@article {pmid41606790,
year = {2026},
author = {Clutter, CH and Leung, DT},
title = {Tracing MR1 expression across tissues to find the perfect MAIT.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiag014},
pmid = {41606790},
issn = {1938-3673},
abstract = {Mucosal associated invariant T (MAIT) cells are part of a T cell subset that is activated upon presentation of B2 vitamin (riboflavin) metabolites by the major histocompatibility complex, class I related (MR1) protein. Though there is a clear relationship between microbial production of riboflavin and MAIT cell development and persistence, little is known about the cells that primarily communicate with MAIT cells and other MR1-restricted T cells. Elegant work by Deng et al demonstrates that it is macrophages from the lung and peritoneum that express the highest amount of MR1 and are the most efficient at presenting vitamin B antigens to MAIT cells. This landmark study not only definitively identifies and maps the key antigen presenting cell populations involved in MAIT cell activation, it also reveals a bidirectional relationship between MR1 expression and the host microbiome. While further work on how these findings translate to human MAIT cell biology is needed, this study has provided us with unprecedented insights into the mechanistic interplay and microbial ecology of MR1 presentation of riboflavin metabolites.},
}

@article {pmid41606773,
year = {2026},
author = {Ross, SM},
title = {Forever Young, Part 3: Urolithin A: A Gut Microbiome-Derived Metabolite and Its Role in Aging.},
journal = {Holistic nursing practice},
volume = {},
number = {},
pages = {},
pmid = {41606773},
issn = {1550-5138},
}

@article {pmid41606595,
year = {2026},
author = {Luan, J and Zhang, X and Chen, T and Pu, S and Shen, Z and Xu, C and Chen, Z and Zhang, J and Chen, D},
title = {Adolescent exposure to polystyrene nanoplastics induces male reproductive damage via the microbiome-gut-testis axis.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04069-y},
pmid = {41606595},
issn = {1477-3155},
support = {ZDXK202219//Jiangsu Province Capability Improvement Project through Science, Technology and Education/ ; PY2025017//Young Scholars Fostering Fund of the First Affiliated Hospital of Nanjing Medical University/ ; PY2023002//Young Scholars Fostering Fund of the First Affiliated Hospital of Nanjing Medical University/ ; 2022ZB730//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; 82103580//National Natural Science Foundation of China/ ; },
abstract = {Polystyrene nanoplastics (PS-NPs), are increasingly associated with reduced male fertility, yet the underlying mechanisms remain poorly defined. Here, we systematically unraveled a novel microbiome-gut-testis axis mediating PS-NPs-induced reproductive toxicity. Adolescent rats exposed to PS-NPs for 5 weeks induced dose-dependent testicular injury, characterized by disrupted spermatogenesis, and compromised blood-testis barrier. Single-cell atlases revealed spermatogenic arrest, abnormal immune microenvironment, and perturbed testicular cell communication upon exposure to PS-NPs. Furthermore, multi-omics analysis highlighted the activation of NF-κB/IL-17/HIF-1 and inhibition of PPAR-γ signaling, contributing to increased DNA damage and apoptosis, suppressed autophagy, and dysregulated energy-lipid metabolism. Additionally, PS-NPs exposure initiated gut microbial dysbiosis, significantly increasing pro-inflammatory bacteria, while reducing beneficial commensals. This microbial disruption compromised intestinal barrier integrity, leading to elevated circulating LPS levels. Subsequent activation of the TLR4/MyD88/NF-κB signaling pathway propagated inflammatory responses to testes. Crucially, FMT from PS-NPs-exposed donors reproduced the damage in healthy recipients, thus suggesting gut microbiota as a causal mediator. Therapeutically, DI intervention effectively mitigated the reproductive toxicity by restoring gut barrier integrity, rebalancing microbial communities, and suppressing inflammation. Our findings unveil a gut microbiome-centric mechanism for nanoplastic-induced male reproductive toxicity, and identify DI as a promising therapeutic candidate, accordingly providing critical insights for environmental risk assessment.},
}

@article {pmid41606550,
year = {2026},
author = {Zhang, X and Xu, J and Chen, M and Wu, Y and Chen, D and Xu, X and He, X},
title = {Aspergillus fumigatus in mechanically ventilated pneumonia- independent mortality risk and synergistic microbiome signatures from a multicenter mNGS cohort.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04131-3},
pmid = {41606550},
issn = {1471-2466},
support = {2022GYX28//Lishui Public Welfare Technology Application Research Program Project/ ; },
}

@article {pmid41606514,
year = {2026},
author = {Hu, S and Luo, C and Wan, S and Zhang, S and Li, N and Liu, G and Zhao, LY},
title = {Modulating the gut microbiome to enhance cancer immunotherapy: a systematic review and Meta-Analysis of probiotics and FMT as adjuncts.},
journal = {BMC cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12885-026-15655-6},
pmid = {41606514},
issn = {1471-2407},
}

@article {pmid41606319,
year = {2026},
author = {Kamitaki, N and Handsaker, RE and Hujoel, MLA and Mukamel, RE and Usher, CL and McCarroll, SA and Loh, PR},
title = {Human and bacterial genetic variation shape oral microbiomes and health.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41606319},
issn = {1476-4687},
abstract = {Human genetic variation influences all aspects of our biology, including the oral cavity[1-3], through which nutrients and microbes enter the body. Yet it is largely unknown which human genetic variants shape a person's oral microbiome and potentially promote its dysbiosis[3-5]. We characterized the oral microbiomes of 12,519 people by re-analysing whole-genome sequencing reads from previously sequenced saliva-derived DNA. Human genetic variation at 11 loci (10 new) associated with variation in oral microbiome composition. Several of these related to carbohydrate availability; the strongest association (P = 3.0 × 10[-188]) involved the common FUT2 W154X loss-of-function variant, which associated with the abundances of 58 bacterial species. Human host genetics also seemed to powerfully shape genetic variation in oral bacterial species: these 11 host genetic variants also associated with variation of gene dosages in 68 regions of bacterial genomes. Common, multi-allelic copy number variation of AMY1, which encodes salivary amylase, associated with oral microbiome composition (P = 1.5 × 10[-53]) and with dentures use in UK Biobank (P = 5.9 × 10[-35], n = 418,039) but not with body mass index (P = 0.85), suggesting that salivary amylase abundance impacts health by influencing the oral microbiome. Two other microbiome composition-associated loci, FUT2 and PITX1, also significantly associated with dentures risk, collectively nominating numerous host-microbial interactions that contribute to tooth decay.},
}

@article {pmid41606239,
year = {2026},
author = {Salem, GM and Azamor, T and Familiar-Macedo, D and Onwubueke, C and Cambou, MC and Chen, W and Nielsen-Saines, K and Foo, SS},
title = {Mechanistic insights into the impact of prenatal viral infections on maternal and offspring immunity.},
journal = {Npj viruses},
volume = {4},
number = {1},
pages = {7},
pmid = {41606239},
issn = {2948-1767},
support = {N/A//Cleveland Clinic/ ; },
abstract = {Global outbreaks of human immunodeficiency virus (HIV) and respiratory viruses - severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza, accounted for ~50 million infections in 2024. Prenatal exposure to these viruses poses substantial risks to maternal and fetal health, yet the underlying immunological mechanisms remain incompletely understood. Despite differences in viral biology and transmission, mounting evidence reveals a convergent theme of maternal immune activation during pregnancy. Even without vertical transmission, virus-elicted maternal immune responses alter the maternal-fetal interface and gut microbiome, reshaping fetal immunity and birth outcomes. These immune perturbations increase susceptibility to infections, neurodevelopmental disorders, and immune-mediated diseases later in life. Here, we discuss viral immune evasion strategies that modulate maternal immunity and review current clinical and emerging therapeutic approaches aimed at mitigating long-term consequences in exposed children. Understanding how prenatal viral exposure shapes lifelong health is critical for developing targeted interventions and reducing postnatal disease burden.},
}

@article {pmid41606218,
year = {2026},
author = {Abdelhameed, A and Hussein, RH and Hatem, ZA and Bağcı, C and Ziemert, N},
title = {From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {65},
pmid = {41606218},
issn = {1573-0972},
mesh = {Humans ; *Multigene Family ; *Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Biosynthetic Pathways/genetics ; Metagenome ; },
abstract = {Diverse microbial communities within the human microbiome perform vital functions which influence both health and disease in hosts. Specialized metabolites produced by microbes via biosynthetic gene clusters (BGCs) drive ecological interactions and offer possibilities for therapeutic application. The biosynthetic capabilities of microorganisms present in human microbiomes are still mostly unexplored despite metagenomics advancements. The study examines the variety of microbial communities and BGC locations through metagenomic data from 1,191 samples across eight human microbiomes taken from the IMG/M database. Kraken2 executed taxonomic classification while antiSMASH v6.1.1 identified BGCs. The study used BiG-SCAPE to build a sequence similarity network while Bracken and Pavian tools analyzed microbial diversity. A total of 25,681 BGCs were identified, of which 97.5%, showed no significant match to existing clusters in MIBIG database, indicating substantial potential for novel biosynthetic discoveries . Showing no match to existing clusters in the MIBiG database which shows huge potential for new biosynthetic discoveries. New strains were discovered that produce unique RiPPs, NRPs, and siderophores primarily within the microbiomes of the large intestine, oral cavity, and skin. The large intestine showed maximum microbial and biosynthetic diversity compared to other areas while the biliary tract and nasal cavity displayed minimal diversity. New BGCs associated with antibiotic, cytotoxic, and immune-modulating functions present potential therapeutic uses. The investigation uncovers essential information about how microbial communities develop specific functions within various body regions. Uncharacterized BGC discoveries present new opportunities for drug development and treatments that target microbiomes.},
}

Humans
*Multigene Family
*Microbiota/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics
Biosynthetic Pathways/genetics
Metagenome

@article {pmid41606121,
year = {2026},
author = {Duttagupta, S and Messaoudene, M and Hunter, S and Desilets, A and Jamal, R and Mihalcioiu, C and Belkaid, W and Marcoux, N and Fidelle, M and Suissa, D and Ponce, M and Geiger, M and Malo, J and Piccinno, G and Punčochář, M and Filin, A and Heidrich, V and Rusu, D and Mbaye, B and Durand, S and Ben Aissa, I and Puller, V and de Lahondès, R and Blais, N and Tehfe, M and Owen, S and Bélanger, K and Parvathy, SN and Shieh, B and Raphael, J and Lenehan, J and Breadner, D and Rothenstein, J and Rozza, N and Maillou, J and Nili, S and Prifti, DK and Pinto, F and Armanini, F and Kim-Schulze, S and Marron, TU and Kroemer, G and Derosa, L and Zitvogel, L and Silverman, M and Segata, N and Vareki, SM and Routy, B and Elkrief, A},
title = {Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41606121},
issn = {1546-170X},
abstract = {Immune checkpoint inhibitors (ICI) have improved outcomes for patients with non-small cell lung cancer (NSCLC) and melanoma, yet over half of patients exhibit primary resistance. Fecal microbiota transplantation (FMT) may overcome resistance to anti-programmed cell death protein 1 (PD-1) therapy. The clinical activity and safety of FMT plus anti-PD-1 in NSCLC or anti-PD-1 plus anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) therapy in melanoma have not been evaluated. Here we report results from FMT-LUMINate, a multicenter, open-label, phase 2 trial assessing healthy donor FMT plus anti-PD-1 in NSCLC (n = 20) or anti-PD-1 plus anti-CTLA-4 (dual ICI) in melanoma (n = 20), in the first-line setting. Eligible patients received a single FMT via oral capsules prior to ICI initiation. The primary endpoint was objective response rate (ORR) in NSCLC. Secondary endpoints included ORR in melanoma, safety and donor-host microbiome similarity. In NSCLC, the ORR was 80% (16/20), meeting the study primary endpoint. In melanoma, the ORR was 75% (15/20). FMT was deemed safe in both cohorts by an independent data and safety monitoring committee, with no grade 3 or higher adverse events (AEs) in NSCLC and 13 (65%) patients experiencing grade 3 or higher AEs in melanoma. Shotgun metagenomic sequencing revealed that responders developed a distinct post-FMT gut microbiome composition, independent of acquired donor-recipient similarity or strain-level engraftment. Responders exhibited significantly greater loss of baseline bacterial species compared to non-responders, with frequent depletion of Enterocloster citroniae, E. lavalensis and Clostridium innocuum. This finding was reproduced across three published FMT oncology trials. We recolonized antibiotic-treated, tumor-bearing mice with post-FMT stool from two responder patients, and reintroduction of the specific bacterial species that were lost after FMT abrogated the antitumor effect of ICI. Taken together, these findings confirm the clinical activity of FMT in combination with ICI and suggest that the elimination of deleterious taxa is required for FMT-mediated therapeutic benefit. ClinicalTrials.gov identifier: NCT04951583 .},
}

@article {pmid41606120,
year = {2026},
author = {Fernandes, R and Jabbarizadeh, B and Rajeh, A and Hong, MMY and Baines, KJ and Ernst, S and Winquist, E and Ali, AS and Penny, S and Figueredo, R and Parvathy, SN and Lenehan, JG and Pinto, DM and Silverman, MS and Maleki Vareki, S},
title = {Fecal microbiota transplantation plus immunotherapy in metastatic renal cell carcinoma: the phase 1 PERFORM trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41606120},
issn = {1546-170X},
support = {1-MR_2022_4884//Lotte and John Hecht Memorial Foundation (Lotte & John Hecht Memorial Foundation)/ ; 203745/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Immune checkpoint inhibitors (ICIs) improve outcomes in metastatic renal cell carcinoma (mRCC) but are hindered by immune-related adverse events (irAEs). Modulation of the gut microbiome may enhance efficacy and mitigate toxicity, yet the safety and mechanisms of healthy donor fecal microbiota transplantation (FMT) in mRCC remain unexplored. In this phase 1 trial, 20 treatment-naive patients with mRCC received encapsulated healthy donor FMT (LND101) combined with ipilimumab/nivolumab (n = 16), pembrolizumab/axitinib (n = 3) or pembrolizumab/lenvatinib (n = 1). The primary endpoint was safety, defined by the incidence and severity of irAEs. Secondary endpoints included clinical response (Response Evaluation Criteria in Solid Tumors version 1.1), gut microbiome and immune correlates and patient-reported quality of life. The safety endpoint was met with 50% (10/20) of patients experiencing grade 3 irAEs and no serious FMT-related toxicities or grade 4 or 5 irAEs. Among evaluable patients, the objective response rate was 50% (9/18), including two complete responses (11%, 2/18). Notably, most treatment responders did not develop any grade 3 or higher irAEs. Alpha (α) diversity improvement and durable engraftment of taxa and metabolic functions associated with anti-inflammatory properties correlated with reduced toxicity and improved response. Conversely, patients experiencing grade 3 irAEs exhibited expansion of Segatella copri, particularly with ipilimumab/nivolumab, and elevated levels of donor-derived microbial enzymes previously linked to pro-inflammatory activity. Resilience to toxicity correlated with the maintenance of protective metabolites and increased levels of immune regulatory cells, whereas the presence of grade 3 irAEs and S. copri enrichment was associated with high immune dysregulation. These findings demonstrate the safety and potential for functional microbiome engraftment to optimize response and minimize toxicity in ICI-treated mRCC. ClinicalTrials.gov identifier: NCT04163289 .},
}

@article {pmid41606119,
year = {2026},
author = {Porcari, S and Ciccarese, C and Heidrich, V and Rondinella, D and Quaranta, G and Severino, A and Arduini, D and Buti, S and Fornarini, G and Primi, F and Stumbo, L and Giannarelli, D and Giudice, GC and Damassi, A and Giron Berríos, JR and Punčochář, M and Barbazuk, TB and Piccinno, G and Pinto, F and Armanini, F and Asnicar, F and Schinzari, G and Derosa, L and Kroemer, G and Sanguinetti, M and Masucci, L and Gasbarrini, A and Tortora, G and Cammarota, G and Zitvogel, L and Segata, N and Iacovelli, R and Ianiro, G},
title = {Fecal microbiota transplantation plus pembrolizumab and axitinib in metastatic renal cell carcinoma: the randomized phase 2 TACITO trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41606119},
issn = {1546-170X},
support = {GR-2018-12365734//Ministero della Salute (Ministry of Health, Italy)/ ; PNRR-POC-2023-12377319//Ministero della Salute (Ministry of Health, Italy)/ ; PNRR-POC-2023-12377319//Ministero della Salute (Ministry of Health, Italy)/ ; 30203//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; FIS00001711//Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)/ ; ERC-StG MicroRestore-101221279//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101052444//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; microTOUCH-101045015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101168810//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ONCOBIOME-825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; IHMCSA-964590//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 1U01CA230551//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Renal cell carcinoma (RCC) is a common malignancy with limited durable responses to first-line immune checkpoint inhibitor (ICI)-based therapies. Emerging evidence implicates the gut microbiome in modulating ICI efficacy. In the investigator-initiated, randomized, double-blind placebo-controlled phase 2a TACITO trial, we evaluated whether fecal microbiota transplantation (FMT) from complete ICI responders enhances clinical outcomes in treatment-naive patients with metastatic RCC (mRCC) receiving pembrolizumab + axitinib. The primary endpoint was the rate of patients free from disease progression at 12 months after randomization (12-month progression-free survival (PFS)). Secondary endpoints were median PFS and median overall survival, objective response rate (ORR), safety and microbiome changes, after randomization. Forty-five patients randomly received donor FMT (d-FMT) or placebo FMT (p-FMT). Although the primary endpoint was not met (70% versus 41% for d-FMT versus p-FMT, respectively, P = 0.053), the secondary endpoint of median PFS was significantly longer with d-FMT (24.0 months in the d-FMT arm versus 9.0 months in the p-FMT arm; hazard ratio = 0.50, P = 0.035). The ORR was 52% of patients in the d-FMT arm and 32% of patients receiving placebo. Microbiome analysis confirmed donor strain engraftment and increased α-diversity and larger microbiome shifts (β-diversity) compared with baseline composition in the d-FMT treatment group. Acquisition or loss of specific strains, but not total engraftment, was associated with the primary endpoint. Our findings support the safety and potential efficacy of selected donor FMT to enhance ICI-based treatment in mRCC, which deserves further investigations. ClinicalTrials.gov identifier: NCT04758507 .},
}

