@article {pmid42043192,
year = {2026},
author = {Knap-Wielgus, W and Knap, A and Pietrzak, B and Suchońska, B and Wielgoś, M},
title = {A Role of the Lower Genital Tract Microbiome in Promoting Cervical Intraepithelial Neoplasia: A Premalignant Precursor of Cervical Cancer-A Literature Review.},
journal = {Viruses},
volume = {18},
number = {4},
pages = {},
pmid = {42043192},
issn = {1999-4915},
mesh = {Humans ; Female ; *Microbiota ; *Uterine Cervical Dysplasia/microbiology/virology/pathology ; *Uterine Cervical Neoplasms/microbiology/virology/pathology ; Papillomavirus Infections/complications/virology/microbiology ; Dysbiosis/microbiology ; *Vagina/microbiology/virology ; Papillomaviridae ; Lactobacillus ; },
abstract = {The cervicovaginal microbiome (CVMB) is pivotal in maintaining the homeostasis of the lower female genital tract and has emerged as a significant modulator of cervical carcinogenesis. Although persistent infection with high-risk human papillomavirus (HR-HPV) is a prerequisite for the development of cervical intraepithelial neoplasia (CIN) and subsequent cervical carcinoma, it remains insufficient alone to drive oncogenesis. Accumulating evidence suggests that alterations in the CVMB composition profoundly impact HPV persistence, local immune responses, and disease progression. A vaginal microbiota dominated by Lactobacillus species, most notably Lactobacillus crispatus, correlates with low microbial diversity, robust immune regulation, and facilitated HPV clearance. Conversely, microbial dysbiosis-characterized by Lactobacillus depletion and a concomitant proliferation of anaerobic taxa, typical of Community State Type (CST) IV and Lactobacillus iners-dominated profiles-is strongly associated with chronic inflammation, oxidative stress, epithelial barrier compromise, and an elevated risk of CIN progression. This review synthesizes current evidence regarding the multifaceted interactions among the cervicovaginal microbiome, HPV pathogenesis, immune dysregulation, and oxidative stress in the etiology of CIN. Elucidating these intricate host-microbiome dynamics may precipitate the discovery of novel microbiome-derived biomarkers, ultimately informing innovative prophylactic and therapeutic interventions for cervical cancer.},
}

Humans
Female
*Microbiota
*Uterine Cervical Dysplasia/microbiology/virology/pathology
*Uterine Cervical Neoplasms/microbiology/virology/pathology
Papillomavirus Infections/complications/virology/microbiology
Dysbiosis/microbiology
*Vagina/microbiology/virology
Papillomaviridae
Lactobacillus

@article {pmid42043303,
year = {2026},
author = {Böswald, LF and Zeyner, A and Santo, MM and Wensch-Dorendorf, M and Sünder, A and Popper, B and Siegert, W},
title = {Feeding Laboratory Mice: Comparing a Standard Versus a Purified Diet - Marked Effects on Digestive Physiology.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.70063},
pmid = {42043303},
issn = {1439-0396},
abstract = {Diet composition and processing have a major impact on its utilisation by the animal, as is known from farm and pet animal species. This includes effects on energy and nutrient digestibility, the intermediary metabolism, and the intestinal microbiome, with all the resulting impacts. For laboratory animals, data is scarce on influencing factors on diet digestibility. In experiments using special diets, either standard diets are used for the control group, or purified control diets. The aim of the present study was to compare a standard diet and a purified control diet (both pelleted) fed ad libitum to C57BL/6J mice and to investigate the potential effect on body weight development, feed conversion, energy and nutrient digestibility and indicators of intestinal fermentation (pH, short-chain fatty acids). Thus, 21 mice each were fed the standard diet (STD) and the purified diet (PD). Results showed a significantly higher apparent digestibility of gross energy and the crude nutrients in group PD (p < 0.001). The weight of the filled cecum and colon was significantly lower in group PD than STD (p < 0.001; p < 0.01). The pH of ingesta was significantly higher in stomach, cecum and colon of group PD (p < 0.0001), likely influenced by the significantly lower concentration of total short-chain fatty acids measures in cecum and colon of PD mice. The high apparent digestibility of the PD implied a lower influx of fermentable substrate into the hindgut, resulting in lower concentrations of microbial metabolites and altered pH milieu.},
}

@article {pmid42043563,
year = {2026},
author = {Chatterjee, S and Dutta, S and Ghosh, J and Saha, S and Mondal, M and Sarkar, J and Mondal, N and Ghosh, W},
title = {Warming responses, antibiosis potentials, and ecological implications of cryo-adapted copiotrophs from a Trans-Himalayan lake-desert ecosystem.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043563},
issn = {1432-072X},
support = {Intramural Faculty Grant//Bose Institute/ ; },
}

@article {pmid42043564,
year = {2026},
author = {Niu, YJ and Liu, LB and Yang, ZD and Xu, CJ and Zhao, TK and Chen, LL and Wang, QQ and Sun, B and Kim, S},
title = {The antimicrobial arsenal of endophytes in Lilium pumilum: active components of Fusarium tricinctum and antifungal mechanisms.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043564},
issn = {1432-072X},
support = {No. 22267011//National Natural Science Foundation of China/ ; 2023-RC-43//The project of the Bureau of Science and Technology of Lanzhou/ ; Y20220198//The Science and Technology Plan Project of Wenzhou, China/ ; 2025CXZX-608//The Gansu Provincial Department of Education: Graduate Student 'Innovation Star' Project/ ; No. 2022CYZC-29//The Industrial Support Plan Project of Colleges and Universities in Gansu Province/ ; },
mesh = {*Fusarium/isolation & purification/metabolism/physiology/chemistry ; Botrytis/drug effects ; *Endophytes/isolation & purification/metabolism/chemistry/physiology ; *Lilium/microbiology ; Plant Diseases/microbiology/prevention & control ; Rhizoctonia/drug effects ; *Antifungal Agents/pharmacology ; Soil Microbiology ; Rhizosphere ; Ascomycota/drug effects ; Antibiosis ; Hypocreales ; },
abstract = {The microbiome of Lilium pumilum represents a valuable resource for developing sustainable biocontrol strategies. This study investigated the potential of these microorganisms to serve as major plant pathogen-antagonistic strains. In this study, 38 strains (18 fungi and 20 actinobacteria) were isolated from L. pumilum and its rhizosphere soil. Among these, the endophytic fungus Z-SD-LJ-2 (Fusarium tricinctum) exhibited remarkable broad-spectrum antifungal activity against five tested plant pathogens, with inhibition rates of 68.07-89.42% and half maximal effective concentration (EC50) values of 16.58-30.97 µg mL[- 1]. Notably, its performance surpassed the commercial fungicide azoxystrobin against Fusarium oxysporum and Botrytis cinerea. Concurrently, the rhizosphere-derived strain Z-SDTR-2 (Purpureocillium lilacinum) demonstrated potent inhibition against Rhizoctonia solani, Sclerotinia sclerotiorum, and Botrytis cinerea, with all inhibition rates exceeding 80% and EC50 values of 17.17-21.80 µg mL[- 1]. Activity-guided isolation from Z-SD-LJ-2 led to the identification of enniatin B as the most active compound, exhibiting EC50 values of 13.78-26.81 µg mL[- 1]. Further studies revealed that enniatin B induces apoptosis in the pathogens by triggering reactive oxygen species (ROS) accumulation and causing mitochondrial dysfunction. In pot experiments, the fermentation broth of Z-SD-LJ-2 (2 × 10[3] mg L[- 1]) effectively controlled lily wilt, reducing the disease index to 30% (14.3% lower than azoxystrobin) and achieving a preventive efficacy of 72.6% (18% higher than the control). Additionally, the treatment promoted lily growth, increasing plant height by 4.4% and stem thickness by 8.71% compared to the control, underscoring its dual-function potential as a novel, effective biopesticide for sustainable agricultural practices.},
}

*Fusarium/isolation & purification/metabolism/physiology/chemistry
Botrytis/drug effects
*Endophytes/isolation & purification/metabolism/chemistry/physiology
*Lilium/microbiology
Plant Diseases/microbiology/prevention & control
Rhizoctonia/drug effects
*Antifungal Agents/pharmacology
Soil Microbiology
Rhizosphere
Ascomycota/drug effects
Antibiosis
Hypocreales

@article {pmid42043853,
year = {2026},
author = {Pucci, N and Mende, DR},
title = {bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization.},
journal = {Microbial genomics},
volume = {12},
number = {4},
pages = {},
pmid = {42043853},
issn = {2057-5858},
mesh = {Humans ; *Milk, Human/metabolism/microbiology ; *Glycoside Hydrolases/genetics/metabolism ; *Polysaccharides/metabolism ; *Bifidobacterium/genetics/enzymology/metabolism ; *Molecular Sequence Annotation/methods ; Bacterial Proteins/genetics/metabolism ; Software ; },
abstract = {Human milk glycan (HMG) metabolism, especially by bifidobacteria, is crucial for infant gut colonization and healthy microbiome development. Bifidobacterial species and even strains are highly variable in their ability and in their enzymatic repertoire for HMG metabolism. The enzymes involved in HMG metabolism often have many non-HMG-related homologues, necessitating fine-grained annotation for accurate assessment of bifidobacterial HMG metabolic capabilities. However, current annotation tools provide only broad glycoside hydrolase (GH) (sub)family classifications. Here, we present bifidoAnnotator, a tool for fine-grained annotation and visualization of bifidobacterial GH genes involved in HMG utilization. bifidoAnnotator leverages MMseqs2 (Many-against-Many sequence searching) to map protein sequences against a manually curated database of over 22,000 bifidobacterial GH proteins, organized into 13 families and 108 functional clusters, each assigned a validation status (i.e. experimentally validated, putative or hypothetical). The tool performs hierarchical annotation at family and cluster levels, identifying consistently annotated protein variants rather than just broad family assignments, and generates publication-ready heatmaps for comparative analysis. Benchmarking on a gold standard dataset demonstrated that bifidoAnnotator has superior performance (95.9% precision, 100% recall) compared with six established tools and is an order of magnitude faster than the most accurate competitor. bifidoAnnotator's superior performance and computational efficiency represent a meaningful advance in high-throughput genomic annotation workflows, enabling detailed characterization of strain-level functional diversity in bifidobacterial HMG metabolism.},
}

Humans
*Milk, Human/metabolism/microbiology
*Glycoside Hydrolases/genetics/metabolism
*Polysaccharides/metabolism
*Bifidobacterium/genetics/enzymology/metabolism
*Molecular Sequence Annotation/methods
Bacterial Proteins/genetics/metabolism
Software

@article {pmid42043859,
year = {2026},
author = {Patel, RA and Harke, SN},
title = {A decade of evidence linking gut microbiome dysbiosis to depression: a computational meta-analysis of mechanistic pathways: 2014-2024.},
journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/15622975.2026.2660311},
pmid = {42043859},
issn = {1814-1412},
abstract = {OBJECTIVES: The gut microbiome-gut-brain axis (MGBA) has been associated in the pathophysiology of depression; however, the expanding literature remains fragmented across metabolic signalling, immune-inflammatory pathways, stress physiology and dysbiosis outcomes.

METHODS: Abstracts were retrieved from bibliographic databases (Lens.org, PubMed, DOAJ, Europe PMC) for studies published between 2014 and 2024 investigating associations between the gut microbiome and depression using 16S rRNA sequencing. Following text preprocessing, Latent Dirichlet Allocation (LDA) was applied to identify latent thematic topics. Topic proportions were subsequently embedded using principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation and projection (UMAP).

RESULTS: Topic modelling revealed distinct interconnected thematic domains within the gut microbiome depression literature, encompassing metabolic and short chain fatty acid pathways, immune inflammatory mechanisms, stress and hypothalamic pituitary adrenal (HPA) axis regulation, probiotic and interventional work, microbial diversity and compositional metrics, neurochemical and neuroplasticity, developmental cohorts, and sequencing- or methodology-focused research.

CONCLUSIONS: Computational synthesis indicates that research on the gut microbiome depression axis is structured around multiple convergent mechanistic themes. This thematic landscape highlights dominant areas of mechanistic focus, providing a conceptual framework to guide future experimental design, mechanistic validation and translational research.},
}

@article {pmid42043941,
year = {2026},
author = {Qu, W and Shi, X and Xu, X and Liu, C and Ding, L and Song, M and Xu, Z and Xu, Y and Mo, F and Ruan, J and Timko, MP and Fan, L and Zheng, S and Jiang, W and Wang, Y and Shen, Y},
title = {BACON: decoding the dynamic social networks of complex microbial communities at single-cell resolution.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {42043941},
issn = {1477-4054},
support = {82402729//National Natural Science Foundation of China/ ; 32200073//National Natural Science Foundation of China/ ; 32250710678//National Natural Science Foundation of China/ ; LQ23H200003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021R01012//Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2024C03005//Pioneer' R&D programs of Zhejiang Province/ ; 2024SSYS0022//Key Research and Development Program of Zhejiang/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholar/ ; },
mesh = {*Quorum Sensing ; Humans ; *Single-Cell Analysis ; *Gastrointestinal Microbiome ; *Microbiota ; Escherichia coli/genetics ; Bacillus subtilis/genetics ; *Computational Biology/methods ; Pseudomonas aeruginosa/genetics ; },
abstract = {Microbial communities function as dynamic societies where intercellular communication governs collective behaviors. However, mapping these interaction networks has remained a fundamental challenge in microbiology. This study aims to decode the social networks of complex bacterial communities at single-cell resolution by developing BACON, a computational framework that infers quorum sensing-mediated communication from single-microbe transcriptomic data. The approach combines a curated database of signaling systems with a statistical model that quantifies communication strength through coordinated expression of signal synthesis and receptor genes. Validation in model systems demonstrated BACON's precision in reconstructing density-dependent communication trajectories in Bacillus subtilis and capturing rapid network reorganization in Escherichia coli under antibiotic stress, revealing distinct sender-receiver subpopulations. Applied to human gut microbiomes, BACON unveiled diurnal fluctuations in cross-species signaling that transcend enterotype boundaries and uncovered conserved metabolic specialization in signal-responsive bacteria. In a clinical context, analysis of an ICU patient's gut microbiome revealed how Pseudomonas aeruginosa establishes a self-reinforcing communication circuit that upregulates virulence pathways. This work provides a unified framework for analyzing bacterial social interactions across diverse ecosystems. It opens new avenues for understanding microbial sociology, combating antimicrobial resistance, and engineering synthetic communities.},
}

*Quorum Sensing
Humans
*Single-Cell Analysis
*Gastrointestinal Microbiome
*Microbiota
Escherichia coli/genetics
Bacillus subtilis/genetics
*Computational Biology/methods
Pseudomonas aeruginosa/genetics

@article {pmid42044092,
year = {2026},
author = {Bloemendaal, M and Mulder, D and Gudden, J and Heikamp-de Jong, I and Ioannou, A and Belzer, C and Emile Natasha, E and Edwin Thanarajah, S and Aatsinki, AK and van Gelder, MMHJ and Arias Vasquez, A},
title = {Development of the gut microbiota throughout the first year of life and its association with socio-emotional development into childhood.},
journal = {Developmental neuroscience},
volume = {},
number = {},
pages = {1-27},
doi = {10.1159/000552189},
pmid = {42044092},
issn = {1421-9859},
abstract = {Introduction Early life is a critical window for the development of many bodily systems, including the gut microbiota and the central nervous system, that are inter-connected through the gut-brain-axis. These early life gut-brain-axis connections are often studied through cross-sectional cohorts, limiting insights into temporal developmental trajectories. This longitudinal cohort study assessed whether gut microbial development over the first year of life is associated with socio-emotional development into childhood. Methods The PRIDE (PRegnancy and Infant DEvelopment) BIOME study (n=81, n=42 males) is a focus cohort within the larger prospective PRIDE Study. Gut microbiome was measured 5 times throughout the first year of life (at 2, 4, 6, 9 and 12 months through V4 16S rRNA sequencing) and socio-emotional development 8 times over 4.5 years, between 6 months and 5 years through the Ages and Stages Questionnaire: Social-Emotional (ASQ-SE). We related the development of the gut microbiota of infants throughout their first year of life with their socio-emotional development into childhood, the latter modelled as a slope per individual (ASQ slope). We assessed effects of time, ASQ slope and its interaction with time on microbial community measures alpha and beta diversity, as well as taxonomy, using linear mixed-effects models and PERMANOVA, correcting for sex, birth weight, gestational age and sequencing depth. Results Expected developmental patterns on the gut microbiota over the first year of life were observed, including increased alpha diversity and clustering of beta diversity before and after solid food introduction. Interestingly, ASQ slope was a significant predictor of beta diversity (F(1,394)=25.90, p=0.001) and Bifidobacterium abundance across the first year of life (b= -0.745, SE= 0.24, pFDR= 0.023). Moreover, we observed a temporal association between ASQ slope and Eggerthella abundance (ASQ slope × timepoint interaction, b=0.709, SE=0.21, pFDR=0.009). That is, Eggerthella abundance decreased across the group, but not in "late concern" infants, with concern about socio-emotional development at more recent timepoints. Discussion This study shows that genera Bifidobacterium and Eggerthella, known to be altered in mental health conditions such as autism spectrum disorder and depression, are already linked to socio-emotional development during early life. Hence, this work contributes to the identification of gut microbial candidates relevant for preventive screening of healthy gut-brain development and microbiota-targeted interventions.},
}

@article {pmid42044128,
year = {2026},
author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D},
title = {Diet and gut microbiome of skipjack tuna (Katsuwonus pelamis) as indicators of environmental changes.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346882},
pmid = {42044128},
issn = {1932-6203},
mesh = {Animals ; *Tuna/microbiology/physiology ; *Gastrointestinal Microbiome ; *Diet ; Pacific Ocean ; *Climate Change ; Ecosystem ; Food Chain ; },
abstract = {Understanding the relationship between environmental changes and marine ecosystem dynamics is crucial, especially under the influence of climate events such as the El Niño Southern Oscillation (ENSO). The diet and gut microbiome of marine predators have the potential to efficiently, timely, and reliably indicate impacts of environmental and ecosystem changes, especially with the assistance of high-throughput sequencing (HTS) technology. This study investigated the gut content and microbiome of skipjack tuna (Katsuwonus pelamis) collected in the central Pacific Ocean during a transitional period of ENSO phases, shifting from a strong La Niña phase to a weak El Niño phase, aiming to evaluate the impacts of ENSO and other environmental factors on marine food webs and microbiome dynamics of skipjack tuna. While prey diversity was unaffected by ENSO events, skipjack tuna exhibited high diversity and opportunistic foraging patterns, with fish as the primary prey. In contrast, gut microbiome diversity was affected by ENSO events and Southern Oscillation Index (SOI). Five microbiome families (Fusobacteriaceae, Bacillaceae, Propionibacteriaceae, Beijerinckiaceae, and Comamonadaceae), which are associated with immune system functionality and nutritional provisioning of the host, displayed the most significant abundance changes between ENSO phases. A random forest model showed potential for ENSO phase classification based on the abundances of these five families, achieve high accuracy in internal validation, though the performance of external validation was mixed due to storage and sampling period differences. This study highlights the potential of skipjack tuna gut microbiome as indicators of rapid environmental changes, while acknowledging that the short sampling period requires longer-term validation across multiple ENSO cycles.},
}

Animals
*Tuna/microbiology/physiology
*Gastrointestinal Microbiome
*Diet
Pacific Ocean
*Climate Change
Ecosystem
Food Chain

@article {pmid42044527,
year = {2026},
author = {Rabasco, JT and Bolyen, E and Caporaso, JG and Sapers, H and Callahan, BJ},
title = {Identify contaminants with decontam on the QIIME 2 Framework.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0126125},
doi = {10.1128/mra.01261-25},
pmid = {42044527},
issn = {2576-098X},
abstract = {Here, we present the integration of the decontam method for contaminant identification and a supplemental approach for identifying the source of contaminants in sequencing data within the QIIME 2 Framework for microbiome data science. We demonstrate its use in a tutorial based on the QIIME 2 "Moving Pictures Tutorial" data.},
}

@article {pmid42044645,
year = {2026},
author = {Shoemark, A and Johnson, ED and Shuttleworth, M and Schwiening, M and Hull, R and Stobo, J and Abo-Leyah, H and Finch, S and Pollock, J and Huang, JTJ and Richardson, H and Perea, L and McIntosh, E and Cant, E and Galloway, R and Choi, H and de Soyza, A and Spinou, A and Ringshausen, FC and Lorent, N and Mallia, P and Johnston, SL and Gierlinski, M and Goeminne, P and Loebinger, MR and Hua Gao, Y and Chotirmall, SH and Dhar, R and Haworth, C and Altenburg, J and Blasi, F and Polverino, E and Shteinberg, M and Strickson, S and Cipolla, D and Teper, A and Fernandez, C and Shih, VH and Mange, K and Singanayagam, A and Aliberti, S and Sibila, O and Long, MB and Chalmers, JD},
title = {Azurocidin-1 as a mediator of bronchiectasis severity, epithelial defence, and target of dipeptidyl peptidase-1 inhibition: an international, multicohort study.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(25)00334-0},
pmid = {42044645},
issn = {2213-2619},
abstract = {BACKGROUND: Dipeptidyl peptidase-1 (DPP1) inhibitors prevent the activation of neutrophil serine proteases and reduce exacerbations in people with bronchiectasis. We previously identified a novel effect of DPP1 inhibitors in reducing the neutrophil pseudoenzyme azurocidin-1 (AZU1). The aim of this study was to investigate the role of AZU1 in the pathophysiology of bronchiectasis.

METHODS: Sputum AZU1 concentrations were analysed in multiple cohorts. These consisted of two observational cohorts of patients with bronchiectasis (EMBARC BRIDGE cohort 1 and cohort 2) and a cohort of patients with chronic obstructive pulmonary disease (COPD; TARDIS COPD cohort) to correlate AZU1 with disease severity and exacerbations. A rhinovirus challenge study was used to investigate AZU1 concentrations during experimental exacerbation in COPD, people who smoke, and controls. A post-hoc analysis of the phase 2 WILLOW trial of brensocatib versus placebo was used to assess the effect of DPP1 inhibition on airway AZU1.

