the gut microbiome: Cases for microbial symbiosis and dysbiosis in parallel contexts.},
journal = {PNAS nexus},
volume = {5},
number = {5},
pages = {pgag132},
pmid = {42099577},
issn = {2752-6542},
abstract = {Microbiomes associated with both the human gut and plant root rhizosphere are essential for the maintenance of host health and function as holobionts where both the host and microbiome operate as an integrated unit. Though substantial differences exist in both host biology and environment, these systems share functional parallels: both are enriched by host-derived nutrients, undergo successional shifts during development, and maintain core microbiomes that are taxonomically variable yet functionally redundant. Central to both systems is the balance that is maintained where beneficial microbes regulate nutrient cycling, modulate host immune response, and suppress pathogens in the presence of biotic and abiotic influences that may serve to disrupt this equilibrium. When dysbiosis occurs, there is a disruption in the composition and/or function of the associated microbiome and a loss of beneficial functional guilds, which results in a reduction in host fitness. These shared dynamics underscore dysbiosis as a cross-kingdom pathology that may be treated with similar interventions. Probiotics and prebiotics mirror microbial inoculants and organic amendments; synbiotics incorporate both biotic and abiotic factors, while fecal and soil microbiome transplants represent parallel strategies to restore a beneficial microbiome. By framing dysbiosis within a "One Health" perspective and illustrating the connectedness between human and plant health, this review advocates for microbial stewardship as a unifying strategy to mitigate disease, enhance resilience, and ensure sustainable health across both systems.},
}

@article {pmid42099587,
year = {2026},
author = {Xie, X and Chen, X and Wang, Z and Chen, Y and Li, J},
title = {The role of gut microbiota-immune-endocrine crosstalk in the pathogenesis of osteoporosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1813653},
pmid = {42099587},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Osteoporosis/immunology/metabolism/microbiology/etiology ; Animals ; Dysbiosis/immunology ; *Endocrine System/immunology/metabolism ; Female ; Bone and Bones/metabolism/immunology ; },
abstract = {Osteoporosis (OP) is a common metabolic bone disorder characterized by decreased bone mass and deterioration of bone microarchitecture that result in increased bone fragility and fracture risk, especially in postmenopausal women and older adults. The gut microbiota-immune-endocrine axis has recently emerged as an important regulator of bone homeostasis, but its mechanistic role in OP pathogenesis remains incompletely understood. This review synthesizes current evidence on how gut dysbiosis, immune dysregulation, and endocrine changes interact to promote bone loss. Clinical and preclinical studies indicate that gut dysbiosis in OP is characterized by reduced microbial diversity and an increased Firmicutes/Bacteroidetes ratio, leading to altered levels of key microbial metabolites-such as decreased short-chain fatty acids (SCFAs) that normally promote bone formation, and increased lipopolysaccharide (LPS) that drives inflammation. Immune changes include chronic low-grade inflammation with elevated pro-inflammatory cytokines [e.g., tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6)] and an imbalanced T-cell profile skewed toward osteoclastogenic T helper 17 (Th17) over anti-osteoclastogenic regulatory T (Treg) cells, which together favor bone resorption. Endocrine factors further modulate this gut-bone crosstalk: estrogen deficiency (in postmenopausal OP) promotes gut dysbiosis and Th17 expansion; excess glucocorticoids compromise the gut barrier and induce dysbiosis; gut-derived incretin hormones [e.g., glucagon-like peptide-1 (GLP-1) and peptide YY (PYY)] are influenced by microbial metabolites like butyrate; and parathyroid hormone (PTH) effects on bone are both regulated by and dependent on the gut microbiota. Overall, OP can be viewed as a multi-system disorder involving an interplay among the gut microbiome, the immune system, and the endocrine system. This integrated perspective on the "gut-bone axis" suggests that interventions targeting the gut microbiota (probiotics, prebiotics, etc.) could complement traditional therapies for OP. Enhancing skeletal health may require a multidisciplinary approach that considers gut microbial status, immune function, and hormonal milieu in tandem.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Osteoporosis/immunology/metabolism/microbiology/etiology
Animals
Dysbiosis/immunology
*Endocrine System/immunology/metabolism
Female
Bone and Bones/metabolism/immunology