@article {pmid41606026,
year = {2026},
author = {Rahat, MTI and Sumi, MSA and Nurejannath, M and Ahmmed, R and Kibria, MK},
title = {Identification of bacterial key genes and therapeutic targets in hypertensive patients with type 2 diabetes through bioinformatics analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36467-5},
pmid = {41606026},
issn = {2045-2322},
abstract = {Hypertension (HTN) coexisting with type 2 diabetes (T2D) significantly increases cardiovascular risk, yet most microbiome studies have focused on these diseases separately and have overlooked their combined microbial gene-level mechanisms. The coexistence of HTN and T2D may create a distinct gut microbial environment where metabolic and vascular pathways intersect but the specific bacterial genes and molecular interactions underlying this dual phenotype remain largely unknown. To address this gap, this study aimed to identify bacterial key genes (bKGs) associated with hypertension coexisting with type-2 diabetes (HTNT2D) and to explore therapeutic agents targeting these bKGs through integrated bioinformatics approaches. A total of 124 gut microbiome samples, including 95 healthy controls (HC) and 29 HTNT2D cases were analyzed. Diversity analysis revealed significantly higher microbial richness and distinct clustering in HTNT2D, indicating altered microbial community structure. Differential abundance analysis identified 19 bacterial genera across four dominant phyla, while functional prediction uncovered 195 enriched metabolic pathways and 257 associated genes. To refine these finding, protein-protein interaction analysis highlighted 10 hub genes (acpP, dnaG, fusA, gltB, guaA, gyrB, lacZ, mdh, purF and tktA) as potential drivers of HTNT2D pathogenesis. Molecular docking analysis of these bKGs revealed binding affinities ranging from - 4.109 to -9.961 kcal/mol and three top-ranked drug candidates named Naringin-fusA (-9.961 kcal/mol), Neohesperidin-mdh (-9.818 kcal/mol), and Bromocriptine-gyrB (-9.446 kcal/mol) were selected as potential drugs based on their binding affinities. Subsequent molecular dynamics simulations performed for 100 ns confirmed the stability of their complexes, supporting their biological relevance. Drug-likeness and ADMET evaluations pointed to Bromocriptine as the most suitable compound though further safety validation will be necessary. Overall, this study provides novel insights into the gut microbiome signatures of HTNT2D and identifies bKGs with therapeutic potential. These computationally identified candidates can be prioritized for experimental validation to advance microbiome-based diagnostics and targeted therapies for HTNT2D management.},
}

@article {pmid41605941,
year = {2026},
author = {Di Grazia, G and Sánchez-Bayona, R and Casals-Pascual, C and Pascual, T and Generali, D and Gennari, A and Vigneri, P and Harbeck, N and Cortés, J and Prat, A and Schettini, F},
title = {Dynamic biomarkers in hormone receptor-positive/HER2-negative breast cancer trials: a new hope for precision oncology.},
journal = {NPJ breast cancer},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41523-026-00904-5},
pmid = {41605941},
issn = {2374-4677},
abstract = {Hormone receptor-positive/HER2-negative breast cancer evolves in response to therapy, demanding smarter, adaptive biomarker-based treatment strategies. We review emerging dynamic biomarkers to guide therapeutic decision-making, spanning tissue and liquid biopsies, metabolic imaging, and microbiome profiling, that capture tumor or host-related changes over time. By contrasting Academic and Industry approaches, we advocate for a cultural shift in clinical trial design and implementation, aiming to move from reactive to proactive Oncology.},
}

@article {pmid41605932,
year = {2026},
author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W},
title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00921-z},
pmid = {41605932},
issn = {2055-5008},
support = {N42A660907//National Research Council of Thailand/ ; },
abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.},
}

@article {pmid41605865,
year = {2026},
author = {Solis, S and Maldonado, EM and Mukhopadhyay, S and Jan, G and Landete, JM and Maluquer de Motes, C and Gutierrez-Merino, J},
title = {Self-aggregating Lactiplantibacillus plantarum enhances type-I interferon responses via the cytosolic sensors NOD2 and cGAS.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2615490},
doi = {10.1080/19490976.2026.2615490},
pmid = {41605865},
issn = {1949-0984},
mesh = {*Interferon Type I/immunology/metabolism/genetics ; *Nod2 Signaling Adaptor Protein/metabolism/genetics/immunology ; Humans ; Gastrointestinal Microbiome ; *Nucleotidyltransferases/metabolism/genetics/immunology ; Macrophages/immunology/microbiology ; *Lactiplantibacillus plantarum/immunology/physiology ; Animals ; Cytosol ; Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase ; },
abstract = {The gut microbiome plays a critical role in health, disease and immunity. To date, we have access to large datasets describing how the microbial diversity present in the gut correlates with many clinical conditions. However, the microbiome composition is taxonomically complex; influenced by many environmental factors; and variable between individuals and communities, thereby limiting functional and mechanistic insights into the microbiota‒host interactions. We are still unsure of the molecular mechanisms by which gut commensal microbes intrinsically possess to interact with the immune system and induce beneficial responses. This study has addressed this important question by revealing that only certain members of Lactobacillaceae, a bacterial family very well known for its probiotic properties, interact very intimately with macrophages because of their ability to simultaneously overexpress adhesive cell wall proteins and to self-aggregate, leading to significant production of type I interferon (IFN-I) cytokines. IFN-I cytokines are essential to confer protection against viral infections and auto-immune disorders. Specifically, we have proved that this enhanced IFN-I feature is strain-dependent and predominantly driven by cGAS, a molecule that activates the cytosolic sensor STING upon the recognition of bacterial DNA. Furthermore, another cytosolic sensor, NOD2, seems to be an additional stimulus to amplify IFN-I production, suggesting the involvement of successive molecular events for a prominent probiotic response. Our findings provide insight into how specific molecules of probiotic bacteria modulate or stimulate host responses, providing a better understanding of the molecular crosstalk between the microbiome and immune cells.},
}

*Interferon Type I/immunology/metabolism/genetics
*Nod2 Signaling Adaptor Protein/metabolism/genetics/immunology
Humans
Gastrointestinal Microbiome
*Nucleotidyltransferases/metabolism/genetics/immunology
Macrophages/immunology/microbiology
*Lactiplantibacillus plantarum/immunology/physiology
Animals
Cytosol
Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase

@article {pmid41605799,
year = {2026},
author = {Lee, H and Lee, MH and Seo, SH and Pak, J and Bae, S and Lee, G and Kim, HS and Kim, K and Kim, JH and Son, HS},
title = {Integrated Microbiome and Metabolomic Profiling to Identify Potential Biomarkers of Major Depressive Disorder.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2512014},
doi = {10.4014/jmb.2512.12014},
pmid = {41605799},
issn = {1738-8872},
mesh = {Humans ; *Major Depressive Disorder/microbiology/diagnosis/blood/metabolism ; *Biomarkers/blood/urine ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Male ; *Metabolomics/methods ; Middle Aged ; Female ; Adult ; *Metabolome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Carnitine/analogs & derivatives/metabolism/blood ; Dysbiosis/microbiology ; Gas Chromatography-Mass Spectrometry ; Fatty Acids/metabolism ; Republic of Korea ; },
abstract = {The pathophysiology of major depressive disorder (MDD) remains incompletely understood, hindering the development of objective diagnostic markers. While the microbiota-gut-brain axis is implicated in MDD, the functional link between gut dysbiosis and systemic metabolism remains largely obscure. To address this, we employed an integrated multi-omics approach combining 16S rRNA gene sequencing, GC-MS analysis of urine and plasma, complemented by UPLC-QTOF-MS profiling of plasma, in a Korean cohort (n = 69). We identified distinct taxonomic shifts, specifically the enrichment of the Eubacterium eligens group and Veillonella in MDD patients. Integrated correlation analysis revealed a functional "gut-lipid axis", where these taxa were strongly associated with alterations in host acylcarnitine and fatty acid metabolism. Notably, diagnostic evaluation demonstrated that the plasma metabolic profile yielded superior predictive accuracy (AUC = 0.862) compared to the gut microbiota (AUC = 0.654). Our findings suggest that while the gut microbiome provides mechanistic insights into lipid dysregulation, the circulating metabolome serves as a more robust, proximal diagnostic readout for MDD.},
}

Humans
*Major Depressive Disorder/microbiology/diagnosis/blood/metabolism
*Biomarkers/blood/urine
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Male
*Metabolomics/methods
Middle Aged
Female
Adult
*Metabolome
Bacteria/classification/genetics/isolation & purification/metabolism
Carnitine/analogs & derivatives/metabolism/blood
Dysbiosis/microbiology
Gas Chromatography-Mass Spectrometry
Fatty Acids/metabolism
Republic of Korea

@article {pmid41605796,
year = {2026},
author = {Park, CK and Bae, SH and Park, HW and Oh, NS and Kim, YJ and Kim, YW and Cho, TJ and Li, Y and Chai, J and Zhao, J and Cho, HT and Jung, JH and Park, J and Kim, TG and Kim, JK},
title = {Development of Large Language Model Specialized into Microbiome Datasets: an Application of Self-Evaluation and Scoring Comparison with Conventional Natural Language Processing Markers.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2511050},
doi = {10.4014/jmb.2511.11050},
pmid = {41605796},
issn = {1738-8872},
mesh = {*Natural Language Processing ; Humans ; Artificial Intelligence ; *Gastrointestinal Microbiome ; *Microbiota ; Computational Biology/methods ; Liver/microbiology/metabolism ; Large Language Models ; },
abstract = {The gut microbiome plays a fundamental role in host metabolism, immune regulation, and disease development. With the rapid accumulation of multi-omics and literature data, the microbiome field now faces the challenge of efficiently extracting scientific insights from massive, heterogeneous datasets. Artificial intelligence (AI) and large language models (LLMs) provide promising tools to address this complexity by enabling integrative analysis and knowledge synthesis across diverse biological sources. In this study, we developed METABOLISM, a microbiome-specialized LLM fine-tuned on 160,000 scientific abstracts to enhance literature-based contextual understanding of microbiome-liver interactions and related biological mechanisms. Using LoRA-based parameter-efficient training, METABOLISM was optimized for domain-specific reasoning and response generation. Model performance was evaluated through both automated Phi-4 scoring (a large language model-based evaluator for relevance, informativeness, and fluency) and structured human expert rubric assessments involving 20 domain specialists. The fine-tuned METABOLISM achieved superior relevance and clarity scores (mean > 7.5 ± 0.06) compared with general-purpose LLMs such as Gemma-3-12B-IT and ChatGPT-4o. Correlation analysis revealed weak to moderate negative relationships (R = -0.65, p < 0.0001) between traditional NLP metrics (BLEU, ROUGE) and human expert rubric scores, with a similar trend observed for correlations with Phi-4-based automated evaluation scores, indicating the limitations of surface-level similarity measures in biomedical contexts. Overall, our findings demonstrate that microbiome-adapted LLMs can effectively distill high-volume scientific data into biologically meaningful insights, supporting more efficient and interpretable research in microbiology and systems biology.},
}

*Natural Language Processing
Humans
Artificial Intelligence
*Gastrointestinal Microbiome
*Microbiota
Computational Biology/methods
Liver/microbiology/metabolism
Large Language Models

@article {pmid41605717,
year = {2026},
author = {Zhang, Y and Zhu, SJ},
title = {Role of bile acid metabolites in regulating viral infections.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.12.008},
pmid = {41605717},
issn = {1878-4380},
abstract = {Gut microbiota-derived bile acids are emerging as pivotal regulators of viral pathogenesis. They exhibit dual roles by directly blocking or promoting viral entry, while also systemically tuning immune responses. This forum discusses how spatiotemporal mapping of these interactions can address unresolved questions and inspire novel microbiome-based antiviral strategies.},
}

@article {pmid41605669,
year = {2026},
author = {Shen, X and Li, SB and Gao, MJ and Cao, JJ and Yang, H and Li, WW and Wei, LC and Chen, M and Liu, JY and Shi, YQ},
title = {Relationship Between Fecal Bile Acid Profile and Intestinal Microbiota in Patients With Chronic Radiation Enteritis.},
journal = {Journal of digestive diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-2980.70029},
pmid = {41605669},
issn = {1751-2980},
support = {82330100//National Natural Science Foundation of China/ ; 82200567//National Natural Science Foundation of China/ ; 2024TD-06//Healthcare lnnovation Capability Enhancement Plan in Shaanxi Province/ ; JSYXM04//Booster Plans of Xijing Hospital/ ; },
abstract = {OBJECTIVE: We aimed to investigate the relationship between fecal bile acid (BA) profile and intestinal microbiota in patients with chronic radiation enteritis (CRE).

METHODS: Altogether 60 patients with cervical cancer (CC) who visited Xijing Hospital between December 2022 and September 2023 were enrolled, including 20 patients who did not undergo any treatment (the CC group), 20 patients who developed CRE after radical radiotherapy (the CRE group), and 20 patients who did not experience CRE after radical radiotherapy (the non-CRE [NRE] group). Patients' characteristics and fecal samples were collected. Fecal BA profiles were quantified, and intestinal microbiota were analyzed by using the 16S rRNA gene sequencing. Differentially expressed BAs and microorganisms were identified across groups, and their correlations were assessed using Spearman's correlation analysis.

RESULTS: In patients with CRE, BA metabolism was characterized by increased proportions of primary BAs and decreased proportions of secondary BAs, particularly lithocholic acid and its isomers. In addition, the abundance of beneficial bacterial genera, such as Bifidobacterium and Megasphaera, was reduced, whereas that of potentially pathogenic genera, including Megamonas and Dorea, was increased. Furthermore, a bidirectional relationship between BA metabolism and intestinal microbiota was observed.

CONCLUSIONS: Patients with CRE present notable alterations in BA metabolism and intestinal microbiota. CRE may trigger a harmful feedback mechanism driven by the interaction between these two factors. Targeted regulation of BA metabolism and intestinal microbiota may be a promising therapeutic approach for the management of CRE.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT05728060.},
}

@article {pmid41605617,
year = {2026},
author = {Vijay-Kumar, M and Yeoh, BS and Gewirtz, AT},
title = {Hydroxylation matters! Microbial bile acid metabolism and colorectal cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337583},
pmid = {41605617},
issn = {1468-3288},
}

@article {pmid41605597,
year = {2026},
author = {Murcia-Soriano, LF and Venegas-Sanabria, LC and Arias-Blanco, D and Baracaldo Gomez, SDP and Borda, MG and Sanchez, G and Buitrago-Garcia, D},
title = {Microbes and ageing beyond the gut: the oral microbiome and frailty, sarcopenia and neurocognitive disorders in the elderly - a scoping review protocol.},
journal = {BMJ open},
volume = {16},
number = {1},
pages = {e106590},
doi = {10.1136/bmjopen-2025-106590},
pmid = {41605597},
issn = {2044-6055},
mesh = {Humans ; Scoping Reviews as Topic ; *Sarcopenia/microbiology ; Aged ; *Aging/physiology ; *Frailty/microbiology ; *Microbiota ; *Neurocognitive Disorders/microbiology ; *Mouth/microbiology ; Research Design ; },
abstract = {INTRODUCTION: Population ageing is a global phenomenon that has resulted in an increase in the number of patients with chronic diseases and geriatric syndromes. Frailty, sarcopenia and neurocognitive disorders are among the most prevalent conditions affecting older adults and have a direct effect on their quality of life, and can impact the burden and budgets of health systems. Recently, the oral microbiome has gained attention as it may be a factor that potentially influences the onset and progression of these syndromes. However, this is still a new line of research that has not been deeply explored. This scoping review protocol aims to explore how the oral microbiome may be associated with the onset of prevalent geriatric syndromes, frailty, sarcopenia and neurocognitive disorders, providing a picture of the current evidence and potential gaps for future research.

METHODS AND ANALYSIS: The scoping review will follow the Johanna Briggs Institute (JBI) methodology and will be reported accordit to the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews guidelines (PRISMA-ScR). Searches will be conducted in Medline, Embase, Cochrane Central, CINAHL, LILACS and Epistemonikos from inception to December 2025. Independent reviewers will perform the study selection and data extraction. A descriptive analysis of information will be conducted, highlighting oral microorganisms associated with these syndromes and emerging trends in the evidence. Original research studies in any language will be included. We will include randomised controlled trials, cohort studies, case-control studies and other relevant designs if they investigate the oral microbiome and its relation to geriatric syndromes in adults aged 65 or older, regardless of geographic location or setting.

ETHICS AND DISSEMINATION: Ethics approval is not required.},
}

Humans
Scoping Reviews as Topic
*Sarcopenia/microbiology
Aged
*Aging/physiology
*Frailty/microbiology
*Microbiota
*Neurocognitive Disorders/microbiology
*Mouth/microbiology
Research Design

@article {pmid41605486,
year = {2026},
author = {Cai, XX and Zhang, HT and Wang, YX and Li, XJ},
title = {[Role and research progress of dental medicine in physical anthropology studies].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {2},
pages = {266-272},
doi = {10.3760/cma.j.cn112144-20251013-00401},
pmid = {41605486},
issn = {1002-0098},
support = {2023YFC2506300//National Key R&D Program of China/ ; 2024C03241//Key Research and Development Program of Zhejiang Praince/ ; RD2022DXKB03//Exploration and Development Project of School of Stomatolog, Zhejiang University School of Medicine/ ; 202505/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Physical anthropology is a discipline that studies human physical characteristics and their evolutionary patterns through the analysis of human biological remains. Oral tissues such as teeth and jawbones, serving as crucial or even exclusive materials among human biological remains, establish dental medicine's central role in this field. This paper reviewed the advances in dental medicine's research on key physical anthropology topics and methodologies, including human origins and evolution, paleopathology, paleodietary reconstruction, and paleomicrobiology. In human origins and evolution research, dental morphology provides crucial evidence for identifying population relationships. Paleopathology reflects ancient survival pressures, subsistence economies, and cultural behavioral patterns through oral diseases. Paleodietary research reconstructs ancient dietary structures using dental microwear, trace elements, stable isotopes, and calculus microfossils (e.g., starch grains, ancient DNA, ancient proteins). Paleomicrobiology explores the evolution of health and disease through the oral microbiome. Current research faces limitations including narrow observation of oral diseases, inconsistent diagnostic criteria, and insufficient interdisciplinary integration. Future efforts should enhance multidisciplinary collaboration among dental medicine, archaeology, anthropology, and other fields. This multi-perspective approach will systematically elucidate the evolutionary trajectory of oral health and disease, enrich the historical context of dental medicine, and provide insights for contemporary prevention and treatment of oral diseases.},
}