FINDINGS: Higher AZU1 sputum concentration was associated with increased bronchiectasis disease severity index (p<0·0001), decreased percentage predicted forced expiratory volume in 1 second (r=-0·4662, p<0·001), and increased exacerbation frequency (p<0·0019; EMBARC cohort 1, n=197). AZU1 was associated with radiological severity (Reiff score), symptoms (quality of life bronchiectasis respiratory symptom score), and bacterial infection (sputum microbiology and 16S microbiome alpha diversity; highest levels of AZU1 were found in airway samples with Pseudomonas aeruginosa; p<0·0001; EMBARC cohort 2, n=144). Bronchiectasis patients with bacterial and viral exacerbations had increased concentrations of AZU1 (p=0·0003; n=96). These findings were extended to COPD, in which AZU1 was related to COPD severity (COPD cohort, n=101), and in patients with COPD challenged with rhinovirus A16, AZU1 was increased at day 9 post-challenge (p<0·001; n=9). In-vitro AZU1 impaired ciliary function and epithelial integrity, suggesting a mechanism by which AZU1 drives disease pathogenesis. In a post-hoc analysis of the WILLOW trial, AZU1 was the most downregulated protein with brensocatib treatment (brensocatib 10 mg, n=71; brensocatib 25 mg, n=73; and placebo, n=71). Over 24 weeks, AZU1 was significantly reduced by DPP1 inhibition (p<0·0001).

INTERPRETATION: AZU1 was identified as a novel marker of disease severity in bronchiectasis, associated with bacterial infection and exacerbation, and targeted by DPP1 inhibition.

FUNDING: EMBARC3 and Insmed.},
}

@article {pmid42044680,
year = {2026},
author = {Maitan Santos, B and Estellé, J and Ramayo-Caldas, Y and Chadi, S and Barone, M and Chain, F and Kropp, C and Bridigi, P and Langella, P and Martín, R},
title = {Sex modulates the long-term effects of delivery mode on microbiota-gut barrier crosstalk and colitis susceptibility in mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2658276},
doi = {10.1080/19490976.2026.2658276},
pmid = {42044680},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Mice ; Disease Susceptibility ; *Colitis/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Sex Characteristics ; Sex Factors ; *Cesarean Section/adverse effects ; *Intestinal Mucosa/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Sexual dimorphism and mode of delivery are key determinants of gut physiology and microbiota development and may differentially affect predisposition to gut-related diseases. Cesarean section delivery markedly shapes early-life microbiota, predisposing individuals to higher risk of immune and metabolic comorbidities later in life. Although both sex and delivery mode are known to influence gut barrier-microbiota crosstalk, whether delivery mode modulates or counter-regulates sex-specific features of this interaction remains, to our knowledge, largely unexplored. Here, we investigated how sex impacts gut barrier-microbiota crosstalk shaped by delivery mode across development until adulthood by reanalyzing existing data. Using a preclinical mouse model, we combined gut barrier analyses with differential abundance and co-occurrence network approaches (LinDA and NetMoss). We found that the impact of CSD on gut barrier-microbiota crosstalk is partially dependent on sex and life stage. During the first days of life, delivery mode dictates immune imprinting and microbial network topology, with only limited sex effects. However, trajectories diverged with age, with CSD males exhibiting colitis reoccurrence in adulthood. By applying integrative strategies to stratify data by sex and development, our study uncovers short- and long-term sex-dependent gut barrier and microbial signatures. These findings reveal that delivery mode might program sex-specific host-microbiota trajectories with consequences for gut health and disease susceptibility, highlighting the need to consider sex and early-life microbial imprinting in future microbiome-targeted interventions.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
Male
Mice
Disease Susceptibility
*Colitis/microbiology
Disease Models, Animal
Mice, Inbred C57BL
Sex Characteristics
Sex Factors
*Cesarean Section/adverse effects
*Intestinal Mucosa/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid42044685,
year = {2026},
author = {Kooima, P and Oesterle, DA and Hematti, Y and Kay, DM and McFarlane, K and Roberts, JL},
title = {Gut microbiota depletion alters functional recovery and bone healing following fracture in mice.},
journal = {Bone},
volume = {},
number = {},
pages = {117907},
doi = {10.1016/j.bone.2026.117907},
pmid = {42044685},
issn = {1873-2763},
abstract = {Bone fracture pain evolves dynamically with tissue repair, yet current analgesic strategies are limited by adverse effects and concerns regarding impaired healing. The gut microbiome is an established regulator of pain and inflammation; however, its contribution to post-fracture recovery remains unclear. We tested whether antibiotic-induced microbiota depletion alters functional recovery and behavior after femoral fractures. Young female C57BL/6J mice received a broad-spectrum oral antibiotic cocktail or control water for two weeks prior to femoral fracture and were assessed longitudinally over 28 days after fracture. Microbiota depletion was associated with prolonged deficits in hindlimb loading and zone clearance performance, and continuous home-cage monitoring revealed decreased vertical rearing activity and voluntary wheel-running, collectively indicating sustained functional and motivational impairment. Despite a hypoinflammatory systemic and intestinal phenotype, microbiota-depleted mice exhibited elevated ipsilateral lumbar DRG expression of Ngf and Cxcl1 at Day 7 post-fracture alongside suppressed DRG Il10. NGF immunoreactivity was also elevated in the ipsilateral lumbar DRG of microbiota-depleted mice at the same timepoint. Microarchitectural analysis of fracture callus were suggestive of delayed secondary fracture healing. Together, these findings indicate that antibiotic-induced microbiota depletion was associated with altered inflammatory, behavioral, and skeletal responses after fracture. These results identify the gut microbiome as a potential contributor to the integrated pain-healing response to skeletal injury.},
}

@article {pmid42044842,
year = {2026},
author = {Al-Awadi, AA and Grove, JI and Bawden, S and Vijay, A and Valdes, AM and Gowland, P and Taylor, MA and Aithal, GP},
title = {The effect of a two-week low glycaemic index, higher fibre diet versus high glycaemic index diet on body composition, ectopic lipids, inflammatory biomarkers, gastrointestinal hormones and gut microbiota in Metabolic dysfunction-associated Steatotic Liver Disease (MASLD): A pilot randomized cross-over study.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {103306},
doi = {10.1016/j.clnesp.2026.103306},
pmid = {42044842},
issn = {2405-4577},
abstract = {Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) is a global health concern. Low glycaemic index (LGI) diets, which tend to be naturally higher in dietary fibre, may reduce liver fat, blood glucose, and gut microbiota imbalance arresting MASLD progression. We hypothesized that in patients with MASLD, an LGI diet, meeting estimated energy requirements, would reduce liver fat more than a high GI (HGI) diet, despite matched energy (isoenergetic) and macronutrient content. To test this, a 2×2 randomized cross-over trial was undertaken involving 7 participants with MASLD randomised (1:1 ratio) to a 2-week either high GI (HGI) or LGI diet followed by a 4-week wash-out period and then the opposite diet. The impact of the LGI diet on liver fat content, measured using Magnetic Resonance Spectroscopy ([1]H-MRS) liver-related blood biomarkers, appetite (using subjective visual analogue scales) and gut microbiome composition was identified. Relative liver fat fraction was markedly reduced following the LGI diet (8.57%).Observations in the LGI group coincided with changes in blood glycaemic biomarkers, including a significant reduction in HOMA-IR (-1.78, p=0.043). Additionally, the LGI diet resulted in significant reductions in body weight (-1.2 kg, p=0.018) and body mass index (-0.38 Kg/m[2], p=0.017), as well as increased pre-meal appetite scores during the middle of the diet period and decreased interleukin 6; IL-6 (-0.9 pg/mL) and glucagon (-13.7 pg/mL) levels (all p<0.05). In agreement with previous work in healthy participants, this study suggests that LGI diets reduce liver fat in patients with MASLD and may be an important factor in preventative care. REGISTRATION: This trial was registered on the website of ClinicalTrials.gov, number NCT04415632.},
}

@article {pmid42044997,
year = {2026},
author = {Sanyaolu, L and Ahmed, H and Santer, M and Jones, S and Hayward, G},
title = {Update to the management of recurrent urinary tract infections in women aged 16 years and older.},
journal = {Drug and therapeutics bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1136/dtb.2025.000042},
pmid = {42044997},
issn = {1755-5248},
abstract = {Recurrent urinary tract infections (rUTIs) are a burdensome condition affecting approximately 6% or 1.7 million women in the UK. UTIs are also a common reason for antibiotic use, with UK data demonstrating that they are the second most common reason for antibiotic prescribing after respiratory tract infections. UTIs also result in significant healthcare costs, with hospital admissions alone estimated to have cost the National Health Service in England over £600 million from 2023 to 2024. This review provides an up-to-date overview of the management of rUTIs, focusing on the updated 2024 National Institute for Health and Care Excellence guidance, which recommends a stepwise approach starting with behavioural measures, then progressing to non-antibiotic and finally antibiotic prevention. It also compares the guidance with international recommendations and outlines the current evidence on pathogenesis, diagnostic approaches and treatment options, including behavioural measures, non-antibiotic interventions (eg, vaginal oestrogen and methenamine hippurate) and antibiotic prophylaxis. Key challenges in primary care are discussed, such as diagnostic uncertainty, patient dissatisfaction and antimicrobial resistance (AMR). Emerging research in point-of-care testing, the urinary microbiome and novel therapies is also highlighted. This review aims to support safe prescribing, improve patient satisfaction and mitigate AMR by promoting antimicrobial and diagnostic stewardship in the management of rUTIs.},
}

@article {pmid42045370,
year = {2026},
author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB},
title = {Author Correction: Unbinned contigs expand known diversity in the global microbiome.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-026-02354-y},
pmid = {42045370},
issn = {2058-5276},
}

@article {pmid42045408,
year = {2026},
author = {Kutuzova, S and Piera Líndez, P and Danielsen, LS and Nielsen, KN and Olsen, NS and Riber, L and Gobbi, A and Forero-Junco, LM and Erdmann Dougherty, P and Westergaard, JC and Browne, PD and Christensen, S and Hestbjerg Hansen, L and Nielsen, M and Nybo Andersen, J and Rasmussen, S},
title = {Improving metagenome binning by integrating intrinsic features and taxonomy.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42045408},
issn = {1546-1696},
support = {NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 7076-00129B//Innovationsfonden (Innovation Fund Denmark)/ ; },
abstract = {A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. State-of-the-art binning methods use coabundance and sequence-based motifs such as tetranucleotide frequencies, whereas taxonomic labels derived from alignment based classification have not been widely used. Here we propose TaxVAMB, a metagenome binning tool based on semisupervised bimodal variational autoencoders, combining tetranucleotide frequencies and contig coabundances with taxonomic information. TaxVAMB outperformed all other binners on CAMI2 human microbiome datasets, returning on average 29% more high-quality assemblies than the next best binner, and performed on par with the best binners on short-read datasets. On a human gut long-read dataset, TaxVAMB recovered 29% more high-quality bins. In a typical single-sample setup, TaxVAMB on average returns 83% more high-quality bins compared to VAMB. Lastly, TaxVAMB binned incomplete genomes better than any other tool, returning on average 300% more high-quality bins of incomplete genomes than the next best binner.},
}

@article {pmid42045433,
year = {2026},
author = {Reisinger, SN and Kong, G and van de Garde, N and Muhammad, A and Adithya, P and Lu, D and Kiridena, P and Gubert, C and Dabscheck, G and Payne, JM and Hannan, AJ},
title = {Gut microbiome alterations are sex-dependently associated with brain abnormalities in a mouse model of Neurofibromatosis type I.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {42045433},
issn = {1476-5578},
abstract = {Neurofibromatosis type 1 (NF1) is a genetic condition presenting with variable symptomatology, however most individuals will demonstrate cognitive and behavioural difficulties, including autism. Using a heterozygous germline knockout mouse model of NF1 (Nf1 +/-), we performed in-depth behavioural evaluations encompassing learning and memory, stereotypy, social interaction, anxiety- and depression-like behaviour. Anatomical and functional studies of the brain and gastrointestinal tract were followed by the first investigation of gut microbiota composition (via full-length 16S rRNA sequencing) in a Nf1 +/- mouse model. The cognitive and autism-like behavioural phenotype seen in Nf1 +/- mice was accompanied by a striking increase in relative brain size which is highly relevant to clinical NF1. Furthermore, brain size was correlated with behaviour, supporting a potential mechanistic link. Nf1 +/- mice showed significant alterations in gut microbiota composition vs. Nf1 +/+ wild-type controls, with males additionally showing significant changes to species abundance of the Clostridium and Blautia genera, and the Lachnospiraceae family, findings which partially overlap with those in preclinical and clinical autism. Composition of associated functional pathways was not globally altered, however +/- mice showed significant changes in a pyrimidine deoxynucleotide biosynthesis pathway. In male Nf1 +/- mice, we also identified a genotype-specific host-microbial signature, pointing towards a mechanistic link between gut microbiome composition and brain size. These findings significantly expand our understanding of brain and behavioural abnormalities in this preclinical model of NF1 and, importantly, have uncovered the gut microbiome as a highly promising new area of research and a potential therapeutic target for these symptom clusters.},
}

@article {pmid42045512,
year = {2026},
author = {Moghadam, Z and Doraghi, M and Fallahizadeh, S and Badeenezhad, A and Alinehjad, N and Parseh, I},
title = {Enhanced phytoremediation of crude oil-contaminated soil using Cynodon dactylon with nutrient and mixed liquid suspended solids amendments.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50261-3},
pmid = {42045512},
issn = {2045-2322},
support = {98065//Behbahan Faculty of Medical Sciences/ ; },
}

@article {pmid42045563,
year = {2026},
author = {Mai, H and Wang, Y and Zhu, Y and Zhao, Y and Chen, Y and Hoeher, L and Al-Maskari, R and Luo, J and Erturk, A},
title = {Whole-mouse immunolabeling at cellular resolution for comprehensive 3D atlases.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {42045563},
issn = {1750-2799},
abstract = {Mapping complex biological systems and tracking disease progression at high resolution across the entire mammalian body has remained technically challenging. Here, to address this, we present wildDISCO (immunolabeling of wild-type mice and DISCO clearing), a comprehensive protocol for whole-body immunolabeling, optical clearing and imaging of mice at cellular resolution using standard IgG antibodies. This protocol optimizes tissue permeabilization using cyclodextrin as a potent enhancer of cholesterol extraction and membrane permeabilization, enabling deep antibody penetration across all organs. We detail procedures for sample preparation, tissue decolorization and decalcification, whole-body immunostaining, clearing, and subsequent 3D imaging, virtual reality visualization and whole-mouse atlas construction. The method allows comprehensive mapping of neuronal, vascular, lymphatic and immune systems, as well as systemic studies in disease models, including cancer and microbiome-host interaction studies. We anticipate that wildDISCO will serve as a broadly applicable platform for generating whole-body cellular atlases, enabling systems-level investigations of health and disease. Only standard immunohistochemistry facilities are required, but successful implementation may require initial technical training, particularly for researchers with limited prior experience in tissue clearing or 3D imaging workflows. From start to finish, the procedure takes 4 weeks.},
}

@article {pmid42045628,
year = {2026},
author = {Snir, A and Schwarzman, P and Wainstock, T and Sheiner, E},
title = {Offspring long-term infectious morbidity following pregnancies with cervical cerclage.},
journal = {Archives of gynecology and obstetrics},
volume = {313},
number = {1},
pages = {},
pmid = {42045628},
issn = {1432-0711},
mesh = {Humans ; Female ; *Cerclage, Cervical/adverse effects/statistics & numerical data ; Pregnancy ; Retrospective Studies ; Adult ; Premature Birth/prevention & control ; Kaplan-Meier Estimate ; Proportional Hazards Models ; Infant, Newborn ; *Uterine Cervical Incompetence/surgery ; Incidence ; Young Adult ; },
abstract = {INTRODUCTION: Cervical cerclage is an acceptable procedure in women with cervical insufficiency and is known to be effective in the prevention of preterm delivery. However, limited data exist regarding long-term health outcomes among offspring exposed to cerclage during pregnancy. Since the presence of a foreign body during pregnancy may change the vaginal microbiome, we aimed to study whether a cervical cerclage is associated with long-term infectious morbidity of the offspring.

STUDY DESIGN: A retrospective population-based cohort study was performed at a tertiary medical center, including all singleton deliveries between the years 1991-2021. Long-term infectious morbidity was compared among offspring after pregnancies with and without cervical cerclage. The diagnoses of infectious morbidities were defined based on ICD-9 codes as recorded in community clinics and hospitalization files. A Kaplan-Meier survival curve was utilized to evaluate the cumulative incidence. A Cox proportional hazards model was used to control for confounders.

RESULTS: Out of 356,356 offspring included in the analysis, 0.4% (n = 1416) were following pregnancies with cervical cerclage. Unadjusted analyses demonstrated no significant difference in total infectious morbidity between the groups (OR 1.0, 95% CI 0.9-1.1; p = 0.369, Table 1). Kaplan-Meier analysis showed no difference in cumulative incidence (log-rank test P-value = 0.19, Fig. 1). In the primary analysis, cerclage was not associated with long-term infectious morbidity. However, in a secondary model, after adjustment for confounders including gestational age, obesity and diabetes, cerclage exposure was associated with a modest reduction in the risk of long-term infectious morbidity (adjusted HR 0.9, 95% CI 0.87-0.99, p = 0.036).

CONCLUSION: In this large population-based cohort, cervical cerclage was not associated with increased long-term infectious morbidity in offspring. A modest association with reduced infectious morbidity was observed after adjustment for confounding factors. These findings should be interpreted cautiously given the observational design and potential residual confounding.},
}

Humans
Female
*Cerclage, Cervical/adverse effects/statistics & numerical data
Pregnancy
Retrospective Studies
Adult
Premature Birth/prevention & control
Kaplan-Meier Estimate
Proportional Hazards Models
Infant, Newborn
*Uterine Cervical Incompetence/surgery
Incidence
Young Adult

@article {pmid42045676,
year = {2026},
author = {Wood, GV and Liddicoat, C and Robinson, JM and Breed, MF},
title = {Restoring soil and sediment microbiomes in the Anthropocene.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42045676},
issn = {1740-1534},
abstract = {Soil and sediment microbiomes have a central role in biogeochemical cycling, climate regulation and ecosystem resilience. However, they are increasingly degraded by land use change, pollution and climate change. Despite their foundational roles in ecosystems, these microbiomes remain under-represented in ecosystem restoration science, practice and policy. Improving the integration of microbiomes across the restoration science-practice-policy nexus is essential for achieving more effective and resilient restoration outcomes. Without this, global restoration risks neglecting the microbial foundations of functional ecosystems and long-term resilience. In this Review, we synthesize the current state of knowledge of soil and sediment microbiome restoration. We describe the major anthropogenic stressors that are degrading these microbiomes, highlighting the linked and context-dependent nature of these impacts, and evaluate existing strategies to restore them. To improve restoration effectiveness, we propose a research workflow that encompasses baseline establishment, degradation diagnostics, designing and testing interventions, research methodology selection and best practice principles. We also outline key theoretical frameworks and propose future research priorities to help soil and sediment microbiome restoration to move towards a predictive, theory-led discipline.},
}

@article {pmid42045695,
year = {2026},
author = {da Silva, JB and Câmara, PEAS and Rosa, LH and Oliveira, VM},
title = {Disentangling bacterial diversity and biogeography in snow-covered regions.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {42045695},
issn = {1573-0972},
abstract = {UNLABELLED: This study investigated the bacterial diversity of snow-inhabiting microbial communities across multiple geographic locations, including Antarctic and temperate regions. Using high-throughput sequencing of the 16S rRNA gene from Antarctic snow samples and comparisons with publicly available datasets from other cold regions worldwide, we assessed patterns of taxonomic diversity and the influence of geographic and environmental factors on snow bacterial communities. Our results revealed that bacterial communities from Martel Inlet (King George Island) exhibited lower diversity compared to other Antarctic sites, likely influenced by the geographic characteristics. In contrast, snow microbial communities from temperate regions such as Austria, Quebec, and Iceland showed higher diversity, potentially driven by overlapping environmental conditions including temperature range, snow dynamics, and seasonal variability. Network analyses revealed distinct interaction patterns among regions, with more dynamic and competitive microbial networks observed in Maritime Antarctic environments, while continental snow ecosystems exhibited more compartmentalized and stable network structures. Overall, our findings highlight the combined influence of geographic distance and environmental conditions in shaping microbial diversity and ecological interactions in snow ecosystems across different regions of the globe.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04918-w.},
}

@article {pmid42045813,
year = {2026},
author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , },
title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05101-9},
pmid = {42045813},
issn = {1471-2180},
}

@article {pmid42045958,
year = {2026},
author = {Huang, J and Chen, Z and Wang, M and Yang, C and Wang, A and Chen, Y},
title = {Efficacy and safety of fecal microbiota transplantation in reducing recurrence of colorectal adenomas after endoscopic resection: study protocol for a multicenter, open-label, randomized, no-treatment-controlled trial.},
journal = {Trials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13063-026-09740-1},
pmid = {42045958},
issn = {1745-6215},
support = {C2401027//Shenzhen Medical Research Fund/ ; },
abstract = {BACKGROUND: Endoscopic resection is the standard treatment for colorectal adenoma (CRA), a key precursor to colorectal cancer (CRC). However, a high rate of recurrence post-procedure poses a significant challenge for long-term CRC prevention. Growing evidence suggests gut microbial dysbiosis contributes to adenoma development and recurrence. This trial will test the hypothesis that restoring a healthy gut microbiome with fecal microbiota transplantation (FMT) can reduce the recurrence of CRA after endoscopic resection.

METHODS: This protocol describes a multicenter, open-label, randomized, no-treatment-controlled trial that will enroll 466 participants with CRA following endoscopic resection. Participants will be randomly assigned in a 1:1 ratio to receive either FMT or no treatment (control). The FMT intervention consists of an initial colonoscopic infusion and oral capsules, followed by oral maintenance capsules at months 3, 6, and 9. The primary outcome is the rate of CRA recurrence at the 12-month follow-up colonoscopy. Key secondary outcomes include the incidence of all polypoid lesions, changes in the gut and mucosal microbiota composition, the incidence of CRC, and a comprehensive assessment of adverse events to evaluate safety.

DISCUSSION: This trial is designed to provide high-quality evidence on the efficacy and safety of FMT for preventing CRA recurrence. The findings may support a novel, microbiome-based strategy for the secondary prevention of CRC and provide mechanistic insights into the role of the gut microbiota in colorectal carcinogenesis.

