@article {pmid42960201,
year = {2026},
author = {Luo, L and Zhao, J and Zhuge, J and Fang, H and Yuan, L and Wang, J and Hua, Z and Cui, Y},
title = {BALF-mNGS-Derived Microbial Detection Profiles and Their Associations with Clinical Severity in Immunocompromised Patients with Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {657668},
pmid = {42960201},
issn = {1178-6973},
abstract = {BACKGROUND: Immunocompromised patients with community-acquired pneumonia (CAP) have heterogeneous pulmonary microbial profiles and frequently experience a severe clinical course. Whether bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS)-derived microbial features are associated with clinical severity in this population remains unclear.

OBJECTIVE: To characterize pulmonary microbial features in immunocompromised patients with CAP and evaluate their association with ICU admission and length of hospital stay (LOHS).

METHODS: This multicenter retrospective study included 1072 patients with CAP who underwent BALF-mNGS at five hospitals (August 2021-June 2025), including 362 immunocompromised and 710 immunocompetent patients. Microbial diversity, composition, and differentially enriched taxa were compared by immune status. Among immunocompromised patients, taxon-outcome associations were assessed using adjusted logistic and negative binomial regression, with sensitivity analyses additionally adjusting for antibiotic and antifungal exposure before BALF.

RESULTS: Immunocompromised patients had higher alpha diversity (P<0.001), with limited overall community separation. Five taxa were enriched: Burkholderia multivorans, Klebsiella pneumoniae, Candida glabrata, Candida tropicalis, and Streptococcus pseudopneumoniae. In primary analyses, B. multivorans abundance was associated with ICU admission (adjusted odds ratio [aOR] 1.400, 95% CI 1.088-1.801; false discovery rate [FDR]-adjusted P=0.045) and longer LOHS (adjusted incidence rate ratio [aIRR] 1.108, 95% CI 1.036-1.186; FDR-adjusted P=0.014). C. glabrata was associated with longer LOHS (aIRR 1.101, 95% CI 1.023-1.185; FDR-adjusted P=0.026). K. pneumoniae showed a nominal ICU association that did not survive FDR correction (FDR-adjusted P=0.084). After additional adjustment for antibiotic and antifungal exposure, the associations of B. multivorans and C. glabrata with longer LOHS remained significant (both FDR-adjusted P=0.044), whereas the association between B. multivorans and ICU admission did not (FDR-adjusted P=0.168).

CONCLUSION: BALF-mNGS-derived microbial features showed limited overall community differences but distinct taxon-specific associations with clinical severity. These exploratory findings require further validation before their prognostic or clinical utility can be established.},
}

@article {pmid42960262,
year = {2026},
author = {Li, Y and Zhang, H and Hu, L and Wang, H},
title = {Multi-Niche Microbiome Alterations in Endometrial Cancer: Drivers, Biomarkers and Translational Targets.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {643435},
pmid = {42960262},
issn = {1179-1411},
abstract = {Endometrial cancer (EC) is the commonest gynecological malignancy in high-income countries and one of the few solid tumors whose incidence and mortality are rising despite advances in oncological care. Conventional hormonal, metabolic and genetic risk factors fail to fully explain EC tumorigenesis, and the multi-niche human microbiome has emerged as a novel, modifiable regulatory axis governing EC onset, progression and immunotherapy responsiveness. However, existing reviews have largely examined individual anatomical sites in isolation, and a cross-compartment synthesis that integrates the gut, cervicovaginal, uterine cavity, and intratumoral niches-together with their mechanistic and therapeutic implications-remains lacking. This narrative review screened English articles from PubMed, Web of Science, Scopus and Google Scholar using keywords covering EC, microbiome, reproductive tract microbiome alterations, the estrobolome and immune checkpoint inhibitors (ICIs), prioritizing prospective cohorts, clinical trials and multi-omics mechanistic studies. We synthesize evidence across four interconnected niches and integrate them into a unified mechanistic framework. Reproducible compartmental signatures characterize EC: cervicovaginal samples show severe Lactobacillus depletion and enrichment of pathogenic anaerobes including Porphyromonas, Prevotella and Atopobium; malignant endometrial tissues display elevated α-diversity dominated by Anaerococcus, Peptoniphilus and Gardnerella, together with poorly explored fungal community shifts; the intratumoral niche harbors distinct taxa that directly modulate tumor proliferation, immune evasion and therapeutic responsiveness; and gut microbiome alterations deplete short-chain fatty acid-producing Firmicutes while expanding β-glucuronidase-rich Enterobacteriaceae, driving estrogen reactivation via the estrobolome and systemic pro-tumor inflammation. The PRIMMO trial further validates gut microbial clusters as predictive biomarkers of pembrolizumab efficacy in recurrent EC. By positioning the intratumoral microbiome as a distinct niche and linking multi-niche alterations to hormonal, inflammatory, immunological and genotoxic pathways, this review provides a new cross-compartment perspective that reframes the microbiome as both a mechanistic contributor and a translational target in EC. Standardized analytical workflows and large-scale prospective cohorts are urgently needed to translate these discoveries into routine clinical practice.},
}

@article {pmid42960341,
year = {2026},
author = {Prokopenko, YA and Faizullina, EA and Serova, OV and Protsenko, SV and Mokrushina, YA and Gong, N and Zheng, H and Kuzmin, YB and Tsarapaev, PV and Malabuiok, DM and Vereveyko, YR and Smirnov, IV and Kushlinskii, NE and Zhang, H and Gabibov, AG and Terekhov, SS},
title = {Optimization of Antibiotic and Antimycotic Compositions for the Eradication of Microorganisms from Cell Cultures.},
journal = {Acta naturae},
volume = {18},
number = {3},
pages = {94-101},
pmid = {42960341},
issn = {2075-8251},
abstract = {Cell cultures underlie the vast majority of in vitro research. Despite strict sterility requirements and the availability of high-tech equipment to prevent contamination, laboratory practice remains associated with a significant risk of contamination of mammalian cell cultures with bacterial and fungal agents. According to the American Type Culture Collection (ATCC), 15-35% of cell lines are contaminated with mycoplasma, posing a high risk of cross-contamination and leading to significant distortions of the experimental data obtained using such cultures. Furthermore, microbial contamination is a major risk factor when working with cell cultures isolated from patient surgical biospecimens. Despite the availability of ready-made solutions for eradicating microorganisms and preventing cell culture contamination, the problem of antibiotic resistance is particularly relevant for such contamination, and commercially available agents are often ineffective. In this study, combinations of antimicrobial agents were selected to address two of the most common practical challenges in cell culture: (i) complete elimination of mycoplasma infection and (ii) preventing contamination of primary cell cultures with bacteria and fungi that are components of the patient microbiome. A combination of tylosin, tetracycline, ciprofloxacin, erythromycin, and chloramphenicol was shown to completely eradicate mycoplasma from infected cell cultures. A combination of levofloxacin, polymyxin B, vancomycin, meropenem, and the antifungals micafungin and voriconazole completely eliminated the risk of microbial contamination during primary culture isolation, including from complex specimens such as surgical resections from colorectal cancer patients. The selected compositions successfully combine low cytotoxicity with a broad spectrum of antimicrobial activity, allowing for their effective use in laboratory practice. Nonetheless, the principle of minimizing the use of antimicrobial agents should be strictly adhered to in order to control the spread of antibiotic resistance.},
}

@article {pmid42960423,
year = {2026},
author = {Rajan, R and Nandakumar, D and Kapoor, N},
title = {Recent advances in polyendocrine metabolic ovarian syndrome and obesity: a comprehensive review.},
journal = {Current opinion in endocrinology, diabetes, and obesity},
volume = {33},
number = {6},
pages = {257-268},
pmid = {42960423},
issn = {1752-2978},
mesh = {Humans ; Female ; *Obesity/metabolism/complications/physiopathology ; Multiomics ; *Metabolic Syndrome/metabolism/complications/therapy/diagnosis ; *Polycystic Ovary Syndrome/metabolism ; Biomarkers/metabolism ; Precision Medicine/trends ; Insulin Resistance ; },
abstract = {PURPOSE OF REVIEW: This review evaluates recent advances in polyendocrine metabolic ovarian syndrome (PMOS), emphasizing its complex association with obesity and the ongoing transition toward precision medicine. The synthesis of current evidence addresses pathophysiology, emerging biomarkers, and multiomics approaches, highlighting their potential to enhance diagnosis, risk stratification, and individualized management.

RECENT FINDINGS: PMOS is a multifactorial disorder involving insulin resistance, hyperandrogenism, genetic predisposition, gut dysbiosis, and environmental factors. Obesity intensifies metabolic and reproductive dysfunction through mechanisms including chronic inflammation, adipose tissue dysfunction, and altered gut-ovary signalling. Traditional phenotype-based classifications do not adequately capture this biological heterogeneity. Multiomics approaches that integrate genomics, transcriptomics, proteomics, metabolomics, and microbiome data have identified distinct molecular subtypes, including insulin-resistant, steroidogenic, inflammatory, and neuroendocrine clusters. Novel biomarkers, including anti-Müllerian hormone, free androgen index, and specific metabolomic and lipidomic signatures, have the potential to improve diagnostic accuracy and phenotyping.

SUMMARY: The integration of multiomics represents a pivotal advancement toward patient-centred care in PMOS by enabling early risk prediction and mechanism-based therapies. While current evidence remains largely exploratory, these developments support a shift from uniform treatment strategies to precision endocrinology, with the potential to substantially improve long-term metabolic and reproductive outcomes.},
}

Humans
Female
*Obesity/metabolism/complications/physiopathology
Multiomics
*Metabolic Syndrome/metabolism/complications/therapy/diagnosis
*Polycystic Ovary Syndrome/metabolism
Biomarkers/metabolism
Precision Medicine/trends
Insulin Resistance

@article {pmid42960740,
year = {2026},
author = {Larysz, K and Ludynia, M and Trzebny, A and Klencz, W and Malcherczyk, N and Sierka, E},
title = {Plant Identity Shapes Core Microbiomes on Green Roofs.},
journal = {Environmental microbiology reports},
volume = {18},
number = {6},
pages = {},
pmid = {42960740},
issn = {1758-2229},
support = {2020/39/B/ST10/00862//National Science Centre, Poland/ ; 119118//Student Research Grants of the European City of Science Katowice/ ; FESL.10.25-IZ.01.0369/23-003//jUŚt transition-Potencjał Uniwersytetu Śląskiego podstawą Sprawiedliwej Transformacji regionu/ ; //Director's Reserve of the Institute of Biology, Biotechnology and Environmental Protection of the University of Silesia in Katowice/ ; },
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Plants/microbiology/classification ; *Lotus/microbiology ; Ecosystem ; Soil Microbiology ; },
abstract = {Extensive green roof substrates support plant-microbe interactions that may contribute to ecosystem functioning. Yet the role of plant identity in shaping substrate-associated microbiomes remains insufficiently resolved beyond Sedum-dominated systems. We examined bacterial and fungal communities associated with three plant species representing contrasting functional groups in sterilized and non-sterilized green roof substrates, integrating taxonomic differentiation with plant functional traits and predicted metabolic pathways. Plant identity was associated with distinct microbial community patterns in sterilized and non-sterilized substrates, and these associations varied with the substrate's initial microbial state. LEfSe identified 13 discriminant fungal genera in ITS data and 65 bacterial genera in V4 data; strong discriminant taxa included Mortierella, Schizothecium, and Serendipita in fungal communities, and Sphingomonas, Brevundimonas, and Tumebacillus in bacterial communities. Lotus corniculatus showed particularly distinct plant-associated microbial patterns, while differences in predicted metabolic pathways provided a complementary functional perspective on taxonomic differentiation. Integrating plant functional traits with bacterial and fungal community analyses provided an ecological framework for interpreting plant-associated microbiome differentiation in extensive green roof substrates. Integrating plant functional traits with microbial community analyses provides an ecological framework for interpreting plant-associated microbiome differentiation in extensive green roof substrates.},
}

*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Plants/microbiology/classification
*Lotus/microbiology
Ecosystem
Soil Microbiology

@article {pmid42961031,
year = {2026},
author = {Sánchez, ICC and Margis-Pinheiro, M and Dias-Oliveira, M and Ponte, LR and Ricachenevsky, FK and Margis, R},
title = {The impact of OsASR5 on rice microbiome: Implications for nutrient cycling and stress response.},
journal = {Genetics and molecular biology},
volume = {49Suppl 3},
number = {Suppl 3},
pages = {e20250064},
pmid = {42961031},
issn = {1415-4757},
abstract = {Plant-microorganism interactions contribute to plant health by enhancing nutrient acquisition. The transcription factor OsASR5 regulates detoxification gene expression under aluminum stress in rice and is implicated as a positive regulator of responses to iron and phosphorus deficiency. Given its role in nutrient regulation, we investigated whether OsASR5 influences the assembly of the rice microbiome. In this study, we characterized the bacteria communities associated with the leaves and roots of OsASR5-RNAi rice plants compared to wild-type Oryza sativa cv. Nipponbare. Notably, OsASR5-RNAi plants showed altered bacterial beta diversity compared with wild type. The bacterial composition of OsASR5-RNAi plants differed in both organs, with decreased Desulfobacteriota and increased in Acidobacteria abundance in leaves. At the genus level, Methylobacterium, a known plant growth promoter, was less prevalent in leaves, while Magnetospirillum, associated with iron cycling, was less abundant in roots. Conversely, several bacteria were more abundant in OsASR5-RNAi plants, including Aneurinibacillus, Anaeromyxobacter, and Methylobacter, which are associated with nitrogen cycling and phosphorus solubilization. Additionally, Geobacter and Geothrix, both known for their role in metal reduction, particularly iron, were more abundant in OsASR5-RNAi plants. These suggest that OsASR5 affects plant-microbe interactions, potentially influencing nutrient cycling and plant stress responses through microbiome modulation.},
}

@article {pmid42961039,
year = {2026},
author = {Hooper, PM and Vincent, WF and Girard, C and Feil, EJ and Bass, D and Jungblut, AD},
title = {Diversity and connectivity of microbial eukaryotes in High Arctic terrestrial and aquatic ecosystems.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag096},
pmid = {42961039},
issn = {1574-6941},
abstract = {High Arctic ecosystems are being rapidly altered by climate change. Increased permafrost thaw and rainfall are making terrestrial landscapes more hydrologically active, increasing the input of organic and inorganic material into freshwater systems and freshening coastal marine ecosystems. Understanding the ecological implications of this environmental change requires an improved taxonomic and ecological resolution for less-studied microbial eukaryote communities. Microbial communities were investigated from freshwater, terrestrial, and coastal marine ecosystems on Ward Hunt Island, Ward Hunt Ice Shelf and Ellesmere Island along the coastal margin of the Last Ice Area, Canadian High Arctic. For the first time, Arctic microbial eukaryotic diversity was assessed using full-length 18S rRNA gene metabarcoding sequencing. Terrestrial microbial eukaryotic richness correlated with soil moisture, extending biogeographical patterns observed in lower latitudes. A greater connectivity between terrestrial and freshwater, than to coastal communities was identified, with a predicted input of terrestrial microbial eukaryotes into the Ward Hunt Lake microplankton. As Arctic catchments become more hydrologically active, increased transport of microbial eukaryotes may strengthen connectivity and homogenisation between terrestrial and freshwater ecosystems, while greater freshwater inputs may alter microbial diversity in adjacent coastal waters.},
}

@article {pmid42961044,
year = {2026},
author = {Chandran, S and Gibson, KE},
title = {Ligilactobacillus salivarius inhibits GII.4[P16] human norovirus replication in zebrafish larvae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0127826},
doi = {10.1128/aem.01278-26},
pmid = {42961044},
issn = {1098-5336},
abstract = {Human gut bacteria can modulate human norovirus (HuNoV) infection, underscoring the need to characterize virus-bacterium interactions. This study evaluated the effect of Ligilactobacillus salivarius on HuNoV GII.4[P16] replication using a zebrafish larva model. A GII.4[P16]-positive stool specimen was resuspended in phosphate-buffered saline (PBS), centrifuged, and the supernatant stored at -80°C. L. salivarius was grown overnight in de Man, Rogosa, and Sharpe broth, from which bacterial cells and cell-free supernatant (CFS) were collected. The overnight broth (OB), cells, and CFS were each mixed with virus suspension at a 1:1 ratio, and 3 nL were microinjected into 3-day post-fertilization larvae; controls received PBS with virus. Daily until 4 days post-infection (dpi), 2 samples of 10 pooled larvae were collected, and RNA was extracted and quantified by droplet digital PCR. Two-way analysis of variance showed that treatment and time significantly influenced viral RNA levels (P < 0.001), with a marginal interaction (P = 0.051) indicating consistent inhibitory trends across the study period. CFS-injected larvae showed replication comparable to controls (P > 0.05), peaking at 5.31 log RNA copies/larva at 1 dpi, whereas cell-containing treatments (cells and OB) significantly reduced replication (P < 0.01) throughout the 4-day period. An in vitro binding assay showed that 67% of the virus inoculum physically bound to L. salivarius. In a further comparison, both live and heat-killed bacteria reduced replication initially; live L. salivarius significantly inhibited replication at 3 dpi (P < 0.05). These findings support the hypothesis that L. salivarius physically binds to HuNoV GII.4[P16] and inhibits viral replication, highlighting its potential as a probiotic intervention for HuNoV infection.IMPORTANCENorovirus remains the leading cause of acute gastroenteritis worldwide, responsible for nearly 700 million cases and substantial economic burden annually, yet no vaccine or antiviral therapy currently exists. This study's findings are significant because they identify a specific probiotic strain, Ligilactobacillus salivarius, capable of directly binding to and inhibiting replication of a clinically relevant norovirus genotype (GII.4[P16]), which is responsible for many recent outbreaks globally. By demonstrating that live bacterial cells-not just secreted metabolites-drive this antiviral effect, the study points toward a mechanistic, cell-mediated mode of action that could inform targeted probiotic formulations. The use of a zebrafish larva model also offers a valuable, scalable in vivo system for studying norovirus-microbiome interactions, addressing a major bottleneck in norovirus research caused by the lack of robust cell culture systems. Together, these findings advance understanding of bacterium-virus interactions and support further development of probiotic-based strategies for preventing or reducing norovirus infection severity.},
}

@article {pmid42961062,
year = {2026},
author = {Lehr, K and Stegemann-Koniszewski, S and Scharlach, M and Thon, C and Lücke, E and Link, A and Schreiber, J},
title = {Changes in respiratory and gut microbiota in asthma and depression associate with disease markers.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0233426},
doi = {10.1128/spectrum.02334-26},
pmid = {42961062},
issn = {2165-0497},
abstract = {Asthma is heterogeneous and frequently accompanied by depression, affecting disease mechanisms and management. Both asthma and depression have been associated with inflammation and microbiota alterations, but their combined impact on microbial compositions remains unclear. Our exploratory study analyzed lung and gut microbiota in patients with asthma and depression to identify associations between microbiota composition and disease markers. This cross-sectional study included 20 healthy controls, 20 patients with asthma, and 20 patients with asthma and comorbid depression. Participants underwent clinical characterization and assessment of asthma control, depression, anxiety, and perceived stress. Induced sputum and fecal samples were collected for microbiota analysis, and inflammatory cytokines were measured in serum and sputum. Microbial profiling was performed using 16S rRNA gene sequencing. Lung function and FeNO levels were comparable between all groups. Asthma control scores were lower, and psychological scores were significantly higher in patients with asthma and comorbid depression compared with asthma alone and controls. Despite similar alpha and beta diversity across groups, sputum and fecal microbiota, particularly of healthy controls and comorbid patients, significantly differed in genus-level taxonomic composition. Correlation analyses demonstrated associations between clinical and psychological parameters and microbial profiles, including a consistent negative correlation between psychological scores and Neisseria abundance in both sputum and fecal samples. Asthma with comorbid depression is associated with distinct alterations in respiratory and gut microbiota, including reduced Neisseria perflava abundance correlating with psychological symptom severity.IMPORTANCEAsthma and depression frequently coexist, yet the potential contribution of microbial alterations to this comorbidity remains poorly understood. Because both respiratory and gut microbiota have been implicated in immune regulation and disease pathophysiology, characterizing microbiota patterns associated with asthma and depression may provide new insights into the biological links between these conditions. In this exploratory study, we investigated respiratory and gut microbiota in individuals with asthma, with and without comorbid depression, and healthy controls. Genus-level community composition differed between groups, particularly between controls and patients with asthma and depression. Notably, reduced abundance of Neisseria perflava in sputum and fecal samples was consistently associated with greater psychological symptom severity. These findings suggest that asthma accompanied by depression is associated with distinct alterations in microbial communities at multiple body sites. Further studies are warranted to determine whether such microbiota-psychological associations contribute to disease mechanisms or may serve as biomarkers of asthma-depression comorbidity.},
}

@article {pmid42961241,
year = {2026},
author = {Wang, Z and Huang, L and Liu, X and Cheng, X and Liang, Y and Chen, J and Ma, R and Song, W and Li, X},
title = {Pathobiont-directed mucosal immunotherapy targets Ruminococcus gnavus and remodels host-microbiota interactions in colitis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2754605},
doi = {10.1080/19490976.2026.2754605},
pmid = {42961241},
issn = {1949-0984},
mesh = {Animals ; *Ruminococcus/immunology ; *Immunotherapy/methods ; Mice ; *Colitis/therapy/microbiology/immunology ; *Host Microbial Interactions/immunology ; Immunity, Mucosal ; Intestinal Mucosa/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Humans ; Disease Models, Animal ; *Colitis, Ulcerative/therapy/microbiology/immunology ; Mice, Inbred C57BL ; Immunoglobulin A, Secretory/immunology ; Eubacteriales ; },
abstract = {Disease-associated pathobionts are recurrently enriched in inflammatory bowel disease (IBD), yet their causal contribution and selective therapeutic control remain incompletely defined. Here, through clinical microbiome profiling and causal animal studies, we identified Ruminococcus gnavus (Rg) as a key ulcerative colitis (UC)-associated pathobiont whose abundance positively correlates with intestinal oxidative stress and inflammatory levels. To selectively constrain Rg, we engineered CP-EV@Ca, an oral microbiota-directed mucosal immunotherapy that combines pathogen-specific immune targeting with redox modulation. CP-EV@Ca enhanced mucosal antigen presentation, promoted T follicular helper cell-germinal-center B-cell responses and induced robust Rg-specific secretory IgA (sIgA). CP-EV@Ca-induced mucosal immune responses, including enhanced Rg-specific sIgA production, were associated with increased immune coating and reduced Rg expansion. In both acute and chronic colitis models, CP-EV@Ca outperformed 5-aminosalicylic acid (5-ASA), suppressing inflammation and restoring microbial, epithelial and immune homeostasis. These findings demonstrate that pathobiont-specific mucosal immunity can be harnessed to selectively constrain disease-associated bacteria and restore intestinal homeostasis.},
}

Animals
*Ruminococcus/immunology
*Immunotherapy/methods
Mice
*Colitis/therapy/microbiology/immunology
*Host Microbial Interactions/immunology
Immunity, Mucosal
Intestinal Mucosa/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Humans
Disease Models, Animal
*Colitis, Ulcerative/therapy/microbiology/immunology
Mice, Inbred C57BL
Immunoglobulin A, Secretory/immunology
Eubacteriales

@article {pmid42961282,
year = {2026},
author = {Coelho, CPES and Munduri, JMS and Oliveira, JAVC and Moreira, MI and Cena, JA and Dame-Teixeira, N},
title = {From enemy to ally: an update for dental professionals on oral microbiome ecology and its systemic implications.},
journal = {Journal of applied oral science : revista FOB},
volume = {34},
number = {},
pages = {e20260384},
doi = {10.1590/1678-7765-2026-0384},
pmid = {42961282},
issn = {1678-7765},
mesh = {Humans ; *Microbiota/physiology ; *Dysbiosis/microbiology ; *Mouth/microbiology ; *Mouth Diseases/microbiology ; },
abstract = {The oral microbiome is a natural and essential component of the human body, maintaining a symbiotic relationship with the host and contributing to health. Rather than being caused simply by the presence of microorganisms, oral diseases are now understood as ecological dysbioses, in which disruption of the oral microbiome precedes and drives the development of clinical signs. This perspective challenges traditional clinical approaches, as strategies focused exclusively on detecting or eliminating specific microorganisms are unlikely to address the ecological nature of oral diseases and may, in some cases, be counterproductive. Furthermore, far beyond local effects, oral dysbiosis may have systemic repercussions. Through mechanisms such as chronic inflammation and interactions along the oral-gut axis, oral dysbiosis may influence systemic health and has been associated with cardiovascular, metabolic, neurodegenerative, and autoimmune diseases. This relationship is bidirectional: oral dysbiosis may contribute to systemic inflammatory and metabolic alterations, while systemic conditions can also modify the oral environment. As oral microbiome discoveries increasingly reach dental professionals, there is a growing need to critically translate this body of evidence into clinically meaningful concepts. This review aims to help bridge the gap between rapidly evolving oral microbiome research and everyday dental practice by providing dental professionals with an integrated ecological perspective of the oral microbiome. By synthesizing emerging concepts in microbiome homeostasis, dysbiosis, resilience, and oral-systemic interactions into clinically relevant principles, this review can support evidence-based decision-making in contemporary dentistry. The role of dental professionals in maintaining oral microbiome balance is part of a broader strategy to support both oral and systemic health. Recognizing oral diseases as ecological dysbiosis highlights the need for a shift in dental practice, in which preserving microbiome eubiosis and ecological stability becomes central to care. In dysbiosis, the microbiome becomes an enemy, so it is better kept on our side.},
}

Humans
*Microbiota/physiology
*Dysbiosis/microbiology
*Mouth/microbiology
*Mouth Diseases/microbiology

