@article {pmid41835236,
year = {2026},
author = {Ariyan, M and Mikryukov, V and Khalil, H and Gohar, D and Hosseyni Moghaddam, MS and Drenkhan, R and Tedersoo, L},
title = {Impact of plant species, mycorrhizal type, and leaf traits on foliar fungal communities (in a common garden experiment).},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e173358},
pmid = {41835236},
issn = {2210-6340},
abstract = {Foliar fungal communities are essential components of the plant microbiome, playing a vital role in maintaining plant health and influencing ecosystem dynamics. Despite increasing interest in plant-microbe associations, the drivers shaping foliar fungal community composition remain poorly understood, including the roles of host phylogeny, functional traits, and belowground mycorrhizal symbiosis. We used the MycoPhylo experimental field, in which plant species are planted in a replicated, phylogenetically diverse design, to investigate the influence of host plant identity, mycorrhizal type, and leaf functional traits on foliar fungal assemblages. We examined foliar fungal communities across 158 plots representing 110 distinct plant species using a metabarcoding approach. The resulting operational taxonomic units (OTUs) were dominated by Dothideomycetes (44.5%), Tremellomycetes (12.7%), and Taphrinomycetes (9.0%). Functional guild analysis revealed that plant pathogens and saprotrophs were the most abundant ecological groups. Foliar fungal alpha diversity and community composition were significantly influenced by plant growth form and mycorrhizal association. Although plant deciduousness did not affect fungal richness, it significantly affected fungal community composition. The measured leaf traits (hairiness and thickness) showed the least influence on fungal richness. Mantel tests revealed weak, guild-dependent relationships between host phylogenetic distance and foliar fungal community dissimilarity. Moreover, plant phylogenetic eigenvectors accounted for up to 25.8% of the variation in fungal richness. These findings indicate that host phylogeny and plant traits contribute to-but do not solely determine-the structure of foliar fungal assemblages under field conditions.},
}

@article {pmid41835377,
year = {2026},
author = {Alsanie, SA},
title = {Integrated omics approaches with non-thermal food fortification: pathways to personalized nutrition solutions.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1778056},
pmid = {41835377},
issn = {2296-861X},
abstract = {The integration of multi-omics technologies with non-thermal food processing represents a paradigm shift from population-based to precision nutrition interventions. This review synthesizes current advances in genomics, transcriptomics, proteomics, metabolomics, and microbiomics alongside emerging non-thermal technologies, including high-pressure processing, pulsed electric fields, cold plasma, ultrasound, and supercritical fluid extraction, to enable the development of personalized fortified foods. Non-thermal processing offers distinct advantages by preserving heat-sensitive nutrients, enhancing bioavailability through matrix modification, and supporting innovative encapsulation systems that overcome limitations of conventional thermal methods. Multi-omics approaches provide insights into genetic polymorphisms, metabolic phenotypes, and microbiome profiles that influence nutrient metabolism, thereby informing targeted fortification strategies for individuals and subpopulations. We examine nutrient-gene interactions, the impact of non-thermal processing on food matrices and fortificant stability, and the integration of complex omics datasets through systems biology. Key challenges include industrial scalability, harmonization of omics data interpretation, regulatory frameworks for personalized products, equitable access, and genetic data privacy. Emerging opportunities involve artificial intelligence for predictive modeling, biosensor-based monitoring, blockchain-enabled traceability, and convergence with precision medicine. This review provides a comprehensive framework to guide researchers, food technologists, healthcare professionals, and policymakers in advancing omics-guided, non-thermally processed fortified foods as innovative strategies for addressing malnutrition, preventing chronic disease, and promoting optimized health across diverse populations.},
}

@article {pmid41836174,
year = {2026},
author = {Lewis, N and Schätzle, S and Cardone, F and Erpenbeck, D and Wörheide, G and Vargas, S},
title = {Species-specific community structure in the microbiomes and eukaryotic communities associated with Mediterranean golf ball sponges.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20452},
pmid = {41836174},
issn = {2167-8359},
mesh = {*Porifera/microbiology ; Animals ; *Microbiota/genetics ; Phylogeny ; Species Specificity ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 16S/genetics ; *Eukaryota/genetics/classification ; },
abstract = {BACKGROUND: Sponges harbor complex and diverse microbiomes that contribute to the host's fitness and, ultimately, the health of the ecosystems sponges inhabit.

METHODS: Using high-throughput 16S and 18S rRNA amplicon sequencing, we explore the prokaryotic and eukaryotic communities associated with three sympatric Mediterranean demosponges, namely Tethya aurantium, Tethya meloni, and Tethya citrina.

RESULTS: We found species-specific prokaryotic and eukaryotic communities despite the close sympatry of the three Mediterranean Tethya species studied. This offers further support for the phylogenetic nature of the sponge microbiome, where microbial communities reflect the evolutionary ancestry of their host species. These patterns are both present in the eukaryotic and prokaryotic sponge-associated communities, since both display similar levels of host species specificity.},
}

*Porifera/microbiology
Animals
*Microbiota/genetics
Phylogeny
Species Specificity
RNA, Ribosomal, 18S/genetics
RNA, Ribosomal, 16S/genetics
*Eukaryota/genetics/classification

@article {pmid41836235,
year = {2026},
author = {Chang, J and Xiao, S and Su, Y and Sherman, SK and Howe, JR and De Andrade, JP and Hoshi, H and Chan, CHF},
title = {Impact of biliary fungal contamination on outcomes after pancreaticoduodenectomy for pancreatic cancer.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1776853},
pmid = {41836235},
issn = {2234-943X},
abstract = {INTRODUCTION: Many patients with cancer of the pancreatic head will have biliary stenting to relieve malignant obstruction. Biliary stenting is associated with increased rates of bacterial and fungal biliary contamination. Little is known regarding the impact of fungal biliary contamination on postoperative and oncologic outcomes of pancreatic cancer. This study aims to evaluate the effects of fungal biliary contamination on postoperative and oncologic outcomes in patients receiving pancreatoduodenectomy for pancreatic ductal adenocarcinoma (PDAC).

METHODS: A retrospective study of a prospectively maintained single tertiary institutional database was performed, identifying patients with a diagnosis of PDAC from 2015 to 2022 who underwent curative-intent resection and had intraoperative biliary fungal cultures. Primary outcome measures assessed included overall survival (OS) and recurrence-free survival (RFS). The secondary outcome measure was postoperative complication rate. The Kaplan method estimated OS and RFS, and survival curves were compared with the log-rank test. Clinicopathologic variables were assessed for association with multivariable Cox hazard ratio.

RESULTS: Among 82 patients included, 87.8% had preoperative stenting. In stented patients, bacterial and fungal contamination had an incidence of 98.7% and 48.6%, respectively. Patients with positive fungal cultures had higher rates of neoadjuvant chemotherapy utilization than those with negative intraoperative fungal bile cultures (p = 0.05). Positive biliary fungal cultures were not independently associated with risk for postoperative complications nor RFS but were associated with worse OS (HR = 2.11 [1.04-4.26], p = 0.04). In the subgroup of patients who received neoadjuvant chemotherapy, positive fungal bile culture was associated with worse OS (HR = 2.70 [1.11-6.60], p = 0.03), but without more pronounced hematological evidence of systemic immunosuppression before and after chemotherapy.

CONCLUSION: Biliary fungal contamination was not associated with increased risk of postoperative complications in patients with pancreatic cancer but was associated with worse OS, particularly in patients who received neoadjuvant therapy. Investigations regarding the causal relationship between biliary fungus and treatment response and outcome in patients with PDAC are warranted.},
}

@article {pmid41836334,
year = {2025},
author = {Corley, C and Swinton, C and McElory, T and Sridharan, B and Thomas, J and Cronin, B and Sridharan, V and Robeson, MS and Allen, AR},
title = {Implications of Cyclophosphamide, Methotrexate, and 5-Flurouracil Chemotherapy on Hippocampal-Dependent Cognition and Gut-Microbiome.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {},
pmid = {41836334},
issn = {2813-4338},
support = {R25 GM083247/GM/NIGMS NIH HHS/United States ; },
abstract = {Chemotherapy-induced cognitive impairment, also called "chemobrain", has been heavily researched as a major side effect of cancer treatment. Although breast cancer has a 91% survival rate in the U.S., this rate is significantly lower in developing countries. Cancer survivors often experience chemobrain which can decrease their quality-of-life post-chemotherapy. The presented study evaluates potential mechanisms for long-term symptoms in cyclophosphamide, methotrexate, and 5-fluorouracil (CMF)-induced cognitive impairments and implications of CMF on the microbiome. Twelve-week-old C57/B6J female mice were treated with a combination of CMF once a week for 4 weeks. Spatial memory was tested with the Morris water maze. Hippocampal tissues were used to probe for immediate-early genes (IEGs) with western blotting techniques. Fecal matter was collected to assess microbial community composition via 16S rRNA gene sequencing. In this study, we showed that chemotherapy impaired spatial memory during the Morris water maze trials and resulted in a significant decrease in immediate early genes (IEGs) c-Fos, Arc, and Zif286 expression. Comparing Alpha diversity, there were no significant differences identified amongst taxa within the CMF group compared to the saline group for Pielou's evenness. However, Beta diversity qualitative metrics, Jaccard and Unweighted Unifrac were significantly different. These results suggest that continual memory deficits may be associated with alterations in synaptic plasticity and long-term potentiation.},
}

@article {pmid41836369,
year = {2026},
author = {Kucharski, R and Kosiński, A and Kalinowski, L and Kaźmierczak-Siedlecka, K},
title = {Ipilimumab, -omics, and head and neck cancers-update in 2025.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1737862},
pmid = {41836369},
issn = {1664-3224},
mesh = {Humans ; *Ipilimumab/therapeutic use/adverse effects ; *Head and Neck Neoplasms/drug therapy/immunology/etiology ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; Nivolumab/therapeutic use ; Immunotherapy/methods ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; CTLA-4 Antigen/antagonists & inhibitors/immunology ; *Antineoplastic Agents, Immunological/therapeutic use ; },
abstract = {Immunotherapy employing immune checkpoint inhibitors (ICIs) represents a pivotal approach for the management of recurrent and metastatic head and neck cancers (HNCs). Ipilimumab is a fully human monoclonal IgG1κ antibody against cytotoxic T-lymphocyte antigen-4 (CTLA-4), which can be introduced as a monotherapy or dual immunological regimen with nivolumab (anti-programmed death protein 1, PD-1). The background of the use of these monoclonal antibodies as combination immunotherapy is strongly associated with their different mechanisms of action. CTLA-4 and PD-1 are able to regulate the function of T cells through different mechanisms. Despite the better efficacy of immunotherapy with ipilimumab + nivolumab in HNCs observed in some cases, the overall effect regarding the comparison of ipilimumab versus ipilimumab + nivolumab is still unclear. The microbiome is one of the biomarkers that affect the response to immunotherapy with ICIs, including ipilimumab. Nevertheless, there is a clear lack of data in this context with regard to HNCs. The beneficial signature of the microbiome contributes to the prevention of the immune-related adverse events caused by ipilimumab. Notably, the incidence of gastrointestinal side effects induced by ICIs is significantly increased in the dual regimen with ipilimumab + nivolumab, which affects its recommendation for patients with HNCs.},
}

Humans
*Ipilimumab/therapeutic use/adverse effects
*Head and Neck Neoplasms/drug therapy/immunology/etiology
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects
Nivolumab/therapeutic use
Immunotherapy/methods
Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects
CTLA-4 Antigen/antagonists & inhibitors/immunology
*Antineoplastic Agents, Immunological/therapeutic use

@article {pmid41836373,
year = {2026},
author = {Kim, GC and Do, JS and Kim, SH and Yoon, JH and Kim, J and Jeon, D and Hitayezu, E and Mauliasari, IR and Koo, N and Kim, JJ and Seo, JY and Lee, SB and Nam, KT and Cha, KH and Kwon, HK and Seong, JK},
title = {Akkermansia muciniphila primes lung-resident antiviral immunity via the gut-lung axis during SARS-CoV-2 infection.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1762843},
pmid = {41836373},
issn = {1664-3224},
mesh = {Animals ; *COVID-19/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Mice ; *SARS-CoV-2/immunology ; *Lung/immunology/virology/pathology/microbiology ; Mice, Transgenic ; *Akkermansia/immunology ; Cytokines ; Humans ; Disease Models, Animal ; },
abstract = {INTRODUCTION: The gut microbiota plays a central role in shaping systemic immunity and modulating the gut-lung axis, which is crucial during respiratory infections such as COVID-19. SARS-CoV-2 infection is known to disrupt the gut microbiome, but the downstream functional impacts on microbial metabolism and host immune responses remain insufficiently understood.

METHODS: Using K18-hACE2 transgenic mice, researchers investigated the effects of SARS-CoV-2 variants (WA and Omicron) on the gut microbiome and host immunity. Microbial composition and functional profiles were assessed post-infection. To test the therapeutic potential of Akkermansia muciniphila (A. muciniphila), live bacteria were administered prophylactically, and various outcomes were evaluated, including weight loss, lung pathology, immune cell phenotypes, and cytokine production.

RESULTS: In K18-hACE2 transgenic mice infected with SARS-CoV-2, there was a marked reduction in gut microbial diversity, accompanied by a consistent enrichment of A. muciniphila. This microbial shift was associated with functional disruptions in key metabolic pathways, particularly those involved in glycosaminoglycan degradation and lipid metabolism, suggesting a broader impact of infection on microbial functionality. Remarkably, prophylactic administration of live A. muciniphila prior to infection led to significant protective effects. Treated mice exhibited reduced weight loss and improved lung histopathology compared to untreated controls. Local antiviral immune responses in the lung were notably enhanced without triggering excessive systemic inflammation. Mice receiving A. muciniphila also demonstrated elevated production of Th2 and Th17 cytokines, robust expansion of tissue-resident memory T cells, and the formation of inducible bronchus-associated lymphoid tissue (iBALT)-all indicative of potentiated mucosal immunity. These findings highlight a functional role for A. muciniphila not only as a microbial signature of COVID-19-associated dysbiosis but also as an active modulator of host immune responses during respiratory viral infections.

DISCUSSION: These findings position A. muciniphila as both a biomarker of COVID-19-related gut dysbiosis and a potent live biotherapeutic candidate for respiratory infections. Its ability to enhance mucosal immune responses through gut-lung axis modulation highlights its promise in prophylactic strategies against viral respiratory diseases, including SARS-CoV-2.},
}

Animals
*COVID-19/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Mice
*SARS-CoV-2/immunology
*Lung/immunology/virology/pathology/microbiology
Mice, Transgenic
*Akkermansia/immunology
Cytokines
Humans
Disease Models, Animal

@article {pmid41836398,
year = {2026},
author = {Li, X and Wang, Q and Yuan, Q and Wang, L},
title = {The intratumoral microbiome in colorectal cancer: origins, microenvironmental interactions, and new horizons in precision medicine.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1795736},
pmid = {41836398},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/immunology ; *Tumor Microenvironment/immunology ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; Animals ; *Microbiota ; },
abstract = {As a key functional component of the tumor microenvironment (TME), the intratumoral microbiome in colorectal cancer (CRC) has revolutionized the traditional paradigm of the "sterile tumor." Far from being mere "bystanders," these intratumoral microbes act as key drivers deeply implicated in remodeling the TME, influencing tumor progression, and determining therapeutic responses, thus necessitating a comprehensive synthesis of their complex biological characteristics and potential for clinical translation. Therefore, this review systematically summarizes the potential origins, community characteristics, and anatomical heterogeneity of the intratumoral microbiome. It further explores the precise mechanisms driving tumor progression, including the induction of genomic instability, metabolic reprogramming, epigenetic regulation, and immune microenvironment remodeling. We highlight the clinical utility of intratumoral microbes in CRC diagnosis, prognosis, and therapeutic prediction, while also introducing novel intervention strategies based on nanomedicine, engineered probiotics, and phage therapy. Finally, critical challenges such as contamination control in low-biomass samples, sampling heterogeneity, and the delineation of causality are scrutinized, aiming to provide new perspectives for the development of microbiome-guided precision medicine in CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/therapy/immunology
*Tumor Microenvironment/immunology
*Precision Medicine/methods
*Gastrointestinal Microbiome
Animals
*Microbiota

@article {pmid41836406,
year = {2026},
author = {Guo, Z and Yang, J and Zang, R and Yang, Y and Wang, Q and Xu, C},
title = {The brain-gut-skin axis in inflammatory and disfiguring skin diseases: mechanistic insights, clinical correlations, and therapeutic strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1737303},
pmid = {41836406},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Skin Diseases/therapy/etiology/metabolism/immunology/microbiology ; *Skin/immunology/metabolism/pathology ; Animals ; *Brain-Gut Axis/immunology ; *Brain/metabolism/immunology ; Inflammation ; Dysbiosis ; },
abstract = {Emerging evidence suggests that the brain-gut-skin axis (BGSA) plays a critical role in the pathogenesis of inflammatory and disfiguring skin diseases. Conditions such as acne, atopic dermatitis, psoriasis, rosacea, vitiligo, and alopecia areata, once regarded as localized disorders driven mainly by cutaneous immune dysfunction, are now recognized as systemic conditions associated with neuroendocrine stress responses, gut microbial dysbiosis, and chronic low-grade inflammation. Mechanistic studies elucidate the intricate interorgan communication mediated by microbial metabolites (e.g., short-chain fatty acids and tryptophan derivatives), cytokine networks, neuropeptides, and hypothalamic-pituitary-adrenal (HPA) axis signaling. Building on these insights, therapeutic strategies are evolving rapidly. Microbiome-directed interventions (probiotics, postbiotics, dietary modification, and fecal microbiota transplantation), together with psychoneuroimmunological approaches, have shown potential to alleviate disease severity. Integrative therapies, including traditional herbal medicine, offer promising effects; however, we emphasize that mechanistic depth and robust clinical validation for these modalities are currently limited. This review integrates mechanistic findings, clinical correlations, and emerging therapeutic approaches, while critically distinguishing between correlation and causation. Future studies should emphasize longitudinal multi-omics analyses and standardized clinical trials to clarify causal pathways and guide precision, patient-centered management for systemic and cutaneous health.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Skin Diseases/therapy/etiology/metabolism/immunology/microbiology
*Skin/immunology/metabolism/pathology
Animals
*Brain-Gut Axis/immunology
*Brain/metabolism/immunology
Inflammation
Dysbiosis

@article {pmid41836424,
year = {2026},
author = {Du, Q and Wang, X and Shi, Z and Chen, H and Zhang, Y and Wang, R and Mou, Z and Kong, L and Zhou, H},
title = {Dysbiosis of intestinal microbiota in patients with neuromyelitis optica spectrum disorders.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1747643},
pmid = {41836424},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Neuromyelitis Optica/microbiology/drug therapy/metabolism/immunology ; Female ; Male ; *Dysbiosis/microbiology ; Adult ; Middle Aged ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Immunosuppressive Agents/therapeutic use ; Longitudinal Studies ; *Bacteria/genetics/classification ; Metabolomics/methods ; Metabolome ; },
abstract = {OBJECTIVE: This study aimed to explore the specific microbial signatures and metabolomic profiles of fecal microbiota in patients with neuromyelitis optica spectrum disorders (NMOSD) and assess the effects of immunosuppressants on their gut microbiota using a longitudinal cohort study.

METHODS: We enrolled 21 treatment-naïve NMOSD patients and 21 matched healthy controls (HCs). Fecal microbial composition and metabolomic profiles were compared between groups using 16S rRNA gene sequencing and ultra-high-performance liquid chromatography-mass spectrometry. Subsequently, fecal samples from NMOSD patients were collected and reassessed after immunosuppressant treatment.

RESULTS: The gut microbial composition and metabolomic profiles of NMOSD patients were distinct from those of HCs. The α-diversity metrics were significantly higher in NMOSD patients than in HCs (P <0.001). Microbiome alterations in NMOSD patients were characterized by increased abundances of Streptococcus and Ruminococcus, and decreased abundances of Faecalibacterium, Ralstonia, and Pseudomonas at the genus level (all with linear discriminant analysis scores > 4 and P < 0.001). Additionally, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis identified 19 differentially abundant metabolites and 44 altered metabolic pathways in NMOSD patients compared to HCs. Immunosuppressive treatment for over six months may reduce these differences, shifting the gut microbiota composition and metabolite profiles of NMOSD patients closer to those of HCs.

INTERPRETATION: Our study revealed significant gut microbiome dysbiosis and metabolic abnormalities in patients with NMOSD, which were markedly alleviated after six months of immunosuppressive treatment. These preliminary findings suggest the gut microbiota biomarkers could serve as potential therapeutic targets in the future.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Neuromyelitis Optica/microbiology/drug therapy/metabolism/immunology
Female
Male
*Dysbiosis/microbiology
Adult
Middle Aged
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Immunosuppressive Agents/therapeutic use
Longitudinal Studies
*Bacteria/genetics/classification
Metabolomics/methods
Metabolome

@article {pmid41836754,
year = {2025},
author = {Gan, G and Chen, R and Zheng, P and Long, K and Cheng, KKY and Sulaiman, JE and Huang, X},
title = {Oral pathogens meet the gut microbiome: new mechanistic insights on systemic disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1673512},
pmid = {41836754},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; Inflammation/microbiology ; Probiotics ; Animals ; Fusobacterium nucleatum/pathogenicity ; },
abstract = {The oral-gut axis represents a critical bidirectional pathway linking oral microbiota to systemic health. Dysbiosis of the oral microbiome, driven by pathogens like Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus species, and Helicobacter pylori, disrupts gut ecology via direct translocation, metabolite signaling (e.g., TMAO, SCFAs), and immune crosstalk (e.g., Th17). This leads to gut barrier dysfunction, systemic inflammation, and metabolic disturbances, contributing to diverse diseases beyond the oral cavity. Evidence supports causal links with conditions including rheumatoid arthritis, cardiovascular diseases, neurodegenerative disorders, metabolic syndrome, and gastrointestinal cancers. Emerging diagnostic tools exploit these oral pathogens as biomarkers for non-invasive disease detection. Therapeutic strategies, such as probiotics, dietary interventions, and periodontal therapy, target this axis to restore microbial homeostasis and ameliorate systemic inflammation. Future research must focus on longitudinal human studies and multi-omics approaches to elucidate mechanistic details and develop effective clinical interventions for preventing and managing systemic diseases linked to oral-gut microbial dysbiosis.},
}

Humans
*Dysbiosis/microbiology
*Gastrointestinal Microbiome
*Mouth/microbiology
Inflammation/microbiology
Probiotics
Animals
Fusobacterium nucleatum/pathogenicity

@article {pmid41836788,
year = {2026},
author = {Cha, JH and Jeong, SA and Ye, BS and Lee, I and Jung, BY},
title = {Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2643036},
pmid = {41836788},
issn = {2000-2297},
abstract = {INTRODUCTION: Dementia poses a growing burden in the aging population, prompting the search for noninvasive biomarkers for early detection.

MATERIALS AND METHODS: We performed shotgun metagenomic sequencing of tongue-coating samples from older adults with dementia (n = 30) and cognitively healthy controls (n = 28) to identify oral microbiome signatures.

RESULTS: The analysis revealed distinct microbial compositions associated with dementia, including an enrichment of Veillonella parvula in dementia patients, whereas Lautropia dentalis was more abundant in healthy controls. We also identified functional alterations in the microbiome in the dementia group, including increased abundance of the histidine degradation and biotin biosynthesis pathways, whereas ubiquinol biosynthesis was more abundant in the healthy control group. The abundance of several microbial taxa and metabolic pathways were correlated with scores on the Korean Mini-Mental State Examination 2nd edition (K-MMSE), a clinical assessment of dementia severity. Prevotella pleuritidis, Actinomyces sp., Leptotrichia buccalis, and Leptotrichia sp. were positively correlated, whereas Oribacterium parvum was negatively associated with K-MMSE scores. Among the metabolic pathways, glutamine/glutamate biosynthesis was positively correlated with cognitive performance.

CONCLUSIONS: These results suggest that specific oral taxa and their metabolic functions are associated with cognitive status and may reflect underlying neurodegenerative processes.},
}

@article {pmid41836789,
year = {2026},
author = {Manzoor, M and Pussinen, PJ and Saarela, RK and Pitkälä, K and Hiltunen, K and Mäntylä, P},
title = {Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2641915},
pmid = {41836789},
issn = {2000-2297},
abstract = {BACKGROUND: The denture-associated oral microbiome (DAOM) may act as reservoirs of pathogenic microorganisms with potential health effects.

OBJECTIVES: To characterize the compositional and functional activity of the DAOM in dentate and edentulous older adults residing in long-term care facilities (LTCFs).

METHODS: Participants (51 dentate and 56 edentulous) aged ≥64 years were recruited from the Finnish Oral Health Studies in Older Adults. Clinical oral examinations were performed, and biofilm samples for shotgun metagenomics were collected from the acrylic surface of removable dentures. Diversity indices, taxonomic composition, and functional pathways were assessed to characterize DAOM.

RESULTS: Alpha diversity was similar, whereas beta diversity showed modest differences between groups. Dentate participants had a higher abundance of Streptococcus mutans, Veillonella parvula, and Parascardovia denticolens, whereas edentulous participants were enriched with Haemophilus parainfluenzae and Propionibacterium acidifaciens. Edentulous participants had reduced microbial network stability and interconnectedness but highly active microbial metabolic functions, particularly those associated with Streptococcus pneumoniae.