TRIAL REGISTRATION: ClinicalTrials.gov NCT06205862. Registered on 16 January, 2024. https://clinicaltrials.gov/study/NCT06205862.},
}

@article {pmid42045979,
year = {2026},
author = {Deng, Y and Chen, R and Gao, X and Wu, H and He, N and Hu, N and Zhang, W and Chen, L and Zheng, X and Jiang, J},
title = {Tissue-resident Limosilactobacillus reuteri modulates intratumoral arachidonic acid metabolism to enhance CD8[+] T cell-mediated anti-PD1 response.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08170-6},
pmid = {42045979},
issn = {1479-5876},
}

@article {pmid42046041,
year = {2026},
author = {Thomas, LF and Panaretos, C and Scott, MA and Valeris-Chacin, R and Cook, WE},
title = {Distinct host-pathogen and microbiome responses of aoudad (Ammotragus lervia) and bighorn sheep (Ovis canadensis) following exposure to Mycoplasma ovipneumoniae with or without co-exposure to leukotoxigenic Pasteurellaceae.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05375-1},
pmid = {42046041},
issn = {1746-6148},
}

@article {pmid42046057,
year = {2026},
author = {Hsu, CY and Abdelgawwad El-Sehrawy, AAM and Alshkarchy, SS and Abdul, AS and Ganesan, S and Gupta, PK and Sharma, R and Nayak, PP and Ebrahimpour, A and Khazaei, Y},
title = {Innovative approaches in the treatment of hematologic malignancies: the role of CRISPR-engineered microbiomes along the gut-immune axis in immunotherapy development.},
journal = {Cancer cell international},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12935-026-04316-0},
pmid = {42046057},
issn = {1475-2867},
}

@article {pmid42046285,
year = {2026},
author = {Miyamoto, S and Yoshimoto, S and Katsumata, N and Mutoh, N and Iwabuchi, N and Odamaki, T and Asaoka, D and Machida, S},
title = {Bifidobacterium longum BB536 is associated with improvements in gastrointestinal symptoms and odor-related metabolites in microbiota-defined subgroups of male athletes consuming a high-protein diet: exploratory randomized double‑blind placebo‑controlled trial.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {23},
number = {1},
pages = {2664664},
doi = {10.1080/15502783.2026.2664664},
pmid = {42046285},
issn = {1550-2783},
mesh = {Humans ; Male ; Double-Blind Method ; *Gastrointestinal Microbiome ; *Probiotics/administration & dosage ; *Bifidobacterium longum ; Adolescent ; *Odorants ; Feces/microbiology/chemistry ; *Diet, High-Protein/adverse effects ; Young Adult ; Athletes ; Volatile Organic Compounds/analysis ; *Gastrointestinal Diseases ; Whey Proteins/administration & dosage ; },
abstract = {BACKGROUND: High‑protein diets are widely used by athletes but may disturb the gut environment and increase production of odor‑related metabolites. Probiotic supplementation has been proposed as a strategy to support gastrointestinal function under such dietary stress. This study aimed to explore the effects of Bifidobacterium longum BB536 on gastrointestinal symptoms, gut microbiota, and odor‑related metabolites in male athletes consuming a high‑protein diet.

METHODS: In an exploratory, randomized, double‑blind, placebo‑controlled trial, 60 healthy male athletes (mean age: 18.62 ± 0.75 years; mean BMI: 22.35 ± 1.80 kg/m[2]) consumed a whey protein supplement (70 g/day) together with either BB536 (46 billion CFU/day, as measured at the start of the intervention) or placebo for 4 weeks. Gastrointestinal symptoms, gut microbiota composition, skin‑emitted volatile compounds, and fecal metabolites were assessed. Subgroup analyses based on responder status and baseline enterotype were conducted post hoc to generate hypotheses regarding microbiota‑dependent responses.

RESULTS: In the overall cohort, no significant between‑group differences were observed across gastrointestinal outcomes, gut microbiota indices, or metabolite profiles. Within the BB536 group, diarrhea‑related scores improved from baseline. Post hoc analyses suggested that increases in Faecalibacterium were evident among responders. Enterotype‑based patterns also emerged: individuals with Ruminococcus‑dominant microbiota showed higher skin‑emitted short‑chain fatty acids after BB536 intake, whereas those with Faecalibacterium‑dominant microbiota exhibited reductions in odor‑related metabolites, including methyl mercaptan and ammonia. Corresponding fecal metabolite shifts were modest.

CONCLUSION: BB536 supplementation was associated with improvements in diarrhea‑related symptoms and odor‑related metabolites in specific microbiota‑defined subgroups. As these findings did not extend to the full cohort, they should be interpreted as exploratory and hypothesis‑generating. Baseline gut microbiota composition may influence probiotic responsiveness, warranting confirmatory trials with prespecified endpoints.},
}

Humans
Male
Double-Blind Method
*Gastrointestinal Microbiome
*Probiotics/administration & dosage
*Bifidobacterium longum
Adolescent
*Odorants
Feces/microbiology/chemistry
*Diet, High-Protein/adverse effects
Young Adult
Athletes
Volatile Organic Compounds/analysis
*Gastrointestinal Diseases
Whey Proteins/administration & dosage

@article {pmid42046303,
year = {2026},
author = {Sun, S and He, Y and Deng, Y and Wang, J},
title = {Urinary Microbiome Characteristics in Kidney Transplant Recipients and Their Clinical Implications: A Narrative Review.},
journal = {Annals of transplantation},
volume = {31},
number = {},
pages = {e952286},
doi = {10.12659/AOT.952286},
pmid = {42046303},
issn = {2329-0358},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Microbiota ; Dysbiosis/microbiology ; *Urinary Tract/microbiology ; Graft Rejection/microbiology ; Transplant Recipients ; Urinary Tract Infections/microbiology ; *Urine/microbiology ; },
abstract = {High-throughput sequencing has overturned the long-standing "sterile urine" paradigm and revealed a low-biomass yet clinically informative urinary tract microbiota. In kidney transplant recipients, immunosuppression, perioperative instrumentation, and antibiotic exposure can reshape urinary microbial communities; however, reported signatures remain heterogeneous across cohorts and methodologies. This narrative review synthesizes evidence on: (1) baseline urobiome patterns and major determinants of inter-individual variability, (2) post-transplant drivers of dysbiosis, and (3) associations between urobiome dynamics and key transplant outcomes, including urinary tract infection (UTI), acute rejection (AR), and chronic allograft dysfunction such as interstitial fibrosis and tubular atrophy (IF/TA). Across studies, dysbiosis commonly manifests as reduced diversity, depletion of putatively protective taxa, and enrichment of opportunistic pathogens; several longitudinal cohort studies further suggest that microbiome shifts can precede clinical events, supporting a potential window for risk stratification and early surveillance. We also summarize translational research directions, including integration of urinary microbial profiles with host biomarkers and multi-omics readouts, as well as microbiome-sparing strategies (antimicrobial stewardship, targeted probiotics/synbiotics, and dietary modulation). Finally, we highlight methodological challenges unique to low-biomass urine samples - especially contamination control, negative controls, and transparent reporting - that are essential for improving reproducibility and enabling clinical implementation. This review aims to provide an up-to-date, clinically oriented synthesis of the post-transplant urobiome and to propose methodological and translational priorities for future research and implementation.},
}

Humans
*Kidney Transplantation/adverse effects
*Microbiota
Dysbiosis/microbiology
*Urinary Tract/microbiology
Graft Rejection/microbiology
Transplant Recipients
Urinary Tract Infections/microbiology
*Urine/microbiology

@article {pmid42046343,
year = {2026},
author = {Jiang, L and Li, T and Wu, J and Lau, HCH and Wong, CC and Zhou, X and Cheung, AHK and Wei, Q and Ren, J and Zhang, X and Li, Q and Nie, Y and Yu, J},
title = {Dietary nitrate drives gastritis by modulating gastric microbiota and metabolites.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0679},
pmid = {42046343},
issn = {2095-3941},
support = {2023ZD0501400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 82472896//National Natural Science Foundation of China/ ; 3133344//Strategic Seed Funding Collaboration Research Scheme CUHK/ ; 3135509//Strategic Impact Enhancement Fund CUHK/ ; 3134277//Impact Case for RAE CUHK/ ; },
abstract = {OBJECTIVE: Dietary nitrate has been increasingly recognized as a potential carcinogen associated with gastritis. In this study the mechanistic role of a high-nitrate diet (NaD) in driving gastritis was elucidated with a focus on modulation of the gastric microbiota composition and metabolomic profiles.

METHODS: Animals were randomly assigned to two dietary intervention groups using a C57BL/6 mouse model: a NaD containing 7.5% nitrate; or a standard normal diet (ND). Gastric microbiota composition was characterized based on full-length 16S rRNA sequencing and gastric metabolite profiles were analyzed using high-performance liquid chromatography-mass spectrometry (HPLC/MS). Finally, the roles of the microbiome and metabolites in gastritis development were validated using the human gastric epithelial cell line (GES-1), as well as conventional and germ-free mouse models.

RESULTS: NaD induced gastritis in conventional mice compared to ND-fed mice. In addition, NaD incited the infiltration of macrophages and neutrophils with elevated levels of inflammatory cytokine genes (IL-17a, Ccl20, Cxcl5, IL-6, and Ccl2). A significant shift in the composition of the gastric microbiota occurred with an increase in pathogenic bacteria (Enterococcus gallinarum, Prevotella timonensis, and Mycobacterium gordona) and a decrease in probiotics (Roseburia hominis, Clostriduim scindens, and Faecalibacterium prausnitzii). Furthermore, NaD induced alterations in the metabolic profile, marked by an elevated level of 5-hydroxyindoleacetate (5-HIAA), a key downstream metabolite of the tryptophan metabolic pathway. Notably, 5-HIAA also upregulated the levels of inflammatory cytokines in the human gastric epithelial GES-1 cell line. In addition, both E. gallinarum colonization and 5-HIAA exposure significantly increased inflammatory responses in conventional and germ-free mouse models.

CONCLUSIONS: NaD drives gastritis in mice by inducing gastric microbial dysbiosis and metabolomic dysregulation with elevated 5-HIAA.},
}

@article {pmid42046474,
year = {2026},
author = {Allaham, S and Mohamed, S and Yusuf, M and Abdillahi, A},
title = {Early-Life Viral Lower Respiratory Tract Infections and Their Impact on Childhood Asthma: Molecular Endotypes and Prevention Strategies.},
journal = {Pediatric allergy, immunology, and pulmonology},
volume = {},
number = {},
pages = {2151321X261445781},
doi = {10.1177/2151321X261445781},
pmid = {42046474},
issn = {2151-3228},
abstract = {Background: Early-life viral lower respiratory tract infections (LRTIs), particularly those caused by respiratory syncytial virus (RSV) and human rhinovirus (HRV), are major contributors to pediatric morbidity and are strongly linked to asthma. RSV causes about 3.6 million hospitalizations and 100,000 deaths annually in children under 5, mainly in low- and middle-income countries. RSV peaks in infancy, while HRV has more impact later in childhood. Mechanisms include viral epithelial injury, genetic susceptibility (e.g., 17q21 variants), and environmental factors (e.g., allergic sensitization). Together, these raise asthma risk. Diagnosis is difficult due to overlapping presentations and reliance on molecular tests. Preventive strategies include maternal RSV vaccination, long-acting monoclonal antibodies such as nirsevimab and palivizumab, and pediatric vaccine candidates. Strategies to limit allergic sensitization may lower HRV-related asthma risk. Long-term effects include persistent wheeze and asthma, making early life a crucial window for prevention.Methods: This review summarizes current evidence on the epidemiology, mechanisms, and long-term impact of early viral LRTIs.Results: It highlights molecular and immunological endotypes of virus-induced asthma and explores the influence of genetic, epigenetic, and microbial factors. Emerging diagnostic tools and preventive strategies-including vaccines, monoclonal antibodies, environmental interventions, and microbiome-targeted therapies-are also discussed as means to reduce the global pediatric asthma burden and improve respiratory health.},
}

@article {pmid42046516,
year = {2026},
author = {Chowdhury, I and Massay, R and Stubbs, A},
title = {Food additives, emulsifiers, microplastics, and ultra-processed foods in rheumatic disease pathogenesis.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000001161},
pmid = {42046516},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: Dietary patterns have changed significantly over time, with ultra-processed foods now comprising a large proportion of daily energy intake in many countries. Ultra-processed foods (UPFs) contain numerous additives and may also increase exposure to processing- and packaging-related contaminants that could influence immune function. This review summarizes why UPFs have drawn growing attention and evaluates their potential relevance to autoimmune inflammation, with a focus on rheumatoid arthritis (RA) and related disorders.

RECENT FINDINGS: Population studies suggest that higher UPF intake is associated with an increased risk of RA after adjustment for obesity and lifestyle factors. Experimental and translational studies suggest that components common in UPF-rich diets (e.g., emulsifiers, thickeners, synthetic colorants, added sugars, excess sodium, and some nonnutritive sweeteners), as well as microplastic exposures, may disrupt gut barrier integrity, remodel the microbiome, and promote low-grade inflammation. These mechanisms overlap with pathways implicated in RA and systemic inflammation, including dysregulation of Treg/Th17 balance, loss of mucosal tolerance, endotoxemia, and innate immune activation.

SUMMARY: Overall, evidence supports biologically plausible mechanisms and epidemiologic associations linking UPF-rich dietary patterns to immune dysregulation relevant to rheumatic disease, but direct RA-specific interventional and mechanistic clinical data remain limited. Dietary exposures may represent modifiable risks; however, stronger longitudinal studies with validated RA phenotyping and pragmatic dietary interventions are needed before firm clinical recommendations can be made.},
}

@article {pmid42046678,
year = {2026},
author = {Dayrit, G and Mabrok, M and Chaiyapechara, S and Rodkhum, C},
title = {Habitat-structured fungal mycobiomes at the water-gill interface of farmed red tilapia in Central Thailand: An internal transcribed spacer rRNA amplicon sequencing study.},
journal = {Veterinary world},
volume = {19},
number = {3},
pages = {1196-1214},
pmid = {42046678},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Tilapia aquaculture is rapidly expanding across Southeast Asia and plays a critical role in regional food security. While bacterial microbiomes of farmed fish have been widely investigated, the fungal component of aquatic microbial communities remains poorly characterized, particularly at the biologically important interface between rearing water and fish gills. Fungi may influence fish health, environmental microbial ecology, and occupational exposure risks within aquaculture systems. This study aimed to characterize fungal mycobiomes associated with rearing water and gills of clinically healthy red tilapia (Oreochromis spp. hybrids) cultured in Central Thailand using internal transcribed spacer (ITS) rRNA amplicon sequencing and to determine how habitat type, farming system, and environmental variables shape fungal community structure.

MATERIALS AND METHODS: Samples were collected from ten tilapia farms located in five provinces of Central Thailand, representing two aquaculture systems: open river cages and closed earthen ponds. A total of 27 rearing water samples and 30 composite gill samples were analyzed. Fungal DNA was extracted and the ITS1 region was amplified and sequenced using the Illumina MiSeq platform. Sequence processing and amplicon sequence variant inference were performed in QIIME2 using the DADA2 pipeline. Alpha diversity indices and beta diversity analyses were used to evaluate community structure, while multivariate statistical approaches assessed the influence of habitat type, geographic location, farming style, and physicochemical water parameters.

RESULTS: Fungal communities displayed considerable taxonomic diversity and differed significantly between habitats. Rearing water samples exhibited significantly higher alpha diversity than gill-associated communities. Dominant genera included Cladosporium, Candida, Aspergillus, Fusarium, and Rhodotorula. Gill communities were relatively enriched in Candida and Fusarium, whereas rearing water contained higher abundances of Cladosporium and Rhodotorula. Beta diversity analyses demonstrated significant effects of sampling source, province, and farming system on fungal community composition. Environmental parameters such as pH, nitrate concentration, and ionic strength were associated with variations in fungal diversity, particularly in rearing water. Several detected genera included taxa with known opportunistic pathogenic potential for fish and humans.

CONCLUSION: This study provides the first ITS-based baseline characterization of fungal mycobiomes associated with red tilapia aquaculture systems in Central Thailand. Distinct fungal assemblages occur at the water-gill interface, with environmental conditions and aquaculture practices influencing community composition. The presence of opportunistic fungal genera highlights the importance of incorporating fungal community monitoring into aquaculture biosecurity and One Health surveillance frameworks to support sustainable fish production, environmental health, and occupational safety.},
}

@article {pmid42046684,
year = {2026},
author = {Dehghan, H and Moghaddaszadeh-Ahrabi, S and Hashemzadeh-Farhang, H and Shahbazi, P and Nobari, B},
title = {Synergistic effects of Ferula asafoetida extract and condensed tannins from raisin pomace on in vitro cecal fermentation kinetics and nutrient digestibility in horses.},
journal = {Veterinary world},
volume = {19},
number = {3},
pages = {905-919},
pmid = {42046684},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The equine hindgut depends on microbial fermentation for efficient nutrient utilization but remains vulnerable to dysbiosis, hindgut acidosis, and suboptimal fiber digestion. Growing restrictions on antibiotic and synthetic feed additives have increased interest in natural phytogenic compounds. Medicinal plant extracts and condensed tannins are promising candidates to modulate microbial activity, improve fermentation efficiency, and enhance nutrient digestibility. This study aimed to investigate the individual and combined effects of hydroalcoholic extract of Ferula asafoetida and condensed tannins extracted from raisin pomace on equine cecal fermentation parameters and nutrient utilization using in vitro gas production and batch culture techniques.

MATERIALS AND METHODS: A 2 × 2 factorial in vitro design was used with four treatments: control (C; basal diet only), F. asafoetida extract (A; 30 mg), condensed tannins from raisin pomace (G; 50 mg), and their combination (A × G). Fecal inoculum was collected from four healthy 14-month-old Arabian geldings adapted for 14 days to a forage-based maintenance diet. Fermentation kinetics were evaluated over 120 h using the in vitro gas production technique and fitted to the Gompertz model. Parallel batch cultures measured pH, ammonia-nitrogen (NH3-N), and apparent disappearances of dry matter (DM), crude protein (CP), acid detergent fiber (ADF), and neutral detergent fiber (NDF). Data were analyzed using PROC GLM in SAS with Tukey-Kramer post-hoc tests (p < 0.05).

RESULTS: Cumulative gas production at 120 h was significantly higher in G (340.5 mL) and A × G (340.3 mL) than in C (228.8 mL) (p < 0.01), with faster fermentation rates and shorter lag times (p < 0.01). Terminal pH values remained stable (6.33-6.40) across treatments with no indication of acidosis. NH3-N concentrations were elevated in G (26.0 mg/dL) and A × G (25.5 mg/dL) compared with C (24.5 mg/dL) (p < 0.01). Apparent digestibility improved markedly: DM increased from 64.5% (C) to 70.3% (G), CP from 60.3% (C) to 66.9% (G), with parallel positive trends observed for ADF and NDF (p < 0.01).

CONCLUSION: Supplementation with F. asafoetida extract and condensed tannins from raisin pomace, especially in combination, enhanced fermentation efficiency, accelerated substrate degradation, and improved nutrient digestibility while maintaining stable pH in an in vitro equine cecal model. These findings indicate strong potential for these phytogenic compounds as sustainable natural feed additives to optimize equine hindgut function. In vivo validation, dose optimization, and long-term microbiome studies are recommended to confirm practical efficacy and safety in horses.},
}

@article {pmid42046757,
year = {2026},
author = {Gao, RY},
title = {Targeting gut immunity as a therapy for steatotic liver disease.},
journal = {eGastroenterology},
volume = {4},
number = {2},
pages = {e100404},
pmid = {42046757},
issn = {2976-7296},
}

@article {pmid42046871,
year = {2026},
author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q},
title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.},
journal = {Journal of Zhejiang University. Science. B},
volume = {27},
number = {4},
pages = {375-389},
pmid = {42046871},
issn = {1862-1783},
support = {2021YFA0805904//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mice ; Germ-Free Life ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Metagenomics ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Mice, Inbred C57BL ; Female ; },
abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.},
}

Animals
*Gastrointestinal Microbiome/genetics
Humans
Mice
Germ-Free Life
*Fecal Microbiota Transplantation/methods
Feces/microbiology
*Metagenomics
Reproducibility of Results
High-Throughput Nucleotide Sequencing
Male
*Metagenome
Mice, Inbred C57BL
Female

@article {pmid42046931,
year = {2026},
author = {Zhang, F and Lard, ML and Khachatryan, L and Guo, C and Sandifer, A and Villafuerte, NM and Nde, DB and Cook, RL and Cormier, SA and Richmond-Bryant, J},
title = {Shifts in soil microbiome surrounding a thermal treatment facility for hazardous waste: the hidden impact of environmentally persistent free radicals.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
pmid = {42046931},
issn = {2050-7895},
abstract = {The disposal of hazardous materials from Superfund sites often involves thermal treatment (TT), generating environmentally persistent free radicals (EPFRs). While substantial evidence links EPFR exposure to negative health outcomes, its effects on the soil microbiome remain underexplored. Since the mid-1980s, a TT facility in Colfax, LA, has employed open-burn and open-detonation to process hazardous waste. In 2023, we collected soil samples from 13 residential sites within a 17-km radius of the TT facility and analyzed microbial communities and EPFR content. Our findings revealed a distinct microbial community near the TT facility (within 5-km), characterized by reduced bacterial abundance and increased fungal presence. Soil EPFR concentrations ranged from 0.81 × 10[16]-4.39 × 10[16] spins per g with g-factor values of 2.0033-2.0040, indicating a mixture of carbon-centered radicals with adjacent oxygen and oxygen-centered radicals. Correlation analysis identified bacterial taxa, particularly Alpha-proteobacteria and Actinobacteria, positively associated with EPFR abundance. In vitro tests showed that laboratory generated EPFRs more strongly inhibited bacterial growth than fungal growth, though some bacterial isolates from the study sites exhibited resistance to EPFR exposure. The differences in microbial responses to EPFR exposure may contribute to the shifts in microbial communities near the TT facility. Our study advances the understanding of EPFR impacts on the soil microbiome and suggests potential long-term effects on environmental and community health.},
}

@article {pmid42047038,
year = {2026},
author = {Marsh, EB and Lavretsky, H and Kasparian, NA and Pike, NA and Doyle, KP and Aggarwal, NT and Fullerton, HJ and Ivy, AS and Dlamini, N and , },
title = {Brain Health Across the Life Span: A Framework for Future Studies: A Scientific Statement From the American Heart Association.},
journal = {Stroke},
volume = {},
number = {},
pages = {},
doi = {10.1161/STR.0000000000000518},
pmid = {42047038},
issn = {1524-4628},
abstract = {The concepts of brain health (ie, optimal functioning of the brain across cognitive, emotional, and behavioral domains throughout life) and cognitive resilience (ie, the ability of the brain to recover after an insult) have become increasingly important as the population ages. Previous research has called attention to vascular risk factors underlying cerebrovascular disease, as well as modifiable variables that contribute to premature aging and cognitive dysfunction. In this scientific statement, we focus on the role of nonvascular physical and psychologic variables that affect brain health across the life span. We provide a broad overview of influences such as chronic medical conditions, inflammation, environmental exposures, and socioeconomic drivers that affect the developing brain, along with factors including sleep quality, the gut microbiome, and mental health that contribute to neurodegeneration. We also review the varying strength of evidence supporting biologic mechanisms and mitigating strategies that may help optimize resilience, with the goal of providing a framework for future studies.},
}