@article {pmid42099620,
year = {2026},
author = {Mo, M and Chen, L and Wang, Y and Lin, X and Li, H and Chen, B and Yuan, J and Tao, E},
title = {The gut-lung axis in childhood asthma: from early-life programming to microbiome-informed precision medicine-a narrative review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1814901},
pmid = {42099620},
issn = {1664-3224},
mesh = {Humans ; *Asthma/microbiology/immunology/etiology/therapy ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; *Lung/immunology/microbiology ; Child ; Dysbiosis ; },
abstract = {The gut-lung axis links early-life microbial programming to long-term respiratory health, offering a pivotal framework for understanding childhood asthma pathogenesis. This review synthesizes current evidence on how disruptions in microbial-immune crosstalk during critical developmental windows shape asthma susceptibility. Perinatal determinants-including maternal diet, delivery mode, antibiotic exposure, and breastfeeding-establish gut microbial communities that educate the developing immune system. Distinguishing itself from recent reviews, this review offers three novel contributions: (i) an integrated multi-omics framework linking early-life microbial maturation trajectories to specific asthma endotypes; (ii) a systematic synthesis of the molecular mechanisms by which microbial metabolites-including short-chain fatty acids, tryptophan derivatives, and bile acids-orchestrate gut-lung immune crosstalk; and (iii) a clinically actionable precision medicine algorithm that translates multi-omics profiling into personalized risk prediction, endotype-driven therapy selection, and targeted preventive strategies. Dysbiosis, characterized by delayed microbial maturation and depletion of short-chain fatty acid-producing taxa, compromises epithelial barrier integrity and skews immune homeostasis toward pro-allergic type-2 responses. Microbial metabolites, particularly short-chain fatty acids (acetate, propionate, butyrate) and tryptophan derivatives (indole-3-lactic acid, indole-3-propionic acid), serve as key molecular mediators that regulate regulatory T cells differentiation, reinforce mucosal barriers, and modulate distal airway inflammation. Microbial signatures correlate with specific asthma endotypes, offering opportunities for patient stratification. We critically evaluate emerging microbiome-targeted interventions-including strain-specific probiotics, prebiotics, postbiotics, and fecal microbiota transplantation-highlighting both therapeutic promise and the need for rigorous, well-powered clinical trials. Integrating multi-omics microbial profiling with host genetics and clinical phenotyping holds potential for microbiome-informed precision medicine, enabling personalized risk prediction, endotype-driven therapy selection, and novel preventive strategies targeting the gut-lung axis from the earliest stages of life.},
}

Humans
*Asthma/microbiology/immunology/etiology/therapy
*Gastrointestinal Microbiome/immunology
Precision Medicine
*Lung/immunology/microbiology
Child
Dysbiosis

@article {pmid42099642,
year = {2026},
author = {Li, J and Chen, H and Zhou, Y and Sun, L and Xing, Y and Sun, Y and Yang, Y and Shi, Y},
title = {Angel or demon? The dual role of branched-chain amino acids in chronic inflammatory and injury-related diseases.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1778455},
pmid = {42099642},
issn = {1664-3224},
mesh = {Humans ; *Amino Acids, Branched-Chain/metabolism ; Animals ; *Inflammation/metabolism ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Signal Transduction ; Diabetes Mellitus, Type 2/metabolism ; Chronic Disease ; },
abstract = {Branched-chain amino acids (BCAAs)-leucine, isoleucine, and valine-are essential nutrients that exhibit context-dependent, paradoxical effects on human health, with mTORC1 (mechanistic target of rapamycin complex 1) signaling serving as a central mechanistic node through which physiological BCAA concentrations support anabolism and repair while chronic pathological elevation drives metabolic and inflammatory injury. While their anabolic properties in promoting muscle protein synthesis, modulating immune responses, and conferring hepatoprotection are well-documented, accumulating evidence demonstrates that chronically elevated circulating BCAA concentrations are strongly associated with the pathogenesis and progression of metabolic, inflammatory, and injury-related diseases, including insulin resistance, type 2 diabetes mellitus (T2DM), cardiovascular disease (CVD), metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD), and certain malignancies. This biological duality is mechanistically rooted in a network of interconnected pathological processes, in which BCAA-mediated modulation of mTORC1 signaling-already introduced above-represents one central hub operating alongside impaired catabolic flux, accumulation of branched-chain α-keto acids (BCKAs) and branched-chain acylcarnitines, mitochondrial redox imbalance, and cellular stress pathway activation. Physiological BCAA concentrations support anabolic processes and cellular repair, whereas chronic pathological elevation is associated with mTORC1 hyperactivation alongside impaired BCKDH-mediated catabolic flux, accumulation of branched-chain α-keto acids (BCKAs) and branched-chain acylcarnitines, mitochondrial redox imbalance, and activation of cellular stress pathways-collectively contributing to disrupted metabolic homeostasis, amplified inflammatory cascades, and mitochondrial dysfunction. The ultimate biological impact of BCAAs is not intrinsic to these amino acids but rather is determined by a complex interplay of factors including: dosage and duration of exposure, individual metabolic status (particularly insulin sensitivity and mitochondrial oxidative capacity), specific disease context, and genetic polymorphisms affecting BCAA metabolism alongside gut microbiome composition. This review comprehensively synthesizes current understanding of BCAA biology and advocates for a paradigm shift toward precision nutrition approaches. Evidence supports therapeutic BCAA supplementation in hypercatabolic conditions such as sarcopenia and hepatic cirrhosis, while suggesting potential adverse metabolic consequences in insulin-resistant or obese individuals. Future nutritional and therapeutic strategies should transition from universal dietary recommendations to personalized interventions based on comprehensive metabolic phenotyping and genetic profiling, thereby optimizing BCAA intake for individual health trajectories and providing novel preventive and therapeutic opportunities for chronic disease management.},
}

Humans
*Amino Acids, Branched-Chain/metabolism
Animals
*Inflammation/metabolism
Mechanistic Target of Rapamycin Complex 1/metabolism
Signal Transduction
Diabetes Mellitus, Type 2/metabolism
Chronic Disease

@article {pmid42099660,
year = {2026},
author = {Leal, F and Filho, RM and Inoue, LT and Heidrich, V and Dos Santos, EX and Bastos, DA and Camargo, AA and Jardim, DLF},
title = {Urinary microbiota diversity and composition in patients with advanced renal cell cancer.},
journal = {BJUI compass},
volume = {7},
number = {5},
pages = {e70186},
pmid = {42099660},
issn = {2688-4526},
abstract = {OBJECTIVES: This study aims to investigate the role of urinary microbiota in renal cell carcinoma; we analysed urinary microbiota in kidney cancer patients and explored its potential role as biomarker.