@article {pmid42961364,
year = {2026},
author = {Alghafri, M and Edwards, L and Moyes, D and Nibali, L},
title = {Antimicrobial Resistance in Periodontal Disease: Rethinking Adjunctive Therapy in the Metagenomics Era, the Pressing Need for Precision Treatment and Periodontal Resistome Mapping.},
journal = {Journal of cellular and molecular medicine},
volume = {30},
number = {21},
pages = {},
pmid = {42961364},
issn = {1582-4934},
mesh = {Humans ; *Metagenomics/methods ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Microbiota/drug effects ; *Periodontal Diseases/microbiology/drug therapy ; *Precision Medicine ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial ; },
abstract = {Systemic antibiotics are effective when used as adjunctive therapy in the treatment of periodontitis; however, their use must be balanced against antimicrobial resistance, which is a major threat to global public health. This review provides an expert synthesis of the literature and a field-level overview of antimicrobial resistance in periodontal therapy, highlighting current knowledge and emerging directions, while examining how adjunctive antibiotic protocols may contribute to resistance within the periodontal microbiome through emerging metagenomic insights. To provide this synthesis, the PubMed database was searched for English-language publications using combinations of the terms periodontitis, systemic antibiotics, antimicrobials, resistance, resistome, therapeutic adjuncts, resistance genes, susceptibility, antibacterial and drug resistance, and the findings are presented as a narrative review. The evidence indicates that a substantial proportion of patients with periodontitis harbour subgingival microbiota that are non-susceptible to at least one antibiotic used in periodontal therapy. Across the included studies, antimicrobial resistance was most frequently reported in Prevotella and Porphyromonas species, while some studies also identified virulence-associated factors in Staphylococcus aureus, a non-classical periodontal organism detected within the subgingival microbiota. Overall, current evidence indicates a high prevalence of antibiotic resistance genes in the subgingival microbiota of patients with periodontitis and highlights the ecological consequences of adjunctive antibiotic use. These findings reinforce the need to optimize antibiotic prescribing protocols within an antibiotic stewardship framework and support further metagenomic investigations to refine understanding of resistance patterns, gene-transfer mechanisms and microbiome disruption, with the aim of advancing precision-based periodontal care.},
}

Humans
*Metagenomics/methods
*Anti-Bacterial Agents/therapeutic use/pharmacology
Microbiota/drug effects
*Periodontal Diseases/microbiology/drug therapy
*Precision Medicine
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial

@article {pmid42961539,
year = {2026},
author = {Ahmad, N and Khan, NA and Shah, AA and Aziz, U and Khan, N and Zhang, L and Yuan, H and Song, Y},
title = {Phytogenic feed additives for climate-resilient camel production in arid and semi-arid regions: current evidence and research priorities.},
journal = {Tropical animal health and production},
volume = {58},
number = {8},
pages = {},
pmid = {42961539},
issn = {1573-7438},
support = {2022YFD1600101-02//Key Technologies Research and Development Program/ ; },
mesh = {Animals ; *Camelus/physiology ; *Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; *Animal Husbandry/methods ; Desert Climate ; *Food Additives ; Dietary Supplements/analysis ; Diet/veterinary ; },
abstract = {Camels play a vital role in supporting food security and livelihoods under the harsh feed, water, and environmental conditions of arid and semi-arid regions (ASARs), owing to their remarkable ability to tolerate heat stress and prolonged dehydration, travel long distances, and efficiently utilize low-quality forage resources available in these regions. Nevertheless, increasing climatic stress, coupled with fluctuating feed availability, infectious and parasitic diseases, and limited access to veterinary services, continues to constrain camel production in ASARs. Phytogenic feed additives are increasingly being explored as nutritional strategies to support foregut function, animal health, and product quality; however, the strength and directness of the available evidence for these effects in camels remain critically underexplored. This structured narrative review, grades available evidence from controlled camel studies, camel-specific mechanistic investigation, other foregut fermenters, and biologically more distant animal models. Its novel contribution is a camel-centered evidence hierarchy that separates demonstrated effects from comparative mechanisms and hypothesis-generating evidence while linking each candidate additive to specific research requirements. Potential applications include the modulation of foregut fermentation, oxidative and inflammatory status, microbial ecology, immune responses, parasite management, and milk and meat quality. However, direct camel evidence remains insufficient to establish effective doses, long-term safety, residues, sensory effects, or economic returns. Phytogenic feed additives therefore merit investigation as potential nutritional interventions, but current evidence does not support their routine use in camels. Future studies should use chemically characterized preparations, dose-response designs, clinically and economically meaningful outcomes, together with integrated assessments of foregut function, immune status, animal health, product quality, safety, and feasibility under dryland production conditions.},
}

Animals
*Camelus/physiology
*Animal Feed/analysis
Animal Nutritional Physiological Phenomena
*Animal Husbandry/methods
Desert Climate
*Food Additives
Dietary Supplements/analysis
Diet/veterinary

@article {pmid42961615,
year = {2026},
author = {Dolker, S and Ghosh, A and Singh, VK and Joshi, BD and Sharma, LK and Thakur, M},
title = {Exploring sex- and captivity-associated gut microbial diversity in Bengal Tigers (Panthera tigris tigris).},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42961615},
issn = {1573-4978},
mesh = {Animals ; *Tigers/microbiology/genetics ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Feces/microbiology ; Bacteria/genetics/classification ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Endangered Species ; },
abstract = {BACKGRO UND: The gut microbiome plays a critical role in host nutrition, immune regulation, metabolic stability, and overall physiological health in wildlife. However, gut microbiome data from large carnivores remain limited, particularly for endangered tiger populations. This study conducted a comparative analysis of fecal microbiomes from captive and wild Bengal tigers, integrated with publicly avai lable datasets from Amur, Malayan, and South China tigers, to understand how captivity and host factors influence microbial assembly. ME THOD S AND RESULTS: Across all tiger subspecies, Firmicutes and Proteobacteria dominated as core bacterial phyla, with Actinobacteriota, Bacteroidota, and Fusob acteriota forming a conserved microbial backbone. Wild Bengal tigers exhibited higher microbial richness and diversity than captive tigers . Beta diversity analyses demonstrated clear clustering by habitat (captive versus wild), but substantial overlap between male and female captive Bengal tigers, indicating that captivity-associated conditions exert influences on gut microbiome structure than sex. Comparative analyses among tiger subspecies revealed broad overlap in microbial community composition, suggesting limited phylogenetic influence. South China and Amur tigers displayed the lowest richness compared to Bengal and Malayan tigers. Furthermore, analysis identified an enrichment of protein fermentation-associated taxa in captive tigers, whereas wild tigers showed a greater abundance of environmentally associated taxa. CONCLUSIONS: The study provides evidences that captivity promotes reduction in gut microbial diversity in Bengal tigers, and highlights the potential utility of microbiome-informed captive management. Integrating gut microbiome monitoring into conservation breeding, zoo exchange and reintroduction programmes may improve adaptive fitness in endangered tiger populations.},
}

Animals
*Tigers/microbiology/genetics
Female
Male
*Gastrointestinal Microbiome/genetics
Phylogeny
Feces/microbiology
Bacteria/genetics/classification
Biodiversity
RNA, Ribosomal, 16S/genetics
Sex Factors
Endangered Species

@article {pmid42961986,
year = {2026},
author = {Tractenberg, RE and Groah, SL and Newcomb, E and Khemmani, M and Joyce, C and Wolfe, AJ and Riegner, CR},
title = {Variation in urobiome composition over time in asymptomatic individuals with spinal cord injury and disease using intermittent catheterization.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0356391},
pmid = {42961986},
issn = {1932-6203},
mesh = {Humans ; *Spinal Cord Injuries/complications/microbiology ; Female ; Male ; *Urinary Tract Infections/microbiology ; *Microbiota ; Adult ; Middle Aged ; *Intermittent Urethral Catheterization ; },
abstract = {Urinary tract infection (UTI) remains the most common infectious complication among individuals with neurogenic lower urinary tract dysfunction (NLUTD) due to spinal cord injury or disease (SCI/D). Despite widespread reliance on microbiological and symptom-based criteria for UTI diagnosis, significant ambiguity persists-especially in distinguishing clinically meaningful change from normal variability in urinary analysis results. This uncertainty contributes to overdiagnosis, inappropriate antibiotic use, and antimicrobial resistance. The present study sought to operationalize "normal variability" of the urinary microbiome (urobiome) among adults with NLUTD due to SCI/D. Using repeated samples collected from asymptomatic individuals over time, we analyzed inter- and intra-individual microbial composition to determine stability and fluctuation under baseline conditions. We observed wide intra- and inter-individual variability, substantial overlap between asymptomatic and pre-symptomatic states, and a consistent predominance of genera conventionally labeled as "uropathogens" including Escherichia/Shigella, Klebsiella, Enterococcus, Staphylococcus, and Streptococcus, even in the absence of symptoms. Bray-Curtis dissimilarities between paired samples ranged from 0 to 1, confirming substantial within-person compositional change over time. These findings suggest that assumptions drawn from cross-sectional studies-linking particular taxa or diversity values to health or disease-are not supported within individuals over time, at least in people with NLUTD due to SCI/D. Empirically characterizing normal within-person variability is a prerequisite both for interpreting urobiome results in this high-risk population and for improving the accuracy and stewardship of UTI diagnosis and treatment.},
}

Humans
*Spinal Cord Injuries/complications/microbiology
Female
Male
*Urinary Tract Infections/microbiology
*Microbiota
Adult
Middle Aged
*Intermittent Urethral Catheterization

@article {pmid42961994,
year = {2026},
author = {Cho, KC and Lee, WJ},
title = {How early microbial encounters shape adult behavior.},
journal = {PLoS biology},
volume = {24},
number = {10},
pages = {e3004101},
doi = {10.1371/journal.pbio.3004101},
pmid = {42961994},
issn = {1545-7885},
abstract = {Microbes are increasingly recognized as modulators of host behavior, but the underlying mechanisms are poorly understood. A new PLOS Biology study reveals a microbiome-to-gut-to-neuron pathway linking developmental microbial exposure to later food avoidance.},
}

@article {pmid42962075,
year = {2026},
author = {Alihosseini, C and Stein, M and Madiedo, ASA and Hesari, R and Kauffman, M and Zaiac, MN},
title = {Asymptomatic Tattoo-Associated Cutaneous Nontuberculous Mycobacterial Infection: Case Report.},
journal = {JMIR dermatology},
volume = {9},
number = {},
pages = {e108587},
pmid = {42962075},
issn = {2562-0959},
mesh = {Humans ; Male ; *Tattooing/adverse effects ; *Mycobacterium Infections, Nontuberculous/etiology/drug therapy/diagnosis/pathology ; Adult ; *Skin Diseases, Bacterial/etiology/drug therapy/pathology/diagnosis/microbiology ; *Mycobacterium abscessus/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Tattoo-associated nontuberculous mycobacterial infections can present in a variety of ways, including papular, pustular, nodular, and abscess-like morphologies. We report the case of an immunocompetent 28-year-old male who presented with diffusely distributed monomorphic papules with collarettes of scale confined to recently tattooed skin. Histopathologic evaluation demonstrated an atypical lichenoid vacuolar interface dermatitis, and tissue culture ultimately confirmed infection with Mycobacterium abscessus complex following prolonged incubation. This case highlights the diagnostic challenges posed by atypical clinical and histopathologic features of tattoo-associated nontuberculous mycobacterial infections, emphasizing the importance of early biopsy, mycobacterial culture, and prolonged combination antimicrobial therapy for optimal patient outcomes.},
}

Humans
Male
*Tattooing/adverse effects
*Mycobacterium Infections, Nontuberculous/etiology/drug therapy/diagnosis/pathology
Adult
*Skin Diseases, Bacterial/etiology/drug therapy/pathology/diagnosis/microbiology
*Mycobacterium abscessus/isolation & purification
Anti-Bacterial Agents/therapeutic use

@article {pmid42962337,
year = {2026},
author = {Dias-Alves, A and Marco, I and Jasso, MV and García-Ulloa, M and Asiimwe, C and Hobaiter, C and Akankwasa, JW and Babweteera, F and Kayaga, E and Malavé, A and Migura-Garcia, L and Aguilar, XF and Martínez-Urtaza, J and Cabezón, O},
title = {Microbiome-based survey of pathogenic bacteria at the chimpanzee-human-livestock interface, Uganda.},
journal = {Veterinary microbiology},
volume = {323},
number = {},
pages = {111251},
doi = {10.1016/j.vetmic.2026.111251},
pmid = {42962337},
issn = {1873-2542},
abstract = {Anthropogenic land-use change is intensifying contact among wildlife, humans, and livestock in tropical ecosystems, increasing opportunities for cross-species transmission of infectious agents. Chimpanzees (Pan troglodytes schweinfurthii), owing to their close phylogenetic relationship with humans, are particularly susceptible to pathogen spillover. We performed a microbiome-based screening of potentially pathogenic bacteria in faecal samples from a chimpanzee-human-livestock interface in western Uganda using full-length 16S rRNA gene sequencing. A total of 21 bacterial genera, categorized as potentially pathogenic, were detected across all three studied host groups, from which several taxa of potential zoonotic or health relevance, including Clostridium perfringens, Salmonella enterica, Shigella spp., and Streptococcus suis, were detected in chimpanzees, humans, and goats. Our findings indicate an overlap in bacterial taxa across the interface. The relative abundance of potentially pathogenic bacterial taxa was descriptively lower in chimpanzees than in humans and livestock, but carried both enteric and respiratory bacterial species previously associated with disease outbreaks in captive and wild populations. These findings support integrating bacterial monitoring into conservation-oriented One Health frameworks.},
}

@article {pmid42962471,
year = {2026},
author = {Zou, D and Fu, Y and Lv, Z and Liu, Z and Huang, Z and Yan, B and Liu, J and Kuang, Y and Li, M and Lin, L and He, M and Jing, T and Huang, S},
title = {Associations of environmental phenols exposure with gut microbiota in a general population from Shenzhen, China.},
journal = {Ecotoxicology and environmental safety},
volume = {326},
number = {},
pages = {120990},
doi = {10.1016/j.ecoenv.2026.120990},
pmid = {42962471},
issn = {1090-2414},
abstract = {The gut microbiota is considered an important target for the toxicity of environmental phenols, yet the epidemiological evidence elucidating their associations in adults remains limited. This study investigated associations between phenol exposure and gut microbiota in 241 adults from Shenzhen, China. We quantified 38 urinary phenols via ultrahigh performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) and profiled the gut microbiome via shotgun metagenomics. Linear regression, permutational multivariate analysis of variance (adonis), and Multivariable Association with Linear Models 2 (MaAsLin2) were used to assess links with α-diversity, β-diversity, microbial taxa, and functional pathways. We found that exposure to environmental phenols was significantly associated with altered gut microbiota diversity, composition and function. Bisphenol C was negatively associated with α-diversity, whereas benzylparaben and ethylparaben were positively associated with it. Exposure to methylparaben, triclosan, isopropylparaben and propylparaben was significantly associated with altered gut microbial community structure. Taxa analysis showed that methylparaben was negatively associated with the relative abundance of two beneficial species, Bacteroides salyersiae and Anaerostipes caccae. Additionally, functional profiling revealed that parabens inhibited amino-acid, carbohydrate and terpenoid metabolism, whereas triclosan up-regulated pathways for aromatic compound degradation and mixed-acid fermentation. Further prospective investigations are warranted to validate our findings.},
}

@article {pmid42962555,
year = {2026},
author = {Cordova, B and Milletich, PL and Jones, MP and McKinley, KL and Mearig, AJ and Triplett, EW and Ludvigsson, J},
title = {Gut microbial functional associations with subsequent irritable bowel syndrome in a prospective, paediatric case-control study.},
journal = {EBioMedicine},
volume = {133},
number = {},
pages = {106521},
doi = {10.1016/j.ebiom.2026.106521},
pmid = {42962555},
issn = {2352-3964},
abstract = {BACKGROUND: The infant gut microbiome undergoes rapid maturation that shapes lifelong gastrointestinal health. Although adults with irritable bowel syndrome (IBS) show characteristic microbial and metabolic alterations, it remains unclear whether these differences precede disease onset. Here, microbiome composition and function in infancy were prospectively associated with future IBS development.

METHODS: Stool samples collected from the All Babies in Southeast Sweden (ABIS) cohort at a mean age of 12.4 (±1.5) months, were analysed using a nested case-control design. Cases included future IBS and/or pelvic and abdominal pain, with the average time between age at stool collection and diagnosis being 11.8 (±5.2) years and a mean age at diagnosis of 12.8 (±5.2) years. Microbial composition was profiled with 16S rRNA gene sequencing (n = 396). Data were processed with DADA2, taxonomically assigned using SILVA database, and predicted functionally with PICRUSt2. Descriptive statistics were analysed using χ[2] or Fisher's exact test, global differences with PERMANOVA, differential abundance with ANCOM-BC2, and pathway enrichment with GSEA.

FINDINGS: Infants with future IBS risk demonstrated microbial divergence, marked by depletion of short-chain fatty acid producers and expansion of facultative and mucosa-disruptive taxa. Inferred functional profiles exhibited reduced fermentative capacity, greater respiratory potential, accelerated degradation of neuroactive aromatic amines, and case-enrichment of cytochrome bc1 complex respiratory unit.

INTERPRETATION: Gut microbiome dysbiosis in infants with IBS risk is present many years prior to diagnosis and includes early disruptions in fermentation, redox balance, and amine metabolism that potentially compromise epithelial resilience and promote visceral hypersensitivity. Early detection of microbiome dysbiosis suggests probiotic-based interventions.

FUNDING: Barndiabetesfonden; Swedish Council for Working Life and Social Research; Swedish Research Council; Östgöta Brandstodsbolag; Medical Research Council of Southeast Sweden; JDRF-Wallenberg Foundation; Linköping University; Horizon Europe INITIALISE grant.},
}

@article {pmid42962574,
year = {2026},
author = {Yu, X and Liu, S and Gutang, Q and Wang, Y and Yin, X and Li, Y and Wang, X},
title = {Unveiling the mechanism of microplastic-mediated antibiotic bioavailability, gut microbiota and antibiotic resistome in marine fish: Importance of microplastic aging and antibiotic-loading.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127177},
doi = {10.1016/j.watres.2026.127177},
pmid = {42962574},
issn = {1879-2448},
abstract = {Microplastics and antibiotics co-occur commonly in coastal aquatic ecosystems. Environmental aging of microplastics and interactions with antibiotics are inevitable, which alter the fate of antibiotics and associated ecotoxicological effects, yet the distinct impacts and underlying mechanisms remain largely unknown. Here, polyethylene (PE) microplastics, derived from a widely used polymer and frequently detected in aquatic environments, were selected to investigate the effects of aging and ciprofloxacin (CIP) loading on CIP bioaccumulation and toxicity in marine medaka (Oryzias melastigma). The intake of microplastics by fish visualized via a novel in situ hyperspectral imaging revealed aged PE (APE) easily accumulated in the fish gut. The presence of microplastics exacerbated CIP-induced gill and intestinal lesions. CIP-loaded pristine PE (PPE-CIP) increased CIP accumulation by 0.87-fold, 1.18-fold and 0.10-fold in the gastrointestinal tract, gill and muscle, respectively, and CIP-loaded aged PE (APE-CIP) further amplified this promoting effect. Conversely, PPE and APE without CIP-loading decreased CIP accumulation in the fish gut, but this clean effect varied with exposure duration, tissue distribution and microplastic aging status. The presence of microplastics altered the gut microbiota composition, and APE-CIP exacerbated the effects of microplastics on the gut microbiota by decreasing the stability of the microbiome network. The presence of PPE-CIP and APE-CIP amplified the abundance of Vibrio and CIP-associated antibiotic resistance genes (i.e., norM gene) in fish feces via enhancing CIP bioaccumulation, increasing the risk of ARGs spread through fish feces. These findings highlight the importance of considering aging and antibiotic-loading when evaluating the carrier effects and toxicity of microplastics.},
}

@article {pmid42962646,
year = {2026},
author = {Zakari, A and Chen, YH and Chen, PJ and Peng, SW and Lan, SC and Shih, YS and Hsiao, TC and Chung, KF and Chuang, KJ and Chang, JH and Chi, KH and Chuang, HC},
title = {Associations of particulate matter-associated microbial profiles with lung and intestinal microbiomes in healthy mice.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143978},
doi = {10.1016/j.jhazmat.2026.143978},
pmid = {42962646},
issn = {1873-3336},
abstract = {Ambient air pollution has detrimental effects on human health. We investigated exposure-related differences and microbial overlap among PM1, lung, and gut microbiomes in mice exposed to PM1, high-efficiency particulate air (HEPA)-filtered air, or clean air. PM1 was characterized for soluble ions, metals, carbonaceous fractions, and oxidative potential, while gaseous pollutants data were obtained from air-quality monitoring stations. PM1, lung, and gut microbiomes were analyzed using 16S rRNA sequencing, and short-chain fatty acids (SCFAs) were quantified by gas chromatography-mass spectrometry (GC-MS). Proteobacteria was the dominant phylum in PM1. PM1 contained diverse chemical constituents, including soluble ions, metals, and oxidative species. Lung microbial diversity remained largely unchanged, whereas the gut microbiome was significantly altered. Compared with control, the PM1 group showed reduced Actinobacteriota and Bacteroidota, while Campylobacterota and Patescibacteria decreased in both HEPA and PM1 groups. Verrucomicrobiota increased in the HEPA group, and Proteobacteria increased in the PM1 group compared with both HEPA and control groups. Correlation analyses identified associations between lung and gut microbiomes, environmental variables, PM1 characteristics, gaseous pollutants, and SCFAs. Eleven bacterial families and six genera overlapped among PM1, lung, and gut microbiomes in the PM1 group. Overall, ambient air pollution was associated with gut dysbiosis in mice.},
}

@article {pmid42962704,
year = {2026},
author = {May, L and Wolstenholme, J and Bajaj, J},
title = {Targeting the Microbiome to Treat Alcohol Use Disorder and Liver Disease.},
journal = {Seminars in liver disease},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2993-3789},
pmid = {42962704},
issn = {1098-8971},
abstract = {Alcohol use disorder and alcohol-associated liver disease represent a global health burden, yet treatment options remain limited. Emerging evidence has shown the intestinal microbiome to be a mediator of alcohol-associated organ injury, establishing gut dysbiosis, intestinal barrier dysfunction, and aberrant microbial metabolite production as drivers of disease. The gut-liver-brain axis provides a mechanistic framework in which microbial products and signals fuel hepatic inflammation, steatosis, fibrosis, and neuroinflammation that drive alcohol consumption. This review discusses current evidence on how chronic alcohol exposure shapes microbial communities, disrupts the gut epithelium, and alters innate immune and metabolic circuits in the liver and the brain. We examine how microbiome-targeted interventions, such as probiotics, prebiotics, synbiotics, fecal microbiota transplantation, non-absorbable antibiotics, and short-chain fatty acid supplementation, can act on mechanistic targets along this axis. Finally, we highlight knowledge gaps, including the roles of causal microbial taxa, sex differences in gut-immune-brain signaling, and windows of reversibility that must be further investigated and understood to translate microbial modulation into effective therapies. In conclusion, this review summarizes the current literature on targeting the microbiome and the gut-liver-brain axis as a treatment approach, with a focus on the mechanisms within this axis and the interventions that target them.},
}

@article {pmid42962970,
year = {2026},
author = {Islam Bhuiyan, MN},
title = {Food as Biological Information: A Testable Dietome Framework for Precision Nutrition and Whole-Food Meal Design.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101909},
doi = {10.1016/j.tjnut.2026.101909},
pmid = {42962970},
issn = {1541-6100},
abstract = {Nutrition science has established the importance of energy, essential nutrients, dietary patterns, and food matrices, yet researchers often study these dimensions separately from the biological systems that transform and interpret a meal. This Perspective proposed the Dietome as a testable, systems-level description of food-derived inputs and the Informational Nutrition Framework (INF), comprising encoding, transmission, decoding, execution, and biological memory. The framework integrates sensory perception and eating behaviour with digestion, microbial metabolism, host signalling, and context-dependent responses. Its novelty is not the claim that food contains a literal code, but the proposal to connect food composition and structure to measurable, falsifiable predictions about meal-level responses. Evidence from personalized postprandial prediction, foodome network analysis, microbial short-chain fatty acid (SCFA)-associated chromatin regulation, and computational diet modelling illustrates both opportunity and limitations. A worked meal example shows how to evaluate minimally processed foods and their combinations before considering engineered formulations. The Perspective also identifies sustainability, developmental nutrition, and food-allergy prevention as domains requiring cautious, evidence-specific application. Dietary microRNAs and long-term nutritional memory remain less established than conventional nutrient and microbial-metabolite pathways. The framework should therefore be judged by prospective validation, causal evidence, clinical utility, cultural acceptability, and environmental performance, not by terminology alone.},
}

@article {pmid42963088,
year = {2026},
author = {Durr, KM and Hum, C and Kain, T and Tran, A and English, S and McIntyre, L},
title = {Randomised controlled trials of faecal microbiota transplantation in adult inpatients: a scoping review study protocol.},
journal = {BMJ open},
volume = {16},
number = {10},
pages = {e122741},
doi = {10.1136/bmjopen-2026-122741},
pmid = {42963088},
issn = {2044-6055},
}

@article {pmid42963223,
year = {2026},
author = {Fu, W and Sun, C and Guo, Q and Lai, H},
title = {Cross-kingdom endosymbiosis rewires the rhizobiome for fungal pathogenicity.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.10.005},
pmid = {42963223},
issn = {1878-4380},
abstract = {Soil-borne fungal pathogens undermine crop health by disrupting the protective rhizosphere microbiome. Zhou et al. uncovered a cross-kingdom endosymbiotic mechanism that enables Fusarium oxysporum f. sp. lycopersici to subvert rhizosphere protection: intracellular bacterial endosymbionts drive fungal metabolic reprogramming to produce a selective toxin, thereby suppressing keystone beneficial rhizobacteria.},
}

@article {pmid42963493,
year = {2026},
author = {van Wesemael, AJ and de Kroon, RR and van Eijk, LMHE and Frerichs, NM and Vermeulen, MJ and van den Akker, CHP and Raets, MMA and Hulzebos, CV and de Boode, WP and van Kaam, AH and de Meij, TGJ and Niemarkt, HJ},
title = {Clinical effects of multi-strain probiotics in extremely preterm infants: a multicenter pre-post implementation study in the Netherlands.},
journal = {European journal of pediatrics},
volume = {185},
number = {11},
pages = {},
pmid = {42963493},
issn = {1432-1076},
mesh = {Humans ; *Probiotics/therapeutic use ; Infant, Newborn ; Netherlands/epidemiology ; *Enterocolitis, Necrotizing/prevention & control/epidemiology ; *Infant, Extremely Premature ; Male ; Female ; Intensive Care Units, Neonatal ; *Infant, Premature, Diseases/prevention & control/epidemiology ; Gestational Age ; Sepsis/prevention & control/epidemiology ; Incidence ; Treatment Outcome ; Streptococcus thermophilus ; },
abstract = {UNLABELLED: Probiotics may reduce the risk of necrotizing enterocolitis (NEC), late-onset sepsis (LOS), and mortality in preterm infants. However, their efficacy in extremely preterm infants (gestational age < 28 weeks) is still regularly questioned due to limited data and safety concerns. In Dutch Neonatal Intensive Care Units (NICUs), a three-strain probiotic product (ProPrems®; Bifidobacterium infantis Bb-02, Bifidobacterium lactis BB-12, and Streptococcus thermophilus TH-4) was implemented as standard of care from 2021 onwards. This study evaluates the clinical effects of these probiotics in extremely preterm infants. Pre- and postimplementation cohorts of extremely preterm infants from 6 Dutch NICUs (2018-2023) were compared. Clinical data from the first 29 days of life were collected. Incidence of NEC (modified Bell's stage ≥ IIA), LOS, and mortality were compared with logistic regression; growth velocity with linear regression; and time to full enteral feeds (tFEF) with survival analyses. In total, 481 extremely preterm infants (212 pre-, 269 post-implementation) were included. After implementation, the adjusted odds ratio was 0.49 (0.25-0.99; p = 0.049) for NEC; 0.87 (0.59-1.28; p = 0.49) for LOS; and 0.67 (0.35-1.27; p = 0.22) for all-cause mortality. Furthermore, tFEF decreased by 2 days (p < 0.001) and probiotic use was associated with an increase in growth velocity of 1.8 g/kg/day (p < 0.001). One infant (0.4%) developed probiotic-associated sepsis.