@article {pmid42047173,
year = {2026},
author = {Zhang, N and Wang, Z and Yang, F and Liu, T and Ji, D},
title = {The causality between gut microbiota and ectopic pregnancy based on genome-wide association: A Mendelian randomization study.},
journal = {African journal of reproductive health},
volume = {30},
number = {8},
pages = {66-75},
doi = {10.29063/ajrh2026/v30i8.7},
pmid = {42047173},
issn = {1118-4841},
mesh = {Humans ; Pregnancy ; Female ; *Gastrointestinal Microbiome/genetics ; *Pregnancy, Ectopic/genetics/microbiology ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Blood Proteins ; },
abstract = {Ectopic pregnancy represents a prevalent gynecological emergency with incompletely characterized pathophysiology, creating substantial clinical challenges in timely diagnosis and effective management. The causal interplay between gut microbiota and ectopic pregnancy, particularly through plasma proteomics mediation, remains undefined. We derived Gut microbiota GWAS data (n=412) from the Dutch Microbiome Project meta-analysis and Ectopic pregnancy data from IEU OpenGWAS and FinnGen project. The results revealed nine kinds of gut microbiotas demonstrating causal associations with ectopic pregnancy risk. A total of 67 plasma proteins causally impact the risk of ectopic pregnancy. In addition, three kinds of gut microbiotas were mediated by 25 kinds of plasma proteins on ectopic pregnancy. Microbiota enriched in L.rhamnose.degradation.I affected ectopic pregnancy through 22 kinds of plasma proteins. This study establishes causal relationships between specific gut microbial pathways and ectopic pregnancy risk, mediated through distinct plasma protein signatures, providing directions for clinical interventions and future research.},
}

Humans
Pregnancy
Female
*Gastrointestinal Microbiome/genetics
*Pregnancy, Ectopic/genetics/microbiology
Genome-Wide Association Study
Mendelian Randomization Analysis
Blood Proteins

@article {pmid42047214,
year = {2026},
author = {Mingolelli, G and Bashatwah, RM and Jurek, MJ and Chauvin, IM and Orjala, J and Riley, AP and Burdette, JE and Henke, MT},
title = {The Human Gut Microbiome Metabolizes Diverse Bioactive Coumarins via α,β-Unsaturated Lactone Reduction.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.6c00329},
pmid = {42047214},
issn = {1520-6025},
abstract = {The gut microbiome can influence drug efficacy through the direct metabolism of bioactive molecules. Despite numerous high-throughput screens for drug-microbiome interactions, the gut microbial metabolism of many bioactive compounds and its impact on treatment efficacy remain uncharacterized. We chose to investigate coumarins, which are a large class of bioactive natural products and chemical scaffolds for synthetic drugs. The core of the class, 1,2-benzopyrone, is metabolized by the microbiome to yield 3,4-dihydrocoumarin and melilotic acid via α,β-unsaturated lactone reduction. To explore the scope of this pathway, we screened a structurally diverse group of 12 bioactive coumarins using semitargeted LC-MS/MS metabolomics and ex vivo cultures of human feces. The culturable gut microbiome can reduce the α,β-unsaturated lactone of isocoumarin, simple, furano, pyrano, and prenylated coumarins with an unsubstituted 3,4-alkene bond. In a monoculture screen of microbiome isolates, we determined that 11 species could metabolize multiple coumarins through this pathway. Further, we demonstrate the direct coumarin-reducing capability of N-ethylmaleimide reductase from Escherichia coli. Finally, gut microbial metabolites of methoxsalen had diminished cytotoxicity against melanoma cancer cells compared to the parent drug. In summary, the human gut microbiome utilizes a single metabolic pathway to modulate the bioactivities of many coumarins.},
}

@article {pmid42047238,
year = {2026},
author = {Cardoso, A and Naghibi, M and Climent, E and Rodenes-Gavidia, A and Lamelas, A and Llobregat, L and Martínez-Blanch, J and Friedman, D and Vijayakumar, V and Day, R},
title = {Effects of Live and Heat-Treated Bifidobacterium longum CECT 7347 in Adults With Allergic Rhinitis: A Randomised, Double-Blind, Placebo-Controlled Trial.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70360},
pmid = {42047238},
issn = {1398-9995},
support = {//Archer Daniels Midland/ ; IDI-20170876//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {BACKGROUND: Allergic rhinitis (AR) is an increasingly common chronic inflammatory condition of the nasal mucosa. While conventional anti-allergy treatments are widely used, they can come with side effects and are not always effective. As a result, AR remains a significant concern for many millions of people worldwide, affecting quality of life and social functioning.

OBJECTIVE: To investigate clinical evidence for the role of probiotics and postbiotics in reducing AR symptoms.

METHODS: In this single-centre, randomized, double-blind, placebo-controlled clinical trial, 72 adults aged 18-60 years with moderate-severe AR, taking first-line medication, were studied. The primary outcome of the trial was to determine the effects of supplementation with the probiotic Bifidobacterium longum CECT 7347 (PRO) and the heat-treated postbiotic of the same strain (POST) on symptoms associated with AR as assessed using the Combined Symptom and Medication Score (CSMS). The secondary outcomes of the study assessed the effects of the interventions over: quality of life (rhinitis quality of life questionnaire [RQLQ]), systemic immune response, local immune response, and faecal microbiota composition.

RESULTS: Statistically significant reduction in total CSMS after 8 weeks of supplementation was observed in the POST group compared to placebo control (CON) (p = 0.022), showing on average a 0.6 greater reduction than placebo (CI: 0.09-1.12), equivalent to a 33.15% greater reduction and exceeding the World Allergy Organization's threshold for minimal clinically significant efficacy.

CONCLUSION: POST intake for 8 weeks was associated with a statistically significant reduction of total CSMS compared to placebo. There was also improvement in RQLQ parameters when compared to baseline. PRO intake for 8 weeks resulted in non-significant beneficial effects on AR-related symptoms.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT05208528.},
}

@article {pmid42047389,
year = {2026},
author = {Adeniji, A and Wassie, M and Madebo, MP and Liang, G},
title = {Harnessing plant-exuded prebiotics as a next-generation strategy for sustainable agriculture.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70275},
pmid = {42047389},
issn = {1744-7909},
support = {//Yunnan Provincial Foreign Experts Project/ ; },
abstract = {Global agriculture urgently needs sustainable strategies to boost crop productivity while reducing environmental impact. Harnessing plant-exuded bioactive metabolites, such as polyphenols, flavonoids, and organic acids, as natural prebiotics offers a powerful yet underexploited avenue for modulating rhizosphere microbiomes. These prebiotics complement existing microbial inoculants by leveraging the plant's own chemistry to selectively recruit beneficial microbes, thereby enhancing disease suppression, nutrient acquisition, and soil health more reliably than introduced consortia, which often fail due to ecological instability. However, translating this promise into practice is hampered by the profound complexity of the soil-root-microbe interface. This review establishes a conceptual framework that positions plant prebiotics as actionable tools for precision microbiome engineering. We summarize the biosynthetic pathways and mechanisms through which these specialized metabolites stimulate specific beneficial microbial functions. Building on this synthesis, we introduce the PRE-DDV pipeline (decode-design-validate), a closed-loop strategy integrating multi-omics profiling, synthetic community design, and iterative field validation. To enable commercial-scale field application, we critically examine key translational considerations: Identifying scalable plant sources (including native flora and agro-industrial byproducts), advancing formulation and precision delivery to ensure stability and targeted release, and assessing the economic feasibility, environmental sustainability, and regulatory frameworks governing industrial-scale production. Together, these contributions position prebiotics within a concrete pathway that bridges biological mechanisms and practical scalability, transforming them from a promising concept into a practical cornerstone of sustainable, climate-resilient agriculture.},
}

@article {pmid42047396,
year = {2026},
author = {Yuan, W and Feng, Z and Zhang, W and Liu, Y and Zhou, Y and Qin, Y and Bai, Y and Zhu, H and Yao, Q},
title = {Keystone taxa of phyllosphere microbiome confer resistance to citrus bacterial canker in pomelo via multiple mechanisms.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70273},
pmid = {42047396},
issn = {1744-7909},
support = {//National Key Research and Development Program of China/ ; },
abstract = {Citrus bacterial canker (CBC) is a globally important citrus disease caused by Xanthomonas citri subsp. citri (Xcc). Increasing evidence shows that the plant microbiome is crucial for host growth performance and health maintenance, among which the keystone taxa stand out due to their indispensable roles in microbiome homeostasis. However, how keystone taxa in the phyllosphere microbiome contribute to disease resistance remains unclear. In this study, we characterized the phyllosphere bacterial community of pomelo across an annual cycle and found that amino acids in leaves were the main drivers of the bacterial community structure. Meanwhile, five OTUs were identified as keystone taxa. A total of 587 phyllosphere bacterial strains were isolated, among which six strains belonging to Methylobacterium, Sphingomonas, Massilia, and Paenibacillus were identified as the corresponding keystone strains. We further constructed a consortium with these six strains to test its role in controlling CBC in planta. Network analysis reveals that consortium inoculation increased the phyllosphere bacterial community stability, whereas Xcc inoculation decreased it. However, dual inoculation of the consortium and Xcc restored community stability compared to the control. Interestingly, the inoculated keystone strains, if not all, still appeared as keystone taxa in the microbiomes of the control, consortium inoculation, and dual inoculation treatments, but not in the Xcc-inoculated treatment. Moreover, the consortium inoculation significantly increased the defense-related enzyme activities such as PPO, POD, and PAL in leaves, suggesting a triggered plant immune response. In vitro assays indicated that these keystone strains showed either antagonistic activity against Xcc or siderophore-producing activity. Finally, the consortium inoculation significantly reduced the disease index by 78% in planta. Taken together, these results suggest that the keystone taxa of the phyllosphere microbiome can confer disease resistance to the host via multiple mechanisms, especially by maintaining phyllosphere microbiome homeostasis.},
}

@article {pmid42047468,
year = {2026},
author = {Liu, Z and Huang, R and Sun, T and Zhu, L},
title = {Probiotic supplementation during pregnancy for vaginal microbiota improvement and pathogen clearance: A systematic review and meta-analysis.},
journal = {Acta obstetricia et gynecologica Scandinavica},
volume = {},
number = {},
pages = {},
doi = {10.1111/aogs.70234},
pmid = {42047468},
issn = {1600-0412},
support = {2025-I2M-XHZY-037//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 2025-I-PY-010//the Independent Research Fund of the State Key Laboratory of Complex, Severe, and Rare Diseases/ ; 82530054//the National Natural Science Foundation of China/ ; },
abstract = {INTRODUCTION: Pregnancy is associated with susceptibility to vaginal dysbiosis, including Group B Streptococcus (GBS), bacterial vaginosis (BV), and vulvovaginal candidiasis (VVC). Probiotic supplementation has emerged as a potential strategy to restore vaginal microecology, yet its effectiveness during pregnancy remains uncertain.

MATERIAL AND METHODS: To evaluate whether probiotic supplementation during pregnancy increases the likelihood of clearance of GBS colonization, BV, and VVC. We systematically searched PubMed, Embase, Cochrane CENTRAL, and Web of Science from inception to 16 April 2025. Eligible studies were randomized or non-randomized studies comparing probiotic supplementation with placebo or no treatment in pregnant women, reporting outcomes related to vaginal microbiota, pathogen decolonization, or infection resolution. Two reviewers independently screened studies and extracted data. Randomized controlled trials (RCT) were evaluated using the Cochrane ROB-1 tool, and the single non-RCT was assessed using ROBINS-I. Meta-analyses were performed for co-primary outcomes, with subgroup analyses by timing, comparator type (placebo-controlled vs. no-treatment control), and duration of intervention.

RESULTS: Eighteen studies (n = 3705) were included. For the co-primary outcomes, a statistically significant increase in the odds of GBS decolonization was observed (OR 1.38, 95% CI 1.08-1.76; I[2] = 2%). This association was no longer statistically significant in analyses restricted to RCTs (OR = 1.28, 95% CI 0.93-1.76; I[2] = 9%) and remained non-significant when further restricted to placebo-controlled RCTs (OR = 1.32, 95% CI 0.94-1.85; I[2] = 31%). No significant effects were found for BV (OR 0.91) or VVC (OR 0.65). An exploratory pooled analysis across infection types showed no significant overall improvement in infection clearance (OR 1.13, 95% CI 0.94-1.36; I[2] = 16%). Subgroup analysis indicated greater efficacy in interventions initiated during the third trimester or lasting ≤4 weeks, though interaction tests were not significant.

CONCLUSIONS: Probiotic supplementation during pregnancy may increase the likelihood of GBS decolonization. However, this association was not statistically significant in sensitivity analyses restricted to randomized and placebo-controlled trials. No consistent benefit was observed for BV or VVC. Standardized probiotic regimens and harmonized diagnostic frameworks are needed.},
}

@article {pmid42047508,
year = {2026},
author = {Li, H and Fei, Y and Zhao, W},
title = {The Control of Canine Halitosis By Sugar Cane Polyphenols: Effects and Potential Mechanisms.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c00022},
pmid = {42047508},
issn = {1520-5118},
abstract = {Halitosis in companion animals lacks safe, effective long-term solutions. This study evaluated sugar cane polyphenols (SP) as an oral deodorizer for dogs using acute and 30 day intervention trials. Efficacy was evaluated by sensory scoring, volatile profiling, microbiome analysis, and mechanistic assays. Oral malodor was significantly reduced in both the acute (0-120 min) spray test and the 30 day SP intervention, accompanied by decreases in volatile sulfur compounds and indole. Mechanistic evidence indicated that SP interacts with odorants through noncovalent interactions and reduces protein surface hydrophobicity. Molecular simulations further supported competitive occupation of hydrophobic and aromatic protein binding regions by SP. Meanwhile, salivary β-glucosidase activity was inhibited in a concentration-dependent manner. SP exposure was also associated with reduced abundances of odor-associated oral taxa, such as Porphyromonas and Fusobacterium. These findings support SP as a food-grade strategy for controlling canine halitosis, with translational relevance to oral care applications.},
}

@article {pmid42047567,
year = {2026},
author = {Seeram, D and Park, H and Abrams, JA and Uhlemann, AC and Freedberg, DE},
title = {Vancomycin-resistant Enterococcus often spreads from hospitalized patients into the local environment and less often spreads from the environment into patients.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag240},
pmid = {42047567},
issn = {1537-6613},
abstract = {BACKGROUND: Uncertainty remains about how gut-based organisms such as vancomycin-resistant Enterococcus (VRE) are spread within the local hospital environment. We hypothesized that, in the medical intensive care unit (ICU), VRE is spread predominantly patient-to-environment rather than environment-to-patient.

METHODS: Medical ICU patients with sepsis and receiving broad-spectrum antibiotics were sampled via deep rectal swabs at ICU admission and on ICU days 3, 7, 14, and 30. Corresponding ICU room environmental samples were taken at the same timepoints. All samples were analyzed with 16S sequencing and selective culture, and VRE isolates were genetically characterized via whole genome sequencing (WGS).

RESULTS: There were 680 samples gathered from 90 unique patients and their ICU rooms. 47/90 (52%) patients and 36/90 (40%) rooms showed VRE colonization at one or more timepoint. On 16S sequencing, Enterococcus relative abundance was enriched in room samples when the room housed a VRE positive patient (0.63% VRE(+) vs. <0.01% VRE(-), p<0.01). In a network analysis, patient and room Enterococcus were connected for VRE positive but not VRE negative patients. WGS identified 23 genetically distinct clusters of VRE. There were 3 events when distinct clusters appeared first in the patient gut and then in the room and 3 events when clusters appeared simultaneously in the gut and room; in no cases was a cluster first detected in the room.

CONCLUSIONS: We detected three events when spread of genetically distinct VRE clusters from hospitalized patients into their local ICU environment but no reverse events. Effectiveness of infection prevention might be increased by gut-targeting interventions.},
}

@article {pmid42047611,
year = {2026},
author = {Capone, K and Kuller, J and Durand, DJ and Tierney, NK and Lund, C},
title = {Exploration of Changes in the Human Skin Microbiome by Mode of Birth and Following First Bath.},
journal = {Pediatric dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/pde.70219},
pmid = {42047611},
issn = {1525-1470},
support = {UL1 TR000004/TR/NCATS NIH HHS/United States ; //Johnson & Johnson Consumer Inc./ ; },
abstract = {BACKGROUND/OBJECTIVES: Microbes colonize the skin soon after birth, and the skin microbiome changes over time. However, the effects of bathing and hygiene products on the infant skin microbiome are not well studied. This randomized, single-center trial analyzed the skin microbiome in neonates born vaginally or via cesarean section (c-section), before and after their first bath with or without a mild baby cleanser.

METHODS: One hundred healthy full-term neonates were randomized to baths with water alone or with mild baby cleanser, stratified by delivery mode. Volar forearm swabs of neonates (before and after first bath) and their mothers were analyzed by 16S rRNA metagenomic sequencing.

RESULTS: At birth, neonates born vaginally had greater overall richness of the skin microbiome versus those born via c-section. Vaginally delivered neonates had similar species richness as their mothers, while neonates delivered via c-section had much lower species richness. Shannon diversity was similar regardless of birth mode, but community structure varied. Species richness was similar before and after bath in vaginally delivered neonates, but those born via c-section had higher species richness after their first bath and showed larger changes in community structures, compared with the vaginal group. Whether water alone or baby cleanser was used for the first bath did not greatly affect skin microbiome composition.

CONCLUSIONS: The mode of birth had the largest effect on the skin microbiome composition, richness, and structure. Neonates born via c-section showed the largest post-bath changes in the skin microbiome, while the use of water or baby cleanser had little effect.},
}

@article {pmid42047845,
year = {2026},
author = {Pereira-Rodrigues, A and Gonçalves, A and Alves, IN and Mendes, CS and Silva, C and Campos, J and Sampaio-Maia, B and Falcão-Pires, I and Araujo, R},
title = {Metabolic and gut microbiota effects of ketogenic diet and exogenous ketone salts in a rat model of metabolic syndrome.},
journal = {European journal of nutrition},
volume = {65},
number = {4},
pages = {},
pmid = {42047845},
issn = {1436-6215},
}

@article {pmid42048286,
year = {2026},
author = {Yan, Q and Yu, X and Wei, J and Fang, C and Zhao, J and Li, X and Fu, Y and Li, X},
title = {Shewanella oneidensis Metabolically Engineered with Prussian Blue for Synergistic Tumor Microenvironment Remodeling and Photodynamic Breast Tumor Elimination.},
journal = {ACS biomaterials science & engineering},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsbiomaterials.6c00087},
pmid = {42048286},
issn = {2373-9878},
abstract = {Microorganism-based tumor therapy has attracted increasing interest due to the intrinsic tumor tropism and metabolic plasticity of certain bacterial species. However, their therapeutic efficacy is often hindered by insufficient metabolic activity within the tumor microenvironment and safety concerns associated with systemic administration. Here, we develop a biohybrid system, termed Ce6@PB@MR-1, to enhance the intrinsic tumor-targeting behavior of chlorin e6 (Ce6) and lactate-metabolizing capability of Shewanella oneidensis MR-1 (MR-1) through engineered material-microbe coupling. In this system, Prussian blue (PB) is metabolically precipitated onto the MR-1 surface during anaerobic respiration, forming an electron-mediating interface in which PB functions as an efficient exogenous electron acceptor to strengthen respiratory electron flux and accelerate the lactate metabolism of MR-1. The PB coating simultaneously attenuates bacterial immunogenicity, enabling the improved in vivo persistence and safety of MR-1. Furthermore, bioconjugated Ce6 enables 660 nm-triggered photodynamic therapy to induce immunogenic cell death and activate antitumor immune responses. In vivo, the biohybrid system achieves durable tumor eradication accompanied by a marked remodeling of the tumor microenvironment. This work establishes a metabolically assisted material-microbe hybridization framework that expands microbial functionality and offers a versatile strategy for developing safe and effective microbe-based cancer therapies.},
}

@article {pmid42048337,
year = {2026},
author = {Bernal Hernández, N and Rodríguez Cabal, HA and Pino, NJ and Ramírez Restrepo, S and Múnera Porras, LM},
title = {Metagenomic and taxonomic profiling of phyllosphere bacteria from Mangifera indica in response to urban air pollutants in Medellín, Colombia.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347959},
pmid = {42048337},
issn = {1932-6203},
mesh = {Colombia ; *Mangifera/microbiology ; *Bacteria/genetics/classification/drug effects ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Air Pollutants/metabolism ; Microbiota/genetics ; *Metagenome ; Phylogeny ; Cities ; },
abstract = {Urban trees and their phyllosphere-associated microbiota constitute a promising nature-based solution for mitigating urban air pollution. In this study, we characterized the taxonomic composition, diversity patterns, and functional potential of bacterial communities inhabiting the phyllosphere of Mangifera indica in two urban sites of Medellín, Colombia, with contrasting pollution levels and across two time points, analyzing a total of 12 samples. We integrated 16S rRNA gene amplicon sequencing, performed on the Illumina MiSeq platform, with shotgun metagenomic sequencing generated on the Illumina NovaSeq 6000 platform to assess community structure and the presence of genes involved in the degradation of airborne organic pollutants. Bacterial assemblages were dominated by Pseudomonadota (Proteobacteria), Actinomycetota, and Bacteroidota, with genera such as Methylobacterium, Pseudomonas, and Serratia consistently prevalent. Alpha diversity was higher in the highly polluted downtown, while beta diversity was shaped primarily by temporal variation. Functional annotation of metagenome-assembled genomes (MAGs) uncovered genes encoding complete aromatic hydrocarbon degradation pathways, including naphthalene, toluene, xylenes, and benzoate. Both ortho- and meta-cleavage routes for catechol degradation were detected, with temporal shifts in pathway dominance linked to changes in the abundance of key degraders taxa. These results reflect genetic potential for xenobiotic degradation within the M. indica phyllosphere microbiota, modulated by environmental conditions. Our findings highlight the ecological role of phyllosphere bacteria as contributors of inferred functional capacity relevant to atmospheric bioremediation and supports their integration into microbiome-informed green infrastructure strategies.},
}