SUBJECTS AND METHODS: Samples were collected from 49 males (28 patients planned to undergo systemic therapy and 21 healthy volunteers). Two samples were collected from each patient, one prior to treatment and one after 8 to 12 weeks of systemic therapy. Microbiota was analysed by 16S rRNA sequencing. Microbiota diversity, taxonomic composition and relative abundance were compared between groups and longitudinal samples.

RESULTS: Amplicon sequence variant (ASV) richness was higher in renal cancer patients (p = 0.042) than controls. Beta diversity also differed between patients and controls by means of Jaccard (p = 0.001), Bray-Curtis (p = 0.008), and nonweighted UniFrac metrics (p = 0.001). Acetobacter, Lacticaseibacillus, Alloscardovia, Brevibacterium and the family Propicionibactericeae had higher relative abundance in cancer patients, while Prevotella, Microbacterium and Sphingomonas were more abundant in controls. Beta diversity differed between pretreatment and posttreatment samples (p = 0.008). After systemic treatment, we found an increased relative abundance for Prevotella, Rothia, Bradyrhizobium, Methylobacterium/Methylobrum, Porphiromonas and Fusobacterium and a decreased one for the Burkeholderia-Caballeronia-Paraburkholderia group. Higher ASV richness was predictive of poor prognosis for RCC patients (p = 0.043) but not of treatment response.

CONCLUSIONS: Urinary microbiota in patients with renal cell carcinoma differed from controls. Changes in microbiota composition were observed after systemic treatment. Urinary microbiota should be further investigated as a potential biomarker in renal cell carcinoma.},
}

@article {pmid42099859,
year = {2026},
author = {Hwang, I and Seo, M},
title = {Complex food matrices reveal microbiota-nutrient balance interactions that modulate gut microbiome diversity in vitro.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101423},
pmid = {42099859},
issn = {2665-9271},
abstract = {Diet-microbiome relationships are often evaluated using isolated nutrients, yet microbes encounter complex food matrices in which nutrient accessibility and baseline microbial community context jointly shape gut fermentation outcomes. This study integrated an in vitro digestion and gut fermentation to examine the nutrient-baseline microbiota interaction to modulate community diversity. Nutrient-defined matrix classes were grouped using free saccharides, free amino acids, and free fatty acids content in food digesta. Two machine learning models-a classification model that predicted nutrient-defined matrix class from genus-level relative abundance changes (0-12 h) and regression models that predicted α-diversity change using nutrient and baseline (0 h) community features-were developed. SHAP-based feature attribution revealed that three nutrient-defined matrix classes exhibited distinct microbial response signatures (Turicibacter/Alistipes/Staphylococcus-centered), suggesting post-digestion nutrient associations with gut microbial restructuring patterns. However, α-diversity shifts within the same nutrient class were bidirectional, and inclusion of baseline microbiota features improved model performance for predicting diversity change from R[2] = 0.34 to R[2] = 0.72, consistent with a role for baseline-nutrient interactions. Fermented food matrices further illustrated that food-associated microbial contexts can modify restructuring trajectories beyond nutrient profiles. Overall, these findings propose that diversity outcomes during fermentation may depend on baseline-conditioned responses to bioaccessible nutrients, highlighting a matrix-specific but context-dependent diet-microbiome effects.},
}

@article {pmid42099956,
year = {2026},
author = {Vigneron, M and Halary, S and Crochemore, S and Plaisance, L and Parthuisot, N and Bettarel, Y},
title = {Uncovering leaf and root microbiomes of mangrove trees in French Guiana.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1782119},
pmid = {42099956},
issn = {2813-4338},
abstract = {Microorganisms are now widely acknowledged as essential contributors to the health and resilience of coastal environments. Yet, mangrove ecosystems, despite offering numerous ecological and economic services, remain relatively overlooked in microbial research. In this study, we examined the bacteriome of the rhizosphere and the phyllosphere of two mangrove tree species: Avicennia germinans and Rhizophora mangle. Both species were sampled along the banks of the Sinnamary estuary in French Guiana. Our results revealed notable differences in microbiome composition between the two organs and between the two tree species. On average, only 0.3% of ASVs were shared between the leaves and roots and 2.2% between A. germinans and R. mangle. The taxonomic differences were characterized mainly by the significant presence of Rhodothermia and Bacteroidia in the leaves and Cyanobacteria and Planctomycetia in the roots. Furthermore, our results showed that the root microbiome of both species was only weakly influenced by the surrounding water and sediment, with an average of less than 0.7% of ASVs shared. Finally, our study indicates a strong specificity in the bacterial communities of both the phyllosphere and rhizosphere and also raises questions regarding the near absence of Gammaproteobacteria in both the leaves and roots, which remain to be elucidated.},
}