@article {pmid41605365,
year = {2026},
author = {Pillay, D and Kuppusamy, UR and Arumugam, B},
title = {Role of terpenes and terpenoids in cross-talk between adipocyte browning and gut microbiome in obesity.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {107113},
doi = {10.1016/j.fitote.2026.107113},
pmid = {41605365},
issn = {1873-6971},
abstract = {Obesity, a major global health concern, is a complex condition characterized by excessive accumulation of fat that can result in various other health complications like cardiovascular disease, type 2 diabetes, and cancer. The intricate interactions between the gut microbiota and adipocyte browning, the process that transforms white adipose tissue (WAT) into metabolically active beige or brown-like adipose tissue (BAT) have gained considerable attention as a therapeutic strategy against obesity and related metabolic disorders. Terpenes and terpenoids have emerged as promising natural compounds to combat obesity and its associated metabolic complications. Terpenoids have been shown to exert anti-adipogenic effects, thus attenuating adipocyte hypertrophy, adipose tissue inflammation and oxidative stress through various mechanisms. The compounds have also been shown to modulate the composition and activity of gut microbiota, promoting the growth of beneficial bacteria while inhibiting the proliferation of harmful ones. These alterations in gut microbiota composition have been linked to improved metabolic parameters, including enhanced energy expenditure, improved insulin sensitivity, and reduced adiposity. Recent studies have highlighted the potential role of gut microbiota in mediating the effects of terpenoids on adipocyte browning, suggesting a complex interplay between these factors. However, the interplay has not been reviewed thus far. Therefore, this review highlights the role and mechanisms of terpenes and terpenoids in the cross-talk between adipocyte browning and the gut microbiome as potential therapeutic strategies for obesity. Studies were identified and screened through academic database searches and synthesized narratively. The review also includes challenges and future perspectives in introducing the compounds as alternate treatments for obesity.},
}

@article {pmid41605326,
year = {2026},
author = {Yuasa, H and Bermudez, DA and Konishi, K and Furukawa, M and Nozaki, R and Morita, S and Ozaki, K and Kondo, H and Hirono, I and Koiwai, K},
title = {Bacterial communities in pond water of kuruma shrimp Penaeus japonicus farms with different reported disease histories.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108555},
doi = {10.1016/j.jip.2026.108555},
pmid = {41605326},
issn = {1096-0805},
abstract = {Penaeid shrimp aquaculture is expanding worldwide, but recurrent infectious diseases remain a major threat to production. Interestingly, some farming environments sustain long-term stable production performance. To investigate the microbial basis of this condition, we performed 16S rRNA gene-based bacterial community analysis of rearing water from two farms with different reported disease histories. The stable production performance farm (Taketomijima) was characterized by a low-diversity bacterial community dominated by unclassified Rhodobacteraceae, whereas the variable production performance farm (Tanegashima) harbored a highly diverse and heterogeneous community. Despite the higher diversity, the variable production performance environment showed less stability across ponds, while the stable production performance farm exhibited a uniform and resilient microbiome structure. These results demonstrate that community composition and dominance of specific taxa, rather than overall diversity, are critical for disease prevalence. Our findings provide new insight into microbial factors of disease outcomes and lay the foundation for microbiome-informed management strategies to improve the sustainability and resilience of shrimp aquaculture.},
}

@article {pmid41605325,
year = {2026},
author = {Domari, MA and Khani, A and Sahebzadeh, N and Najimi, M and Mehrabadi, M},
title = {Gut microbes modulate Helicoverpa armigera immunity and affect its susceptibility to microbial pathogens.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108553},
doi = {10.1016/j.jip.2026.108553},
pmid = {41605325},
issn = {1096-0805},
abstract = {Emerging research underscores the critical roles of host-associated microbiota in modulating immunity and disease resistance in insects. However, the interplay between gut microbes and innate immune pathways remains incompletely understood in lepidopteran pests. This study investigates if manipulation of the gut microbiome affects immune responses and pathogen susceptibility in Helicoverpa armigera larvae. To do this, the gut microbiome of the larvae was removed using antibiotic treatment. Subsequently, the expression of antimicrobial peptides (AMPs) including attacin and defensin, and antioxidant genes including superoxide dismutase (SOD), dual oxidase (DUOX) and NADPH oxidase (NOX)were assessed following challenge with Bacillus thuringiensis (Bt) and Beauveria bassiana (Bb). Our results revealed that microbiome depletion reduced the expression of attacin and defensin in fat body and gut, and suppressed SOD gene expression in the gut. The bioassay tests showed that depletion of microbiota resulted in increased larval vulnerability to the pathogens compared to the control larvae. We also tested whether microbial infection affects gut microbiota and found that intrahemocoelic microbial injection induced both humoral and gut immunity, resulting in suppression of gut microbiota, highlighting a crosslink between humoral and gut immunity. Together, these results underscore a conserved requirement for microbiota-derived signals in priming specific innate immune pathways and provide insight into how microbiome manipulation may impact the success of biological control strategies. These findings suggest that targeted manipulation of the gut microbiome could be harnessed to enhance pest susceptibility to biocontrol agents, thereby offering a promising avenue for improving microbial pest control.},
}

@article {pmid41605271,
year = {2026},
author = {Akhtara, N and Bharali, MK},
title = {Recurrent amoxicillin exposure disrupts colonic homeostasis through oxidative stress, DNA repair dysregulation, and gut dysbiosis-driven inflammation.},
journal = {Chemico-biological interactions},
volume = {427},
number = {},
pages = {111939},
doi = {10.1016/j.cbi.2026.111939},
pmid = {41605271},
issn = {1872-7786},
abstract = {The present study investigated the impact of recurrent amoxicillin exposure on colonic health in a mouse model, applying a multi-parametric approach. Twenty animals were randomly divided into two groups, out of which one group received oral amoxicillin (100 mg/kg BW), administered every other week for twelve weeks. Histological and ultra-structural analyses (SEM and TEM) of colonic tissues revealed crypt degeneration, mucosal thinning, and inflammatory cell infiltration in the treated group. Biochemical assays demonstrated significantly elevated lipid peroxidation along with reduced antioxidant defences, indicative of oxidative stress. Immunohistochemistry confirmed oxidative DNA damage, accompanied by aberrant expression of DNA repair genes, indicating impaired genomic maintenance. Faecal microbiota profiling showed a pronounced loss of microbial load and enrichment of opportunistic pathogens, alongside a paradoxical increase in short-chain fatty acid levels. These alterations correlated with significantly upregulated inflammatory gene expression (TNF-α, IFN-γ, IL-6, IL-17 & IL-1β), indicating microbiome destabilization and heightened inflammatory signalling. Overall, recurrent amoxicillin exposure disrupted colonic homeostasis through dysbiosis, oxidative stress, genotoxicity, and inflammation, underscoring the potential risks of antibiotic therapy.},
}

@article {pmid41605131,
year = {2026},
author = {Kindtler, NL and Sheikh, S and He, R and Fonseca, RRD and Laursen, KH and Ekelund, F},
title = {Microbial diversity loss affects old and modern barley cultivars differently under varying nitrogen sources.},
journal = {Microbiological research},
volume = {306},
number = {},
pages = {128458},
doi = {10.1016/j.micres.2026.128458},
pmid = {41605131},
issn = {1618-0623},
abstract = {Soil microbial diversity is crucial for plant nutrition and health, yet how its loss affects plant performance remains unclear. We used a dilution-to-extinction approach to test how declining rhizo-microbiome diversity influences two barley cultivars: the modern RGT Planet and the older Babushka. Plants were grown in sterilized systems amended with mineral or organic nitrogen and inoculated with microbiome treatments (10[-][1], 10[-][3], 10[-][5], and 10[-][7] dilutions), plus a no-inoculum treatment. We used amplicon sequencing (16S, ITS, 18S) to profile rhizosphere communities, and quantified plant biomass, shoot nitrogen, and chitin mineralization. Protists and fungi were present in 10[-][1] and 10[-][3] but absent in all others. Microbiome inoculum and nitrogen source explained most variation in rhizo-microbiome composition, with cultivar having a smaller effect. Under organic nitrogen, Babushka showed a marked decline in biomass with decreasing diversity, whereas RGT was largely unaffected, indicating that the older cultivar relied more on a diverse microbiome to maintain growth. At intermediate diversity, when protists and fungi were lost, both cultivars showed improved growth and shoot nitrogen, coinciding with shifts in bacterial composition and loss of potential pathogens. Hence, reduced diversity did not always impair growth, suggesting functional compensation. Under mineral nitrogen, both cultivars were less sensitive to diversity loss. Overall, nitrogen source and cultivar identity modulated plant responses to microbial diversity loss. Diverse microbiomes promoted efficient use of organic nitrogen, particularly for the older cultivar, while the modern cultivar maintained growth at lower diversity. Our results demonstrate that the consequences of diversity loss are context-dependent and cultivar-specific.},
}

@article {pmid41605120,
year = {2026},
author = {Shakir Shakir, HN and Alias-Castillo, AJ and Bertini-Pérez, D and Rueda-Ruzafa, L and Roman, P and Cardona, D},
title = {Effectiveness of probiotic supplementation in managing depressive symptoms and inflammatory status in patients with depression: A systematic review and meta-analysis.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {58},
number = {},
pages = {106554},
doi = {10.1016/j.clnu.2025.106554},
pmid = {41605120},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: Depression is a multifactorial disorder influenced by genetic, biochemical, psychological, and environmental factors, and it significantly impacts quality of life. Probiotics, especially Lactobacillus and Bifidobacterium strains, have been proposed as adjunct therapies due to their capacity to modulate gut microbiota and the gut-brain axis. This systematic review and meta-analysis aimed to evaluate the effectiveness of probiotic supplementation on depressive symptoms and inflammatory status in individuals with depression.

METHODS: Articles were identified through searches in databases including PubMed, Scopus, CINAHL, and Zenodo, using terms related to depression, microbiome, and probiotics. The search, conducted between January and February 2025, yielded 780 articles. After removing duplicates and applying eligibility criteria, 13 studies were included in the systematic review and 7 in the meta-analysis.

RESULTS: Probiotic supplementation was significantly associated with improvement in depressive symptoms (p < 0.00001). However, no significant changes were found in inflammatory biomarkers, including interleukin-6 (p = 0.45) and tumor necrosis factor-alpha (p = 0.21).

CONCLUSIONS: These results suggest that probiotics may help alleviate depressive symptoms, although their effect on inflammation remains uncertain. Further high-quality studies are necessary to clarify underlying mechanisms and determine the clinical relevance of probiotics as adjunctive therapy in depression..},
}

@article {pmid41605069,
year = {2026},
author = {Vijayasimha, M and Srikanth, M},
title = {From association to action: Advancing microbiome evidence toward decision-grade insights in Japanese encephalitis virus research.},
journal = {Veterinary microbiology},
volume = {314},
number = {},
pages = {110901},
doi = {10.1016/j.vetmic.2026.110901},
pmid = {41605069},
issn = {1873-2542},
}

@article {pmid41604931,
year = {2026},
author = {Tanunchai, B and Schröder, O and Schädler, M and Noll, M},
title = {Dynamics of the plastisphere microbiome in agricultural soils under changing climatic conditions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141151},
doi = {10.1016/j.jhazmat.2026.141151},
pmid = {41604931},
issn = {1873-3336},
abstract = {Plastic pollution is a growing environmental concern, particularly in agricultural soils where plastics are widely used. Biodegradable plastics such as polybutylene succinate (PBS) and polybutylene adipate-co-terephthalate (PBAT) are increasingly promoted as sustainable alternatives, yet their environmental fate under changing climate and land-use conditions remains poorly understood. This study investigated the plastisphere microbiome associated with PBS, PBAT, and polyethylene (PE) as a reference, under conventional and organic farming systems and both ambient and simulated future climate scenarios. We assessed microbial colonization, plastic degradation, and bacterial-fungal interactions over one year of soil exposure. Agricultural practices significantly influenced the PBS plastisphere microbiome and PBAT bacterial richness, while climate effects were minor and limited to specific time points. No treatment significantly affected the molar mass loss of biodegradable plastics, although PBS degraded faster than PBAT. Microbial community composition shifted over time, with bacterial and fungal richness peaking at 160 or 270 days, and gene copy numbers highest at 60 or 365 days. Early colonization was dominated by a few genera, including Sphingomonas, Hymenobacter, Massilia, Vishniacozyma, Alternaria, and Mycosphaerella, many of which are known plastic colonizers and potential degraders. Co-occurrence networks revealed positive associations between dominant bacterial and fungal taxa. These findings provide new insights into the temporal dynamics and environmental drivers of plastisphere microbiomes in agricultural soils. Understanding microbial succession and interactions on biodegradable plastics is essential for assessing their degradation potential and environmental risks, particularly regarding microplastic formation and the persistence of plastic residues in terrestrial ecosystems.},
}

@article {pmid41604430,
year = {2026},
author = {de Jong, MJ and Zhou, J and Derikx, LAAP and Darwish Murad, S and van der Meer, AJ and de Vries, AC},
title = {Management of Inflammatory Bowel Disease Associated With Primary Sclerosing Cholangitis Pre- and Post-liver Transplantation.},
journal = {Transplantation},
volume = {},
number = {},
pages = {},
pmid = {41604430},
issn = {1534-6080},
abstract = {Primary sclerosing cholangitis (PSC)-associated inflammatory bowel disease (IBD) is considered a distinct IBD phenotype, with probably a distinct pathogenesis according to genome-wide association studies and mucosal immunology and microbiome studies. Management of IBD in patients with PSC presents with specific monitoring and therapeutic challenges. Both IBD-related and treatment-related complications have to be carefully considered in the context of hepatobiliary disease, end-stage liver disease, and liver transplant recipients. Standard IBD drug therapies are generally effective and well-tolerated in PSC-IBD, both pre- and post-liver transplantation. However, evidence of direct benefit on PSC progression is limited and largely based on surrogate endpoints such as alkaline phosphatase reduction. Vedolizumab and adalimumab have shown modest biochemical improvements in selected cohorts, although no therapy has demonstrated consistent disease-modifying effects on PSC. Based on current available data, vancomycin seems promising to improve IBD and PSC outcomes. In patients with an indication for colectomy, counseling on functional outcome in general and on disease-specific risks of recurrent intestinal inflammation, neoplasia, and PSC progression is warranted. Immunosuppressive regimens posttransplant and persistent intestinal inflammation influence graft survival and PSC recurrence. Thus, management in patients with PSC and IBD requires a tailored, risk-adapted approach, integrating control of intestinal inflammation, hepatobiliary monitoring, and cancer surveillance. This contemporary review aimede to elucidate the current understanding regarding the efficacy and safety of medical and surgical therapies used for IBD in light of the pre- and posttransplant course of patients with PSC-IBD.},
}

@article {pmid41604220,
year = {2026},
author = {Yao, ML and Lin, P and Hua, K and Zhang, W},
title = {The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jimb/kuag005},
pmid = {41604220},
issn = {1476-5535},
abstract = {Specialized metabolites encoded by biosynthetic gene clusters (BGCs) in the oral microbiome remain largely unexplored in the context of oral health and disease. Previous genome-centric surveys have identified hundreds of uncharacterized BGCs in the oral cavity associated with health and disease, but these studies relied on reference genomes and did not capture strain-level variation or the native distribution of BGCs. Here, we assembled three independently sourced metagenomic datasets from healthy and dental caries samples, extracted BGCs, and quantified their metagenomic abundance and transcriptional activity. We found that aryl polyene, ribosomally synthesized and post-translationally modified peptide (RiPP), and nonribosomal peptide (NRP) encoding BGCs were the most prominent BGCs identified across the three metagenomic datasets. We grouped the identified BGCs into homology-based gene cluster families (GCFs) and found that specific GCFs were consistently associated with either health or caries across diverse taxa, suggesting that some specialized metabolites may perform conserved ecological functions. Conversely, other BGCs showed more restricted taxonomic distributions and were linked to disease-associated taxa, such as Propionibacterium acidifaciens, suggesting niche-specific biosynthetic capacities within the oral environment. Applying elastic-net regression to the metatranscriptomic dataset further identified a subset of 51 BGCs out > 3 000 that distinguished healthy from caries samples, reinforcing the discriminatory power of BGC expression patterns. Together, these results demonstrate that BGCs provide functional resolution beyond taxonomic profiling and that BGC expression, rather than genomic presence alone, differentiates oral microbial community states. This underscores the relevance of specialized metabolism to oral health and supports the use of BGC-centric analyses to interrogate microbial interactions underlying community stability and disease-associated shifts.},
}

@article {pmid41604186,
year = {2026},
author = {Molasy, B and Wrzosek, M},
title = {The Wound Microbiome in Chronic Wounds: A Biomarker and Therapeutic Target.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag025},
pmid = {41604186},
issn = {1365-2672},
abstract = {Chronic wounds, including diabetic foot ulcers, venous leg ulcers, and pressure ulcers, remain a major global healthcare challenge, associated with substantial morbidity, risk of limb loss, and high healthcare costs. Increasing evidence indicates that the wound microbiome modulates inflammation, tissue repair, and responses to therapy, thereby influencing clinical outcomes. This review summarizes current knowledge on the composition and function of chronic wound microbial communities and discusses their clinical relevance as prognostic biomarkers and therapeutic targets. Microbiome structure is shaped by wound etiology, chronicity, anatomical site, and host comorbidities. Dysbiosis and biofilm formation contribute to persistent inflammation, antimicrobial tolerance, and delayed healing. Advances in sequencing and multi-omics technologies have improved microbial characterization and enabled the identification of candidate microbial signatures associated with healing trajectories. Emerging microbiome-modulating strategies such as probiotics, bacteriophages, topical oxygen approaches and nanotechnology-based interventions show potential to shift wound ecosystems toward a pro-healing state; however, robust clinical validation remains limited. Further clinical studies are needed to validate microbiome-guided diagnostics and interventions and to establish standardized protocols for their application in clinical practice.},
}

@article {pmid41604101,
year = {2026},
author = {Nihel, AB and Rania, AD and Hamadou, OH and Ghiles, G and Imen, B and Fatma, A and Ali, A and Basma, M and Hayet, S and Radhouan, G and Leila, AK and Mokdad-Gargouri, R},
title = {Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {47},
pmid = {41604101},
issn = {1678-4405},
support = {952583//H2020 European Research Council/ ; },
}

@article {pmid41604057,
year = {2026},
author = {Silveira, KA and Ramiro-Garcia, J and Lawless, C and Espinosa-Vazquez, JM and Fermoso, FG and Collins, G and O'Flaherty, V},
title = {Mutual dosing of tungsten, molybdenum and selenium impact anaerobic digestion microbiome.},
journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine},
volume = {},
number = {},
pages = {},
pmid = {41604057},
issn = {1572-8773},
support = {861088//H2020 Marie Skłodowska-Curie Actions/ ; },
abstract = {Metals are critical in anaerobic digestion, but their co-occurrence effects on microbiome structure and function are underexplored. This study hypothesized that exposure of methanogenic granules to a trace element (TE) mixture alongside molybdenum (Mo), tungsten (W) or selenium (Se)-would alter (i) extracellular polymeric substances (EPS) protein and carbohydrate content, (ii) microbial composition and function (iii) methanogenic pathways.To test this, anaerobic batch reactors (n = 35) were set up in a fed batch mode, with sacrificial reactors (n = 14) used to collect biomass for analyses, including DNA: RNA co-extraction, amplicon sequencing, and determination of the concentrations of total and soluble metals, Scanning Electron Microscopy- Energy Dispersive X-ray (SEM-EDX) and EPS extraction over a 24-day period.The results reveal that, Mo and W increased the concentration of soluble Fe in abiotic controls, enhancing Fe and S retention. The presence of W, Mo, W + Se, and Se had a positive effect on methane production, with W + Se and W enhancing acetoclastic methanogenesis. Additionally, Se increased EPS protein and carbohydrate contents in the biomass. Shifts in the microbiome composition were mainly driven by Mo and Se, with typically dominant Anaerolineacaeae, Capriciproducens, Macelibacteroides and Clostridium sensu stricto 5 taxa. Functional potential suggested an enrichment of nucleotide metabolism and, importantly, Vitamin (B12, B6 and B9) metabolic potential.These finding inform Anaerobic digestion (AD) stakeholders about the impacts of Fe, W, Mo, and Se co-dosing on process performance and microbiome structure and function, offering insights to optimize biogas production through tailored metal supplementation combinations, given demonstrations at lab and pilot scales.},
}

@article {pmid41603727,
year = {2026},
author = {Hoedt, EC and Burns, GL and Kang, S and Bruce, J and Morrison, M and Keely, S and Talley, NJ},
title = {Altered Duodenal Mucosa-Associated Microbiota and Immune Profiles in Functional Dyspepsia: A Study of Host-Microbiome Homeostasis.},
journal = {Neurogastroenterology and motility},
volume = {38},
number = {1},
pages = {e70238},
doi = {10.1111/nmo.70238},
pmid = {41603727},
issn = {1365-2982},
support = {//National Health and Medical Research Council/ ; },
mesh = {Humans ; *Dyspepsia/immunology/microbiology/pathology ; *Gastrointestinal Microbiome/immunology/physiology ; Female ; Male ; Homeostasis/immunology ; Middle Aged ; Adult ; *Intestinal Mucosa/microbiology/immunology/pathology ; *Duodenum/microbiology/immunology/pathology ; Leukocytes, Mononuclear/immunology ; },
abstract = {BACKGROUND: Recent work suggests an altered duodenal mucosa-associated microbiota (d-MAM) in patients with functional dyspepsia (FD) when compared to controls. This may reflect alterations in host-microbiome homeostasis. Given the specific mucosal immune signatures identified in FD, we hypothesize that these signatures are associated with specific microbial changes. We aim to profile the d-MAM to identify microbes associated with known changes in FD mucosal and peripheral immunity.