CONCLUSION:  This multicenter pre-postimplementation study showed that multi-strain probiotic administration was associated with lower NEC incidence, shorter tFEF, and greater growth velocity in extremely preterm infants during the first four weeks of life. Probiotic-associated sepsis was rare. These results support continued use of probiotics in this vulnerable population.

WHAT IS KNOWN: • Certain probiotic strains effectively reduce incidence of necrotizing enterocolitis (NEC) in preterm infants, but the efficacy and safety for extremely preterm infants (GA < 28 weeks) remain under debate.

WHAT IS NEW: • This study shows that a multi-strain probiotic supplement was associated with lower NEC incidence, shorter time to full enteral feeds, and greater early postnatal growth in a Dutch multicenter cohort of extremely preterm infants. • The incidence of probiotic-associated sepsis in extremely preterm infants was very low in our cohort with just 1 case (0.4%), consistent with the rare occurrence reported previously.},
}

Humans
*Probiotics/therapeutic use
Infant, Newborn
Netherlands/epidemiology
*Enterocolitis, Necrotizing/prevention & control/epidemiology
*Infant, Extremely Premature
Male
Female
Intensive Care Units, Neonatal
*Infant, Premature, Diseases/prevention & control/epidemiology
Gestational Age
Sepsis/prevention & control/epidemiology
Incidence
Treatment Outcome
Streptococcus thermophilus

@article {pmid42963768,
year = {2026},
author = {Khan, HW and Iqbal, MA and Reyer, H and Trakooljul, N and Hadlich, F and Oster, M and Kuhla, B and Keiler, J and Wimmers, K and Ponsuksili, S},
title = {Breed and housing system shape jejunal transcriptome and digesta microbiota in German Landrace and Saddleback pigs.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42963768},
issn = {2524-4671},
abstract = {BACKGROUND: Sustainable pig farming balances animal welfare, productivity, and social acceptance. Organic systems offer enriched environments for the pigs and represent a model for sustainable production, but require an understanding of how breed, intestinal microbiome, and housing interact. In this study, we compared a commercial breed (German Landrace, GL) and a traditional breed (German Saddleback, GS) reared in different housing systems (Conventional, CON; Organic, ECO). Jejunal mucosa transcriptomes (n = 56) and digesta microbiota (n = 100) were collected from growing pigs at 70 days of life; 54 samples overlapped between the two datasets and were used for all integrated host-microbiome analyses. Data from RNA-seq and 16 S-seq were evaluated through differential expression analysis, microbial community profiling, and DIABLO-based data integration.

RESULTS: Jejunal transcriptome variation was influenced primarily by breed. GL pigs exhibited a profile supporting anabolic pathways, including upregulated oxidative phosphorylation, whereas GS pigs showed a profile focused on lipid metabolism and a shift toward energy storage as an adaptation. In contrast, the housing system was the main driver of microbial composition, with ECO housing enriching fermentative taxa such as Lactobacillus and Campylobacter, presumably due to outdoor exposure, while CON housing enriched fewer Lactobacillus but more Clostridium. Breed-Housing combinations analysis revealed distinct adaptive strategies: the modern GL breed responded strongly to housing conditions at both the transcriptional and microbial levels, whereas the traditional GS breed, while also transcriptionally responsive, maintained a more stable microbial community phenotype across environments. Integrated host-microbiome analysis identified a core set of host genes (e.g., PCSK9 and SCD) that were strongly correlated with housing-specific microbes, defining a lipid-inflammation axis.

CONCLUSION: Breed and rearing environment jointly shape the porcine jejunal transcriptome and microbiota through distinct strategies. Together, these data provide molecular insight into how traditional and modern breeds differentially respond and potentially adapt to divergent husbandry systems, with implications for health and productivity.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid42963927,
year = {2026},
author = {Chang, H and Gu, C and Zou, D and Wang, X and Xu, R and Zheng, S and Ran, M and Wang, T and Zhao, Y and Wang, D},
title = {Host seasonal trophic strategies linked to dietary-microbiota coupling: A potential mechanism mediating the coexistence of sympatric small rodents.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70383},
pmid = {42963927},
issn = {1365-2656},
support = {//Double-First Class Initiative of the School Life Sciences Shandong University/ ; 31970417//National Natural Science Foundation of China/ ; 32330012//National Natural Science Foundation of China/ ; },
abstract = {The coexistence mechanisms of sympatric species have long attracted widespread research attention. However, it remains unclear whether sympatric species experiencing the same seasonal conditions exhibit convergent or host-specific gut microbiota responses. We compared the herbivorous Brandt's vole (Lasiopodomys brandtii) and the granivorous Mongolian gerbil (Meriones unguiculatus), two sympatric rodent species with divergent trophic strategies inhabiting the grasslands of Inner Mongolia, China. By integrating plant DNA metabarcoding, gut microbiota profiling and microbial functional output analyses across seasons, we investigated seasonal dietary-microbiome associations. Our results revealed that although seasonal dietary variation affects the composition of the host gut microbiota, the taxonomic and functional plasticity of gut microbiota is strongly influenced by host trophic strategies. Brandt's voles maintained a fermentation-oriented microbiota tightly coupled with seasonal shifts in Poaceae and Cyperaceae intake, exhibiting coordinated changes in microbial taxa, short-chain fatty acid production and cellulase activity. In contrast, Mongolian gerbils exhibited substantial seasonal dietary turnover between Chenopodiaceae and Caragana plants, while maintaining comparatively stable microbial functional outputs, suggesting metabolic buffering. Host trophic strategy, rather than shared environmental seasonality, is related to the strength and functional consequences of the coupling between diet and microbiome. Our results emphasize the gut microbiome as a potential key mechanism underlying trophic niche differentiation and ecological coexistence in wild mammalian communities.},
}

@article {pmid42964032,
year = {2026},
author = {Li, H and Hou, C and Pan, Y},
title = {Targeting the gut-tumor axis: probiotic therapy as an adjunct strategy in colorectal cancer treatment.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1873871},
pmid = {42964032},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/therapy/drug therapy ; *Probiotics/therapeutic use/pharmacology ; Multiomics ; Apoptosis/drug effects ; Cell Survival/drug effects ; Metabolomics ; Proteomics ; Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; Cell Line, Tumor ; Systems Biology ; Signal Transduction/drug effects ; Caco-2 Cells ; Gene Expression Profiling ; Butyrates/pharmacology ; Indoleacetic Acids ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is a multifactorial disease driven by interactions among host genetics, immune dysregulation, environmental factors, and gut microbiota. The gut-tumor axis regulates CRC progression through inflammatory signaling, oxidative stress, epithelial barrier disruption, and immune imbalance. Probiotic-derived metabolites act as bioactive molecules capable of restoring host-microbiome homeostasis and modulating tumor-associated pathways.

OBJECTIVE: To evaluate probiotic metabolites as adjunct therapeutic agents in CRC using integrative multi-omics analysis and in vitro validation.

METHODS: A systems biology approach integrating network pharmacology, transcriptomics, proteomics, metabolomics, and microbiome profiling was applied. Twelve probiotic metabolites yielded 428 predicted targets, with 162 overlapping CRC-associated genes. CRC cell lines (HCT116, HT-29, Caco-2, SW480) were treated and analyzed for viability, apoptosis, gene/protein expression, cytokines, metabolites, and microbial composition.

RESULTS: Sodium butyrate (5 mM) reduced cell viability by 35.5-42.3% (p < 0.001) and increased apoptosis from 8.6% to 32.4%, reaching 41.2% when combined with indole-3-acetic acid (IAA, 100 μM), suggesting a synergistic pro-apoptotic effect. RNA-seq identified 1,248 DEGs, with upregulation of BAX and CASP3 (log2FC +1.8 to +2.3) and downregulation of IL6, TNF, and NFKB1 (-1.5 to -2.1). Proteomics revealed 412 differentially expressed proteins, including downregulation of AKT1 (-1.6-fold), MAPK1 (-1.4-fold), and EGFR (-1.3-fold), and upregulation of CASP3 (+1.7-fold) and BAX (+1.5-fold). Cytokines IL-6, TNF-α, and IL-1β decreased by 48.2%, 44.7%, and 39.5%, respectively, while IL-10 increased by 26.3%. Metabolomics showed a 2.8-fold increase in butyrate and ~35% reduction in oxidative stress. Microbiome diversity improved (Shannon index 2.8-3.6).

CONCLUSION: Probiotic-derived metabolites modulate NF-κB, PI3K-Akt, MAPK, and apoptosis pathways, supporting their potential role as adjunct therapeutic agents in CRC management.},
}

Humans
*Colorectal Neoplasms/therapy/drug therapy
*Probiotics/therapeutic use/pharmacology
Multiomics
Apoptosis/drug effects
Cell Survival/drug effects
Metabolomics
Proteomics
Gastrointestinal Microbiome/drug effects
Cytokines/metabolism
Cell Line, Tumor
Systems Biology
Signal Transduction/drug effects
Caco-2 Cells
Gene Expression Profiling
Butyrates/pharmacology
Indoleacetic Acids

@article {pmid42964048,
year = {2026},
author = {Rahman, MA and Islam, SMS and Alabdallah, NM and Latif, S and Hoque, M and Hasan, MM},
title = {New insights into root 2-naphtholic acid exudation, microbiome recruitment, and designing of drought-smart future crops.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1938013},
pmid = {42964048},
issn = {1664-462X},
}

@article {pmid42964076,
year = {2026},
author = {Pandey, S and Skidmore, J and Dhillon, J},
title = {A systematic review of the effects of diet on the gut microbiota in individuals at elevated risk for colorectal cancer.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1818522},
pmid = {42964076},
issn = {2296-861X},
abstract = {BACKGROUND: Colorectal cancer (CRC) poses a major public health concern, with emerging evidence highlighting the critical role of the gut microbiota in CRC progression. Considering that diet is a major modifiable factor influencing CRC risk, partly through its interaction with the gut microbiome, this systematic review evaluated the effects of dietary intervention RCTs, including supplements, functional foods, whole foods, and dietary patterns, on the gut microbiome in elevated-risk individuals.

METHODS: A search of PubMed, Scopus, and Web of Science, and manual sourcing of systematic reviews, meta-analyses, and reference lists of relevant papers identified 5,558 records.

RESULTS: Following screening, seven studies met inclusion criteria, focusing on microbial diversity and taxonomic composition. Findings demonstrate that effects on microbial diversity metrics were minimal and were observed only with a general healthy eating dietary pattern, navy bean powder interventions, and with one rice bran intervention. No consistent patterns emerged by intervention type (functional compounds, whole foods, or dietary pattern), intervention duration, or by diversity metric. In contrast, genus-level compositional shifts were more frequently reported, although directionality varied by dietary exposure. Enrichment of Faecalibacterium, Bifidobacterium, and Lactobacillus was reported in some rice bran and navy bean interventions, whereas reductions in Akkermansia, Ruminococcus, Bacteroides, Prevotella, and Porphyromonas were observed in others. Among the four trials assessing microbial-derived metabolites, some were associated with increased short-chain fatty acids and plant-derived metabolites while others reported reductions in secondary bile acids, p-cresol sulfate, and branched-chain bacterial fatty acids.

CONCLUSION: Overall, this review highlights the potential of dietary strategies to modulate the gut microbiome in populations at risk for CRC, while also addressing critical gaps in the current evidence and offering direction for the development of evidence-based dietary interventions that incorporate microbiome assessment. Limited RCTs and heterogeneity in outcomes limit generalizability. Future research should conduct rigorous RCTs across the lifespan, using microbiome and metabolite analyses such as shotgun metagenomics, meta-transcriptomics, or metabolomics and examining understudied dietary patterns to guide CRC prevention.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024530038, identifier CRD42024530038.},
}

@article {pmid42964104,
year = {2026},
author = {Ramos-Nino, ME and Doshi, A and Ramdass, PVAK},
title = {The emerging oral microbe-host axis in endometriosis: a systematic review of Fusobacterium nucleatum.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1994934},
pmid = {42964104},
issn = {2235-2988},
mesh = {*Endometriosis/microbiology ; Humans ; Female ; *Fusobacterium nucleatum/pathogenicity/physiology ; Animals ; *Fusobacterium Infections/microbiology/complications ; *Mouth/microbiology ; Microbiota ; *Host Microbial Interactions ; },
abstract = {BACKGROUND: Fusobacterium nucleatum, an oral-associated bacterium implicated in several extraoral diseases, has recently been proposed as a potential contributor to endometriosis through microbial translocation, inflammation, and fibrosis. However, the consistency and clinical significance of this association remain uncertain. This systematic review evaluated the human and experimental evidence linking F. nucleatum with endometriosis and assessed the plausibility of a proposed oral microbe-host axis.

METHODS: PubMed/MEDLINE, Embase, Web of Science, and Google Scholar were searched from inception through August 31, 2026, following PRISMA 2020 guidelines. Human and animal studies reporting F. nucleatum or historically related F. nucleatum-complex taxa in relation to endometriosis were included. Risk of bias was assessed using a prespecified adapted ROBINS-I framework for human observational studies and SYRCLE for animal studies. Owing to substantial heterogeneity in anatomical compartments, detection methods, and outcomes, meta-analysis was not appropriate and findings were synthesized qualitatively.

RESULTS: Four human studies encompassing 384 participants at the study level were included, although analysis-specific denominators varied. Direct tissue evidence came from two studies and was conflicting: Muraoka et al. reported Fusobacterium positivity in 64.3% of endometrial samples from women with endometriosis versus 7.1% of controls in a 42-versus-42 tissue subset, whereas Graciano-España et al. found no significant case-control difference in F. nucleatum abundance among 55 cases and 37 controls. Indirect microbiome studies reported oral Fusobacterium enrichment in moderate/severe endometriosis and vaginal F. animalis depletion in chronic pelvic pain with endometriosis. All human studies were judged at serious overall risk of bias, and certainty of evidence was very low. Experimental evidence suggesting TGF-β-mediated lesion growth and fibrosis derived principally from one translational study and lacked independent replication.

CONCLUSIONS: Current evidence supports biological plausibility but not a consistent or causal association between F. nucleatum and endometriosis. Direct tissue evidence is limited to two conflicting studies, while non-tissue microbiome findings are indirect. Standardized contamination-controlled sampling, paired anatomical-site sampling, strain-level analyses, and longitudinal studies are required before microbial translocation, temporality, causality, or antimicrobial treatment can be established.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420261337885.},
}

*Endometriosis/microbiology
Humans
Female
*Fusobacterium nucleatum/pathogenicity/physiology
Animals
*Fusobacterium Infections/microbiology/complications
*Mouth/microbiology
Microbiota
*Host Microbial Interactions

@article {pmid42964215,
year = {2026},
author = {Ali, WH and Omar, A and Ali, AH and Hefny, HM and Nabil, G and Mahmoud, Y and Nasr, AEA and Abdelhamid, SM and Amin, HM and Omar, MM and El-Attar, LM and Mohamed, FS and Elgamal, R and Ibrahem, M and Abdelmotogaly, HSM},
title = {Targeted Quantitative Polymerase Chain Reaction Analysis of Gut Microbiota and Its Association With Feeding and Mealtime Behavior and Intestinal Permeability in Children With Autism Spectrum Disorder.},
journal = {Journal of clinical medicine research},
volume = {18},
number = {10},
pages = {759-769},
pmid = {42964215},
issn = {1918-3003},
abstract = {BACKGROUND: Gastrointestinal (GI) symptoms and feeding and mealtime problems are common in children with autism spectrum disorder (ASD). It is important to note that the gut microbiome is a hypothesized mechanism of action, but it is not yet known if specific bacterial profiles and markers of intestinal barrier function predict feeding problems in the target group of ASD.

METHODS: This is a cross-sectional case-control study that examined 70 children with ASD (aged 3-12 years) and 70 matched neurotypical children. Autism was evaluated using the Childhood Autism Rating Scale (CARS), and mealtime behaviors were evaluated using the Brief Autism Mealtime Behavior Inventory (BAMBI). Six important bacterial taxa were quantified using real-time polymerase chain reaction (PCR), and fecal zonulin and calprotectin were quantified by enzyme-linked immunosorbent assay (ELISA).

RESULTS: Children with ASD had significantly higher levels of fecal zonulin and calprotectin than controls (both at P < 0.001) and lower abundances of beneficial taxa (Prevotella, Bifidobacterium, Lactobacillus) and higher abundances of Clostridium difficile and Bacteroidetes (all P < 0.01). The overall BAMBI scores did not differ among the groups, but within the ASD group, feeding problem severity was highly correlated with lower Bifidobacterium (r = -0.68) and higher Clostridium difficile (r = 0.74) and was not significantly correlated with autism severity, zonulin, or calprotectin.

CONCLUSION: Children with ASD have increased levels of gut dysbiosis and barrier dysfunction compared to their non-autistic peers, but the severity of their feeding and mealtime problems tracked the degree of gut microbial imbalance rather than the severity of their ASD symptoms in general. This suggests that feeding behavior is a characteristic that has been under-recognized as a component of the ASD phenotype and is related to the microbiome; if confirmed in longitudinal studies, these microbial associations could represent a candidate target for future gut-directed intervention research.},
}

@article {pmid42964395,
year = {2026},
author = {Xue, L and Chen, Y and Zhong, Y and Wan, C},
title = {Microclimate characteristics, temporal dynamics of soil bacterial communities, and potential co-occurrence network differences between greenhouse and open-field cultivation environments.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1988234},
doi = {10.3389/fmicb.2026.1988234},
pmid = {42964395},
issn = {1664-302X},
abstract = {INTRODUCTION: Greenhouse cultivation modifies agricultural microclimates and may be associated with temporal changes in soil microbial communities. We investigated a representative vegetable greenhouse and an adjacent open-field site in the subtropical red-soil region of Jiangxi Province, China.

METHODS: Air temperature and relative humidity were monitored continuously for one year in both environments, while soil temperature and volumetric water content were monitored within the greenhouse. Monthly soil samples were analyzed using 16S rRNA gene amplicon sequencing.

RESULTS: The greenhouse exhibited pronounced daytime warming, nighttime heat retention, and generally higher relative humidity. Soil bacterial community composition differed significantly between greenhouse and open-field soils, while alpha-diversity differences varied among seasons. Month-resolved analyses revealed significant temporal dynamics. Air temperature and relative humidity jointly explained 15.59% of the variation in bacterial community structure. Potential co-occurrence networks also differed between the two environments in topology and in the proportions of positive and negative correlations.

DISCUSSION: The results document year-round differences in microclimate and soil bacterial community dynamics between greenhouse and open-field cultivation environments. The measured atmospheric microclimate variables showed statistically detectable but limited associations with bacterial community composition, providing a basis for soil microbiome monitoring and environmental management in subtropical protected agriculture.},
}

@article {pmid42964681,
year = {2026},
author = {Al-Beltagi, M},
title = {Clinical guidelines for the diagnosis and management of pediatric fecal incontinence: A comprehensive review and treatment algorithm.},
journal = {World journal of clinical pediatrics},
volume = {15},
number = {4},
pages = {120203},
doi = {10.5409/wjcp.120203},
pmid = {42964681},
issn = {2219-2808},
abstract = {Pediatric fecal incontinence (FI) is a multifactorial condition with functional, neurodevelopmental, and organic etiologies. Despite its prevalence, FI remains underdiagnosed, stigmatized, and associated with significant psychosocial and family burden. This review synthesizes current evidence on the diagnosis, pathophysiology, and management of pediatric FI and proposes practical, algorithm-based guidance for frontline clinicians and subspecialists. A structured literature search of PubMed, Scopus, and Cochrane databases was conducted, focusing on pediatric FI, functional and organic subtypes, neurodevelopmental comorbidities, and multidisciplinary interventions. Emphasis was placed on evidence-based management strategies, emerging therapeutic innovations, and psychosocial considerations. Functional retentive FI often responds to structured disimpaction, maintenance laxatives, and behavioral interventions, whereas non-retentive forms require tailored psychological and behavioral therapies. Organic etiologies often require long-term, multidisciplinary care, surgical intervention, or neuromodulation. Special populations-including children with autism spectrum disorder, attention-deficit/hyperactivity disorder, developmental delay, and postoperative anorectal conditions-require individualized, developmentally adapted programs. Psychosocial impacts on children and families are significant and require coordinated counseling. Emerging research highlights the gut-brain axis, microbiome modulation, digital behavioral applications, and precision bowel management as future directions. Limitations include heterogeneous study designs, lack of long-term pediatric randomized controlled trials, and variable outcome measures. Pediatric FI is a complex condition requiring early recognition, subtype-specific management, and multidisciplinary care. Algorithm-based, individualized strategies that integrate physiological, behavioral, and psychosocial components optimize long-term continence, psychosocial well-being, and quality of life. Future research should focus on standardized outcomes, neuromodulatory interventions, and precision, technology-enhanced therapies.},
}

@article {pmid42804785,
year = {2026},
author = {Kailasam, S and Panigrahi, R},
title = {Phylogeny and ecosystem jointly shape metabolite sensing by structured noncoding RNAs.},
journal = {Genome},
volume = {69},
number = {},
pages = {1-17},
doi = {10.1139/gen-2026-0048},
pmid = {42804785},
issn = {1480-3321},
mesh = {*Riboswitch ; Animals ; *Ecosystem ; *Phylogeny ; *RNA, Untranslated/genetics/metabolism ; *Microbiota/genetics ; Humans ; Bacteria/genetics/classification/metabolism ; },
abstract = {Noncoding RNAs (ncRNAs) regulate gene expression through diverse structural and sequence-based mechanisms, often acting without protein intermediates. Riboswitches are cis-regulatory ncRNAs that directly sense small molecule metabolites to control gene expression. Many riboswitches operate through kinetic control, meaning the rate at which a ligand binds to the aptamer domain determines whether gene expression is turned ON or OFF. Here, we present a comparative survey of riboswitch repertoires across eight microbiomes: human gut, oral, skin, vaginal, mouse gut, pig gut, sheep rumen, and marine environment, spanning 13 946 prokaryotic genomes. Using covariance models, we identified 86 485 riboswitches across 12 916 genomes (92.6%), representing 23 metabolite-sensing classes, with six dominant classes accounting for ~70% of all riboswitch hits. Riboswitch composition varied significantly across ecosystems, but variance partitioning showed this structure is driven primarily by phylogeny: phylum explained 25.5% of compositional variance, whereas the fraction uniquely attributable to ecosystem after conditioning on taxonomy was only 2.2%. Overall riboswitch distributions reflect both phylogenetic and ecological influences, highlighting their role in shaping metabolite-responsive regulatory strategies across microbial life.},
}

*Riboswitch
Animals
*Ecosystem
*Phylogeny
*RNA, Untranslated/genetics/metabolism
*Microbiota/genetics
Humans
Bacteria/genetics/classification/metabolism

@article {pmid42954653,
year = {2026},
author = {Busturia, I and Martín-Cardoso, H and Domingo, C and Garcia-Molina, A and San Segundo, B},
title = {Decoding microbial diversity in roots of rice plants under flooded conditions: influence of the host genotype, root compartment, and mycorrhizal association.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0167126},
doi = {10.1128/aem.01671-26},
pmid = {42954653},
issn = {1098-5336},
abstract = {UNLABELLED: Rice is a vital staple for more than half of the world's population, uniquely adapted to grow under flooded conditions. Our current understanding of root-associated microbiomes in rice plants under flooded conditions (anaerobic rice) is, however, limited. While rice plants are capable of establishing symbiotic associations with arbuscular mycorrhizal (AM) fungi, also under flooded conditions, little is known about the impact that mycorrhizal associations might have on the root microbiome. Here, we used metagenomic sequencing to characterize the root-associated microbiomes of cultivated rice grown under flooded conditions. The root endosphere and rhizosphere compartments were found to harbor distinct microbial communities, with bacterial taxa comprising approximately 95% of the total microbial community. At the phylum level, the root bacteriome was primarily composed of Pseudomonadota (Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria), followed by Actinomycetota. The fungal microbiome was dominated by Ascomycota (Sordariomycetes, Eurotiomycetes, and Dothideomycetes) and Basidiomycota. Both root compartment and host genotype significantly influenced microbiome composition, with most genotype-specific recruitment occurring at the species level. These associations were further reshaped in plants pre-inoculated with the AM fungus Rhizophagus irregularis. Co-occurrence networks revealed a genotype-dependent effect in the complexity of microbial taxa in mycorrhizal rice plants. Key microbial species primarily involved in methane production and nutrient cycling (e.g., phosphate-solubilizing bacteria and nitrogen-cycling bacteria) residing in roots of flooded rice were identified. Functional analysis of gene abundance related to those microbial communities revealed compartmentalization, with nutrient-cycling bacteria being more prevalent at the endosphere. Overall, this study demonstrated that the rice genotype, root compartment, and mycorrhizal condition shape the root microbiome in rice plants, ultimately influencing holobiont dynamics in flooded rice fields.