@article {pmid42099957,
year = {2026},
author = {Alali, MA and Shori, AB},
title = {Understanding the human gut microbiome: from composition to disease association.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1717288},
pmid = {42099957},
issn = {2813-4338},
abstract = {The human gut microbiota is critical for regulating host metabolism, immune responses, epithelial integrity, and systemic homeostasis, and disturbance has been linked to metabolic, inflammatory, and immune-mediated illnesses. Despite significant advances in microbiome research, the interpretation of gut microbiota-disease relationships is still limited by an overreliance on taxonomic profiling and observational study designs, which frequently overlook functional, strain-level, and mechanistic aspects of host-microbiota interactions. Growing research suggests that microbial functional capacity, metabolic activity, and ecological features such as resilience and functional redundancy are better markers of gut health than compositional measurements alone. Nonetheless, significant inter-individual variability, methodological heterogeneity, and dependence on fecal-based analysis continue to limit reproducibility and causal inference across studies. This review integrates current evidence on gut microbiota composition, functional features, and important influencing variables, while emphasizing mechanistic linkages between microbial dysbiosis and major human illnesses, filling significant conceptual gaps in modern microbiome research.},
}

@article {pmid42099988,
year = {2026},
author = {Minhajuddin, F and Colgan, SP and Cartwright, IM},
title = {Impact of Neutrophils on the Tissue Microenvironment During Intestinal Inflammation.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {540855},
pmid = {42099988},
issn = {1178-7031},
abstract = {Neutrophils (polymorphonuclear leukocytes, PMN) are abundant innate immune cells that rapidly accumulate at mucosal surfaces during inflammation. While their antimicrobial functions are essential for host defense, sustained PMN activation profoundly alters the tissue microenvironment, driving epithelial barrier disruption, ECM remodeling, metabolic imbalance, and microbiome dysbiosis. In chronic inflammatory diseases such as inflammatory bowel disease (IBD), these processes contribute to persistent tissue injury and therapeutic resistance. In this review, we synthesize evidence from human mucosal biopsies, experimental models of intestinal inflammation, and emerging single-cell, spatial, and metabolic approaches to define how PMN shape the inflamed mucosal microenvironment. We highlight mechanisms governing PMN recruitment, retention, and survival; effector programs including reactive oxygen species production, protease release, and PMN extracellular trap formation; and bidirectional crosstalk with epithelial, stromal, and immune cell compartments. We further discuss how PMN-driven metabolic and microbiome alterations reinforce chronic inflammation and influence responses to biologic therapy. Collectively, these insights reframe PMN as context-dependent regulators of mucosal pathology and repair and identify PMN-centered pathways as promising targets for precision therapies aimed at restoring barrier function and promoting durable inflammatory resolution.},
}

@article {pmid42100045,
year = {2026},
author = {Panwar, N and Stewart, JE and Ibarra Caballero, JR and Szczepaniec, A},
title = {Characterizing fungal community shifts associated with Amauromyza karli Hendel (Diptera: Agromyzidae) infestation in quinoa.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1741091},
pmid = {42100045},
issn = {1664-462X},
abstract = {INTRODUCTION: Fungal communities are central elements of phytobiomes, yet their roles in mediating plant-insect interactions remain poorly understood. Here, we addressed this knowledge gap in quinoa, which has recently suffered significant losses due to a stem-boring pest.

METHODS: We used culture-based isolation from stems and amplicon-based profiling of rhizosphere soils to characterize quinoa-associated fungi across six site-year combinations in Colorado and to relate community patterns to abundance of stem-boring fly Amauromyza karli Hendel (Diptera: Agromyzidae).

RESULTS: Eighteen stem endophytes dominated by Ascomycota were isolated. Soil sequencing resolved 23 core amplicon sequence variants detected across all site-years; the core was primarily Ascomycota, with Fusarium spp., Alternaria spp., and Plectosphaerella spp. comprising over half of relative abundance of the entire community. Alpha diversity (richness, Shannon, inverse Simpson) differed significantly among site-years, and beta-diversity analyses revealed clustering by site and year. Abundance of adult A. karli was correlated positively with soil fungal richness and Shannon diversity and was also significantly associated with differences in community composition. Indicator and differential-abundance analyses identified taxa linked to low fly abundance (e.g., Cladosporium herbarum, Alternaria spp.) versus high abundance (e.g., Fusarium solani, Microdochium spp.). Fusarium spp., and Alternaria spp. were more prevalent in fields with high larval abundance, whereas antagonistic endophytes such as Gibellulopsis piscis and Heydenia spp. dominated in low-abundance fields.