CONCLUSION: Although tooth loss does not markedly alter the overall microbial diversity of DAOM, it is associated with distinct taxonomic and functional shifts. Edentulous individuals have less stable and less interconnected microbial networks alongside heightened metabolic activity, reflecting notable changes in the DAOM of older adults living in LTCFs.},
}

@article {pmid41837390,
year = {2026},
author = {Abagnale, V and Palacin-Lizarbe, C and Paul, D and Kerttula, J and Ronkainen, J and Siljanen, HMP},
title = {Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70279},
pmid = {41837390},
issn = {1462-2920},
support = {342362//Academy of Finland/ ; 346516//Academy of Finland/ ; 361980//Academy of Finland/ ; 337550//Academy of Finland/ ; 357905//Academy of Finland/ ; 359343//Academy of Finland/ ; 202400252//Maj ja Tor Nesslingin Säätio/ ; 20231200//OLVI-Säätiö/ ; },
mesh = {*Picea/microbiology ; *Lichens/microbiology ; *Nitrous Oxide/metabolism ; Finland ; Oxidoreductases/genetics/metabolism ; Taiga ; *Bacteria/metabolism/genetics/isolation & purification/classification ; Forests ; Oxidation-Reduction ; Oxygen/metabolism ; },
abstract = {The nitrous oxide (N2O) dynamics in boreal forests are better known at the ecosystem scale, with greater uncertainty associated with specific ecosystem compartments. We investigated the N2O dynamics of the lichen Platismatia glauca in boreal forests near Kuopio, North Savo, Finland. At the study sites, P. glauca is the most abundant lichen colonising Norway spruce (Picea abies). Despite their abundance, the contribution of epiphytic lichens like P. glauca to N2O dynamics in boreal forests has received little attention. By incubating P. glauca, we assessed the effects of moisture, temperature, and oxygen availability on its N2O dynamics. We observed net N2O consumption potential, particularly at +5°C at aerobic condition. Quantitative real-time PCR analysis targeting the N2O reductase gene fragment (nosZ) revealed that it was present and active in both in situ and incubated lichens. nosZ transcription was higher at +5°C. Clade I nosZ was dominant, with most sequences affiliated with the order Rhizobiales. We confirmed the presence of nosZ gene with targeted metagenomics sequencing. Our results demonstrate that P. glauca acts as a net consumer of N2O, with potential ranging between 0.1 and 0.4 ng N2O-N g DW[-1] h[-1] under aerobic conditions.},
}

*Picea/microbiology
*Lichens/microbiology
*Nitrous Oxide/metabolism
Finland
Oxidoreductases/genetics/metabolism
Taiga
*Bacteria/metabolism/genetics/isolation & purification/classification
Forests
Oxidation-Reduction
Oxygen/metabolism

@article {pmid41837427,
year = {2026},
author = {Xu, J and Zhang, Y and Shi, L and Wang, H and Zeng, M and Lu, Z},
title = {Comparative analysis of the lung microbiota in patients with lung cancer, chronic obstructive pulmonary disease, and community-acquired pneumonia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0045025},
doi = {10.1128/spectrum.00450-25},
pmid = {41837427},
issn = {2165-0497},
abstract = {Respiratory diseases pose a significant global public health challenge. Extensive research indicates that respiratory conditions are influenced by lung microbiota; however, the relationships between alterations in pulmonary microbiota and various respiratory diseases remain unclear. This study explores the characteristics and distinctions of lung microbial communities in patients with lung cancer (LC), chronic obstructive pulmonary disease (COPD), and community-acquired pneumonia (CAP). The research involved 114 patients and employed culturomics and 16S rRNA gene sequencing to analyze bronchoalveolar lavage fluid samples. Through culturomics, 168 bacterial species were identified, with variations in bacterial profiles observed across the different diseases. Sequencing results indicated that the dominant phyla among the three groups were Bacillota, Bacteroidota, Pseudomonadota, Actinomycetota, and Fusobacteriota, consistent with the culturomics findings. Notably, the CAP group exhibited higher species richness compared to the LC and COPD groups, with significant differences in beta-diversity among the three groups. Specific bacterial genera, such as Alloprevotella, Abiotrophia, and Mycoplasma, were distinguished as indicative taxa for the LC, COPD, and CAP groups, respectively. Utilizing random forest modeling and receiver operating characteristic curve analysis, several key bacterial genera were identified as capable of differentiating between these diseases. The study highlights distinct differences in lung microbiota among patients with LC, COPD, and CAP, potentially serving as a reference for diagnosis, suggesting that disease-specific microenvironments may influence local microbial communities, thus providing evidence for associations between lung microbiota and various respiratory diseases that warrant further investigation.IMPORTANCEThe human lung microbial community plays a crucial role in various respiratory diseases by regulating the lung's immune system and maintaining lung homeostasis. However, there is a paucity of comparative studies examining the characteristics of the pulmonary microbiome in common respiratory diseases, such as lung cancer (LC), chronic obstructive pulmonary disease (COPD), and community-acquired pneumonia (CAP). This study aims to explore the differences in lung microbiomes among these conditions. By employing culturomics and 16S rRNA sequencing technology, we identified significant variations in their lung microbiota. Notably, Alloprevotella, Abiotrophia, and Mycoplasma were identified as indicative taxa for the LC, COPD, and CAP groups, respectively. This research is essential for enriching the database of cultivable lung bacteria and investigating the interactions between specific strains and diseases at the species level, and identifying potential biomarkers and therapeutic targets.},
}

@article {pmid41837476,
year = {2026},
author = {Jung, DH and Cha, JM and Kim, HN and Lee, YR and Nam, GM and Lee, CK and Kim, CH and Lim, HS and Lee, JY and Lim, HS},
title = {Effect of Low-Lactose Processed Milk on Clinical Symptoms and Gut Microbiome Modulation in Lactose-Intolerant Adults.},
journal = {Journal of medicinal food},
volume = {29},
number = {2},
pages = {61-70},
doi = {10.1177/1096620X251412892},
pmid = {41837476},
issn = {1557-7600},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Lactose Intolerance/microbiology/diet therapy/metabolism ; Adult ; *Lactose/metabolism/analysis ; Female ; Male ; Middle Aged ; *Milk/metabolism/chemistry ; Breath Tests ; Animals ; Body Composition ; Feces/microbiology ; Young Adult ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {This study aimed to evaluate the effects of low-lactose processed milk consumption on body composition, clinical indicators, hydrogen breath levels, and gut microbiome changes in Korean adults with lactose intolerance. A total of 32 participants diagnosed with lactose intolerance, as determined by a hydrogen breath test, were enrolled in the study. During the 30-day intervention period, participants consumed one serving per day of banana-flavored milk containing 10.2 g of lactose. Stool and breath samples were collected before and after the intervention to assess changes in gut microbiota composition and lactose malabsorption. Following the intervention, significant improvements were observed in body composition, including reductions in body fat percentage (P < .001) and increases in fat-free mass (P < .001), skeletal muscle mass (P < .001), and soft-tissue lean mass (P < .001). Blood pressure also decreased; however, no significant changes were observed in hematological markers. Hydrogen breath test results demonstrated a significant reduction in hydrogen breath levels, and 40.6% of participants were reclassified as negative for lactose intolerance post-intervention. While no significant changes were observed in alpha diversity or overall microbial composition across all participants, a significant increase in the relative abundance of the Weissella confusa group (P = .007) was detected in individuals who tested negative for lactose intolerance after consuming the intervention food. These findings suggest that consuming low-lactose processed milk improves lactose intolerance, body composition, and gut microbiota composition, providing a feasible dietary strategy for managing lactose intolerance in adults.},
}

Humans
*Gastrointestinal Microbiome
*Lactose Intolerance/microbiology/diet therapy/metabolism
Adult
*Lactose/metabolism/analysis
Female
Male
Middle Aged
*Milk/metabolism/chemistry
Breath Tests
Animals
Body Composition
Feces/microbiology
Young Adult
Bacteria/classification/isolation & purification/genetics

@article {pmid41837494,
year = {2026},
author = {Liu, S and Wang, S and Zhang, J and Tao, C and Xu, X and Wang, Z and Lv, N and Dong, M and Shen, Z and Li, C and Yang, J and Li, R and Shen, Q and Kowalchuk, GA},
title = {Host-mediated rhizosphere microbiome transfer suppresses Fusarium oxysporum in banana.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71071},
pmid = {41837494},
issn = {1469-8137},
support = {ZDYF2024KJTPY003//The key research and development program of Hainan Province, China/ ; ZDYF2025XDNY087//The key research and development program of Hainan Province, China/ ; KJJQ2025018//Fundamental Research Funds for the Central Universities/ ; KJYQ2025053//Fundamental Research Funds for the Central Universities/ ; 2023YFD1901402//National Key Research and Development Program of China/ ; //Priority Academic Program Development of the Jiangsu Higher Education Institutions (PAPD)/ ; HZ610X25070//Achievement Transformation Fund project of Sanya Research Institute of Nanjing Agricultural University/ ; 42477316//National Natural Science Foundation of China/ ; },
abstract = {A plant's phenotype is determined by the traits of both the plant itself and its associated microbiome. However, we still have a poor understanding of the extent to which plant microbial recruitment contributes to disease resistance. We conducted a cross-inoculation experiment in which rhizosphere microbiomes from Fusarium wilt-resistant and susceptible banana varieties were collected and used to colonize the next planting cycle, and microbiome dynamics during recruitment and transfer were tracked. Culture-based approaches were used to construct synthetic microbial communities (SynComs) and test the effects of variety-specific metabolites on isolated strains. Transferring the rhizosphere microbiome from a highly resistant variety to a susceptible variety reduced Fusarium wilt pathogen abundance by 37.65% compared with transferring the susceptible plant's microbiome, while sterilized microbiomes had no detectable effect. Constructed SynComs recapitulated the suppressive effects of their source microbiomes, and metabolites derived from the highly resistant variety, characterized by enrichment of shikimic acid, stearic acid, and D-(-)-ribofuranose, promoted the growth of these beneficial microbes. Our results highlight that plant resistance levels are largely determined by the plant's ability to recruit a disease-suppressive microbiome, suggesting that enhancing microbial recruitment may represent an avenue to improve the disease resistance of susceptible varieties.},
}

@article {pmid41837593,
year = {2026},
author = {Mailem, RC and Tsai, PW and Tayo, L and Hsueh, CC and Hsieh, CY and Chen, BY},
title = {Uncovering the Redox and Immunoregulatory Basis of the Chinese Herbal Formula Ping An Fang Yu Yin using Network Pharmacology and In Silico Target Profiling.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113816128418247251211153057},
pmid = {41837593},
issn = {1873-4286},
abstract = {INTRODUCTION: Ping An Fang Yu Yin (PAFYY) is a traditional Chinese herbal tea formula commonly used to treat respiratory infections, including COVID-19. Previous research indicates potential antiinflammatory activities; however, the underlying mechanisms remain unclear. This study aimed to investigate the mechanisms underlying the therapeutic effects of PAFYY, specifically its electron-transport and bioenergetic properties, through network pharmacology, electrochemical analysis, and Microbial Fuel Cell (MFC) assessments.

METHODS: Active compounds and their respective targets were identified via database searches. Proteinprotein interaction networks were constructed using the STRING database and further analyzed using Cytoscape and MCODE software. Molecular docking was employed to assess the binding affinity between identified key compounds and their targets. Cyclic voltammetry (CV) and MFC assays evaluated the electrontransport characteristics of PAFYY water and ethanol extracts.

RESULTS: The analysis identified 298 active compounds associated with 1,940 biological targets, highlighting key targets including EP300, CREBBP, ESR1, AKT1, MAPK3, MAPK1, and STAT3. GO and KEGG pathway enrichment analyses revealed that PAFYY significantly influences immune system processes and neuronal signaling pathways. Molecular docking confirmed the anti-inflammatory and antiviral potential of the identified active compounds. Additionally, electrochemical studies demonstrated that PAFYY contains electroactive substances mediating electron-driven redox reactions.

DISCUSSION: Recent studies have demonstrated that traditional Chinese herbal teas contain electron shuttles capable of mediating electron transfer in electrogenic bacteria. Emerging evidence further indicates that electroactive plant polyphenols can modulate microbial ecology through redox-mediated mechanisms. Our findings suggest that PAFYY may act on the microbiota-immune axis, with its electron-shuttling constituents contributing not only to direct cellular effects and antioxidant activity but also to modulation of the gut microbiome in ways that support antiviral immunity and attenuate inflammation. These results may inform future research into the mechanistic basis of medicinal herbs, while highlighting the potential of MFCs as a functional screening platform for identifying bioactive redox compounds.

CONCLUSION: The anti-COVID-19 properties of PAFYY may be largely attributed to its electron-transport capabilities, mediated through electroactive compounds. These findings provide novel insights into the mechanistic basis of traditional Chinese medicine prescriptions, potentially enhancing their therapeutic application.},
}

@article {pmid41837716,
year = {2026},
author = {Pantiukh, K and Krigul, KL and Aasmets, O and Org, E},
title = {Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0011426},
doi = {10.1128/msystems.00114-26},
pmid = {41837716},
issn = {2379-5077},
abstract = {UNLABELLED: Metagenomic profiling has advanced the understanding of microbe-host interactions. However, widely used read-based approaches are limited by incomplete reference databases and the inability to resolve strain-level variation. Here, we present a scalable, genome-resolved framework that integrates population-specific metagenome-assembled genomes (MAGs) to discover novel species, within-species diversity, and disease associations. From 1,878 deeply sequenced samples in the Estonian Microbiome Cohort (EstMB-deep), we reconstructed 84,762 MAGs representing 2,257 species, including 353 (15.6%) previously uncharacterized species reaching up to 30% relative abundances in some individuals. We integrated these MAGs with the Unified Human Gastrointestinal Genome collection to create an expanded reference (GUTrep), enabling profiling of 2,509 EstMB individuals and testing associations with 33 prevalent diseases. Of the 25 diseases with significant associations, 8 involved newly identified species, underscoring the value of population-specific MAGs. To quantify within-species diversity, we developed the genome unit number (GUN), a novel MAG-based metric that informed within-species analyses. Based on normalized GUN, we prioritized Odoribacter splanchnicus, a prevalent species with the lowest within-species heterogeneity, yielding sufficient power for a within-species association study. We identified two dominant genome units, GU-N1 and GU-N2, with distinct gene repertoires and divergent disease associations. Notably, GU-N1 was negatively associated with gastritis, duodenitis, and hypertensive heart disease, associations undetected at the species level. Our study expands the human gut reference landscape, demonstrates the importance of population-specific MAGs for uncovering novel microbial diversity, and reveals new disease associations at the within-species level obscured at higher taxonomic levels, highlighting the need for genome-resolved approaches in microbiome research.

IMPORTANCE: Microbiome studies increasingly recognize that species-level profiles can mask critical within-species differences relevant to health and disease. However, our work shows that within-species diversity varies drastically across gut microbes, with some species exhibiting almost as many distinct within-species clusters as recovered genomes, making association studies at the within-species level essentially intractable. To address this, we introduce the genome unit number (GUN), a scalable metric for quantifying within-species structure. Using GUN, we demonstrate that only species with limited within-species diversity, such as Odoribacter splanchnicus, currently allow for robust within-species association testing. These findings emphasize the need to systematically evaluate species structure across the gut microbiome and call for the development of new computational and statistical approaches to enable meaningful within-species analyses in highly diverse species.},
}

@article {pmid41837772,
year = {2026},
author = {Yilmaz, A and Ashrafi, N and Guerra, Z and Goniwiecha, D and Saiyed, N and Gordevičius, J and Krinickis, K and Gabrielaite, M and Osentoski, T and Schumacher, N and Khan, S and Pai, A and Ruff, S and Maddens, ME and Imam, K and Monastero, R and Graham, SF},
title = {Salivary metabolomics for early detection of vascular contributions to cognitive impairment and dementia: Exploring microbiome dysbiosis and sex differences.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261423158},
doi = {10.1177/13872877261423158},
pmid = {41837772},
issn = {1875-8908},
abstract = {BackgroundVascular factors contribute to dementia in approximately 20 million individuals, notably in vascular contributions to cognitive impairment and dementia (VCI). However, the lack of specific molecular biomarkers to differentiate VCI from normal aging and Alzheimer's disease (AD) impedes early diagnosis and treatment.ObjectiveTo date the use of saliva for VCI diagnosis has not been previously reported. In this small proof-of-concept study, we aim to explore the feasibility of screening novel salivary diagnostic biomarkers for VCI.MethodsUsing both proton nuclear magnetic resonance ([1]H NMR) spectroscopy and liquid chromatography coupled with mass spectrometry (LC-MS) we biochemically profiled saliva samples collected from individuals with VCI (n = 26) and compared them with cognitively healthy controls (n = 37).ResultsOf the 167 salivary metabolites 56 of them are found to be at significantly different concentrations in the saliva of individuals with VCI as compared to controls. Subsequently, we developed predictive models capable of distinguishing VCI from controls with 0.92 accuracy. Moreover, sex-stratified analysis revealed the perturbation of different metabolic pathways in the saliva of individuals with VCI.ConclusionsThis study underscores the promising role of salivary metabolomics as a non-invasive tool for the early detection of VCI. Our findings suggest that oral microbiome dysbiosis may contribute to VCI pathogenesis, offering novel mechanistic insights. Given the accessibility of saliva, further validation of these robust salivary biomarkers could facilitate scalable, cost-effective screening for VCI, aiding in timely intervention strategies.},
}

@article {pmid41838175,
year = {2026},
author = {Erkert, L and Haag, LM and Becker, C},
title = {Paneth cells as orchestrators of epithelial barrier defense and emerging therapeutic targets in inflammatory bowel disease.},
journal = {Seminars in immunopathology},
volume = {48},
number = {1},
pages = {},
pmid = {41838175},
issn = {1863-2300},
abstract = {First described by Joseph Paneth in 1888 in the small intestine, particularly in the crypts of Lieberkühn, Paneth cells have since emerged as a critical subtype of intestinal epithelial cells (IECs), which together constitute the body’s largest interface with the external environment, continuously exposed to pathogens, dietary components, and toxins. Paneth cells represent a unique, long-lived secretory IEC population located at the crypt base, where they play indispensable roles in antimicrobial defense and stem cell niche maintenance. Their differentiation, positioning, and survival are governed by tightly regulated signaling networks, including the Wnt and Notch pathway. Although traditionally viewed as terminally differentiated, emerging evidence suggests Paneth cells possess a certain level of plasticity, enabling functional adaptation or dedifferentiation under stress or injury. These characteristics position Paneth cells as central regulators of intestinal homeostasis and epithelial barrier integrity. Over the last decades, accumulating evidence has established that Paneth cell dysfunction is closely linked to microbial dysbiosis and the development of inflammatory bowel disease (IBD), highlighting their contribution to disease pathogenesis. Recent discoveries on how Paneth cell dysfunction contributes to intestinal inflammation are uncovering new therapeutic approaches aimed at reestablishing Paneth cell homeostasis and alleviating IBD progression. In this review, we comprehensively summarize current knowledge on Paneth cell differentiation, function, and their role in gut host defense and epithelial barrier maintenance. We further discuss mechanisms by which Paneth cell dysfunction disrupts intestinal homeostasis, promoting IBD development, and highlight emerging therapeutic strategies that target Paneth cells to reestablish barrier integrity and restore gut health.},
}

@article {pmid41838229,
year = {2026},
author = {Jones, OX and Kelly, KD and Khoo, SK and Kelly, RR and Sidles, SJ and LaRue, AC},
title = {The PTSD-Bone Axis: Evidence, Mechanisms, and Management.},
journal = {Current osteoporosis reports},
volume = {24},
number = {1},
pages = {},
pmid = {41838229},
issn = {1544-2241},
abstract = {PURPOSE OF REVIEW: This review explores the relationship between post-traumatic stress disorder (PTSD) and bone health, focusing on how chronic psychological stress influences skeletal integrity through neuroendocrine, immune, and behavioral pathways.

RECENT FINDINGS: Clinical and preclinical studies demonstrate PTSD is associated with reduced bone mineral density, impaired healing, and fracture risk. Mechanistic insights implicate hypothalamic-pituitary-adrenal (HPA) axis dysregulation, sympathetic nervous system (SNS) overactivation, and chronic inflammation in disrupting bone remodeling. Additional risk modifiers include sex-specific biology, early-life adversity, and glucocorticoid sensitivity. However, selective serotonin reuptake inhibitors (SSRIs), serotonin-norepinephrine reuptake inhibitors (SNRIs), anti-inflammatory agents, and emerging tools like exosomal profiling and microbiome modulation show promise in mitigating stress-related bone loss.

SUMMARY: PTSD contributes to skeletal fragility through complex, multisystem mechanisms. Trauma-informed care integrating bone health screening and personalized interventions may improve psychological and musculoskeletal outcomes. Future research should prioritize longitudinal, mechanistic studies to guide holistic management of trauma-related disease.},
}

@article {pmid41838256,
year = {2026},
author = {Bahar, A and Moazzen, M and Khazaei, M and Yosefi, S and Tahmasebi, H},
title = {Control of HELLP syndrome and pre-eclampsia with microbiota.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41838256},
issn = {1573-4978},
}

@article {pmid41838730,
year = {2026},
author = {Bayrón-Ho, DI and Rivera-Rodríguez, AJ and Morales-Cintrón, AJ and Cardona-Sierra, HA and Rodríguez-Morales, RE},
title = {Brain and Gut Dissection in Surface Fish and Cavefish Populations of Astyanax mexicanus.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {228},
pages = {},
doi = {10.3791/70412},
pmid = {41838730},
issn = {1940-087X},
mesh = {Animals ; *Brain/surgery/anatomy & histology ; *Characidae/anatomy & histology ; *Dissection/methods ; Caves ; Gastrointestinal Microbiome ; *Gastrointestinal Tract/surgery/anatomy & histology ; },
abstract = {Teleost fish are used to answer a wide range of research questions spanning from development to genetics and neuroscience, and more recently, to understand the complexities of the gut-brain axis, and even in a wider context, the gut-brain-liver axis. The Mexican tetra, Astyanax mexicanus, has been increasingly used in comparative and developmental evolution frameworks due to the availability of morphologically and physiologically distinct morphotypes, including river-dwelling surface fish and cave-adapted, blind cavefish. Adaptation to cave habitats is associated with changes in morphological traits, behavioral traits, and gut microbiota diversity that are also found in laboratory conditions. This has opened up the possibility to ask questions about the interactions between the microbiome, metabolic activity, neural adaptation, and complex behavioral outputs. These interactions can now be addressed through whole-brain mapping studies with cleared brains and gut microbiota sequencing to detect bacterial diversity associated with surface and cave-adapted phenotypes. However, most of these studies would benefit from intact, carefully dissected, and preserved whole organs and tissues, which allow for post-processing in downstream applications. This protocol describes a step-by-step method for brain and gut dissection, where the whole brain and abdominal organs are removed and isolated for both surface fish and cavefish morphotypes.},
}

Animals
*Brain/surgery/anatomy & histology
*Characidae/anatomy & histology
*Dissection/methods
Caves
Gastrointestinal Microbiome
*Gastrointestinal Tract/surgery/anatomy & histology

@article {pmid41838875,
year = {2026},
author = {Chen, Q and Zhang, B and Peng, C and Huang, J and Liu, Z and Shen, X and Jiang, C},
title = {Kun-peng enables scalable and accurate pan-domain metagenomic classification.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {41838875},
issn = {1477-4054},
support = {82341109//National Natural Science Foundation of China/ ; 82173645//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Databases, Genetic ; *Software ; Computational Biology/methods ; Algorithms ; },
abstract = {Comprehensive pan-domain metagenomic classification is increasingly constrained by the memory and runtime costs of building and querying the rapidly expanding reference genome space. We introduce Kun-peng, a taxonomic classifier powered by an intelligent block-partitioned database structure and optimized search strategies, enabling ultra-scalable, memory-efficient pan-domain profiling. Using the Critical Assessment of Metagenome Interpretation II benchmark, Kun-peng substantially reduces the memory usage of database-building and querying by up to 24-fold, and accelerates sample classification by up to 4.73-fold compared with Kraken2. Kun-peng achieves competitive accuracy with fewer false positives than Kraken2, Centrifuger, and even KrakenUniq, while maintaining consistently high sensitivity across diverse datasets. In a real-world evaluation of 586 metagenomic samples spanning air, water, soil, and human-associated environments, we performed classification using a 4.3 TB pan-domain database comprising 204,477 genomes, which was built by Kun-peng with only 4.1 GB peak memory. Kun-peng processed each sample in 0.2-11.2 min with 4.0-35.4 GB peak memory, corresponding to a 54-473-fold reduction in memory usage relative to Kraken2. Compared with Sylph, Kun-peng achieved up to a 46-fold speedup while requiring 21-fold less memory. Kun-peng classified 69.8%-94.3% of reads, improving coverage by 20%-60% over the standard Kraken2 database with 62,026 genomes. This improvement reflects expanded reference coverage, although a small fraction of false positives is inherent to k-mer-based methods. Overall, Kun-peng effectively eliminates the long-standing memory bottleneck in pan-domain database building and classification, enabling rapid and scalable pan-domain taxonomic analysis of complex environmental, ecological, and exposomic sequencing datasets.},
}

*Metagenomics/methods
*Metagenome
Humans
Databases, Genetic
*Software
Computational Biology/methods
Algorithms

@article {pmid41839322,
year = {2026},
author = {Danese, T and Asti, V and Ablondi, M and Raspa, F and Cavallini, D and Valle, E},
title = {Clinical nutrition in equine colic: a scoping review from an equine nutritionist's perspective.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {105852},
doi = {10.1016/j.jevs.2026.105852},
pmid = {41839322},
issn = {0737-0806},
abstract = {BACKGROUND: Colic represents one of the leading causes of morbidity and mortality in equine medicine, with nutritional management recognized as a key modifiable factor influencing postoperative recovery. However, guiding principles for nutritional enteral support in horses after colic remain limited, and current practices are largely empirical.

OBJECTIVES: This scoping review aimed to (1) examine enteral nutritional support protocols reported in literature through a scoping review to map the available evidence on equine clinical nutrition in the context of colic, and (2) propose a physiology-based interpretative framework to consider when formulating dietary plans for post-colic horses, from a clinical nutritionist's perspective.