METHODS: Upper gastrointestinal biopsies were collected from 11 outpatient controls and 17 FD patients. Specific biopsies were collected for 16S rRNA sequencing, histology, and mucosal lamina propria mononuclear cell (LPMC) isolation. Where available, peripheral blood mononuclear cells (PBMC) were isolated. PBMC and LPMC populations were analyzed for T-cell populations by flow cytometry.

KEY RESULTS: Comparing the histological and immune measures between FD and controls revealed significant differences with decreased villi goblet cells and increased LPMC CD4 Central Memory, LPMC CD8, and PBMC CD4+ Central Memory Th17 in FD patients. Specific microbiome associations found that in controls, villi goblet cells positively correlated with Massilia and negatively with Exiguobacterium. Additionally, controls had a negative correlation between LPMC CD4 Central Memory and Veillonella. Notably, FD patients demonstrated a significant negative correlation between LPMC CD8 and Sulfophobococcus, and a positive correlation between PBMC CD4+ Central Memory Th17 and both Gemella and Fusobacterium.

CONCLUSIONS AND INFERENCES: Our findings contribute to a growing body of evidence, indicating FD patients exhibit distinct alterations in d-MAM and immune profiles compared to controls. Furthermore, the immune-microbiome associations within control populations were absent in FD patients, suggesting a loss of host-microbiome homeostasis that may contribute to FD pathophysiology.},
}

Humans
*Dyspepsia/immunology/microbiology/pathology
*Gastrointestinal Microbiome/immunology/physiology
Female
Male
Homeostasis/immunology
Middle Aged
Adult
*Intestinal Mucosa/microbiology/immunology/pathology
*Duodenum/microbiology/immunology/pathology
Leukocytes, Mononuclear/immunology

@article {pmid41603631,
year = {2026},
author = {Díaz, S and Eisfeld, AJ and Palma-Cuero, M and Dinguirard, N and Owens, LA and Ciuoderis, KA and Pérez-Restrepo, LS and Chan, JD and Goldberg, TL and Hite, JL and Hernandez-Ortiz, JP and Kawaoka, Y and Zamanian, M and Osorio, JE},
title = {Gut microbiota and parasite dynamics in an Amazonian community undergoing urbanization in Colombia.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0078825},
doi = {10.1128/msphere.00788-25},
pmid = {41603631},
issn = {2379-5042},
abstract = {Studies on human gut microbiota have recently highlighted a significant decline in bacterial diversity associated with urbanization, driven by shifts toward processed diets, increased antibiotic usage, and improved sanitation practices. This phenomenon has been largely overlooked in the Colombian Amazon, despite rapid urbanization in the region. In this study, we investigate the composition of gut bacterial microbiota and intestinal protozoa and soil-transmitted helminths (STHs) in both urban and rural areas of Leticia, located in the southern Colombian Amazon. Despite their geographic proximity, the urban population is predominantly non-indigenous, while indigenous communities mostly inhabit the rural area, resulting in notable lifestyle differences between the two settings. Our analyses reveal a reduction in bacterial families linked to non-processed diets, such as Lachnospiraceae, Spirochaetaceae, and Succinivibrionaceae, in the urban environment compared to their rural counterparts. Prevotellaceae, typically associated with non-processed food consumption, shows a significantly higher abundance in urban Leticia. STH infections were primarily detected in rural Leticia, while intestinal protozoa were ubiquitous in both rural and urban areas. Both types of parasites were associated with higher gut bacterial richness and diversity. Additionally, microbial metabolic prediction analysis indicated differences in pathways related to unsaturated fatty acid production and aerobic respiration between rural and urban bacterial microbiomes. This suggests a tendency toward changes in the urban microbiota that may lead to increased susceptibility to non-communicable chronic diseases. These findings provide new insights into the impact of urbanization on gut microbiota dynamics in the Amazonian context and underscore the need for further research into any associated health outcomes.IMPORTANCEChanges in the diversity and composition of gut microbiota in urban populations have been linked to the rise of non-communicable chronic diseases, such as autoimmune conditions, diabetes, and cancer. As developing countries undergo a demographic shift toward increased urbanization, accompanied by changes in diet, housing, and medication use, there is a concerning loss of microbial diversity. Therefore, it is essential to investigate microbiota changes in overlooked populations, such as indigenous communities in the Colombian Amazon basin. A better understanding of local and generalizable changes in gut microbial composition through urbanization may facilitate the development of targeted programs aimed at promoting lifestyle and diet changes to prevent diseases that healthcare systems may be ill-equipped to effectively address.},
}

@article {pmid41603538,
year = {2026},
author = {Retherford, SA and Woodruff, KL and Harstine, BR and Dittoe, DK and Block, J},
title = {The Bull Reproductive Microbiome: A Comparative Analysis of Microbial Communities within Semen and Organs of the Bull Reproductive System†.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioag025},
pmid = {41603538},
issn = {1529-7268},
abstract = {Semen from mature, healthy bulls contains commensal microbes. Potential internal sources of seminal microbes have not been extensively evaluated. Objectives were to 1) assess whether the testes of the bull contain commensal microbes and to compare the composition of the putative testicular microbiome to that of semen and rumen fluid and 2) determine whether other organs of the bull reproductive system contain microbial populations. Here, we demonstrate that the testes of the bull contain a low biomass, yet diverse, microbiome. Interestingly, the microbial composition of rumen fluid, semen and testicular tissue were each dissimilar from one another, indicating that each source contains a unique microbiota. Only four core amplicon sequence variants, Acinetobacter, Enterobacteriaceae (E. coli), Jeotgalicoccus, and Kiritimatiellae WCHB1-41, were shared between semen and the testes. Along with the testes, microbial populations were also present within the penile and pelvic urethra, seminal vesicles and epididymis of mature bulls. Of these anatomic niches, the microbial populations within the penile and pelvic urethra were the most diverse and shared the greatest number of core taxa (n = 72). The microbiota of the seminal vesicles, epididymis and the testes were significantly dissimilar from each other. Only one core taxa, Mycoplasma, was shared between the testes and epididymis. Collectively, our results demonstrate that semen and organs of the bull reproductive tract contain unique microbial populations. Further research is necessary to determine whether the microbial composition of organs of the bull reproductive system, such as the testes and epididymis, influence sperm viability and bull fertility.},
}

@article {pmid41603371,
year = {2026},
author = {McAbee, GN and Morse, AM},
title = {Symptomatic Vitamin and Nutrient Deficiencies of Autism Spectrum Disorder and the Potential for Treatment.},
journal = {Journal of child neurology},
volume = {},
number = {},
pages = {8830738251413826},
doi = {10.1177/08830738251413826},
pmid = {41603371},
issn = {1708-8283},
abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurobehavioral disorder. Children with ASD often have restrictive diets that can be due to food aversion, sensory sensitivities, ritualistic behavior, or comorbid gastrointestinal issues. Diet and nutritional status play a critical role in the health of neurodevelopment, and the microbiome, and can affect cognition, motor and sensory status, behavior, and sleep. Children with ASD are 5 times more likely to develop eating problems and secondary vitamin and nutritional deficiencies. Such dietary restriction has been causative of vitamin and nutritional deficiencies that can lead to permanent sequelae if not adequately identified and treated. Symptoms of these deficiencies can be subtle and misleading and, thus, underrecognized. This review discusses various symptomatic vitamin and nutrient deficiencies associated with dietary restrictions that can occur in children and adolescents with ASD of which clinicians need to be aware. With treatment, symptoms can be reversible. Without timely treatment, sequelae can be permanent.},
}

@article {pmid41603333,
year = {2026},
author = {Tiwari, P and Gupta, A and Kaushik, M and Dwivedi, R and Tripathi, M and Dada, R},
title = {Association of yoga with cognitive and gut microbiome changes in Alzheimer's disease: An exploratory case-control study.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261415612},
doi = {10.1177/13872877261415612},
pmid = {41603333},
issn = {1875-8908},
abstract = {BackgroundAlzheimer's disease (AD) is marked by cognitive decline, depressive symptoms, and gut microbial dysbiosis. Yoga may support cognitive and emotional health while modulating gut microbiota, but integrative clinical evidence is limited.ObjectiveTo evaluate the effects of a 12-week yoga intervention on cognition, depressive symptoms, and gut microbial diversity, composition, and function in Indian patients with mild AD.MethodsIn this hospital-based case-control study, 16 AD patients and 17 cognitively healthy controls (HCs) were recruited at AIIMS, New Delhi. AD diagnosis followed NIA-AA criteria, supported by Montreal Cognitive Assessment (MoCA) and Patient Health Questionnaire-9 (PHQ-9) assessments. AD participants underwent 60-min supervised yoga sessions daily for 12 weeks. Cognitive performance, depressive symptoms, and stool microbiota were assessed pre- and post-intervention. Metagenomic sequencing enabled taxonomic and functional profiling, with alpha diversity, beta diversity (Bray-Curtis distance), and differential abundance analyses performed using standard bioinformatics tools.ResultsYoga was associated with improved cognition (MoCA: 22.33 ± 2.34 → 25.44 ± 2.01; p = 0.001) and reduced depressive symptoms (PHQ-9: 5.78 ± 3.11 → 2.22 ± 1.71; p = 0.007). Alpha diversity remained stable, while beta diversity shifted post-yoga AD samples toward the HC cluster. Beneficial taxa (Faecalibacterium prausnitzii, Roseburia intestinalis, Bifidobacterium, Akkermansia) increased, whereas pro-inflammatory taxa (Collinsella aerofaciens, Klebsiella spp.) decreased. Functional analysis showed partial recovery of metabolic and short-chain fatty acid pathways.ConclusionsA 12-week yoga intervention was associated with cognitive and mood improvements and partial normalization of gut microbial function in mild AD. Larger randomized trials with lifestyle monitoring and multi-omics integration are warranted to confirm causal mechanisms.},
}

@article {pmid41602763,
year = {2025},
author = {Xu, J and Li, J and Kong, X and Zhang, C and Qi, B and Zhu, X and Zhu, Y and Xu, Y},
title = {Dysbiosis and metabolic pathway shifts in the gut microbiome of children with sepsis: a comparative analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1715990},
pmid = {41602763},
issn = {1664-302X},
abstract = {BACKGROUND: The newly published Phoenix Sepsis Score in 2024 for assessing sepsis in children mainly focuses on respiratory, cardiological, coagulation and neurological indicators, whereas the gut microbiome also plays key roles in the occurrence and progression of sepsis. Additionally, emerging evidence suggests that specific biomarkers in gut microbiome are associated with disease progression. This study aimed to explore the differences in gut microbiome diversity, composition and function between septic and healthy children, and to establish correlations with clinical indicators and outcomes, providing new possibilities for the diagnosis and treatment of sepsis.

RESULTS: Analysis of gut microbiome was performed in 20 sepsis children and 9 healthy controls aged between 3 and 18 years old. The anal swab samples were analyzed by metagenomic next-generation sequencing. Significant differences were observed in α and β diversity of gut microbiome between sepsis group and healthy controls groups. Especially, Shannon diversity was significantly correlated with white blood cell count, serum lactate, length of pediatric intensive care unit stay and length of hospital stay (all R > 0, p < 0.05). Firmicutes and Bacteroidetes were both dominant in most of children in SG and HC groups, while three in SG showed extremely low combined abundances of Firmicutes and Bacteroidetes (<10%), which might be associated with chemistry therapy and death outcome. Bacteria associated with nosocomial infections, including genus taxa Acinetobacter, Prevotella, Escherichia, Klebsiella, Bacteroides, and Corynebacterium, can be dominant (relative abundance>70%) in sepsis group, which were absent in healthy control group. Enterococcus abundance not only predicted sepsis risk (AUC = 0.85) but also was correlated with 28-day mortality (R > 0, p = 0.004). Gene function prediction based on Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated significant differences profile in SG and sepsis-deaths groups. The enriched gut microbiome genes were related to cellular proliferation, energy metabolism, signal transduction, the oxidative stress response and arginine metabolism.

CONCLUSION: Significant differences in diversity, taxa composition and gene function in the gut microbiome existed between septic and healthy children. The associations between gut microbiome dysbiosis and clinical indicators were identified. Enterococcus could be a biomarker to predict sepsis risk.},
}

@article {pmid41602754,
year = {2025},
author = {Deng, L and Chen, X and Pan, S and Huang, W and Yin, Y and Wei, X and Zhang, H and Zhu, C},
title = {The developmental changes of fecal microbial composition and diversity in emu (Dromaius novaehallandiae) at early growth stages.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1744168},
pmid = {41602754},
issn = {1664-302X},
abstract = {The early postnatal period plays a crucial role in the establishment and maturation of the gut microbiome in avian hosts, significantly influencing their metabolic processes and overall health. This study was carried out to characterize the ontogenetic development of fecal microbiota in emus (Dromaius novaehollandiae) during critical early growth stages from days 7 to 28 post-hatch using 16S rRNA gene sequencing. The results indicated that rank abundance and rarefaction curves confirmed adequate sequencing depth for capturing microbial diversity across all age groups. The dominant phyla of fecal microbiota in emus included Firmicutes, Proteobacteria, and Bacteroidetes, with successional shifts observed at order, family, and genus levels. As emus advanced in age, fecal microbiota underwent significant changes in microbial community, diversity, and function. The α-diversity indices (Observed species, Shannon, PD whole tree, Chao1, and ACE) in the feces of emus peaked significantly at d 21 (p < 0.05). The β-diversity analysis revealed significant structural differences in microbial communities between different ages, particularly between d14 and d7, d21 vs. d7, and d14 vs. d28 (p < 0.05). Linear discriminant analysis Effect Size (LEfSe) identified 26 discriminative biomarkers with stage-specific enrichments, including Turicibacter (d7/d28), Erysipelotrichaceae (d7/d14), Bacteroidetes (d21), and Corynebacteriaceae as well as Actinobacteria (d28). T-test validation confirmed significant temporal variations in phylum (Firmicutes, Actinobacteria, and Bacteroidetes) and genus-level abundances (e.g., Bacteroides and Lactobacillus) in the feces of emus (p < 0.05). PICRUSt functional prediction indicated age-dependent metabolic pathway enrichment, including amino and nucleotide sugar metabolism (d7), oxidative phosphorylation (d14), ABC transporters and cysteine metabolism (d21), and genetic information processing pathways (d28). These results demonstrated dynamic, stage-specific restructuring of the fecal microbiota and its metabolic potential during early development in emus. This research presented the initial longitudinal assessment of fecal microbiota development in emus throughout their crucial early developmental stage, revealing age-dependent alterations in microbial composition and metabolic activity that could guide enhanced nutritional and health approaches for ratites.},
}

@article {pmid41602751,
year = {2025},
author = {Wu, Y and Zhou, M and Wan, Y and Wei, K and Ma, S and Cheng, L and Lin, T and He, L and He, Y and Zhou, F},
title = {The microbial conductor of cancer hallmarks: intratumoral microbiome as a multidimensional oncogenic modulator.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1695187},
pmid = {41602751},
issn = {1664-302X},
abstract = {The intratumoral microbiome, comprising diverse bacteria, fungi, and viruses residing within tumor tissues, is increasingly recognized as a multidimensional oncogenic modulator, acting akin to a "microbial conductor" orchestrating key cancer hallmarks. Its compositon exhibits substantial heterogeneity across individuals and is closely associated with the host immunity, the tumor microenvironment (TME), and therapeutic efficacy. Specific microbial species can "conduct" pro-tumorigenic processes by producing carcinogenic metabolites, dysregulating inflammatory signaling, or facilitating immune evasion. Conversely, other microorganisms may exert anti-tumorigenic effects by stimulating anti-tumor immunity or directly inhibiting cancer cell proliferation. Furthermore, the intratumoral microbiome can influence therapeutic outcomes by modulating the metabolism of chemotherapeutic agents or altering the efficacy of immunotherapies. Therefore, a deeper understanding of the intratumoral microbiome and its complex interplay with tumors holds immense potential to unravel fundamental mechanisms of cancer development and progression, while simultaneously revealing novel avenues for precision oncology strategies. This review outlines the biological roles of the microbiota in modulating the hallmarks of cancer hallmarks, summarizes current knowledge on its multidimensional interactions driving tumor progression, and discusses the translational potential of targeting or leveraging the intratumoral microbiome based on recent advancements. Future research integrating multi-omics profiling, spatial technologies, and functional validation will be essential for resolving methodological limitations and accelerating the clinical translation of microbiome-based interventions.},
}

@article {pmid41602744,
year = {2025},
author = {Karpe, AV and Hegde, P and Bletotu, C and Qiu, Z},
title = {Editorial: Antimicrobial resistance: causes, mechanisms and mitigation strategies for gut dysbiosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1765239},
pmid = {41602744},
issn = {1664-302X},
}