DISCUSSION: These results indicated that community composition impacted pest pressure, with pathogenic fungi coinciding with higher fly abundance and entomopathogenic fungi enriched where larval pressure was lower. These findings identify candidate taxa for microbiome-informed integrated pest management and underscore the potential of site-specific practices (e.g., intercrops, organic amendments) to foster fungal communities that enhance quinoa resilience.},
}

@article {pmid42100046,
year = {2026},
author = {Li, X and Zhao, D and Zhao, J and Li, C and Deng, W and Gao, S and Chen, G and Hu, H},
title = {Response of Morus alba L. to cadmium stress with potential for restoration: physiological and microbiological perspectives.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1795556},
pmid = {42100046},
issn = {1664-462X},
abstract = {Cadmium (Cd) contamination threatens plant productivity and the stability of soil ecosystems. However, the mechanisms by which woody plants tolerate Cd stress remain incompletely understood. In this study, one-year-old Morus alba L. saplings were exposed to a gradient of Cd concentrations to investigate plant physiological responses, metal allocation patterns, cellular ultrastructure, and rhizosphere microbial communities. Increasing Cd concentrations progressively reduced plant growth, nutrient status, pigment content, and photosynthetic performance, while oxidative stress and membrane damage increased. In contrast, low Cd exposure induced a mild hormetic response, characterized by enhanced antioxidant activity, osmotic regulation, and a temporary increase in photosynthetic capacity. Bioaccumulation indices together with ultrastructural observations revealed a dose-dependent change in Cd handling. Under lower Cd exposure, Cd was more readily translocated to shoots, whereas higher Cd levels promoted root sequestration and intracellular compartmentalization. Despite Cd treatment, rhizosphere bacterial α-diversity remained relatively stable, although several Cd-tolerant taxa increased in relative abundance. Overall, these results demonstrate the tolerance capacity of M. alba to Cd stress and highlight its potential for the phytoremediation of mildly to moderately Cd-contaminated soils.},
}

@article {pmid42100057,
year = {2026},
author = {Gimignani, G and Borello, A and Panetta, C and Lucchetti, L and Caorsi, R and Gattorno, M and Conforti, A},
title = {Age-Related Microbiota Signatures in Inflammatory Diseases: Comparative Insights into Paediatric and Adult Crohn's Disease, Ulcerative Colitis, and Spondyloarthritis.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {1},
pages = {146-155},
pmid = {42100057},
issn = {2529-198X},
abstract = {OBJECTIVES: The study investigated the relationship among the human microbiota in the development and progression of inflammatory bowel diseases (IBD), specifically Crohn's Disease (CD) and Ulcerative Colitis (UC), as well as Spondyloarthritis (SpA), comparing paediatric and adult populations.

METHODS: The research elaborated the distinct characteristics and impacts of CD, UC, and SpA across age groups. It further explored the developmental stages of the paediatric microbiota, identifying factors like delivery method, feeding, and antibiotics as critical influencers. It examined specific dysbiosis patterns in paediatric IBD and SpA associated to disease activity. Subsequently, it addressed the adult microbiota's stability and variations due to diet, lifestyle, and medications, detailing microbial alterations in adult CD, UC, and SpA.

RESULTS: A comparative analysis underscores age-related differences in microbiota composition, clinical manifestations, and treatment responses, indicating greater yet weaker microbial populations in adults. In paediatric patients, there was a marked decrease in Faecalibacterium prausnitzii and other bacteria responsible for producing short-chain fatty acids. In contrast, adults tended to show a more persistent form of dysbiosis and lower microbiome resilience. These disparities in microbial and metabolic phenotypes were strongly associated with the activity of the disease and the response to the treatment, which suggests the potential of microbiota-based biomarkers to create age-specific diagnostic and therapeutic approaches.

CONCLUSION: This research found that microbiota play a great role in the inflammatory diseases and they can be of great use in the current treatments as well as serve as a biomarker. The new targeted therapies underscored the necessity of patient specific microbiome studies to enhance diagnostics and therapies of these disorders throughout the lifespan.},
}

@article {pmid42100141,
year = {2026},
author = {Doyle, WJ and Schumacher, SM and Gates, MR and Sofaly, N and Angelo, E and Hedelius, H and Johnson, DR and Wells, J and Perlmutter, M and Caradonna, K and Ochoa-Repáraz, J},
title = {Sexual dimorphism in the colonic microbiome and host's transcriptomics profiles of a murine model of multiple sclerosis.},
journal = {Clinical immunology communications},
volume = {9},
number = {},
pages = {102-114},
pmid = {42100141},
issn = {2772-6134},
support = {P20 GM148321/GM/NIGMS NIH HHS/United States ; R15 NS107743/NS/NINDS NIH HHS/United States ; },
abstract = {BACKGROUND: Multiple Sclerosis is a chronic autoimmune disease that attacks the myelin sheath in the central nervous system, with a higher prevalence among female patients. We and others have documented significant changes in microbial taxa in response to the induction of active experimental autoimmune encephalomyelitis (EAE), an MS model.

OBJECTIVE: To evaluate sex as a biological variable in both the host and colonic microenvironment during active EAE.

METHODS: We conducted colonic transcriptomics and microbiota analysis of colonic fecal content in male and female EAE C57BL/6 J mice and controls at the time of disease induction, pre-onset, and peak disease.