METHODS: PRISMA 2020-ScR guidelines were applied in Scopus and Web of Science databases using "horse colic" AND "clinical nutrition." Inclusion criteria comprised English-peer-reviewed studies reporting nutritional interventions in horses with colic. Data were extracted into predefined different categories.

RESULTS: Twenty-three studies met the inclusion criteria, revealing marked heterogeneity. Early reintroduction of enteral nutrition (12-24 h postoperatively) was associated with faster recovery, whereas parenteral nutrition was reserved for severe intestinal dysfunction. Evidence supports the use of forage-based, low-starch diets to promote intestinal motility and microbiome stability, while prolonged fasting or high-NSC feeds increase the risk of dysmotility and recurrence. Post-colic horses benefit from the "feed pyramid" approach-maximizing forages, low-NSC, balanced supplements, avoiding fasting and offering small frequent meals in wet, digestible feed forms.

CONCLUSIONS: Current evidence underscores the central role of early, forage-based enteral feeding in post-colic management. The integration of nutritional planning within multidisciplinary decision-making is essential to balance clinical, metabolic, and nutritional priorities.},
}

@article {pmid41839398,
year = {2026},
author = {Kawuribi, V and Awere-Duodu, A and Adjei, FA and Osman, AH and Bomansaan, H and Madadi, MM and Tampuri, JU and Adu-Amankwaah, J},
title = {The gut-tumor metabolic axis: A comprehensive exploration of bidirectional crosstalk in cancer immunotherapy.},
journal = {Critical reviews in oncology/hematology},
volume = {222},
number = {},
pages = {105280},
doi = {10.1016/j.critrevonc.2026.105280},
pmid = {41839398},
issn = {1879-0461},
abstract = {The gut-tumor metabolic axis represents a bidirectional immunometabolic network in which tumor-derived metabolites reshape microbial ecology, while gut microbiome-derived metabolites recalibrate systemic and intratumoral immunity, ultimately influencing cancer progression and immunotherapy outcomes. Tumor aerobic glycolysis generates excess lactate and acidity that suppress cytotoxic immune function, remodel the tumor immune microenvironment, and indirectly perturb intestinal microbial composition. In turn, microbial metabolites including short-chain fatty acids, bile acid derivatives, tryptophan catabolites, inosine, and trimethylamine N-oxide signal through defined host pathways such as GPR109A, AHR, and adenosine A2A receptors to regulate antigen presentation, T-cell differentiation, macrophage polarization, and immune checkpoint sensitivity. Preclinical and emerging clinical evidence demonstrates that dietary modulation, rational probiotics, and fecal microbiota transplantation can enhance immune checkpoint inhibitor efficacy in selected contexts. However, metabolite effects are highly context dependent, with dose, timing, tumor type, and immune state critically shaping therapeutic benefit or resistance. This review integrates mechanistic insights and clinical evidence, highlights translational challenges including safety, donor heterogeneity, and biomarker validation, and proposes a framework for biomarker-guided microbiome-based strategies to advance precision cancer immunotherapy.},
}

@article {pmid41839407,
year = {2026},
author = {Chen, S and Zhao, A and Zhang, W and Liu, Q and Li, D},
title = {Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134433},
doi = {10.1016/j.biortech.2026.134433},
pmid = {41839407},
issn = {1873-2976},
abstract = {The persistence of antibiotic resistance genes (ARGs) and pathogens during manure composting poses critical risks within the One Health framework. However, the ecological and metabolic mechanisms by which microbiome engineering disrupts the dissemination of these biohazards remain poorly understood. This study evaluated a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum) in mitigating these risks. KEGG analysis highlighted a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly. This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities. Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation. While thermophilic hosts temporarily enriched specific ARGs, SynCom ultimately achieved a significant reduction in multidrug resistance genes and virulence factors by intensifying thermophilic fermentation. Mantel correlation analysis revealed the SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification were critical environmental drivers, restricting ARGs and alleviating co-selection pressure on metal resistance genes. Network analysis demonstrated SynCom induced a structural collapse of high-risk interactomes (reducing potential host-gene associations by 26.6%), effectively disrupting ARG and mobile genetic element connections by suppressing key recombinases (XerD, IntI1) and eliminating Pseudomonadota hub hosts. Consequently, deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors. These findings indicate that SynCom provides a robust microbiome engineering strategy to disrupt the genetic dissemination of biohazards and ensure organic fertilizer biosafety.},
}

@article {pmid41839432,
year = {2026},
author = {Martínez-Guzmán, O and Cáceres-Chacón, M and Rivera-López, M and Hernández-Busot, G and Forty-Díaz, J and Haddock-Martínez, HG and Sierra-Mercado, D},
title = {Mild concussion impairs extinction of avoidance and alters respective brain circuits in male rats.},
journal = {Experimental neurology},
volume = {},
number = {},
pages = {115734},
doi = {10.1016/j.expneurol.2026.115734},
pmid = {41839432},
issn = {1090-2430},
abstract = {Concussive brain injury is a risk factor for anxiety disorders. Pre-clinical models demonstrate that concussion increases passive fear responses, such as conditioned freezing, yet provide limited insight to active responses like avoidance of perceived threats. This is important because persistent avoidance is characteristic of anxiety disorders. Moreover, brain injury can induce an imbalance of the gut microbiome, which can alter emotions. Adult male rats were trained on a platform-mediated avoidance task where they learned to step onto a platform to avoid a foot shock following a conditioned auditory tone. A sucrose reward was provided via a lever press that is opposite to the platform. Next, closed head injury was delivered to produce a mild concussion. After recovery, separate cohorts of rats were tested to dissociate between changes in avoidance expression and extinction-related processes. Cellular activity was assessed using c-Fos immunohistochemistry in brain regions implicated in avoidance: amygdala, medial prefrontal cortex, insular cortex, ventral striatum, and ventral hippocampus. Fecal pellets were collected to extract genetic material to identify potential changes in populations of bacteria in the gut microbiome. Closed head injury induced persistent avoidance by impairing extinction. Injured rats showed decreased activity in the basomedial amygdala and the CA1 subregion of the ventral hippocampus, increased activity in the rostral insular cortex and ventral striatum, and no change in the medial prefrontal cortex. Closed head injury did not induce changes in gut microbiota. Understanding mechanisms of concussion-induced avoidance is crucial for developing rehabilitation strategies for mental health disorders impacted by brain injury.},
}

@article {pmid41839435,
year = {2026},
author = {Liu, H and Liang, J and Du, X and Lee, Y and Lee Binti Abdullah, A and Tay, YJ and Han, M},
title = {Toxic Effects of Tire Wear Particle Leachate on Benthic Fish Misgurnus anguillicaudatus: An Integrated Assessment of Immunosuppression, Metabolic Disruption, and Microbiome Dysbiosis Across Concentration Gradients.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127958},
doi = {10.1016/j.envpol.2026.127958},
pmid = {41839435},
issn = {1873-6424},
abstract = {Tire wear particles (TWPs) are a major source of microplastic pollution, entering aquatic environments via stormwater runoff, and other transport mechanisms. Their leachate contains heavy metals and organic contaminants that exert diverse toxic effects on aquatic organisms. However, the toxic effects of TWP leachate on the benthic fish Misgurnus anguillicaudatus remain poorly understood. In this study, we used an integrative multi-omics approach to investigate the effects of TWP leachate exposure on M. anguillicaudatus. TWP leachate downregulated type I interferon signaling, impairing antiviral defense and immune function. It also significantly increased levels of lysophosphatidylcholines (LPCs) and lysophosphatidylethanolamines (LPEs), which are biomarkers of membrane damage and excessive inflammatory cytokine production. Furthermore, concentration-dependent compensatory mechanisms were triggered, including enhanced biosynthesis of cholesterol and long-chain fatty acids to maintain membrane stability. TWP exposure also altered gut microbiota composition and interaction networks, with reduced abundances of immunomodulatory taxa and increased proliferation of energy metabolism-related families. These findings indicate that TWP leachate disrupts immune competence, cellular structural homeostasis, and energy metabolism in M. anguillicaudatus through interconnected molecular pathways. Our study provides essential evidence to guide mitigation strategies in aquaculture and offers a reference for ecological risk assessment of TWP leachate contamination across concentration gradients.},
}

@article {pmid41839452,
year = {2026},
author = {Rautemaa-Richardson, R and Sobel, JD and Stone, N and De Seta, F and Cassone, A and Vieira-Baptista, P and Comar, M and Warris, A and Roselletti, E},
title = {State-of-the-Art Review: Managing Vulvovaginal Candidiasis.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {82},
number = {3},
pages = {371-382},
doi = {10.1093/cid/ciaf673},
pmid = {41839452},
issn = {1537-6591},
support = {//MRC Centre for Medical Mycology/ ; MR/N006364/2//University of Exeter/ ; MR/V033417/1//University of Exeter/ ; NIHR203320//NIHR Exeter Biomedical Research Centre/ ; //Department of Health and Social Care/ ; },
mesh = {Humans ; *Candidiasis, Vulvovaginal/drug therapy/diagnosis/microbiology/therapy/physiopathology ; Female ; *Antifungal Agents/therapeutic use ; Risk Factors ; Recurrence ; Microbiota ; Vagina/microbiology ; Candida/drug effects ; },
abstract = {Vulvovaginal candidiasis is one of the most prevalent infections in women worldwide. Together with its recurrent form, it affects millions of women annually, causing significant symptoms and severely impacting quality of life. This review examines the pathophysiology, risk factors, microbiome interactions, clinical manifestations, and challenges in diagnosing and managing vulvovaginal candidiasis, with emphasis on recurrent vulvovaginal candidiasis. While Candida albicans is the primary cause, non-albicans species are increasingly common. Multiple factors contribute to both forms, including hormonal changes, diabetes, antibiotic use, immune dysfunction, and genetics. The vaginal microbiome plays a key role in maintaining homeostasis and preventing Candida overgrowth. Symptoms such as itching, discharge, and soreness overlap with other conditions, complicating the diagnosis. Standard treatment involves topical or systemic antifungals, but recurrence and resistance are frequent. Emerging strategies include novel antifungals, immunomodulators, and vaccines. Future approaches should focus on modulating host and environmental factors to prevent recurrence, reduce resistance, and improve outcomes.},
}

Humans
*Candidiasis, Vulvovaginal/drug therapy/diagnosis/microbiology/therapy/physiopathology
Female
*Antifungal Agents/therapeutic use
Risk Factors
Recurrence
Microbiota
Vagina/microbiology
Candida/drug effects

@article {pmid41839646,
year = {2026},
author = {Byrd, MC and Wang, M and Li, G and Bhaumik, D and Gibson, K and Su, CL and Salzman, E and Head, JR and Mody, L and Foxman, B},
title = {Clinical Predictors of Nose/throat Bacteriome and Fungal Colonization in Skilled Nursing Facility Residents.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag166},
pmid = {41839646},
issn = {1537-6613},
abstract = {BACKGROUND: Microbiomes resist or facilitate pathogen invasion and modulate host immune responses and infection susceptibility. We describe nose/throat bacteriome composition and predicted functional changes associated with Candida albicans colonization, antibiotic use, and medical devices among adults receiving short-term sub-acute care in a skilled nursing facility (SNF).

METHODS: We collected combined nose/throat swabs from 301 adults every three days for up to five visits. Bacteriome composition was detected via 16S rRNA amplicon sequencing and C. albicans colonization by qPCR. Functional potential was inferred using PICRUSt2. We used ADAPT software to evaluate bacteriome compositional and functional differences by C. albicans colonization adjusting for age, sex, antibiotic exposure, and medical device presence.

RESULTS: C. albicans colonization was more common among participants with devices and antibiotic use, but not statistically significantly. Participants had mean age 77 years, 63.8% female, 48.5% received antibiotics, and 20.3% had device at entry. Nose/throat bacteriome was significantly less diverse and rich in the presence of C. albicans, antibiotic exposure, and device use (p<0.05), but composition varied little during follow-up. With C. albicans, predicted bacteriome function favored acid-tolerant, biofilm-forming species (S. wiggsiae, L. fermentum; p<0.01), and depleted glycolate degradation (log10fold change -0.45; adjusted p=0.01).

CONCLUSION: Nose/throat bacteriome composition and function were significantly associated with C. albicans colonization and C. albicans colonization was strongly associated with antibiotic exposure and medical device use. These findings underline the importance of integrating fungal colonization assessment and clinical factors into microbiome studies aimed at preserving bacteriome resilience and reducing infection risk in vulnerable populations.},
}

@article {pmid41839668,
year = {2026},
author = {Nadeem, SA and Ali, I and Hussain, H and Ullah, I and Ali, W and Alzahrani, KJ and Ali, H and Khan, ZI and Abass, KS and Rahman, RU},
title = {Metagenomic analysis of bacterial and viral communities of Aedes aegypti and Aedes albopictus.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {1},
pages = {100643},
pmid = {41839668},
issn = {2090-5920},
abstract = {BACKGROUND: The complicated relationship between the Aedes mosquito microbiome, arbovirus transmission and essential physiological processes, is extremely important. Microbial community plays a vital role in shaping vector biology, impacting critical aspects such as parasite replication within the vector, vector longevity, and ultimately, vector competence. Understanding the composition and function of the Aedes microbiome is therefore crucial for developing novel strategies to control arboviral diseases. Therefore, we aimed to identify prevalent bacterial and viral communities in Aedes mosquitoes from Pakistan.

METHODS: Ae. aegypti and Ae. albopictus were collected and from three different regions of Khyber Pakhtoonkhwa, Punjab and federal capital Islamabad. We isolated DNA and sequenced two pools of each species and conducted metagenomic analysis, identifying a variety of bacteria and viruses.

RESULTS: We found diverse bacterial and viral communities in both studied species. In Ae. aegypti, the most abundant bacterial species was Klebsiella pneumoniae followed by Acinetobacter baylyi. Ae. albopictus presented Pseudomonas putida as the most abundant bacterial species followed by Brevundimonas diminuta. Similarly in Ae. aegypti, we found that Escherichia phage HK639 was the most abundant viral species while in Ae. albopictus, it was Lactobacillus phage 2. It is important to mention that the prevalent viruses in both Aedes species belong to the Siphoviridae genus.},
}

@article {pmid41840154,
year = {2026},
author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A},
title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {41840154},
issn = {1678-4405},
support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnología/ ; CAR-21861//Universidad Autónoma de Yucatán/ ; },
abstract = {UNLABELLED: The gut microbiota of insects plays a crucial role in host health and is thought to have co-evolved with each species. In stingless bees, a general understanding of these associations has begun to emerge; however, several important knowledge gaps remain. In this study, we employed amplicon sequencing to compare the gut microbiota of individual specimens from two closely related and sympatric Neotropical stingless bee species from the Maya region, Melipona beecheii and Melipona yucatanica. Our results revealed that (i) most amplicon sequence variants (ASVs) in both species were transient; (ii) the core microbiota of these species was almost entirely distinct, sharing only one ASV out of a total of 31; and (iii) despite this divergence, all core ASVs identified in both species belonged to only four bacterial orders. This pattern suggests that, while their microbiota have differentiated at finer taxonomic scales, it likely originated from a shared ancestral community. We contextualize these findings within the current understanding of stingless bee microbiotas and highlight future directions for exploring their evolution and diversity.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-026-01905-z.},
}

@article {pmid41840216,
year = {2026},
author = {Glascock, A and Maguire, C and Phan, HV and Lydon, EC and Schaenman, J and Calfee, CS and Melamed, E and Greenland, J and Corry, DB and Kheradmand, F and Baden, LR and Sekaly, R and McComsey, GA and Haddad, EK and Cairns, CB and Geng, LN and Pulendran, B and Fernandez-Sesma, A and Simon, V and Metcalf, JP and Agudelo Higuita, NI and Messer, WB and Davis, MM and Nadeau, KC and Kraft, M and Bime, C and Erle, DJ and Atkinson, MA and Brakenridge, SC and Ehrlich, LIR and Montgomery, RR and Shaw, AC and Hough, CL and Hafler, DA and Augustine, AD and Becker, PM and Peters, B and Ozonoff, A and Hoch, A and Kim-Schulze, S and Krammer, F and Bosinger, S and Eckalbar, W and Altman, MC and Wilson, M and Guan, L and Maecker, H and Steen, H and , and Diray-Arce, J and Rouphael, N and Kleinstein, SH and Jayavelu, ND and Reed, EF and Levy, O and Chu, VT and Langelier, CR},
title = {Empiric azithromycin alters the upper respiratory microbiome and resistome without anti-inflammatory benefit in COVID-19.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41840216},
issn = {2058-5276},
abstract = {Azithromycin is a widely used antibiotic and was frequently used to treat hospitalized patients during the COVID-19 pandemic. The impact of empiric azithromycin use on the respiratory microbiome in patients with viral respiratory infections is unclear. Here we used longitudinal metatranscriptomics on nasal swabs from a prospective multicentre cohort of 1,164 patients hospitalized for COVID-19. We compared the upper respiratory microbiome, resistome and systemic immune response in patients treated with azithromycin (n = 366) with those who received no antibiotics (n = 474) or other antibiotics (n = 324). We found that azithromycin altered microbiome composition and increased the expression and relative proportion of macrolide/lincosamide/streptogramin (MLS) resistance genes. These changes occurred after 1 day of exposure and persisted for over a week. MLS resistance gene expression was associated with commensals and potential pathogens, while there were no differences in host inflammatory gene expression in blood and airways. This demonstrates that empiric azithromycin treatment impacts the upper respiratory microbiome and resistome without apparent anti-inflammatory benefit.},
}

@article {pmid41840217,
year = {2026},
author = {Chapman, JA and Masi, AC and Beck, LC and Watson, H and Young, GR and Browne, HP and Shao, Y and Kiu, R and Nelson, A and Doyle, JA and Palmowski, P and Lengyel, M and Connolly, JPR and Lamb, CA and Porter, A and Lawley, TD and Hall, LJ and Embleton, ND and Perry, JD and Berrington, JE and Stewart, CJ},
title = {Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41840217},
issn = {2058-5276},
support = {221745/Z/20/Z//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
abstract = {Infant gut microbiome development is strongly impacted by breastmilk and human milk oligosaccharides (HMOs), which can protect preterm infants against pathologies including necrotizing enterocolitis. HMO metabolism in bifidobacteria is well characterized and linked to health outcomes, but the scope of HMO-utilizing species remains unclear. Here, using a combination of genomics, proteomics and metabolomics, we show that Clostridium species isolated from preterm infants (born at <32 weeks gestation), in particular Clostridium perfringens lacking the toxin perfringolysin O (PfoA), metabolized HMOs. Clostridium species produced beneficial metabolites including short-chain fatty acids and tryptophan catabolites at higher quantities than Bifidobacterium species in vitro. Cell-free supernatant from C. perfringens was non-toxic to colonic cell lines, promoted the growth of commensal bifidobacteria and inhibited growth of pathobionts isolated from the preterm infant gut in vitro. It also suppressed inflammation in preterm-derived intestinal organoids. These findings expand our understanding of HMO-metabolizing microbes and suggest that pfoA[-] C. perfringens strains could contribute to healthy infant gut development.},
}

@article {pmid41840421,
year = {2026},
author = {Liu, S and Tan, S and Li, Q and He, D and Xu, L and Zhang, H and Wang, R and Guan, Y and Cheng, Z and Wu, J and Xu, W and Zhang, H and Tang, M and Fan, J and Liu, L and Xie, J},
title = {PagMYB74 orchestrates flavonoid-mediated plant-microbe feedback for drought resilience in poplar.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71086},
pmid = {41840421},
issn = {1469-8137},
support = {2025D01E61//Xinjiang Science Fund for Distinguished Young Scholars/ ; },
abstract = {The interactions between plants and the soil microbiome play critical roles in regulating plant resistance to stresses. However, the process partly results from the complex interaction between root exudates and microbes, a relationship that remains poorly understood. Here, we investigated the interconnected responses of the root microbiome associated with the perennial tree Populus under drought stress. This was achieved via molecular genetics approaches and multi-omics analyses, combined with integrative comparisons of microbiome structure against both the host plant's metabolomic profiles and transcriptomic data, using samples collected over a 13-wk period of progressive drought treatment. We demonstrate that progressive drought triggers a phased transcriptional cascade in roots, culminating in the activation of a flavonoid biosynthesis program. Moreover, we confirm that Pseudomonas is strongly associated with flavonoid biosynthesis and identify that gene PagMYB74 is critical for quercetin and kaempferol secretion. We further found that Pseudomonas putida S110 colonization establishes positive feedback through enhanced phenylpropanoid metabolism and activation of nutrient transport pathways in PagMYB74-overexpressing plants, reinforcing the symbiotic interaction. Our findings establish a complete mechanistic continuum from a single host gene to metabolite-driven recruitment and symbiotic reprogramming, facilitating the improvement of environmental adaptation by regulating their interaction with beneficial soil microorganisms.},
}

@article {pmid41840446,
year = {2026},
author = {You, T and Parmar, P and Decke, G and Baikie, K and Ryckewaert, L and Marette, A and Niculita-Hirzel, H},
title = {Water-vapor treatment of shower systems in healthcare facilities: reshaping built-environment microbiomes to improve Legionella control and protect at-risk patients.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02355-3},
pmid = {41840446},
issn = {2049-2618},
support = {61963.1 INNO-EE//Swiss Innovation Agency Innosuisse/ ; 61963.1 INNO-EE//Innosuisse - Schweizerische Agentur für Innovationsförderung/ ; },
abstract = {BACKGROUND: Legionnaires' disease (LD) is a severe form of pneumonia caused by inhalation of aerosols containing Legionella spp., most commonly L. pneumophila, which proliferates within protozoa embedded in established biofilms of engineered water systems, such as shower systems. Despite water management plans, durable control of L. pneumophila at terminal outlets remains challenging, partly because the effects of disinfection treatments on microbial community assembly, ecological interactions, and functional organization within biofilms are poorly understood. This study aimed to investigate how an emerging water/vapor disinfection treatment reshapes shower biofilm microbiomes at critical developmental stages - from early adhesion and biomass peak when L. pneumophila first appears, to mature biofilms associated with pathogen persistence - relative to conventional hot water disinfection, and to identify microbial taxa and functions selectively affected by these interventions.

RESULTS: We applied a sequential water flushing followed by high-pressure vapor (120℃) protocol either during early biofilm formation or on mature biofilms, all grown on standardized shower systems installed in healthcare, nursing home, and residential buildings subject to L. pneumophila routine control. Compared with conventional thermal disinfection of shower systems (65 °C, 10 min), water-vapor treatment more effectively removed established biofilm communities as supported by scanning electron microscopy, flow cytometry of residual cells, and culture. Amplicon sequencing of the V3-V4 region of 16S rRNA genes revealed treatment-specific shifts in microbial community composition and predicted functional profiles (R[2] = 0.285, p = 0.001). Beyond Legionella removal, water-vapor treatment disrupted 70 metabolic pathways (FDR < 0.05), including pathways related to lipopolysaccharide synthesis, central metabolism, and the Legionella-specific CMP-legionaminate pathway, indicating selective impacts on biofilm integrity and pathogen-supportive functions.

CONCLUSION: Water-vapor treatment induces substantial ecological restructuring of shower biofilm microbiomes, affecting both taxonomic composition and functional capacity associated with biofilm resilience and pathogen persistence. These findings support that perturbation of key ecological functions within built-environment microbiomes can influence opportunistic pathogen dynamics and encourage the development of microbiome-informed strategies to complement conventional water safety management, particularly in healthcare settings. Video Abstract.},
}

@article {pmid41840696,
year = {2026},
author = {Roca, C and Hemphill, CC and Speen, AM and Jaspers, I and Wolfgang, MC and Drummond, MB},
title = {Dysbiosis of the nasal microbiome is associated with prospective acute exacerbation of COPD.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02357-1},
pmid = {41840696},
issn = {2049-2618},
support = {R01 HL150081/HL/NHLBI NIH HHS/United States ; R01HL150081/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is often associated with respiratory viral infection and the need for increased medical intervention. The nasal mucosa plays a critical role in infection susceptibility and severity, with the nasal microbiome shaping mucosal immunity. This study investigated the association between the bacterial nasal microbiome and AECOPD. Participants included 41 individuals with COPD and 15 healthy non-COPD controls. Nasal microbiome composition was assessed from nasal epithelial lining fluid and compared at baseline between healthy participants and individuals with COPD, stratified by AECOPD history. COPD subjects who experienced one or more AECOPD in the year prior to enrollment were categorized as Ever AECOPD. COPD participants without a history of AECOPD in the prior year were categorized as Never AECOPD. Prospective exacerbation data were collected and used in a case-control analysis to identify clinical and microbiological markers predictive of future AECOPD in COPD-diagnosed subjects.

RESULTS: We found two distinct nasal microbiome architectures with enrichment of protective taxa (healthy signature) or pathobionts (pathogenic signature). Nasal microbiome analysis demonstrated significant differences in nasal bacterial composition between COPD-diagnosed individuals with prior AECOPD (Ever AECOPD) compared to healthy controls. For COPD individuals with no prior AECOPD (Never AECOPD), we identified two underlying community structures; Cluster 1 subjects harbored a nasal microbiome significantly similar to healthy controls (healthy signature) and Cluster 2 subjects were significantly similar to the Ever AECOPD cohort (pathogenic signature). We evaluated the baseline microbiome of COPD-diagnosed participants based on the occurrence of at least one AECOPD 1-year after baseline sample collection (prospective AECOPD) and found that the nasal microbiome was associated with the occurrence of future AECOPD events. Prospective exacerbation was associated with reduced relative abundance of Dolosigranulum pigrum. Further analysis by qPCR showed that decreased D. pigrum abundance was associated with lower lung function and higher risk of future AECOPD.