IMPORTANCE: Plant roots harbor a large diversity of microorganisms that strongly influence plant health and improve stress tolerance. Among them, root colonization by arbuscular mycorrhizal (AM) fungi enhances mineral nutrition and mitigates environmental stress. Although most rice cultivated worldwide is grown under anaerobic conditions (flooded fields), investigation of microbial communities inhabiting root-associated compartments of flooded rice, including AM fungi, has received only little attention. Here, we demonstrated that the rice genotype, root compartment, and mycorrhizal condition markedly influence the microbiome in roots of rice plants in flooded conditions, thus illustrating the potential of the rice plant to shape its root-associated microbiome. Differential root-associated microbiomes of commercial rice varieties include microbes primarily associated with methane production and nutrient cycling. Elucidation of factors influencing root-associated microbiomes in flooded rice systems, including their association with AM fungi, offers practical guidance for exploiting root-associated microbial communities for sustainable rice cultivation while reducing reliance on agrochemicals.},
}

@article {pmid42954768,
year = {2026},
author = {Debnath, D},
title = {The gut-ovary axis in polyendocrine metabolic ovarian syndrome: Mechanisms, microbiome dysbiosis, and emerging therapeutic strategies.},
journal = {International journal of gynaecology and obstetrics: the official organ of the International Federation of Gynaecology and Obstetrics},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijgo.71478},
pmid = {42954768},
issn = {1879-3479},
abstract = {Polycystic ovary syndrome (PCOS), recently termed polyendocrine metabolic ovarian syndrome (PMOS), is a heterogeneous endocrine-metabolic disorder characterized by reproductive, metabolic, and hormonal disturbances. Increasing evidence suggests that interactions between the gut microbiota and host physiology may be relevant to PMOS through pathways involving intestinal barrier function, inflammation, insulin sensitivity, steroid hormone metabolism, bile acid signaling, and gut-brain-ovary communication. This narrative review synthesizes current human and preclinical evidence on the gut-ovary axis in PMOS, with particular emphasis on microbial dysbiosis, proposed mechanistic pathways, microbiome-related metabolic and endocrine interactions, and emerging therapeutic approaches. Human studies generally report associations between altered microbial composition and metabolic or reproductive features of PMOS, although findings vary considerably according to population characteristics, bodyweight, diagnostic criteria, sequencing methods, and analytical approaches. Experimental studies provide additional support for potential roles of microbial metabolites, intestinal permeability, immune signaling, and metabolic pathways, but these mechanisms have not been established as causal in humans. Microbiome-targeted interventions, including probiotics, prebiotics, synbiotics, and dietary approaches, show potential, whereas fecal microbiota transplantation remains largely experimental. Conventional metabolic therapies, including glucagon-like peptide-1 receptor agonists, should be considered separately from microbiome-targeted approaches. Overall, the gut-ovary axis represents a promising framework for understanding the systemic features of PMOS, but substantial heterogeneity, limited longitudinal human evidence, and underrepresentation of diverse populations currently limit translation into clinical practice.},
}

@article {pmid42954932,
year = {2026},
author = {Plisko, OL and Chapel, VS and Sekela, JJ and Talbert, JA and Townsend, SD and Zemel, BS and Wu, GD and R Redinbo, M},
title = {Human milk oligosaccharides are distinctly processed by early life gut microbial sialidases.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748788},
doi = {10.1080/19490976.2026.2748788},
pmid = {42954932},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Oligosaccharides/metabolism/chemistry ; *Neuraminidase/metabolism/genetics/chemistry ; Infant ; Adult ; Lactose/analogs & derivatives/metabolism ; *Bacteria/enzymology/genetics/classification ; Metagenome ; },
abstract = {The infant gut microbiome in early life is shaped by numerous factors, including feeding method. Exclusively breastfed and formula-fed infants exhibit distinct microbiome compositions. While these effects are well-established, the underlying mechanisms that drive these differences are not fully understood. Here, we examine the removal of sialic acid from human milk oligosaccharides (HMOs) influenced by human microbial sialidases in early life. We identify 351 and 214 unique sialidase sequences from adult and infant microbiome metagenomes, respectively, and characterize a diverse, representative set in vitro using sialylated HMOs normally present in human breastmilk. We find these proteins exhibit distinct abilities to metabolize 3'- and 6'-sialyllactose, which are the most abundant sialylated HMOs in breastmilk, and distinctly process other more complex substrates, as well. We provide structural insights into these functional differences by pinpointing active site features uniquely present in efficient enzymes and show that these results extend to activities on complex mixtures of sialylated HMOs purified from human breastmilk. Finally, we demonstrate in human clinical data that distinct profiles of sialidase-encoding bacterial taxa are observed in breastfed and formula-fed infants at 1 and 4 months of age, prior to the introduction of solid foods. Together, these findings show that specific bacterial sialidases are influential in shaping the early gut microbiome, data that may improve the supplementation of infant formulas for enhanced developmental outcomes.},
}

Humans
*Milk, Human/chemistry/metabolism
*Oligosaccharides/metabolism/chemistry
*Neuraminidase/metabolism/genetics/chemistry
Infant
Adult
Lactose/analogs & derivatives/metabolism
*Bacteria/enzymology/genetics/classification
Metagenome

@article {pmid42955029,
year = {2026},
author = {Stevens, T and Salani, M},
title = {The Crossroads Between the Kidney and Gastrointestinal Disorders: Core Curriculum 2026.},
journal = {American journal of kidney diseases : the official journal of the National Kidney Foundation},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.ajkd.2026.08.005},
pmid = {42955029},
issn = {1523-6838},
abstract = {The kidney and gastrointestinal (GI) tract are closely linked through a bidirectional system involving complex interactions called the gut-kidney axis. Within this system, alterations in the gut microbiome can promote progression of chronic kidney disease (CKD) while uremic toxins from advanced kidney dysfunction can adversely affect intestinal health. Incretin hormones, particularly glucagon-like peptide 1 (GLP-1), play an important role in this gut-kidney signaling and will be explored here. We also examine how this physiology helps explain the connection between GI illness and IgA nephropathy, along with the kidney manifestations seen in inflammatory bowel disease. Furthermore, we will review how CKD and end-stage kidney disease increase the risk of GI disease and complicate its management, and how CKD therapies affect GI symptoms. In this AJKD Core Curriculum, we use a case-based format to illustrate the intricate interplay between the kidneys and the GI tract.},
}

@article {pmid42955175,
year = {2026},
author = {de Lima Núñez, TA and de Moraes, RS and de Cerqueira Júnior, JCN and Ribeiro, D and Reyes, RPR and Andreatti Filho, RL and Melchert, A and Guimarães-Okamoto, PTC and Okamoto, AS},
title = {Constructing a Perspective of Probiotic Bacteria in the Management of Urinary Tract Infection in Cats: A Scoping Review.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42955175},
issn = {1867-1314},
abstract = {Feline lower urinary tract disease (FLUTD) and urinary tract infections (UTIs) pose a significant clinical challenge in companion animal medicine. Increasing antimicrobial resistance and emerging insights into the feline urinary microbiome highlight the potential of probiotic-based therapeutic strategies. However, the scope and quality of existing evidence in feline medicine remain unclear. This study aimed to systematically map and characterize the literature on probiotic microorganisms (particularly Lactobacillus spp. and Bifidobacterium spp.) in feline urinary health, identifying research domains, evidence gaps, and future priorities. A scoping review identified peer-reviewed studies addressing FLUTD, urinary microbiota, antimicrobial resistance, and probiotic interventions. Studies were categorized into four domains: clinical burden, microbiome evidence, clinical probiotic evidence, and mechanistic probiotic evidence. Fifty-three studies met inclusion criteria. The main finding of this review is that there is limited to no direct evidence on the use of probiotics for the management of FLUTD or UTIs in cats: only nine studies addressed probiotics (clinical probiotic evidence: n = 5; mechanistic probiotic evidence: n = 4), and no randomized controlled trials specifically assessing probiotic efficacy in cats were identify. Most literature focused on clinical burden (n = 37), comprising epidemiological surveys and antimicrobial resistance reports, whereas microbiome investigations were limited (n = 7). The high prevalence of Escherichia coli and increasing antimicrobial resistance underscore the need for alternative strategies. Addressing this gap through well-designed clinical trials in cats is essential before probiotic-based strategies can be recommended to improve both clinical outcomes and animal welfare in feline patients.},
}

@article {pmid42955188,
year = {2026},
author = {Saqr, A and Mohamed, ME and Staley, C and Onyeaghala, G and Vo, D and Remmel, RP and Teigen, L and Guan, W and Oetting, WS and El-Rifai, R and Dorr, CR and Gupta, K and Matas, AJ and Israni, AK and Jacobson, PA},
title = {Microbiome-Mediated Pharmacokinetics and Informed Dosing of Mycophenolate in Kidney Transplantation.},
journal = {Clinical pharmacokinetics},
volume = {},
number = {},
pages = {},
pmid = {42955188},
issn = {1179-1926},
support = {5R01AI140303//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND AND OBJECTIVES: The gut microbiome contributes to interindividual variability in drug pharmacokinetics; however, its role in guiding dose adjustments remains unclear. Mycophenolic acid (MPA), the active metabolite of the immunosuppressant mycophenolate mofetil (MMF), exhibits high pharmacokinetic variability, potentially linked to microbial activity. This study aimed to characterize the gut microbiome effect on MPA pharmacokinetics and determine if these effects necessitate dose modifications.

METHODS: In 84 kidney transplant recipients, plasma and urine concentration-time profiles for MPA and its glucuronide metabolites were characterized using population pharmacokinetic modeling in NONMEM[®]. Stool samples were collected within 2 days of pharmacokinetic sampling for microbiome shotgun metagenomic sequencing. Machine learning was used to identify microbial species associated with pharmacokinetic variability. The impact of these species and clinical covariates was evaluated using full fixed-effect modeling. Simulations were conducted to assess the effect of microbial relative abundance on MPA therapeutic target attainment across various MMF doses.

RESULTS: Five bacteria were associated with the magnitude or duration of enterohepatic circulation (EHC). High relative abundance of Eubacterium callanderi increased EHC and MPA exposure by 29-63%, requiring a 17% lower MMF dose. Conversely, high Faecalibacterium SGB15315 abundance reduced EHC and MPA exposure by 13-26%, requiring a 50-75% higher dose. While Gemmiger formicilis and Eisenbergiella tayi prolonged EHC by >100% and Anaerostipes caccae decreased it by 30%, these taxa did not clinically impact therapeutic target attainment.

CONCLUSION: We identified several stool microbial species affecting MPA pharmacokinetics. Specifically, Eubacterium callanderi and Faecalibacterium SGB15315 may identify patients who require additional therapeutic drug monitoring or possible dose modifications to reach target concentrations.

CLINICAL TRIAL REGISTRATION: Clinicaltrials.gov, NCT04953715.},
}

@article {pmid42955203,
year = {2026},
author = {Sagawa, T and Hirakawa, M and Nagashima, H and Fujikawa, K},
title = {Gut Microbiome Signatures and Immune Checkpoint Inhibitor Response in Gastrointestinal Cancers: Reproducibility and Translational Readiness.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42955203},
issn = {1534-6269},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Neoplasms/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; Reproducibility of Results ; Translational Research, Biomedical ; },
abstract = {PURPOSE OF REVIEW: Gut microbial features have been associated with immune checkpoint inhibitor (ICI) outcomes, but whether these signatures are robust across gastrointestinal (GI) tumor types, treatment regimens, and populations remains uncertain. This critical narrative review assesses human evidence, experimental mechanisms, longitudinal sampling, and the criteria needed for clinical implementation.

RECENT FINDINGS: A gastric cancer cohort showed different response-associated microbial features for immunotherapy alone, chemotherapy alone, and combined treatment. Cross-cancer strain-resolved analyses found that signature transportability was strongly conditional on matching ICI regimens. A large primary liver cancer cohort analyzed 315 patients and 777 serial samples and explored a baseline score derived from on-treatment species selection; later samples were available only in a selected subgroup, complicating interpretation. Experimental studies link selected microbes and metabolites with antitumor immunity, but these mechanistic findings do not establish therapeutic efficacy in humans. Fecal microbiota transplantation (FMT) studies in melanoma demonstrate feasibility yet do not establish benefit in GI malignancies. Stool profiles may not represent mucosal or tumor-adjacent communities in upper GI cancer. No stool microbiome signature is currently validated to select ICI therapy in GI oncology. Meaningful translation requires standardized assays, non-ICI comparators to establish treatment-effect prediction, strict separation of discovery and external validation, prospectively handled missingness, and randomized clinical-utility studies.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Neoplasms/drug therapy/microbiology/immunology
*Gastrointestinal Microbiome/drug effects/immunology
Reproducibility of Results
Translational Research, Biomedical

@article {pmid42955208,
year = {2026},
author = {Shen, WH and Zheng, LP and Zhou, JQ and Wang, JW},
title = {Exploring endophytic actinomycetes from Shiraia fruiting bodies to enhance fungal hypocrellin A biosynthesis.},
journal = {Bioresources and bioprocessing},
volume = {13},
number = {1},
pages = {},
pmid = {42955208},
issn = {2197-4365},
support = {82073955//National Natural Science Foundation of China/ ; 81773696//National Natural Science Foundation of China/ ; 900520246116//Start-up Funding for Research of Jiangsu Medical College/ ; },
abstract = {The medicinal fruiting bodies of Shiraia harbor diverse microbial communities that are increasingly recognized as important regulators of fungal secondary metabolism. While endophytic bacteria and fungi associated with Shiraia have recently attracted considerable attention, the diversity and functional roles of endophytic actinomycetes remain largely unexplored. Here, we combined culture-dependent isolation with high-throughput 16 S rRNA amplicon sequencing to investigate the endophytic actinomycete community associated with Shiraia fruiting bodies. A total of 28 actinomycete isolates representing four genera were recovered, with Streptomyces being the predominant culturable genus. Functional screening identified the native endophyte S. pseudogriseolus A6 as the most effective elicitor of fungal hypocrellin A (HA) biosynthesis. Genome analysis revealed abundant carbohydrate-active enzymes and 27 secondary metabolite biosynthetic gene clusters, indicating a strong genetic potential for fungal colonization and metabolite-mediated communication. Co-cultivation with live strain A6 markedly enhanced both intracellular and extracellular HA accumulation without significantly affecting fungal biomass. Under the optimized co-cultivation conditions, total HA production reached 296.0 mg/L, representing a threefold increase over the monoculture control. Furthermore, A6 coordinately upregulated the expression of HA biosynthetic genes and metabolite transport genes. This study provides the first characterization of endophytic actinomycetes associated with Shiraia fruiting bodies and identifies actinomycete elicitors capable of stimulating fungal HA biosynthesis. These findings expand current knowledge of the Shiraia microbiome and highlight endophytic actinomycetes as promising microbial resources for enhancing fungal perylenequinone production.},
}

@article {pmid42955256,
year = {2026},
author = {Bastaminejad, S and Bakhtiyari, S and Heidari, A and Ebrahimi, E},
title = {Gut microbiota as a key player in diabetes mellitus: mechanisms, dysbiosis, and emerging interventions.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42955256},
issn = {1874-9356},
abstract = {The gut microbiome has emerged as a critical regulator of metabolic and immune homeostasis, with significant implications for diabetes mellitus. This narrative review synthesizes findings from selected landmark original investigations published from 2000 to 2026, examining the role of the gut microbiome in both type 1 diabetes (T1D) and type 2 diabetes (T2D). As a narrative rather than a systematic review, this synthesis does not follow a registered protocol or an exhaustive, reproducible search strategy. Observational studies frequently report dysbiosis, characterized by reduced microbial diversity and altered taxa, as a feature of both prediabetes and diabetes, correlating with poor glycemic control and complications, although the specific taxa and dysbiotic signatures implicated vary across geographically and ethnically distinct populations, indicating that dysbiosis is not a uniform, population-invariant hallmark of disease. Mechanistic studies highlight pathways such as short-chain fatty acid production, immune modulation, and gut barrier integrity, which mediate microbial effects on insulin sensitivity and glucose metabolism, with short-chain fatty acid (SCFA) signaling and gut barrier integrity identified as the most significant pathways driving these effects. Interventional approaches, including probiotics, prebiotics, dietary modifications, fasting, exercise, and bariatric surgery, show preliminary, proof-of-concept potential to reshape the microbiome and improve diabetic outcomes, although none of these interventions has yet been validated in large-scale, adequately powered, multi-center randomized controlled trials with hard clinical endpoints, and none should be regarded as an established treatment. Notably, T1D research emphasizes autoimmune interactions, while T2D focuses on metabolic dysfunction. Despite advances, challenges like establishing causality and addressing inter-individual variability persist. This review underscores the microbiome's therapeutic promise pending confirmation in the larger trials outlined above, and advocates for personalized, multi-omics-driven strategies to enhance diabetes management.},
}

@article {pmid42955320,
year = {2026},
author = {Martin-Loeches, I and Povoa, P and Robba, C and Bandera, A and Guglielmi, A and Citerio, G},
title = {Ventilator-associated pneumonia after traumatic brain injury: a timing-sensitive ecological framework of neuroimmune-pulmonary vulnerability.},
journal = {Intensive care medicine},
volume = {},
number = {},
pages = {},
pmid = {42955320},
issn = {1432-1238},
abstract = {BACKGROUND: Ventilator-associated pneumonia (VAP) is frequent after traumatic brain injury (TBI), but its biological meaning and outcome impact remain incompletely defined. Traditional models emphasise mechanical ventilation, aspiration, colonisation, endotracheal tube biofilm, and hospital pathogens. These mechanisms remain essential, but they do not fully explain the early clustering, heterogeneous susceptibility, changing bacteriology, and variable mortality effect observed after TBI.

MAIN TEXT: Severe brain injury creates an early vulnerable host state through impaired consciousness and airway protection, neuroimmune dysregulation, autonomic and endocrine activation, altered pulmonary immune surveillance, and, in many patients, extracranial trauma, shock, transfusion, or thoracic injury. These processes interact with ventilation, antibiotic pressure, and rapid respiratory microbiome disruption. Early VAP may reflect abrupt loss of control after injury and intubation, whereas late VAP may reflect persistent or secondary failure driven by biofilm maturation, antibiotic selection, multidrug-resistant pathogens, and intensive care unit (ICU)-acquired immune dysfunction. Clinically, VAP consistently prolongs ventilation, ICU stay, antibiotic exposure, and resource use, while its independent effect on mortality is phenotype- and context-dependent.

CONCLUSIONS: This model proposes a timing-sensitive ecological framework in which established mechanisms may converge early and with particular clinical intensity after severe TBI, creating a vulnerable host-microbe state that may lower the threshold for clinically apparent infection. Future studies should distinguish isolated TBI from polytrauma, compare TBI with other acute brain injuries and non-neurological ventilated populations, and incorporate dynamic immune, microbial, and trajectory-based outcomes.

HIGHLIGHTS: VAP after TBI should be viewed as a timing-sensitive interaction between ventilator exposure and early host vulnerability, not as a distinct disease entity or as a pneumonia pathway unique to traumatic brain injury. The TBI-focused contribution lies in the early convergence of otherwise non-unique mechanisms: impaired airway control, aspiration risk, neuroimmune-endocrine activation, treatment exposure, dysbiosis, and extracranial injury burden, rather than in any single TBI-specific mechanism. Isolated TBI and TBI with polytrauma are biologically different phenotypes and should be separated in future studies. Early and late VAP may represent different phases of loss of pulmonary host-microbe containment; this distinction is probabilistic rather than TBI-specific in itself and requires validation in TBI-stratified cohorts. Mortality remains clinically relevant but context-dependent; VAP more consistently modifies recovery trajectory, ventilator dependence, ICU stay, antibiotic exposure, and possibly neurological recovery.},
}

@article {pmid42955366,
year = {2026},
author = {Ketehouli, T and Trub, MR and Goss, EM and Martins, SJ},
title = {Pseudomonas spp.-based synthetic microbial community effects on nutrient dynamics in citrus plants under induced dysbiosis.},
journal = {Planta},
volume = {264},
number = {6},
pages = {},
pmid = {42955366},
issn = {1432-2048},
support = {2022-68015-36721//National Institute of Food and Agriculture/ ; },
mesh = {*Pseudomonas/physiology ; Rhizosphere ; *Citrus/microbiology/metabolism ; *Microbiota ; Soil Microbiology ; *Dysbiosis/chemically induced ; Nutrients/metabolism ; Potassium/metabolism ; Streptomycin/pharmacology ; Anti-Bacterial Agents/adverse effects/pharmacology ; Plant Roots/microbiology ; },
abstract = {A targeted Pseudomonas-based synthetic microbial community reshaped rhizosphere bacterial communities and altered potassium partitioning under stress conditions, suggesting a potential role in mitigating antibiotic-induced dysbiosis. Sustainable agriculture primarily relies on biological practices to improve crop yield and resilience. Synthetic bacterial communities (SynComs) are a promising approach to promote plant growth; however, their effectiveness in situ is influenced by interactions with native microbial ecosystems and by environmental stressors, such as low pH and antibiotic use. In this context, beneficial microorganisms like Pseudomonas may enhance nutrient availability and mitigate antibiotic-induced dysbiosis by supporting microbial community reassembly and functional stability, thereby improving plant health. This study evaluated the effects of a Pseudomonas-based SynCom on nutrient accumulation and rhizosphere microbial dynamics in citrus plants subjected to streptomycin-induced dysbiosis and low-pH conditions. Selected Pseudomonas strains, chosen for their compatibility and adaptability to low-pH conditions, and through whole-genome sequencing, were applied at equal concentrations (OD600 = 0.1). SynCom treatment increased Chloroflexota abundance in the rhizosphere while reducing Actinomycetota and Pseudomonadota after 24 days. By Day 45, the abundance of Actinomycetota decreased, with slight increases in the other two phyla. At the genus level, SynCom application reduced the abundance of Pseudomonas and Agrobacterium, while enriching the Klebsiella community. Plants treated with SynCom under stress exhibited a 25% increase in leaf potassium levels, accompanied by a 29% decrease in root potassium (essential for stomatal regulation, osmotic adjustment, and photosynthetic efficiency, which are fundamental to tree growth and stress resilience) levels. Overall, our findings demonstrate that a targeted Pseudomonas-based SynCom can reshape rhizosphere communities and improve nutrient dynamics under abiotic stress, highlighting its potential as a sustainable strategy to mitigate antibiotic-induced dysbiosis and enhance citrus resilience.},
}

*Pseudomonas/physiology
Rhizosphere
*Citrus/microbiology/metabolism
*Microbiota
Soil Microbiology
*Dysbiosis/chemically induced
Nutrients/metabolism
Potassium/metabolism
Streptomycin/pharmacology
Anti-Bacterial Agents/adverse effects/pharmacology
Plant Roots/microbiology

@article {pmid42955378,
year = {2026},
author = {Gschwendtner, S and Maison, N and Illi, S and von Mutius, E and Rosenboom, I and Tümmler, B and Dittrich, AM and Weckmann, M and Abdo, M and Waschki, B and Kopp, MV and Hansen, G and Brinkmann, F and Rabe, K and Schaub, B and Schloter, M and , },
title = {Exploratory analysis of nasal and gut microbial community structure in preschool children with recurrent wheeze.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42955378},
issn = {1432-184X},
mesh = {Humans ; *Respiratory Sounds/etiology ; *Bacteria/classification/isolation & purification/genetics ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Pilot Projects ; Cross-Sectional Studies ; Female ; Infant ; Male ; *Nose/microbiology ; *Gastrointestinal Microbiome ; Recurrence ; *Microbiota ; DNA, Bacterial/genetics ; },
abstract = {Early-life wheezing has been associated with microbial alterations along the gut-airway axis, yet few studies have examined bacterial communities in both compartments within the same children. This cross-sectional exploratory pilot study (n=25) characterized nasal and stool bacterial communities in children aged 1-4 years with recurrent wheeze and healthy controls using 16S rRNA gene metabarcoding. Across participants, nasal and stool bacteriomes were highly individualized and taxonomically diverse. Overall richness, evenness, and global community composition did not differ significantly between healthy controls and children with recurrent wheeze in either compartment. Nasal communities in the recurrent-wheeze group showed greater within-group dispersion, although the comparison did not reach the conventional significance threshold (p=0.054). Exploratory distance-based stratification identified a subgroup with nasal profiles farther from the healthy-control centroid; these profiles had lower richness and evenness, higher Moraxella abundance, and lower abundances of Prevotella spp., Alloprevotella, and Veillonella. No statistically supported genus-level differences were detected in stool samples. Community-assembly and co-occurrence analyses yielded group-specific descriptive patterns in both compartments. Different sets of cross-compartment correlations passed the multiple-testing threshold in healthy controls and children with recurrent wheeze, including correlations of stool Lactococcus with several nasal taxa in the recurrent-wheeze group. Because these analyses were performed in small groups, they are considered hypothesis-generating. These findings identify nasal microbial heterogeneity and exploratory differences in community organization in preschool children with recurrent wheeze, while providing no evidence for causal or Moraxella-driven effects. Larger longitudinal studies with functional measurements are required for validation.},
}

Humans
*Respiratory Sounds/etiology
*Bacteria/classification/isolation & purification/genetics
Child, Preschool
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Pilot Projects
Cross-Sectional Studies
Female
Infant
Male
*Nose/microbiology
*Gastrointestinal Microbiome
Recurrence
*Microbiota
DNA, Bacterial/genetics

@article {pmid42955504,
year = {2026},
author = {Catalogna, A and Agostoni, C and Barni, S and Canani, RB and Carucci, L and Ciliberti, L and Coppola, S and Corsello, A and Milani, GP and Mori, F and Nocerino, R and Pinto, BS and Spolidoro, GCI and Giovannini, M and Munblit, D},
title = {Breast Milk and Allergic Disease Development: Immunological Factors Associated with Eczema, Food Allergy and Wheezing/Asthma.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42955504},
issn = {1534-6315},
mesh = {Humans ; *Milk, Human/immunology ; *Food Hypersensitivity/immunology ; Female ; *Eczema/immunology ; *Respiratory Sounds/immunology ; *Asthma/immunology ; Infant ; Cytokines/metabolism ; *Hypersensitivity/immunology ; },
abstract = {PURPOSE OF REVIEW: Human milk (HM) contains a diverse array of immunological, microbial, and metabolic bioactive factors that may influence early immune maturation and allergic disease susceptibility. This narrative review examines current evidence linking major HM bioactives with eczema, food allergy, and wheezing/asthma, integrating mechanistic findings with human observational and clinical data.