RESULTS: Analysis showed significant sex-specific differences in colonic gene expression during EAE. As disease severity increased, the profiles of colon microbiome and transcriptomics became less distinct.

CONCLUSIONS: Our results suggest early changes in colonic inflammatory pathways, with notable differences between males and females associated with microbiota alterations triggered by disease induction.},
}

@article {pmid42100225,
year = {2026},
author = {Tang, Q and Qiu, D and Wen, C and Bu, Z and Huang, Y and Zou, C and Wu, H and Chen, F and Liu, L and Li, Z and Xie, X and Huang, H and Gan, K and Liu, Y},
title = {Effects of dietary rumen-degradable protein on growth performance, nitrogen metabolism, and rumen microbiome in dairy buffalo heifers.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1806578},
pmid = {42100225},
issn = {2297-1769},
abstract = {INTRODUCTION: Buffaloes are globally important dairy animals, but their low feed nitrogen utilization efficiency and excessive dietary rumen-degradable protein (RDP) results in aggravated nitrogen pollution and high breeding costs. Studies on the optimal RDP levels for 7-10-month-old dairy buffalo heifers remain scarce, limiting precise nutritional management.

MATERIALS AND METHODS: Dairy buffalo heifers (n = 36, 7-10-month-old, 193.39 ± 4.10 kg) were selected, and randomly assigned to six groups (n = 6 heifers/group, with one heifer in each replicate; Dietary RDP: 60.85-88.90 g/kg). The 73-day trial (15-day adaptation) included measurements of growth performance, nitrogen metabolism, serum indices, rumen parameters, and microbiome (16S rRNA/ITS sequencing).

RESULTS: (1) No differences in initial/final body weight or dry matter intake were found among the groups (p > 0.05). The low-RDP group (LP-1, 67.31 g/kg) had the highest average daily gain (0.79 kg/d) and lowest feed-to-gain ratio (7.88) (p < 0.05). (2) With a decrease in dietary RDP levels, intake nitrogen (IN), urinary nitrogen (UN), digested nitrogen, and UN /IN efficiency decreased (p < 0.05). The low-RDP group (LP-1) had the highest retention nitrogen/IN efficiency (32.31%) (p < 0.05). (3) The serum total protein and urea levels decreased with decreasing dietary RDP levels (lowest in LP-2: 64.52 g/L and 5.15 mmol/L, p < 0.05), with no differences in liver or kidney function or glucose-lipid metabolism (p > 0.05). (4) LP-1 had the highest rumen total volatile fatty acids, acetate, and butyrate levels (p < 0.05), while rumen pH and NH3-N decreased with RDP (p < 0.05). (5) Dietary RDP levels significantly altered the rumen microbial structure. Pichia in LP-1 was 28.81-fold and 39.68-fold higher than in HP-1 and MP-1 groups, respectively (p < 0.05), along with the presence of group-specific taxa.

DISCUSSION: An optimal dietary RDP level for 7-10-month-old dairy buffalo heifers was 67.31 g/kg, which improved the ADG and nitrogen utilization efficiency without compromising health, while also altering the rumen microbial structure. Therefore, when formulating diets for buffaloes, it is advisable to consider to note only meet the DCP requirements but also appropriately regulate the dietary RDP levels.},
}

@article {pmid42100351,
year = {2026},
author = {Hu, Y and Yan, X and Gao, F and Xu, D and Yang, Y and Cheng, J and Chen, S and Cui, Z},
title = {Probiotic-driven microbiome remodeling is associated with coordinated immune and metabolic responses, improving growth and disease resistance in farmed tongue sole (Cynoglossus semilaevis).},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100600},
pmid = {42100351},
issn = {2666-5174},
abstract = {In flatfish aquaculture, labour-intensive tank cleaning represents a major operational challenge, limiting sustainability due to its high labour requirements and associated costs. We tested a new semi-closed recirculating aquaculture system (RAS) protocol for Cynoglossus semilaevis (tongue sole), replacing manual cleaning with post-feeding water exchange (80% drained) and probiotic application. Compared with control groups, the probiotic-water exchange protocol significantly improved growth (+0.18%/day) and survival (+7.9%), while shifting the gut microbiota from a Vibrio-dominated configuration to a Photobacterium-dominated one. Metagenomics revealed that Photobacterium damselae became the predominant taxon (86%) in the probiotic group, accompanied by the enrichment of quorum sensing pathways, CAZymes (CEs, AAs), and nutrient metabolism functions. Histological examination showed improvements in the intestinal muscular layer and villi structure. Multi-tissue transcriptomics identified systemic changes in immune and metabolic pathways, including activation of intestinal immune networks (IgA production, NF-κB signaling) and antimicrobial peptide genes. Liver, gill, and skin transcriptomes revealed enhanced DNA repair, cytokine signaling, and barrier pathways. JAK-STAT pathway was also activated, linking microbial metabolite sensing to growth promotion (stat5b, igf2bp3). The probiotic-integrated protocol modifies the gut microbiome by shifting microbial composition through changes in competitive interactions and microbial signaling pathways. It also improves the intestinal wall, overall immunity, and nutrient absorption. These findings provide insights into the microbiome-host interaction under probiotic treatment and suggest that this strategy may offer potential benefits under farm conditions, but further studies are needed to validate its safety and ecological implications.},
}