CONCLUSIONS: Our data indicates that the nasal microbiome is associated with AECOPD phenotypes. Moreover, participants with decreased nasal Dolosigranulum pigrum abundance had lower lung function and a higher risk of future exacerbations. These findings suggest that D. pigrum may serve as a biomarker for AECOPD risk; however, validation of these findings in a larger multicenter cohort is needed. Video Abstract.},
}

@article {pmid41840712,
year = {2026},
author = {Xu, L and Liu, C and Chen, S and Mao, A and Zi, X and Li, J and Ge, X and Liu, Q and Wang, S and Li, X and Wu, Q and Wan, J and Zhang, Z and Xu, H and Li, J and Lin, Q and Cao, Z},
title = {Characterization of age-related changes in the gut microbiome and metabolome of Kunming dogs and their associations with police performance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02388-8},
pmid = {41840712},
issn = {2049-2618},
support = {2023YNPKLANF004//Open Foundation of the Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science/ ; YNWR-QNBJ-2018-137//Young Talent of Yunnan Xingdian Support Project for High Level Talents/ ; 202305AC160040//Yunnan Provincial Middle-Young Academic and Technical Leader Candidate/ ; },
abstract = {BACKGROUND: Gut microbiota plays a pivotal role in regulating the host's central nervous system (CNS) activity and behavior. However, its influence on the police performance of Kunming dogs and the underlying mechanisms remain largely unexplored. This study was the first to apply multi-omics technologies to investigate the dynamic variations in gut microbiota and their metabolic profiles across different ages of Kunming dogs. Furthermore, we systematically examined the associations between these microbial alterations and police performance metrics, providing a theoretical foundation for enhancing the working capabilities of Kunming dogs through targeted modulation of intestinal microecology.

RESULTS: The study showed that puppies, young dogs and adult dogs had significantly better police performance than elderly dogs, with young dogs exhibiting the highest scores. Analysis of 16S rRNA sequencing demonstrated that gut microbial diversity and stability were highest during the young dog stage, gradually declining with age. Metagenomic analysis revealed that the abundance of Lactobacillus acidophilus, Lactobacillus johnsonii, Limosilactobacillus reuteri, Ligilactobacillus animalis and Muribaculum gordoncarteri were strongly correlated with police performance. The results of metagenome-assembled genomes (MAGs) indicated that the above species have functional genes involved in GABAergic and glutamatergic synapse pathways. Furthermore, metabolomic analysis showed that differential metabolites were enriched in the neuroactive ligand-receptor interaction pathway, in which GABA (γ-aminobutyric acid), histamine and tyramine metabolites were positively correlated with the above species and police performance.

CONCLUSION: The species L. acidophilus, L. johnsonii, L. reuteri, L. animalis, and M. gordoncarteri, which were enriched in the gut of puppies and young Kunming dogs, may potentially influence the nervous system through the production of neurotransmitters and neuromodulators, suggesting a possible association with police performance. Video Abstract.},
}

@article {pmid41840729,
year = {2026},
author = {Mori, H and Fujisawa, T and Higashi, K and Tanizawa, Y and Nakagawa, Z and Nishide, H and Fujiyoshi, M and Nakamura, Y and Uchiyama, I and Matsui, M and Yamada, T},
title = {Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02385-x},
pmid = {41840729},
issn = {2049-2618},
support = {JPMJND2206//Japan Science and Technology Agency/ ; },
abstract = {BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications.

RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were >95% completeness and <1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.

CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.},
}

@article {pmid41841008,
year = {2026},
author = {Peng, T and Zhang, Z and Ding, N and Zhang, J},
title = {Mechanistic Investigation of Exercise Interventions in Rodent Models of Alzheimer's Disease and Prospects for Clinical Translation.},
journal = {Neural plasticity},
volume = {2026},
number = {1},
pages = {e6718671},
doi = {10.1155/np/6718671},
pmid = {41841008},
issn = {1687-5443},
support = {2025023//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Alzheimer Disease/therapy/physiopathology/metabolism ; Animals ; Disease Models, Animal ; Gastrointestinal Microbiome/physiology ; *Physical Conditioning, Animal/physiology ; *Exercise Therapy/methods ; Humans ; Translational Research, Biomedical ; Mice ; Brain/metabolism ; Mice, Transgenic ; Neuronal Plasticity/physiology ; },
abstract = {Alzheimer's disease (AD) is a progressive and debilitating neurodegenerative disorder for which existing pharmacotherapies are inadequate to arrest pathological progression, highlighting the imperative to identify safe and effective nonpharmacological interventions. Exercise, as a multi-target therapeutic modality, has been shown to reverse multiple facets of AD-related neuropathology through diverse mechanisms. In this systematic review, we synthesize evidence on the effects of voluntary running, structured swimming, and modulation of the gut microbiota in transgenic murine models of AD. Exercise was found to ameliorate AD pathology by modulating amyloid precursor protein (APP) processing and β-amyloid (Aβ) production/clearance, restoring mitochondrial integrity and function, attenuating neuroinflammatory responses, enhancing synaptic plasticity, and upregulating neurotrophic factors. Moreover, exercise reshapes the intestinal microbiome and thereby modulates the gut-brain axis, further promoting neuroimmune homeostasis and cognitive resilience. Through RNA sequencing data analysis, key genes such as Tlr4, Cdc42, and F13a1 were identified, which may play significant roles in neuroimmune regulation and cognitive protection. By integrating multi-omics evidence, we propose a coordinated "exercise-microbiota-brain" mechanistic framework that offers theoretical support for personalized, exercise-based therapeutic strategies and translational applications in AD. We also emphasize the necessity of future studies combining exercise with complementary interventions to accelerate the clinical translation of multimodal therapeutic approaches.},
}

*Alzheimer Disease/therapy/physiopathology/metabolism
Animals
Disease Models, Animal
Gastrointestinal Microbiome/physiology
*Physical Conditioning, Animal/physiology
*Exercise Therapy/methods
Humans
Translational Research, Biomedical
Mice
Brain/metabolism
Mice, Transgenic
Neuronal Plasticity/physiology

@article {pmid41841157,
year = {2026},
author = {Ruiz-Malagón, AJ and Herraiz-Vilela, M and Pinazo-Bandera, J and Toro-Ortiz, JP and López-Gómez, C and Ho-Plagaro, A and Garrido-Sánchez, L and Robles-Díaz, M and Taminiau, B and Daube, G and Sanabria-Cabrera, J and Matilla-Cabello, G and Lucena, MI and Andrade, RJ and García-Fuentes, E and García-Cortes, M and Rodriguez-Diaz, C},
title = {An Exploratory Study on the Pathogenic Role of Faecal Extracellular Vesicles in Metabolic Dysfunction-Associated Steatotic Liver Disease Progression and in Drug-Induced Liver Injury.},
journal = {Journal of extracellular vesicles},
volume = {15},
number = {3},
pages = {e70240},
doi = {10.1002/jev2.70240},
pmid = {41841157},
issn = {2001-3078},
support = {101095679//Horizon 2020 Framework Programme/ ; FORT23/00013//Instituto de Salud Carlos III/ ; PI18/01804//Instituto de Salud Carlos III/ ; PI19/00883//Instituto de Salud Carlos III/ ; PI21/01248//Instituto de Salud Carlos III/ ; PI-0285-2016//Consejería de Salud y Consumo, Junta de Andalucía/ ; PI18-RT-3364//Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía/ ; UMA18-FEDERJA-194//Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucía/ ; },
mesh = {Humans ; *Extracellular Vesicles/metabolism ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Chemical and Drug Induced Liver Injury/metabolism/microbiology/pathology ; Male ; Female ; Hep G2 Cells ; Middle Aged ; *Fatty Liver/metabolism/microbiology/pathology ; Disease Progression ; Aged ; Adult ; },
abstract = {The role of extracellular vesicles secreted by the gut microbiota present in faeces (fEVs) is not well known in metabolic dysfunction-associated steatotic liver disease (MASLD) and idiosyncratic drug-induced liver injury (DILI). We identify the microbiome profiles of fEVs in these liver diseases, and analyse the effects of fEVs from MASLD, without (F≤2) or with (F≥3) significant liver fibrosis, and DILI patients on inflammation, steatosis and mitochondrial function. DILI patients showed a consistent pattern in fEVs, characterised by a decrease in Paraprevotella and an increase in AAP99, Acinetobacter, Actinobacillus, Aerococcus and Anaeroglobus. A higher presence of 16S rDNA was observed in plasma EVs from MASLD and DILI patients. HepG2 cells treated with DILI and MASLD F≥3 fEVs increased TLR4, TLR5, IL6 and CASP3 expression, and accumulation of lipid droplets. DILI fEVs enhanced the hepatotoxic impact of diclofenac on the response to microbial components (TLR4, TLR5), inflammatory response (IL1B, IL6), accumulation of lipid droplets and mitochondrial dysfunction (OPA1, DNM1L). In conclusion, bacterial EVs enter the bloodstream and could modulate the immune response. DILI and MASLD F≥3 fEVs are drivers of the pro-inflammatory response and hepatocyte steatosis. DILI fEVs have a distinct bacterial profile that enhances the hepatotoxic potential of diclofenac.},
}

Humans
*Extracellular Vesicles/metabolism
*Feces/microbiology
Gastrointestinal Microbiome
*Chemical and Drug Induced Liver Injury/metabolism/microbiology/pathology
Male
Female
Hep G2 Cells
Middle Aged
*Fatty Liver/metabolism/microbiology/pathology
Disease Progression
Aged
Adult

@article {pmid41841328,
year = {2026},
author = {Akachoud, O and Langrand, J and Bouamama, H and Facon, N and Laruelle, F and Qaddoury, A and Lounès-Hadj Sahraoui, A},
title = {Comparative Analysis of Lavandula Dentata Rhizosphere Microbiota Across Different Developmental Stages in a Semi-Arid Area.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70318},
doi = {10.1111/1758-2229.70318},
pmid = {41841328},
issn = {1758-2229},
support = {45884PG//PHC-TOUBKAL/21/115-Campus France/ ; //VPMA4 Moroccan project/ ; //CPER Alibiotech and BiHauts Eco de France projects/ ; //Bio-TEAM project (ANR-25-PRIM-0002)/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Lavandula/microbiology/growth & development ; *Bacteria/classification/genetics/isolation & purification ; Morocco ; Mycorrhizae/classification/isolation & purification/genetics ; Biomass ; Fungi/classification/genetics/isolation & purification ; Desert Climate ; Plant Roots/microbiology ; },
abstract = {The positive effects of soil microbiota on plant growth and stress tolerance are well established. However, their role in aromatic and medicinal plants, particularly under arid conditions, remains underexplored. This study examined rhizospheric microbial community dynamics across developmental stages of wild Lavandula dentata L., a semi-arid species threatened with extinction in Morocco. Results showed total microbial biomass peaked at senescence, mainly due to increases in Gram-negative (25.02 μg/g) and Gram-positive (18.11 μg/g) bacterial biomasses. Beta diversity analysis revealed consistent dominance of Actinobacteria, with peaks during senescence and the vegetative phase. Saprotrophic fungi (8.81 μg/g) and arbuscular mycorrhizal fungi (AMF) (4.16 μg/g) biomasses peaked at flowering. The fungal community was dominated by the Ascomycota phylum, with no significant variation across stages. The AMF genus Glomus remained most abundant throughout development. Senescence featured the most complex interkingdom interaction network and high ecological niche heterogeneity, reflected by more negative associations. Overall, the rhizospheric microbial community of L. dentata shifts with plant development, with flowering and senescence as key phases for microbial biomass accumulation and community diversification. Flowering and senescienceez stages seem to represent promising targets for developing biostimulant consortia to improve soil health and crop productivity in arid environments.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
*Lavandula/microbiology/growth & development
*Bacteria/classification/genetics/isolation & purification
Morocco
Mycorrhizae/classification/isolation & purification/genetics
Biomass
Fungi/classification/genetics/isolation & purification
Desert Climate
Plant Roots/microbiology

@article {pmid41841409,
year = {2026},
author = {Chu, J and Xu, X and Xu, Y and Hu, K and Chan, HF and Chen, W and Cheung, KH and Ning, X and Yung, KKL},
title = {Bioengineered Probiotic-Prebiotic Hierarchical Microspheres With pH-Responsive Architecture Reprogram Immunometabolism in Obesity-Related Disorders.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e14910},
doi = {10.1002/smll.202514910},
pmid = {41841409},
issn = {1613-6829},
support = {82361168640//National Natural Science Foundation of China/ ; XJ2024043//Hong Kong Scholars Program/ ; 2021YFF1000700//National Key Research and Development Program of China/ ; N_EdUHK205/23//Joint Research Scheme/ ; JSTJ-2025-292//Jiangsu Youth Science and Technology Talent Support Program/ ; 20220ZB23//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; 82361168640//Joint Research Fund for Overseas Chinese Scholars and Scholars in Hong Kong and Macao/ ; },
abstract = {Obesity is increasingly recognized as a chronic immunometabolic disorder driven by dysregulated gut-adipose communication and microbiota imbalance. Here, we present bioengineered pH-responsive probiotic-prebiotic hierarchical microspheres (MicroSym) that coordinate localized microbial restoration with systemic immune reprogramming to treat obesity-related disorders. MicroSym is fabricated via microfluidic-assisted phase separation coupled with electrostatic spraying, embedding probiotic bacteria within a lotus-derived prebiotic matrix to form a protective yet responsive microenvironment that preserves viability during gastric transit. At intestinal pH, the hierarchical architecture selectively disassembles to release probiotics and prebiotic substrates, fostering beneficial colonization and metabolite production. This symbiotic modulation reshapes the gut immune landscape, suppresses proinflammatory macrophage polarization, and restores adipose tissue homeostasis. In diet-induced obese mice, oral treatment with MicroSym remodels the gut microbiota, improves glucose tolerance, reduces lipid accumulation, and normalizes cytokine profiles without overt toxicity. Transcriptomic profiling and microbiome analyses further validate comprehensive systemic immunometabolic benefits. Collectively, this work establishes a biofabricated symbiotic microsphere platform for controlling microbiota-immune-metabolic crosstalk and offers a translatable therapeutic strategy for obesity-associated immunometabolic disease.},
}

@article {pmid41841412,
year = {2026},
author = {Sabuz, O and Folz, J and Deepika, D and Blanco, J and Schuhmacher, M and Aichinger, G and Kumar, V},
title = {Microbiota-Driven Metabolic Alterations Induced by BPA, TDCPP and PFOA in an Ex Vivo Human Fecal Fermentation Model.},
journal = {Chemical research in toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrestox.5c00516},
pmid = {41841412},
issn = {1520-5010},
abstract = {The gut microbiome is increasingly recognized as a key contributor to chemical toxicity. Endocrine-disrupting chemicals (EDCs) such as bisphenol A (BPA), tris(1,3-dichloro-2-propyl) phosphate (TDCPP), and perfluorooctanoic acid (PFOA) are widespread environmental contaminants with the potential to affect host health. To characterize microbiota-specific response to these compounds, we employed an ex vivo fecal fermentation model using samples from healthy adult donors. Fecal slurries were exposed to BPA, TDCPP and PFOA (75 μM) for up to 24 h under anaerobic conditions. Targeted LC-MS/MS quantified parent compounds over time, while untargeted metabolomics profiled microbial metabolic alterations at 4 and 24 h. TDCPP levels decreased similarly in fecal and abiotic controls, suggesting a nonmicrobial loss (e.g., instability or adsorption), whereas PFOA levels remained stable across donors. Untargeted metabolomics revealed compound- and time-dependent perturbations, with PFOA eliciting the strongest metabolic shifts. A curated set of 124 annotated metabolites indicated disruptions in bile acid transformation short-chain fatty acid production, nucleotide turnover, redox balance, and phytochemical catabolism. Several altered metabolites have been previously linked to immunomodulatory processes, suggesting potential implications for host-microbiota interactions. Overall, this study demonstrates the utility of ex vivo fermentation systems for assessing microbiota-mediated metabolic responses to xenobiotics and highlights the relevance of incorporating microbiome-related end points into chemical risk assessment.},
}

@article {pmid41841444,
year = {2026},
author = {Yin, P and Qiu, B and Xu, L and Xie, S and Zhang, S and Zhang, J and Berglund, B and Yao, M and Li, L},
title = {Ligilactobacillus salivarius Li01 enhances gut microbiota-derived indole-3-propionic acid to alleviate 5-fluorouracil-induced diarrhea in mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00050a},
pmid = {41841444},
issn = {2042-650X},
abstract = {As a widely applied chemotherapeutic agent, 5-fluorouracil (5-FU) frequently causes significant gastrointestinal side effects, particularly diarrhea, a process in which the gut microbiome serves as a crucial mediator. In this study, we evaluated the effect of oral administration of Ligilactobacillus salivarius Li01 (Li01) on 5-FU-induced intestinal mucositis in mice. We discovered that intake of Li01 was associated with alleviated diarrheal symptoms by mitigating inflammation, reducing oxidative stress, and restoring intestinal barrier function. Moreover, transcriptome analysis revealed that the Th17 signaling pathway was significantly suppressed. We also confirmed the essential contribution of the gut microbiota in mediating these effects, since the protective benefits of Li01 were not observed when the gut microbiota was depleted by antibiotics. Furthermore, administration of Li01 markedly increased the production of indole-3-propionic acid (IPA) by the gut microbiota. This key molecule was shown to contribute to the protection against 5-FU-associated diarrhea by activating the pregnane X receptor (PXR). Additionally, a close correlation was identified between IPA levels and the abundance of two bacterial species that form a mutualistic relationship with strain Li01: Lactobacillus reuteri and Lactobacillus johnsonii. In conclusion, our study demonstrates that Li01 alleviates 5-FU-induced diarrhea and microbiota dysbiosis by enhancing gut microbiota-derived IPA, supporting its potential as a probiotic.},
}

@article {pmid41841524,
year = {2026},
author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y},
title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2645267},
doi = {10.1080/19490976.2026.2645267},
pmid = {41841524},
issn = {1949-0984},
mesh = {*Mucins/metabolism ; Animals ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; },
abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.},
}

*Mucins/metabolism
Animals
*Gastrointestinal Microbiome
Humans
Feces/microbiology
Metagenome
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics

@article {pmid41841608,
year = {2026},
author = {Farsi, DN and Cotillard, A and Wilson, B and So, D and Gibson, PS and Slater, R and Probert, C and Morris, S and Scott, SM and Quinquis, L and Pichaud, M and Shetty, S and Tap, J and Le Nevé, B and Rossi, M and Whelan, K},
title = {Gut Microbiome Composition and Function, Diet and Clinical Factors in Relation to Fermentable Carbohydrate-Induced Bloating: A Double-Blind, Randomized, Crossover Trial.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000003997},
pmid = {41841608},
issn = {1572-0241},
abstract = {BACKGROUND: Specific foods are associated with abdominal bloating, which can significantly impact quality of life.

OBJECTIVE: To identify responders to fiber-induced bloating and the mechanisms underpinning clinical and microbial responses.

DESIGN: Double-blind, placebo-controlled, randomized, 2-period, 2-challenge crossover trial in 41 individuals with functional bloating. Participants were randomized to 8 g/d of fructan or α-galacto-oligosaccharides (α-GOS) for 7 days with a 21-day washout. Clinical, nutritional, microbial (shotgun sequencing, metatranscriptomics) and fermentation (short-chain fatty acids, volatile organic compounds, breath hydrogen) profiles were characterized prior to each challenge to identify factors predicting response, and after the challenge to elucidate mechanisms underpinning food-induced bloating.

RESULTS: Thirty-nine participants completed both challenges (39 fructan, 40 α-GOS). Overall, seven (7/39, 17.9%) participants were fructan responders and eight (8/40, 20%) were α-GOS responders (experienced fiber-related symptom induction). Clinical metrics indicative of bloating distinguished responders and non-responders to both challenges, including greater abdominal girth (fructan, p = 0.009; α-GOS, p = 0.030). α-GOS responders had higher breath hydrogen (H2) pre-challenge than α-GOS non-responders (p = 0.011). Trends were identified within metagenomic and metatranscriptomic gut microbial analyses, with higher carbohydrate active enzyme (CAZyme) diversity in fructan responders (pre-challenge, adjusted p-value (padj) = 0.024; post-challenge, padj = 0.042), and greater increase in gene expression for gamma-aminobutyric acid (GABA) degradation in α-GOS responders (padj = 0.041).

CONCLUSION: A higher burden of GI symptoms predicts clinical response to fermentable fibers in functional bloating, while for α-GOS, higher repeated fasting breath H2 is also a predictor. Gut microbiome function and fermentation is associated with functional bloating; however, further investigations are required to draw firm conclusions for the microbial influence in this interplay.ClinicalTrials.gov (Identifier: NCT04802798).},
}

@article {pmid41841712,
year = {2026},
author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE},
title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.},
journal = {Biomeditsinskaia khimiia},
volume = {72},
number = {1},
pages = {62-74},
doi = {10.18097/PBMCR1644},
pmid = {41841712},
issn = {2310-6972},
mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology/drug therapy ; *Microbiota ; Adult ; Case-Control Studies ; *Vagina/microbiology ; Recurrence ; Lactobacillus/genetics/isolation & purification ; Prevotella ; },
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.},
}

Humans
Female
*Candidiasis, Vulvovaginal/microbiology/drug therapy
*Microbiota
Adult
Case-Control Studies
*Vagina/microbiology
Recurrence
Lactobacillus/genetics/isolation & purification
Prevotella

@article {pmid41841726,
year = {2026},
author = {Laakso, H and Hashem Taha, M and Flegal, M and Surette, J and Mysara, M and Klokov, D},
title = {Impact of chronic low-dose external gamma- and internal tritium beta-irradiation on the gut microbiome in the context of intestinal tumorigenesis in Apc[Min/+] mice.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0115625},
doi = {10.1128/msystems.01156-25},
pmid = {41841726},
issn = {2379-5077},
abstract = {UNLABELLED: The gut microbiome (GM) plays an essential role in health, and its dysbiosis can increase the risk of colon cancer. While the detrimental effects of high-dose ionizing radiation on GM have been documented, little is known about the effects of low doses, including from internal exposure to tritium, which is produced by nuclear power generation and emits beta radiation, making it a public concern. We examined the effects of chronic irradiation with internal tritium beta radiation or external [60]Co gamma radiation on GM and intestinal tumorigenesis in the Apc[Min/+] mouse model of colorectal cancer. Mice were exposed to tritiated drinking water (HTO) or gamma radiation at cumulative doses of 0, 10, 100, and 2,000 mGy, followed by intestine, blood plasma, and fecal sample collections at 12, 16, and 20 weeks of age. HTO- and gamma-exposed cohorts had distinct tumor size and multiplicity patterns, with non-monotonous dose-responses. Complex patterns of blood cytokine changes with age, dose, and type of irradiation were recorded. GM analyses using 16S rRNA amplicon sequencing revealed significant changes in alpha and beta diversity in irradiated mice compared to controls, indicating altered microbial dynamics. HTO and gamma radiation induced distinct microbiome changes that did not correlate with tumor and blood cytokine readouts. Our results suggest that chronic exposure to low-dose gamma- or internal HTO beta radiation can affect GM in a radiation type and dose-dependent non-linear manner. Our results provide novel insight into the effects of low-dose gamma- and tritium beta radiation on GM and a possible association with tumorigenesis.