Colombia
*Mangifera/microbiology
*Bacteria/genetics/classification/drug effects
Metagenomics
RNA, Ribosomal, 16S/genetics
*Air Pollutants/metabolism
Microbiota/genetics
*Metagenome
Phylogeny
Cities

@article {pmid42048459,
year = {2026},
author = {He, D and Zhou, Y and Li, M and Wang, M and Yu, W and Shao, C and Singh, SK and Gu, M and Wang, Y and Yuan, J and Wu, X and Zheng, S and Xie, Y and Chen, L and Morcillo, RJL and Yang, Y and Vílchez, JI and Zhang, JL and Miao, Y and Macho, AP and Zhang, H},
title = {Perception of a bacterial quorum sensing signal activates a tripartite plant immune strategy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {18},
pages = {e2532423123},
doi = {10.1073/pnas.2532423123},
pmid = {42048459},
issn = {1091-6490},
mesh = {*Quorum Sensing ; *Arabidopsis/immunology/microbiology/genetics ; *Pseudomonas aeruginosa/physiology ; Arabidopsis Proteins/metabolism/genetics ; *Plant Immunity ; Signal Transduction ; Protein Serine-Threonine Kinases/metabolism/genetics ; Plant Diseases/microbiology/immunology ; Acetophenones/metabolism ; Plant Roots/microbiology/immunology ; Disease Resistance ; },
abstract = {Bacterial quorum sensing (QS) signals an increasing threat during pathogenesis. How plants deploy timely defenses through QS perception is poorly understood. Here, we report that Arabidopsis thaliana perceives 2'-aminoacetophenone (2'-AA), a volatile QS signal from Pseudomonas aeruginosa, and mounts a multilayered defense. This response comprises BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-dependent intracellular immunity, extracellular quorum quenching through the release of acetic acid, and ecological remodeling of the root microbiome to suppress Pseudomonas. Our findings demonstrate that plants can translate the detection of a specific bacterial QS molecule into a coordinated, preemptive disease resistance strategy.},
}

*Quorum Sensing
*Arabidopsis/immunology/microbiology/genetics
*Pseudomonas aeruginosa/physiology
Arabidopsis Proteins/metabolism/genetics
*Plant Immunity
Signal Transduction
Protein Serine-Threonine Kinases/metabolism/genetics
Plant Diseases/microbiology/immunology
Acetophenones/metabolism
Plant Roots/microbiology/immunology
Disease Resistance

@article {pmid42048700,
year = {2026},
author = {Aycan, M and Fakhet, D and Picazo, PJ and Bodur, S and Nagano, H and Asiloglu, R and Aranjuelo, I and Mitsui, T},
title = {Plant-microbiome interactions are associated with enhanced salinity tolerance and methane emissions in rice.},
journal = {Plant physiology and biochemistry : PPB},
volume = {234},
number = {},
pages = {111324},
doi = {10.1016/j.plaphy.2026.111324},
pmid = {42048700},
issn = {1873-2690},
abstract = {Salinity is a severe environmental stressor that reduces crop performance, alters soil microbial communities, and influences greenhouse gas emissions such as methane (CH4). Climate change is expected to further increase salinity globally. Although plants have evolved physiological and molecular mechanisms to cope with salinity, the role of plant-microbiome interactions in salinity tolerance and their link to CH4 emissions remain poorly understood. Here, we investigated the interactions among plant salinity tolerance, rhizobiome, and CH4 emission under salinity stress. We used salt-tolerant and salt-sensitive rice genotypes grown in nutrient-poor paddy field soil and nutrient-rich commercial nursery soil under climate-controlled greenhouse conditions with salinity stress until harvesting. Salt-sensitive genotypes exhibited decreases in early biomass and gas exchange due to salinity stress under nutrient-rich nursery soil. However, salinity effects were mitigated by plant-microbiome interactions, which improved plant growth performance. Rhizosphere microbiome analysis revealed that Rhizobacteria, including Cyanobacteria, were associated with plant development and salinity tolerance. Salinity altered methanogenic archaeal communities, especially Methanobacteria and Methanocellia, with salt-tolerant genotypes releasing more CH4 during stress. Gas exchange and antioxidant enzyme activity were positively correlated with CH4 emissions, suggesting an association between improved physiological performance under salinity and microbial methanogenesis. Gene expression profiling revealed a significant upregulation of hormone- and ion-transport-related genes in paddy soil, which may be associated with stress tolerance, microbial activity, and CH4 emissions. This study proposes a mechanistic framework that links plant salinity tolerance, rhizosphere microbial dynamics, and methane production, illustrating how these interconnected processes shape plant performance and the environmental outcomes. These findings emphasize the necessity of balancing agricultural productivity with CH4 emissions and soil resilience under climate-induced stress.},
}

@article {pmid42048934,
year = {2026},
author = {Gaafar, AM and Stolberg-Mathieu, G and Roager, HM and La Barbera, G},
title = {A validated chiral LC-MS/MS method for enantioselective quantification of aromatic lactic acids in human faeces.},
journal = {Journal of chromatography. A},
volume = {1779},
number = {},
pages = {466997},
doi = {10.1016/j.chroma.2026.466997},
pmid = {42048934},
issn = {1873-3778},
abstract = {Bifidobacterium, a key genus of the infant gut microbiome, produces d- and l- enantiomers of aromatic lactic acids that may influence early-life immune development through stereochemistry-dependent biological activity. No validated analytical methods currently enable their accurate enantio‑separation and quantification in human biological samples. We report the first validated, targeted, liquid chromatography-mass spectrometry method using a chiral column for the enantioselective separation and quantification of d- and l- forms of phenyllactic acid (PLA), 4-hydroxyphenyllactic acid (4OH-PLA), and indolelactic acid (ILA) in faecal samples. The method achieves baseline separation of all enantiomers within 10 min, with resolution values of 2.66 (PLA), 1.77 (4OH-PLA), and 2.42 (ILA). Solid-phase extraction reduces matrix effects (>80 %) and improves analyte recovery (>80 %). Limits of quantification range from 2.9 to 6.7 ng mL[-1], and calibration curves show excellent linearity (R[2] > 0.99). Inter- and intra-day precision expressed as %RSD are < 15 % for most analytes. The method was successfully applied to infant faecal samples, enabling sensitive and stereospecific quantification of aromatic lactic acids, thus establishing a foundation for exploring the biological relevance of these enantiomers in infant health.},
}

@article {pmid42049031,
year = {2026},
author = {Wong, O and Zheng, Z and Wang, M and Cao, A and Chan, FKL and Ng, SC and Su, Q},
title = {Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102780},
doi = {10.1016/j.xcrm.2026.102780},
pmid = {42049031},
issn = {2666-3791},
abstract = {Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.},
}

@article {pmid42049134,
year = {2026},
author = {Gajendiran, TY and Ganamurali, N and Sabarathinam, S},
title = {The host-steroid-microbiome axis: Microbial remodeling of steroid scaffolds and its implications for metabolic and endocrine disorders.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {104683},
doi = {10.1016/j.drudis.2026.104683},
pmid = {42049134},
issn = {1878-5832},
abstract = {Steroids, chemically conserved yet functionally diverse, integrate metabolic, endocrine and microbial networks. Beyond host hormones acting via specific receptors, the gut microbiome edits steroid scaffolds, yielding metabolites that reshape systemic signaling. We introduce the host-steroid-microbiome axis, framing steroids as holobiont currencies coordinating metabolism, immunity and endocrine balance. This continuum links endogenous steroidogenesis, microbial transformations (via hydroxysteroid dehydrogenases, sulfatases and β-glucuronidases) and host receptor modulation (farnesoid X, TGR5, estrogen, androgen and glucocorticoid receptors), impacting bile acid signaling, glucose/lipid metabolism and hormone-related diseases. Steroidomics, multiomics, cryo-EM, artificial intelligence (AI) modeling and digital twins illuminate these interactions, enabling precision endocrinology informed by the microbiome, diet and genetics. A roadmap unites microbial ecology, steroid chemistry and AI for therapeutic targeting.},
}

@article {pmid42049248,
year = {2026},
author = {Jose, A and Apewokin, S and Ollberding, NJ and Duan, Q and Trannguyen, J and Prisco, SZ and Thenappan, T and Hemnes, AR and Elwing, JM},
title = {Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70161},
doi = {10.1002/cph4.70161},
pmid = {42049248},
issn = {2040-4603},
support = {K23HL16497/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; 2022 Research Award//Team Phenomenal Hope/ ; },
mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; *Lactobacillus/physiology ; Prospective Studies ; Middle Aged ; *Pulmonary Arterial Hypertension/microbiology/physiopathology ; Adult ; Aged ; *Hypertension, Pulmonary/microbiology ; Ventricular Dysfunction, Right ; },
abstract = {BACKGROUND: Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.

METHODS: This was a prospective cohort study of patients with pulmonary arterial hypertension undergoing right heart catheterization, with pulmonary artery blood subject to nuclear magnetic resonance metabolomics, and simultaneous stool sample shotgun metagenomics. Validation of metabolite levels with disease severity was done in an independent cohort of pulmonary arterial hypertension patients with blood samples from right heart catheterization testing.

RESULTS: The presence of Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients was associated with less severe pulmonary hemodynamics and echocardiographic right ventricular dysfunction. Higher threonine levels were associated with more favorable pulmonary hemodynamic characteristics in both prospective and independent validation cohorts of pulmonary arterial hypertension patients.

CONCLUSIONS: Detectable Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients are associated with more favorable pulmonary hemodynamic and right ventricular characteristics. Circulating gut-derived metabolites may also be involved. Further investigation into the relationship between gut microbial Lactobacillus, circulating metabolites, disease severity, and clinical outcomes in pulmonary arterial hypertension may be warranted.},
}

Humans
Male
Female
*Gastrointestinal Microbiome/physiology
*Lactobacillus/physiology
Prospective Studies
Middle Aged
*Pulmonary Arterial Hypertension/microbiology/physiopathology
Adult
Aged
*Hypertension, Pulmonary/microbiology
Ventricular Dysfunction, Right

@article {pmid42049393,
year = {2026},
author = {Iorra, FQ and Loebens, LAS and Auler, A and Nascimento, ECT and Schaan, BD and Bock, PM},
title = {Effects of Weight Loss Interventions on Gut Microbiota-Derived Metabolites Linked to Cardiometabolic Health: A Systematic Review and Meta-Analysis.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70151},
doi = {10.1111/obr.70151},
pmid = {42049393},
issn = {1467-789X},
support = {//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {BACKGROUND: Gut microbiota-derived metabolites are emerging as potential mediators between obesity and cardiometabolic conditions. While weight loss interventions modify microbiota composition, their effects on systemic microbial metabolites remain unclear.

OBJECTIVE: To evaluate the effect of weight loss interventions on circulating levels of key gut-derived metabolites in individuals with overweight or obesity, through a systematic review and meta-analysis.

METHODS: Searches were performed in MEDLINE, EMBASE, and The Cochrane Library up to July 17, 2024. We included intervention studies in individuals with overweight/obesity undergoing weight loss strategies, with measurement of serum lipopolysaccharides (LPSs), trimethylamine N-oxide (TMAO), secondary bile acids, short-chain fatty acids (SCFAs), or indole derivatives. Meta-analysis used the standardized mean difference (SMD) with a random-effects model, stratified by intervention type (non-surgical or surgical).

RESULTS: Sixty-seven studies were included. Non-surgical interventions were associated with reduced TMAO (n = 8 studies; SMD: -0.56; 95% CI -0.90 to -0.22; I[2] = 74.7%), but not LPS (n = 10 studies; SMD: -0.11; 95% CI -0.58 to 0.35; I[2] = 91.2%). Surgical interventions were associated with decreased LPS (n = 7 studies; SMD: -0.47; 95% CI -0.80 to -0.14; I[2] = 78.8%), and increased TMAO (n = 8 studies; SMD: 0.49; 95% CI 0.08 to 0.90; I[2] = 81.8%) and secondary bile acids (n = 13 studies; SMD: 0.48; 95% CI 0.30 to 0.66; I[2] = 58.8%). Evidence on SCFAs and indole derivatives was limited.

CONCLUSION: Weight loss strategies have distinct effects on gut microbiota-derived metabolites, underscoring the complexity of microbiota-host interactions and the potential for personalized approaches to obesity treatment.},
}

@article {pmid42049453,
year = {2026},
author = {Voyiatzis, I and Vatsellas, G and Valakos, D and Stavropoulos, G and Lamia, A and Stamatogianni, C and Athanasiadis, E and Anagnostopoulos, AK and Alexiou, L},
title = {Effects of a Greek Yoghurt-based Complex on the Human Facial Skin Microbiome.},
journal = {In vivo (Athens, Greece)},
volume = {40},
number = {3},
pages = {1852-1863},
doi = {10.21873/invivo.14339},
pmid = {42049453},
issn = {1791-7549},
mesh = {Humans ; *Yogurt/microbiology ; *Microbiota/drug effects/genetics ; Female ; Male ; Adult ; Middle Aged ; *Skin/microbiology/drug effects ; Aged ; *Face/microbiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Skin Microbiome ; },
abstract = {BACKGROUND/AIM: Natural ingredient-containing complexes are used in dermo-cosmetics to ameliorate facial characteristics, yet human experimental approaches and trials demonstrating their efficacy remain limited. This study assessed the effects of a Greek yoghurt-based complex on the human facial skin microbiome.

MATERIALS AND METHODS: Thirty-one volunteers (27 females, 4 males; 20-65 years) with stressed facial skin and 15 volunteers (10 females, 5 males) with balanced skin were enrolled in a 28-day clinical study. At baseline, skin swabs were collected from both groups. Participants with stressed skin were treated in a split-face design with a yoghurt-based complex applied to the right cheek and placebo to the left cheek for 28 days, with follow-up sampling on days 7, 14, and 28. Bacterial DNA was analyzed by 16S rRNA gene amplicon sequencing. Bioinformatic analyses assessed microbial composition, diversity, and relative abundance. Baseline differences between skin types and treatment effects versus placebo were evaluated over time.

RESULTS: A lowered microbiota diversity was observed in "stressed" facial skin, compared to the "balanced" group, on day 0. The four most abundant microbiota genera were Corynebacterium, Propionibacterium, Staphylococcus and Actinomyces spp. A significant difference in the relative abundance of these species was noted in the two groups (stressed vs. balanced) at baseline, as well as a consistent increase in mean bacterial diversity after intervention with the yogurt-based complex.

CONCLUSION: A gradual restoration of the skin's microbial balance essential for a healthy skin function and appearance, was noted following the yoghurt-based complex application.},
}

Humans
*Yogurt/microbiology
*Microbiota/drug effects/genetics
Female
Male
Adult
Middle Aged
*Skin/microbiology/drug effects
Aged
*Face/microbiology
RNA, Ribosomal, 16S/genetics
Young Adult
Skin Microbiome

@article {pmid42049487,
year = {2026},
author = {El-Assaad, F and El-Omar, EM},
title = {Gut-peritoneal-multisystem axis in endometriosis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337490},
pmid = {42049487},
issn = {1468-3288},
}

@article {pmid42049488,
year = {2026},
author = {Lan, K and Bai, D and Yuan, L and Luo, H and Jin, J and Li, SC and Wu, LF and Sun, XS and Liu, SL and Chen, QY and Mai, HQ and Liu, YX and Tang, LQ},
title = {Metagenomic identification of gut microbiome signatures for accurate diagnosis and prognostic prediction of Epstein-Barr virus-associated nasopharyngeal carcinoma.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338223},
pmid = {42049488},
issn = {1468-3288},
abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. The gut microbiome can influence outcomes of viral infections but the potential links among the gut microbiome, EBV infection and NPC remain unclear.

OBJECTIVE: To characterise gut microbiome alterations in EBV-associated NPC, evaluate microbiome-based diagnostic performance (alone and in combination with EBV markers), and explore associations between microbial features, EBV DNA burden, prognosis and the tumour microenvironment.

DESIGN: We conducted a large-scale shotgun metagenomic study including 516 patients with EBV-associated NPC and 263 healthy controls. Microbiome dysbiosis, functional pathways and associations with plasma EBV DNA were assessed. Species-level markers were used to build a random forest classifier for NPC diagnosis, and performance was evaluated alone and in combination with EBV-specific markers. Survival analyses were performed to identify microbial features associated with NPC-related mortality and relationships with an immune-suppressive tumour microenvironment were explored.

RESULTS: NPC was characterised by gut microbiome dysbiosis, including depletion of short-chain fatty acid-producing species and reduced butanoate metabolism, which were significantly associated with plasma EBV DNA. A random forest classifier based on species-level markers distinguished NPC from controls with an area under the curve (AUC) of 0.917; performance improved to an AUC of 0.984 when combined with EBV-specific markers. Specific microbial species were associated with NPC-related mortality and prognostic microbial features were linked to an immune-suppressive tumour microenvironment.

CONCLUSION: EBV-associated NPC is associated with distinct gut microbiome and functional alterations that correlate with plasma EBV DNA. Microbial markers show strong diagnostic potential, particularly when integrated with EBV-specific markers, and prognostic microbial features may be linked to an immune-suppressive tumour microenvironment, supporting a potential role of the gut microbiome in NPC tumourigenesis.},
}

@article {pmid42049541,
year = {2026},
author = {Yang, M and Liu, T and Qin, Y and Cai, R and Yang, X and Tang, C},
title = {Role of gut microbiota modulation in preventing and treating sarcopenia in patients with liver cirrhosis: A narrative review.},
journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajg.2026.03.005},
pmid = {42049541},
issn = {2090-2387},
abstract = {Sarcopenia, a common and serious complication in patients with liver cirrhosis, is associated with high morbidity and mortality. Accumulating evidence highlights the gut-liver-muscle axis as a key regulatory pathway underlying muscle wasting in cirrhosis, with disruptions in the gut microbiome taking center stage. This review systematically summarizes the mechanisms by which gut microbiota dysregulation contributes to sarcopenia in cirrhosis, examining how compromised intestinal integrity, inflammatory responses, and disrupted metabolism of key compounds, such as short-chain fatty acids, branched-chain amino acids, and bile acids, play pivotal roles in this pathological process. We also critically examine the scientific evidence supporting approaches that target gut microbiome health, aiming to provide a comprehensive and up-to-date overview for clinicians and researchers.},
}

@article {pmid42049610,
year = {2026},
author = {Barrientos, G and Fahlbusch, FB and Conrad, ML},
title = {Microbes, molecules, and the maternal-fetal interface: rethinking the gut-placenta axis.},
journal = {Trends in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.it.2026.03.010},
pmid = {42049610},
issn = {1471-4981},
abstract = {Placental biology is increasingly framed through a signaling paradigm in which maternal microbiome-derived mediators-rather than microbial colonization-affect the function of the interface. This review synthesizes evidence that circulating microbial signals, including short-chain fatty acids, tryptophan-derived indoles, bile-acid-linked ligands, microbe-associated molecular patterns, and bacterial extracellular vesicles, are associated with placental vascular development, immune regulation, nutrient transport, and endocrine programs-processes central to pregnancy outcomes. We integrate mechanistic insights from gnotobiotic and supplementation models with limitations of human evidence and identify key translational gaps. The current evidence supports a model in which maternal microbial ecology shapes a network of circulating mediators that converge on interlinked placental pathways essential for placental function and fetal development.},
}

@article {pmid42049611,
year = {2026},
author = {Gurumurthy, G and Gurumurthy, J and Gurumurthy, S and Reynolds, L and Thachil, J},
title = {Dysbiosis and immunothrombosis - How platelets and the gut microbiome interact.},
journal = {Blood reviews},
volume = {},
number = {},
pages = {101395},
doi = {10.1016/j.blre.2026.101395},
pmid = {42049611},
issn = {1532-1681},
abstract = {Platelets are classically recognised for their role in haemostasis and thrombosis. They are now increasingly recognised as modulators of the immune system, referred to as immunothrombosis, and are thought to be closely associated with the gut microbiome. The gut microbiome shapes platelet phenotype through receptor-mediated sensing of microbial ligands and circulating metabolite-driven priming. Dysbiosis and barrier disruption increase systemic exposure to microbial-associated molecular patterns (MAMPs) which, in turn, engage platelet and vascular pattern-recognition receptors. Prothrombotic metabolites such as trimethylamine N-oxide has also been shown to modulate platelet activation by amplifying calcium-dependent activation and downstream inflammatory crosstalk. Other metabolites, such as phenylacetylglutamine, have been shown to increase platelet activation through adrenergic receptor-mediated pathways. In contrast, short-chain fatty acids may reduce this thromboinflammatory platelet phenotypes through anti-inflammatory signalling and potential effects on megakaryopoiesis and platelet reactivity. Therapeutic options that target these pathways between platelets and the microbiota have been explored. Examples include dietary modifications and microbiome-based interventions. Yet, whilst promising, significant gaps remain in understanding the long-term impacts of these strategies on platelet behaviour and overall disease outcomes.},
}

@article {pmid42049674,
year = {2026},
author = {Velarde-Salcedo, AJ and Serrato-Alemán, O and Barba-de la Rosa, AP},
title = {Food-Derived Peptides: Neuropeptides and the Diet-Microbiome-Brain Axis.},
journal = {Annual review of food science and technology},
volume = {17},
number = {1},
pages = {79-101},
doi = {10.1146/annurev-food-053124-011258},
pmid = {42049674},
issn = {1941-1421},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neuropeptides/metabolism/chemistry ; *Brain/physiology/metabolism ; *Diet ; *Peptides/chemistry/metabolism ; Animals ; Dietary Proteins/metabolism ; },
abstract = {Food-derived peptides are short chains of amino acids encrypted in the proteins of several plant sources. Several functions of food-derived peptides, or bioactive peptides (BPs), such as antioxidant, antihypertensive, antidiabetic, antiobesity, and antimicrobial, have been well studied. However, at the beginning of the twenty-first century, due to stressful situations such as prolonged aging and pandemic diseases, the study of BPs with the potential to mitigate the impact of anxiety, cognitive impairment, and the progression of neurodegenerative diseases has received increased attention. Classical processes such as enzymatic hydrolysis, fermentation, the use of probiotics, and the simulation of gastrointestinal digestion are used to release BPs. Heating, high pressure, and in silico design are methods proposed to obtain novel peptides. In addition, gut microbiota play a key role in the metabolism of dietary proteins; therefore, through cross-kingdom communication, the diet-gut-brain axis is a fundamental mechanism in maintaining health status that is only just beginning to be understood. Furthermore, attention is being paid to small peptides, or noncoding peptides, which can be found in dietary foods, as new players capable of modulating the diet-gut-brain axis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Neuropeptides/metabolism/chemistry
*Brain/physiology/metabolism
*Diet
*Peptides/chemistry/metabolism
Animals
Dietary Proteins/metabolism