RECENT FINDINGS: Transforming growth factor-β (TGF-β), secretory IgA (sIgA), human milk oligosaccharides (HMOs), cytokines, fatty acids, short-chain fatty acids, the HM microbiome, and extracellular vesicles have all been implicated in pathways relevant to epithelial integrity, microbial colonization, and immune tolerance. However, associations with allergic outcomes are heterogeneous and frequently context dependent. Findings vary according to lactation stage, maternal characteristics, infant susceptibility, microbial exposures, and outcome definition. Mechanistic evidence is often stronger than prospective clinical evidence, and no individual HM component or bioactive profile has yet emerged as a reproducible predictor of allergy protection. Current evidence supports viewing HM as a dynamic maternal-milk-infant biological network rather than as a source of isolated protective factors. Future studies should integrate repeated HM sampling, rigorous allergic phenotyping, and multi-omic approaches to distinguish causal mediators from biomarkers of maternal or infant biology.},
}

Humans
*Milk, Human/immunology
*Food Hypersensitivity/immunology
Female
*Eczema/immunology
*Respiratory Sounds/immunology
*Asthma/immunology
Infant
Cytokines/metabolism
*Hypersensitivity/immunology

@article {pmid42956094,
year = {2026},
author = {Kakabra, K and Patel, S and Temko, A and Claesson, MJ},
title = {Taxonova: Deep learning enables fast and confidence-aware microbiome species-level amplicon classification.},
journal = {PLoS computational biology},
volume = {22},
number = {10},
pages = {e1014912},
doi = {10.1371/journal.pcbi.1014912},
pmid = {42956094},
issn = {1553-7358},
abstract = {Accurate species-level taxonomic classification of microbial amplicon sequences remains challenging due to the difficulty of resolving subtle variations within conserved ribosomal regions. Traditional similarity-based methods struggle with short amplicons and sequences with poor database representation. No existing method performs robustly across the full spectrum of amplicon lengths, limiting applicability across diverse sequencing platforms and variable-region targets. We present Taxonova, a deep learning framework for both short- and long-read ribosomal amplicons. Evaluated across physical and biome-simulated mock communities representing seven biomes (via the accompanying benchmark tool Taxobench), Taxonova attains species-level F-measures of 0.76-1.00 (median 0.94) for short-read and 0.82-0.99 (median 0.97) for long-read amplicons spanning 250 bp to 4,900 bp, reduces the species-level abundance-estimation error (L1 norm) by a median of 0.52 to 1.50 depending on amplicon region, and has a species-level false-positive rate that is a median of 16.2 × 10-4 lower than that of the other classifiers. Species-level assignment is expected to be most reliable for well-characterised communities, such as human-associated microbiomes. To demonstrate real-world applicability, we also compared amplicon-derived taxonomic profiles to paired shotgun whole-genome sequencing from gut, soil and vaginal microbiomes; Taxonova achieves the strongest species-level concordance (Jaccard) in all three studies, with a species-level Jaccard index 0.009 to 0.022 higher than that of the next-best classifier across both high- and low-complexity communities. Taxonova runs at a throughput of roughly 100 sequences per second on a single CPU core, making it suitable for routine deployment in research settings.},
}

@article {pmid42956359,
year = {2026},
author = {Shabbir, A and Parvinzadeh Gashti, M},
title = {Advanced cannabidiol delivery platforms: smart biomaterials, controlled release systems, and 3D-bioprinted therapeutic technologies.},
journal = {Journal of drug targeting},
volume = {},
number = {},
pages = {1-29},
doi = {10.1080/1061186X.2026.2755447},
pmid = {42956359},
issn = {1029-2330},
abstract = {Cannabidiol (CBD), a non-psychoactive phytocannabinoid derived from Cannabis sativa L. has gained significant attention in biomedical research due to its broad spectrum of therapeutic properties, including anti-inflammatory, antimicrobial, antioxidant, neuroprotective, and anticancer activities. However, its clinical translation remains limited by poor aqueous solubility, low bioavailability, rapid metabolism, and instability under physiological conditions. To overcome these challenges, advanced drug delivery platforms based on 3D bioprinting technologies have emerged as promising strategies for controlled and site-specific delivery of CBD. This review provides a comprehensive overview of state-of-the-art CBD delivery systems, including polymeric biomaterials such as PLGA, PEG derivatives, chitosan, alginate, and cellulose-based hybrids, which enhance drug stability and enable sustained release profiles. Nano- and microstructured systems, including liposomes, nanoparticles, nanoemulsions, microspheres, and electrospun nanofibers, are discussed for their ability to improve bioavailability and facilitate targeted delivery at the cellular level. Hydrogel-based platforms, particularly injectable and stimuli-responsive systems, are highlighted for their role in localised therapy and tissue engineering applications. Furthermore, the integration of 3D bioprinting technologies enables the fabrication of patient-specific scaffolds and implantable constructs for precision medicine and regenerative therapies. Stimuli-responsive systems, including pH-, temperature-, enzyme-, and externally triggered release platforms, further enhance on-demand drug release in diseased microenvironments. The biomedical applications of CBD-based systems are critically evaluated in antimicrobial therapy, wound healing, tumour-targeted cancer therapy, immunomodulation, microbiome regulation, and regenerative medicine. Finally, this review addresses current translational challenges such as drug loading efficiency, stability issues, scalability, and regulatory barriers, while highlighting future perspectives involving artificial intelligence-guided design, personalised nanomedicine, and advanced biomanufacturing technologies. Overall, CBD-based smart biomaterial platforms represent a highly promising approach for next-generation therapeutic systems with improved efficacy, safety, and clinical potential.},
}

@article {pmid42956460,
year = {2026},
author = {Araujo, LDC and da Silva, RAB and Messora, MR and Furlaneto, FAC and Salvador, SL and Radaic, A and Kamarajan, P and Kapila, YL and Nelson-Fillho, P and Gomes-Moura, AP and da Silva, LAB},
title = {Intracanal administration of Bifidobacterium animalis subsp. lactis HN019 modulates the microbiota of periapical lesions in male rats.},
journal = {Archives of oral biology},
volume = {193},
number = {},
pages = {106788},
doi = {10.1016/j.archoralbio.2026.106788},
pmid = {42956460},
issn = {1879-1506},
abstract = {OBJECTIVE: The oral microbiome comprises a complex microbial community that plays a fundamental role in maintaining oral health by preventing the proliferation of pathogenic microorganisms. This study aimed to investigate whether the probiotic strain Bifidobacterium animalis subsp. lactis HN019 (B. lactis HN019) can modulate the microbiota associated with periapical lesions.

DESIGN: Thirty-one Wistar rats were randomly allocated into four groups (n = 8/group): healthy teeth; periapical lesion infection; periapical lesion treated with vehicle (2% carboxymethylcellulose [CMC]); and periapical lesion treated with a probiotic solution containing 2.7 × 10⁹ CFU of B. lactis HN019 in 2% CMC. On days 7 and 14 after infection, 600 μL of vehicle or probiotic solution was applied in root canal orifice and aspirated, followed by placement of 5 μL inside the root canal before restoration. After euthanasia, hemimandibles were processed for histological analysis. Laser capture microdissection was used to isolate periapical lesion samples for DNA extraction and bacterial identification by 16S rRNA sequencing. Alpha diversity was analyzed using one-way ANOVA and Kruskal-Wallis tests (5% significance).

RESULTS: Healthy teeth exhibited a characteristic resident microbiota, with Staphylococcus aureus, Cutibacterium acnes, and Streptococcus oralis as the most abundant species. In the infection group, Streptococcus agalactiae predominated. In the probiotic group, Streptococcus agalactiae and Bacteroides fragilis remained predominant, while Lactobacillus reuteri significantly increased compared with the infection group (p = 0.033).

CONCLUSION: B. lactis HN019 modulated the microbiota associated with periapical lesions, supporting its potential as an adjunctive strategy to promote microbial balance and tissue recovery.},
}

@article {pmid42956531,
year = {2026},
author = {Kramer, ML and Bradbury, M and Ho, AK and Lamprecht, E and Finlay, KA},
title = {The good participant paradox: BenevolentMisrepresentation as a response to research exclusion.},
journal = {Social science & medicine (1982)},
volume = {411},
number = {},
pages = {119937},
doi = {10.1016/j.socscimed.2026.119937},
pmid = {42956531},
issn = {1873-5347},
abstract = {RATIONALE: Research participation fraud is typically framed as incentive-driven dishonesty, yet altruistic motivation is near-universal among research candidates. A paradox is created when well-intentioned individuals misrepresent their eligibility information to join studies they believe will help others, rather than for personal gain. This phenomenon, termed benevolent misrepresentation, is poorly understood and increasingly consequential as online research recruitment and screening become more widespread.

OBJECTIVE: This study examined when and why well-intentioned individuals misrepresent their eligibility during health research screening.

METHODS: A sequential mixed-methods design was employed, including observational analysis of 10,734 screening submissions from a large-scale urinary microbiome study, qualitative analysis of excluded candidate correspondence (n = 25), and a quantitative survey of individuals from the same patient population (n = 438).

RESULTS: Misrepresentation was predominantly situational rather than a reflection of persistent underlying dishonesty. A Two-Stage Model emerged: emotional responses, altruistic salience, and perceived eligibility predicted whether individuals resisted exclusion, while perceived eligibility alone differentiated whether resistance took the form of legitimate challenge or misrepresentation. 24.01% misrepresented their eligibility in at least one scenario. Exclusion criteria that dismissed experiential knowledge in favour of clinical diagnosis elicited the highest misrepresentation rates; unspecified exclusion criteria elicited the lowest.

CONCLUSION: These findings, grounded in procedural justice and moral self-licensing theory, challenge fraud-detection models by suggesting misrepresentation is strongly associated with perceived injustice rather than intentional dishonesty. The psychological mechanisms of benevolent misrepresentation in unremunerated research are explored through the lens of a Two-Stage Model of Benevolent Misrepresentation, and practical recommendations are provided to help researchers avoid the identified triggers.},
}

@article {pmid42956717,
year = {2026},
author = {Bork, P and Bowler, C and Tedersoo, L and Kuhn, M and , and Abiven, S and de Vargas, C and Bertucci, PY},
title = {Toward planetary microbial systems biology.},
journal = {Cell},
volume = {189},
number = {22},
pages = {6907-6921},
doi = {10.1016/j.cell.2026.09.019},
pmid = {42956717},
issn = {1097-4172},
mesh = {*Systems Biology/methods ; *Earth, Planet ; *Microbiota ; Ecosystem ; Multiomics ; },
abstract = {Microorganisms underpin Earth's biosphere, sustaining life, shaping biogeochemical cycles, and maintaining ecosystem stability. In an era of scientific and geopolitical fragmentation, we advocate for a "planetary microbial systems biology" (PMSB) framework to uncover the mechanisms and organizational principles governing Earth's interconnected microbial systems across scales of matter, space, and time and in relation to underlying natural and anthropogenic drivers. PMSB combines molecular and cellular technologies, multi-omics data, artificial intelligence (AI), and integrated transdisciplinary research across ecosystems. By federating open data and combining field observations, experimentation, and modeling, PMSB enables predictive understanding of microbiome dynamics across planetary scales, thus filling a critical knowledge gap in our understanding of the co-evolution of life and the Earth-system.},
}

*Systems Biology/methods
*Earth, Planet
*Microbiota
Ecosystem
Multiomics

@article {pmid42956747,
year = {2026},
author = {Kadoki, M and Nanki, K and Szamosvári, D and Mohamed, AMT and Stražar, M and Thurimella, K and Lee, J and Shin, YH and Ung, P and Shuai, M and Zimmerman, S and Park, J and Nambu, A and Avila-Pacheco, J and Mashin, E and Carey, KL and Li, B and Pishchany, G and Clish, CB and Clardy, J and Graham, DB and Xavier, RJ},
title = {Microbial products trigger chemosensory dialogues through intestinal G protein-coupled receptors.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.10.002},
pmid = {42956747},
issn = {1934-6069},
abstract = {Organismal reactions to changing environmental conditions require information relays that sense cues and elicit appropriate responses. G protein-coupled receptors (GPCRs), including olfactory receptors, comprise the largest receptor family that recognizes environmental cues, consisting of over 800 genes in the human genome. Here, by screening libraries of gut metabolites and natural products using a multiplexed GPCR reporter system, GPCR-seq, we reveal multiple intestinal chemosensory pathways. Among these, we determine that a cyclic fatty acid promotes serotonin production from enterochromaffin cells via olfactory receptor OR51E1. Two additional gut microbe-derived molecules, a β-carboline and 6-hydroxynicotinic acid (6-HNA), function as agonists for GPR35, a receptor linked to inflammatory bowel disease (IBD). The IBD-associated GPR35 risk variant, T108M, shows aberrant responses to 6-HNA, while Enterocloster bolteae, a species increased in IBD, generates high levels of 6-HNA. This approach provides an accelerated path to mapping critical chemosensory pathways and host physiological responses.},
}

@article {pmid42956754,
year = {2026},
author = {Bhuiyan, MNI and Hossain, SJ},
title = {Artificial Intelligence for Predictive Microbiome Engineering: Integrating Community Design and Environmental Validation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {6},
pages = {},
pmid = {42956754},
issn = {1758-2229},
mesh = {*Artificial Intelligence ; *Microbiota ; Ecosystem ; Microbial Consortia ; Multiomics ; },
abstract = {Microbial ecosystems can now be measured across genomic, transcriptomic, proteomic, metabolomic, and environmental dimensions, yet their emergent functions remain difficult to predict and control. Artificial intelligence (AI) can integrate heterogeneous data, but predictive accuracy alone does not establish causality, transferability, or controllability. This review developed a five-layer framework: observe, infer, predict, design, and learn that connects microbial measurement to prospective intervention and experimental feedback. We critically synthesise evidence from sequence and protein learning, multi-omics integration, metabolic modelling, synthetic microbial communities, environmental biotechnology, and temporal forecasting. Recent primary studies illustrate progress in forecasting community trajectories, predicting microbial competition and designing consortia for pollutant degradation; they also reveal important boundaries between model performance and demonstrated ecosystem control. We examine risks arising from compositional data, information leakage, dependent observations, batch effects, uncertain calibration, sparse perturbation data, ecological instability, and evolutionary change. We propose operational criteria for ecosystem programmability and a staged validation pathway from controlled systems to field-relevant environments. Progress will depend on standardised context-rich data, hybrid AI-mechanistic models, prospective benchmarks, independent replication, and safety-constrained design.},
}

*Artificial Intelligence
*Microbiota
Ecosystem
Microbial Consortia
Multiomics

@article {pmid42956980,
year = {2026},
author = {Wang, K},
title = {Microplastics and antibiotic toxicity in aquatic organisms: Exposure, interactions and mechanisms.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110726},
doi = {10.1016/j.cbpc.2026.110726},
pmid = {42956980},
issn = {1532-0456},
abstract = {Micro- and nanoplastics co-occur with antibiotic residues in aquatic environments, but whether particles increase antibiotic hazard remains unresolved. We conducted a structured qualitative synthesis of original aquatic co-exposure studies identified through Europe PMC searches to 25 September 2026, a complementary OpenAlex search and citation chasing. Experiments were compared by organism, particle properties, both contaminant concentrations, exposure route, comparator design and endpoint. Reported outcomes include amplification, attenuation and dose- or endpoint-dependent reversals. Marine bivalve and other invertebrate studies extend this evidence to low antibiotic concentrations, but low antibiotic exposure does not by itself establish realistic particle exposure. Microbiome shifts were distinguished from host injury and fitness impairment. A mixture response exceeding either single treatment does not establish synergy, and increased tissue accumulation does not alone establish particle-mediated delivery. Our study-level appraisal separates conditional co-exposure findings from designs capable of identifying an interaction and from evidence supporting a specific mechanism. The five-level hierarchy is proposed as a framework for evaluating current claims and designing future research; its highest levels are evidentiary targets, not a claim that the existing literature has already established causal pathways at environmentally realistic exposures.},
}

@article {pmid42957030,
year = {2026},
author = {Hu, J and Xing, N and Bao, G and Yuan, Y and Bao, L and Sana, S},
title = {A new risk to food security: Co-transport, accumulation, and deterioration of nutritional quality mediated by surface charge of nanoplastics and flame retardants in the soil-crop system.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126041},
doi = {10.1016/j.envres.2026.126041},
pmid = {42957030},
issn = {1096-0953},
abstract = {The pervasive coexistence of nanoplastics (NPs) and organophosphorus flame retardants (OPFRs) in agro-ecosystems poses direct threats to food security and environmental sustainability, yet the underlying synergistic toxicities remain largely unknown. This study explores how surface-charge properties may mediate the combined toxicity of carboxylated (PS-COOH) and aminated (PS-NH2) polystyrene NPs with the OPFR triethyl phosphate (TEP) in rye. Through integrated short-term hydroponics and full-life-cycle soil cultivation coupled with multi-dimensional analyses, we demonstrate that positively charged PS-NH2 exerts significantly greater toxicity than PS-COOH. Mechanistically, our results suggest that TEP may promote the formation of NP-containing complexes via van der Waals-type interactions, potentially serving as a carrier to enhance root uptake and translocation of PS-NH2 into grains. This synergistic-like response triggered severe oxidative stress (H2O2 levels 10-fold higher than control), disrupted metabolic homeostasis, and altered the rhizosphere microbiome, with elevated relative abundances of taxa such as Comamonadaceae under TEP-containing treatments. Transcriptomics revealed specific activation of phenylpropanoid biosynthesis and repression of ion transport and energy metabolism pathways. Consequently, the PS-NH2 + TEP co-exposure delayed heading by 22 days, reduced 1000-grain weight by 28.89%, slashed grain crude fat by 55.58%, and increased indigestible fiber by 62.67%. These findings underscore that NP surface charge is a critical determinant of phytotoxicity. The resultant cascade of physiological disruptions may compromise crop yield and nutritional integrity, creating plausible entry points for contaminants into the food chain and ultimately raising concerns for global food security and ecosystem resilience.},
}

@article {pmid42957060,
year = {2026},
author = {Kanj, AN and Wireko, FW and Zhao, CY and Limper, AH and Skalski, JH},
title = {Respiratory and Gastrointestinal Mycobiome Profiles Identify Distinct Patient Clusters Associated with Asthma Control.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {109240},
doi = {10.1016/j.rmed.2026.109240},
pmid = {42957060},
issn = {1532-3064},
abstract = {PURPOSE: The human microbiome contributes to asthma pathogenesis, yet most studies have focused on bacterial communities. This pilot study aimed to characterize fungal communities across multiple body sites in adults with asthma and evaluate whether integrated multisite mycobiome profiles are associated with asthma control.

PATIENTS AND METHODS: We enrolled 24 adults with asthma evaluated at Mayo Clinic between 2020 and 2022. Oral wash, nasal swab, sputum, and stool samples were collected, and fungal communities were characterized using ITS2 sequencing. Multisite mycobiome data were integrated using an unsupervised clustering approach , with a two-cluster solution selected for exploratory clinical comparisons. Clusters were compared with respect to fungal composition, site-specific diversity metrics, and asthma control.

RESULTS: Two patient clusters with distinct multisite mycobiome profiles were identified. Cluster 1 demonstrated poorer asthma control, with lower Asthma Control Test scores than Cluster 2 (median [IQR], 15.0 [13.0-17.5] vs. 18.0 [17.0-19.0]; p = 0.040). Compared with Cluster 2, Cluster 1 exhibited a higher relative abundance of Cladosporium in nasal and sputum samples, and greater sputum fungal diversity (p = 0.016). In contrast, Cluster 2 exhibited a higher relative abundance of Candida in stool and sputum samples. No significant differences in fungal diversity were observed in oral, nasal, or stool samples.

CONCLUSION: Integrated multisite mycobiome profiling identified distinct fungal community patterns associated with asthma control, highlighting the need for larger, longitudinal studies to define their clinical relevance.},
}

@article {pmid42957456,
year = {2026},
author = {Faisal, M and Abdelfattah, N and Yun, K},
title = {Multilayered mechanisms driving sexual dimorphism in antitumor immunity.},
journal = {Trends in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.it.2026.09.007},
pmid = {42957456},
issn = {1471-4981},
abstract = {Biological sex is a major variable associated with cancer incidence and treatment response, but how it affects antitumor immunity is not well understood. This review highlights the multilayered mechanisms driving sex differences in antitumor immunity. At the molecular level, tumor suppressor and oncogene alterations can be sex-biased and lead to the activation of noncanonical, immune-altering pathways. At the tissue level, resident immune niches and the commensal microbiome modulate sex-biased inflammation. Finally, at the organismal level, sex hormones and chromosomes, which act systemically across tissues, drive divergent inflammatory responses. Together, these mechanisms drive sex-specific antitumor responses, including differences in immunotherapy efficacy and toxicity. Further elucidating these mechanisms will advance precision oncology through sex-stratified treatment strategies and improve preclinical and clinical study designs.},
}

@article {pmid42957500,
year = {2026},
author = {Ma, Y and Liu, Q},
title = {Cross-kingdom volatile networks shape plant resilience.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2026.09.014},
pmid = {42957500},
issn = {1878-4372},
abstract = {Volatile organic compounds (VOCs) are interpreted as transient, unidirectional signals in plant-microbe interactions. We argue that this reductionist framing obscures their emergent role as regulators of ecological network dynamics, influencing stability-associated properties of plant-microbe systems. We propose a conceptual framework based on five principles (gradient logic, blend emergence, feedback reciprocity, threshold switching, and multiscale coupling) and use it to generate falsifiable predictions for how plant-derived and microbial VOCs operate as a cross-kingdom regulatory network shaping microbiome assembly, plant physiological plasticity, and multitrophic interactions. Key mechanistic gaps are critically evaluated alongside testable approaches for probing volatile-mediated ecological dynamics. Viewing volatile networks as adaptive ecological infrastructure reframes plant-microbiome resilience with implications for sustainable agriculture and ecological restoration under global change.},
}

@article {pmid42957522,
year = {2026},
author = {Zhou, D and Li, D and Zhong, C and Li, Q and Chen, P and Yang, S and Liang, H and Chen, Z and He, H and Zhang, H and Zeng, X and Chen, M and Lin, Y and Xu, M and Liu, X and Cai, M and Deng, Y},
title = {Gut microbiota-derived UDP-GlcNAc co-opts the host O-GlcNAcylation system to fuel breast tumour progression.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2026.10.022},
pmid = {42957522},
issn = {2095-9281},
abstract = {The gut microbiome is increasingly linked to breast cancer (BC) progression; however, specific microbial metabolites and their direct mechanistic connections to oncogenic signalling remain poorly defined. Here, using multi-omics analyses in treatment-naïve patients with BC, we identified gut microbiota-derived uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) as a circulating oncometabolite associated with therapeutic response. We further showed that Ruminococcus lactaris is a key intestinal commensal capable of de novo UDP-GlcNAc biosynthesis, and that microbial-derived UDP-GlcNAc acts as an independent tumour-promoting metabolite, even though the host hexosamine pathways generate the majority of circulating UDP-GlcNAc pools. Mechanistically, UDP-GlcNAc systemically activates O-GlcNAc transferase (OGT), stabilizing the transcription factor NFIB, and triggers a feed-forward loop that upregulates OGT and the proto-oncogene KIT, thereby driving BC progression. Genetic or pharmacological inhibition of OGT disrupts this signaling axis and suppresses tumour growth, even in the presence of UDP-GlcNAc-producing bacteria. These findings reveal a gut microbiota-metabolite-host signalling circuit, in which a microbial metabolite hijacks a core host post-translational modification pathway to promote BC progression, providing novel opportunities for microbiome-targeted diagnosis and therapy.},
}

@article {pmid42957639,
year = {2026},
author = {Lista, S and Emanuele, E and Cuperlovic-Culf, M and Mahdi, A and Singh, V and López-Ortiz, S and Khoramipour, K and Merino-País, M and Minoretti, P and Cisale, GY and Heslegrave, A and Imbimbo, C and Sancesario, GM and Bendlin, BB and Imbimbo, BP and Zetterberg, H and Santos-Lozano, A},
title = {Artificial intelligence applications in microbiota-gut-brain axis research: Implications for Alzheimer's disease.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261500124},
doi = {10.1177/13872877261500124},
pmid = {42957639},
issn = {1875-8908},
abstract = {Alterations in the gut microbiota (GM) are increasingly implicated in Alzheimer's disease (AD) pathogenesis through the microbiota-gut-brain axis (MGBA), influencing neuroinflammation, amyloid-β deposition, and tau aggregation. The inherent complexity of microbiota data necessitates artificial intelligence (AI) and machine learning (ML) to identify novel biomarkers and therapeutic targets. In this narrative review, we examined AI applications in AD-related GM research, including metataxonomic and metagenomic approaches. AI methods facilitate microbial signature identification and enterotype characterization associated with AD progression, enable multi-omics integration clarifying molecular pathways linking GM dysbiosis to neurodegeneration, support predictive modeling for early AD detection, and inform personalized MGBA-targeted interventions. Employed techniques include classical ML (e.g., random forests) for taxonomic classification, deep learning (e.g., neural networks) for complex pattern recognition, and explainable AI for identifying key bacterial taxa and metabolic functions. Significant challenges persist regarding methodological standardization, larger longitudinal cohorts, and ethical considerations in clinical applications. Future priorities include developing interpretable models, integrating longitudinal multi-omics data to establish causality, and validating AI-derived insights for precision AD prevention and treatment. AI uniquely enables high-dimensional, non-linear analyses that advance understanding of microbiome-brain interactions, though clinical translation requires rigorous validation and interdisciplinary collaboration.},
}