IMPORTANCE: Low-dose ionizing radiation is one of the few environmental stressors that simultaneously reshapes host physiology and the structure-function landscape of resident microbiomes, yet mechanistic insight at ecologically relevant doses has been scarce. By integrating longitudinal 16S rRNA profiling, multiplex cytokine analyses, and quantitative tumor phenotyping in the Apc[Min/+] mouse model, our study demonstrates that continuous exposure to either external [60]Co γ-photons or tritium beta particles perturbs gut microbial community structure in radiation-quality-specific ways and that these shifts track with, and sometimes precede, complex, non-monotonic changes in intestinal tumor burden. The work expands the traditional radiobiology focus from host-centric DNA damage to a systems-level view in which microbe-host-radiation interactions form a dynamic network influencing early colorectal carcinogenesis.},
}

@article {pmid41841743,
year = {2026},
author = {Deblais, L and Derippe, G and Horvat, M and Ranjit, S and Moulia, V and Jimenez Madrid, AM and Kauffman, M and Rotondo, F and Ivey, MLL and Miller, SA and Rajashekara, G},
title = {Dairy manure, glyphosate, and antimicrobials (copper, streptomycin, and triazole) modulated the composition of antimicrobial resistance at the gene and microbial levels in a processing tomato field.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0200325},
doi = {10.1128/spectrum.02003-25},
pmid = {41841743},
issn = {2165-0497},
abstract = {Intensive pesticide use drives antimicrobial resistance (AMR) in agriculture, yet the effects of specific practices remain poorly understood. This study evaluated the impact of dairy manure and agrochemicals (glyphosate, copper, streptomycin, and propiconazole) on the composition of culturable AMR bacteria (CARB), AMR genes (ARGs; n = 87), and the microbiome in a processing tomato field (n = 64 experimental plots). Glyphosate-treated plots harbored the lowest levels of CARB, but the highest prevalence of ARGs (especially tetA, tetB, OXA-50, and OXA-58) in the tomato leaves (P < 0.05). Manure-treated plots had the highest levels of CARB and ARGs in the soil and in tomato leaves (especially ACT-1, LAT, MIR, aadA1, and aphA6). The prevalence of multiple ARGs (IMP-12, ACT-1, DHA, MIR, MOX, OXA-58, OXA-60, ermB, oprj, and oprm) was lower in streptomycin- or propiconazole-treated plots compared to non-treated plots. Shifts in the soil and leaf microbiome correlated with changes in ARG composition, particularly aminoglycoside-, fluoroquinolone-, and beta-lactamase-associated genes. These findings show that dairy manure, glyphosate, and propiconazole significantly alter the tomato field microbiome and ARG landscape, indicating that fungicide and herbicide applications may contribute to AMR development and dissemination similar to conventional antibacterial agents in agricultural ecosystems.IMPORTANCEPlant agricultural practices are commonly used by farmers to assure the yield and quality of crops; however, they are also associated with the emergence and dissemination of antimicrobial-resistant (AMR) pathogens. AMR is a critical concern in plant agriculture, as it can affect food safety, security, and sustainability. To combat this issue, it is critical to understand the impact of agricultural practices on AMR. Our study demonstrated that biological amendment (dairy manure) and pesticides (glyphosate, copper, streptomycin, and propiconazole) significantly exacerbated the AMR burden in the applied tomato field, which could increase the food safety risk of the fruit. Findings from this study will raise awareness among farmers, policymakers, and consumers, promote responsible and judicious use of antimicrobial agents in plant agriculture, and prioritize the development of sustainable practices to mitigate current and future AMR challenges.},
}

@article {pmid41841761,
year = {2026},
author = {Ward, B and Bindels, LB and Balligand, J-L and Bearzatto, B and Bommer, G and Cani, PD and De Greef, J and Dewulf, JP and Gatto, L and Haufroid, V and Jodogne, S and Kabamba, B and Pyr Dit Ruys, S and Vertommen, D and Yombi, JC and Belkhir, L and Elens, L},
title = {Association of nasopharyngeal Dolosigranulum pigrum and Corynebacterium species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0231325},
doi = {10.1128/spectrum.02313-25},
pmid = {41841761},
issn = {2165-0497},
abstract = {This longitudinal study investigated the differential composition of the nasopharyngeal microbiome in patients presenting different COVID-19 infectious phenotypes and its evolution during convalescence, with a focus on post-acute sequelae of SARS-CoV-2 (PASC) and its potential microbiome-related mechanisms. Microbiota composition was assessed for a cohort of healthy participants (n = 25), influenza patients (n = 24), and patients with moderate (n = 50) and severe (n = 57) COVID-19. Samples were collected at two time points: during the acute infection phase and at approximately 3-month follow-up. From collected nasopharyngeal swab samples, metagenomics using shotgun sequencing was performed and the microbiota composition was analyzed. Alpha and beta diversity analyses revealed no significant differences in overall community diversity between patient groups across visits. However, differential abundance testing identified specific species, such as Dolosigranulum pigrum and various Corynebacterium species, whose profiles correlated with PASC development. Furthermore, the analysis of microbial co-associations identifies commensal species, including D. pigrum and Corynebacterium species, which are less abundant in patients who develop PASC, consistent with a potential protective role suggested by experimental studies but not proven by our observational data. Antibiotic use was associated with lower levels of key protective taxa, which may increase susceptibility to PASC in case of superinfection. These findings highlight the potential importance of the nasopharyngeal microbiome in acute COVID-19 disease outcomes and suggest that preserving or restoring a balanced respiratory microbiome could mitigate the risk of COVID-19 persistent symptoms and PASC development. Our results may set the stage for future clinical interventions involving probiotics or microbial-derived metabolites to promote respiratory health post-COVID-19.IMPORTANCEThis study highlights the importance of bacteria naturally found in the upper respiratory tract, particularly the nasopharynx (the nasopharyngeal microbiome), in shaping how severely COVID-19 affects patients and whether they experience persistent symptoms, also called long-COVID or post-acute sequelae of SARS-CoV-2 (PASC). By examining microbiome samples from healthy people, influenza patients, and individuals with COVID-19 during acute and convalescent phases, we found that certain commensal bacteria, namely, Dolosigranulum pigrum and Corynebacterium species, were less abundant in individuals who developed long-COVID and more abundant in those who fully recovered. We also observed that antibiotic treatment was associated with lower abundances of these commensal taxa, in turn coinciding with a higher frequency of PASC. These findings suggest that the composition of the nasopharyngeal microbiome is associated with recovery trajectories after COVID-19 and motivate future research into treatments aimed toward the microbiome to improve respiratory health following infection.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05557539.},
}

@article {pmid41842611,
year = {2026},
author = {Chen, Y and Pan, J and Li, R and Lin, W and Ye, Y and Chen, B and He, H},
title = {Microbiota-Derived Butyrate Preserves Epithelial Integrity Through SIRT1-Mediated Metabolic-Epigenetic Crosstalk in Vulvar Lichen Sclerosus.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {6},
pages = {e71670},
doi = {10.1096/fj.202502946RR},
pmid = {41842611},
issn = {1530-6860},
support = {Y20240609//Wenzhou Science and Technology Bureau/ ; },
mesh = {Female ; Humans ; *Sirtuin 1/metabolism/genetics ; Animals ; *Vulvar Lichen Sclerosus/metabolism/microbiology/genetics/pathology ; Mice ; *Epigenesis, Genetic ; *Butyrates/metabolism/pharmacology ; *Microbiota ; Adult ; Middle Aged ; Gastrointestinal Microbiome ; },
abstract = {Vulvar lichen sclerosus (VLS) is increasingly understood as a disorder shaped by systemic immune-metabolic disturbances and microbiome dysregulation. This study investigated how temporal changes in the gut and reproductive tract microbiota influence gene expression, metabolic status, and therapeutic responses in VLS. Fecal and vaginal samples from 20 VLS patients and 20 healthy women were collected at baseline and four follow-up time points and analyzed using multi-omics profiling. VLS patients exhibited consistently reduced microbial diversity, with increased abundances of Prevotella and Gardnerella and decreased Bifidobacterium and Lactobacillus. These microbial shifts were accompanied by significant upregulation of inflammatory genes (IL-6 and TNF-α) and downregulation of metabolic regulators (FOXO3 and SIRT1), with dynamic changes closely paralleling clinical progression. Metabolomic analysis further revealed marked disruptions in lipid and carbohydrate metabolism, particularly reduced levels of short-chain fatty acids (SCFAs). Functional assays demonstrated that patient-derived microbiota impaired cellular homeostasis by suppressing proliferation, enhancing apoptosis, and amplifying inflammatory signaling in vulvar epithelial and fibroblast models. In vivo, SCFA supplementation most effectively restored SIRT1 expression, reduced inflammatory cytokines, and improved metabolic balance in a DMBA-induced VLS mouse model. Together, these findings highlight a mechanistic link between microbiome dysbiosis, inflammatory activation, and metabolic dysfunction in VLS. They also underscore the therapeutic potential of targeting microbial and metabolic pathways, providing a foundation for microbiome-informed and personalized interventions for VLS.},
}

Female
Humans
*Sirtuin 1/metabolism/genetics
Animals
*Vulvar Lichen Sclerosus/metabolism/microbiology/genetics/pathology
Mice
*Epigenesis, Genetic
*Butyrates/metabolism/pharmacology
*Microbiota
Adult
Middle Aged
Gastrointestinal Microbiome

@article {pmid41842880,
year = {2026},
author = {González-Mercado, VJ and Jean Lim, S and Kumar Singh, P and Sales-Martinez, S and Fernandez-Cajavilca, M and Marrero, LM and Pedro, E and D'Eramo Melkus, G},
title = {Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study.},
journal = {Puerto Rico health sciences journal},
volume = {45},
number = {1},
pages = {3-10},
pmid = {41842880},
issn = {2373-6011},
mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology ; Male ; Female ; Middle Aged ; Pilot Projects ; *Gastrointestinal Microbiome ; *Diet ; Cross-Sectional Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metagenomics ; Neoadjuvant Therapy ; },
abstract = {OBJECTIVE: Examining whether gut microbial taxa abundances and predicted functional pathways correlate with dietary quality scores at the end of neoadjuvant chemoradiotherapy (nCRT) for rectal cancer (RC); identifying differentially abundant bacterial species from the pantothenate and acetyl-coenzyme A biosynthesis pathways that differ among dietary quality groups in a subset of participants.

METHODS: RC patients (n = 30) provided stool samples for 16S rRNA gene sequencing. To validate pathway predictions from the 16S rRNA gene data, stool samples from a subset of 17 participants underwent shallow shotgun metagenomics sequencing (SMS). Dietary quality was calculated using the Prime Diet Quality Score (PDQS; 24-hour recall). 16S rRNA gene data were analyzed using QIIME2, and SMS data were analyzed using HUMAnN2.

RESULTS: At the genus level, Parvimonas, Caproiciproducens, and uncultured Eggerthellaceae abundances positively correlated (Spearman's rho = 0.36 to 0.50) with PDQS scores, whereas abundances of Prevotella, Rothia, Peptostreptococcus, Paeniclostridium, Enterococcus, and Howardella correlated negatively (Spearman's rho = -0.43 to 0.36). Predicted pathways, including those related to B-vitamin biosynthesis and enzyme cofactor biosynthesis (e.g., B5/pantothenate [phosphopantothenate biosynthesis I]), were correlated with higher PDQS scores. Mean abundances of species predicted to encode the vitamin B5-CoA pathway were greater in the high- diet-quality group.

CONCLUSION: Findings suggest important associations between the taxa abundances of gut bacteria and the abundances of predicted B-vitamin biosynthesis pathways and dietary quality at the end of nCRT. Three bacterial species encoding vitamin B5-CoA biosynthesis pathways were prominent in high-dietaryquality participants.},
}

Humans
*Rectal Neoplasms/therapy/microbiology
Male
Female
Middle Aged
Pilot Projects
*Gastrointestinal Microbiome
*Diet
Cross-Sectional Studies
Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Metagenomics
Neoadjuvant Therapy

@article {pmid41843072,
year = {2026},
author = {Tavassoli Razavi, F and Yazdanpanah, E and Shadab, A and Emami, A and Haghmorad, D},
title = {The crosstalk between iron metabolism and immune tolerance in autoimmunity.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {75},
number = {1},
pages = {},
pmid = {41843072},
issn = {1420-908X},
mesh = {Humans ; Animals ; *Iron/metabolism/immunology ; *Immune Tolerance ; *Autoimmunity ; *Autoimmune Diseases/immunology/metabolism ; },
abstract = {BACKGROUND: Iron metabolism has emerged as a critical regulator of immune homeostasis, influencing both innate and adaptive immune responses. Dysregulation of iron balance is increasingly recognized as a key driver of autoimmunity, contributing to oxidative stress, ferroptosis, immune cell dysfunction, and the breakdown of immune tolerance.

FINDINGS: This review explores the complex interplay between iron metabolism and autoimmune diseases, including multiple sclerosis (MS), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE). We highlight how iron overload and deficiency impact immune cell differentiation, macrophage polarization, Treg/Th17 balance, and B cell activation, thereby promoting chronic inflammation and tissue damage. Moreover, we discuss disease-specific mechanisms such as iron accumulation in the CNS in MS, synovial iron overload in RA, and hepcidin-driven anemia and ferroptosis in SLE.

CONCLUSIONS: Emerging therapeutic approaches, including iron chelation, hepcidin modulation, ferroptosis inhibition, and microbiome-targeted interventions, are examined as potential strategies to restore immune tolerance and mitigate autoimmune pathology. Finally, we emphasize the need for precise iron-targeted therapies, integration with immunomodulatory treatments, and the development of reliable iron-related biomarkers to optimize clinical management of autoimmunity.},
}

Humans
Animals
*Iron/metabolism/immunology
*Immune Tolerance
*Autoimmunity
*Autoimmune Diseases/immunology/metabolism

@article {pmid41833046,
year = {2026},
author = {Baghel Chauhan, S and Jaitawat, DPS and Jain, C and Singh, I},
title = {Synergistic Neuroimmune Modulation by Cannabidiol and Probiotics for Therapeutic Advancement in CNS Disorders: A Systematic Review.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273411035251111055748},
pmid = {41833046},
issn = {1996-3181},
abstract = {INTRODUCTION: The gut-brain axis (GBA) is a complex, bidirectional communication network connecting the gastrointestinal tract and central nervous system. Cannabidiol (CBD) and probiotics have shown promising neuroprotective, anti-inflammatory, and immunomodulatory effects. However, the synergistic potential of these agents on the GBA has not been fully explored.

METHODS: A systematic review of recent preclinical and clinical studies was conducted using databases such as PubMed, Scopus, Web of Science, Science Direct, and Google Scholar. The review focused on the individual and combined effects of CBD and probiotics on gut microbiota composition, neuroinflammation, neurotransmitter modulation, and immune signalling. Mechanistic insights involving the endocannabinoid system and microbiome-derived metabolites were also analyzed.

RESULTS: Evidence suggests that both CBD and probiotics can enhance gut microbial diversity, regulate pro-inflammatory cytokines, and increase neuroactive metabolites like serotonin and short-chain fatty acids. These effects may improve vagus nerve activity and gut-brain communication, indicating therapeutic potential for managing anxiety, depression, and neurodegenerative conditions. However, human studies remain limited in scale and duration.

DISCUSSION: The observed benefits of CBD and probiotics suggest a synergistic mechanism through gut-brain axis modulation, addressing both neurological and immunological pathways. While animal studies are promising, translation to clinical practice requires further evidence.

CONCLUSION: CBD and probiotics represent a novel combinatorial approach for managing central nervous system disorders through GBA modulation. Future clinical trials should establish optimal dosing, long-term safety, and therapeutic efficacy to validate their use in neuroimmune conditions.},
}

@article {pmid41833200,
year = {2026},
author = {Roach, T and Stegner, M and Clara, D and Ametrano, CG and Compant, S and Gerna, D},
title = {Seed ageing increases the influence of native microorganisms on germination.},
journal = {Microbiological research},
volume = {308},
number = {},
pages = {128493},
doi = {10.1016/j.micres.2026.128493},
pmid = {41833200},
issn = {1618-0623},
abstract = {Improper seed storage conditions, such as elevated temperature and moisture, accelerate ageing and compromise seed quality. However, the impacts of ageing on the seed microbiome and the resulting consequences for germination performance remain poorly understood. Here, we characterised how ageing soybean (Glycine max) seeds at 45 °C and 75% RH affects seed fungal communities, metabolism relevant to microbial growth, and sensitivity of germination to fungal challenge. Additionally, we assessed a role for endophytic bacteria in controlling pathogenic fungi. Amplicon sequencing revealed that ageing decreased fungal richness and reshaped community structure and composition of dominant taxa in seeds. Fusarium and Rhizopus isolates inhibited germination of non-aged seeds, whereas Sarocladium, Plectosphaerella, and Cladosporium impaired germination of aged seeds only. During imbibition, ageing increased seed metabolite leakage, including pinitol, glucose, and fructose, which promoted fungal growth in vitro. Among 39 endophytic bacteria previously isolated from soybean seeds, Bacillus toyonensis C55 and B. pumilus AM26 antagonised fungal growth, consistent with genomic regions associated with antifungal activity. Ageing oxidised the seed cellular redox state, and fungi tolerated oxidative growth conditions better than bacteria. In two cultivars, seed inoculation with B. toyonensis C55 increased germination, supporting a role in regulating fungal infections, whereas B. pumilus AM26 impaired germination. Notably, neither Bacillus strain affected germination of high-vigour non-aged seeds. Fluorescence in situ hybridisation microscopy revealed that both strains recolonised the seed endosphere following ageing. We conclude that oxidation during seed ageing contributes to increased sensitivity to fungal pathogens, which can be modulated by certain bacteria.},
}

@article {pmid41833276,
year = {2026},
author = {Cao, J and He, K and Chen, X and Wang, J and Yin, Q and Ouyang, W and Wang, H and Lin, J and Fan, C},
title = {Multi-omics profiling complements physicochemical monitoring by revealing functional signatures of dissolved oxygen status in the Xijiang River.},
journal = {Water research},
volume = {297},
number = {},
pages = {125609},
doi = {10.1016/j.watres.2026.125609},
pmid = {41833276},
issn = {1879-2448},
abstract = {This study established a multi-level diagnostic framework for dissolved oxygen (DO) variation and associated degradation risk by integrating conventional water quality analysis, untargeted metabolomics, and microbiome profiling. This framework aims to identify DO-related functional degradation signals that are difficult to resolve using conventional indicators alone. The results show that, although nutrient concentrations were broadly comparable between high-DO waters (6.14 ± 0.9 mg/L) and low-DO waters (3.52 ± 0.6 mg/L), pronounced differences were observed in microbial community structure and metabolic profile composition. Among the 794 metabolites identified, 79 metabolites were significantly associated with DO variation, with nitrogen-containing organic compounds and short-chain fatty acids showing systematic enrichment under low-DO conditions, suggesting reduced efficiency of aerobic organic matter transformation. Further integration of differential analysis and correlation analysis enabled the construction of a DO-associated network consisting of six key microbial functional groups (|log2FC| = 0.58-2.53, |r| = 0.51-0.83) and 32 differential metabolites, which was primarily linked to aerobic transformation processes of steroids and xenobiotic organic compounds. At the pathway level, the arginine-proline metabolic axis exhibited a stable association with DO variation, and the intermediate metabolite N-carbamoylputrescine showed a significant positive correlation with DO concentration (|r| = 0.57), indicating its potential as a process-related indicator of oxygen consumption status. Overall, this study expands the scope of DO-oriented water quality diagnosis from molecular, microbial, and metabolic pathway perspectives, and provides multi-omics diagnostic clues that may inform the development of process-informed approaches for earlier detection and refined assessment of DO-related water-quality risks.},
}

@article {pmid41833509,
year = {2026},
author = {Brinker, P and Salles, JF and Beukeboom, LW and Fontaine, MC},
title = {Host-Associated Bacterial Community Changes After Laboratory Introduction Vary With Wolbachia Presence.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70265},
pmid = {41833509},
issn = {1462-2920},
support = {//Adaptive Life scholarship of the University of Groningen, The Netherlands/ ; },
mesh = {*Wolbachia/physiology/genetics ; Animals ; *Wasps/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Female ; *Host Microbial Interactions ; },
abstract = {Translocating organisms from their natural habitats to laboratories can significantly alter their microbial communities, yet this impact is often overlooked. While common in research, the effects on microbiomes and how laboratory findings relate to natural field dynamics require further study. Symbionts may stabilise microbial communities or increase susceptibility to change, influencing results. This study investigates the effects of laboratory translocation on host-microbiome interactions using the parasitic wasp Asobara japonica and its endosymbiont Wolbachia. Three infected (asexual) and three uninfected (sexual) lines, each with seven iso-female lines, were introduced into the laboratory to track microbial community changes over four generations via 16S rRNA gene sequencing. Our results show laboratory translocation reduces bacterial diversity, with stochastic processes driving changes in the microbial community. Changes in bacterial composition differed between sexual and asexual lines. Over four generations, the asexual wasps' bacterial community became more similar, while sexual wasps exhibited greater diversity. Notably, changes in bacterial communities emerged over generations rather than in the first generation. Finally, Wolbachia abundance varied following laboratory introduction, likely impacting bacterial community structure and assembly over time. Overall, our research highlights how laboratory conditions can affect host-associated microbial communities in different ways, potentially impacting their functions and host interactions.},
}

*Wolbachia/physiology/genetics
Animals
*Wasps/microbiology
*Bacteria/classification/genetics/isolation & purification
Symbiosis
*Microbiota
RNA, Ribosomal, 16S/genetics
Female
*Host Microbial Interactions

@article {pmid41833536,
year = {2026},
author = {Li, H and Cai, LQ and Mou, Q and Sun, YF and Yang, KY and Liang, YS and Li, HS and Pang, H},
title = {A free-living Serratia symbiotica strain enhances aphid development, potentially through alteration of host nutritional composition.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70719},
pmid = {41833536},
issn = {1526-4998},
support = {//Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; //National Natural Science Foundation of China/ ; //National Key Research and Development Program of China/ ; JCYJ20250604175510013//the Shenzhen Science and Technology Program/ ; },
abstract = {BACKGROUND: Aphids harbor diverse microbial communities that influence their development, reproduction, and stress tolerance. In our previous work, we identified a free-living strain of Serratia symbiotica, SsMj, which is highly abundant in the gut of Megoura crassicauda. However, the biological effects of SsMj on its aphid host remain largely unknown.

RESULTS: In this study, SsMj- M. crassicauda were generated by rearing newly hatched nymphs separately from their parthenogenetic SsMj+ parents. Absolute quantification of the microbiome revealed that, apart from the loss of SsMj, the overall bacterial abundance and diversity did not differ significantly between SsMj- and SsMj+ aphids. Nevertheless, SsMj- individuals exhibited slower development, smaller body size, reduced survival, and produced more offspring compared to their SsMj+ counterparts. Metabolomic analyses further showed that SsMj- aphids accumulated higher levels of several sugars but lower concentrations of multiple amino acids. Consistently, the insulin-like peptide (ILP) gene showed elevated expression across developmental stages in SsMj- aphids, which is likely to reflect a response to nutrient imbalance. RNA interference targeting ILP significantly delayed development, confirming its regulatory role in aphid growth. Comparative genomics showed that the SsMj genome contains a high number of genes involved in amino acid synthesis pathways than both obligate and facultative S. symbiotica strains, a pattern consistent with other free-living strains.

CONCLUSION: Our findings indicate that S. symbiotica plays an essential role in aphid nutrient metabolism, and is likely to be facilitating the conversion of dietary sugars into amino acids to support host development. The fitness benefits conferred by this free-living S. symbiotica strain suggest a close, mutualistic-like association with its aphid host, highlighting its ecological and physiological significance in insect-microbe interactions. © 2026 Society of Chemical Industry.},
}

@article {pmid41833558,
year = {2026},
author = {Karampela, AI and Druce, M},
title = {The Relationship Between Polycystic Ovary Syndrome (PCOS) and Depression.},
journal = {Clinical endocrinology},
volume = {},
number = {},
pages = {},
doi = {10.1111/cen.70124},
pmid = {41833558},
issn = {1365-2265},
abstract = {OBJECTIVE: Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder, frequently accompanied by psychological comorbidities including depression. The aim of this narrative review is to summarise the latest research regarding potential contributors to and underpinning mechanisms of this relationship.

DESIGN: A detailed search of the PubMed database was carried out beginning with systematic reviews and using the 'snowballing' method to identify further studies. The results yielded were assessed for quality using the GRADE framework. Depression in all studies was assessed using validated questionnaires.

RESULTS: The association of PCOS and depression is bidirectional and multifactorial. The role of biological factors such as hyperandrogenism, metabolic dysregulation, chronic low-grade inflammation, gut microbiome, and genetic and epigenetic factors are highlighted. Also, psychosocial contributors includingillness perception (obesity, acne and hirsutism), menstruation, infertility issues, and sexual dysfunction, as well as eating disorders have a prevalent role. The majority of the studies included were systematic reviews and cross-sectional original research studies.

CONCLUSION: Given the complex pathophysiology underpinning both diseases independently as well as in combination, despite evolving research, there is no single unifying link. However, this highlights the need for mental health risk stratification, addressing possible contributing factors, and offering the support required for patients with PCOS and depression.},
}

@article {pmid41833567,
year = {2026},
author = {De la Vega-Camarillo, E and Quattrone, AC and Okumoto, S and Rajan, N and Hernández-Rodríguez, C and Bernal, JS and Antony-Babu, S},
title = {Bridging the Cultivation Gap in Plant Microbiomes: A Comparative Study of Aerial Root Mucilage Microbiome Characterization by Conventional Isolation, Prospector High-Throughput Cultivation, and Molecular Profiling.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70268},
doi = {10.1002/mbo3.70268},
pmid = {41833567},
issn = {2045-8827},
support = {13322389//USDA NIFA-AFRI/ ; 2208267//USDA NIFA-AFRI/ ; 20240945//SIP projects/ ; 20251163//SIP projects/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Plant Roots/microbiology ; *Sorghum/microbiology ; High-Throughput Nucleotide Sequencing ; Phylogeny ; DNA, Bacterial/genetics ; *Plant Mucilage ; },
abstract = {The "great plate count anomaly" represents a fundamental challenge in microbiome research, with vast microbial diversity remaining uncultivable. We systematically compared three methodological approaches for characterizing plant-associated bacterial communities: conventional plate cultivation, the high-throughput Prospector platform, and full-length 16S rRNA nanopore sequencing. Using mucilage-associated bacteria from teosinte and sorghum as model systems, we evaluated efficiency, taxonomic coverage, and inherent biases. The Prospector platform dramatically outperformed conventional cultivation, achieving 8x to 13.5x improvements in isolate recovery (342 vs. 43 isolates from sorghum; 379 vs. 28 from teosinte) and 1.5x to 1.8x improvements in genus-level detection. While metabarcoding detected 82 total genera, cultivation methods captured only 35.4% of this diversity, with Prospector recovering 16.9%-25.7% compared to 11.3%-14.3% for conventional methods. Each approach exhibited distinct taxonomic biases: conventional plating favored fast-growing taxa (Pseudomonas, Pantoea, Bacillus), Prospector accessed slower-growing bacteria (Sphingomonas, Curtobacterium), while metabarcoding exclusively detected 59-85 cultivation-resistant genera. We propose an integrated framework leveraging complementary strengths: metabarcoding for comprehensive profiling, Prospector for enhanced cultivation efficiency, and conventional isolation for targeted applications. Together, our findings establish quantitative benchmarks for method comparison and support an integrative framework that combines metabarcoding for comprehensive profiling, the Prospector platform for enhanced cultivation efficiency, and conventional isolation for targeted applications, highlighting how methodological choices fundamentally shape our understanding of microbial diversity.},
}

*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Plant Roots/microbiology
*Sorghum/microbiology
High-Throughput Nucleotide Sequencing
Phylogeny
DNA, Bacterial/genetics
*Plant Mucilage

@article {pmid41833719,
year = {2026},
author = {Zheng, L and Huang, J and Ni, H and Kuang, X and Liao, J and Qu, Z and Liu, H and Huang, C and Yu, L and Dai, L and Leung, EL},
title = {Systematic profiling of human gut bacteria with cyclic di-AMP secretion to enhance anti-tumor immunity.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.03.013},
pmid = {41833719},
issn = {2090-1224},
abstract = {INTRODUCTION: Gut microbiota-derived metabolites play pivotal roles in clinical tumor treatment and progression. Cyclic di-AMP serves as both a bacterial signaling molecule and an immune activator of the STING pathway. However, knowledge on cyclic di-AMP production by gut commensals remains limited, hindering the rational application of gut bacteria in cancer therapy.