@article {pmid42049694,
year = {2026},
author = {Joung, JY and Choi, HS and Oh, NS},
title = {Emerging Roles of Postbiotics in Gut-Brain-Microbiome Axis Modulation and Neurobiological Pathways of Chronic Stress-Related Brain Dysfunction.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2603010},
doi = {10.4014/jmb.2603.03010},
pmid = {42049694},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Stress, Psychological/microbiology/physiopathology ; Animals ; *Brain/physiopathology ; Dysbiosis ; Hypothalamo-Hypophyseal System ; Probiotics ; Pituitary-Adrenal System ; *Brain-Gut Axis ; },
abstract = {Chronic psychological stress disrupts the gut-brain-microbiome axis (GBMA) through gut dysbiosis, intestinal and blood-brain barrier disruption, hypothalamic-pituitary-adrenal (HPA) axis dysregulation, and neuroinflammation, collectively impairing neurotransmitter signaling and neuroplasticity. Addressing these interconnected pathological processes requires therapeutic strategies capable of acting across multiple nodes of the GBMA simultaneously. Postbiotics, defined as preparations of inanimate microorganisms and/or their components that confer a health benefit on the host, have emerged as promising candidates for restoring GBMA homeostasis under chronic stress. Key postbiotic classes, including short-chain fatty acids, tryptophan metabolites, GABA-related compounds, heat-killed bacteria, and bacterial extracellular vesicles, attenuate neuroinflammation, reinforce barrier integrity, normalize neurotransmitter balance, and promote brain-derived neurotrophic factor (BDNF)-dependent neuroplasticity. Preclinical evidence has consistently demonstrated behavioral and neurochemical improvements following postbiotic administration, and limited clinical data suggest preliminary reductions in cortisol, inflammatory biomarkers, and stress-related symptom severity. However, clinical translation remains constrained by the absence of standardized postbiotic characterization and limited mechanistic data from human trials. This review provides an integrated account of the neurobiological pathways by which chronic stress disrupts the GBMA and examines the emerging roles of postbiotics in modulating these pathways, with the goal of informing future postbiotic-based strategies for chronic stress-related brain dysfunction.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Stress, Psychological/microbiology/physiopathology
Animals
*Brain/physiopathology
Dysbiosis
Hypothalamo-Hypophyseal System
Probiotics
Pituitary-Adrenal System
*Brain-Gut Axis

@article {pmid42039801,
year = {2026},
author = {Hanlon, M and Van Beeck, W and Wei, L and Tosta, I and Liao, R and Marco, ML and DiCaprio, E},
title = {Consumer knowledge and motivations for consumption of fermented foods.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1789825},
pmid = {42039801},
issn = {1664-302X},
abstract = {Non-alcoholic fermented foods (FFs) are a popular food group with consumers; however limited studies exist evaluating the motivations for consuming FFs and the frequency of consumption. To begin to address this gap in knowledge, we developed an online survey to assess participant familiarity with different types of fermented products, determine consumption frequency, and gain insight into the motivation for consumption. A total of 751 participants completed the survey. Yogurt was the most frequently identified fermented food (n = 658; 87.62% of respondents). Participants reported consuming fermented cereal grains (n = 307; 46.17%), fruits and vegetables (n = 281; 42.26%), dairy products (n = 204; 39.70%), soy/rice products (n = 250; 37.60%) and fermented meats (n = 204; 30.68%). Reported daily consumption was highest for categories of fermented cereal and dairy products, compared to the other categories which typically were consumed on a weekly or monthly basis. The primary motivator for consumption was taste (n = 337; 50.68%) compared to health benefits (n = 235; 35.34%) and cultural reasons (n = 80; 12.03%). The most highly selected health benefits associated with FF consumption were "improved gut microbiome" (n = 513; 77.14%), "digestive benefits" (n = 508; 76.39%), and "probiotic" (n = 458; 68.87%). Participants associated health benefits with all fermented products listed in the survey. Therefore, consumers may assume that all fermented foods confer the same health benefits. The motivations for consumption (sensory attributes, health benefits, cultural reasons) did not vary when individuals were asked to respond for FFs as a broad category versus specifically for non-alcoholic, fermented fruits and vegetables. This suggests that consumers view FFs similarly regardless of the starting ingredients and fermentative process involved.},
}

@article {pmid42039807,
year = {2026},
author = {Liu, X and Tang, W and Li, C and Jiao, Y and Bai, Y and Xiang, L and Wu, Z},
title = {Vaginal microbiota in assisted reproduction: determinants, dynamics, and impact on clinical outcomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1770446},
pmid = {42039807},
issn = {1664-302X},
abstract = {The vaginal microbiota (VMB), predominantly composed of Lactobacillus genus, plays a crucial role in maintaining female reproductive health through acid production, immune modulation, and protection against pathogens. However, substantial inter-individual variability exists in its composition and stability. In assisted reproduction, the vaginal microenvironment is increasingly recognized as an important factor influencing embryo implantation and pregnancy outcomes. Emerging evidence suggests that the composition and dynamics of the vaginal microbiome are not only predictive biomarkers but also potential regulatory targets influencing assisted reproduction outcomes. This review outlines vaginal microbial community types, key behavioral and host-related determinants, and their links to ART outcomes. We also discuss current limitations, including methodological heterogeneity, unclear causal mechanisms, and the lack of standardized intervention strategies. Finally, we highlight the need for longitudinal and multi-omics studies to support the clinical translation of vaginal microbiome research in reproductive medicine.},
}

@article {pmid42039826,
year = {2026},
author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C},
title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797687},
pmid = {42039826},
issn = {1664-302X},
abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.

METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.

RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 × 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.

CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.},
}

@article {pmid42039832,
year = {2026},
author = {Sola, L and Candeliere, F and Busi, E and Raimondi, S and Amaretti, A and Rossi, M},
title = {A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761627},
pmid = {42039832},
issn = {1664-302X},
abstract = {INTRODUCTION: Clostridia is a major microbial class in the human gut, crucial for fermenting undigested carbohydrates and proteins, which produce short-chain fatty acids essential for gut health and immune balance. This study revised the taxonomic classification and phylogeny of all the species of intestinal Clostridia catalogued in the Unified Human Gastrointestinal Genome database using a whole-genome approach and assessed butyrate and propionate producing species.

METHODS: A total of 1,897 Clostridia species, including those with recognised binomial nomenclature and those lacking formal taxonomic classification, were retrieved and reclassified using GTDB-Tk. Their phylogeny was determined by identifying, concatenating, and aligning the 120 ubiquitous single-copy proteins defined in the GTDB. Average amino acid identity (AAI), percentage of conserved proteins (POCP), and phylogenetic relationships were used to organize the species into genera and families. The presence of enzymes belonging to the biosynthetic pathways for butyrate and propionate production was investigated in all genomes with the tool GapSeq.

RESULTS: Reclassification of the genomes resulted in 404 recognised species and 1,493 species lacking formal taxonomic classification. Oscillospirales and Lachnospirales encompassed most of the species. The pathways leading to butyrate and propionate production were analyzed in their entirety, revealing 519 species as potential butyrate producers, 257 as potential propionate producers and 77 capable of producing both. To assess the abundance of each species, 151 faecal metagenomes of healthy subjects were profiled, indicating that butyrate producing Clostridia accounted on average for 28.0% of each microbiome.

CONCLUSIONS: This study offers a comprehensive overview of intestinal Clostridia diversity, emphasising their role in gut ecosystems and their potential for butyrate and propionate production.},
}

@article {pmid42039839,
year = {2026},
author = {Chonnacháin, CN and Gibney, ER and Feeney, EL and Rooney, M and O'Connor, A and Noronha, N and Crispie, F and Cotter, PD and FitzGerald, JA},
title = {Unmelted, melted, and deconstructed Cheddar cheese: effects on the gut microbiome from a human dietary intervention study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1702111},
pmid = {42039839},
issn = {1664-302X},
abstract = {INTRODUCTION: Cheddar cheese is a nutritionally dense food matrix containing nutrients and bioactives with the potential to influence gut microbial characteristics. Food matrices influence nutrient absorption and digestibility, therefore the dairy matrix may affect gut microbial responses to dairy food intake. This research aims to identify gut microbial responses to Cheddar cheese consumption, considering aspects of the dairy matrix.

METHODS: Secondary analysis was conducted on a subset (n = 69) of participants' data collected during a 6-week parallel 3-armed intervention study. Interventions involved daily consumption of one of the following: (A) 120 g unmelted Cheddar cheese; (B) 120 g melted Cheddar cheese; (C) butter (49 g), calcium caseinate powder (30 g), and Ca supplement (500 mg). Demographics, anthropometry, dietary intake and fecal samples were collected at baseline (V1) and post-intervention (V2). Fecal samples underwent 16S rRNA gene sequencing, followed by bioinformatic processing and statistical analysis.

RESULTS: At V1, 52% were female, mean age was 58.2 ± 5.4 years, with no significant differences between groups or timepoints. Following sequencing, 12,098 unique bacterial taxa in total were identified. Under a False Discovery Rate (FDR) cutoff of 0.1, Dorea (W = 0.568, FDR = 0.079) and Erysipelotrichaceae UCG-003 (W = 0.887, FDR = 0.097) were significantly increased from V1 to V2 in the unmelted cheese group. At V2, Bacteroides was differentially more abundant in the unmelted cheese group, relative to the melted group (W = 0.587, FDR = 0.034). Bacterial alpha diversity (Shannon, Simpson) significantly increased in the unmelted cheese group only from V1 to V2 (p < 0.05). Beta diversity analysis showed a significant group effect considering both timepoints (F = 1.505, p < 0.01). Considering V2 only, Principal Coordinate Analysis showed the unmelted group clustered more closely relative to the other groups, although the effect was not significant.

DISCUSSION: Unmelted Cheddar cheese modulated the gut microbiome by increasing alpha diversity and abundance of several fermenting bacteria. Overall community structure also became more similar following consumption of unmelted cheese, relative to the other groups. Heating cheese and altering its physical structure disrupts the dairy matrix, potentially influencing downstream gut-nutrient interactions and subsequent gut microbial response.},
}

@article {pmid42039844,
year = {2026},
author = {Duff, AF and Bailey, MT},
title = {Abnormal intestinal microbial colonization in prenatally stressed offspring is related to lung and intestinal cytokine expression.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1813467},
pmid = {42039844},
issn = {1664-302X},
abstract = {INTRODUCTION: Prenatal stress (PNS) is associated with deleterious effects on childhood health and wellbeing. Among these consequential health repercussions, PNS-exposed children are at increased risk for acquiring early-life infections, with respiratory infections frequently reported. Stress-induced perturbations in the maternal microbiome during pregnancy represent a key link between stress in utero and aberrant offspring development and can drive abnormal pioneer colonization of offspring microbiomes.

METHODS: Using a mouse model of PNS, we aimed to understand the extent to which these early-life intestinal microbial perturbations are related to intestinal and lung cytokine gene expression. The intestinal microbiome alongside intestinal and lung tissue gene expression were assessed over the first five weeks of life in PNS-exposed offspring to characterize basal cytokine differences in relation to intestinal microbial composition.

RESULTS: In addition to significant changes in microbiome diversity and differential abundance, PNS offspring exhibited significant differences in ileal and lung cytokines characterized by overall increased interferon and proinflammatory gene signatures. PNS-associated microbiome changes also correlated to gene expression in both the ileum and lung. Finally, PNS-associated cytokine differences were not observed in MyD88[-/-] offspring which lack the ability to initiate inflammatory responses through microbially-stimulated toll-like receptor signaling.

CONCLUSION: These findings suggest that PNS-mediated changes in the early-life microbiome are linked to respiratory and ileal immune development and the microbe-immune interactions are MyD88 pathway-dependent.},
}

@article {pmid42039845,
year = {2026},
author = {Muscò, A and Tarracchini, C and Rizzo, SM and Viappiani, A and Ventura, M and Turroni, F},
title = {Exploring the molecular crosstalk between the sex steroids drospirenone and ethinylestradiol with vaginal lactobacilli.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1725887},
pmid = {42039845},
issn = {1664-302X},
abstract = {INTRODUCTION: The vaginal microbiota, dominated by the genus Lactobacillus spp., plays a crucial role in maintaining vaginal homeostasis and protecting against infection through lactic acid production, antimicrobial compound secretion and competitive exclusion of pathogens. Although hormonal fluctuations are known to influence microbial composition, the molecular mechanisms underlying these interactions remain largely unexplored. The aim of this study was to investigate the direct effects of the synthetic sex hormones drospirenone and ethinylestradiol, key components of hormonal contraceptives, on representative vaginal Lactobacillus species.

METHODS: Representative Lactobacillus species associated with different vaginal Community State Types (CSTs) were exposed to drospirenone and ethinylestradiol under simulated vaginal conditions. Lactobacilli responses were assessed using growth assays and RNA-seq transcriptome profiling to evaluate species-specific transcriptional changes following hormonal exposure.

RESULTS: Among the tested strains, Lactobacillus crispatus PRL2021 showed the most pronounced transcriptomic modulation. In this strain, hormone treatment led to the upregulation of genes involved in cell wall biosynthesis, amino acid and carbohydrate metabolism, and stress adaptation. Specifically, expression of the histidine kinase gene sasA_1, part of a two-component regulatory system potentially involved in environmental sensing, was induced. Additionally, the ribBA and ribE genes, predicted to be involved in riboflavin biosynthesis and associated with antioxidant defense and mucosal protection, were upregulated.

CONCLUSION: These findings demonstrate that drospirenone and ethinylestradiol can directly modulate bacterial gene expression, revealing a previously underinvestigated molecular crosstalk between host endocrine signals and the vaginal microbiota. This interaction may contribute to the maintenance of vaginal eubiosis and has potential implications for the development of microbiome-targeted strategies to support women's health. Further studies are needed to elucidate the broader functional consequences of hormone-microbiota interactions and their clinical relevance.},
}

@article {pmid42039849,
year = {2026},
author = {Weng, N and Pinela, E and Shakeri Yekta, S and Moestedt, J and Westerholm, M},
title = {Interplay of iron and sulfur with syntrophic propionate oxidation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798413},
pmid = {42039849},
issn = {1664-302X},
abstract = {In anaerobic environments, different chemical forms of iron and sulfur influence microbial community composition and functions. This study employs mesophilic and thermophilic ammonia-tolerant syntrophic propionate-oxidizing (SPO) cultures to investigate how different iron and sulfur species influence propionate oxidation, as well as downstream syntrophic acetate oxidation and methanogenesis. Elevated concentrations of both Fe[3+] and Fe[2+] species strongly inhibited SPO activity and suppressed propionate oxidation by the mesophilic culture. In contrast, FeSO4 addition to the thermophilic SPO culture markedly enhanced propionate oxidation and methane formation. Notably, neither Na2SO4 nor FeCl2 alone produced comparable stimulation, suggesting that the observed response was driven by a synergistic effect of Fe[2+] and SO4 [2-] on the SPO microbial network. Following Fe[2+] amendment of thermophilic cultures, a bacterium associated with the glycine cleavage pathway became enriched. Subsequently, with the onset of syntrophic propionate and acetate oxidation, the SPO candidate "Candidatus Thermosyntrophopropionicum ammoniitolerans," a syntrophic acetate-oxidizing bacterium affiliated with the family Thermacetogeniaceae, and a hydrogenotrophic methanogen affiliated with the genus Methanothermobacter increased in relative abundance. Overall, the study demonstrates that predicting the outcomes of iron amendments to the anaerobic microbiome demands careful consideration of the prevailing iron and sulfur chemical speciation and their relative molar concentrations, as these factors drive divergent microbial responses under mesophilic and thermophilic conditions. The outcomes support developing targeted strategies to optimize anaerobic digestion and enhance renewable methane yields in high-ammonia biogas systems.},
}

@article {pmid42039890,
year = {2026},
author = {Feng, F and Choi, J and Ahn, D and Truong, TMT and Yim, KJ and Kim, HJ and Jung, MY and Lee, HW and Kim, DS and Kang, I},
title = {Marine-derived extracts of Peyssonnelia caulifera Okamura and Meristotheca papulosa demonstrate differential efficacy in modulating obesity-related metabolic skewing revealed by integrative analysis of extract metabolomics and microbiome profiles.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1749413},
pmid = {42039890},
issn = {2296-861X},
abstract = {This study investigated the anti-obesity efficacy of Peyssonnelia caulifera Okamura extract (PCE) and Meristotheca papulosa extract (MPE) in a high-fat diet (HFD)-induced obese mouse model. Both extracts improved hyperinsulinemia, adipocyte hypertrophy, and adipose/hepatic inflammation. PCE significantly reduced fasting glucose and hepatic triglyceride levels, while MPE effectively normalized colonic histopathology. Both extracts restored tight junction protein expression and mitigated gut barrier disruption. At the phylum level, both supplementations decreased Bacteroidota and increased Verrucomicrobiota; At the genus level, MPE significantly enriched Lachnospiraceae NK4A136, Dubosiella, Faecalibaculum, and Ruminococcaceae NK4A214, while PCE showed modest, non-significant increase. PCE more potently suppressed LPS-induced cytokines expression and adipogenesis than MPE in vitro. UPLC-QTOF-MS revealed distinct metabolite fingerprints for each extract, and correlation analysis linked key metabolites (e.g., carnitine, valyl isoleucine) to inflammatory and metabolic indices. These findings identify PCE and MPE confer metabolic benefits in HFD-induced obesity through coordinated effects on gut, hepatic, and adipose tissue responses, with PCE showing superior efficacy.},
}

@article {pmid42040226,
year = {2026},
author = {Francomano, E and Aci, MM and Mosca, S and Mohamed, NZ and Agosteo, GE and Li Destri Nicosia, MG and Malacrinò, A and Schena, L},
title = {Plant health in the era of global changes, holobiont biology, and microbiome-based solutions.},
journal = {Horticulture research},
volume = {13},
number = {4},
pages = {uhaf364},
pmid = {42040226},
issn = {2662-6810},
abstract = {Agriculture faces unprecedented challenges due to climate change, increasing food demand, and resource scarcity, which needs sustainable and innovative solutions. This review explores the emerging paradigm of holobiont biology (host and its microbiome as biological unit) in the context of emerging plant health challenges driven by global changes. We highlight three critical challenges: the rise of complex plant syndromes, the emergence and re-emergence of plant diseases, and the consequences of dysbiotic plant microbiomes. We discuss how microbiome-based strategies can enhance plant resilience, reduce reliance on agrochemicals, and foster sustainable agriculture. Integrating these strategies with advanced frameworks, such as holo-omics and machine learning, opens avenues for microbiome-based solutions to address agricultural challenges in the era of global changes, ensuring resilient crop systems and planetary health.},
}

@article {pmid42040306,
year = {2026},
author = {Yang, R and Zhu, J and Zhang, Y and Liu, Y and Li, Z and Zhang, H and Li, Q and Wang, X and Chen, X and Chen, D and Liu, Q},
title = {Organic amendments boost maize yield (Zea mays L.) in karst soils via a hierarchical process driven by soil phosphorus enhancement and microbial-mediated nutrient cycling.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1782544},
pmid = {42040306},
issn = {1664-462X},
abstract = {INTRODUCTION: Sustainable food production in fragile karst landscapes requires moving beyond input-intensive agriculture.

METHODS: This study investigated how long-term organic amendments affected maize yield, using a 15-year field trial on karst yellow soil. Integrating soil analysis, metagenomics, and causal modeling, revealed that adding farmyard manure or bio-organic fertilizer to mineral NPK increased yield by 12.08% and 11.48%, respectively, and improved key soil properties, most notably available phosphorus.

RESULTS: Organic inputs shifted the soil microbiome toward copiotrophic taxa and enriched genes for organic matter decomposition and phosphorus mobilization. However, statistical modeling revealed that these biological changes did not directly drive yield. Instead, the primary pathway was hierarchical: amendments first enhanced the soil's chemical habitat, which then directly boosted crop growth while simultaneously shaping the microbial community and its functional potential. The interaction of soil, microbes, and genes together explained 81% of the yield variation.

DISCUSSION: Our findings demonstrate that in phosphorus-limited karst soils, organic amendments act foremost as soil conditioners. Microbial processes, though crucial, are secondary mediators that translate improved soil conditions into efficient nutrient cycling. Therefore, sustainable intensification in these vulnerable agroecosystems should prioritize managing soil health over directly targeting microbial processes.},
}

@article {pmid42040322,
year = {2026},
author = {Tong, J and Li, Y and Zhang, Y and Zhang, P and Wang, K and Zou, Q and Shen, S},
title = {Genotype-matched mapping reveals consistent regional flavour signatures and rhizosphere microbial correlates in spring-flush Yunnan large-leaf tea.},
journal = {Food chemistry: X},
volume = {35},
number = {},
pages = {103869},
pmid = {42040322},
issn = {2590-1575},
abstract = {Microbial correlates of tea terroir are often confounded by cultivar. Using eight SNP-confirmed genotype-matched pairs large-leaf tea cultivar pairs across Menghai and Pu'er, we tested whether rhizosphere communities covary with flavour chemistry during the spring flush. Under genotype control, the volatile Signature Index (VSI) was consistently higher in Menghai in all pairs, with a β-caryophyllene detection/non-detect contrast (7/8 detected in Pu'er vs 0/8 in Menghai). Non-volatiles chemistry showed a two-tier response: EGCG increased in Menghai, whereas nitrogen-associated taste allocation varied by pair. Bulk soil nitrogen and enzyme activities did not directly explain leaf patterns, while bacterial and fungal communities showed significant regional separation and cross-kingdom concordance. Within this strict genotype-matched framework, the results identify spring-flush regional flavour signatures and their microbial correlates as association-level patterns, providing candidate targets for subsequent mechanistic study.},
}

@article {pmid42041114,
year = {2026},
author = {Chen, J and Liang, T and Xu, X and Yu, X and Li, Z and Zheng, X and Liu, Y and Yang, S and Meng, Z and Zhou, Y and Ye, C and Tu, H and Cao, G and Chen, H and Chen, L and Li, B and Nie, Y and Sun, S and Zhang, Y and Lu, Y and Zhang, X and Yu, G and Lv, Y and Jia, H and Deng, Z and Pei, N and Shi, Y and Yang, Y},
title = {Characterization of the intrahepatic microbiome in patients with HBV-Related end-stage liver disease.},
journal = {Virulence},
volume = {},
number = {},
pages = {2665492},
doi = {10.1080/21505594.2026.2665492},
pmid = {42041114},
issn = {2150-5608},
abstract = {BACKGROUND: Dysregulated microbiota is a hallmark of end-stage liver disease (ESLD). This study aimed to elucidate the intrahepatic microbiome in hepatitis B virus (HBV)-related ESLD.