@article {pmid42957705,
year = {2026},
author = {Anani, H and Destras, G and Semanas, Q and Martin, FP and Petrier, M and Oddoux, E and Burfin, G and Bulteau, S and Poulain, C and Sinha, D and Motos, A and Gourain, V and Cremet, L and Montassier, E and Bressollette-Bodin, C and Roquilly, A and Josset, L},
title = {Identification of functional bacterial-viral pneumotypes associated with airway inflammation and all-cause mortality in critically ill patients.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957705},
issn = {2041-1723},
mesh = {Humans ; *Critical Illness/mortality ; Female ; Male ; Klebsiella pneumoniae/genetics/virology ; *Lung/microbiology/virology ; Middle Aged ; Bacteriophages/genetics/isolation & purification/pathogenicity ; Aged ; Microbiota/genetics ; Cross Infection/microbiology/mortality/virology ; Metagenomics ; Dysbiosis/microbiology ; Streptococcus/genetics ; },
abstract = {Alterations in lung virome and bacteriome compositions have been associated with hospital-acquired pneumonia in critically ill patients, but data on lung microbiome functions underlying progression to severe complications remain unclear. Here, we analyse 184 endotracheal aspirates (ETAs) collected in 94 intubated critically ill patients enrolled in a clinical trial (NCT04793568). Combining viral-metagenomics with metatranscriptomics analyses, we identify a high-risk functional pneumotype observed before the onset of hospital-acquired pneumonia and associated with lung inflammation and mortality. This unfavourable pneumotype is characterised by enrichment in virulent Streptococcus-bacteriophages and temperate Klebsiella-bacteriophages, decreased transcriptional activity of commensal taxa such as Streptococcus and Alloprevotella, and increased transcriptional activity of Klebsiella pneumoniae. Machine-learning models define two-viral- and four-bacterial-factor signatures predicting unfavourable pneumotype (AUC 0.8 and 0.7, respectively). Validation in an independent cohort (NCT02003196) of 117 ICU patients (239 ETAs) demonstrates the robustness of the association of these signatures with the risk of mortality. Causal inference identifies virulent bacteriophages associated with Streptococcus and host genes including IL18R1, ADM and PTX3, as key regulators of severe lung dysbiosis linked to mortality in critically ill patients.},
}

Humans
*Critical Illness/mortality
Female
Male
Klebsiella pneumoniae/genetics/virology
*Lung/microbiology/virology
Middle Aged
Bacteriophages/genetics/isolation & purification/pathogenicity
Aged
Microbiota/genetics
Cross Infection/microbiology/mortality/virology
Metagenomics
Dysbiosis/microbiology
Streptococcus/genetics

@article {pmid42957707,
year = {2026},
author = {Pulliam, C and Xu, M and Holandez-Lopez, K and Xue, D and Shang, Z and Gupta, G and Dioli, OE and Xiao, H and Gou, L and Wu, C and Brodbelt, JS and Wu, E and Peng, X and Chen, H and Li, J},
title = {Genome mining of the tumor microbiome reveals biosynthetic diversity and potential pathology-modulating metabolites.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957707},
issn = {2041-1723},
support = {1R35GM150565//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM139658//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F-1155//Welch Foundation/ ; },
mesh = {Humans ; *Neoplasms/microbiology/metabolism/pathology ; *Microbiota/genetics ; Multigene Family ; Fusobacterium/genetics/metabolism ; Metagenome ; Biosynthetic Pathways/genetics ; Genome, Bacterial ; },
abstract = {Human tumor-associated microbes - the tumor microbiome - have demonstrated an increasingly important role in human health due to their relevance to cancer progression and treatment response. While the metabolism at the host-microbiota interface, such as in the human gut, has been extensively investigated in recent years, the specialized metabolites from the tumor microbiome remain uncharted territory. To address this knowledge gap, we report a survey of the biosynthetic potential of the human tumor microbiome. Utilizing high-quality microbial metagenome-assembled genomes from 3,526 human tumor tissue samples, we identify 528 biosynthetic gene clusters with the potential to encode specialized metabolites relevant to tumor pathology. We reveal that the tumor microbiome encodes known and unknown metabolites spanning multiple biosynthetic classes. From this diverse biosynthetic landscape, we express a conserved family of biosynthetic genes from the genus Fusobacterium, which has a well-established role in cancer, and discover distinct families of long-chain fatty acyl amides. We subsequently find that one of these fatty acyl amides, oleoyl γ-aminobutyric acid, has immunomodulatory and G-protein-coupled receptor partial agonist activities, potentially supporting the influence of Fusobacterium in tumor pathology. The findings of our investigation lay a foundation for further research into the roles of tumor microbe-derived metabolites in cancer.},
}

Humans
*Neoplasms/microbiology/metabolism/pathology
*Microbiota/genetics
Multigene Family
Fusobacterium/genetics/metabolism
Metagenome
Biosynthetic Pathways/genetics
Genome, Bacterial

@article {pmid42957744,
year = {2026},
author = {Ghiotto, G and Zampieri, G and Orellana, E and Chatzis, A and Kougias, PG and Camargo, A and Roux, S and Campanaro, S and Kyrpides, NC and Treu, L},
title = {Author Correction: Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
doi = {10.1038/s41467-026-79140-1},
pmid = {42957744},
issn = {2041-1723},
}

@article {pmid42957759,
year = {2026},
author = {Nasr, EMT and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, KT and Ferrari, E and Griffin, TJ and Grüning, BA and Hiltemann, S and Hyde, CJ and Jagtap, PD and Kumar, A and Malla, MA and Mehta, S and Métris, KL and Momin, S and Nelson, T and Oba, AJ and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, AP and van Heusden, P and Vohra, M and Zierep, PF and Batut, B},
title = {Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42957759},
issn = {2399-3642},
support = {ANR-11-INBS-0013//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-MPGA-0013//Agence Nationale de la Recherche (French National Research Agency)/ ; U41HG006620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U24AI183870//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 75N92023P00302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U41HG006620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; INV-046492//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV-079648//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 228162/Z/23/Z//Wellcome Trust (Wellcome)/ ; LIBIS/de.NBI Freiburg,//Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg (Ministry of Science, Research and Art Baden-Württemberg)/ ; HORIZON-INFRA-2021-EOSC-01-04//European Commission (EC)/ ; REA.B.3, BGE 101059492//European Commission (EC)/ ; REA.B.3, BGE 101059492//European Commission (EC)/ ; },
mesh = {Reproducibility of Results ; *Microbiology ; *Computational Biology/methods ; Microbiota ; Proteomics ; *Software ; },
abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyse it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab (MGL): a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports the creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbiological data analysis. The MGL enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org , .eu , .org.au , . fr).},
}

Reproducibility of Results
*Microbiology
*Computational Biology/methods
Microbiota
Proteomics
*Software

@article {pmid42957763,
year = {2026},
author = {Karim, A and Ahmad, F and Qaisar, R},
title = {The gut-muscle-joint axis in osteoarthritis: Mechanistic insights and therapeutic perspectives.},
journal = {European journal of clinical nutrition},
volume = {},
number = {},
pages = {},
pmid = {42957763},
issn = {1476-5640},
abstract = {Emerging evidence highlights a complex crosstalk between the gut microbiota, musculoskeletal tissues, and the joint microenvironment, revealing osteoarthritis (OA) as a systemic disorder rather than a localized cartilage disease. The gut-muscle-joint interaction integrates microbial dysbiosis, chronic inflammation, and metabolic dysregulation to influence cartilage homeostasis, muscle strength, and neuromuscular stability. Building upon previously described gut-osteoarthritis and gut-muscle interactions, the Gut-Muscle-Joint (GMJ) axis is presented as an integrative framework linking intestinal permeability, microbial metabolites, systemic inflammatory signaling, neuromuscular health, skeletal muscle function, and joint integrity. Perturbations in this axis amplify oxidative stress, mitochondrial dysfunction, and extracellular matrix degradation across musculoskeletal tissues. Understanding GMJ axis-driven mechanisms offers novel preventive and therapeutic strategies that target microbiome restoration, metabolic reprogramming, and neuromuscular health through probiotics, postbiotics, AMPK-SIRT1 activators, and structured exercise. This integrative perspective positions the GMJ axis as a unifying framework for intervention, enabling precision approaches to preserve joint function, reduce sarcopenia, and attenuate OA progression.},
}

@article {pmid42957838,
year = {2026},
author = {Abaresh, S and Ivantsova, E and Parmar, MS},
title = {Glymphatic Dysfunction as a Multisystem Pathway Linking Systemic Health Conditions to Alzheimer's Disease: Mechanisms, Risk Factors, and Therapeutic Opportunities.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42957838},
issn = {1559-1182},
mesh = {Humans ; *Glymphatic System/pathology/metabolism/physiopathology ; *Alzheimer Disease/therapy/physiopathology/metabolism/pathology ; Animals ; Risk Factors ; *Health ; },
abstract = {The glymphatic system is a glia-associated perivascular pathway involved in cerebrospinal fluid (CSF)-interstitial fluid (ISF) exchange and the transport and clearance of neurotoxic metabolites, including amyloid-β (Aβ) and tau, from the central nervous system. Growing evidence suggests that alterations in glymphatic and perivascular clearance are associated with Alzheimer's disease (AD) pathology and may contribute to the accumulation of neurotoxic proteins and neurodegeneration. This review examines the role of the glymphatic system in AD and explores how aging, sleep disturbances, hypertension, ischemic heart disease, high-fat diet, diabetes, and gut microbiome dysbiosis impair glymphatic transport. A recurring mechanism across experimental models is the loss of perivascular AQP4 polarization, while vascular, metabolic, and inflammatory conditions may converge on related perivascular and neurovascular processes that impair CSF-ISF exchange and solute handling. Neuroimaging studies using markers such as DTI-ALPS, perivascular space burden, and free-water measurements provide evidence of alterations in glymphatic-related and perivascular processes in AD and demonstrate associations with amyloid deposition, neurodegeneration, and cognitive decline. Furthermore, glymphatic dysfunction may interact with neuroinflammation and tau pathology, creating a self-reinforcing cycle that accelerates disease progression. Emerging therapeutic strategies, including continuous theta-burst stimulation, positive airway pressure therapy for obstructive sleep apnea, pharmacological enhancement of AQP4 function, and nutritional interventions, have shown potential in experimental and early translational studies to influence glymphatic-related processes and may mitigate AD-related pathology. Collectively, current findings suggest that glymphatic and perivascular clearance pathways may represent an important link between systemic health conditions and AD. Because related pathways are implicated across multiple systemic conditions, interventions targeting glymphatic and perivascular dysfunction may have broader relevance to brain health, but their clinical effects remain to be established.},
}

Humans
*Glymphatic System/pathology/metabolism/physiopathology
*Alzheimer Disease/therapy/physiopathology/metabolism/pathology
Animals
Risk Factors
*Health

@article {pmid42957839,
year = {2026},
author = {Molina, MA and Zhang, Y and Steenbergen, RDM and Melchers, WJG and Du, J},
title = {Towards a sequential microbiome therapy for HPV-associated cervicovaginal dysbiosis.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42957839},
issn = {2399-3642},
mesh = {Female ; Humans ; *Dysbiosis/therapy/microbiology ; *Microbiota ; *Papillomavirus Infections/therapy/microbiology/virology/complications ; *Human Papillomavirus Viruses ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; Uterine Cervical Neoplasms/prevention & control/virology ; },
abstract = {Persistent high-risk human papillomavirus (hrHPV) infections are the principal cause of cervical cancer, and are increasingly associated with ecological instability of the cervicovaginal microbiome. Multiomics studies indicate that hrHPV persistence is linked to reduced Lactobacillus dominance, increased anaerobic taxa, and metabolic alterations that may compromise epithelial integrity and antiviral immunity. In this Perspective article, we introduce a sequential microbiome therapy (SMT) framework designed to restore cervicovaginal ecological balance and support viral clearance. SMT is a two-phase, strain-resolved strategy. The first phase targets dysbiotic communities using antimicrobials, biofilm-disrupting or microbiota-modulating approaches to create a window for ecological reset. The second phase introduces health-associated Lactobacillus species selected for their acidification capacity, competitive fitness, and ability to stabilize the mucosal environment. We outline the ecological principles underpinning SMT and discuss its development as a potentially scalable microbiome-directed strategy for restoring cervicovaginal health and managing hrHPV-associated disease within existing cervical cancer prevention frameworks.},
}

Female
Humans
*Dysbiosis/therapy/microbiology
*Microbiota
*Papillomavirus Infections/therapy/microbiology/virology/complications
*Human Papillomavirus Viruses
*Vagina/microbiology/virology
*Cervix Uteri/microbiology/virology
Uterine Cervical Neoplasms/prevention & control/virology

@article {pmid42957847,
year = {2026},
author = {Cui, X and Zhang, X and Feng, S and Chen, J and Zhang, S and Sampedro, GR and Gao, H and Irnov, I and Lu, Q and Baldridge, MT and Boon, ACM and Cadwell, K and Torres, VJ and Bubeck Wardenburg, J and Chen, M and Liang, G and Virgin, HW and Stallings, CL and Wang, YT},
title = {Autophagy in macrophages curtails IL-1α-mediated immune priming against lung infections.},
journal = {Nature immunology},
volume = {},
number = {},
pages = {},
pmid = {42957847},
issn = {1529-2916},
support = {32522036/32370804//National Natural Science Foundation of China (National Science Foundation of China)/ ; JQ24032//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
abstract = {Host resistance to infection is initially determined by how well primed the innate immune system is to respond on first exposure to an invader, yet the mechanisms underlying this priming remain incompletely understood. Here we found that basal autophagy suppressed the expression of Il1a in alveolar macrophages (AMs) and an otherwise protective innate immune priming against Staphylococcus aureus and influenza A virus (IAV), independently of the microbiome and adaptive immunity. Inactivating autophagy genes in AMs led to elevated expression of IL-1α in AMs, which subsequently enhanced IL-1R-MyD88 signaling in neutrophils and increased the recruitment of myeloid cells to the lung. As a result, autophagy-deficient mice showed more efficient clearance of S. aureus along with reduced lung damage and inflammation. Similar to genetic inactivation of autophagy, overexpression of IL-1α in AMs conferred broad spectrum protection against S. aureus and IAV, suggesting a possible strategy to fine-tune immune responses to combat important respiratory infections.},
}

@article {pmid42957850,
year = {2026},
author = {Roux, S and Neri, U and Bushnell, B and Fremin, BJ and George, NA and Gophna, U and Hug, LA and Camargo, AP and Wu, D and Ivanova, N and Kyrpides, NC and Eloe-Fadrosh, EA},
title = {Planetary-scale metagenomic analysis reveals CRISPR targeting dynamics across ecosystems.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42957850},
issn = {2058-5276},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; ERC-AdG 787514//European Commission (EC)/ ; 2016-03686//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; },
abstract = {Interactions between microorganisms and their mobile genetic elements (MGEs), including viruses and plasmids, impact microbiome dynamics. CRISPR-Cas systems are important regulators of these host-MGE interactions, but a global understanding of the diversity, activity and roles of CRISPR spacers across Earth's biomes is still lacking. Here we develop a computational approach to search short-read data and collect 794 million CRISPR spacers across 367,609 public metagenomes, from which we identified 1.18 billion hits between 41 million spacers and 2.5 million viruses and plasmids. While spacers were highly variable across samples, those matching known viruses were more prevalent and conserved, consistent with a positive selection pressure associated with phage targeting. Among these, however, we find evidence suggestive of recurrent entry of phage genomes into non-host microbial cells, further blurring the line between CRISPR targeting and virus-host interactions. These results highlight key drivers of CRISPR targeting patterns likely to influence strain-level diversification and selection processes in microbiomes.},
}

@article {pmid42957855,
year = {2026},
author = {Teheran-Sierra, LG and de Carvalho, LAL and Mejia-Alvarado, FS and Chaves-Sierra, C and Pinheiro, DG and Arias, NAA},
title = {From Soil to Leaves: Decoding the Microbiome of Oil Palm in Colombia.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42957855},
issn = {1432-184X},
mesh = {Colombia ; *Plant Leaves/microbiology ; *Arecaceae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; *Microbiota ; *Fungi/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Archaea/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Rhizosphere ; },
abstract = {Plant microbiomes are shaped by hierarchical ecological filters in which compartmentalization through the progressive selection of microbial communities along the soil-root-leaf continuum, emerges as the strongest structuring force. Despite the agronomic importance of oil palm (Elaeis guineensis Jacq.) as an important oil crop, compartment-resolved characterizations of its microbiome remain scarce, and the microbiome of the interspecific hybrid OxG (E. oleifera × E. guineensis), widely planted in Latin America to sustain production in disease-affected areas, had not been previously described. Here, we used 16S rRNA (V3-V4) and ITS (ITS2) metabarcoding to survey bacterial, archaeal, and fungal communities across bulk soil, rhizosphere, roots, and leaves of productive plots of E. guineensis and OxG hybrid palms under two soil consociations in Colombia. Sequencing produced 10,298,116 raw reads, of which 79.83% were assigned to amplicon sequence variants (ASVs). Compartment was the dominant force structuring both prokaryotic and fungal communities (PERMANOVA p < 0.01), with alpha diversity decreasing along the bulk soil-rhizosphere-roots-leaves continuum and the leaf compartment being the most distinct and least diverse. Compartment-specific biomarkers included Acidobacteriota and Saitozyma in soil, Bradyrhizobium and Pseudomonas in roots, and Methylocella and Pseudocladosporium in leaves. Predicted functional potential inferred with PICRUSt2 closely tracked the taxonomic gradient, with compartment explaining 85.87% of the variance in KEGG composition. Additionally, we found that OxG hybrid exhibited recurrent enrichment of Acidobacteriota and Ascomycota, along with more fragmented co-occurrence networks than E. guineensis. However, palm species effects were consistently weaker than compartment effects and varied with locality.},
}

Colombia
*Plant Leaves/microbiology
*Arecaceae/microbiology
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
*Microbiota
*Fungi/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Archaea/classification/genetics/isolation & purification
Plant Roots/microbiology
Rhizosphere

@article {pmid42957890,
year = {2026},
author = {Kapoor, S and Yang, YT and Bone, M and Jex, AR and Baxter, S and Oxley, APA and Harvey, ML and Batterham, P and Gasser, RB and Bowles, VM and Perry, T and Anstead, CA},
title = {Comparative microbiome analysis of parasitic and necrophagous subspecies of Lucilia cuprina.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {42957890},
issn = {1432-0614},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Lucilia cuprina/microbiology/classification ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Phylogeny ; Australia ; DNA, Bacterial/genetics ; Myiasis/veterinary/parasitology ; Sheep/parasitology ; Sequence Analysis, DNA ; *Diptera/microbiology ; },
abstract = {Blowflies of the genus Lucilia (Insecta: Diptera: Calliphoridae) are important in forensic science, medical research, and agriculture, particularly due to their role as facultative ectoparasites of domesticated sheep. The Australian sheep blowfly, L. cuprina dorsalis, is a primary causative agent of cutaneous myiasis, leading to substantial economic losses to the wool industry. In contrast, the closely related subspecies L. cuprina cuprina does not induce myiasis in sheep, but functions as a necrophagous subspecies in urban regions of Australia. Differences in the physiology, behavior, and host interactions of these subspecies might be attributed to their bacterial community structures as demonstrated in other blowfly species. However, our understanding of the bacterial communities associated with these flies is limited. This study aimed to characterize the microbiomes of two geographically distinct subspecies of L. cuprina-L. c. dorsalis (rural) and L. c. cuprina (urban) using 16S rRNA gene sequencing. The findings indicate that, while both subspecies harbor broadly similar microbial compositions, their respective urban and rural environments influence the prevalence of specific bacterial genera. The bacterial communities of these flies were predominantly composed of members of the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. The genus Ignatzschineria was highly abundant in L. c. dorsalis, whereas Pseudomonas was more prevalent in L. c. cuprina, highlighting distinct microbial compositions between the two subspecies. These findings provide fundamental insights into the microbial composition of Lucilia species, contributing to a broader understanding of their ecological and biological roles, with potential applications in forensic entomology, medical research, and agricultural pest management. KEY POINTS: • The microbial communities of Lucilia cuprina dorsalis and Lucilia cuprina cuprina have a broadly similar composition, but the abundance of particular bacterial genera is notably different. • Proteobacteria is the most abundant phylum in both subspecies. • The genus Ignatzschineria is notably abundant in Lucilia cuprina dorsalis, while Pseudomonas is predominant in Lucilia cuprina cuprina, emphasizing differences between the microbial community members between these subspecies.},
}

Animals
RNA, Ribosomal, 16S/genetics
*Lucilia cuprina/microbiology/classification
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Phylogeny
Australia
DNA, Bacterial/genetics
Myiasis/veterinary/parasitology
Sheep/parasitology
Sequence Analysis, DNA
*Diptera/microbiology

@article {pmid42958014,
year = {2026},
author = {Li, J and Aoki, T and Miyata, S and Fukaya, A and Hayashi, Y and Hirao, H and Yoshimoto, S and Nagaoka, K},
title = {Fecal microbiome-based clustering identifies distinct disease subtypes with differing metabolomic profiles and treatment outcomes in canine chronic enteropathy.},
journal = {The veterinary quarterly},
volume = {46},
number = {1},
pages = {2744638},
doi = {10.1080/01652176.2026.2744638},
pmid = {42958014},
issn = {1875-5941},
mesh = {Animals ; Dogs ; *Dog Diseases/microbiology/metabolism/drug therapy ; *Feces/microbiology/chemistry ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; Chronic Disease/veterinary ; Treatment Outcome ; *Gastrointestinal Microbiome ; Metabolomics ; Metabolome ; *Intestinal Diseases/veterinary/microbiology ; Cluster Analysis ; Diarrhea/veterinary/microbiology ; },
abstract = {Canine chronic enteropathy (CE) is a heterogeneous disorder with variable clinical outcomes. We aimed to identify fecal microbiome and metabolomic signatures associated with CE severity and treatment outcomes. Fecal samples from dogs with CE (n = 56), acute diarrhea (n = 8), and healthy controls (n = 126) were analyzed by 16S rRNA gene sequencing and GC-MS-based untargeted metabolomics. CE dogs exhibited significantly reduced microbial diversity compared with the other groups, and unsupervised Partitioning Around Medoids clustering identified two microbiome clusters within the CE cohort. Cluster 2 was characterized by dysbiosis, with enrichment of Streptococcus, Enterococcus, and Klebsiella, and depletion of short-chain fatty acid producers, including Fusobacterium and Blautia. Among dogs with baseline Canine Chronic Enteropathy Clinical Activity Index (CCECAI) > 3, 10 of 12 Cluster 1 dogs (83.3%) achieved remission (CCECAI ≤ 3) after treatment, compared with 7 of 18 Cluster 2 dogs (38.9%; p = 0.0256). CCECAI scores decreased significantly after treatment in Cluster 1 (p = 0.0005) but not in Cluster 2 (p = 0.077). Fecal propanoic acid and kynurenic acid levels also differed between clusters. These findings suggest that gut microbiota and associated metabolites may contribute to differences in CE severity and treatment outcomes.},
}

Animals
Dogs
*Dog Diseases/microbiology/metabolism/drug therapy
*Feces/microbiology/chemistry
Female
RNA, Ribosomal, 16S/genetics
Male
Chronic Disease/veterinary
Treatment Outcome
*Gastrointestinal Microbiome
Metabolomics
Metabolome
*Intestinal Diseases/veterinary/microbiology
Cluster Analysis
Diarrhea/veterinary/microbiology

@article {pmid42958032,
year = {2026},
author = {Chen, H and Liu, J and Hou, R and Chen, F and Qi, D and Chen, Y and Bi, W and Zhou, Y and Gu, J and Lan, G and Wu, W and Zhang, K and Ma, R},
title = {Ecological succession and topological rewiring of the oral microbiome in giant panda cubs.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42958032},
issn = {1471-2180},
support = {ZYN2024057//Southwest Minzu University/ ; 32400405//National Natural Science Foundation of China/ ; 2024CPB-Y05//Chengdu Giant Panda Breeding Research Foundation/ ; },
mesh = {Animals ; *Ursidae/microbiology ; *Microbiota ; *Mouth/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Saliva/microbiology ; Dental Plaque/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In specialized herbivores retaining a carnivorous digestive tract, such as the giant panda, early-life oral microbiome assembly is crucial for lifelong health, yet remains poorly understood. Here, we longitudinally tracked the saliva and supragingival plaque microbiomes of captive cubs (180 matched samples) from birth to one year using microbiome sequencing and topological cartography. We demonstrate a profound spatial-temporal divergence driven by deterministic succession. Initial plaque colonization exhibited transient priority effects reflecting maternal imprints, rapidly superseded by autogenic niche reconstruction and deep anaerobic maturation. Host ontogeny, notably deciduous tooth eruption, triggered intense microbial exchange, causing significant transient habitat homogenization (peak Mantel correlations at months 6 and 8, p < 0.001). Mature plaque selectively enriched for peptidoglycan biosynthesis and complex carbohydrate degradation, establishing a pre-adaptive metabolic reservoir for the impending high-fiber bamboo diet. Crucially, topological analysis (interaction edges expanded 3.4-fold) revealed that early pioneers evade competitive exclusion by shifting their ecological niche to become inter-module connectors (Pi > 0.62), providing spatial scaffolds for late-arriving climax communities. These findings decipher the deterministic assembly rules of saliva and plaque microbiomes during the extreme milk-to-bamboo dietary transition, advancing our understanding of giant panda adaptive evolution and identifying native keystone targets for preventive veterinary interventions.},
}

Animals
*Ursidae/microbiology
*Microbiota
*Mouth/microbiology
*Bacteria/classification/genetics/isolation & purification
Saliva/microbiology
Dental Plaque/microbiology
Ecosystem
RNA, Ribosomal, 16S/genetics

@article {pmid42958040,
year = {2026},
author = {Barsila, SR and Gotoh, Y and Takizawa, S and Fukuda, Y and Kakihara, H and Pakhrin, WT and Ogura, S},
title = {Rumen fraction type (solid vs. liquid) modulates diet-driven patterns of bacterial diversity and composition in sheep.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42958040},
issn = {1471-2180},
mesh = {Animals ; *Rumen/microbiology ; Sheep/microbiology ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Animal Feed/analysis ; *Diet/veterinary ; DNA, Bacterial/genetics ; Biodiversity ; Sequence Analysis, DNA ; *Gastrointestinal Microbiome ; Phylogeny ; Fermentation ; },
abstract = {BACKGROUND: The rumen microbiota is essential to substrate digestion and fermentation of nutrients, which has a direct impact on animal sustainability and productivity. It is further known that diet composition has an impact on rumen microbial communities, while the proportional roles of feed types and rumen fraction type (solid vs. liquid) to the diversity of bacterial communities in sheep kept indoors are still lacking. This study examined the impact of rumen sample fractions (solid vs. liquid) and diet composition (single vs. mixed) on the diversity and structure of the sheep's rumen bacterial community.