@article {pmid42100398,
year = {2026},
author = {Akintola, A and Dareng, EO and Adebamowo, SN and , and Adebamowo, CA},
title = {Impact of educational intervention on the uptake of self-sampling for HPV test-based cervical cancer screening.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1810950},
pmid = {42100398},
issn = {2234-943X},
abstract = {BACKGROUND: Self-sampling for HPV testing is increasingly adopted for cervical cancer screening globally, including in Sub-Saharan Africa. However, concerns remain regarding women's willingness and ability to collect samples and the effectiveness of educational interventions. Although prior studies in Africa and Nigeria have examined acceptability and barriers, there is limited evidence on whether structured educational interventions can modify women's attitudes toward HPV self-sampling in routine screening contexts. We evaluated the effect of a structured educational intervention on women's attitudes toward self-sampling and, secondarily, explored baseline correlates of willingness to self-sample among Nigerian women.

METHODS: We conducted a single-group pre-post quasi-experimental study nested within the African Collaborative Center for Microbiome and Genomics (ACCME) prospective cohort study in central Nigeria. A total of 220 eligible women undergoing cervical cancer screening were enrolled. Baseline measurements were obtained prior to the intervention. The standardized educational intervention, delivered by trained research staff, included brochures, leaflets, an instructional video, verbal instructions, and hands-on familiarization with the Evalyn[®] self-sampling brush. Participants subsequently performed self-sampling privately at participating screening facilities. Post-intervention measurements were collected immediately after the educational session and procedure. Samples were analyzed using DEIA/LIPA HPV assays.

RESULTS: Most participants were married (63.2%), belonged to the middle socioeconomic group (69.5%), had prior knowledge of cervical cancer (61.8%), and had never undergone screening (89.5%). At baseline, 91.8% were willing to self-sample. The intervention significantly improved mean attitude scores from 42.6 (SD 8.3) to 50.8 (SD 9.8) (p<0.001). Among women unwilling to self-sample, 50.0% (9/18) were in the lower SES group compared with 12.9% (26/202) among willing participants (p<0.001). In exploratory analyses, younger age (OR 0.95, 95% CI 0.90-1.00), cervical cancer knowledge (OR 1.42, 95% CI 1.00-1.99), middle SES (OR 3.69, 95% CI 1.07-12.66), and pre-intervention attitude (OR 0.89, 95% CI 0.81-0.99) were associated with willingness.

CONCLUSIONS: A structured educational intervention significantly improved attitudes toward HPV self-sampling. Baseline willingness was high, and exploratory analysis indicate that younger age, better knowledge, and middle SES are associated with willingness. These findings support context-specific educational strategies to optimize HPV self-sampling uptake in Nigeria and similar low-resource settings.},
}

@article {pmid42100420,
year = {2026},
author = {Zhang, J and Zhi, J and Li, J and Li, L and Zhang, S and Niu, J and Wang, W},
title = {Gut microbiome restructuring in laryngeal squamous cell carcinoma identifies stable microbial biomarkers with diagnostic potential.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1788705},
pmid = {42100420},
issn = {2234-943X},
abstract = {BACKGROUND: Alterations in the gut microbiota have been reported in various malignancies, but its role in laryngeal squamous cell carcinoma (LSCC) remains unclear.

METHODS: This retrospective study included 101 patients undergoing laryngeal surgery (46 benign, 55 malignant). Preoperative fecal samples were collected and subjected to 5R 16S rRNA sequencing. Sequencing data were processed using DADA2 and QIIME2, followed by α/β diversity analysis, differential abundance detection (Wilcoxon test, LEfSe, random forest), and LASSO regression. Functional pathway differences were inferred using PICRUSt2.

RESULTS: There were no significant differences in α diversity metrics between groups, whereas β diversity analysis revealed significant separation between Benign and LSCC (PERMANOVA, P<0.01). Distinct community composition differences were observed: Malignant cases showed enrichment of genera such as Streptococcus and Lactobacillus, while Benign cases exhibited enrichment of genera including Bacteroides and Lachnospira. Multimethod integration identified 17 core bacterial genera, which were further refined via LASSO regression to select a stable set of genera (e.g., Streptococcus, Eubacterium, Lachnospira) capable of reliably distinguishing benign from malignant cases. The logistic regression model based on stable genera demonstrated excellent diagnostic performance (AUC > 0.8), particularly in distinguishing benign from LateLSCC. Functional prediction revealed pathway imbalances: malignant cases showed enrichment in cell wall and amino acid synthesis pathways, while benign cases favored vitamin and steroid metabolism pathways.