OBJECTIVES: This study systematically characterizes the metabolic profiles and genotypes associated with cyclic di-AMP synthesis in human gut commensals. We further validate the immune-activating and anti-tumor effects of high cyclic di-AMP-producing probiotics in both in vitro and in vivo non-small cell lung cancer models.

METHODS: Cyclic di-AMP levels (intracellular and extracellular) were quantified via LC-MS in 51 representative gut bacterial species derived from 442 strains isolated from 119 human fecal samples. STING pathway activation was assessed by co-culturing THP-1 cells with supernatants from high cyclic di-AMP-producing gut probiotics. Anti-tumor efficacy was evaluated in a non-small cell lung cancer mouse model.

RESULTS: Screening of 51 gut bacterial species identified 24 high cyclic di-AMP producers, with 18 exhibiting robust secretion capacity. Bioinformatic annotation revealed genes governing cyclic di-AMP synthesis, degradation, and secretion. Two food-grade probiotics, Limosilactobacillus fermentum DA785 and Lacticaseibacillus rhamnosus R7970, demonstrated efficient cyclic di-AMP secretion. Their supernatants significantly upregulated STING pathway-related gene expression and IFN-β secretion in THP-1 cells. Oral administration of these strains suppressed tumor growth in mice by activating immune responses within the tumor microenvironment. And Limosilactobacillus fermentum DA785 suppresses tumor growth via the STING pathway.

CONCLUSION: This study highlights the therapeutic potential of food-grade probiotics with high cyclic di-AMP production to augment anti-tumor immunity, offering a novel microbiome-based strategy for cancer treatment.},
}

@article {pmid41833797,
year = {2026},
author = {Pinos-Tamayo, EA and Domínguez-Borbor, C and Morales, I and Ramírez, M and Sonnenholzner, S and Rodríguez, J},
title = {Breaking paradigms: Reconsidering the role of harmless vibrios in shrimp health.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108597},
doi = {10.1016/j.jip.2026.108597},
pmid = {41833797},
issn = {1096-0805},
abstract = {Vibriosis is a leading cause of economic losses in the shrimp industry worldwide, affecting both larvae and juveniles. Vibrio species (Vibrio spp.) are ubiquitous in marine and aquaculture environments, and their ability to thrive in warm, nutrient-rich conditions makes them omnipresent in shrimp microbiota. While pathogenic species such as Vibrio parahaemolyticus are responsible for acute hepatopancreatic necrosis (AHPND), there is increasing evidence on non-pathogenic Vibrio strains that can naturally limit the proliferation of pathogenic species. This review examines the environmental and ecological factors that help explain the predominance of Vibrio spp. in aquaculture systems and synthesizes the current knowledge on how microbial imbalance caused by pathogenic vibrios, particularly V. parahaemolyticus, affects shrimp health. We highlight the emerging evidence that beneficial Vibrio strains can improve microbiota stability, modulate immune responses, and competitively exclude pathogens. The focus is on Vibrio diabolicus (Ili strain) and its potential role in strengthening shrimp resilience against pathogenic Vibrio spp. Biosecurity considerations and challenges in incorporating beneficial Vibrio spp. into vibriosis management strategies are also addressed. By reframing vibrios as both threats and potential allies, this review proposes a new perspective for developing microbiome-based approaches for the sustainable control of vibriosis in shrimp aquaculture.},
}

@article {pmid41833938,
year = {2026},
author = {Li, D and Qu, ZS and Wang, C and Peng, ZH and Zhou, X and Cai, L},
title = {The Anna Karenina principle in the assembly of plant microbiome under pathogen stress.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00964-2},
pmid = {41833938},
issn = {2055-5008},
support = {U24A20343//National Natural Science Foundation of China/ ; 32300009//National Natural Science Foundation of China/ ; 32330002//National Natural Science Foundation of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.},
}

@article {pmid41833944,
year = {2026},
author = {d'Haens, EJ and Debast, SB and Rossen, JWA and Visser, DH and Bergman, KA and Termote, JUM and Wolfs, TFW and Loeffen, YGT and Hutten, MC and Lorente Flores, C and Kornelisse, RF and Bekker, V and Nijholt, IM and Hemels, MAC},
title = {Short Antibiotic Treatment for Coagulase-negative Staphylococcal Sepsis in Premature Infants: A Multicenter Noninferiority Study.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000005209},
pmid = {41833944},
issn = {1532-0987},
abstract = {BACKGROUND: Optimizing antibiotic duration in neonatal intensive care units is essential for antimicrobial stewardship and microbiome preservation. However, the safety of short antibiotic courses for uncomplicated late-onset coagulase-negative staphylococcal (CoNS) sepsis remains uncertain.

AIM: To determine whether short (≤96 hours) antibiotic treatment of uncomplicated CoNS sepsis in premature infants admitted to a neonatal intensive care unit is noninferior to long treatment (>96 hours) by comparing relapse rates.

METHODS: This multicenter, observational cohort study reviewed all proven neonatal CoNS sepsis in premature births <32 weeks admitted to 8 neonatal intensive care units in the Netherlands between 2017 and 2020. Uncomplicated CoNS sepsis was defined as clinical recovery within 24-48 hours, no central venous line in place or removed after the onset of sepsis, no signs of necrotizing enterocolitis or infected thrombus, and no Staphylococcus lugdunensis bacteremia. Data on patient characteristics, antibiotic treatment and relapse rates were systematically collected. The incidence of relapse (<72 hours after discontinuation of treatment) was calculated as the proportion (%) of the total. The noninferiority margin was set at 2%. A Pnoninferiority value <0.025 was considered significant.

RESULTS: A total of 669 proven late-onset CoNS sepsis were identified. Of these, 390 were uncomplicated. Among uncomplicated cases, 172 were treated ≤96 hours and 218 >96 hours. Patient characteristics showed no significant differences. One relapse occurred in the short-treatment group (0.58%), none in the long-treatment group, with a significant Pnoninferiority value of 0.007.

CONCLUSIONS: The relapse rate in uncomplicated CoNS sepsis was extremely low (<1%), even with short-course treatment. In premature infants with uncomplicated CoNS sepsis, shorter antibiotic treatment is noninferior to longer treatment, confirming its safety and effectiveness.},
}

@article {pmid41834018,
year = {2026},
author = {Straub, D and Englert, T and Beller, A and Stadelmaier, J and Stahl, M and Kilian, J and Borzym, J and Rotermund, C and Akbuğa-Schön, T and Krakau, S and Czemmel, S and Weiler, S and Pettenkofer, M and Pettenkofer, J and Maser, U and Dammeier, S and Nieß, AM and Enderle, MD and Nahnsen, S},
title = {Resistance Training Reshapes the Gut Microbiome in a Longitudinal 8-Week Intervention in Sedentary Adults.},
journal = {Sports medicine - open},
volume = {12},
number = {1},
pages = {},
pmid = {41834018},
issn = {2199-1170},
abstract = {BACKGROUND: The gut microbiome plays a critical role in metabolism, immunity, and aging. While endurance training has been shown to beneficially modulate the microbiome, the effects of resistance training remain less clear, with some studies reporting minimal changes. This project aims to investigate whether structured resistance training elicits significant changes in gut microbiome composition and diversity in sedentary, healthy adults. 150 participants (85 female, 63 male), between 24 and 61 years of age, completed an 8-week supervised resistance training program between May 2022 and July 2023 in the cities of Tübingen and Rottenburg, Germany. Session-level training data, including weights and repetitions, were recorded alongside metrics like load and compliance. Fecal samples were collected throughout the study period at designated timepoints for 16S rRNA gene amplicon sequencing to assess microbiome composition and for metabolomics analyses to evaluate microbial metabolic activity.

RESULTS: No differences in microbial diversity were observed, and there were no significant changes in microbial community composition or fecal metabolomics across all participants post-training. However, within-individual microbial community changes significantly correlated with strength improvement (Pearson correlation coefficient r = 0.167, p = 0.0004), and significantly stronger shifts in beta diversity were observed in participants with ≥ 33% average strength gains compared to those with ≤ 12.2% gains (Kruskal-Wallis rank sum test, p = 0.08). In these high responders, differential abundance analysis revealed time-dependent microbial changes, with 27 taxa enriched or depleted by week 8 of training (ANCOM-BC2, ≥ 2-fold change, p ≤ 0.05). Notably, Faecalibacterium and Roseburia hominis-both associated with a healthier, anti-inflammatory microbiome-were significantly enriched. Many differentially abundant taxa belonged to the Lachnospiraceae family.

CONCLUSIONS: Resistance training drives significant, time-dependent gut microbiome changes, particularly in those demonstrating greater improvements in strength. These shifts mirror endurance training effects and may reflect improved overall health.},
}

@article {pmid41834265,
year = {2026},
author = {Bradley, R and A Staab, C and E Jamieson, P and O Langley, B and O Metz, T and F Stevens, J},
title = {Safety and Tolerability of Xanthohumol in Adults With Crohn's Disease: Results of a Triple-Masked, Randomized, Placebo-Controlled Phase 2 Trial.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {6},
pages = {e70438},
pmid = {41834265},
issn = {1613-4133},
support = {R01HL146549/HL/NHLBI NIH HHS/United States ; R01AT010271/AT/NCCIH NIH HHS/United States ; K24AT011568/AT/NCCIH NIH HHS/United States ; },
mesh = {Humans ; *Propiophenones/adverse effects/therapeutic use ; *Crohn Disease/drug therapy ; Adult ; Male ; Female ; *Flavonoids/adverse effects/therapeutic use ; Middle Aged ; Double-Blind Method ; Young Adult ; gamma-Glutamyltransferase/blood ; Body Mass Index ; Humulus/chemistry ; },
abstract = {Xanthohumol (XN), a flavonoid from hops (Humulus lupulus), exhibits mucosal anti-inflammatory, antioxidant, and microbiome-modulating effects, making it a candidate therapeutic for inflammatory bowel disease. We assessed the safety and tolerability of XN in adults with Crohn's disease (CD) over 8 weeks. In this randomized, triple-masked, placebo-controlled phase 2 trial, 20 adults with unremitted CD received either 24 mg/day XN or placebo for 8 weeks. Primary outcomes included clinical laboratory toxicology parameters, vital signs and adverse events (AEs). Disease activity was screened and assessed using the Crohn's Disease Activity Index (CDAI). XN was well tolerated, with adherence exceeding 95%. Neither halting nor stopping criteria were met, and all laboratory elevations were minor and transient in both groups. There were no attributable serious AEs in either group, and all moderate AEs were short-term and self-resolving. Between-group comparisons demonstrated differences for changes in BMI and gamma-glutamyltransferase (GGT), favoring XN: BMI: -0.67 (0.0, 1.3), p = 0.04 and GGT: -4.8 U/L, 95% CI 0.8-8.8, p = 0.02, which may reflect beneficial effects on hepatic and metabolic health in CD. XN at 24 mg/day was safe and well tolerated in adults with active CD, supporting further research in inflammatory bowel disease.},
}

Humans
*Propiophenones/adverse effects/therapeutic use
*Crohn Disease/drug therapy
Adult
Male
Female
*Flavonoids/adverse effects/therapeutic use
Middle Aged
Double-Blind Method
Young Adult
gamma-Glutamyltransferase/blood
Body Mass Index
Humulus/chemistry

@article {pmid41834313,
year = {2026},
author = {Giacomo Fassini, P and Rezzi, S},
title = {Omega-3 fatty acids and human health: why strong claims remain on fragile consensus.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCO.0000000000001224},
pmid = {41834313},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: Omega-3 (ω-3) polyunsaturated fatty acids (PUFAs) consumption remains widespread despite inconsistent reported health benefits. This review discusses multiple issues related to the efficiency of ω-3 PUFAs on human health including factors driving ω-3 PUFAs bioavailability and growing concerns about product quality.

RECENT FINDINGS: Recent clinical research reports ω-3 PUFAs benefits in various areas including cardiometabolic health, inflammation, cognitive protection, pregnancy outcomes, cancer and certain neuropsychiatric conditions. However, effects on healthy individuals and dietary recommendations need stronger clinical evidence. Heterogeneity in supplementation response involves genetic variability, microbiome, oxidative stress, diet and differences in supplementation protocols. Moreover, some of ω-3 PUFAs products are prone to significant oxidative degradation which can drastically reduce health benefits while possibly being detrimental. Yet ω-3 PUFAs oxidation status of products remains rarely reported and the effects of long-term consumption of oxidized lipids in humans still need to be established.

SUMMARY: Future clinical practices and research should shift toward biomarker-guided and personalized ω-3 PUFAs intervention strategies with mandatory prerequisite knowledge about product quality, e.g. dietary supplements and ω-3 PUFAs rich/fortified foods, and baseline blood-based ω-3 PUFAs nutritional status. Standardized reporting of formulation, oxidation status, and participant baseline characteristics is essential to clarify dose-response relationships and optimize therapeutic efficacy of ω-3 PUFAs.},
}

@article {pmid41834342,
year = {2026},
author = {Wade, SJ and Kumar, AA and Nitschke, SO and Joyce, P and Minaei, E and Reuter Lange, SE and Penney, C and Warren, H and Shepherd, R and Dinoro, JN and Wallace, GG and Dosseto, A and Ansar, S and Islam, N and Lochhead, A and Sharbeen, G and Phillips, PA and Aghmesheh, M and Hawthorne, WJ and Vine-Perrow, KL},
title = {Efficacy and Safety Assessment of 5-Fluorouracil, Irinotecan and Oxaliplatin-Loaded Implants in Mouse and Pig Models for Pancreatic Cancer Therapy.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e22617},
doi = {10.1002/adma.202522617},
pmid = {41834342},
issn = {1521-4095},
support = {APP1165978//Pancare Foundation (administered by Cancer Australia)/ ; 2020/CDF1093//Cancer Institute NSW/ ; RSP-292-2024//Tour de Cure/ ; 2021/CBG0003//Sydney Partnership for Health, Education, Research and Enterprise/ ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains highly resistant to treatment, with mortality rates largely unchanged despite advances in cancer therapies. For ∼80% of borderline, non-resectable, or metastatic cases, chemotherapy is predominantly palliative, underscoring the need for improved drug delivery approaches. This study presents the development, characterization and in vivo evaluation of a novel polymeric implant loaded with 5-fluorouracil, irinotecan, and oxaliplatin (FIRINOX). Scanning electron microscopy of FIRINOX implants showed internal microstructure was preserved upon drug loading, while micro-CT and X-ray imaging revealed valuable insights into the morphology and degradation of implants retrieved from in vivo experiments. In murine PDAC models, dose-escalation identified 4 × FIRINOX implants as the maximum tolerated dose, while 2 × implants achieved significant therapeutic efficacy at lower doses than IV administration, without compromising animal safety. In healthy pigs, 20 × FIRINOX implants were well-tolerated, as confirmed by histopathology and blood analysis. Finally, laser ablation-inductively coupled plasma-mass spectrometry imaging and microbiome analysis confirmed localized drug perfusion within tissues, and minimal off-target effects, including preservation of gut microbiota diversity. These findings support the potential of this implantable platform to improve outcomes in borderline or non-resectable PDAC and enhance tolerability of cytotoxic chemotherapy through localized, controlled delivery, addressing a key gap where current treatment options are limited.},
}

@article {pmid41834639,
year = {2026},
author = {Soliman, MS and Abbas, AM and Algebaly, HF and El-Kholy, AA and Soliman, NS},
title = {Metagenomics profiling of the lower respiratory tract microbiome and relevant respiratory pathogens in pediatric intensive care unit patients: a pilot exploratory study in Egypt.},
journal = {Acute and critical care},
volume = {41},
number = {1},
pages = {136-147},
pmid = {41834639},
issn = {2586-6060},
abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of mortality in children. These infections disrupt the equilibrium of lower respiratory tract (LRT) microbiota, allowing respiratory pathogens to dominate. The conventional culture method has limitations in describing complex microbiomes and may fail in the detection of respiratory pathogens. In the present study, we sought to use the advanced technology of 16S metagenomics next-generation sequencing (16SmNGS) to characterize the LRT microbiome among children with LRTIs and to identify the underlying respiratory pathogens that commonly evade detection by traditional culture.

METHODS: Twenty LRT specimens from hospitalized children with LRTIs were analyzed using 16SmNGS, as well as standard microbiological culture.

RESULTS: The 16SmNGS taxonomical analysis revealed the highest relative abundances for Streptococcus (27.7%) and Escherichia (13.3%) genera, which belong to the phyla of Firmicutes (45.4%) and Proteobacteria (45.3%), respectively. Streptococcus pneumoniae (45%), Escherichia coli (45%), Pseudomonas aeruginosa (15%), Staphylococcus aureus (10%), Acinetobacter baumannii (5%), and Haemophilus influenzae (5%) were the primary respiratory pathogens. Conventional culture failed to detect growth in 100%, 77.7%, and 55.5% of 16SmNGS-positive specimens for H. influenza, S. pneumoniae, and E. coli, respectively.

CONCLUSIONS: The 16SmNGS technique revealed a predominance of Streptococcus and Escherichia genera belonging to the phyla of Firmicutes and Proteobacteria in pediatric LRTIs. In this exploratory study, 16SmNGS was able to enhance the identification of significant respiratory pathogens, particularly those difficult to isolate in culture. However, to rule out contamination by flora, it is advisable not to interpret metagenomics results independently from culture, clinical, and radiological data. In addition, further clinical correlations are desired to reach appropriate clinical decisions.},
}

@article {pmid41834846,
year = {2025},
author = {Jiang, Y and Xiao, D and Zhou, J and Zhang, F and Xiong, Z and Shen, Q and Xiong, X},
title = {Role of probiotic supplementation in preventing ventilator-associated pneumonia among critically ill patients-a critical umbrella review of meta-analyses of randomized controlled trials.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1719310},
pmid = {41834846},
issn = {2296-861X},
abstract = {BACKGROUND: In critically ill patients, gut microbiome balance is often disrupted by antibiotics and disease-related stress. Probiotics may strengthen gut barrier function and lower the risk of ventilator-associated pneumonia (VAP), but their effectiveness in mechanically ventilated patients remains unclear. This umbrella review synthesizes evidence from systematic reviews on the association between probiotic therapy and VAP incidence.

METHODS: A comprehensive search was conducted in PubMed, Embase, Web of Science, the Cochrane Library, Scopus, and China National Knowledge Infrastructure (CNKI) for systematic reviews published from database inception to July 20, 2025. Data were extracted using a standardized form that had been pilot-tested prior to use. Data were synthesized using both narrative and quantitative approaches. The study protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) (registration ID: CRD420251034247).

RESULTS: This umbrella review included 24 meta-analyses of randomized controlled trials (RCTs) involving 92,711 mechanically ventilated critically ill patients. Using a measurement tool to assess systematic reviews, version 2 (AMSTAR 2) tool, the methodological quality varied-a total of 4 were rated critically low, 12 were rated low, 1 was rated moderate, and 9 were rated high. Probiotic supplementation was associated with a reduced risk of VAP [odds ratio (OR) = 0.67, 95% confidence interval (CI): 0.61-0.75; relative risk (RR) = 0.74, 95% CI: 0.69-0.80] and nosocomial infections (OR = 0.81, 95% CI: 0.73-0.90; RR = 0.84, 95% CI: 0.80-0.88). Probiotics showed modest reductions in intensive care unit (ICU) stay [weighted mean difference (WMD) = -1.30 days, 95% CI: -1.59 to-1.02], overall hospital stay (WMD = -1.29 days, 95% CI: -1.79 to -0.79), duration of mechanical ventilation (WMD = -1.64 days, 95% CI: -2.07 to -1.22), and antibiotic use (WMD = -1.26 days, 95% CI: -2.25 to -0.28). The risk of diarrhea decreased based on OR estimates (OR = 0.77, 95% CI: 0.67-0.88), whereas RR estimates did not show a statistically significant difference (RR = 0.98, 95% CI: 0.94-1.01). Probiotic use was associated with a statistically significant reduction in ICU mortality (OR = 0.86, 95% CI: 0.79-0.94; RR = 0.94, 95% CI: 0.90-0.98), whereas hospital mortality was reduced only in RR analyses (RR = 0.92, 95% CI: 0.88-0.97) and not in OR Analyses (OR = 0.92, 95% CI: 0.84-1.01).

CONCLUSION: Probiotics may offer potential benefits for mechanically ventilated, critically ill patients by reducing infections and improving certain clinical outcomes; however, the overall quality of the available evidence remains insufficient to support definitive conclusions.

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD420251034247, CRD420251034247.},
}

@article {pmid41834861,
year = {2026},
author = {Zhang, Z and Hu, X and Ma, Y},
title = {Gut microbiota and ulcerative colitis: a bibliometric analysis of knowledge structure, research hotspots, and future directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1765748},
pmid = {41834861},
issn = {1664-302X},
abstract = {BACKGROUND: Ulcerative colitis (UC), a globally prevalent immune-mediated colonic disorder, is fundamentally linked to intestinal dysbiosis. Despite the exponential growth in related papers, systematic, data-driven bibliometric analyses including global productivity trends, international collaboration networks, citation impact distributions, and the temporal evolution of research topics remain lacking.

METHODS: We conducted a comprehensive bibliometric analysis of 5,879 articles and reviews sourced from the Web of Science Core Collection (WOSCC) and Dimensions (2004-2025). Publication outputs, international collaboration networks, institutional productivity, and keyword evolution were visualized using R-bibliometrix, VOSviewer, and CiteSpace. Lotka's law and Bradford's law were applied to assess author and journal productivity distributions, respectively. Burst detection algorithms identified emerging research frontiers.

RESULTS: Annual publications demonstrated exponential growth, escalating from 36 in 2004 to a projected 819 in 2024. Geographically, China dominated absolute output (n = 2,559), followed by the USA (n = 1,181), with these two nations collectively accounting for 63.6% of global publications, justifying their prominence as the two major hubs in this research field. Harvard Medical School exhibited the highest citation efficiency (296.6 citations per publication), contrasting with volume leaders like Zhejiang University (92 publications). Co-occurrence clustering revealed 18 distinct knowledge domains, converging on five accelerating frontiers: "fecal microbiota transplantation (FMT)," "short-chain fatty acids," "traditional Chinese medicine," "intestinal barrier mechanisms," and "nanoparticle-based microbiota modulation." Burst analysis confirmed these themes-initiated citation surges post-2017, with "nanoparticles" and "intestinal barrier" exhibiting the strongest recent momentum (2023-2025), indicating a paradigm shift from descriptive microbiome profiling to mechanistic, precision-targeted interventions.

CONCLUSION: The UC-microbiome research agenda has transitioned from correlative association studies to multi-layered therapeutic modulation. Future efforts should prioritize standardizing FMT protocols through randomized controlled trials, establishing multi-ethnic longitudinal cohorts to address population-specific microbiome signatures, elucidating dose-response relationships of microbial metabolites, and converging nanodelivery systems with microbiome engineering to optimize therapeutic precision and sustain remission.},
}

@article {pmid41834868,
year = {2026},
author = {Niu, M and Pan, J and Guo, Y and Zhang, F and Guan, H and Yang, X and Li, H and Xiong, H and Zhang, Y and Chen, Y},
title = {Neonatal jaundice and the infant gut microbiome: an integrated shotgun metagenomics and bidirectional Mendelian randomization study in Xinjiang.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761712},
pmid = {41834868},
issn = {1664-302X},
abstract = {BACKGROUND: Neonatal jaundice is a common condition, yet inter-individual variation in its onset and severity cannot be fully explained by traditional clinical risk factors. Emerging evidence suggests that the infant gut microbiome may modulate bilirubin metabolism, but its compositional and functional signatures in jaundiced neonates remain incompletely defined. This study aimed to characterize the taxonomic and functional features of the gut microbiome in neonatal pathologic jaundice and to explore potential causal links using Mendelian randomization (MR).

METHODS: We conducted a case-control study of term infants with pathologic jaundice and matched healthy controls. Stool samples were subjected to shotgun metagenomic sequencing to assess microbial diversity, taxonomic composition, functional gene repertoires, and carbohydrate-active enzyme families, and publicly available genome-wide association study summary statistics were used to perform bidirectional MR between microbiome-related traits and neonatal jaundice.

RESULTS: Alpha diversity indices did not differ significantly between groups, whereas beta diversity based on Bray-Curtis dissimilarity showed clear separation of jaundiced and control infants, indicating a restructured microbial community rather than a simple loss of richness. Jaundiced neonates exhibited increased relative abundance of Gram-negative taxa, including Escherichia coli, and reduced levels of putatively beneficial genera such as Bifidobacterium and Lactobacillus. Functionally, pathways involved in bile acid synthesis and metabolism, carbohydrate and energy metabolism, and cofactor and vitamin biosynthesis were enriched in the jaundiced group, accompanied by marked shifts in carbohydrate-active enzyme profiles. Forward MR suggested that several microbial metabolic pathways exert genetically predicted effects on jaundice risk, whereas reverse MR provided little evidence that genetic liability to jaundice substantially alters microbiome traits.