@article {pmid41602620,
year = {2025},
author = {Yang, SB and Moon, JH},
title = {Microbial therapeutics for canine periodontal disease: current status and future perspectives.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1748968},
pmid = {41602620},
issn = {2297-1769},
abstract = {Periodontal disease in dogs arises from ecological disruption of the oral microbiome. Sequencing-based studies and quantitative molecular analyses reveal characteristic dysbiotic transitions in affected dogs, with coordinated increases in Porphyromonas gulae, Prevotella, and Treponema, along with Treponema denticola and Tannerella forsythia, together with a loss of commensal-dominated genera such as Moraxella, Capnocytophaga, and members of the Neisseriaceae family. Rather than being driven by a single dominant pathogen, accumulating evidence indicates that canine periodontitis is driven by polymicrobial synergy within dysbiotic biofilms. This ecological perspective has stimulated growing interest in microbial therapeutics aimed at modulating community structure and function instead of relying solely on broad-spectrum antibiotics. Probiotics and postbiotics show potential in reducing halitosis and modulating epithelial innate immune responses. Bacteriophage-based approaches and predatory bacteria exhibit strain-specific antimicrobial activity in preclinical human or in vitro models, although their relevance to canine oral disease remains unvalidated. Synthetic biology and CRISPR-based antimicrobial systems provide conceptual frameworks for genotype-targeted modulation of virulence. Remaining challenges include transient microbial persistence, limited veterinary clinical evidence, biosafety concerns, and the absence of standardized regulatory pathways. Collectively, emerging microbial therapeutics highlight the potential but also the current limitations of ecology-guided, non-antibiotic strategies for canine periodontal therapy.},
}

@article {pmid41602541,
year = {2025},
author = {Adkar-Purushothama, CR and Chettimada, A and Murali, TS and Muthusamy, A and Bouarab, K and Perreault, JP},
title = {Non-chemical control of fungal pathogens in crops: a one-health perspective on strategies, mechanisms, and future directions.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1746521},
pmid = {41602541},
issn = {1664-462X},
abstract = {Fungal pathogens threaten global crop production, food security, and environmental and human health. Though the reliance on chemical fungicides has provided effective control, but raises concerns over environmental contamination, toxic residues, and the rapid emergence of fungicide-resistant strains. These challenges, along with regulatory pressures, highlight the need for safer, more sustainable disease-management strategies. This review incorporates advances in non-chemical approaches for controlling fungal plant diseases, including cultural practices, biological control agents, natural plant metabolites, RNA-based technologies, nanotechnology, and microbiome engineering. We evaluate each strategy's mechanisms, strengths, limitations, and remaining knowledge gaps. An integrated pest management framework is proposed to combine complementary methods, reduce dependence on chemical inputs, enhance crop resilience, and support human and ecosystem health.},
}

@article {pmid41602533,
year = {2025},
author = {Vieira, CK and Rozmoš, M and Kotianová, M and Hršelová, H and Bukovská, P and Jansa, J},
title = {Low spatial mobility of associated microbes along the hyphae limits organic nitrogen utilization in the arbuscular mycorrhizal hyphosphere.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1706684},
pmid = {41602533},
issn = {1664-462X},
abstract = {BACGROUND: Arbuscular mycorrhizal (AM) fungi enhance plant nutrient acquisition from soil; however, their ability to exploit organic nutrient forms in the absence of associated microbes capable of mineralization remains unclear.

METHODS: To test if the AM fungi carry their beneficial bacterial partners into nutrient-rich zones, we conducted three controlled experiments manipulating the microbial inputs, diversity and composition in plant-AM fungus-soil systems, ranging from open pots to semi-sterile mesocosms. We manipulated soil microbial diversity by imposing a microbial diversity gradient (complex communities fractionated by size, resulting in fractions passing through 1 µm to 1000 µm sieves) and cultivated Andropogon gerardii in previously sterilized substrate together with a bacterial-free Rhizophagus irregularis. In each experiment, [15]N-labeled chitin or mineral nitrogen (N) compartments were installed in the root-free zone of each mesocosm.

RESULTS: With decreasing microbial inputs into the root-free zone, the N uptake from chitin to plants, facilitated by the AM fungal hyphae, decreased. Upon complete absence of microbes in the root-free zone, AM hyphal foraging preferences assessed by quantitative PCR indicated that exploration of the mineral N compartments was more effective than that of the chitin compartments. The AM fungal hyphae were ineffective in priming mineralization of organic N even if provided with complex soil microbiomes at a distance from the compartment.

CONCLUSIONS: In summary, chitin-enriched compartments become attractive for the AM fungi only when previously mineralized by competent microbes. Such microbes, however, were not effectively transported to spatially restricted organic resources in soil via AM hyphal highways in our experiments.},
}

@article {pmid41602516,
year = {2026},
author = {Badero, OJ and Meribole, ES and Omokore, O and Quadri, IO and Kingdom, P and Ifeanyichukwu, OC and Ogunnoiki, SO and Samuel-Ogunnoiki, PM and Adeyoola, O and Osibowale, B and Chima-Ogbuiyi, N and Buari, MO and Umeh, J and Adeyemi, A},
title = {Gut Microbiota and Colorectal Cancer: Is Microbial Dysbiosis in Carcinogenesis an Emerging Risk Factor?.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e102283},
pmid = {41602516},
issn = {2168-8184},
abstract = {The gut microbiome has emerged as a critical factor in colorectal cancer (CRC) development, offering significant potential for early diagnosis and novel approaches. Current screening methods like colonoscopy and faecal immunochemical tests (FIT), while effective, face limitations in accessibility and patient compliance. Recent research has identified distinct microbial signatures associated with CRC, including elevated levels of Fusobacterium nucleatum and specific metabolic byproducts, which could serve as non-invasive diagnostic biomarkers. The integration of microbiome analysis with existing screening techniques shows promise for improving early detection rates, particularly in underserved populations. Furthermore, advances in multi-omics technologies are revealing novel mechanistic insights into how gut dysbiosis contributes to CRC progression, opening new avenues for targeted therapies and personalised prevention strategies. However, significant challenges related to standardisation and clinical implementation must be addressed to realise the full potential of these microbiome-based approaches in routine CRC care.},
}

@article {pmid41602199,
year = {2026},
author = {Luo, L and Yang, B and Zhao, J and Li, X and Qiao, W and Zhang, M and Tian, L and Chen, L},
title = {Regulation of infant gut microbiota and metabolic pathways by human milk oligosaccharides: a multi-omics investigation.},
journal = {RSC advances},
volume = {16},
number = {6},
pages = {5641-5651},
pmid = {41602199},
issn = {2046-2069},
abstract = {The third-most solid component in breast milk is human milk oligosaccharides (HMOs)-crucial for the growth and development of infants. HMOs are divided into three main categories: fucosylated, nonfucosylated, and sialylated HMOs. However, comparative studies evaluating the variations of the impact of in vitro fermentation of these typical or dominant HMOs on the metabolic functions of an infant's gut microbiome remain limited. Therefore, we systematically analyzed the role of three typical HMOs-2'-fucosyl lactose, lactose-N-tetrose, and 3'-sialyllactose-in the structural reshaping of the infant intestinal flora; we also explored their impact on short-chain fatty acid (SCFA) production and metabolism, as well as their overall metabolic spectrum. We found that HMOs aided the growth of beneficial microorganisms, such as Bifidobacterium, Lactobacillus, and Enterococcus, while also reducing the number of harmful bacteria, including Escherichia-Shigella. Further, HMOs had a substantial impact on amino acid, purine, and lipid metabolic pathways and significantly increased SCFA levels. Correlation analyses revealed significant associations between Bifidobacterium and multiple lipid metabolites. Positive correlations between Lactobacillus and amino acid derivatives, as well as close links between Bacteroides and acetate production, were detected. Overall, these findings indicate that the gut flora-metabolite interplay is central to HMO function, and different HMOs variably regulate the gut microbiota composition and metabolic pathways. This study provides a theoretical basis for optimizing HMOs' fortification strategies in infant formulas.},
}

@article {pmid41602156,
year = {2025},
author = {Andrusiów, S and Dratwa-Kuzmin, M and Łacina, P and Bochen, P and Gładysz, K and Szponar, B and Koszewicz, M and Bogunia-Kubik, K},
title = {Genetic and metabolic inflammation signatures in chronic inflammatory demyelinating polyneuropathy: the role of IL18 polymorphisms and short-chain fatty acids.},
journal = {Frontiers in molecular neuroscience},
volume = {18},
number = {},
pages = {1738817},
pmid = {41602156},
issn = {1662-5099},
abstract = {INTRODUCTION: Chronic inflammatory demyelinating polyneuropathy (CIDP) remains diagnostically challenging, with limited biological markers to aid phenotyping and differential diagnosis, particularly at the CIDP-diabetes mellitus (DM) interface.

METHODS: We investigated inflammatory genetic and metabolic readouts in CIDP by integrating interleukin 18 (IL-18) promoter variation with cytokines and short-chain fatty acids (SCFAs). 32 untreated CIDP patients and 15 controls underwent clinical scoring, nerve-conduction studies (NCS), IL-18 genotyping (rs187238, rs1946518, rs1946519), serum cytokine profiling (IL-2, tumor necrosis factor α (TNF-α), IL-18), and SCFA quantification in stool, serum, and cerebrospinal fluid (CSF).

RESULTS: No group-level differences emerged for IL-2, TNF-α, or IL-18 in serum or CSF, and CIDP subgroups (DM+ vs DM-; classical vs atypical) did not differ in NCS severity or electromyography (EMG) denervation. In contrast, IL18 promoter variation showed various associations: rs1946518 G allele correlated with peroneal nerve shorter compound motor action potential (CMAP) distal latency and lower ulnar nerve sensory nerve action potential (SNAP) amplitude. Additionally, carriers of the rs187238 C allele showed significantly higher CSF protein concentrations, whereas the rs1946518 G allele was associated with a trend toward lower CSF protein levels. Moreover, the rs187238 C and rs1946518 T alleles were associated with lower CSF butyrate levels. A haplotype analysis indicated that GGG (rs187238, rs1946518, rs1946519) aligned with shorter peroneal nerve CMAP distal latency, lower disability (INCAT), and a lower CSF protein, whereas CTT associated with higher CSF protein and lower CSF butyrate concentrations. We confirmed the presence of acetate, propionate, and butyrate in human CSF and demonstrated serum-CSF equivalence for these SCFAs, while stool concentrations were higher, as expected.

DISCUSSION: Collectively, IL18 polymorphisms and SCFAs readouts emerge as biologically grounded candidates for patient stratification in CIDP; these findings warrant validation in larger, multicenter cohorts integrating electrophysiology with CSF/serum biomarkers and microbiome profiling.},
}

@article {pmid41602129,
year = {2025},
author = {Gautam, AK and Kumar, V and Sonkar, AB and Singh, A and Yadav, D and Rajan, N and Kumar, P and Singh, S and Saha, S and Mahalingam Rajamanickam, V},
title = {Metabolites involvement in the growth and spread of liver cancer.},
journal = {Liver research (Beijing, China)},
volume = {9},
number = {4},
pages = {286-297},
pmid = {41602129},
issn = {2542-5684},
abstract = {Hepatocellular carcinoma (HCC), commonly known as primary liver cancer, is a leading cause of cancer-related mortality worldwide, primarily attributed to changing lifestyles and dietary habits. HCC arises from liver cirrhosis, hepatic fibrosis, or hepatitis B virus infection, and is caused by disruptions in protein and lipid metabolism. These metabolic alterations, recognized as a hallmark of cancer, are pivotal in the progression of chronic liver disease to HCC. Due to its asymptomatic nature in early stages, HCC is often diagnosed at advanced stages when treatment options are limited. Despite being a potentially curative option, liver transplantation remains hindered by high costs and donor scarcity, further compounded by suboptimal long-term success rates. This review examines the critical metabolites that play a part in developing HCC, focusing on their roles as possible biomarkers for disease progression and therapeutic targets. Additionally, the influence of the gut microbiome on HCC development is discussed, highlighting its interplay with metabolic pathways. Understanding the roles of metabolites and the gut microbiome in HCC progression underscores the importance of their potential use in early detection and the development of targeted therapies, offering new avenues for improving patient outcomes.},
}

@article {pmid41602108,
year = {2025},
author = {Mehta, SD and Zulaika, G and Osire, E and Agingu, W and Paul, S and Akinyi, C and Green, SJ and van Eijk, AM and Bhaumik, RK and Otieno, FO and Phillips-Howard, PA},
title = {Sub-optimal menstrual materials and vaginal microbiome disruption in women relying on sex for livelihood.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1662237},
pmid = {41602108},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology ; Cross-Sectional Studies ; *Microbiota ; Adult ; Young Adult ; Sexual Behavior ; *Menstruation ; Vaginosis, Bacterial/microbiology/epidemiology ; Sexually Transmitted Diseases/microbiology/epidemiology ; *Menstrual Hygiene Products/adverse effects ; RNA, Ribosomal, 16S/genetics ; Adolescent ; },
abstract = {BACKGROUND: Sub-optimal menstrual materials (MM), such as using cloths, cotton balls, or tissues, can adversely affect the vaginal microbiome (VMB). Women who rely on sex for economic livelihood often use sub-optimal materials to conceal menstruation and avoid loss of income. We hypothesized that among women who rely on sex for economic livelihood, those using sub-optimal MM would be more likely to have non-optimal VMB than those with adequate MM.

METHODS: This cross-sectional analysis used baseline data from women participating in a trial assessing the impact of reusable menstrual discs on the VMB, Bacterial vaginosis (BV), and sexually transmitted infections (STIs). Data on sociodemographics, menstrual materials, and sexual practices were collected via interviewer-administered survey. Clinician-collected vaginal samples were tested for BV, STI, and VMB. VMB was assessed via 16S rRNA gene amplicon sequencing. A suite of statistical approaches identified factors associated with sub-optimal MM (use of cotton balls, tissue, or cloth) and VMB composition.

RESULTS: 407 women were enrolled February through October 2023, with median age 27 years, 24.7% were HIV-positive, 42.2% had BV, and 21.9% had STI (composite of chlamydia, gonorrhea, trichomoniasis). Vaginal community state type (CST) was primarily diverse (CST-IV; 63.5%), or Lactobacillus iners dominated (CST-III; 28.1%), while CST-I (L. crispatus dominated) was uncommon (7.9%). Sub-optimal MM was reported by 42.0% of participants and in multivariable modeling, was more common among women with indicators of economic strain. In multivariable analyses, alpha diversity was higher with sub-optimal MM and indicators of economic strain. Sub-optimal MM was associated with CST-IV in crude analyses but was attenuated and non-significant when adjusted for age, educational attainment, amount paid at last sexual encounter, number of sex partners, and HSV-2. Non-targeted machine learning algorithms identified non-optimal VMB taxa with greater relative abundance among women with sub-optimal MM.

DISCUSSION: Sub-optimal menstrual materials were used commonly and associated with non-optimal VMB composition. Reusable menstrual discs that may be worn during sex may address the economic factors driving sub-optimal MM that are associated with non-optimal VMB.},
}

Humans
Female
*Vagina/microbiology
Cross-Sectional Studies
*Microbiota
Adult
Young Adult
Sexual Behavior
*Menstruation
Vaginosis, Bacterial/microbiology/epidemiology
Sexually Transmitted Diseases/microbiology/epidemiology
*Menstrual Hygiene Products/adverse effects
RNA, Ribosomal, 16S/genetics
Adolescent

@article {pmid41602101,
year = {2025},
author = {Deng, Q and Liu, Y and Zhang, J and Zhang, H and Zhang, Y and Wang, M and Jia, M and Ding, D and Fang, Y and Wang, Y and Gu, H and Wang, H},
title = {Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1730098},
pmid = {41602101},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Nanopore Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; *Precision Medicine/methods ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Metagenomics/methods ; Microbiota ; Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Pulmonary infections are common in patients with lung cancer (LC), complicating diagnosis and treatment. This study explored the diagnostic performance and clinical utility of targeted nanopore sequencing (TNPseq) for detecting pathogens in LC-related pulmonary infections.

METHODS: A total of 143 patients with LC or benign pulmonary diseases complicated by pulmonary infections were included and stratified into diagnostic and therapeutic cohorts. Sputum samples underwent conventional culture, metagenomic next-generation sequencing (mNGS), and TNPseq analyses. Microbiota profiles were compared across disease groups and correlated with tumor therapy responses. In the therapeutic cohort, clinical outcomes were assessed between empirical therapy and TNPseq-guided therapy.

RESULTS: TNPseq identified a significantly higher proportion of clinically relevant pathogens compared to mNGS (48.76% vs. 16.80%, p < 0.001) and demonstrated superior sensitivity (81.25% vs. 68.75%), with a 40.7% reduction in turnaround time (16 hours vs. 27 hours). Both sequencing methods revealed an enrichment of Lactobacillus species in non-initial diagnosis lung cancer (NDLC) patients (p < 0.01). Patients exhibiting partial response or stable disease (PR/SD) showed increased abundance of Neisseria, Veillonella, and Prevotella species (p < 0.05). Clinical remission was achieved in all patients; however, 68.4% of those initially receiving empirical therapy subsequently required a switch to TNPseq-guided treatment due to its ineffectiveness. Compared to this empirical-to-TNPseq group, the median treatment duration was significantly shorter under direct TNPseq guidance (total: 6 days vs. 13 days, p < 0.01; LC subgroup: 5 days vs. 15.5 days, p < 0.05), thereby reducing unnecessary antibiotic exposure.

CONCLUSIONS: By enabling rapid pathogen detection and profiling of the pulmonary microbiome, TNPseq facilitates targeted therapy and reduces antibiotic overuse in LC patients. These findings highlight the potential of TNPseq as a promising, rapid, and non-invasive diagnostic candidate for first-line use, offering a comprehensive view of both infection and host-microbe interactions in immunocompromised patients.},
}

Humans
*Lung Neoplasms/complications/microbiology
*Nanopore Sequencing/methods
Male
Female
Middle Aged
Aged
Sputum/microbiology
*Precision Medicine/methods
High-Throughput Nucleotide Sequencing
*Respiratory Tract Infections/diagnosis/microbiology/drug therapy
Metagenomics/methods
Microbiota
Bacteria/genetics/isolation & purification/classification
Sensitivity and Specificity
Adult
Aged, 80 and over

@article {pmid41601983,
year = {2025},
author = {Zhang, Y and Zhang, Y and Wang, L and Liu, B and Zheng, J and Cao, J and Xie, L and Shen, N and Wang, J},
title = {Serum valeric acid stimulates lung epithelial cilia assembly and improves prognosis in patients with severe respiratory infections.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1761517},
pmid = {41601983},
issn = {1663-9812},
abstract = {INTRODUCTION: Globally, respiratory infections remain a leading cause of mortality, with treatment efficacy increasingly challenged by antimicrobial resistance. This study aimed to investigate the role of serum metabolites in the prognosis of severe human pneumonia.