METHODS: We collected liver tissue samples from patients undergoing liver transplantation due to decompensated cirrhosis (DC) (n = 20) or acute-on-chronic liver failure (ACLF) (n = 24), as well as 18 samples from donors. Metatranscriptomic sequencing was performed to profile liver microbiome and transcriptome.

RESULTS: 2208 bacterial species were detected across 13 phyla and 165 genera. Metatranscriptomic profiling revealed that Proteobacteria and Actinobacteria dominated the intrahepatic microbiome, with Escherichia coli and Pseudomonas most prevalent across groups. Principal coordinate analysis showed distinct microbial community structures among donors, DC, and ACLF patients. Compared with donors, both groups exhibited increased abundance of Bacteroides heparinolyticus, Moraxella osloensis, and Gardnerella vaginalis, while ACLF patients were further enriched with Alcaligenes faecalis and Burkholderia insecticola, and DC patients had higher B. heparinolyticus. Most taxa originated from the gut, with additional oral- and respiratory-derived species. Despite similar abundance between groups, E. coli in ESLD displayed marked functional activation, including nutrient acquisition systems and virulence factors linked to adhesion, invasion, and toxin production. Integrated host - microbiome analysis revealed taxa-specific associations with impaired hepatic metabolic, immune, and structural integrity.

CONCLUSION: This study delineates the compositional and functional reprogramming of the intrahepatic microbiome in patients with ESLD and its coupling with liver metabolic, immune, and structural pathways. These findings suggest the intrahepatic microbiome as a promising therapeutic target for ESLD.},
}

@article {pmid42041249,
year = {2026},
author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS},
title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.},
journal = {mBio},
volume = {},
number = {},
pages = {e0286825},
doi = {10.1128/mbio.02868-25},
pmid = {42041249},
issn = {2150-7511},
support = {F32 AI186285/AI/NIAID NIH HHS/United States ; L40 HD116358/HD/NICHD NIH HHS/United States ; R01 AI153332/AI/NIAID NIH HHS/United States ; R21 AI186346/AI/NIAID NIH HHS/United States ; },
abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.},
}

@article {pmid42041258,
year = {2026},
author = {Nieciecki, V and Seitz, VA and Burcham, ZM and Otto, K and Cantrell, K and Kirkland, J and Ackermann, G and Knight, R and Lynne, A and Metcalf, JL and Bucheli, S},
title = {Insects shape the cadaver decomposition microbiome and postmortem interval estimation accuracy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0068125},
doi = {10.1128/msystems.00681-25},
pmid = {42041258},
issn = {2379-5077},
abstract = {The breakdown and recycling of carrion is a crucial ecological process that largely relies on a community of necrophagous insects and microbes. Recent work has shown that a specialized microbial network, likely dispersed throughout the environment by insects, assembles during cadaver decomposition to break down flesh regardless of climate and geography. Because of their broad distribution and successional nature, decomposer microbes have been used in machine learning models to predict the postmortem interval (PMI) of human remains, an important contribution to the field of forensics. How factors such as an indoor environment, which alters insect activity, impact the composition of microbial communities decomposing human remains is unclear. Here, we investigate the effects of enclosed shelter on microbial community assembly and successional patterns during human decomposition and provide important considerations for PMI modeling. Compared to outdoor cadavers, we show that indoor cadavers experienced delayed colonization of key decomposer microbes over the course of decomposition due to restricted insect access. Consequently, machine learning models trained on outdoor cadavers frequently underestimated the PMI of cadavers decomposing indoors. Delayed colonization by blow fly maggots (Diptera: Calliphoridae) was correlated with higher PMI prediction errors, suggesting that insects are an important source of microbial decomposers that drive PMI model predictions. Incorporating microbial data from indoor cadavers and insect activity into PMI models significantly improved prediction capabilities for both indoor and outdoor decomposition environments. Ultimately, we demonstrate the important role insects play in the maintenance and distribution of microbes that help to recycle vertebrate remains.IMPORTANCEMicrobes are critical for the decomposition and recycling of organic matter. Recently, microbiome-based models have shown promising performance in estimating the postmortem interval (PMI). However, many deaths occur indoors, yet no studies have investigated the impact of enclosed shelter on the cadaver microbiome in a controlled setting. Here, cadavers were decomposed indoors, and we found that blow fly maggots serve as an important source of decomposer taxa that significantly alter the cadaver microbiome following infestation. Notably, PMI estimation models trained on outdoor data sets failed to accurately predict the PMI when insect colonization was delayed. We show that incorporating 16S rRNA amplicon data from cadavers decomposing indoors, along with environmental variables, significantly improves PMI estimates, suggesting a microbiome-based forensic tool may be feasible across decomposition environments. Importantly, this research demonstrates the critical ecological role insects play in the dispersal of specialized microbes that are involved in the breakdown and recycling of vertebrate remains.},
}

@article {pmid42041314,
year = {2026},
author = {Ma, H and Zhang, L and Wang, L and Yang, Z and Liu, J and Sun, H and Ge, S and Quan, C},
title = {Antibiotic Mechanisms and Resistance: Molecular Insights and Therapeutic Strategies.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041314},
issn = {2079-6382},
support = {2022020332-JH2/1013//Applied Basic Research Project of Liaoning Provincial Science and Technology Department/ ; LJKMZ20220401//Basic scientific research projects of Liaoning Provincial Department of Education/ ; },
abstract = {Antibiotic resistance is a critical global health threat, already causing over 1.27 million deaths annually and projected to exceed 10 million by 2050. This crisis is compounded by stagnation in novel antibiotic discovery, highlighting the need for mechanism-based innovation. Here, we provide an integrative framework linking antibiotic mechanisms of action, bacterial resistance pathways, and emerging therapeutic strategies. Antibiotics are systematically categorized by their molecular targets, cell wall synthesis, membrane integrity, nucleic acid replication, protein synthesis, and metabolic pathways, while resistance mechanisms are outlined in parallel, including enzymatic degradation, target modification, efflux, and permeability barriers. We further highlight novel approaches such as structure-guided drug design, synergistic combinations, nanoparticle delivery, and artificial intelligence-driven discovery. Precision medicine and microbiome modulation are also emphasized as next-generation interventions. By bridging molecular mechanisms with translational strategies, this review outlines opportunities to guide antibiotic innovation and advance precision therapies against the escalating threat of antimicrobial resistance.},
}

@article {pmid42041360,
year = {2026},
author = {Hashim, NT and Babiker, R and Rahman, MM and Mohammed, R and Padmanabhan, V and Islam, MS and Elsheikh, M and Abduljalil, SMA and Mahmoud, G and Chaitanya, NCSK and Siriwardena, BSMS and Ahmed, A and Gismalla, BG},
title = {Targeting Bacterial Infections in Periodontal Disease: From Conventional Antibiotics to Next-Generation Therapeutics.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041360},
issn = {2079-6382},
abstract = {Periodontitis is a highly prevalent chronic inflammatory disease with significant oral and systemic consequences, including associations with cardiovascular disease, diabetes, and adverse pregnancy outcomes. Although mechanical debridement remains the cornerstone of therapy, adjunctive antibiotic use is increasingly limited by antimicrobial resistance, biofilm-associated tolerance, pharmacokinetic constraints, and disruption of the commensal microbiome, leading to inconsistent outcomes and disease recurrence. This review highlights the mechanistic limitations of conventional antibiotic therapies in periodontitis and critically examines emerging next-generation therapeutic strategies aimed at overcoming these challenges. Specifically, it explores antimicrobial peptides, quorum sensing inhibitors, nanotechnology-based drug delivery systems, host modulation approaches, and microbiome-targeted therapies, with emphasis on their molecular mechanisms, clinical relevance, and translational potential. By integrating microbial, host, and pharmacological perspectives, this review provides a comprehensive framework for advancing precision-guided periodontal therapy and supports the shift toward targeted, sustainable, and personalized treatment strategies.},
}

@article {pmid42041380,
year = {2026},
author = {Alvaro, ME and Caserta, S and Martino, EA and Skafi, M and Bruzzese, A and Amodio, N and Lucia, E and Olivito, V and Labanca, C and Mendicino, F and Vigna, E and Morabito, F and Gentile, M},
title = {Gut Microbiota and Acute Myeloid Leukemia: State of the Art, Clinical Signals, and Translational Opportunities.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041380},
issn = {2079-6382},
abstract = {Acute myeloid leukemia (AML) remains a highly morbid malignancy in which outcomes are constrained not only by disease refractoriness and relapse, but also by therapy-related toxicity-particularly infections, mucosal injury, and delayed hematopoietic reconstitution. The gut microbiota has emerged as a potentially modifiable layer of host vulnerability and resilience during AML treatment. Microbiome disruption is detectable already at diagnosis, even in antibiotic-naïve patients, and is often characterized by reduced community diversity, depletion of anaerobic taxa linked to short-chain fatty acids (SCFAs) production, and enrichment of pathobiont-associated profiles. During induction, cytotoxic therapy and antimicrobials precipitates diversity loss, domination events, and persistent shifts beyond discharge. Clinically, the most consistent translational signal is the association between baseline or early-treatment microbiome features and infectious outcomes, while emerging data suggest that diagnosis-time microbiome structure may also relate to hematologic recovery kinetics. Mechanistic models converge on pathways linking barrier integrity, microbial metabolites (notably butyrate and other SCFAs), immune calibration, and inflammatory translocation of microbial products. These insights support hypotheses: antimicrobial stewardship may preserve microbiome function; ecosystem repair strategies such as autologous fecal microbiota transfer (A-FMT) are feasible and can restore community structure; and metabolite or nutritional interventions merit evaluation in immunocompromised hosts. Regimen-specific microbiome effects and microbiome-drug interactions suggest that treatment choice could have downstream microbiome-mediated consequences. We synthesize evidence, outline interventional concepts, and define methodological priorities for next-generation trials assessing causality and clinical benefit. Progress will require longitudinal sampling, multi-omic integration (metabolomics, resistomics, and barrier/inflammatory biomarkers), and interventional designs linking microbiome dynamics to clinically meaningful outcomes.},
}

@article {pmid42041382,
year = {2026},
author = {Malinoski, L and Silva, GG and Rodrigues, LKI and Carneiro, LF and Gomes, MP},
title = {How Glyphosate and Its Derivatives Influence Antimicrobial Resistance Emergence and Transmission: A One Health Perspective.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041382},
issn = {2079-6382},
support = {302226/2022-2//National Council for Scientific and Technological Development/ ; SUS2025831000005//Fundação Araucária/ ; },
abstract = {Background/Objectives: Glyphosate-based formulations are globally pervasive pollutants increasingly recognized as potential contributors to antimicrobial resistance (AMR) in environmental microbiomes. Although glyphosate is designed to inhibit plant 5-enolpyruvylshikimate-3-phosphate synthase, it also affects microbial metabolism, stress response, and genetic exchange. This review synthesizes the pathways through which glyphosate, its metabolite aminomethylphosphonic acid (AMPA), and commercial mixtures influence resistance-associated phenotypes and the dissemination of antibiotic resistance (ABR). Methods: A critical synthesis of the literature was conducted to evaluate the mechanistic and ecological interactions between glyphosate exposure and bacterial resistance in soil, aquatic, and host-associated microbiomes. Results: Experimental evidence showed that sublethal glyphosate exposure induced oxidative stress, altered membrane permeability, activated multidrug efflux pumps, and promoted tolerance phenotypes that could modify antibiotic susceptibility. It also enhances mutation rates and horizontal gene transfer processes associated with the emergence of resistance under controlled conditions. At the community level, glyphosate exposure is associated with microbiome restructuring and enrichment of resistance determinants, often without major shifts in overall diversity of the microbiome. These effects have been reported at environmentally relevant concentrations, although the evidence remains largely derived from laboratory and mesocosm studies. Conclusions: Glyphosate acts as both a biochemical modulator of resistance-related phenotypes and an environmental selective pressure that shapes microbial communities. Its widespread use and environmental persistence position it as a context-dependent contributor to the emergence and dissemination of AMR through interacting mechanistic and ecological pathways. Integrating AMR endpoints into pesticide risk assessments and surveillance frameworks is warranted, in addition to expanded field-based validation.},
}

@article {pmid42041383,
year = {2026},
author = {Dahdah, M and Ettouil, Y and Issa, H and Koussih, L and Almutairi, MH and Rouabhia, M and Semlali, A},
title = {Evaluation of the Antifungal Activity of the Polyphenol Formulation Viroelixir Against Candida albicans.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {42041383},
issn = {2079-6382},
abstract = {UNLABELLED: Candida albicans (C. albicans) is an opportunistic fungal pathogen capable of causing a wide range of infections, including mucosal and systemic candidiasis. In the oral cavity, fungi represent a minor component of the microbiome but can significantly contribute to morbidity, particularly under conditions of dysbiosis or immunosuppression. Treatment remains challenging due to increasing multidrug resistance. This study investigates the in vitro antifungal potential of Viroelixir, a standardized polyphenol blend derived from green tea and pomegranate and enriched in catechins (including epigallocatechin gallate, EGCG), ellagitannins (notably punicalagin), ellagic acid, and flavonoids, with particular focus on its potential anti-virulence mechanisms.

METHODS: The effect of Viroelixir on C. albicans growth was assessed using MTT assay, optical density measurements, colony formation, carbohydrate quantification, and pH variation analysis. Biofilm formation, morphological transition, ROS production, necrosis, virulence gene expression, adhesion, and host immune responses were also evaluated.

RESULTS: Viroelixir significantly inhibited C. albicans growth and reduced colony formation compared with untreated controls. The formulation also inhibited biofilm formation and markedly reduced pseudohyphal development, reaching up to 94% reduction under specific treatment conditions. Flow cytometry analysis showed an increase in dead fungal cells, reaching approximately 88% following exposure to Viroelixir at the highest tested concentration. In addition, Viroelixir reduced the transcript levels of several virulence-associated genes, including SAP1-SAP9 and EAP1. In epithelial cell co-culture models, pre-treatment of C. albicans with Viroelixir reduced fungal adhesion and attenuated epithelial inflammatory responses, including IL-6, IL-8, and hBD-2 production, and was associated with reduced activation of the TLR4-NF-κB signaling pathway.

CONCLUSIONS: These findings suggest that the antifungal and anti-virulence effects observed may be associated with the polyphenolic compounds present in the Viroelixir formulation, highlighting its potential as a promising in vitro antifungal candidate against C. albicans.},
}

@article {pmid42041444,
year = {2026},
author = {Gu, BC and Jiang, GY and Tseng, CH and Chen, YJ and Wu, CY and Lin, ZX and Yeh, ZW and Wu, CC},
title = {Rapid Electrochemical Profiling of Fecal Short-Chain Fatty Acids Using Esterification/Dissociation Fingerprints and Artificial Neural Networks.},
journal = {Biosensors},
volume = {16},
number = {4},
pages = {},
pmid = {42041444},
issn = {2079-6374},
support = {112-2221-E-005-087//National Science and Technology Council/ ; 113-2622-E-005-005//National Science and Technology Council/ ; 113-2221-E-005-058//National Science and Technology Council/ ; 114-2221-E-005-047-MY2//National Science and Technology Council/ ; },
mesh = {*Neural Networks, Computer ; *Feces/chemistry ; *Fatty Acids, Volatile/analysis ; Humans ; Esterification ; *Electrochemical Techniques ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Microbiome ; *Biosensing Techniques ; },
abstract = {Short-chain fatty acids (SCFAs) are key biomarkers of gut microbiota activity; however, routine quantification in fecal samples relies largely on chromatography, which is instrument-intensive and throughput-limited chromatography techniques. Herein, we present a rapid machine-learning-assisted electroanalysis platform for SCFAs profiling that integrates a disposable three-electrode planar gold chip with voltammetric fingerprinting and artificial neural network (ANN)-based signal decoupling. To generate orthogonal chemical information and improve the discrimination of structurally similar species, a dual pretreatment strategy combining acid-catalyzed esterification and alkaline dissociation was employed prior to electrochemical analyses. Differential pulse voltammetry (DPV) and cyclic voltammetry (CV) were employed to acquire high-dimensional fingerprints, from which current-, potential-, and area-based descriptors were extracted using a cross-information feature strategy. A hierarchical modeling framework improved total SCFAs prediction by incorporating ANN-predicted propionate and butyrate concentrations as auxiliary inputs. While linear calibration was achievable in standard mixtures, direct linear models performed poorly in real fecal matrices due to strong sample-dependent matrix interference. In contrast, the ANN captured nonlinear relationships among multifeature inputs and suppressed matrix effects. Validation against gas chromatography-mass spectrometry in an independent fecal test cohort (n = 30) demonstrated excellent agreement and low prediction errors, with mean absolute error/root mean square error values of 0.063/0.072 mM (propionic acid), 0.029/0.034 mM (butyric acid), and 0.135/0.202 mM (total SCFAs). The DPV/CV acquisition requires only minutes per sample, whereas pretreatment takes 1~3 h depending on the target route but can be performed in parallel for batch processing; thus, overall throughput is determined mainly by batch pretreatment rather than per-sample instrument time. This electrochemical-ANN workflow provides a portable, high-throughput alternative to chromatography for fecal SCFAs profiling in clinical screening and microbiome research.},
}

*Neural Networks, Computer
*Feces/chemistry
*Fatty Acids, Volatile/analysis
Humans
Esterification
*Electrochemical Techniques
Gas Chromatography-Mass Spectrometry
Gastrointestinal Microbiome
*Biosensing Techniques

@article {pmid42041525,
year = {2026},
author = {Bertoni, G and Ristori, S and Monti, D},
title = {Immunosenescence and Inflammaging as Drivers of Neurodegeneration: Cellular Mechanisms, Neuroimmune Crosstalk, and Therapeutic Implications.},
journal = {Cells},
volume = {15},
number = {8},
pages = {},
pmid = {42041525},
issn = {2073-4409},
support = {DM 1557 11.10.2022//Next Generation EU/ ; },
mesh = {Humans ; *Immunosenescence/immunology ; *Neurodegenerative Diseases/immunology/pathology/therapy ; *Inflammation/immunology/pathology ; Animals ; *Aging/immunology ; *Neuroimmunomodulation ; },
abstract = {Aging is accompanied by profound alterations in immune function, termed immunosenescence, and by a chronic, low-grade inflammatory state known as inflammaging. These processes are increasingly recognized as central drivers of age-related neurodegenerative diseases, including Alzheimer's Disease, Parkinson's Disease, Amyotrophic Lateral Sclerosis and Multiple Sclerosis. In the central nervous system, senescent microglia and astrocytes lose their homeostatic and neuroprotective functions, while systemic immune aging and blood-brain barrier dysfunction further amplify neuroinflammation and impair protein aggregate clearance. This sustained pro-inflammatory environment promotes synaptic dysfunction, neuronal loss and cognitive decline. Here, we synthesize current knowledge of the mechanistic links among immunosenescence, inflammaging, and neurodegeneration, highlighting innate and adaptive immune dysregulation, mitochondrial impairment, and failed resolution pathways. We further discuss emerging therapeutic strategies, including senolytics, immunoceuticals, microbiome-based interventions and advanced drug delivery systems, aimed at restoring immune homeostasis and enhancing brain resilience. By integrating mechanistic and translational insights, this review provides a framework for developing novel interventions to target immune aging in neurodegenerative diseases.},
}

Humans
*Immunosenescence/immunology
*Neurodegenerative Diseases/immunology/pathology/therapy
*Inflammation/immunology/pathology
Animals
*Aging/immunology
*Neuroimmunomodulation

@article {pmid42041582,
year = {2026},
author = {Chandra, H and Yadav, B and Kuhnell, D and Langevin, S and Biesiada, J and Medvedovic, M and Yadav, JS},
title = {Exosomal microRNAs from Alveolar Macrophages Reveal a Protective Role of the Lung Microbiome Against Oncogenic Signaling During PAH Exposure.},
journal = {Cells},
volume = {15},
number = {8},
pages = {},
pmid = {42041582},
issn = {2073-4409},
support = {P30ES006096//NIH /NIEHS/ ; },
mesh = {Animals ; *MicroRNAs/metabolism/genetics ; *Exosomes/metabolism/genetics/drug effects ; *Macrophages, Alveolar/metabolism/drug effects ; Mice ; *Lung/microbiology/drug effects ; Signal Transduction/drug effects ; *Microbiota/drug effects ; Benzo(a)pyrene/toxicity ; Receptors, Aryl Hydrocarbon/metabolism ; Mice, Inbred C57BL ; *Polycyclic Aromatic Hydrocarbons/toxicity ; *Carcinogenesis/drug effects/genetics ; Lung Neoplasms/genetics ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs), such as benzo[a]pyrene (B[a]P), are major risk factors for lung cancer and other diseases, acting through the aryl hydrocarbon receptor (AHR). Alveolar macrophages (AMs) help regulate the lung microenvironment by responding to inhaled toxicants and resident microbiota. Although small extracellular vesicles (sEVs, aka exosomes) released by AMs mediate intercellular communication and immune responses, the influence of lung microbiota on sEV biogenesis and the mechanisms underlying sEV dysregulation during PAH exposure remain unknown. Here, we investigated the interplay between AMs, B[a]P, and lung microbiota, focusing on sEV-associated miRNAs (exo-miRNAs). Murine AMs (MH-S) were exposed to varying B[a]P concentrations in the presence or absence of murine lung microbiota with or without an AHR antagonist. sEVs from each condition were characterized and profiled for miRNA. Distinct miRNA signatures emerged: high-dose B[a]P enriched miRNAs linked to cancer progression, whereas lung microbiota alone or with low-dose B[a]P induced tumor-suppressor miRNAs that limit proliferation and metastasis and promote apoptosis, an effect enhanced by AHR antagonism. Lung microbiota appeared to counteract high-dose B[a]P by modulating tumor-suppressive exo-miRNAs. This study demonstrates that lung microbiota-induced exo-miRNAs critically shape AM-derived sEV-miRNA signaling during PAH exposure. The identified exosomal miRNAs could serve as important exposure biomarkers and therapeutic targets for mitigating B[a]P-induced toxicity and cancer development.},
}