CONCLUSIONS: Neonatal pathologic jaundice is associated with distinctive compositional and functional alterations in the gut microbiome. Genetic evidence from MR supports a potential causal contribution of specific microbial pathways to jaundice risk, highlighting candidate targets for microbiome-based prevention or adjunctive therapy in early life.},
}

@article {pmid41834873,
year = {2026},
author = {Duan, Y and Zhang, H and He, C and Gao, G and Tang, Q},
title = {Effects of different rotation crops on soil physicochemical properties and microbial community structure in continuous cotton fields.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1740768},
pmid = {41834873},
issn = {1664-302X},
abstract = {Cotton monoculture is widespread in the oasis cotton-growing region of Xinjiang. Long-term continuous cropping has led to declines in soil fertility and imbalances in microbial communities, constraining sustainable, green production. Crop rotation is an effective agronomic practice to mitigate the deleterious effects of continuous cropping; however, the selection of rotation crops and the regulatory mechanisms by which rotation reshapes the soil micro-ecology require systematic clarification. Using continuous cotton (CK) cropping as the control, we combined high-throughput amplicon sequencing with soil physicochemical analyses to evaluate the effects of four previous-crop schemes-cotton → peanut (CPC), cotton → soybean (CSC), cotton → rapeseed (CRC), and cotton → maize (CMC)-on soil properties and the microbial community structure. Relative to CK, the CPC, CSC, and CRC treatments led to significantly reductions in yield and gross output value ranging from 38.72 to 62.23% and 34.54 to 55.35%, respectively. Although the net profit under CPC treatment decreased by 36.27% relative to CK, the benefit-cost ratio showed no significant difference. CPC significantly increased soil organic matter, available phosphorus, NH4[+]-N, and NO3[-]-N, while decreasing the pH and electrical conductivity, demonstrating the best overall improvement in soil fertility. In the fungal community, under CPC, Basidiomycota and Mortierellomycota significantly increased by 17.15 and 52.37%, respectively, whereas Basidiomycota significantly increased under CSC and CRC (by 17.15 and 20.58%). Functional guild analysis indicated that all four rotation schemes significantly reduced the relative abundance of plant pathogen fungi, with the greatest decrease under CPC (36.80%), with statistically significant differences. In the bacterial community, CPC significantly increased Actinobacteriota, Gemmatimonadota, and Firmicutes by 16.20, 15.75, and 29.73%, respectively, while CRC rose substantially Bacteroidota by 28.58%. Bacterial metabolism constituted the major predicted functional category (79.27-79.68%), no significant differences between treatments. Redundancy analysis identified soil moisture and the N/P ratio as key drivers of the variation in the fungal community, while bacterial communities were regulated by N/P, pH, and organic matter. Overall, rotation alleviated continuous-cropping constraints by optimizing soil properties and the soil microbial structure. The results provide an empirical basis for improving soil microbiomes and designing sustainable planting strategies in oasis cotton systems.},
}

@article {pmid41834875,
year = {2026},
author = {Yang, L and Li, T and Liu, R and Zhang, Y and Ainiwaer, M and Wang, S and Liu, Z and Yang, K and Wang, C},
title = {Effects of letrozole supplementation on growth performance, blood indexes, ruminal fermentation parameters, and microbiome composition of hu lambs.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1734219},
pmid = {41834875},
issn = {1664-302X},
abstract = {This study aimed to explore the effects of dietary letrozole (LE) supplementation on growth performance, rumen microbiota, fermentation profiles, and blood metabolites in Hu lambs, providing insights into its potential for enhancing animal production. Twenty-eight male Hu lambs (20.21 kg ± 0.56 kg, 70 days old) were randomly assigned to four groups, with seven replicates per group: a control group (CON), and three test groups (T1, T2, T3). Lambs in the CON group were fed a basal diet, while T1, T2, and T3 groups received 0.05, 0.1, and 0.2 mg/kg BW of LE, respectively, in addition to the basal diet. The experiment lasted for 46 days. The findings were as follows: (1) There were no significant differences among groups in Initial Body Weight (IBW), Final Body Weight (FBW), Average Daily Feed Intake (ADFI), Average Daily Gain (ADG), and feed conversion ratio throughout the entire trial (P > 0.05). (2) Compared with the CON group, plasma testosterone (T) concentrations in Groups T2 and T3 were significantly elevated at 0 h post-supplementation (P < 0.05). Compared with the control group, nitric oxide (NO) levels in Groups T1 and T2 were significantly reduced 4 h after LE supplementation (P < 0.05). (3)Nitric oxide (NO) levels in experimental groups exhibited a secondary change 4 h after supplementation (P < 0.05). There were no significant differences in plasma Total Antioxidant Capacity (T-AOC), Catalase (CAT), Superoxide Dismutase (SOD), Glutathione Peroxidase (GSH-Px), or Malondialdehyde (MDA) levels between 0 h pre-supplementation and 4 h post-supplementation across all experimental groups (P > 0.05). At 0 h before and 4 h after supplementation, Total Protein (TP), Albumin (ALB), and Globulin (GLB) levels in all experimental groups showed no significant differences compared to the CON group (P > 0.05). (4) Ammonia nitrogen (NH3-N) levels were extremely significantly higher in all test groups compared to the CON group (P < 0.05). Propionic acid and isovaleric acid concentrations in Group T3 were significantly higher than in the CON group (P < 0.01), while the ethyl-to-propyl ratio was significantly lower (P < 0.01). (5) At the phylum level, LE-treated groups showed a higher relative abundance of Firmicutes than the CON group (21.04%), with increases proportional to the LE dose: Group T3 (37.88%), Group T2 (32.74%), and Group T1 (30.66%). At the family level, the relative abundance of Prevotellaceae was significantly lower in all test groups compared to the CON group (P < 0.05), while Lachnospiraceae abundance was significantly higher in the test groups (P < 0.01). Under the experimental conditions, supplemental feeding of LE did not significantly affect the overall growth performance of lambs. but it did increase plasma testosterone concentration, elevated the relative abundance of Firmicutes in the rumen, reduced the relative abundance of Bacteroidetes, and altered the rumen fermentation pattern. This shift occurred by decreasing the acetate-to-propionate ratio, increasing isovaleric acid concentration, and promoting a propionic acid fermentation pattern, thereby improving feed utilization. Among all groups, the optimal supplemental feeding rate was determined to be 0.2 mg/kg BW.},
}

@article {pmid41834876,
year = {2026},
author = {Iqbal, M},
title = {Microbial biocontrol agents and the rhizosphere microbiome: integrating ecological function and climate resilience in sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771649},
pmid = {41834876},
issn = {1664-302X},
abstract = {The growing challenges of food insecurity, soil degradation, and climate-induced stresses are exposing the limitations of chemically intensive crop protection systems. In this context, the rhizosphere microbiome, comprising complex microbial networks that regulate plant growth, nutrient acquisition, and immune responses, has emerged as a promising focus for more sustainable agricultural practices. Microbial biocontrol agents (BCAs) are increasingly recognized not only for their pathogen-suppressive properties but also for their potential to modulate rhizosphere microbial communities and contribute to plant tolerance to abiotic stressors. This review synthesizes recent advances in understanding the ecological and mechanistic interplay between BCAs and the rhizosphere microbiome, highlighting how microbial inoculants can influence community assembly, functional processes, and microbiome resilience under biotic and abiotic stress conditions. Drawing on molecular and ecological evidence, the synthesis integrates current knowledge of BCA-mediated regulation of plant defense signalling, nutrient cycling, and stress-associated responses. Key knowledge gaps related to inoculant persistence, ecological compatibility, and microbiome-level trade-offs that limit field-scale effectiveness are also identified. To address these challenges, a microbiome-informed conceptual framework is proposed, emphasizing precision-designed synthetic microbial communities (SynComs), trait-based screening, host-microbiome co-optimization, and integration of BCAs into resilient Integrated Pest Management (IPM) strategies. In summary, this review provides a systems-level perspective on how rhizosphere microbiome dynamics can be leveraged to support sustainable climate-smart crop production.},
}

@article {pmid41834955,
year = {2026},
author = {Zhou, X},
title = {[The Oral Microecological Theory of Dental Caries].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {1},
pages = {1-7},
pmid = {41834955},
issn = {1672-173X},
mesh = {*Dental Caries/microbiology/prevention & control ; Humans ; *Microbiota/physiology ; *Mouth/microbiology ; Homeostasis ; Dysbiosis/microbiology ; Oral Health ; },
abstract = {The microecological theory represents the current understanding of dental caries etiology, emphasizing that the dynamic balance of the structure and function of the oral microbial community plays a central role in the initiation and progression of caries. This theory posits that dental caries is not caused by a single specific pathogen, but rather results from dysbiosis-an imbalance-of the entire oral microecosystem. By redefining caries from an "infectious disease" to an "ecological imbalance disorder," the microecological theory offers a novel perspective for caries prevention, early intervention, and precision treatment. It underscores that maintaining the homeostasis of the oral microecology is more critical than simply eradicating bacteria, and that ecological approaches represent a key strategy for population-level caries prevention. Homeostatic medicine emphasizes that the dynamic equilibrium of the body's internal environment is fundamental to health. As a major microbial habitat and immunological interface, the oral cavity plays a pivotal role in the body's overall homeostatic network. The stability of the oral microbiome is thus a crucial node in systemic homeostasis. Homeostatic medicine provides a systems-oriented framework for understanding dental caries, shifting the paradigm ofcaries management from "fighting pathogens "toward "preserving ecological balance". This integrative approach aims to achieve the broader goal of promoting systemic homeostasis through local oral health promotion.},
}

*Dental Caries/microbiology/prevention & control
Humans
*Microbiota/physiology
*Mouth/microbiology
Homeostasis
Dysbiosis/microbiology
Oral Health

@article {pmid41834958,
year = {2026},
author = {Wan, K and Yang, C and Chen, N and Chen, F},
title = {[The Impact of Oral Microecology on the Development of Inflammatory Bowel Disease].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {1},
pages = {30-36},
pmid = {41834958},
issn = {1672-173X},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Mouth/microbiology ; *Dysbiosis/microbiology/complications ; *Microbiota ; Gastrointestinal Microbiome ; Fusobacterium nucleatum ; Porphyromonas gingivalis ; },
abstract = {This article systematically reviews the associations and mechanisms between the oral microbiome and inflammatory bowel disease (IBD). Relevant literature was retrieved from the PubMed database from January 2000 to October 2025, and 77 articles meeting the criteria for inductive analysis were selected. The results confirm a bidirectional causal relationship between oral dysbiosis and IBD: patients with IBD exhibit reduced oral microbial diversity, increased abundance of pathogenic bacteria (such as Fusobacterium nucleatum and Porphyromonas gingivalis), and a more active oral immune environment. Oral pathogens can migrate to the gut via the oral-gut axis, directly disrupting the intestinal barrier and microbial homeostasis or activating systemic and intestinal immune responses through pathways such as miRNAs carried by exosomes and immune cell migration, thereby exacerbating IBD. However, current studies have several limitations, including small sample sizes, high heterogeneity in conclusions, lack of longitudinal data, and insufficient technical compatibility. Future research should expand investigations into the roles of oral fungi and viruses and integrate multiomics technologies to advance the clinical translation of oral microbiota in IBD diagnosis and treatment.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/immunology
*Mouth/microbiology
*Dysbiosis/microbiology/complications
*Microbiota
Gastrointestinal Microbiome
Fusobacterium nucleatum
Porphyromonas gingivalis

@article {pmid41834964,
year = {2026},
author = {Ma, T and Lian, B and Wu, Z and Zhao, J},
title = {[Differences in Oral and Gut Microbiome Composition Among Preschool Children in Urumqi During the Deciduous and Mixed Dentition Periods].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {1},
pages = {82-89},
pmid = {41834964},
issn = {1672-173X},
mesh = {Humans ; Child, Preschool ; *Tooth, Deciduous/growth & development/microbiology ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; *Dentition, Mixed ; Saliva/microbiology ; Male ; Female ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; China ; },
abstract = {OBJECTIVE: To analyze the oral and gut microbial composition in preschool children during the deciduous and mixed dentition stages, and to investigate the characteristics of microbiota across different dentition stages.

METHODS: Using 16S rRNA gene-based third-generation sequencing, this study analyzed saliva and fecal samples collected from 10 children with deciduous dentition and 10 with mixed dentition. The composition and differences in oral and gut microbiota between the two groups were compared.

RESULTS: The differences in microbial richness (Chao1 index) and evenness (Shannon index) between the oral cavity and intestine were statistically significant (P = 0.001). Firmicutes, Proteobacteria, and Bacteroidetes were the three dominant phyla at both sites. At the genus level, Neisseria and Streptococcus were abundant in the oral cavity, while Bacteroides and Faecalibacterium predominated in the gut. o_Lactobacillus (LDA = 5.04, P < 0.001) was identified as a marker genus in the oral cavity during the deciduous dentition period, while g_Neisseria (LDA = 5.15, P < 0.001) served as an oral marker genus in children with mixed dentition. In the gut, marker genera during the deciduous dentition period included o_Bacteroides (LDA = 5.17, P < 0.001) and f_Lachnospiraceae (LDA = 5.16, P < 0.001), whereas f_Ruminococcus (LDA = 5.09, P < 0.001) and g_Faecalibacterium (LDA = 5.03, P < 0.001) were marker genera during the mixed dentition period. Upregulation of pathways including lactose degradation and nitrate reduction was observed in the oral microbiota, in contrast to the gut microbiota, where enhanced activity of the methanogenesis from acetate pathway was noted.

CONCLUSION: The composition of oral and gut microbiota varies among children at different dentition stages. As dentition changes, the structural diversity and metabolic functions of both oral and gut microbiota also change.},
}

Humans
Child, Preschool
*Tooth, Deciduous/growth & development/microbiology
*Mouth/microbiology
*Gastrointestinal Microbiome
*Dentition, Mixed
Saliva/microbiology
Male
Female
Feces/microbiology
RNA, Ribosomal, 16S/genetics
China

@article {pmid41834973,
year = {2026},
author = {Zhang, S and Li, Y and Yang, Z and Huang, H and Pan, Y},
title = {[Recent Research Progress and Prospects on Periodontitis Affecting Systemic Comorbidities via the Oral-Gut Axis].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {1},
pages = {15-23},
pmid = {41834973},
issn = {1672-173X},
mesh = {Humans ; *Periodontitis/complications/microbiology ; Animals ; *Gastrointestinal Microbiome ; Comorbidity ; *Mouth/microbiology ; Arthritis, Rheumatoid/epidemiology ; Cardiovascular Diseases/epidemiology/etiology ; Diabetes Mellitus/epidemiology/etiology ; Dysbiosis ; Inflammatory Bowel Diseases/epidemiology/etiology ; Inflammation ; },
abstract = {Periodontitis is a prevalent chronic infectious and inflammatory disease worldwide, which imposes harms extending far beyond the oral cavity. A large body of research has demonstrated that periodontitis is closely associated with various systemic diseases, such as diabetes mellitus, cardiovascular diseases, inflammatory bowel disease, and rheumatoid arthritis. Serving as a crucial pathway connecting the oral cavity to the entire body, the oral-gut axis becomes the core mechanism through which periodontitis affects systemic health, primarily via the ectopic colonization of salivary microbiota, intestinal dysbiosis, intestinal barrier disruption, and systemic inflammation. This review summarizes recent studies focusing on how periodontitis influences systemic comorbidities via the oral-gut axis, encompassing clinical studies, animal experimental and in vitro research. We summarize the research progress regarding how periodontitis perturbs intestinal homeostasis through ectopic colonization of oral pathogenic bacteria, immunoinflammation, host factor regulation, and metabolic disorders, and eventually affects systemic diseases via the oral-gut axis. This review aims to provide a new perspective for the prevention and treatment of periodontitis-related systemic comorbidities.},
}

Humans
*Periodontitis/complications/microbiology
Animals
*Gastrointestinal Microbiome
Comorbidity
*Mouth/microbiology
Arthritis, Rheumatoid/epidemiology
Cardiovascular Diseases/epidemiology/etiology
Diabetes Mellitus/epidemiology/etiology
Dysbiosis
Inflammatory Bowel Diseases/epidemiology/etiology
Inflammation

@article {pmid41834983,
year = {2026},
author = {Shang, X and Wang, Z and Ge, S},
title = {[Research Progress on Microbiome-Driven Mechanisms and Intervention Strategies for Oral Malodor].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {1},
pages = {37-43},
pmid = {41834983},
issn = {1672-173X},
mesh = {*Halitosis/microbiology/prevention & control/therapy ; Humans ; *Microbiota/physiology ; *Mouth/microbiology ; Probiotics/therapeutic use ; Porphyromonas gingivalis/metabolism ; Fusobacterium nucleatum/metabolism ; Antimicrobial Peptides/therapeutic use ; Periodontitis/microbiology ; },
abstract = {Oral malodor, a common oral symptom, is primarily caused by the metabolic activities of oral microorganisms. The characteristic odors mainly originate from volatile sulfur compounds produced and released by oral bacteria (such as Fusobacterium nucleatum and Porphyromonas gingivalis) through specific enzymatic systems that break down sulfur-containing amino acids in saliva, gingival crevicular fluid, and food debris. Research indicates that various factors, including periodontitis, fungal infections, smoking, and obesity, can worsen oral malodor by altering the oral microenvironment. For prevention and treatment, novel interventions such as plant extracts, antimicrobial peptides, and probiotics demonstrate superior microbiological safety compared to traditional antimicrobial drugs. These approaches specifically inhibit pathogenic bacteria, disrupt biofilm structures, and regulate oral microbial balance. This review summarizes relevant research advances to provide new theoretical foundations and practical directions for the precise prevention and treatment of oral malodor.},
}

*Halitosis/microbiology/prevention & control/therapy
Humans
*Microbiota/physiology
*Mouth/microbiology
Probiotics/therapeutic use
Porphyromonas gingivalis/metabolism
Fusobacterium nucleatum/metabolism
Antimicrobial Peptides/therapeutic use
Periodontitis/microbiology

@article {pmid41835006,
year = {2026},
author = {Ho, YS and Christidis, M},
title = {Commentary: Global research on the crosstalk between intestinal microbiome and colorectal cancer: a visualization analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779577},
pmid = {41835006},
issn = {2235-2988},
}

@article {pmid41835010,
year = {2026},
author = {Mei, S and Ye, J and Teng, Y and Chen, Y and Long, Y and Zhao, X and Cen, X and Zhang, X and Zhu, C},
title = {Longitudinal associations between PM2.5 with gestational diabetes mellitus mediated by gut microbiome and potential mechanism: based on a prospective pregnant women cohort in China.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1749504},
pmid = {41835010},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; *Diabetes, Gestational/epidemiology/etiology/microbiology ; *Particulate Matter/adverse effects ; *Gastrointestinal Microbiome/drug effects ; China/epidemiology ; Adult ; Feces/microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Air Pollutants/adverse effects ; Dysbiosis ; Bacteria/classification/genetics/isolation & purification ; Longitudinal Studies ; },
abstract = {BACKGROUND: Exposure to particulate matter pollution with aerodynamic diameters < 2.5 μm (PM2.5) has been linked to gestational diabetes mellitus (GDM) and gut microbiota dysbiosis. However, few studies have illustrated the associations among PM2.5 exposure, gut microbiota, blood metabolites, circular RNAs (circRNAs) and GDM risk. This study aimed to explore the moderating effects of the gut microbiota on the association between PM2.5 exposure and GDM, and to analyze the interaction network of PM2.5 exposure, gut microbiota, blood metabolites and circRNAs.

METHODS: Participants (n = 1,248) were selected from the Pregnancy Metabolic Disease and Adverse Pregnancy Outcome (PMDAPO) cohort in Guangzhou, China. Demographic information, blood and fecal samples were collected from the participants. The fecal microbial composition and relative abundance were characterized using 16S rRNA gene sequencing, while blood differential metabolites and circRNAs of pregnant women with GDM were assessed using non-targeted metabolomics and RT-qPCR, respectively. Exposure levels of air pollutants were assessed using data from the nearest monitoring station. Spearman correlation and regression models were conducted to estimate the associations among PM2.5 exposure, gut microbiota, blood metabolites, circRNAs and GDM.

RESULTS: Elevated PM2.5 exposure levels were significantly associated with an increased risk of GDM, impaired glucose homeostasis and gut microbiota dysbiosis. Solobacterium and Escherichia_Shigella showed a positive effect modification on the association between PM2.5 exposure and fasting blood glucose, while Fusicatenibacter, Ruminococcaceae_UBA1819, Raoultibacter, Anaerofustis and Phascolarctobacterium showed a negative effect modification on the association between PM2.5 exposure and 2-h OGTT glucose. GDM-associated gut microbiota, including Catabacter, Angelakisella, Romboutsia and Fusicatenibacter, were associated with both GDM-associated metabolites (such as sphinganine-1-phosphate, sphingomyelin) and GDM-associated circRNAs (such as hsa_circ_0006732 and hsa_circ_0001439), which were involved in glycerophospholipid metabolism, sphingolipid metabolism and insulin signaling pathway.

CONCLUSIONS: The gut microbiota may moderate the associations between PM2.5 exposure and blood glucose levels, and both PM2.5 exposure and gut microbiota may be related to GDM, potentially involving pathways such as glycerophospholipid metabolism, sphingolipid metabolism and the insulin signaling pathway. However, lifestyle factors (diet and physical activity) and residential mobility were not measured, and the fecal microbiota was assessed at a single time point in mid-pregnancy. Thus, these limitations may contribute to residual confounding, exposure misclassification, and limited causal inference.},
}

Humans
Female
Pregnancy
*Diabetes, Gestational/epidemiology/etiology/microbiology
*Particulate Matter/adverse effects
*Gastrointestinal Microbiome/drug effects
China/epidemiology
Adult
Feces/microbiology
Prospective Studies
RNA, Ribosomal, 16S/genetics
Air Pollutants/adverse effects
Dysbiosis
Bacteria/classification/genetics/isolation & purification
Longitudinal Studies

@article {pmid41835129,
year = {2026},
author = {Milke, F and Garcia, SL and Simon, M and Pacheco-Valenciana, A and Lennartz, ST},
title = {Microbial cohorts: bringing ecological meaning to the modularity concept of co-occurrence networks.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag037},
pmid = {41835129},
issn = {2730-6151},
abstract = {Microbial communities are structured through complex interactions that are difficult to observe directly. Co-occurrence networks offer a way to infer community structure, revealing (not exclusively) potential biotic interactions. Such networks have been inferred for diverse biomes and repeatedly found to be modular, yet the ecological significance of this modularity remains underexplored. We tested whether clusters within co-occurrence networks ("cohorts"), are universal and ecologically meaningful units by assessing their ubiquity, stability, and environmental specificity across diverse ecosystems. Our meta-analysis spans 25 previously published 16S rRNA gene amplicon sequencing datasets (14 160 samples) and covers high environmental variability ranging from aquatic, terrestrial to anthropogenic environments. Microbial co-occurrence networks consistently exhibited high modularity across biomes. Inferred cohorts were ubiquitous and represented up to 90% of the community composition. Our findings demonstrate that modularity is a fundamental and generalizable feature of microbial community organization, indicating the existence of stable subcommunities. Highly similar cohorts were inferred even across different, unconnected environments and datasets, and showed consistent responses to environmental gradients, indicating that their composition is to a large degree deterministic and predictable. The overall cohort structure and environmental preferences were independent of the sample size and the inference algorithm, underlining the robustness and applicability of the results. Recognizing these microbial cohorts as a meaningful level of microbial organization will refine microbial community ecology, cultivation strategies, and predictive modelling of microbial dynamics.},
}

@article {pmid41835221,
year = {2026},
author = {Malykhina, AP},
title = {Shaping the future of abdominal and pelvic pain research with novel scientific and technological advances.},
journal = {Frontiers in pain research (Lausanne, Switzerland)},
volume = {7},
number = {},
pages = {1738762},
pmid = {41835221},
issn = {2673-561X},
abstract = {Abdominal and pelvic pain often originates from one or more visceral organs of the gastrointestinal, musculoskeletal (pelvic floor), urinary, or reproductive systems. Over the past decade, research efforts on abdominal and pelvic pain have advanced considerably, driven by the discovery of new molecular targets, signaling pathways, targeted genetic editing, the use of human tissues, and comprehensive multiomic analyses. Increasingly, the field prioritizes combinatorial and integrative studies that bridge human clinical research with relevant animal models to accelerate the development of novel therapies for affected patients. In addition to established areas of pain research-such as the modulatory role of the central nervous system in chronic pelvic pain (CPP), stress-induced visceral hypersensitivity, sex differences, brain-gut interactions, microbiome influences, comorbidities, and neuromodulation-new research directions continue to emerge. These include exploring the effects of inflammaging and immune regulation in transition from acute to CPP, applying microphysiological systems (MPS) in pain research studies, integrating multiomics analyses, and employing combined artificial intelligence (AI) approaches. This article presents current perspectives on cutting-edge scientific trends and technological innovations shaping the field of abdominal and pelvic pain research.},
}

@article {pmid41835234,
year = {2026},
author = {Mandolini, E and Szedlacsek, S and Abramczyk, B and Szucs, A and Staykova, A and Seybold, A and Knapp, M and Pawłowska, J and Ladurner, P and Peintner, U},
title = {Cryptocalciella - a new Mortierellaceae genus from Alpine glacier forefields.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e177912},
pmid = {41835234},
issn = {2210-6340},
abstract = {Mortierellaceae are cosmopolitan, soil-inhabiting fungi that can be found in nearly all terrestrial habitat types and are therefore considered an essential part of the core soil microbiome. Many species of this family are known to endure harsh environments, including highly exposed and nutrient-depleted terrains such as glacier forefields. In these environments, microbial communities are taxonomically and functionally diverse, greatly contributing to nutrient cycling, soil organic matter formation, and plant establishment. However, there is growing understanding that Mortierellaceae diversity in these habitats remains largely undescribed. In this study, we isolated multiple fungal strains belonging to a previously unknown Mortierellaceae taxon from early stages of soil development in calcareous glacier forefields of the Alps and comprehensively characterized them using different tools: physiological tests, detection of associated bacteria, and microscopic observations (e.g., light, fluorescence, and scanning electron microscopy) to visualize their morphology and surface structure. Additionally, whole-genome sequencing and phylogenomics were used to determine their placement within Mortierellaceae. Our results show that the isolated strains represent a new species within a previously undescribed fungal genus. Due to the strains' origin in hidden, calcareous sediments of the earliest soil developmental stages at glacier forefields, we propose the name Cryptocalciella humilis Mandolini, Szedlacsek & Peintner for this fungus.},
}