METHODS: Eight adult sheep were used in two different feeding groups: mixed feeding (hay, straw, and silage) and single feeding (orchard grass silage only). The solid and liquid fractions of the rumen were separated after 21 days of feeding. The V4 region of the 16 S rRNA gene was sequenced using the Illumina MiSeq platform after microbial DNA was extracted from both fractions. The SILVA database was used to assign amplicon sequence variants (ASVs) for bioinformatic analysis, which was carried out using QIIME2. Using R, analyses of differential abundance, beta diversity, and alpha diversity were performed.

RESULTS: While microbial richness stayed consistent across diets (P = 0.065), mixed feeding increased species richness compared to single feeding (P = 0.0076. On the other hand, the rumen sample fraction had a greater impact on microbial community structure: liquid fractions were dominated by taxa linked to fermentation of soluble carbohydrates, while solid fractions showed greater richness (P = 0.012) and were enriched with bacteria associated with fibre (P< 0.001). Significant compositional differences between solid and liquid fractions were found via beta-diversity analysis (PERMANOVA, R² = 0.553, P < 0.001), but remained similar across the feeding regimens (R² = 0.139, P = 0.099). The phyla Bacteroidota (54.82%) and Bacillota (19.17%) dominated the rumen microbiota in all samples, with Prevotella being the most prevalent genus (18.74%). Dietary differences in volatile fatty acid profiles were negligible, suggesting functional redundancy in spite of taxonomic changes in the rumen bacterial community.

CONCLUSION: Under the conditions examined, this study shows that the rumen sample fraction (solid vs. liquid) is a more important determinant of the composition of the microbial community than the effects of diet composition. Microbial richness is increased by mixed feeding, while different and functionally complementary bacterial communities are present in solid and liquid rumen fractions. These results emphasize how crucial it is to include both rumen sample fractions in microbiome research and offer insightful information for the improvement of feeding practices or sudden dietary changes meant to enhance nutrient utilization in sheep under indoor conditions.},
}

Animals
*Rumen/microbiology
Sheep/microbiology
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Animal Feed/analysis
*Diet/veterinary
DNA, Bacterial/genetics
Biodiversity
Sequence Analysis, DNA
*Gastrointestinal Microbiome
Phylogeny
Fermentation

@article {pmid42958298,
year = {2026},
author = {Akbari-Ardabili, S},
title = {Postbiotic-related host transcriptomic axes link tumour immune microenvironment, stage and survival in colorectal cancer.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42958298},
issn = {1479-5876},
mesh = {*Tumor Microenvironment/genetics/immunology ; Humans ; *Colorectal Neoplasms/genetics/immunology/pathology/microbiology ; *Transcriptome/genetics ; Neoplasm Staging ; Gene Expression Regulation, Neoplastic ; Survival Analysis ; Tryptophan/metabolism ; },
abstract = {BACKGROUND: The tumour immune microenvironment shapes colorectal cancer progression and therapeutic vulnerability, but host metabolic programmes linked to immune-inflamed tumour states remain incompletely defined. Microbiome-derived and postbiotic-related metabolites influence epithelial, stromal and immune signalling, yet their downstream tumour transcriptomic readouts have rarely been assessed as host-side indicators of immune microenvironment state.

METHODS: Four mechanistically defined postbiotic-related host axes were curated: short-chain fatty acid, tryptophan/AhR, polyamine and ferroptosis/redox. Axis scores were calculated as mean z-standardized expression of curated genes in TCGA colorectal cancers and evaluated in GSE39582. Associations with marker-based immune/stromal signatures, microsatellite instability, cytolytic activity, stage and overall survival were tested using Spearman correlations, Wilcoxon tests and Cox models with false-discovery-rate correction.

RESULTS: In TCGA, the tryptophan/AhR axis showed the strongest coupling to marker-based immune and myeloid signatures, including macrophage-, Treg-, NK-cell-, CD8 T-cell-, Th1-like and cytolytic-activity programmes. Tryptophan/AhR, short-chain fatty acid and ferroptosis/redox axes were enriched in MSI-H and immune-high tumours, whereas the polyamine axis showed weaker immune associations. Short-chain fatty acid and ferroptosis/redox axes decreased recurrently in advanced-stage disease across cohorts. No universal prognostic axis emerged, although the short-chain fatty acid axis retained a stage-adjusted association with improved overall survival in GSE39582.

CONCLUSIONS: Postbiotic-related host transcriptomic axes provide interpretable tumour-level readouts connecting metabolic cues with immune microenvironment states in colorectal cancer. They should be considered hypothesis-generating host-side immune-context readouts rather than ready-to-use clinical signatures.},
}

*Tumor Microenvironment/genetics/immunology
Humans
*Colorectal Neoplasms/genetics/immunology/pathology/microbiology
*Transcriptome/genetics
Neoplasm Staging
Gene Expression Regulation, Neoplastic
Survival Analysis
Tryptophan/metabolism

@article {pmid42958357,
year = {2026},
author = {Bruyant, P and Gillespie, LM and Doré, J and Courty, PE and Moënne-Loccoz, Y and Almario, J},
title = {Helotiales fungi as potential nutritional partners for non-mycorrhizal plants: a machine learning and experimental approach.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42958357},
issn = {2049-2618},
mesh = {*Mycorrhizae/physiology/genetics ; Symbiosis ; *Machine Learning ; Phosphorus/metabolism ; Plant Roots/microbiology ; Phylogeny ; Brassicaceae/microbiology ; *Ascomycota/classification/genetics/physiology ; Microbiota ; },
abstract = {BACKGROUND: Most land plants benefit from the ancestral arbuscular mycorrhizal (AM) symbiosis for phosphorus (P) acquisition. However, several plant lineages have independently lost this symbiosis, raising fundamental questions about how these 'non-mycorrhizal' plants meet their nutritional requirements without this crucial partnership.

RESULTS: Comparative genomic analyses confirmed that Cyperaceae, Caryophyllaceae, and Brassicaceae lack genes essential for AM symbiosis, indicating that these lineages independently abandoned this association 90-122 million years ago. Field surveys of 42 wild populations across seven sites revealed that non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors. To identify fungal taxa potentially associated with P nutrition in non-mycorrhizal plants, we applied a machine-learning approach to predict plant P-accumulation from root microbiome composition. The model explained substantial variance in plant P-accumulation (57-69%), and identified 85 fungal taxa as key predictors of shoot P-accumulation, predominantly belonging to the Helotiales (28%) and Pleosporales (23%) orders. Experimental validation of two phylogenetically distant Helotiales lineages (Tetracladium maxilliforme OTU29 and Helotiales sp. OTU7), using isotopic tracing, demonstrated their capacity to enhance plant growth and transfer P (and N) to their native non-mycorrhizal hosts under P-limiting conditions.

CONCLUSIONS: Our findings suggest that non-mycorrhizal plants engage in nutritional partnerships with diverse Helotiales lineages that could collectively contribute to their mineral nutrition. However, given the widespread distribution of these Helotiales fungi, including in roots of AM plants, they may play a broader role in plant nutrition, i.e. also in mycorrhizal hosts. This study provides proof of concept for a novel framework integrating machine-learning predictions with experimental validation to identify functionally important microbial partnerships in natural plant communities. Video Abstract.},
}

*Mycorrhizae/physiology/genetics
Symbiosis
*Machine Learning
Phosphorus/metabolism
Plant Roots/microbiology
Phylogeny
Brassicaceae/microbiology
*Ascomycota/classification/genetics/physiology
Microbiota

@article {pmid42958435,
year = {2026},
author = {Rao, B and Liu, S and Cui, G and Jiang, J and Li, N and Hu, J and Sun, R and Li, A and Zhang, R and Lu, H and Wen, P and Xue, J and Aji, T and Wang, H and Chen, X and Zheng, S and Yu, Z and Ren, Z},
title = {Multikingdom and functional gut microbiota markers for cholangiocarcinoma.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42958435},
issn = {1756-994X},
support = {82570691//National Natural Science Foundation of China/ ; 81672422//National Natural Science Foundation of China/ ; 82470654//National Natural Science Foundation of China/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2025ZD01906305//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; HNCMS202423//Henan Province "Three 100" Program, Special Project for Clinical Medical Scientist Cultivation/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/diagnosis ; Female ; Metagenomics/methods ; Male ; Middle Aged ; Feces/microbiology ; Liver Neoplasms/microbiology/diagnosis ; Biomarkers, Tumor ; Metagenome ; Carcinoma, Hepatocellular/microbiology ; Aged ; },
abstract = {BACKGROUND: While the association between gut microbiota and cholangiocarcinoma (CCA) has been explored, existing research has been limited to bacterial components. The alterations in non-bacterial members (fungi, archaea, and viruses) and their functional characteristics in CCA remain unclear. This study aimed to comprehensively characterize the multi-kingdom gut microbiota and functional profiles in CCA patients and develop a non-invasive diagnostic model.

METHODS: We performed metagenomic sequencing on 700 fecal samples collected from three distinct regions in China, comprising 289 CCA patients, 312 healthy controls, and 99 hepatocellular carcinoma (HCC) patients. Multi-kingdom microbial composition and functional profiles were analyzed. We integrated multiple machine learning algorithms to generate 117 distinct modeling schemes for constructing and screening the optimal CCA diagnostic model. The model was validated across three independent cohorts and tested for specificity against HCC. We also benchmarked the model against established diagnostic approaches by reviewing 15 CCA clinical practice guidelines/consensus statements and their cited evidence and by evaluating model detection in CA19-9-positive and CA19-9-negative patients.

RESULTS: Extensive alterations were identified in CCA patients across multi-kingdom and functional layers, including 198 archaeal, 154 bacterial, 78 fungal, and 120 viral species, as well as 278 genes, 99 pathways, and 151 carbohydrate-active enzymes (CAZymes). A panel of 21 multi-kingdom and functional markers demonstrated superior diagnostic accuracy with an average AUC of 91% across three validation cohorts, outperforming any single-kingdom model. The model exhibited high specificity in distinguishing CCA from HCC, achieving an AUC of 99.74% with a false positive rate of 11.11%. Benchmarking supported a complementary role as a noninvasive screening aid, the model showed pooled sensitivity and specificity of 96.2%, and 78.5%, respectively, and detected 97.6% of CA19-9-negative CCA cases.

CONCLUSIONS: This study represents the first comprehensive characterization of multi-kingdom gut microbiome and functional markers in cholangiocarcinoma. Gut multi-kingdom and functional microbial signatures represent a promising noninvasive tool that may aid the screening and early identification of cholangiocarcinoma in high-risk populations, complementing existing diagnostic approaches.},
}

Humans
*Cholangiocarcinoma/microbiology/diagnosis
*Gastrointestinal Microbiome
*Bile Duct Neoplasms/microbiology/diagnosis
Female
Metagenomics/methods
Male
Middle Aged
Feces/microbiology
Liver Neoplasms/microbiology/diagnosis
Biomarkers, Tumor
Metagenome
Carcinoma, Hepatocellular/microbiology
Aged

@article {pmid42958441,
year = {2026},
author = {Nackers, F and Polnay, K and Almey, R and Daled, S and Djibo, AD and Saeger, S and Deforce, D and Dhaenens, M and Gansemans, Y and Glorieux, G and Guindo, O and Jenkins, B and Koulman, A and Lang, HJ and Langendorf, C and Laukens, D and Mambula, C and Mukagatare, I and Parkington, D and Tassiou, EI and Biesen, WV and De Wiele, TV and Massenhove, JV and Nieuwerburgh, FV and Adehossi, I and Briend, A and Gonzales, GB},
title = {Multi-omics, multi-tissue analysis reveal role of extracellular matrix remodeling and sphingolipid homeostasis in edematous malnutrition (kwashiorkor).},
journal = {Biomarker research},
volume = {14},
number = {1},
pages = {},
pmid = {42958441},
issn = {2050-7771},
abstract = {BACKGROUND: Edematous malnutrition, aka kwashiorkor, is a phenotype of severe malnutrition whose pathophysiology remains poorly understood.

METHODS: In this case-control study, we employed plasma lipidomics, metabolomics, and proteomics, urine metabolomics and gut microbiome profiling to delineate molecular features specific to kwashiorkor in 60 children aged 6-59 months from Niger compared to marasmus (n = 60) and non-malnourished children (NAM) (n = 60) matched by age, sex, and clinical triage score. Features were defined as kwashiorkor-specific if they also correlated with edema severity and normalized following nutritional rehabilitation.

RESULTS: We identified a plasma proteomic factor featuring lumican, gelsolin, and tetranectin and a lipidomic factor enriched in sphingolipids. Both differed in kwashiorkor compared to marasmus and NAM, were associated with edema grade, and trended towards normalcy after nutritional treatment, which are consistent with ECM remodeling and sphingolipid dysregulation. In contrast, neither (plasma and urine) metabolomic profiles nor gut microbiome composition showed kwashiorkor-specific signatures, although our urine and gut microbiome analyses may be underpowered.

CONCLUSION: These findings advance understanding of kwashiorkor pathophysiology beyond nutrient deficiency and highlight ECM and sphingolipid features associated with its distinct clinical and molecular characteristics compared to marasmus.},
}

@article {pmid42958554,
year = {2026},
author = {Zhou, Y and Zhang, G and Shi, Q and Liu, J and Lu, Y and Song, J},
title = {Probiotic-hydrogel systems for microbiome-associated diseases: design principles, preclinical evidence, and translational challenges.},
journal = {Journal of biological engineering},
volume = {20},
number = {1},
pages = {},
pmid = {42958554},
issn = {1754-1611},
support = {YDZJSX20231A064//Shanxi Province/ ; },
abstract = {The human microbiome provides a robust ecosystem for mucosal barrier function, immune regulation, metabolism, and resistance to pathogen infection. Dysbiosis causes inflammatory bowel disease, oral inflammation, wound damage, skin disease, and cancer-related immune dysregulation. Current probiotic therapy is limited by low survival during storage and administration, low oral bioavailability, short retention time, and insufficient targeting. Probiotic-hydrogel systems combine viable microorganisms with natural or synthetic polymer networks to promote probiotic protection, local retention, and controlled release. They can also incorporate prebiotics, engineered bacteria, oxygen-releasing agents, antioxidants, growth factors, drugs, or advanced manufacturing techniques such as microfluidics and 3D printing. Recent preclinical studies suggest that probiotic-hydrogel can modulate local microbes, suppress pathogens, control inflammation, support barrier repair, and promote tissue regeneration. However, most evidence is far from clinical, and human data are limited to a small number of oral and periodontal applications. In this review, we summarize the design strategies, encapsulation approaches, mechanistic frameworks, disease-based evidence, and translational challenges of probiotic-hydrogel. In particular, we paid attention to evidence level, safety, manufacturing, regulatory classification, product stability, clinical trial design. Such issues need to be well understood before probiotic-hydrogel can move from experimental platforms to clinically applicable microbiome treatments.},
}

@article {pmid42958581,
year = {2026},
author = {Paul, S and Kentatchime, F and Andres-Bray, T and Ghosh, T and Couto, GNP and Njabo, K and Gonder, MK},
title = {Optimizing a human forensic STR panel for non-invasive genetic monitoring of chimpanzees (Pan troglodytes).},
journal = {BMC research notes},
volume = {19},
number = {1},
pages = {},
pmid = {42958581},
issn = {1756-0500},
mesh = {Animals ; *Pan troglodytes/genetics ; *Microsatellite Repeats/genetics ; Female ; Humans ; Male ; *Forensic Genetics/methods ; *Genotyping Techniques/methods ; Genotype ; Cameroon ; DNA/genetics ; Polymerase Chain Reaction/methods ; Alleles ; Feces/chemistry ; },
abstract = {OBJECTIVE: Accurate molecular genotyping is essential for conservation genetics, population monitoring, pedigree reconstruction, and wildlife forensic investigations in endangered primates. Although SNP-based approaches are increasingly available, microsatellites remain among the most practical tools for non-invasive individual identification because of their high allelic diversity and strong discriminatory power from relatively few loci. Here, we present a standardized optimization framework for adapting the human forensic GlobalFiler™ PCR Amplification Kit to non-invasive chimpanzee genotyping.

RESULTS: Using blood and fecal DNA from captive and wild chimpanzees in Cameroon, we integrated DNA quality screening, chimpanzee-specific allele binning, replicate consensus genotyping, statistical evaluation of locus performance, and composite marker ranking to develop a robust 16-locus panel for individual identification. Estimated marginal means were calculated from the fitted beta regression models to assess amplification success, allelic dropout, and false allele rates across sample types and loci. These metrics, combined with measures of discriminatory power, identified D10S1248, FGA, D2S441, and D3S1358 as the highest-performing loci. The optimized panel achieved 95.4% amplification success with low allelic dropout (0.08) and false allele (0.02) rates. It identified 64 unique individuals (39 males and 25 females) and showed high discriminatory power (PID(sibs) = 1.2 × 10⁻⁶). This workflow is easily transferable and can complement SNP genotyping, metabarcoding, microbiome analyses, and other molecular approaches in a wide range of non-invasive genetic studies.},
}

Animals
*Pan troglodytes/genetics
*Microsatellite Repeats/genetics
Female
Humans
Male
*Forensic Genetics/methods
*Genotyping Techniques/methods
Genotype
Cameroon
DNA/genetics
Polymerase Chain Reaction/methods
Alleles
Feces/chemistry

@article {pmid42958627,
year = {2026},
author = {Sharma, P and Nhokwara, T and Singh, J and Bala, K and Kamra, K},
title = {Microbiome-Immune Crosstalk in Inflammatory Skin Diseases: Mechanisms and Therapeutic Potential of Probiotics.},
journal = {Immunity, inflammation and disease},
volume = {14},
number = {10},
pages = {},
pmid = {42958627},
issn = {2050-4527},
mesh = {Humans ; *Probiotics/therapeutic use ; *Dermatitis, Atopic/immunology/microbiology/therapy ; Animals ; Skin Microbiome ; *Psoriasis/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; *Acne Vulgaris/immunology/microbiology/therapy ; Skin/immunology/microbiology ; *Microbiota/immunology ; },
abstract = {BACKGROUND: The gut-skin axis links intestinal microbial activity with inflammatory skin disease, yet findings across atopic dermatitis, acne vulgaris, and psoriasis remain inconsistent. This review examines how disease biology and host context shape microbiome-related effects and responses to probiotics.

MATERIALS AND METHODS: Published clinical and experimental evidence on gut microbiota, immune and metabolic signaling, barrier dysfunction, inter-organ communication, and probiotic interventions was narratively reviewed across atopic dermatitis, acne vulgaris, and psoriasis.

RESULTS: Microbiome-related mechanisms differ by disease. In atopic dermatitis, they intersect with barrier dysfunction and altered immune regulation. In acne vulgaris, metabolic, hormonal, dietary, and neuroendocrine factors modify their effects. In psoriasis, gut dysbiosis occurs within a broader setting of systemic immune activation. Probiotic outcomes are similarly variable and depend on strain, host characteristics, disease context, and study design.

DISCUSSION: Gut-skin communication is better interpreted as part of an interconnected physiological network rather than a uniform linear pathway. Disease-specific evaluation of microbiome changes and probiotic interventions may help explain conflicting findings and guide more targeted future studies.},
}

Humans
*Probiotics/therapeutic use
*Dermatitis, Atopic/immunology/microbiology/therapy
Animals
Skin Microbiome
*Psoriasis/immunology/microbiology/therapy
*Gastrointestinal Microbiome/immunology
*Acne Vulgaris/immunology/microbiology/therapy
Skin/immunology/microbiology
*Microbiota/immunology

@article {pmid42958634,
year = {2026},
author = {de Medeiros Oliveira, E and Meyer, E and Lovato, PE and Guerra, MP and Gris, T and de Almeida, AFN and Mayer, JLS},
title = {Beyond Mycorrhizae: A Multi-Kingdom Community in Epiphytic Orchid Roots Reveals Cyanobacteria Intracellular and a Velamen Microbial Refuge.},
journal = {Environmental microbiology reports},
volume = {18},
number = {6},
pages = {},
pmid = {42958634},
issn = {1758-2229},
mesh = {*Plant Roots/microbiology ; *Mycorrhizae/genetics/classification/physiology/isolation & purification ; *Orchidaceae/microbiology ; *Cyanobacteria/classification/genetics/isolation & purification/physiology ; *Microbiota ; Symbiosis ; Phylogeny ; Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; },
abstract = {Orchid biology has long been dominated by the paradigm of mycorrhizal dependency; however, the nutrient acquisition strategies of epiphytic orchids in canopy niches remain poorly understood. Using an integrated approach of multilocus metabarcoding (16S, ITS, 18S) and advanced microscopy (SEM, TEM, CLSM), we characterised the root microbial community of the threatened epiphytic orchid Cattleya purpurata. We report the discovery of intracellular Nostoc-like cyanobacteria within cortical cells, coexisting with the mycorrhizal fungus Tulasnella at a root colonisation rate of 18%. Furthermore, we identified: (1) a diverse velamen-associated microbiome hosting plant growth-promoting bacteria (e.g., the Burkholderia-Caballeronia-Paraburkholderia complex), nematodes and microalgae; and (2) a vast unknown fungal diversity, with over 39 genera and numerous ASVs unmatched in databases. We demonstrate that C. purpurata roots sustain a complex multi-kingdom community. We propose that the root velamen acts as a multi-kingdom microbial refuge, expanding the concept of symbiosis in orchids beyond fungi. Based on the intracellular presence of Nostoc-like cyanobacteria and their known diazotrophic capacity in other plant symbioses, we hypothesise a previously little-known nitrogen pathway mediated by cyanobacteria in a canopy environment, to be functionally tested in future studies.},
}

*Plant Roots/microbiology
*Mycorrhizae/genetics/classification/physiology/isolation & purification
*Orchidaceae/microbiology
*Cyanobacteria/classification/genetics/isolation & purification/physiology
*Microbiota
Symbiosis
Phylogeny
Bacteria/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification

@article {pmid42958637,
year = {2026},
author = {Paramita, L and Teng, CH and Ma, MC and Hashimoto, M and Tang, YA and Pan, HA and Sun, HS},
title = {Elevated Level of Fannyhessea vaginae Correlated with Implantation Outcomes in Women undergoing in vitro fertilization Treatment.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2606022},
doi = {10.4014/jmb.2606.06022},
pmid = {42958637},
issn = {1738-8872},
mesh = {Female ; Humans ; *Fertilization in Vitro ; *Vagina/microbiology ; *Embryo Implantation ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Adult ; Embryo Transfer ; Taiwan ; Bacteria/classification/genetics/isolation & purification ; Lactobacillus/isolation & purification/genetics ; Vaginosis, Bacterial/microbiology ; },
abstract = {The vaginal microbiome plays a significant role in reproductive health. While maintaining a balanced vaginal microbiome is crucial for successful in vitro fertilization (IVF) outcomes, the specific bacteria associated with adverse outcomes may vary by region and are largely unknown. This study aims to investigate the bacterial profiles and their influence on embryo implantation, thereby supporting the development of microbiome-based therapies. One hundred women undergoing IVF provided vaginal swabs at three stages: oocyte retrieval, embryo transfer, and hCG pregnancy testing. An in-house 16S rRNA gene amplicon sequencing and bioinformatics pipeline was used to profile the vaginal microbiota. Bacterial communities were constructed, and the transitions across IVF stages were analyzed. We also used custom quantitative PCR assays to validate NGS results and provide species-level resolution for selected bacterial species. Unlike other regions where Lactobacillus crispatus predominates, we found that Lactobacillus iners is the main vaginal microbiota across all IVF stages in Taiwan. Nevertheless, significant shifts in bacterial community types were correlated with hormonal changes during IVF treatment. Importantly, while Lactobacillus levels didn't predict pregnancy success, higher levels of bacteria associated with bacterial vaginosis, particularly Fannyhessea vaginae, significantly correlated with implantation failure and early embryonic loss. The strong association between elevated F. vaginae levels and adverse implantation rate in Taiwanese women highlights the potential benefit of incorporating routine screening for this pathogen. Personalized microbiome interventions targeting F. vaginae may improve embryo implantation for women undergoing assisted reproductive technologies.},
}

Female
Humans
*Fertilization in Vitro
*Vagina/microbiology
*Embryo Implantation
Pregnancy
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Adult
Embryo Transfer
Taiwan
Bacteria/classification/genetics/isolation & purification
Lactobacillus/isolation & purification/genetics
Vaginosis, Bacterial/microbiology

@article {pmid42958964,
year = {2026},
author = {Zhai, R and Ma, T and Su, M and Wang, H and Li, J and Xing, J and Huang, X and Yu, P and Qiu, J and Liu, T and Xiao, X and Li, Y and Gu, Y and Zhang, Y},
title = {DiseaseCIO: a multi-omics atlas for characterizing clinical intervention outcomes across diverse diseases.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1044},
pmid = {42958964},
issn = {1362-4962},
support = {62372141//National Natural Science Foundation of China/ ; 20240101040366//Science and Technology Program of the Health Commission of Heilongjiang Province/ ; QMSI2024B-02//Qiqihar Medical University Young Doctor Special Research Fund Project/ ; LH2024F020//Joint Guidance Project of Heilongjiang Provincial Natural Science Foundation/ ; 2022-KYYWF-0294//Harbin Medical University Innovation Scientific Research Fund/ ; 2022ZX06C13//Heilongjiang Provincial Department of Science and Technology Project/ ; },
abstract = {Heterogeneity in clinical intervention outcomes across patients is a major barrier to precision medicine. The integration of multidimensional high-throughput omics can help reveal the molecular basis of differences in clinical interventions and provide insights into outcome prediction, prognostic stratification, regulatory patterns, and resistance mechanisms. We present DiseaseCIO (Disease Clinical Intervention Outcomes, http://db.edbc.org/DiseaseCIO/), a database that integrates microbiome, transcriptome, and epigenome data with human disease intervention outcomes. It is designed to characterize the molecular landscape associated with disease intervention outcomes at the individual patient level. DiseaseCIO encompasses 42 798 pretreatment samples from 94 disease states, covering 510 treatment regimens involving 377 pharmacological and non-pharmacological interventions. These samples comprise four types of specimens collected from eight sampling locations. Using the customized iMOD workflow for multi-omics data processing, we generated 20 categories of molecular features and identified >1.84 million candidate feature-outcome associations. DiseaseCIO also provides interactive tools for differential analysis, prognostic evaluation, cross-omics correlation analysis, and cross-cohort integrative analysis of multidimensional features as well as enrichment analysis and signature construction for user-submitted feature sets. DiseaseCIO provides a molecular-level resource for exploring intervention outcome heterogeneity across diseases and identifying candidate multi-omics biomarkers associated with treatment response and prognosis.},
}

@article {pmid42959082,
year = {2026},
author = {Zhang, Y and Pei, C and Zhang, D and Liu, J},
title = {Microbiome-driven precision psychiatry: integrating multi-omics, artificial intelligence, and personalized interventions along the gut-brain axis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1957715},
pmid = {42959082},
issn = {2296-858X},
abstract = {INTRODUCTION: This scoping review maps evidence for microbiome-driven precision psychiatry in depression and anxiety.