Animals
*MicroRNAs/metabolism/genetics
*Exosomes/metabolism/genetics/drug effects
*Macrophages, Alveolar/metabolism/drug effects
Mice
*Lung/microbiology/drug effects
Signal Transduction/drug effects
*Microbiota/drug effects
Benzo(a)pyrene/toxicity
Receptors, Aryl Hydrocarbon/metabolism
Mice, Inbred C57BL
*Polycyclic Aromatic Hydrocarbons/toxicity
*Carcinogenesis/drug effects/genetics
Lung Neoplasms/genetics

@article {pmid42041649,
year = {2026},
author = {Cheng, AY and Zheng, FM and Chen, J and Chu, CH},
title = {Addressing Research Gaps in Early Childhood Caries: A Comprehensive Review.},
journal = {Dentistry journal},
volume = {14},
number = {4},
pages = {},
pmid = {42041649},
issn = {2304-6767},
support = {17104123//Research Grant Council General Research Fund/ ; },
abstract = {Background: Early childhood caries (ECC) is one of the most common chronic diseases in children and remains unevenly distributed across populations. It is associated with pain, impaired function, and long-term health consequences. Although advances have been made in understanding its aetiology and prevention, important gaps in evidence limit progress in prevention, early detection, and equitable care. Objective: To examine current evidence on ECC and identify key research gaps across biological, behavioral, social, and health system domains. Methods: This narrative review draws on peer-reviewed literature addressing ECC epidemiology, pathogenesis, risk factors, diagnosis, management, and service delivery. The literature was examined to identify areas where evidence is limited, inconsistent, or insufficient to inform clinical practice and public health policy. Results: Research on ECC remains uneven across levels. Longitudinal evidence linking microbiome dynamics, host susceptibility, and lesion progression is limited, restricting causal understanding. Genetic and epigenetic contributions are incompletely defined, particularly in diverse populations. Although socioeconomic gradients are well established, integrative models connecting structural determinants with biological mechanisms are scarce. Emerging diagnostic tools, including biomarkers and artificial intelligence, lack robust evidence demonstrating improved clinical or behavioral outcomes. Implementation research addressing scalability, cost-effectiveness, and equity impact is underdeveloped, especially in low-resource settings. Long-term systemic and developmental consequences of ECC remain insufficiently characterized. Conclusions: Addressing ECC requires integrated and equity-oriented research frameworks that bridge biological, social, diagnostic, and implementation domains. Clarifying these gaps is essential to inform coherent prevention strategies and reduce persistent disparities in child oral health.},
}

@article {pmid42041656,
year = {2026},
author = {Abbinante, A and Barile, G and Antonacci, A and Basso, M and Pascale, F and Bartolomeo, N and Agneta, MT and D'Albis, G and Corsalini, T and Capodiferro, S and Corsalini, M},
title = {Probiotics and Ozonated Olive Oil to Maintain Oral Eubiosis in Stage I and II Periodontitis Patients: A Randomized Triple-Blind Clinical Trial.},
journal = {Dentistry journal},
volume = {14},
number = {4},
pages = {},
pmid = {42041656},
issn = {2304-6767},
abstract = {Background: Researchers are now focusing on new and less invasive therapies to improve the domiciliary maintenance phase of periodontitis. Ozonated olive oil as an alternative to common local antiseptics and the assumption of probiotics to maintain a eubiotic oral microbiome show promising results. However, the literature is still limited on this topic. This RCT aims to investigate the clinical benefits of combining ozonated olive oil products (mouthwash and toothpaste) with probiotics on oral health status in patients with stage I and II periodontitis following the active phase of therapy. Methods: The study followed a triple-blind RCT design. Patients with stage I and II periodontitis were enrolled and randomly assigned to three groups: group A (placebo), group B (effective ozonated olive oil mouthwash and toothpaste), and group C (combined protocol with effective ozonated olive oil and probiotics). Clinical assessment was performed at the first visit and after 30 days, considering Full-Mouth Plaque Score (FMPS), Full-Mouth Bleeding Score (FMBS), and Probing Pocket Depth (PPD). Results: The FMPS percentages showed a significative reduction (p = 0.0002) of 24%, 33%, and 62% observed in group A, group B, and group C, respectively. Also, the FMBS percentages were significantly decreased (p < 0.0001): -15%, -20%, and -49% observed in group A, group B, and group C, respectively. The mean PPD showed significant differences (p < 0.0001): -0.10 mm, -0.40 mm, and -1.10 mm observed in group A, group B, and group C, respectively. Overall, group C showed the best improvement among the considered clinical indexes. Conclusions: The findings of this clinical trial support the use of a combined regime of the antimicrobial and anti-inflammatory effects of ozonated olive oil and the modulation of the oral microbiome of probiotic supplements as an adjunctive domiciliary strategy for patients affected by stage I and II periodontitis.},
}

@article {pmid42041792,
year = {2026},
author = {Lee, S and Welch, CB and Zinka, K and Evans, M and Park, HJ and Lozada-Fernandez, VV and West, FD},
title = {Distinct Gut Microbiome Characteristics Associated with Mental Health Symptoms of Healthy Adults.},
journal = {Brain sciences},
volume = {16},
number = {4},
pages = {},
pmid = {42041792},
issn = {2076-3425},
support = {HATCH #GEO001002//Georgia Experimental Agricultural Station/ ; },
abstract = {Background/Objectives: Mental health conditions, including stress, anxiety, depression, and sleep problems, represent a significant health concern globally. Mounting evidence suggests a link between mental health and the gut microbiome via the gut-brain axis. However, discrepancies in human microbiome data exist due to the heterogeneity in study design and analytical approaches. Thus, this study aimed to explore the gut microbial characteristics associated with self-reported mental health symptoms using multiple analytical methods. Methods: A total of 44 healthy adults, defined as individuals without any major chronic medical conditions, were assessed for mental health symptoms using self-reported questionnaire data. To evaluate gut microbial characteristics, stool samples were collected at six time points over 28 days and underwent 16S rRNA gene sequencing. Differential abundance was assessed via ANCOM-BC, and a random forest classifier was implemented to rank features important for the classification of mental health symptoms. Participants who did not report anxiety, stress, depression, or sleep problems served as the reference group for microbiome comparisons. Results: The proportion of participants with self-reported mental health symptoms was 11.4% (stress), 27.3% (depression), 31.8% (anxiety), and 15.9% (sleep problems). Participants reporting mental health symptoms showed differences in gut microbiome composition compared to asymptomatic participants, including variation in alpha- and beta-diversity. Differential analysis identified specific taxa with higher or lower relative abundance in participants reporting specific mental health symptoms. Random forest feature ranking identified partially overlapping taxa across methods, suggesting candidate associations warranting further investigation. Conclusions: These exploratory findings suggest that self-reported mental health symptoms in otherwise healthy adults are associated with differences in the gut microbiome. The taxa identified in this study represent candidates for validation in larger, independent cohorts.},
}

@article {pmid42041827,
year = {2026},
author = {Day, R and Friedman, D and Cardoso, A and Naghibi, M and Pont, A and Martinez-Blanch, J and Lamelas, A and Chenoll, E and Kakilla, C and Rea, K and Vijayakumar, V},
title = {A Randomised, Double-Blind, Placebo-Controlled Trial of Probiotic and Postbiotic Strains in Healthy Adults with Self-Reported Anxiety: Effects on Mood, Vitality, Quality of Life and Perceived Stress.},
journal = {Brain sciences},
volume = {16},
number = {4},
pages = {},
pmid = {42041827},
issn = {2076-3425},
support = {N/A//Archer Daniels Midland (United States)/ ; },
abstract = {Background: Subclinical psychological symptoms-such as low mood, perceived stress, and poor sleep-affect a large portion of the population and can impair quality of life despite remaining below clinical thresholds. The gut-brain axis has emerged as a promising target for interventions that support emotional and psychological resilience. Probiotics and postbiotics are gaining attention for their potential to modulate mood and stress via microbiome-related mechanisms, but human evidence remains limited, particularly in non-clinical populations. Objectives: We aimed to assess the effects of a two-strain combination of live microorganisms alongside a two-strain combination of heat-treated inactivated microorganisms on outcomes associated with anxiety, mood, perceived stress, and quality of life in healthy adults experiencing mild stress. Methods: This study was conducted in two parts. In Part I, a randomized, double-blind, placebo-controlled study, 100 participants were randomized to receive either a blend of live microorganisms (Bifidobacterium longum CECT 7347 and Lactobacillus rhamnosus CECT 8361) or an identical placebo once daily for 12 weeks. In Part II, a pilot feasibility study, a subset of eight placebo non-responders from Part I received the heat-inactivated preparation of the same bacterial strains in a 6-week trial extension phase. For Parts I and II, the primary outcome was the change in the Hamilton Anxiety Rating Scale (HAM-A). Secondary outcomes included measures of mood (Beck Depression Inventory (BDI); Patient Health Questionnaire-9 (PHQ-9)), stress (state and trait anxiety inventory (STAI); Perceived Stress Scale (PSS)), sleep (Pittsburgh Sleep Quality Index (PSQI)), quality of life (36-item Short Form Survey (SF-36)), gastrointestinal symptoms (Gastrointestinal Symptom Rating Scale (GSRS)), salivary cortisol and microbiome modulation. Results: In Part I, there were no significant effects of the live blend on the HAM-A, indicating that the primary endpoint was not met. In addition, no significant effects were seen on the STAI or PSS scores when compared to the placebo. However, participants consuming the live blend trended toward a reduction in total PHQ-9 scores compared to placebo (p = 0.089), whilst preliminary exploratory analyses suggested an improvement in anhedonia (p = 0.045). Furthermore, there was a significant improvement in the vitality domain of the SF-36 compared to placebo (p = 0.017). On microbiome analysis, it was noted that consumption of the live blend was linked to the preservation of butyrate-producing bacteria, particularly members of the Pseudoflavonifractor genus and the Clostridium SGB6179 species. Furthermore, the abundance of B. longum species was found to be inversely associated with the total PSS Scores. In Part II, supplementation with the inactivated preparation resulted in significant within-group improvements for the vitality (p = 0.006) and social functioning (p = 0.010) domains of the SF-36 and improvements in PSS scores compared to baseline (p = 0.050). Conclusions: Supplementation with either the dual-strain live or inactivated formulations was associated with significant improvements in the vitality domain of the SF-36, whilst participants receiving the inactivated formulation demonstrated lower perceived stress and improved social functioning compared to baseline. Overall, the findings from this pilot study suggest that these two biotic consortia are well-tolerated and may be associated with improvements in measures of vitality in individuals with subclinical psychological symptoms. The subtle observations detected for stress and anhedonia suggest that further well-powered trials are needed to better characterize these findings, potentially in populations with greater baseline symptomatology.},
}

@article {pmid42041878,
year = {2026},
author = {Carlone, J and Ribeiro, ÁCDS and Parisi, A and Giampaoli, S and Fasano, A},
title = {Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041878},
issn = {2079-7737},
abstract = {The growing interest in the role of the gut microbiome in athletic performance has led to the application of various sequencing technologies in this field. This review critically examines the sequencing methodologies used in microbiome studies on physical performance and sport, comparing their advantages, limitations, and applicability. In particular, the focus is on 16S metabarcoding and shotgun metagenomics, evaluating how these methodological approaches influence the interpretation of results in sports contexts. Close attention is directed toward technical challenges, methodological biases, and future perspectives, including emerging technologies and multi-omics approaches. This review aims to bridge the gap between methodological rigor and sports-specific applicability, providing evidence-based methodological guidance to support researchers in designing robust athlete microbiome studies and translating sequencing-derived findings into concrete applications for performance and sports health.},
}

@article {pmid42041903,
year = {2026},
author = {Dogra, S and Arukha, AP and Koul, B and Rabbee, MF},
title = {Redox Reprogramming of the Diseased Liver by Dietary Flavonoids: From Molecular Signalling to Gut-Liver Crosstalk.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041903},
issn = {2079-7737},
abstract = {Liver diseases, including fatty liver, hepatitis, and cirrhosis, remain major global health challenges due to their disruption of metabolic homeostasis and detoxification processes. Redox imbalance plays a central role in liver disease progression by promoting inflammation, hepatic stellate cell activation, mitochondrial dysfunction, and fibrogenesis. Although flavonoids have historically been considered direct reactive oxygen species (ROS) scavengers, emerging evidence indicates that their biological effect at physiological concentrations are primarily mediated through modulation of intracellular redox signalling rather than simple radical neutralisation. This review highlights flavonoids as redox-modulating agents capable of restoring hepatic redox homeostasis through coordinated regulation of molecular pathways. Mechanistically, flavonoids activate the Nrf2-Keap1 axis to enhance endogenous antioxidant defences, including heme oxygenase-1 and glutathione biosynthesis enzyme, while suppressing NF-κB-mediated pro-inflammatory signalling and modulating MAPK and PI3K/Akt pathways. They also regulate mitochondrial redox balance, supporting mitophagy, metabolic adaptation, and cellular resilience to oxidative stress. In addition, flavonoid biotransformation by the gut microbiome improves intestinal barrier integrity, reduces endotoxin-driven hepatic inflammation, and contributes to gut-liver crosstalk. Collectively, these mechanisms position dietary flavonoids as multi-target redox modulators with promising therapeutic potential in chronic liver disease, although further studies are needed to improve their bioavailability and clinical translation.},
}

@article {pmid42041913,
year = {2026},
author = {Wang, T and Wang, Z and Yang, X and Zhang, L},
title = {From Microbial Ecology to Functional Components in Microbe-Host Interactions.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041913},
issn = {2079-7737},
support = {82370785//National Natural Science Foundation of China/ ; tscy20190612//TaiShan Industrial Experts Program/ ; tshw20120206//TaiShan Scholars Program of Shandong Province/ ; },
abstract = {Microbiome research is shifting from a focus on "whole microorganisms" to an emphasis on microbial functional components. This review systematically describes how the effects of microbial communities on the host are mediated by bioactive functional components released by microbes. These components primarily exert their effects through interactions with host Pattern Recognition Receptors (PRRs) and metabolic sensing receptors, thereby regulating host immune, metabolic, and barrier function networks. The biological effects of these functional components are highly context-dependent. Under homeostasis, metabolites such as SCFAs and bile acids promote mucosal immune tolerance and maintain epithelial barrier integrity. However, the same signals can become deleterious under dysbiosis, driving inflammation and contributing to colorectal tumorigenesis. Mechanistic dissection of individual components, such as lipopolysaccharide (LPS), is now propelling a transition in clinical translation from whole-microbe-based interventions toward component-oriented diagnostics and therapeutics. Component-oriented diagnostics and therapeutics use defined microbial molecules rather than whole microorganisms. Microbial nucleic acids (e.g., HPV DNA), metabolites (e.g., SCFAs), and proteins can serve as biomarkers for disease risk, diagnosis, and prognosis. Therapeutic strategies include targeted modulation of beneficial components, neutralization of harmful molecules, and engineered microbial delivery.},
}

@article {pmid42041929,
year = {2026},
author = {Ma, Y and Hu, Y and Zhang, J and Sun, Q and Wang, H and Liu, X and Tian, W and Wang, W and Ma, X and Shao, D and Liu, K and Li, B and Qiu, Y and Ma, Z and Li, Z and Wei, J},
title = {The Gut Microbiome and Metabolome of Domestic Cats Were Altered by the Oral Administration of Complex Probiotics.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
pmid = {42041929},
issn = {2079-7737},
abstract = {Probiotics are commonly applied to maintain the balance of gut microbiota and regulate the intestinal metabolic function of companion animals. In the present study, complex probiotics (Bacillus coagulans SNZ-1969, Bacillus subtilis, and Bacillus licheniformis) were added into the basal diet of domestic cats to investigate their influence on the intestinal microbiome and metabolic characteristics. Results revealed that the alpha diversity of the gut microbiota in the probiotic group was enhanced when compared to the control group. The beta diversity of the gut microbiota was also altered by the oral consumption of the complex probiotics. Compared to the control group, the relative abundance of beneficial microbes (such as Clostridium, Bacteroides, Phocaeicola, and Ruminococcus) in the probiotic group was enhanced, while the relative abundance of opportunistic pathogens (such as Escherichia, Gallibacter, Corynebacterium) was decreased. Additionally, the intestinal metabolic characteristics of domestic cats were also changed. The metabolomic analysis identified 408 differential metabolites between the two groups, and the KEGG function pathway analysis proved that the dominant pathway related to the differential metabolites were the amino acid metabolism, lipid metabolism, carbohydrate metabolism, energy metabolism, endocrine system, digestive system, immune system, and other metabolic pathways. Spearman's correlation analysis revealed that the beneficial microbes had positive correlations with the differential metabolites. In conclusion, the current study demonstrated that oral administration of complex probiotics could regulate overall health and well-being in domestic cats through modulating the gut microbiome and metabolic characteristics.},
}

@article {pmid42042209,
year = {2026},
author = {Guryanova, SV and Belogurova-Ovchinnikova, OY and Ovchinnikova, TV},
title = {Human and Marine Host Defense Peptides for Healthy Skin.},
journal = {Marine drugs},
volume = {24},
number = {4},
pages = {},
pmid = {42042209},
issn = {1660-3397},
support = {22-14-00380-P//Russian Science Foundation/ ; },
mesh = {Humans ; *Aquatic Organisms/chemistry ; *Skin/drug effects/metabolism ; Animals ; Skin Aging/drug effects ; *Antimicrobial Peptides/pharmacology ; *Biological Products/pharmacology ; Wound Healing/drug effects ; *Antimicrobial Cationic Peptides/pharmacology ; Immunity, Innate ; *Peptides/pharmacology ; },
abstract = {The skin serves as the first line barrier of innate immunity, protecting the body from external influences and maintaining its homeostasis. Exogenous and endogenous stress factors alter the structure and functional properties of the skin. The search for compounds capable of counteracting these processes has allowed the identification of peptides as promising ingredients of products for medicinal and cosmetic applications. This review comprehensively examines the mechanisms of action and dermatological applications of two distinct classes of natural products-endogenous human peptides and those derived from marine organisms. Human peptides exhibit numerous biological functions, including antimicrobial and immunomodulatory ones, as well as promoting antioxidant protection and wound healing. Microbiome-associated peptides are an underestimated but powerful regulator of skin aging through immunomodulation, inflammation control, barrier function maintenance, and selection of the proper microbial community. Peptides from marine organisms exhibit significant structural diversity and a broad spectrum of biological activity, including regenerative effects and effects on antibiotic-resistant microorganisms. This review summarizes current data obtained from in vitro, ex vivo, and clinical studies demonstrating a broad potential of peptides for maintaining skin health. Both peptide classes represent powerful, targeted strategies for innovative dermatological interventions aimed at promoting skin rejuvenation, protection, and overall homeostasis.},
}

Humans
*Aquatic Organisms/chemistry
*Skin/drug effects/metabolism
Animals
Skin Aging/drug effects
*Antimicrobial Peptides/pharmacology
*Biological Products/pharmacology
Wound Healing/drug effects
*Antimicrobial Cationic Peptides/pharmacology
Immunity, Innate
*Peptides/pharmacology

@article {pmid42042323,
year = {2026},
author = {Granata, G and Petrosillo, N},
title = {Newer Therapeutics to Selectively Kill Clostridioides difficile and Restore the Microbiome.},
journal = {Infectious disease reports},
volume = {18},
number = {2},
pages = {},
pmid = {42042323},
issn = {2036-7430},
abstract = {BACKGROUND: The antibiotic ibezapolstat and the live biotherapeutic product live-JSLM are promising future approaches for treating Clostridioides difficile infection. Ibezapostat is a highly specific antibiotic for Clostridioides difficile, with minimal impact on the intestinal flora. Live-JSLM is designed to restore healthy intestinal microbiota, thus preventing recurrence of Clostridioides difficile infection. In this narrative review, we reviewed available data on ibezapostat and live-JSLM, considering that they are prototypes of two distinct, unique mechanisms of action against Clostridioides difficile.

METHODS: Data sources: PubMed and SCOPUS databases were searched from 1 January 2012 to 15 November 2025. Original articles reporting data on ibezapolstat and live-JSLM were included.

RESULTS: 31 studies were included. When compared to conventional anti-Clostridioides difficile antibiotics, ibezapolstat had a similar level of effectiveness and minimal impact on the gut microbiota. The available data confirm live-JSLM safety and efficacy in restoring the gut microbiota following the conclusion of the standard anti-Clostridioides difficile antibiotic regimen.

CONCLUSIONS: The results on ibezapolstat efficacy are promising, but require confirmation in larger patient populations through double-blind, randomised phase III trials. In the near future, an integrated approach may enhance the management of Clostridioides difficile infection: starting with highly specific antibiotics, i.e., ibezapolstat, followed by microbiome-based therapies such as live-JSLM.},
}

@article {pmid42042338,
year = {2026},
author = {Jiang, H and Xu, H and Meng, Z and Hao, K and Yang, Y and Zhao, Y and Yao, Q and Li, M},
title = {Field Root-Associated Microbiome Characteristics of Astragalus membranaceus and Its Transcriptomic Response to Purpureocillium lilacinum BP2-7 Treatment.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {4},
pages = {},
pmid = {42042338},
issn = {2309-608X},
support = {[2022ZD01]//Inner Mongolia Natural Science Foundation/ ; },
abstract = {Astragalus membranaceus suffers severe yield and quality losses due to root rot caused by Fusarium solani. To address this, we analyzed the root-associated microbial communities of healthy and diseased plants in northwest China using high-throughput sequencing. Combining community analysis with pot experiments and transcriptomic profiling, we elucidated the molecular mechanisms by which the biocontrol fungus Purpureocilliu lilacinum BP2-7 suppresses root rot. Root rot reshaped root-associated microbial structure, affecting fungal diversity more than bacterial diversity. The antagonistic effect of P. lilacinum BP2-7 against F. solani reached 71.43% in plate assays and 63.7% control efficacy in pot experiments, representing the first report of P. lilacinum application for managing root rot in A. membranaceus. Transcriptomic analysis revealed that P. lilacinum BP2-7 promotes the transition of plants from a damaged to a recovering state by modulating translation and metabolic processes, and enhancing protein homeostasis, while moderately downregulating defense-related responses to alleviate pathogen-induced excessive defense mechanisms. Additionally, twenty candidate genes involved in the direct inhibition of F. solani were identified, suggesting a role in enhancing host resistance. This study supports eco-friendly biocontrol strategies and advances understanding of plant-microbe interactions for managing soil-borne diseases in other important crops.},
}