METHODS: Untargeted and targeted serum metabolomics were performed on intensive care unit (ICU) patients. Experimental validation was conducted in a murine bacterial infection model and cellular models. RNA sequencing was used for mechanistic exploration to identify the signaling pathways regulated by the key metabolite.

RESULTS: Valeric acid, a short-chain fatty acid, was significantly elevated in survivors compared with non-survivors of severe pneumonia. In the murine Klebsiella pneumoniae model, valeric acid treatment alleviated infection severity, reduced body weight loss, lung inflammation, and bacterial load. Mechanistically, RNA sequencing revealed that valeric acid suppresses IL-17-associated inflammation and upregulates pathways related to mucociliary clearance. We further delineated the underlying mechanism, finding that valeric acid acts as a histone deacetylase (HDAC) inhibitor, specifically targeting HDAC3. This inhibition activates the canonical Wnt/β-catenin signaling pathway, leading to the upregulation of the master transcriptional regulator Foxj1 and subsequent promotion of cilia assembly and function in airway epithelia.

DISCUSSION: The findings establish a protective role for the gut microbiome-derived valeric acid in respiratory infections via the novel HDAC-Wnt-FOXJ1 axis, revealing its potential as a therapeutic agent to improve clinical outcomes.},
}

@article {pmid41601696,
year = {2025},
author = {Yi, S and Luo, L and Dong, Z and Wang, K and Zhu, Z and Gao, Q and Jiang, Y and Yang, X and Hei, F},
title = {Study on the characteristics and correlation of fecal microbiota and metabolites in patients with acute lung injury after cardiopulmonary bypass based on 16S rRNA sequencing and non-targeted metabolomics analysis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1713650},
pmid = {41601696},
issn = {1664-3224},
mesh = {Humans ; Male ; Female ; *Cardiopulmonary Bypass/adverse effects ; Metabolomics/methods ; *Feces/microbiology ; Middle Aged ; *Acute Lung Injury/metabolism/etiology/microbiology ; Aged ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Prospective Studies ; *Metabolome ; *Bacteria/genetics/classification ; },
abstract = {Acute lung injury (ALI) is a severe complication following cardiopulmonary bypass (CPB), associated with high mortality and impaired patient prognosis. At present, there is no effective therapeutic strategy for ALI after CPB. Although the gut microbiota has been implicated in ALI, the biological significance of these associations remains largely elusive. A prospective, single-center, case-control design was adopted. A total of 53 post-CPB patients were enrolled, including 21 in the ALI group and 32 in the non-ALI (NALI) group. Postoperative fecal samples were collected for microbiome and metabolomic analyses, which were subsequently correlated with clinical data. Results revealed that β diversity analysis indicated distinct differences in microbial community structure (Anosim: R = 0.14, P = 0.004; Permanova: R[2] = 0.058, P = 0.008). ALI patients exhibited a significant increase in the Bacillota, alongside reductions in Bacteroidota and Actinomycetota. At the genus level, Streptococcus and Enterococcus were enriched in the ALI group, while Bacteroides and Akkermansia were diminished. Metabolomics analysis identified 130 differentially expressed metabolites, 109 of which were significantly reduced in the ALI group, primarily involving amino acid metabolic pathways such as phenylalanine, tryptophan, and tyrosine. A random forest model identified genera such as Bacteroides, Corynebacterium, and Lactobacillus as having high predictive value for ALI (AUC > 0.7). Combined microbiota-metabolite analysis revealed significant correlations between specific genera and differentially expressed metabolites, suggesting a potential role for the gut-lung axis in the development of ALI following CPB. Patients with postoperative ALI following CPB exhibit marked gut microbiota structural disruption and metabolic dysfunction, both closely associated with adverse clinical outcomes. Genera such as Bacteroides and their associated metabolites may serve as early predictive biomarkers, offering novel therapeutic targets for the prevention and management of ALI.},
}

Humans
Male
Female
*Cardiopulmonary Bypass/adverse effects
Metabolomics/methods
*Feces/microbiology
Middle Aged
*Acute Lung Injury/metabolism/etiology/microbiology
Aged
*Gastrointestinal Microbiome
*RNA, Ribosomal, 16S/genetics
Case-Control Studies
Prospective Studies
*Metabolome
*Bacteria/genetics/classification

@article {pmid41601648,
year = {2025},
author = {Pan, S and Cui, W and Lin, J and Wang, Z and Li, Z and Liu, B},
title = {The infection-microbiome-immunity axis in bladder cancer: mechanistic insights and therapeutic perspectives.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1716230},
pmid = {41601648},
issn = {1664-3224},
mesh = {Humans ; *Urinary Bladder Neoplasms/immunology/microbiology/therapy/etiology ; Animals ; Tumor Microenvironment/immunology ; Dysbiosis/immunology ; *Microbiota/immunology ; Gastrointestinal Microbiome/immunology ; },
abstract = {Bladder cancer (BC) represents a paradigm of infection-associated malignancy in which microbial dysbiosis, immune aging, and tumor microenvironmental remodeling converge to shape disease progression. Increasing evidence highlights the dual role of the urinary and gut microbiota in modulating bladder carcinogenesis through infection-driven inflammation and immune dysfunction. Chronic exposure to uropathogens and microbial imbalance disrupts epithelial integrity, promotes extracellular matrix degradation, and reprograms local immune signaling, collectively fostering a tumor-permissive niche. Concurrently, immunosenescence exacerbates microbial persistence and impairs antitumor immunity, reinforcing a pathogenic feedback loop between infection and immune decline. This review integrates current insights from microbiome research, tumor immunology, and microbial pathogenesis to delineate the mechanistic continuum linking infection, dysbiosis, and immune remodeling in BC. Finally, we discuss emerging microbiome-targeted and immunomodulatory strategies aimed at restoring microbial-immune equilibrium and improving therapeutic efficacy. Together, these perspectives provide a refined conceptual framework for understanding infection-driven oncogenesis and guiding precision interventions in BC.},
}

Humans
*Urinary Bladder Neoplasms/immunology/microbiology/therapy/etiology
Animals
Tumor Microenvironment/immunology
Dysbiosis/immunology
*Microbiota/immunology
Gastrointestinal Microbiome/immunology

@article {pmid41601564,
year = {2025},
author = {Alavian, F and Safaeian, M},
title = {How the gut microbiome shapes learning and memory: A comprehensive review.},
journal = {IBRO neuroscience reports},
volume = {19},
number = {},
pages = {491-506},
pmid = {41601564},
issn = {2667-2421},
abstract = {Cognitive functions, such as learning and memory processes, are closely related to the gut microbiome. The gut-brain axis (GBA), a complex network of bidirectional communications between the central nervous system and the gastrointestinal tract, plays an important role in regulating these functions. This study aims to investigate the impact of the gut microbiome on learning and memory and to provide new insights into the role of the GBA in these cognitive processes. This narrative review explores various mechanisms through which the gut microbiome affects cognitive functions by reviewing scientific articles related to the gut microbiome, GBA, learning, and memory. The focus is on studies that have investigated the relationship between the gut microbiome, changes in microbial composition, and cognitive functions. The results indicate that the gut microbiome influences brain function and behavior through various mechanisms, such as vagus nerve signaling, effects on the enteric nervous system, the production of neurotransmitters, the regulation of inflammation and the immune system, and the production of metabolites such as short-chain fatty acids (SCFAs). Dysbiosis of the gut microbiota affects hippocampal function, learning, and stress regulation. Additionally, probiotics and prebiotics, along with nutritional status, affect the composition and function of the gut microbiome; therefore, maintaining the balance of the gut microbiome and paying attention to the GBA may lead to improved cognitive functions and the prevention of learning and memory-related disorders. Microbiome-based interventions, such as probiotics and dietary changes, have the potential to increase performance.},
}

@article {pmid41601555,
year = {2025},
author = {Yang, H and Gong, W and Hou, Y and Wang, Y and He, P and Yu, Q},
title = {Genetically predicted immune cell-mediated causal associations between 473 gut microbiome species and neurodevelopmental disorders.},
journal = {IBRO neuroscience reports},
volume = {19},
number = {},
pages = {894-902},
pmid = {41601555},
issn = {2667-2421},
abstract = {BACKGROUND: Neurodevelopmental disorders (NDD) are a class of complex diseases whose underlying pathogenesis has not been fully elucidated. Previous observational studies have reported that gut microbiota dysbiosis may be one of the potential risk factors for the development of NDD, however, causal relationships and the potential mediating role of immune cells have yet to be established.

METHODS: Bidirectional two-sample Mendelian randomization (TSMR) and two-step Mendelian randomization (two-step MR) methods, mainly using inverse variance weighting (IVW), were used to explore the potential associations between gut microbiota and NDD, as well as the mediating role of immune cells in the causal pathway. Bayesian weighted Mendelian randomization (BWMR) method was additionally used to validate positive causality. Sensitivity analyses under different statistical assumptions were conducted to assess association robustness.

RESULTS: Based on the IVW and BWMR methods, we identified 5 and 4 gut microbiota taxonomic units exhibiting significant causal associations with ADHD and ASD, respectively. These included the negative modifying effect of family Syntrophorhabdaceae abundance on ADHD risk (OR: 0.4440, 95 % CI = 0.2620-0.7523, P = 0.0025), the significant protective effect of species ER4 sp002437735 on ASD (OR: 0.2996, 95 % CI = 0.1504-0.5968, P = 0.0004) and the stimulatory effect of species Agathobacter sp000434275 on ASD (OR: 1.7426, 95 % CI = 1.1496-2.6415, P = 0.0089). P values derived from Cochran's Q test, Egger's regression intercept test, and global test for pleiotropy and outliers did not suggest statistical significance. Further two-step MR revealed that Syntrophorhabdaceae could reduce the risk of ADHD, with Unswitched memory B cell %lymphocyte mediating 6.35 %. Additionally, 2.49 % and 1.91 % of the causal associations between ER4 sp002437735 and Agathobacter sp000434275 with ASD were mediated by BAFF-R⁺ switched memory B cells and activated/secreting CD4 regulatory T cell percentage of CD4 regulatory T cells, respectively.

CONCLUSION: Our study reveals direct evidence that NDD is influenced by specific gut microbiota, while its causal effects may be mediated by immune cell traits.},
}

@article {pmid41601518,
year = {2025},
author = {Sgarbossa, C and Chinna Meyyappan, A and Forth, E and Bromley, H and Milev, R},
title = {Assessing the long-term effects of microbial therapeutics as treatment within psychiatry: a systematic review.},
journal = {Frontiers in psychiatry},
volume = {16},
number = {},
pages = {1663719},
pmid = {41601518},
issn = {1664-0640},
abstract = {BACKGROUND: The management and treatment of psychiatric disorders by manipulating the gut microbiome and utilizing microbial therapeutics, via modulation of the gut-brain-axis, has been a rapidly growing field of research. Given the novelty of using microbial therapeutics within psychiatry, a growing number of studies have investigated their use as treatment for various psychiatric disorders and symptoms. However, few studies have explored the longitudinal efficacy of these treatments. This review aims to summarize the findings of any studies assessing the long-term effects of gut-related interventions on mood and psychiatric symptoms.

METHODS: A systematic search of 4 databases (Embase, PsycINFO, Medline, Web of Science) from inception to May 28, 2025, informed by Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, and using key words relating to microbial therapeutics, psychiatric disorders, and long-term effects was conducted. Findings were included or excluded using pre-determined eligibility criteria such as being been written in English and published by a peer-reviewed journal, assessed for quality using the Cochrane Handbook for Systematic Reviews of Interventions Risk of Bias tool, and qualitatively evaluated.

RESULTS: The search yielded 4175 studies, of which 1274 duplicates were removed. All remaining studies underwent abstract screening, from which 70 records were full-text screened and a total of ten clinical studies (n = 10) met eligibility criteria and were included in the review. The majority of studies explored the effects of microbial therapeutics such as fecal microbiota transplant and probiotics, as treatment for disorders of the gastrointestinal tract as the primary scope, with additional outcome measures assessing psychiatric well-being. The review presented with mixed findings: many studies reported a sustained improvement in symptoms of depression and anxiety ranging from 3- to 18-months post-treatment, while others reported the opposite with no sustained long-term improvement in mood-related symptoms. There was also a lack of consistency across follow-up duration between studies, making it difficult to compare findings.

CONCLUSIONS: Overall, this review highlighted the need for more placebo-controlled studies with larger sample sizes to effectively evaluate the longitudinal potential of microbial therapeutics as treatment for mood-disturbances and psychiatric symptoms. With consideration for the limitations of this field, these results provide evidence that there may be long-term benefits of targeting the gut microbiome as treatment for mood-related disturbances.},
}

@article {pmid41601370,
year = {2025},
author = {Tu, S and Zhang, Y and Zhang, L and Zhu, SJ},
title = {Commensal bacteria play a fundamental role in maintaining gut immune homeostasis.},
journal = {Journal of Zhejiang University. Science. B},
volume = {27},
number = {1},
pages = {101-104},
pmid = {41601370},
issn = {1862-1783},
support = {323B200243, 32172864 and U21A20261//the National Natural Science Foundation of China/ ; 2022YFD1800804//the National Key Research and Development Plan of China/ ; },
mesh = {*Homeostasis/immunology ; Humans ; *Gastrointestinal Microbiome/immunology ; T-Lymphocytes, Regulatory/immunology ; Inflammatory Bowel Diseases/immunology/microbiology ; Animals ; Intestinal Mucosa/immunology/microbiology ; Immune Tolerance ; Symbiosis ; },
abstract = {The intestinal microbiome, which is a key factor in the maintenance of host gut homeostasis, enhances intestinal mucosal barrier function and immune tolerance (Rooks and Garrett, 2016; Skelly et al., 2019). However, the specific immunomodulatory functions of microbiota-derived metabolites in mucosal inflammatory responses remain largely unknown. The effects of microbial metabolites may vary across different immune cell types and host homeostasis (Hu et al., 2023; Zhao et al., 2023). Hence, it is fundamental to understand how specific intestinal microbes and their metabolic small molecules cause or mitigate gut-related diseases like inflammatory bowel disease (IBD). It has been uncovered that during the pathogenesis of IBD, excessive T helper 1 cell (Th1)/Th17 activation and impaired function of colonic regulatory T cells (Tregs) occur (Subramanian, 2020). Given that colonic Tregs play an important role in inhibiting IBD via secreting immunosuppressive cytokines, the molecular mechanisms linking certain intestinal microbes and their metabolites to Treg-mediated immune tolerance are yet to be fully understood.},
}

*Homeostasis/immunology
Humans
*Gastrointestinal Microbiome/immunology
T-Lymphocytes, Regulatory/immunology
Inflammatory Bowel Diseases/immunology/microbiology
Animals
Intestinal Mucosa/immunology/microbiology
Immune Tolerance
Symbiosis

@article {pmid41601318,
year = {2026},
author = {Muñoz-Hernández, J and Peralta-Maraver, I and Cavieres, G and Gutiérrez-Cortés, I and Rezende, EL and Rivera, DS},
title = {Phylosymbiosis and functional redundancy in the Drosophila (Diptera: Drosophilidae) gut microbiome and its implications for host fitness.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {1},
pages = {},
pmid = {41601318},
issn = {1536-2442},
support = {11190637//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 21241747//Universidad Mayor Doctoral Fellowship and the ANID National Doctoral Fellowship/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Drosophila/microbiology/physiology/genetics/growth & development ; *Symbiosis ; RNA, Ribosomal, 16S/analysis ; Chile ; *Genetic Fitness ; Female ; Phylogeny ; },
abstract = {The gut microbiome plays a fundamental role in host ecophysiology. Numerous studies have examined microbiome composition and functionality to understand the ecological and evolutionary factors shaping host-microbe interactions. However, the consequences of these patterns for animal ecology remain poorly understood. Here, we examined how variations in the gut microbiome influence fitness differences among Drosophila species sharing a common dietary niche. Using 16S rRNA gene sequencing, we analyzed the gut microbial taxonomy and predicted functional profiles of 4 Drosophila species collected in central Chile. Our results revealed a strong signal of phylosymbiosis in the microbial taxonomy, while functionality was highly redundant across the studied fly species. Functional biomarkers analysis indicated that the gut microbiome supports the nutritional requirements of D. simulans (Sturtevant), D. hydei (Sturtevant), and D. repleta (Wollaston); whereas, this was less evident in D. melanogaster (Meigen). To assess the potential contribution of the microbiome to host performance, we compared egg-to-adult viability between 2 species with the greatest physiological divergence: D. simulans and D. hydei. Notably, D. simulans exhibited significantly higher egg viability and shorter development time than D. hydei. Strikingly, the D. simulans microbiome contained more taxonomic and functional biomarkers previously demonstrated to enhance fly fitness, whereas the D. hydei microbiome harbored taxa and functions potentially detrimental to host performance. These findings suggest that the gut microbiome contributes to host fitness and may shape the evolutionary ecology of Drosophila species, with broader implications for community dynamics, including interspecific competition and species displacement.},
}

Animals
*Gastrointestinal Microbiome
*Drosophila/microbiology/physiology/genetics/growth & development
*Symbiosis
RNA, Ribosomal, 16S/analysis
Chile
*Genetic Fitness
Female
Phylogeny

@article {pmid41601294,
year = {2026},
author = {Song, CH and Kim, N and Nam, RH and Choi, H and Jin, I and Kim, EH and Ha, S and Kang, K and Lee, W and Choi, H and Kim, YR and Seok, YJ and Lee, HK and Shin, CM and Lee, DH},
title = {Sex-Dependent Microbial and Host Profiles Following Fecal Microbiota and Bifidobacterium longum Treatment in Stress-Induced Gut Dysbiosis.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl250440},
pmid = {41601294},
issn = {2005-1212},
abstract = {BACKGROUND/AIMS: Irritable bowel syndrome (IBS) is a chronic functional gastrointestinal disorder influenced by stress, microbial dysbiosis, and immune activation. Microbiota-directed therapies, including fecal microbiota transplantation and probiotics, show promise, but their sex-specific effects remain unclear. We compared the therapeutic effects of lyophilized fecal microbiota (LFM) with Bifidobacterium longum BBH016 in male and female Wistar rats subjected to repeated water avoidance stress.

METHODS: Fecal pellet output (FPO), colonic mast cell infiltration, and fecal short-chain fatty acids were measured. Gut microbial composition and function were analyzed by 16S rRNA sequencing and Kyoto Encyclopedia of Genes and Genomes pathway prediction.