METHODS: Following JBI guidance and PRISMA-ScR, we searched PubMed/MEDLINE and PubMed Central from inception to July 2026, supplemented by Google Scholar and backward citation searching. Human primary studies were screened and charted; findings were synthesized narratively.

RESULTS: Of 58 identified records, 49 remained after deduplication, 35 full texts were assessed, and 28 studies were included. The evidence was predominantly observational. Taxonomic findings varied across populations, while studies of microbial functions, metabolites, multi-omics signatures, and treatment response suggested potential for biological stratification. Microbiome-targeted interventions and artificial intelligence models remain exploratory.

DISCUSSION: Microbiome-derived biomarkers and predictive models require standardized methods, independent validation, and prospective evidence of clinical utility before routine psychiatric use.},
}

@article {pmid42959084,
year = {2026},
author = {Kang, Y and Fan, Y and Ma, Q and Yu, L and Liu, J and Liu, Y and Zhou, Z and Zhao, H and Yang, Z and Xun, Y and Jia, M and Zhao, B and Ma, X and Wang, W and Guo, Y},
title = {An oral-origin Streptococcus salivarius associated with schizophrenia reshapes intestinal T-cell immunity and promotes IL-17A-dominated inflammation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1978713},
pmid = {42959084},
issn = {1664-3224},
mesh = {Animals ; *Interleukin-17/immunology/metabolism ; *Schizophrenia/immunology/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; *Streptococcus salivarius/immunology ; Th17 Cells/immunology ; Inflammation/immunology/microbiology ; Intestinal Mucosa/immunology/microbiology/metabolism ; T-Lymphocytes, Regulatory/immunology ; *Gastrointestinal Microbiome/immunology ; Dysbiosis/immunology/microbiology ; },
abstract = {BACKGROUND: Emerging evidence suggests that oral microbial dysbiosis contributes to neuropsychiatric disorders through microbiome-immune interactions. We previously identified an oral-origin Streptococcus salivarius enriched in individuals with schizophrenia (SCZ) and demonstrated its ability to become enriched in the intestine after oral administration. However, whether this disease-associated bacterium remodels host adaptive immunity remains unclear. Here, we investigated the effects of S. salivarius on intestinal CD4[+] T-cell homeostasis and inflammatory responses.

METHODS: Male C57BL/6 mice were orally administered S. salivarius for 14 days with or without prior antibiotic-mediated depletion of resident microbiota. Intestinal enrichment of S. salivarius was confirmed by quantitative PCR. Colonic lamina propria mononuclear cells (LPMCs) and mesenteric lymph node (MLN) cells were analyzed using single-cell RNA sequencing and flow cytometry to characterize CD4[+] T cell responses. Cytokine levels in colon tissues and serum were quantified by ELISA.

RESULTS: Single-cell transcriptomic analysis demonstrated that intestinal enrichment of S. salivarius altered Treg-associated transcriptional programs, with reduced Treg-stability signatures and increased Type-17-associated features. Flow cytometry confirmed increased Th17 cells, reduced Treg frequencies, and disruption of intestinal Th17/Treg homeostasis. Similar immune alternations were observed in MLNs, indicating extension of gut-associated immune remodeling beyond the intestinal mucosa. S. salivarius exposure was further associated with selective IL-17A in colonic tissues and serum, whereas IL-6, IL-1β, IL-10, and TGF-β remained largely unchanged. Comparable immune changes were observed in both antibiotic-pretreated and conventional SPF mice, indicating that these immunological effects were not restricted to microbiota-depletion condition.

DISCUSSION: These findings identify an SCZ-associated oral-origin S. salivarius as a modulator of intestinal adaptive immunity. Intestinal enrichment of S. salivarius was associated with coordinated remodeling of Treg-associated transcriptional programs, Th17-biased immune polarization, and an IL-17A-dominated inflammatory response, Together, these results define an intestinal immune mechanism through which a disease-associated oral bacterium may contribute to oral-gut immune interactions and provide experimental support for one immunological component of the oral-gut-brain axis relevant to schizophrenia.},
}

Animals
*Interleukin-17/immunology/metabolism
*Schizophrenia/immunology/microbiology
Male
Mice
Mice, Inbred C57BL
*Streptococcus salivarius/immunology
Th17 Cells/immunology
Inflammation/immunology/microbiology
Intestinal Mucosa/immunology/microbiology/metabolism
T-Lymphocytes, Regulatory/immunology
*Gastrointestinal Microbiome/immunology
Dysbiosis/immunology/microbiology

@article {pmid42959094,
year = {2026},
author = {Feng, Y and Tang, F and Ma, Q and Ao, Z and Xiong, Q and Qin, W and Yang, Y and Tao, S and Guo, R},
title = {Oral microbial and metabolic alterations in acute exacerbations of COPD across fungal status.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1843568},
pmid = {42959094},
issn = {2235-2988},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism ; Prospective Studies ; *Mouth/microbiology ; Male ; Female ; Candida ; Microbiota ; *Dysbiosis/microbiology ; Aspergillus/isolation & purification ; Multiomics ; Metabolome ; },
abstract = {BACKGROUND: Oral dysbiosis has been associated with inflammatory processes in acute exacerbations of chronic obstructive pulmonary disease (AECOPD). However, whether Aspergillus-associated or Candida-positive status is associated with distinct oral multi-omics profiles, and whether these profiles change following treatment, remains unclear.

METHODS: In this prospective cohort study (August 2024 to July 2025), 18 AECOPD patients were enrolled and stratified into non-fungal exacerbators (n=6), Aspergillus-associated AECOPD (n=6), and Candida-positive AECOPD (n=6). Oral samples were collected before treatment and, where available, after treatment. The primary analyses compared pretreatment microbial and metabolic profiles across fungal-status groups, whereas longitudinal pre/post-treatment analyses were secondary and exploratory and were performed only in groups with sufficient paired samples.

RESULTS: Baseline characteristics were comparable across groups. At pretreatment, Aspergillus-associated AECOPD showed significantly reduced α diversity and distinct microbial community separation from non-fungal exacerbators (Bray-Curtis R = 0.378, P = 0.009), whereas Candida-positive AECOPD showed no significant global shift. At the genus level, exploratory LEfSe analysis identified distinct subgroup-associated candidate taxonomic signatures. PICRUSt2-based predicted functional profiles were broadly similar across groups. Metabolomic profiling showed the most pronounced baseline differences in the Aspergillus-associated group, with 11 upregulated and 90 downregulated metabolites versus the non-fungal group. Differential metabolites in this baseline comparison were predominantly mapped to sphingolipid metabolism, purine metabolism, one-carbon metabolism, and cAMP/cGMP signaling pathways. In secondary exploratory longitudinal analyses, metabolic shifts were observed in the non-fungal group (4 upregulated and 78 downregulated metabolites) and the Candida-positive group (14 upregulated and 8 downregulated metabolites). No formal longitudinal analysis was performed in the Aspergillus-associated group because only two post-treatment samples were available. O2PLS identified shared cross-omics variation distinguishing pretreatment Aspergillus-associated from non-fungal AECOPD, with several microbial and metabolite features contributing to the shared latent component.

CONCLUSION: Compared with non-fungal and Candida-positive AECOPD, Aspergillus-associated AECOPD showed the most pronounced pretreatment oral microbial dysbiosis and metabolic alterations. These findings support the presence of a distinct oral microbial-metabolic phenotype associated with Aspergillus status and provide candidate signatures for future validation in larger longitudinal cohorts.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/hvshowproject.html?id=250288&v=1.0, identifier ChiCTR2400083090.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/metabolism
Prospective Studies
*Mouth/microbiology
Male
Female
Candida
Microbiota
*Dysbiosis/microbiology
Aspergillus/isolation & purification
Multiomics
Metabolome

@article {pmid42959114,
year = {2026},
author = {Saghi, M and Van Holm, W and Zayed, N and Lauwens, K and Teughels, K and Boon, N and Bernaerts, K and Teughels, W},
title = {Probiotic toothpastes and mouthrinses: probiotic presence, viability, culturability, label accuracy, and effectiveness in vitro.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1936217},
pmid = {42959114},
issn = {2673-4842},
abstract = {OBJECTIVE: Per their design, several oral hygiene products have antimicrobial properties to influence the oral microbiome. However, due to overconsumption, resistance to these antimicrobials is developing. In contrast, as a pro-microbial approach, probiotics hold promise for rebalancing the oral microbiome towards a symbiotic state. Despite the availability of probiotic oral products, uncertainties about the probiotic presence, culturability, and reliability of labels persist. This study assessed the culturability, effectiveness, and accuracy of probiotics listed in commercially available probiotic toothpastes and mouth rinses.

METHODS: A total of 16 probiotic toothpastes and 6 probiotic mouthrinses, available on the European and American markets, were analysed for the number of culturable (CFU; agar plating), live (viability qPCR), and total bacteria (qPCR), and if they indeed contain the probiotic species proclaimed (16S rRNA sequencing). The products with viable probiotics were further evaluated for their impact on an in vitro oral biofilm model. Additionally, culturable probiotic isolates from these products were tested for potential inhibitory effects against individual oral pathogens.

RESULTS: Not all of the examined products contained viable bacteria; instead, they contained ferments or inactivated probiotics. Only 2 toothpastes were found to contain culturable bacteria consistent with the probiotic species declared on their labels. Additionally, traces of DNA from actual probiotics were detected in 68% of the toothpastes and 50% of the mouthrinses. Furthermore, the tested products did not show any beneficial effect on an in vitro oral biofilm model. Similarly, the culturable probiotic isolates recovered from the products showed no inhibitory activity against selected oral pathogens.

CONCLUSIONS: This study highlights that in contrast to probiotic lozenges, which are widely used for oral probiotic delivery, currently available probiotic toothpastes and mouthrinses may not consistently meet established probiotic criteria. These findings highlight the need to critically reassess their use in scientific research and the commercial use of the term probiotic, while recognizing that the present findings are specific to the product batches analysed and may not represent each brand as a whole.},
}

@article {pmid42959296,
year = {2026},
author = {Zhang, X and Yuan, Y and Shi, Y and Chen, S and Gao, Z and Yang, Q and Hou, H and Feng, B},
title = {Crop-associated differentiation of rhizosphere microbial communities and soil functional traits in saline-alkaline farmland.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1952914},
pmid = {42959296},
issn = {1664-302X},
abstract = {INTRODUCTION: Saline-alkaline soils constrain crop production, yet it remains unclear how different crops shape rhizosphere conditions, plant ion allocation and microbial communities when grown under the same field background.

METHODS: We compared eight crops under uniform saline-alkaline field and management conditions and integrated rhizosphere physicochemical properties, enzyme activities, plant nutrient and ion traits, and bacterial and fungal community characteristics using a multivariate framework.

RESULTS: Crop identity was associated with pronounced differences in nutrient status, salinity, moisture, enzyme activity and Na[+] and K[+] allocation, and explained 78.1% and 83.5% of bacterial and fungal community variation, respectively. Multiple factor analysis further separated the eight crops into two stable multivariate profiles, one characterized mainly by nutrient and enzyme traits and the other by higher salinity and greater contributions from Na[+] allocation traits.

DISCUSSION: These findings demonstrate that crop-associated differentiation in saline-alkaline farmland reflects coordinated variation among soil conditions, plant ion regulation and microbial organization, providing an integrated basis for crop comparison and saline-alkaline soil management.},
}

@article {pmid42959427,
year = {2026},
author = {Xue, X and Qiu, S and Zheng, J and Kong, Y and Gao, L and Zhan, W and Guo, W and Chen, J and Li, L},
title = {Radiation-induced oral mucositis as an immune hub: from innate immune sensing to adaptive immune dysregulation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1905406},
pmid = {42959427},
issn = {1664-3224},
mesh = {Humans ; *Radiation Injuries/immunology/etiology ; *Stomatitis/immunology/etiology ; *Immunity, Innate/radiation effects ; Animals ; *Adaptive Immunity/radiation effects ; Innate Immunity Recognition ; Radiotherapy/adverse effects ; Microbiota/radiation effects/immunology ; },
abstract = {Radiation-induced oral mucositis (RIOM) has traditionally been viewed as a cytotoxic injury to rapidly proliferating epithelial cells caused by radiotherapy. Recent studies have revealed that RIOM is fundamentally a pivotal radiotherapy-triggered, damage signal-driven dysregulation event of local and systemic immune homeostasis. The severity of RIOM dynamically and directly affects patients' oral health-related quality of life (OHRQoL), serving as an intuitive reflection of their local immune-inflammatory status. Key immunological events include the release of unique damage-associated molecular patterns (DAMPs) by radiotherapy, which actively initiate and shape the intrinsic immune recognition program; functional shifts and imbalances in critical immune subsets such as neutrophils, macrophages, and T cells, forming the core circuitry of sustained injury and impaired repair; and the chronic immune microenvironment, which not only drives local pathology profoundly influencing systemic antitumor immune responses and long-term complications. This review aims to establish the emerging interdisciplinary framework of radioimmunomucosology, providing a novel perspective for optimizing comprehensive cancer therapy. Additionally, systematic studies have revealed that radiotherapy induces predictable ecological dysbiosis in the oral microbiome, characterized by depletion of commensal bacteria and expansion of opportunistic pathogens. This suggests that RIOM involves radiation-triggered disruption or confrontation between host immunity and commensal microorganisms.},
}

Humans
*Radiation Injuries/immunology/etiology
*Stomatitis/immunology/etiology
*Immunity, Innate/radiation effects
Animals
*Adaptive Immunity/radiation effects
Innate Immunity Recognition
Radiotherapy/adverse effects
Microbiota/radiation effects/immunology

@article {pmid42959445,
year = {2026},
author = {Zhou, E and Zhan, C and Li, Y and Zeng, Y and Luo, R and Ouyang, X and Liu, S and Yang, R and Yan, N and Jiang, L},
title = {Atherosclerosis: From Pathogenesis to Therapeutic Interventions.},
journal = {MedComm},
volume = {7},
number = {11},
pages = {e71095},
pmid = {42959445},
issn = {2688-2663},
abstract = {Atherosclerosis is no longer viewed solely as a lipid-storage disorder but rather as a complex multisystem inflammatory disease driven by interactions among the vascular, immune, metabolic, and nervous systems. This review integrates recent concepts, including trained immunity, the neuroimmune cardiovascular interface, vascular cell plasticity, and the microbiome-vascular axis, that reshape the understanding of plaque initiation, progression, and instability. We summarize how established lipid-lowering, antidiabetic, antihypertensive, and revascularization strategies influence atherosclerotic disease and discuss emerging interventions, including RNA therapeutics, anti-inflammatory agents, gene therapy, and cell-based approaches. Key ongoing clinical trials that may clarify the cardiovascular benefits and safety of these strategies are also reviewed. Despite therapeutic advances, residual cardiovascular risk persists because of limitations in animal models, sex-related differences in plaque phenotype, and the lack of clinically applicable biomarkers. Nanotechnology, human microphysiological systems, spatial multiomics, and artificial intelligence may help bridge these translational gaps. Successful clinical implementation will nevertheless require biomarker-guided patient selection, rational combination therapy, validated surrogate endpoints, long-term safety assessment, and attention to health economics. In summary, these advances will shape future translational research and clinical trial design, ultimately advancing personalized management of atherosclerosis.},
}

@article {pmid42959510,
year = {2026},
author = {Saheb, F},
title = {Post-COVID Gastrointestinal Symptoms and Disorders of Gut-Brain Interaction: A Focus on Persistent Diarrhea.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e117111},
pmid = {42959510},
issn = {2168-8184},
abstract = {Persistent gastrointestinal (GI) symptoms after SARS-CoV-2 infection include diarrhea, abdominal pain, dyspepsia, constipation, nausea, and other disorders of gut-brain interaction (DGBIs), but these entities should not be treated as interchangeable. In a meta-analysis of long-COVID studies, any GI symptom was reported in approximately 22% of patients and diarrhea in 10%, although heterogeneity was very high. In a large US Veterans Affairs cohort, post-acute COVID-19 was associated with incident diarrhea (hazard ratio {HR}:
1.58, 95% CI: 1.52-1.65; excess burden 7.99 per 1,000 persons at one year) and irritable bowel syndrome (HR: 1.54, 95% CI: 1.28-1.86). Prospective Rome IV cohorts report lower absolute rates of formally diagnosed DGBIs; one study found persistent DGBI symptoms in 6.6% at six months, with functional diarrhea in 2.2% and irritable bowel syndrome (IBS) in 2.5% at three months. Mechanistic evidence supports intestinal involvement during acute infection and demonstrates associations with epithelial/angiotensin-converting enzyme 2 (ACE2) perturbation, immune activation, barrier dysfunction, altered microbial taxa, and impaired microbial metabolite production. However, persistent viral RNA or antigen, dysbiosis, and gut-lung signaling remain proposed or associative mechanisms rather than established causes of chronic diarrhea. Treatment evidence specific to post-COVID functional diarrhea is sparse. A large synbiotic trial improved a broad "gastrointestinal upset" domain in post-acute COVID syndrome, but did not enroll a defined chronic diarrhea or Rome-positive population; probiotic and fecal microbiota transplantation trials showing GI effects were largely conducted during acute COVID-19. Therefore, current care should first exclude organic and medication-related causes, then apply phenotype-based management extrapolated from established diarrhea-predominant irritable bowel syndrome (IBS-D) and functional-diarrhea practice while clearly acknowledging the limited post-COVID-specific evidence. Standardized definitions, pre-infection GI data, appropriate controls, functional microbiome measures, and dedicated randomized trials are priorities for future research.},
}

@article {pmid42959563,
year = {2026},
author = {De Jaegher, S and Podrini, C and D'Aguanno, M and Santoro, F and Biazzo, M},
title = {Building biologically relevant in vitro models of the human gut microbiota: methodological considerations, current challenges, and future perspectives.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1949973},
pmid = {42959563},
issn = {1664-302X},
abstract = {The human gut microbiota (HGM) plays a pivotal role in human health by regulating metabolic, immune, and neurological processes and contributes to the susceptibility to various diseases. The increasing interest in microbiota-targeted therapies has highlighted the need for in vitro models capable of accurately reproducing the composition, function, and ecological dynamics of the intestinal microbial ecosystem. This review examines the methodological factors that determine the biological relevance of HGM in vitro models, emphasizing that reliable experimental outcomes depend not only on the choice of fermentation system (including batch and continuous fermentation systems), but also on the optimization of inoculum preparation, culture media, environmental control, and strategies that preserve microbial stability and reproducibility. We further discuss how these methodological decisions influence the interpretation of experimental results and determine the suitability of each model for different biological applications. The application of these models in dietary, prebiotic, probiotic, and pharmacological interventions is explored, demonstrating their potential to predict microbiota responses and elucidate mechanistic links between microbial activity and host responses. We propose that rigorous methodological standardization, rather than increasing technological complexity alone, represents the principal requirement for generating biologically relevant and reproducible in vitro gut microbiota models. Finally, we discuss emerging host-microbe co-culture systems, along with the integration of multi-omics and computational approaches, which are expected to expand the physiological relevance and translational applicability of these models. Unlike reviews primarily organized around individual fermentation technologies, this review adopts a workflow-based perspective and examines how methodological decisions interact to determine ecological fidelity, functional stability and reproducibility.},
}

@article {pmid42959623,
year = {2026},
author = {Muneeb, M and Tharwat, M and Shaukat, A and Nassar, N and Qu, Y and Khan, AY and Alshanbari, FA},
title = {Formulation, stability, and delivery of bacteriophage cocktails in veterinary medicine: a review of physicochemical constraints and therapeutic outcomes in production animals.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1988130},
pmid = {42959623},
issn = {2297-1769},
abstract = {Intensive food animal production is at risk due to the ever-increasing antimicrobial resistance (AMR) of veterinary pathogens, and it is time to look at alternatives to antibiotics. Bacteriophage (phage) cocktails, which involve the use of several bacteriophages with different host ranges and resistance profiles, are a new and exciting biologic approach. Nevertheless, there are significant physicochemical barriers in the animal host and during feed processing that hinder the translation of promising in vitro bacteriolysis to consistent in vivo therapeutic efficacy. The review critically addresses the interrelated issues of gastric acidity, enzymatic digestion, exposure to bile salts, thermal stress during feed pelleting and osmotic fluctuations, which all contribute to the destruction of orally administered phage titers. We systematically examine formulation technologies such as lyophilization, spray-drying, and alginate, chitosan, lipid nanoparticles and hydrogel encapsulation to protect phages from these destructive environments. When comparing the delivery routes of oral, parenteral, intramammary and aerosol, it is observed that each route places different priorities on biopharmaceutical requirements. Critical evaluation of therapeutic outcomes in poultry, swine, ruminants, and aquaculture has shown that the use of formulations optimized for the gastrointestinal physiology of the target species can lead to significantly reduced target bacterial loads and mortality rates, but failures often occur when in vitro stability data is not supported by an understanding of the pharmacokinetic parameters. For ruminants, there is a remarkable difference between the success of acid-resistant encapsulation in monogastrics and the inability of such methods to work in ruminants due to premature release and inactivation of phages by the forestomach microbiome. We emphasize the need for standardized assays of phage titer in different laboratories, well-defined regulatory processes, and physiologically-based pharmacokinetic/pharmacodynamic models that can predict the temporal and spatial dynamics of phage-bacteria interactions in vivo. This synthesis provides a roadmap for the rational design of phage cocktail products that can reliably reduce antibiotic dependence in veterinary medicine.},
}

@article {pmid42959646,
year = {2026},
author = {Xin, Y and Wang, X and Wu, Y and Liu, Q and Ren, Q and Wang, H and Zhai, J},
title = {Gastric Cancer: Epidemiology, Risk Factors, Pathogenesis, Clinical Features, Diagnosis, and Management.},
journal = {MedComm},
volume = {7},
number = {11},
pages = {e71100},
doi = {10.1002/mco2.71100},
pmid = {42959646},
issn = {2688-2663},
abstract = {Gastric cancer is a multifactorial disease shaped by diverse risk factors and a complex pathogenesis spanning from chronic atrophic gastritis to invasive malignancy. Its global incidence shows marked geographic disparities, and advances in understanding its pathogenic mechanisms have improved diagnosis and treatment. Although the relationship between gastric cancer and macrophages has been extensively investigated, a systematic review integrating the entire clinical and biological continuum of gastric cancer, from epidemiology to management, with a focus on macrophages remains lacking. This review summarizes the epidemiology and multidimensional risk factors for gastric cancer, including infectious, dietary, genetic, microbiome, and metabolite-related factors. We describe the evolution of precancerous conditions, molecular alterations such as miRNA expression, and the bidirectional interactions between gastric cancer cells and macrophages that drive tumor progression within the tumor microenvironment. We also review clinical features, diagnostic approaches based on screening and endoscopy, and current management strategies, including surgery, systemic therapies, targeted therapies, immunotherapy, macrophage-targeted therapies, macrophage metabolic reprogramming, and recent preclinical and clinical advances. Overall, this review integrates evidence from epidemiology, molecular biology, immunology, and pathology to provide a comprehensive framework for understanding gastric cancer pathogenesis and current as well as emerging therapeutic strategies.},
}

@article {pmid42959674,
year = {2026},
author = {Sharma, J and Kumar, KS and Sharma, A and Sheikh, MK and Shukla, AK and Shaikh, SS},
title = {Clinical, Immunological, and Environmental Determinants of Pediatric Respiratory Disorders: A Comprehensive Review of Long-Term Health Outcomes.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e117121},
pmid = {42959674},
issn = {2168-8184},
abstract = {Pediatric respiratory disorders remain a major source of childhood morbidity, healthcare utilization, impaired quality of life, and long-term pulmonary vulnerability. The background of this review centers on the complex interaction between early-life clinical susceptibility, immune maturation, environmental exposure, respiratory infections, and social determinants in shaping pediatric airway health. The objective was to synthesize evidence on clinical, immunological, infectious, environmental, and social determinants relevant to pediatric asthma, recurrent wheeze, and associated long-term respiratory outcomes, including disease persistence, impaired lung-function trajectories, and later respiratory vulnerability. The methodology involved a structured literature search of studies published from 2015 to 2025 in PubMed, Scopus, Web of Science, Embase, and Google Scholar, including observational studies, clinical studies, systematic reviews, meta-analyses, and high-quality narrative reviews focused on infants, children, and adolescents. The evidence indicates that early-life respiratory vulnerability, recurrent viral infections, atopic and inflammatory pathways, microbiome alterations, environmental exposures, and social disadvantage may interact across childhood and contribute to heterogeneous long-term respiratory trajectories. Longitudinal cohort findings further show that some children maintain persistent airflow impairment into adulthood, whereas others demonstrate partial improvement over time. Because the available evidence is stronger for associations and prognostic trajectories than for intervention efficacy, preventive and clinical strategies should be interpreted cautiously, with emphasis on appropriate diagnosis, phenotype- and severity-based management, reduction of avoidable exposures, age-appropriate pulmonary-function monitoring, and equitable access to follow-up.},
}