CONCLUSION: LSCC patients exhibit structural remodeling of their gut microbiota, characterized by distinct taxonomic and functional alterations. Stable microbial signatures holding potential as a foundation for the future development of non-invasive diagnostic and staging biomarkers, though their clinical translation necessitates further large-scale validation.},
}

@article {pmid42100577,
year = {2026},
author = {Chen, H and Chen, Y and Liu, Y and Chen, C},
title = {Oral microbiota and urinary system diseases: from mechanistic insights to clinical implications-a comprehensive review.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1803961},
pmid = {42100577},
issn = {2673-4915},
abstract = {The human oral microbiome has attracted considerable attention due to its role in oral health and potential implications for systemic diseases. Oral microbes provide real-time insights into health and disease status, making them valuable for early disease risk stratification and treatment outcome prediction. Accumulating evidence indicates that oral microbiota contribute to the pathogenesis of urinary system diseases. Notably, in pediatric populations, the oral microbiome-shaped by age, feeding patterns, and immune maturation-may modulate susceptibility to renal-related systemic conditions; clinical observations specifically link untreated early childhood caries to an increased risk of Henoch-Schönlein purpura nephritis (HSPN). This review critically appraises the existing literature to clarify the nature and magnitude of the association between the oral microbiome and urinary system diseases, including chronic kidney disease, urolithiasis, benign prostatic hyperplasia, and urologic cancers, as well as pediatric HSPN. We also analyze the potential mechanisms through which the oral microbiota are involved in the pathogenesis and progression of these relevant diseases, and explore its potential implications for the prevention, diagnosis, and management of urinary system disorders.},
}

@article {pmid42100652,
year = {2026},
author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C},
title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1799729},
pmid = {42100652},
issn = {2235-2988},
mesh = {Animals ; *Probiotics/administration & dosage ; Rats, Wistar ; Male ; Metagenomics ; Rats ; Feces/microbiology/chemistry ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Liver Failure ; Cytokines ; Ammonia/blood ; Dysbiosis ; Galactosamine ; },
abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.

METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 μg/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1×10⁸ CFU/day) and high (1×10⁹ CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.

RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6±6.8 to 512.4±48.9 U/L), AST (78.3±9.5 to 684.7±62.1 U/L), and plasma ammonia (38.9±5.2 to 128.6±14.3 μmol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7±41.6 U/L (low dose) and 248.9±32.4 U/L (high dose). Ammonia levels decreased to 86.4±9.7 μmol/L and 59.8±7.6 μmol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8±4.2 to 63.9±6.4 mM), lower ammonia (8.9±1.1 to 3.7±0.5 mM), improved intestinal barrier integrity (TEER: 462±38 to 721±44 Ω·cm²), and reduced TNF-α (214.6±22.8 to 74.9±12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.},
}

Animals
*Probiotics/administration & dosage
Rats, Wistar
Male
Metagenomics
Rats
Feces/microbiology/chemistry
Disease Models, Animal
*Gastrointestinal Microbiome
*Liver Failure
Cytokines
Ammonia/blood
Dysbiosis
Galactosamine

@article {pmid42100658,
year = {2026},
author = {Wu, J and Lu, Y and Zheng, Z and Zheng, J and Fu, Q},
title = {A primary study: high-throughput sequencing analysis of amniotic fluid microbiota in 50 high-risk pregnant women during the second trimester.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1748232},
pmid = {42100658},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology ; *Pregnancy Trimester, Second ; High-Throughput Nucleotide Sequencing ; Adult ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Amniocentesis ; *Pregnancy, High-Risk ; Gestational Age ; DNA, Bacterial/genetics ; Maternal Age ; },
abstract = {OBJECTIVE: Whether bacteria exist in the pregnancy uterus without pathological infection has long been a controversial topic. Through this study, we aim to determine whether characteristic amniotic fluid microbiota exists in the uterus of high-risk pregnant women during the second trimester.

METHODS: This study recruited high-risk pregnant women in the second trimester from September 1, 2024, to August 30, 2025, and recorded their age and gestational age. Amniotic fluid samples were obtained through amniocentesis under strictly sterile conditions, and 16S rRNA high-throughput sequencing was performed on the samples. The inclusion criteria mainly consisted of: advanced maternal age, non-invasive prenatal test results indicating chromosomal abnormalities, abnormal fetal ultrasound findings, history of adverse pregnancy outcomes, and high-risk Down syndrome screening results.

RESULTS: This study included a total of 50 high-risk pregnant women who underwent amniocentesis. The results showed that bacteria were present in all amniotic fluid samples, primarily composed of Actinobacteriota and Proteobacteria. There was no difference in amniotic fluid microbiota diversity between pregnant women under 35 years old and those 35 years or older; however, the abundances of Cutibacterium and Leifsonia differed between the two groups. A slight difference in microbiota diversity was observed between women with gestational ages below 20 weeks and those at 20 weeks or above, but no significant difference was found in microbial composition between the two groups.

CONCLUSION: There was bacterial DNA in amniotic fluid of high-risk pregnant women in the second trimester, with Actinobacteriota and Proteobacteria being the predominant phyla, showing limited correlation with maternal age or gestational age. This study provided evidence for the presence of microorganisms in amniotic fluid during pregnancy and might offer some preliminary data for future research related to eugenics and reproductive health.},
}

Humans
Female
Pregnancy
*Amniotic Fluid/microbiology
*Pregnancy Trimester, Second
High-Throughput Nucleotide Sequencing
Adult
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Amniocentesis
*Pregnancy, High-Risk
Gestational Age
DNA, Bacterial/genetics
Maternal Age