RESULTS: Both interventions significantly reduced FPO and mast cell infiltration in males but had less pronounced effects in females. Microbiota analyses revealed sex-dependent responses, with distinct microbial trajectories in each treatment group. Using linear discriminant analysis effect size, we identified seven key taxa with treatment- or sex-specific enrichment. Alistipes onderdonkii and Bacteroides uniformis consistently increased in both LFM- and B. longum-treated groups, regardless of sex. Bacteroides finegoldii and Barnesiella intestinihominis were specifically enriched in the LFM group. In males, Blautia faecis and Fusicatenibacter saccharivorans were enriched following the interventions, whereas Parabacteroides goldsteinii appeared exclusively in stressed males. Functional predictions revealed the enrichment of estrogen signaling and bile acid pathways in males and the attenuation of proinflammatory pathways in females following LFM. Correlations between microbial taxa and host outcomes were predominantly observed in male rats.

CONCLUSIONS: These findings highlight sex-specific microbial and host responses to microbiota-targeted therapies in a stress-induced IBS model, emphasizing sex as a biological variable in designing personalized microbiome-based treatments.},
}

@article {pmid41601223,
year = {2025},
author = {Liu, ZY and Zhao, XC and Chen, L and Wu, RG and Yuan, MQ and Chen, XH and Zhao, J and Xu, QY and Liu, CH and Sun, HY and Liu, C},
title = {[Recommendations for the Standardization of Forensic Microbiological Analysis].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {482-493},
doi = {10.12116/j.issn.1004-5619.2025.550501},
pmid = {41601223},
issn = {1004-5619},
mesh = {Humans ; *Forensic Medicine/standards/methods ; Reproducibility of Results ; *Microbiological Techniques/standards/methods ; Reference Standards ; *Bacteria/isolation & purification ; *Microbiota ; },
abstract = {With advances in microbiome research and the continuous advancement of detection technologies, the application of microorganisms in forensic medicine has become increasingly widespread, covering areas such as individual identification, body fluid source inference, biogeographical analysis, postmortem interval estimation, and determination of the cause and location of death. However, due to the lack of a comprehensive standardized system, batch effects and inter-laboratory differences have led to low reproducibility of analysis results. This problem is particularly evident in low-quality forensic samples, which compromise the reliability and evidential value of forensic microbiological analyses. Therefore, based on domestic and international research progress and practical experience, this paper systematically summarizes and discusses the standardization of forensic microbiological analysis, aiming to improve the reliability of results and promote the standardization of forensic microbiological analysis.},
}

Humans
*Forensic Medicine/standards/methods
Reproducibility of Results
*Microbiological Techniques/standards/methods
Reference Standards
*Bacteria/isolation & purification
*Microbiota

@article {pmid41601221,
year = {2025},
author = {Zou, HY and Lei, YL and Xia, RC and Shi, Y and Li, CT},
title = {[Exploring Microbial Detection of Psychoactive Substances in Wastewater Based on Micobiome Analysis].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {468-476},
doi = {10.12116/j.issn.1004-5619.2025.550803},
pmid = {41601221},
issn = {1004-5619},
mesh = {*Wastewater/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Psychotropic Drugs/analysis ; Tandem Mass Spectrometry/methods ; Chromatography, Liquid/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Water Pollutants, Chemical/analysis ; DNA, Bacterial/genetics ; },
abstract = {OBJECTIVES: To explore the potential wastewater microbiome analysis for detecting psychoactive substances by using full-length 16S rRNA gene sequencing with liquid chromatography - tandem mass spectrometry (LC-MS/MS).

METHODS: LC-MS/MS was used to qualitatively detect psychoactive substances in 21 wastewater samples suspected to contain such compunds. Based on the results, the samples were categorized into two groups: a positive group (containing psychoactive substances) and a negative group (free of psychoactive substances). Subsequently, bacterial communities in all samples were analyzed using full-length 16S rRNA gene sequencing. This analysis characterized the species composition, α diversity (Shannon and Simpson indices), and β-diversity (PCoA and NMDS). Significantly different operational taxonomic units (OTUs) were screened using linear discriminant analysis effect size (LEfSe), and optimal OTU features were iteratively selected via recursive feature elimination (RFE). A random forest prediction model was built with these two OTU subsets as input features.

RESULTS: The composition and structure of the bacterial communities showed marked differences between the two groups. The sample diversity in the positive group was higher than that in the negative group. The permutational ultivariate analysis of variance (PERMANOVA) revealed a statistically significant difference in β-diversity between the two groups. Random Forest models achieved a prediction accuracy of 83.3%, with areas under the ROC curve of 0.89 and 0.83, respectively.

CONCLUSIONS: Integrating wastewater bacterial community analysis with chemical analysis techniques may provide a more comprehensive approach for monitering the presence of psychoactive substances.},
}

*Wastewater/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Psychotropic Drugs/analysis
Tandem Mass Spectrometry/methods
Chromatography, Liquid/methods
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
*Water Pollutants, Chemical/analysis
DNA, Bacterial/genetics

@article {pmid41601220,
year = {2025},
author = {Chen, J and Zhao, YR and Huang, X and Qu, YL and Lu, YF and Xing, Y and Zhang, H and Zeng, JY and Li, SL and Zhang, SH},
title = {[Effect of Temperature on Microbial Succession in Different Tissues of Cadavers and Estimation of Postmortem Interval].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {456-467},
doi = {10.12116/j.issn.1004-5619.2025.450404},
pmid = {41601220},
issn = {1004-5619},
mesh = {*Postmortem Changes ; Animals ; RNA, Ribosomal, 16S/genetics ; Male ; *Temperature ; Rats ; Cadaver ; *Microbiota ; Female ; Rectum/microbiology ; Lung/microbiology ; Time Factors ; Rats, Sprague-Dawley ; *Bacteria/genetics/classification/isolation & purification ; Testis/microbiology ; Uterus/microbiology ; Proteobacteria/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {OBJECTIVES: To explore the distribution characteristics of microbial communities in various rat tissues under different temperature conditions and their dynamic changes over the postmortem interval(PMI), and to analyze the effects of temperature and tissue type on microbial succession in cadavers.

METHODS: A total of 96 rats were sacrificed by cervical dislocation and then placed under room temperature (20 ℃, n=48), high temperature (40 ℃, n=24), and low temperature (-20 ℃, n=24) conditions. Tissue samples from the diaphragm, lung, rectum, testis, and uterus were collected at various PMIs. Microbial community composition was analyzed using 16S rRNA high-throughput sequencing of the 16S rRNA gene V3-V4 regions. α-diversity, β-diversity, phylum- and genus-level species distributions, PMI-associated biomarkers analysis and species differential analysis were employed to systematically compare the effects of temperature and tissue type on microbial succession.

RESULTS: Under room temperature, microbial diversity exhibited a nonlinear trend, initially increasing and then decreasing. High temperature condition accelerated microbial succession and resulted in a significant decrease in microbial diversity within 24 hours. Low temperature slowed the succession, maintaining relatively high diversity and stable species distribution. The rectal microbial community differed significantly from those in other tissues. The phylum Proteobacteria, especially the genus Proteus, showed a significant increase in relative abundance in various tissues after 48 hours at room temperature and 24 hours at high temperature.

CONCLUSIONS: The dynamic succession patterns of microbial communities in multiple tissues under different temperature conditions confirm the significant regulatory effect of temperature on microbial diversity and species distribution, providing an important basis for optimizing microbiome-based PMI estimation methods.},
}

*Postmortem Changes
Animals
RNA, Ribosomal, 16S/genetics
Male
*Temperature
Rats
Cadaver
*Microbiota
Female
Rectum/microbiology
Lung/microbiology
Time Factors
Rats, Sprague-Dawley
*Bacteria/genetics/classification/isolation & purification
Testis/microbiology
Uterus/microbiology
Proteobacteria/isolation & purification/genetics
High-Throughput Nucleotide Sequencing

@article {pmid41601219,
year = {2025},
author = {Zhang, H and Huang, X and Chen, AQ and Chen, J and Lu, YF and Zeng, JY and Wang, X},
title = {[Skin Microbiome： Expanding Dimensions and Challenges in Forensic Evidence].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {443-455},
doi = {10.12116/j.issn.1004-5619.2025.550403},
pmid = {41601219},
issn = {1004-5619},
mesh = {Humans ; *Skin/microbiology ; *Microbiota/physiology ; *Forensic Medicine/methods ; *Forensic Sciences/methods ; Skin Microbiome ; },
abstract = {The skin microbiome, characterized by its vast abundance, high diversity, pronounced individual specificity, and dynamic traceability, serves as a significant biological marker of the host. Its composition and variation are influenced by both the host's physiological states and external environmental factors, exhibiting a close "mirror" relationship with host phenotypes. This unique "microbial fingerprint" not only expands the sources of forensic evidence but also offers new perspectives and opportunities for the advancement of forensic research and practice. This paper reviews the physiological and structural foundations underlying skin microbial diversity and the mechanisms that shape individual specificity, analyzes its unique advantages and technical approaches in forensic applications, outlines recent research progress, explores the future potential and major challenges of using skin microbiome markers in forensic science, and proposes practical recommendations.},
}

Humans
*Skin/microbiology
*Microbiota/physiology
*Forensic Medicine/methods
*Forensic Sciences/methods
Skin Microbiome

@article {pmid41601145,
year = {2026},
author = {Jiao, Y and Liu, Y and Sun, F and Wang, W and Li, H and Gao, Q and Li, Y and Lu, N and Tian, X and Ding, X and Du, J},
title = {Genetically Modified Plant Beneficial Microorganisms: A Sustainable Solution or a New Challenge for Agriculture.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14342},
pmid = {41601145},
issn = {1520-5118},
abstract = {Plant diseases significantly impact crop yield and quality, while conventional pesticide treatments often disrupt beneficial plant microbiota essential for pathogen prevention and immune regulation. Although plant beneficial microorganisms (PBMs) show promise as disease control agents, their effectiveness is constrained by strain-dependent variations, survival challenges, and inconsistent immune responses. Recent advances in genetic engineering, particularly CRISPR-Cas systems combined with complementary technologies like RecE/T, enable precise modifications of PBMs to enhance their protective potential. Enhanced PBMs improve functionality via multiple mechanisms: targeted gene-expression-mediated colonization, specific antimicrobial activity, and immune regulation. Studies demonstrate that genetically modified PBMs can prevent and control plant diseases through competitive exclusion, antibiotic production, barrier reinforcement, and immune modulation. We analyzed the considerations for the environmental release of engineered PBMs to reduce risks. Future research should focus on optimizing PBMs for specific applications while addressing biosafety concerns, thereby unlocking their full potential in safeguarding plant health.},
}

@article {pmid41509254,
year = {2026},
author = {Ramos, MAA and Gutkin, S and David, M and Shabat, D and Balskus, EP},
title = {Chemiluminescent probes allow for the rapid identification of colibactin-producing bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41509254},
issn = {2692-8205},
abstract = {The pks (or clb) gene cluster, which produces the genotoxic natural product colibactin, is encoded by human gut Enterobacteriaceae, including many commensal strains of E. coli. Colibactin crosslinks DNA and is implicated in colorectal cancer development, highlighting the importance of identifying colibactin-producing gut bacteria within biological samples. In this study, we develop phenoxy-dioxetane chemiluminescent probes that selectively react with a critical colibactin biosynthetic enzyme, the serine peptidase ClbP. We show that these chemiluminescent probes have superior sensitivity, speed, and detection capabilities compared to previously reported fluorescent ClbP probes. Furthermore, we employ these chemiluminescent probes to detect pks [+] E. coli directly in complex stool suspensions. These probes will enable multiple applications requiring detection of colibactin-producing bacteria, including the identification of ClbP inhibitors and the screening of clinical samples.},
}

@article {pmid41454342,
year = {2025},
author = {Song, H and Ma, Y and Peng, L and Gao, F and Fan, X and Yang, M and Hua, T and Yang, Y and Fan, R and Li, Z and Yuan, H},
title = {Platinum-doped emodin carbon dots mitigate sepsis-induced lung injury by targeting the gut-lung axis.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {84},
pmid = {41454342},
issn = {1477-3155},
support = {82471239//National Natural Science Foundation of China/ ; JDLCZDZK//Military clinical key specialty project fund/ ; },
abstract = {UNLABELLED: Sepsis-induced acute lung injury is a life-threatening complication with limited therapeutic options. Although the gut-lung axis is crucial in sepsis pathogenesis, effective interventions targeting this pathway remain scarce. Here, we developed multi-enzymatic platinum-doped emodin carbon dots (Pt-ECDs) via a hydrothermal method. Pt-ECDs exhibited superior catalase, superoxide dismutase, glutathione peroxidase and peroxidase-like activities, enabling potent reactive oxygen species (ROS) scavenging. In a murine sepsis model, oral Pt-ECDs significantly improved survival, reduced systemic inflammation, and ameliorated lung injury. Transcriptomic analysis revealed that Pt-ECDs suppressed oxidative stress and macrophage pyroptosis in lung tissues. Mechanistically, integrated metabolomic and microbiome analyses demonstrated that Pt-ECDs modulated the gut microbiota, specifically inhibiting g_Bacteroides-derived palmitic acid (PA) production. We further confirmed that PA exacerbates macrophage pyroptosis and pro-inflammatory polarization by directly binding to NOX2 and NLRP3. Crucially, fecal microbiota transplantation from Pt-ECDs-treated mice attenuated septic lung injury, whereas microbiota depletion abolished the therapeutic benefits. Collectively, our findings identify Pt-ECDs as a promising nanotherapeutic that alleviates septic lung injury by targeting the gut microbiota-palmitic acid-pyroptosis axis.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12951-025-03972-0.},
}

@article {pmid41082399,
year = {2026},
author = {Ravenscraft, A and Coon, KL},
title = {Transient Microbes in Insects: Fleeting but Functional.},
journal = {Annual review of entomology},
volume = {71},
number = {1},
pages = {253-273},
doi = {10.1146/annurev-ento-121423-013446},
pmid = {41082399},
issn = {1545-4487},
mesh = {Animals ; *Insecta/microbiology ; *Gastrointestinal Microbiome ; Symbiosis ; },
abstract = {Many insects' gut microbiota derive partly or wholly from environmental sources. These microbes may be transient, passing through in a matter of hours, days, a developmental stage, or a host generation. There is increasing recognition of the presence of transient microbes in the insect gut, but it is often assumed that these microbes are commensal and serve no function for their hosts. Here, we explore different definitions of microbial transience and review results from diverse insect systems showing that transience does not always preclude, and in some cases enables, important contributions of environmentally acquired microbes to host fitness. Moving past the assumption that microbes must always be tightly associated with a host to serve beneficial functions will help us develop a more accurate and nuanced understanding of the functions of the gut microbiota in insects and other animals.},
}

Animals
*Insecta/microbiology
*Gastrointestinal Microbiome
Symbiosis

@article {pmid40925006,
year = {2026},
author = {Hu, Y and Moreau, CS},
title = {Nutritional Symbiosis Between Ants and Their Symbiotic Microbes.},
journal = {Annual review of entomology},
volume = {71},
number = {1},
pages = {35-49},
doi = {10.1146/annurev-ento-121423-013513},
pmid = {40925006},
issn = {1545-4487},
mesh = {*Ants/microbiology/physiology ; *Symbiosis ; Animals ; *Microbiota ; },
abstract = {Nutritional symbioses with microorganisms have profoundly shaped the evolutionary success of ants, enabling them to overcome dietary limitations and thrive across diverse ecological niches and trophic levels. These interactions are particularly crucial for ants with specialized diets, where microbial symbionts compensate for dietary imbalances by contributing to nitrogen metabolism, vitamin supplementation, and the catabolism of plant fibers and proteins. This review synthesizes recent advances in our understanding of ant-microbe symbioses, focusing on diversity, functional roles in host nutrition, and mechanisms of transmission of symbiotic microorganisms. Despite progress, most research has concentrated on a few ant genera, and further exploration of microbial roles in different ant morphs and life stages and across various ant species is needed. Expanding research to include a broader array of ant lineages and integrating genomic data with additional experimental data will provide deeper insights into the metabolic strategies that facilitate ant success across diverse ecological habitats.},
}

*Ants/microbiology/physiology
*Symbiosis
Animals
*Microbiota

@article {pmid41601032,
year = {2026},
author = {Wang, X and Yan, W and Fan, G and Han, Z and Xia, M and Liu, J and Wang, Y and Rensing, C and Augustyniak, M and Zhang, Z and Wu, H},
title = {Earthworms reduce the accumulation of soil-borne pathogens in strawberry by altering the gut microbiome and physiological characteristics.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119595},
doi = {10.1016/j.ecoenv.2025.119595},
pmid = {41601032},
issn = {1090-2414},
mesh = {*Oligochaeta/physiology/microbiology ; Animals ; *Fragaria/microbiology ; *Gastrointestinal Microbiome ; *Soil Microbiology ; Fusarium/physiology ; Alternaria/physiology ; *Plant Diseases/microbiology/prevention & control ; Soil/chemistry ; },
abstract = {Pathogenic fungi cause economic loss to many crops including strawberry, highlighting the need for control using sustainable eco-friendly strategies. Earthworm casts effectively reduce the occurrence of soil-borne diseases. However, the interactions between earthworms and soil-borne pathogenic fungi and their underlying mechanisms remain insufficiently understood in strawberry. This study investigated the effects of the pathogenic fungi Fusarium oxysporum and Alternaria alstroemeriae on the structure and composition of the microbial communities in the drilosphere soil and earthworm gut using high-throughput sequencing. The impact of these pathogenic fungi on functional gene expression in earthworms was determined using transcriptomic analysis. Applying F. oxysporum and A. alstroemeriae with earthworms significantly altered the physicochemical properties of the drilosphere soil, reduced the fungal alpha diversity therein, and increased the abundance of potentially beneficial Pseudomonas spp. and Bacillus spp. The presence of the pathogenic fungi increased the alpha diversity and habitat niche breadth of the fungal community in the earthworm gut. However, there was a significant reduction in the relative abundance of potentially pathogenic fungi to plants and animals in the earthworm gut. Earthworms had a positive legacy effect on the abundance of beneficial bacteria in the rhizosphere and enhanced strawberry biomass. Transcriptomic analysis demonstrated that earthworms activated α-linolenic acid and glycerophospholipid metabolism but downregulated the Toll-like receptor pathway, mitigating excessive immune responses. In summary, earthworms suppress soil-borne pathogenic fungi in strawberry via an integrated mechanism involving the restructuring of the gut microbiota, enrichment of biocontrol agents in the drilosphere, and coordination of host immunity, offering a novel paradigm for pest management and sustainable means for strawberry cultivation.},
}

*Oligochaeta/physiology/microbiology
Animals
*Fragaria/microbiology
*Gastrointestinal Microbiome
*Soil Microbiology
Fusarium/physiology
Alternaria/physiology
*Plant Diseases/microbiology/prevention & control
Soil/chemistry