@article {pmid41828642,
year = {2026},
author = {Sadurski, J and Ostrowska, M and Staniszewski, A and Waśko, A},
title = {Genomic Plasticity and Functional Reweighting Facilitate Microbial Adaptation During the Ripening of Artisanal Goat Cheese.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
pmid = {41828642},
issn = {1422-0067},
mesh = {*Cheese/microbiology ; Animals ; Goats ; *Genome, Bacterial ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Metagenome ; Food Microbiology ; Phylogeny ; },
abstract = {This study presents a genome-resolved shotgun metagenomic analysis of artisanal raw-milk goat cheese from the Masurian region of Poland, addressing the limited understanding of strain-level diversification and functional restructuring during traditional cheese ripening. While microbial succession in cheese has been widely described, comprehensive genome-resolved analyses integrating strain-level genomic heterogeneity, pathway reweighting, and mobile genetic elements in artisanal goat cheese remain scarce. By combining taxonomic profiling with metagenome-assembled genome (MAG) reconstruction and pathway-level functional analysis, we characterised microbial succession and genome plasticity across ripening stages. Genome reconstruction yielded 37 MAGs during early ripening and 141 MAGs in mature cheese, revealing increased genome recoverability and pronounced strain-level heterogeneity within dominant taxa, including Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, and Lactococcus lactis. Alpha diversity increased in mature samples, consistent with progressive community restructuring. Functional profiling demonstrated coordinated metabolic reweighting, particularly within carbohydrate metabolism, while amino acid and lipid metabolism remained proportionally stable. Genome-resolved analyses further identified tetracycline- and sulfonamide-associated resistance determinants and diverse bacteriophages targeting lactic acid bacteria, highlighting the role of mobile genetic elements in horizontal gene transfer and microevolutionary adaptation during ripening.},
}

*Cheese/microbiology
Animals
Goats
*Genome, Bacterial
*Adaptation, Physiological/genetics
Metagenomics/methods
Metagenome
Food Microbiology
Phylogeny

@article {pmid41828645,
year = {2026},
author = {Smolińska, K and Tomaszewska, E and Hułas-Stasiak, M and Muszyński, S and Szopa, A and Serefko, A and Dobrowolski, P},
title = {The Regulatory Role of FABP4 in Microbiome-Brain-Gut Communication Under High-Fat-Diet Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
pmid = {41828645},
issn = {1422-0067},
mesh = {*Fatty Acid-Binding Proteins/metabolism ; *Gastrointestinal Microbiome ; Humans ; *Diet, High-Fat/adverse effects ; Animals ; *Brain/metabolism ; Dysbiosis/metabolism ; Inflammation/metabolism ; },
abstract = {High-fat diets (HFDs) are major environmental factors influencing metabolic homeostasis, immune regulation, and brain function, largely through their effects on gut microbiota and intestinal barrier integrity. Disruption of the microbiome-brain-gut axis has been increasingly implicated in systemic and neuroinflammatory processes; however, the molecular mediators that integrate dietary lipid signals with microbial and host responses remain incompletely defined. This review synthesizes the current evidence on the role of fatty acid-binding protein 4 (FABP4) as an integrative node linking HFD-induced gut dysbiosis to systemic and central inflammatory signaling. We critically evaluated experimental and translational studies addressing HFD-driven alterations in gut microbiota composition, intestinal barrier function, and inflammatory pathways, with particular emphasis on FABP4-mediated mechanisms across epithelial, immune, and neural compartments. The available data indicate that FABP4 responds to dietary and microbiome-derived cues and contributes to coordinated metabolic and inflammatory responses, affecting both peripheral tissues and the central nervous system. These findings support a model in which FABP4 participates in diet-driven feedback loops that amplify gut barrier dysfunction, immune activation, and neuroinflammation. In conclusion, FABP4 emerges as a central molecular mediator within the microbiome-brain-gut axis under HFD conditions, highlighting its potential relevance in understanding the pathophysiology of metabolic and neuroinflammatory disorders and guiding future integrative research strategies.},
}

*Fatty Acid-Binding Proteins/metabolism
*Gastrointestinal Microbiome
Humans
*Diet, High-Fat/adverse effects
Animals
*Brain/metabolism
Dysbiosis/metabolism
Inflammation/metabolism

@article {pmid41828691,
year = {2026},
author = {Oršolić, N and Toljanić, B and Odeh, D and Čuljak, N and Šešelja, K and Baus Lončar, M and Đikić, D and Leboš Pavunc, A and Kos, B},
title = {Anti-Atherogenic Activities of Exopolysaccharides and Their Producing Strain Limosilactobacillus fermentum MC1 in Mice.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
pmid = {41828691},
issn = {1422-0067},
support = {IP-2019-04-2237 and IP-2024-05-6548//The Croatian Science Foundation/ ; },
mesh = {Animals ; *Limosilactobacillus fermentum/metabolism/chemistry ; Mice ; *Atherosclerosis/metabolism/prevention & control/drug therapy/pathology ; *Polysaccharides, Bacterial/pharmacology ; Male ; Biomarkers ; Gastrointestinal Microbiome/drug effects ; Lipid Metabolism/drug effects ; },
abstract = {Atherosclerosis, the leading cause of death worldwide, is a chronic inflammatory disease leading to the accumulation of lipid-rich plaques within the artery wall. Accumulating evidence indicates that intestinal microbiota plays an important regulatory role in atherosclerosis at all stages of the disease. Through numerous metabolites, the intestinal microbiota can regulate immune and inflammatory cells and their mediators, as well as lipid metabolism, thereby contributing to the development and progression of atherosclerosis. With these assumptions in mind, we investigated the possibility of using Limosilactobacillus fermentum MC1 (L. fermentum MC1) and its exopolysaccharides (EPSs) in the reduction of lipid and atherogenic parameters as a preventive strategy in preventing the occurrence of cardiovascular diseases (CVD). We investigated the effect of L. fermentum MC1 and its EPSs on the health status of mice by monitoring the following parameters: body weight, colon length and weight, relative weight of organs, hematological (Hgb, WBC, number of erythrocytes, MCHC, MCV, MCH), and biochemical blood parameters including glucose, serum enzymes (ALT, ALP, amylase), urea, creatinine and lipid profile (total cholesterol, triglycerides, HDL, VLDL, LDL), different atherogenic parameters, blood biomarkers such as lymphocyte-to-monocyte (LMR) and neutrophil-to-lymphocyte (NLR) ratios, molecular inflammatory markers (IL1β, IL6, MCP1, IL1α, TLR4, TNFα, CD68, TGFβ), apoptosis markers (BCL2, AIFM1, IGF-1R), and endoplasmic reticulum stress markers (CHOP and GRP94) as well as oxidative stress (NOX2) markers in the colon. Furthermore, the level of lipid peroxidation, nitric oxide and glutathione concentrations in the liver, kidneys and spleen were measured. L. fermentum MC1 and its EPSs may prevent the development of atherosclerosis and the progression of CVD through antioxidant, anti-inflammatory, immunomodulatory activities, and regulation of the gut microbiome and lipid metabolism. The observed reduction in lipid and atherogenic determinants suggests that L. fermentum MC1 and its EPSs may contribute to atheroprotection and confer multiple health benefits.},
}

Animals
*Limosilactobacillus fermentum/metabolism/chemistry
Mice
*Atherosclerosis/metabolism/prevention & control/drug therapy/pathology
*Polysaccharides, Bacterial/pharmacology
Male
Biomarkers
Gastrointestinal Microbiome/drug effects
Lipid Metabolism/drug effects

@article {pmid41828882,
year = {2026},
author = {Kurashov, EA and Krylova, JV and Chernova, AM and Bataeva, YV and Belyakov, EA and Lapirov, AG and Anikina, VV and Grebennikov, VA and Yavid, EY},
title = {Major Low-Molecular-Weight Metabolites from Freshwater Aquatic Macrophytes: Ecological Aspects.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {5},
pages = {},
pmid = {41828882},
issn = {1420-3049},
support = {Scientific topic №: 124032100076-2//The topic of the state assignment of the Institute of Biology of Inland Waters of the Russian Academy of Sciences/ ; },
mesh = {*Fresh Water ; Gas Chromatography-Mass Spectrometry ; *Metabolome ; Molecular Weight ; Ecosystem ; Metabolomics/methods ; *Aquatic Organisms/metabolism ; },
abstract = {Freshwater macrophytes shape not only the morphological "architecture" of shallow-water ecosystems but also their chemical milieu via low-molecular-weight organic compounds (LMWOCs) that may regulate phytoplankton, periphyton, and the microbiome within the leaf/shoot diffusive boundary layer and the surrounding water column. In this study, GC-MS (gas chromatography-mass spectrometry) was used to identify major LMWOCs of the low-molecular-weight metabolome (LMWM) in 11 widely distributed macrophyte species (Myriophyllum spicatum L., Sparganium emersum Rehm., Sparganium gramineum Georgi, the hybrid Sparganium × foliosum A. A. Bobrov, Volkova, Mochalova et Chemeris, Persicaria amphibia (L.) Delarbre, Potamogeton perfoliatus L., Nuphar lutea (L.) Sibth. & Sm., Potamogeton pectinatus L., Potamogeton natans L., Lobelia dortmanna L., and Ceratophyllum demersum L.). Compounds contributing more than 1% to the total LMWOCs pool were considered major, increasing the ecological realism of interpretations by focusing on metabolites more likely to reach effective concentrations in the plant microenvironment. For interspecific comparisons, the maximum recorded values of relative abundance and concentrations were used to estimate species "potential". In total, 137 major LMWOCs were detected (four remained unidentified), and their numbers varied markedly among taxa (from 11 in N. lutea to 71 in P. perfoliatus). Similarity analyses (Jaccard, Sørensen-Czekanowski, Morisita-Horn) indicated that similarity based on compound lists and similarity based on dominance structure may diverge, reflecting differences between the "LMWOCs set" and the quantitative architecture of LMWOCs within the LMWM. Fatty acids formed the core of the major fraction in all species: they were among the top three compounds in all 11 macrophytes and ranked first or second in 10 of 11, highlighting the lipid module as a universal "structure-signaling-defense/allelopathy" hub in aquatic plants. Also, an analysis of the ecological-biochemical role of the main major LMWOCs in the studied aquatic macrophytes is presented. Overall, the data offer a comparable, ecologically oriented framework for interpreting chemical regulation of communities in macrophyte-dominated habitats and for selecting target compounds/species for subsequent bioassay and field studies.},
}

*Fresh Water
Gas Chromatography-Mass Spectrometry
*Metabolome
Molecular Weight
Ecosystem
Metabolomics/methods
*Aquatic Organisms/metabolism

@article {pmid41828913,
year = {2026},
author = {Tian, K and Zhu, J and Qi, R and Yang, Y and Li, J and Tian, W and Tan, Q and Hu, B and Jian, Y},
title = {Associations Between Fine Particulate Matter-Associated Bacteria and Respiratory Tract Microbiota in Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {5},
pages = {},
pmid = {41828913},
issn = {2076-2615},
support = {NCTIP-XD/B07//National Center of Technology Innovation for Pigs/ ; },
abstract = {Environmental health and biosecurity in pig farms and surroundings are increasingly threatened by pathogenic bacteria carried by fine particulate matter with an aerodynamic diameter of 2.5 μm or less (PM2.5) in enclosed piggeries. However, limited attention has been given to these pathogens and their association with the respiratory microbiome of pigs. Using high-throughput sequencing, we investigated the overall and pathogenic bacterial communities attached to PM2.5 in pig houses, as well as those in the upper (URT) and lower respiratory tracts (LRT) of healthy fattening pigs. Concentrations of PM2.5, particulate matter with an aerodynamic diameter of 10 μm or less (PM10), ammonia (NH3), total volatile organic compounds (TVOCs), and hydrogen sulfide (H2S) were significantly higher inside the piggery than in the surrounding environment. The composition of PM2.5-associated bacteria varied with sampling height and showed greater similarity to the microbiota of the URT, particularly the oropharynx, than to that of the LRT. Additionally, 140 core potential bacterial pathogens were identified via Venn analysis in both PM2.5 and respiratory tracts. Co-occurrence network analysis and community assembly patterns revealed that microbial communities in PM2.5 and the respiratory tract exhibit distinct interaction and assembly characteristics. These findings highlight the potential role of PM2.5 as a vector for respiratory pathogens and underscore the importance of air quality management in pig farming to safeguard environmental health.},
}

@article {pmid41828957,
year = {2026},
author = {Guan, X and Ma, H and Liu, R and Xu, Y and Gnagna, D and Yin, X and Zhang, Y and Li, Y},
title = {Impact of Exposure of Dairy Cow Feed to Polystyrene Microplastics on 24 h In Vitro Rumen Fermentation Responses, Microbiota Biodegradation Potential and Metabolic Pathways.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {5},
pages = {},
pmid = {41828957},
issn = {2076-2615},
support = {2023YFD2000700//National Key Research and Development Program of China/ ; ZL2024C018//the Joint key project of Natural Science Foundation of Heilongjiang Province/ ; },
abstract = {Microplastic pollution is increasingly serious worldwide, threatening human and animal health. The cow rumen is a key organ for nutrient digestion and absorption, and its fermentation is closely related to rumen microorganisms. Here, we investigated how polystyrene microplastics (PS-MPs) with varying particle sizes and concentrations affect rumen fermentation and the biodegradability of PS-MPs by rumen fermentation. The results reveal that exposure to PS-MPs lowered gas production and gas concentrations, as well as volatile fatty acid content, and these decreases were positively correlated with PS-MP concentration. However, higher PS-MP concentration and larger particle size increased the activity of carboxymethyl cellulose, β-glucosidase, and xylanase. Furthermore, PS-MP exposure reduced the abundance of certain rumen microorganisms and altered metabolic pathways and metabolites linked to PS-MP biodegradation. It was also found that PS-MP content decreased significantly after 24 h fermentation. Therefore, PS-MPs can inhibit rumen fermentation by affecting the rumen microbiome, and rumen microorganisms and their secreted enzymes can biodegrade PS-MPs to produce styrene and derivatives; such small molecules may further disrupt rumen homeostasis, thereby affecting lactation performance. In addition, rumen microbial degradation of PS-MPs provides a new idea to resolve future microplastic contamination challenges.},
}

@article {pmid41828960,
year = {2026},
author = {Yu, H and Dong, S and Wang, L and Liu, S},
title = {Integrated Gut Microbiome and Metabolome Analysis in Largemouth Bass (Micropterus salmoides) Following Viral Infection.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {5},
pages = {},
pmid = {41828960},
issn = {2076-2615},
abstract = {Largemouth bass (Micropterus salmoides) is an important aquaculture species increasingly threatened by viral diseases, particularly largemouth bass virus (LMBV), which can cause significant mortality. However, integrative analyses linking LMBV-induced gut microbiota dysbiosis to metabolomic dysfunction are limited. In this study, we profiled the intestinal microbiome and metabolome alterations in largemouth bass following LMBV infection and conducted an integrated analysis. Infected fish showed reduced alpha diversity and significant shifts in community structure, including increased relative abundances of Bacteroidota and Fusobacteriota and a decrease in Proteobacteria. Opportunistic taxa, such as Pseudomonas and Mycobacterium, were enriched after infection. Metabolomic profiling revealed differential metabolites primarily involved in amino acid and carbohydrate metabolism. Integrative correlation analyses further identified significant associations between opportunistic bacteria and putative harmful metabolites, suggesting that LMBV-induced dysbiosis disrupts host metabolic homeostasis and contributes to immune dysfunction. These findings may clarify the microbiota-metabolite landscape during LMBV infection.},
}

@article {pmid41828967,
year = {2026},
author = {Taylor, S and Tewson, C and Edmondson, V},
title = {Resolution of Chronic Diarrhoea Following Treatment of Periodontal Disease in a Cat.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {5},
pages = {},
pmid = {41828967},
issn = {2076-2615},
abstract = {An association between periodontal disease and comorbid disorders, including gastrointestinal signs, has been reported in cats and investigated in humans, where a bidirectional relationship between oral and gastrointestinal microbiomes exists. A 5-year-old neutered female domestic shorthair cat was presented with a 2-year history of small-bowel diarrhoea. The cat's appetite was reduced, and coat quality had deteriorated. On examination, the cat was found to have periodontal disease affecting multiple teeth and a matted coat. Biochemistry revealed mild hyperproteinaemia, haematology was unremarkable, cobalamin was normal, folate was elevated, and retroviral testing was negative. Abdominal ultrasound showed diffuse muscularis thickening without other abnormalities, and dental examination and radiography revealed missing teeth, a root remnant, stage 4 periodontal disease, and tooth resorption. Multiple extractions were performed, and multimodal analgesia was provided, including locoregional dental blocks. The cat's appetite, body condition, energy levels, and coat quality improved after the procedure, and the diarrhoea completely resolved within a month of the procedure without any changes in diet, physical, social environment, or the use of any medications, and did not recur during the following 7 months. This case illustrates the potential role of periodontal disease in the development of gastrointestinal disease and the benefits outside the oral cavity of managing dental disease in cats.},
}

@article {pmid41829039,
year = {2026},
author = {Luo, L and Li, J and Li, M},
title = {Intratumoral Staphylococcus pseudintermedius Promotes Proliferation and Migration of CMT-U27 Cells Through the TLR2/PI3K/Akt Signaling Pathway.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {5},
pages = {},
pmid = {41829039},
issn = {2076-2615},
support = {32402964//Young Scientists Fund of the National Natural Science Foundation of China/ ; 840003//Jiangsu Qinglan Project/ ; 804127//Meng Li's Nanjing Agricultural University Research Start-up Fund/ ; },
abstract = {Increasing evidence suggests that intratumoral microorganisms and their metabolites can modulate cancer initiation and progression. However, the composition and functional role of intratumoral bacteria in canine mammary tumors (CMTs) remain unclear. In this study, we investigated the functional significance of tumor-derived Staphylococcus in CMTs, focusing on its effects on the proliferation and migration of CMT-U27 cells. 16S rRNA sequencing revealed reduced alpha diversity in CMT tissues, with Staphylococcus pseudintermedius identified as the most frequently isolated species. Functional assays, including CCK-8, wound healing, RT-qPCR, and Western blot analyses, demonstrated that intratumoral Staphylococcus pseudintermedius significantly enhanced cellular proliferation and migration. Mechanistically, Staphylococcus pseudintermedius significantly upregulated the expression of TLR2, as well as the phosphorylation levels of PI3K, Akt and P70S6K. The inhibition of TLR2 using C29 suppressed the mRNA expression of VEGF, MMP9, MMP2, and EGFR. Collectively, these findings indicate that intratumoral Staphylococcus pseudintermedius promotes the proliferation and migration of CMT-U27 cells through activation of the TLR2/PI3K/Akt pathway, highlighting a functional link between tumor-associated bacteria and cancer progression.},
}

@article {pmid41829048,
year = {2026},
author = {Liu, X and Ying, C and Ma, F and Yang, Y and Liu, K},
title = {Gut Microbiome Signatures Across Migratory, Sedentary, and Aquaculture Ecotypes of Coilia nasus.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {5},
pages = {},
pmid = {41829048},
issn = {2076-2615},
support = {2022YFF0608201//National Key R&D Program of China/ ; ZF2022-18-0399//Monitoring of aquatic resources in key waters of Anhui province/ ; NO.2023TD11//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; },
abstract = {Coilia nasus, a typical species with migratory-sedentary polymorphism, shows different intestinal microbiota characteristics among its different ecotypes. This is attributed to differences in feeding habits and habitat environments (such as water temperature, salinity, etc.). This study constructed a database of intestinal microbiota for three ecological types of C. nasus, namely migratory type (comprising marine populations and freshwater populations), sedentary type and aquaculture-reared type, through 16S rRNA amplicon sequencing technology. This study investigates the ecological mechanisms underlying microbiota differentiation, focusing on three key drivers: environmental selection, host nutritional metabolism requirements, and host life history strategies. The results showed that the core flora of C. nasus consisted of Firmicutes, Proteobacteria, and Actinobacteria. Both the depletion of microbial taxa and the enrichment of marine-adapted bacterial lineages-including Proteobacteria and Psychrobacter-are associated with elevated salinity in the migratory marine population of C. nasus. In contrast, the elevated relative abundance of Actinobacteria in aquaculture-reared C. nasus is likely attributable to dietary supplementation with protein- and lipid-rich artificial feed. Functional correlation analysis holds promise for partially predicting the microbiota's metabolic functional succession patterns. The dominance of Pseudomonas_E in the migratory freshwater population is consistent with its well-documented physiological versatility and adaptive capacity in dynamically fluctuating aquatic habitats. The elevated abundance of Cyanobacteria in the sedentary population C. nasus coincides with the water bloom in their habitat, suggesting that the structure of the microbiota may serve as a novel biomarker for indicating the ecosystem. In conclusion, this study identifies potential molecular markers for tracing genetic resources and distinguishing ecological types of C. nasus, while establishing a theoretical foundation for elucidating the co-evolutionary dynamics between fish hosts and their associated microbiota-and thereby informing both conservation strategies for wild populations and microbiota-informed aquaculture practices.},
}

@article {pmid41829053,
year = {2026},
author = {Nopparatmaitree, M and Loor, JJ and Arjin, C and Hwanhlem, N and Sudchamrong, P and Buapa, B and Intawicha, P and Incharoen, T},
title = {Phytosynbiotic Containing Double-Layer Microencapsulated Pediococcus acidilactici V202 and Tiliacora triandra Leaf Extract Improve Growth Performance and Gut Health in Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {5},
pages = {},
pmid = {41829053},
issn = {2076-2615},
support = {R2567B037//Naresuan University (NU) and the National Science, Research and Innovation Fund (NSRF)/ ; R2569A014//Reinventing University Program 2026, the Ministry of Higher Education, Science, Research and Innovation, Thailand/ ; R2569C002//Frontier Research and Innovation Cluster Fund, Naresuan University/ ; 2278//Fundamental Fund 2026, University of Phayao/ ; },
abstract = {This study investigated the effects of a novel phytosynbiotic feed supplement derived from double-layer microencapsulated Pediococcus acidilactici V202 and Tiliacora triandra leaf extract (DMP) on the growth performance, nutrient utilization, gut fermentation, intestinal morphology, and cecal microbiota of broiler chickens. A total of 250 one-day-old male Ross 308 broilers were randomly assigned to five dietary treatments: basal control diet, antibiotic growth promoter (AGP) with chlortetracycline at 0.07%, and DMP supplementation at 0.25, 0.50, or 1.00% (w/w) for 42 days. Compared with the control diet, feeding the DMP led to linear or quadratic responses (p < 0.05) on average daily gain, feed efficiency, productive index, and economic returns. Apparent digestibility of dry matter, crude protein, and apparent metabolizable energy was enhanced in DMP-fed broilers, indicating improved nutrient utilization efficiency. These performance responses were accompanied by pronounced alterations in cecal fermentation, characterized by increased lactic acid, total volatile fatty acids, and particularly acetic and butyric acid levels (p < 0.01). Microbiome analysis revealed that the DMP selectively enriched fermentative SCFA-producing bacterial orders, including Lachnospirales, Oscillospirales, and Lactobacillales. It also reduced the relative abundance of less desirable taxa. As evidenced by an increased villus height and surface area in the duodenum and jejunum, along with a higher villus height-to-crypt depth ratio in the ileum, feeding the DMP also enhanced small intestinal morphology. These coordinated morphological adaptations are indicative of enhanced epithelial maturation and reduced crypt hyperplasia, likely mediated by elevated microbial SCFA production in the gut. In conclusion, the DMP improved broiler growth performance by coordinating the modulation of the gut microbiota, SCFA levels, and intestinal morphology, resulting in enhanced nutrient digestibility and productivity. This phytosynbiotic strategy represents a sustainable plant-based alternative to antibiotic growth promoters for environmentally responsible poultry production.},
}

@article {pmid41829073,
year = {2026},
author = {Yuan, S and Tu, R and Shan, B and Liu, Y and Jiang, X and Zheng, M and Yang, L and Liu, H and Zhao, T and Yang, P and Zhai, Q and Mao, J and Liu, S and Liu, X},
title = {Turning-Modulated Vertical CO2 Gradients Drive Microbial Stratification and Amadori Product Accumulation in Winter Daqu.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
pmid = {41829073},
issn = {2304-8158},
support = {22138004//the National Natural Science Foundation of China/ ; 2024YFFK0436//the Key Research and Development Program of Sichuan Province/ ; },
abstract = {High-temperature Daqu (HTD)'s quality determines the characteristics and yield of the Chinese sauce-aroma baijiu. However, winter production frequently encounters challenges such as fermentation instability and metabolic fluctuations, primarily stemming from complex, unmonitored microenvironmental changes within the HTD pile. This study established a closed-loop system linking the microenvironment, HTD quality, microbiome, and metabolome. Through continuous monitoring of the winter fermentation pile's microenvironmental conditions and integrating multi-omics analyses, we revealed that CO2 concentration within fermentation piles is the core factor causing quality variations in HTD. By breaking the respiratory bottleneck formed by carbon dioxide (CO2) accumulation through the turning anaerobic stress can be alleviated, thereby driving metabolic succession. The study found that vertical CO2 concentration heterogeneity severely restricts the enrichment of aerobic core functional microbial communities such as the Bacillus species. This directly blocks key metabolic pathways including amino acid metabolism and energy supply via ABC transporters. Moreover, the specific accumulation of Amadori products further confirms that this low-temperature environment under CO2 stress causes the Maillard reaction to stall at intermediate stages. Consequently, this study proposes a steady-state control strategy centered on oxygen and CO2 gas characteristics. By actively regulating the gaseous microenvironment to eliminate metabolic heterogeneity, it provides theoretical support for standardizing traditional fermentation processes.},
}