@article {pmid41600738,
year = {2026},
author = {Yachida, M and Itoh, M and Morita, Y},
title = {Comparative Effects of Raw Milk and Milk Replacer Feeding on Gut Microbiota Diversity and Function in Cryptosporidium parvum-Infected Neonatal Dairy Calves on a Japanese Farm.},
journal = {Veterinary sciences},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/vetsci13010082},
pmid = {41600738},
issn = {2306-7381},
support = {24K09209//Japan Society for the Promotion of Science/ ; 5 chiku-ni-kyo hatsu dai 27//Japan Association for Livestock New Technology/ ; },
abstract = {Neonatal diarrhea is a major health concern in the livestock industry, and Cryptosporidium parvum is a key pathogen responsible for this condition in calves. Milk management and gut microbiome regulation may play important roles in preventing cryptosporidiosis symptoms. This study analyzed the gut microbiota of neonatal calves fed raw milk (BM) or milk replacer (MR) using a total of 58 fecal samples collected on the same farm in 2022 and 2024. In milk replacer-fed calves, alpha diversity was significantly higher in C. parvum-positive (P) calves without diarrhea (N) (PN, n = 5) than in C. parvum-positive calves with diarrhea(D) (PD, n = 18) (Shannon p = 0.0358; Chao1 p = 0.0598). Beta diversity also differed between PN and PD (PERMANOVA, R[2] = 0.1763, p = 0.0092). Predicted microbial taxa such as Faecalibacterium (ALDEx2, effect size = 2.31, p = 0.00003) and Butyricicoccus (effect size = 1.31, p = 0.0041) were enriched in PN calves in MR. Comparison between milk types (BM vs. MR) further showed higher species richness in PN calves in MR than in those (n = 5) in BM(Chao1, p = 0.0088), along with significant differences in beta diversity (R[2] = 0.4112, p = 0.0069). These findings suggest that microbial diversity and the presence of specific taxa may be associated with reduced diarrheal symptoms. Predicted metabolic pathway profiling using a computational functional profiling approach showed the distinct metabolic pathways, including amino acid, carbohydrate, lipid, and vitamin biosynthesis, were enriched in healthier calves in both groups. These results suggest certain functional features of the microbiome could be associated with anti-inflammatory activity and short-chain fatty acid production, potentially mitigating diarrheal symptoms.},
}

@article {pmid41600714,
year = {2026},
author = {Jin, A and Zhou, S and Cheng, S and Yang, Y and Sun, Y and Sun, Z and Zhao, Y and Chen, X},
title = {Effects of Dietary Supplementation with Whole Lamb Omasum on Gut Health and Metabolism in Shiba Inu Dogs.},
journal = {Veterinary sciences},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/vetsci13010058},
pmid = {41600714},
issn = {2306-7381},
support = {CSTB2025TIAD-KPX0079//Chongqing Key Special Project for Technological Innovation and Application Development/ ; CQMAITS202513//Chongqing Herbivorous Livestock Industry Technology System/ ; },
abstract = {The growing pet economy boosts demand for fiber-enriched functional foods to improve canine gut motility and metabolic health. However, low-bioavailability commercial fibers often falter in high-energy diets. Whole lamb omasum-from grass-fed sheep omasum and gastric contents-repurposes a discarded byproduct for waste reduction and sustainable livestock production. This study evaluated the short-term effects of WLO supplementation on gut health and metabolism in healthy adult Shiba Inu dogs. Twelve dogs were randomly assigned to control or WLO groups in a randomized controlled trial. WLO supplementation significantly reduced fecal scores by 8.91% (p < 0.05), increased apparent crude fat and fiber digestibility by 3.70% and 11.55% (p < 0.05), and elevated serum IgA by 35.79-36.15% and T-AOC by 30.53-35.71% (p < 0.05). Serum metabolome revealed 13 between-group and 8 within-subject differences related to lipid and endocrine modulation. Fecal microbiota analysis indicated enrichment of the Bacillota phylum and Blautia genus (p < 0.05). These findings support WLO as a functional food that enhances gut and metabolic health in small-breed dogs.},
}

@article {pmid41600684,
year = {2025},
author = {Mgeni, MS and Zhang, L and Chen, Y and Dong, X and Xiu, Z and Zhang, J and Chen, J and Sun, Y},
title = {Effects of Dandelion Extracts on the Ruminal Microbiota, Metabolome, and Systemic Inflammation in Dairy Goats Fed a High-Concentrate Diet.},
journal = {Veterinary sciences},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/vetsci13010028},
pmid = {41600684},
issn = {2306-7381},
support = {22532J//This research was funded by chongqing performance incentive guide special project 22532J/ ; },
abstract = {This study examined the effect of dandelion extracts on the ruminal microbiota, metabolome, and inflammatory response in dairy goats fed a high-concentrate diet. Eighteen Guanzhong dairy goats were assigned to three groups: low-concentrate diet group (L group, F:C = 60:40), high-concentrate diet group (H group, F:C = 35:65), and dandelion group (D) with 1% dandelion extracts based on the H group. Over six weeks, milk, blood, and ruminal fluid were collected to analyze pH, volatile fatty acids (VFAs), inflammatory markers, microbiome, and metabolome. Feed intake was significantly higher in the H and D groups than in the L group. Ruminal pH decreased in the H group, acetate was significantly higher in the L and D groups, and serum IgA was higher in D group. Bacteroidetes and Firmicutes were dominant rumen phyla, and dandelion supplementation significantly increased Proteobacteria. Prevotella abundance was enriched in the L and D groups and showed a positive correlation with acetate. Dandelion extracts also increased the production of trans-3-Hydroxy-L-proline and 7-Ethyl-5,6-dihydro-1,4-dimethylazulene in the rumen while improving amino acid and lipid metabolism. Overall, supplementation of dandelion extracts positively influenced rumen microbiota, enhanced production of beneficial metabolites, and positively influenced immune function in dairy goats fed high-concentrate diet.},
}

@article {pmid41600605,
year = {2026},
author = {De Rosa, M and Canepari, S and Tranfo, G and Giampaoli, O and Patriarca, A and Smolinska, A and Marini, F and Massimi, L and Sciubba, F and Spagnoli, M},
title = {Unveiling the Metabolic Fingerprint of Occupational Exposure in Ceramic Manufactory Workers.},
journal = {Toxics},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/toxics14010056},
pmid = {41600605},
issn = {2305-6304},
support = {BRIC ID 52//Istituto Nazionale per l'Assicurazione Contro gli Infortuni sul Lavoro/ ; },
abstract = {In this study, for the first time urinary NMR-based metabolomics was applied to investigate the physiological alterations associated with occupational exposure in ceramic manufacturing workers. Multivariate analysis revealed a distinctive metabolic signature with exposure, characterized by a depletion of both aliphatic and aromatic amino acids and a concomitant accumulation of branched-chain amino acid catabolites. Alterations in tricarboxylic acid (TCA) cycle intermediates, including citrate and succinate, suggest an involvement of mitochondrial energy metabolism, reflecting adaptive responses to oxidative stress and increased protein turnover. Notably, glycine levels were found increased, consistent with its central role in antioxidant defense and xenobiotic detoxification. Furthermore, changes in urinary host-microbiome co-metabolites, such as 4-hydroxyphenylacetate and phenylacetylglycine, indicate the potential modulation of gut microbial activity in response to occupational exposure. While limited by the small cohort, this study demonstrates the feasibility of NMR-based urinary metabolomics for the non-invasive biomonitoring of workers and suggests its potential as a useful tool for detecting subtle metabolic perturbations associated with complex occupational exposures.},
}

@article {pmid41600411,
year = {2026},
author = {Tiwari, AK and Gupta, MK and Mishra, SK and Meena, R and Patolsky, F and Narayan, RJ},
title = {Nanobiosensors: A Potential Tool to Decipher the Nexus Between SARS-CoV-2 Infection and Gut Dysbiosis.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {2},
pages = {},
doi = {10.3390/s26020616},
pmid = {41600411},
issn = {1424-8220},
mesh = {*Dysbiosis/diagnosis/virology/microbiology ; Humans ; *COVID-19/diagnosis/virology/complications ; *Biosensing Techniques/methods ; *SARS-CoV-2/isolation & purification/pathogenicity ; *Gastrointestinal Microbiome ; *Nanotechnology/methods ; },
abstract = {The emergence of SARS-CoV-2 posed a great global threat and emphasized the urgent need for diagnostic tools that are rapid, reliable, sensitive and capable of real-time monitoring of SARS-CoV-2 infections. Recent investigations have identified a potential connection between SARS-CoV-2 infection and gut dysbiosis, highlighting the sophisticated interplay between the virus and the host microbiome. This review article discusses the eminence of nanobiosensors, as state-of-the-art tools, to investigate and clarify the connection between SARS-CoV-2 pathogenesis and gut microbiome imbalance. Nanobiosensors are uniquely advantageous owing to their sensitivity, selectivity, specificity, and reliable monitoring capabilities, making them well-suited for identifying both viral particles and microbial markers in biological samples. We explored a range of nanobiosensor platforms and their potential use for concurrently monitoring the gut dysbiosis induced by different pathological conditions. Additionally, we explore how advanced sensing technologies can shed light on the mechanisms driving virus-induced dysbiosis, and the implications for disease progression and patient outcomes. The integration of nanobiosensors with microfluidic devices and artificial intelligence algorithms has also been explored, highlighting the potential of developing point-of-care diagnostic tools that provide comprehensive insights into both viral infection and gut health. Utilizing nanotechnology, scientists and healthcare professionals may gain a more profound insight into the complex interaction dynamics between SARS-CoV-2 infection and the gut microenvironment. This could pave the way for enhanced diagnostic and prognostic approaches, treatment courses, and patient care for COVID-19.},
}

*Dysbiosis/diagnosis/virology/microbiology
Humans
*COVID-19/diagnosis/virology/complications
*Biosensing Techniques/methods
*SARS-CoV-2/isolation & purification/pathogenicity
*Gastrointestinal Microbiome
*Nanotechnology/methods

@article {pmid41600136,
year = {2026},
author = {Song, X and Xia, X and Yang, S and Hao, C and Sun, H and Li, F and Xu, X and Zhang, H and Lu, X},
title = {The Influence of Transgenic Insect-Resistance and Herbicide-Tolerance Soybean KM2208-23 on the Rhizosphere Micro-Biome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/plants15020329},
pmid = {41600136},
issn = {2223-7747},
support = {2023ZD04062//Biological Breeding-Major Projects/ ; 2024LZGC010//the Agricultural Variety Improvement Project of Shandong Province/ ; ZR2021QC207//Shan-dong Province Natural Science Foundation Young Project/ ; },
abstract = {The consequences of stacking multiple insect-resistance and herbicide-tolerance genes, particularly across the entire plant life cycle, remain inadequately understood. This study investigated the impact of stacked-trait transgenic soybeans on rhizosphere microbial communities across five growth stages (pre-sowing, V3, R3, R5, R8). Using 16S rRNA and ITS sequencing, we compared the rhizosphere microbiome of the transgenic modified soybean (GMO) with its non-transgenic control check (CK). Results showed transient but significant shifts in soil properties (e.g., available nitrogen) and microbial beta diversity during the V3 stages. However, plant developmental stage was the predominant factor shaping microbial succession, with its effect outweighing that of the transgene. No persistent changes in microbial alpha diversity were observed. We conclude that the influence of this stacked-trait soybean on the rhizosphere is growth-stage-specific and represents a minor, recoverable perturbation rather than a sustained ecological impact. These findings contribute to the ecological safety assessment of multi-gene transgenic crops.},
}

@article {pmid41599966,
year = {2026},
author = {Nedeva, I and Assyov, Y and Duleva, V and Karamfilova, V and Kamenov, Z and Naydenov, J and Handjieva-Darlenska, T and Denchev, V and Kolevski, A and Pencheva, V and Vodenicharov, V},
title = {Distinct Gut Microbiome Profiles Underlying Cardiometabolic Risk Phenotypes in Individuals with Obesity.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020353},
pmid = {41599966},
issn = {2072-6643},
support = {contract D-300/18.12/2023//Stimulating Excellence in Scientific research, Medical university Sofia/ ; 2025//National program " For Women in Science 2025"/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Obesity/microbiology/complications ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; Adult ; Phenotype ; *Metabolic Syndrome/microbiology ; Cardiometabolic Risk Factors ; *Cardiovascular Diseases/microbiology ; },
abstract = {Background: Obesity-related cardiometabolic disorders have been linked to alterations in selected gut microbiome components, yet clinically relevant microbial signatures remain incompletely defined. Objectives: This study investigated associations between selected gut bacterial taxa and cardiometabolic risk phenotypes in individuals with obesity. Methods: In this cross-sectional study, 100 adults with obesity were stratified according to metabolic syndrome status. Gut microbiome composition was assessed using targeted multiplex real-time PCR of functionally relevant bacterial taxa. Associations with anthropometric and cardiometabolic parameters were examined using correlation analysis, ROC curves, and multivariable logistic regression models. Results: Reduced relative abundance of Lachnospiraceae was associated with metabolic syndrome, lower Faecalibacterium abundance with arterial hypertension, and increased Prevotella abundance with dyslipidemia. ROC analyses identified cohort-specific discriminative thresholds with moderate accuracy. Conclusions: Selected taxon-specific gut microbiome signatures are associated with cardiometabolic risk phenotypes in obesity. These findings are exploratory and require validation in longitudinal and independent cohorts.},
}

Humans
*Gastrointestinal Microbiome
*Obesity/microbiology/complications
Male
Female
Cross-Sectional Studies
Middle Aged
Adult
Phenotype
*Metabolic Syndrome/microbiology
Cardiometabolic Risk Factors
*Cardiovascular Diseases/microbiology

@article {pmid41599961,
year = {2026},
author = {Lietz, A and Dapprich, J and Fischer, T},
title = {Carnivore Diet: A Scoping Review of the Current Evidence, Potential Benefits and Risks.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020348},
pmid = {41599961},
issn = {2072-6643},
mesh = {Humans ; Animals ; },
abstract = {Background: The Carnivore Diet (CD) is an almost exclusively animal-based dietary pattern that has gained increasing popularity on social media. Despite numerous health-related claims, a standardized definition is lacking, and scientific evidence regarding the long-term effects of this diet remains unclear. Methods: The literature search for this scoping review was conducted in accordance with PRISMA guidelines (PRISMA-ScR) using the databases PubMed, LIVIVO, Web of Science, and the Cochrane Library. Results: Nine human studies were included. Individual publications reported positive effects of the CD, such as weight reduction, increased satiety, and potential improvements in inflammatory or metabolic markers. At the same time, potential risks of nutrient deficiencies, particularly in vitamins C and D, calcium, magnesium, iodine, and dietary fiber, as well as elevated low-density-lipoprotein (LDL-) and total cholesterol (TC) levels, were identified, along with one case describing a deterioration in health status. Overall, the quality of evidence is very limited due to small sample sizes, short study durations, and the absence of control groups. Conclusions: The CD may offer short-term health benefits but carries substantial risks of nutrient deficiencies, reduced intake of health-promoting phytochemicals, and the development of cardiovascular disease. At this time, long-term adherence to a CD cannot be recommended.},
}

Humans
Animals

@article {pmid41599910,
year = {2026},
author = {Park, SH},
title = {Recent Research on the Role of Lactobacilli Probiotics in Cancer Management.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020297},
pmid = {41599910},
issn = {2072-6643},
mesh = {*Probiotics/therapeutic use ; Humans ; *Neoplasms/therapy/microbiology ; *Lactobacillus ; Gastrointestinal Microbiome ; Animals ; Apoptosis ; },
abstract = {Lactobacilli strains are one of the major groups belonging to probiotics. Lactobacilli strains are known to be beneficial microbes widely studied and utilized for their health benefits and applications in various fields. Recently, Lactobacilli strains have emerged as promising agents in cancer management due to their ability to influence various physiological processes. Lactobacilli strains have shown potential in producing tumor-suppressive compounds, enhancing immune responses, and reshaping gut microbiota balance for the management of various cancer types. Lactobacilli strains demonstrated tumor-suppressive activity through mechanisms including induction of apoptosis, inhibition of migration, and regulation of key oncogenic signaling pathways. However, the effects of Lactobacilli strains appear to be strain- and cancer-type-dependent, necessitating further research to identify the most effective strains for the proper cancer type with the optimal treatment regimens. In this review article, we focus on Lactobacilli strains studied between 2021 and 2025 that have demonstrated tumor-suppressive properties in various experimental models. In addition, this article explores the current limitations in research methodologies and proposes potential avenues for future investigations in this area of study.},
}

*Probiotics/therapeutic use
Humans
*Neoplasms/therapy/microbiology
*Lactobacillus
Gastrointestinal Microbiome
Animals
Apoptosis

@article {pmid41599902,
year = {2026},
author = {Plaza-Diaz, J and Herrera-Quintana, L and Olivares-Arancibia, J and Vázquez-Lorente, H},
title = {Personalized Nutrition Through the Gut Microbiome in Metabolic Syndrome and Related Comorbidities.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020290},
pmid = {41599902},
issn = {2072-6643},
mesh = {Humans ; *Metabolic Syndrome/microbiology/prevention & control/diet therapy/therapy ; *Gastrointestinal Microbiome/physiology ; Exercise ; *Precision Medicine/methods ; Comorbidity ; Diet ; },
abstract = {Background: Metabolic syndrome, a clinical condition defined by central obesity, impaired glucose regulation, elevated blood pressure, hypertriglyceridemia, and low high-density lipoprotein cholesterol across the lifespan, is now a major public health issue typically managed with lifestyle, behavioral, and dietary recommendations. However, "one-size-fits-all" recommendations often yield modest, heterogeneous responses and poor long-term adherence, creating a clinical need for more targeted and implementable preventive and therapeutic strategies. Objective: To synthesize evidence on how the gut microbiome can inform precision nutrition and exercise approaches for metabolic syndrome prevention and management, and to evaluate readiness for clinical translation. Key findings: The gut microbiome may influence cardiometabolic risk through microbe-derived metabolites and pathways involving short-chain fatty acids, bile acid signaling, gut barrier integrity, and low-grade systemic inflammation. Diet quality (e.g., Mediterranean-style patterns, higher fermentable fiber, or lower ultra-processed food intake) consistently relates to more favorable microbial functions, and intervention studies show that high-fiber/prebiotic strategies can improve glycemic control alongside microbiome shifts. Physical exercise can also modulate microbial diversity and metabolic outputs, although effects are typically subtle and may depend on baseline adiposity and sustained adherence. Emerging "microbiome-informed" personalization, especially algorithms predicting postprandial glycemic responses, has improved short-term glycemic outcomes compared with standard advice in controlled trials. Targeted microbiome-directed approaches (e.g., Akkermansia muciniphila-based supplementation and fecal microbiota transplantation) provide proof-of-concept signals, but durability and scalability remain key limitations. Conclusions: Microbiome-informed personalization is a promising next step beyond generic guidelines, with potential to improve adherence and durable metabolic outcomes. Clinical implementation will require standardized measurement, rigorous external validation on clinically meaningful endpoints, interpretable decision support, and equity-focused evaluation across diverse populations.},
}

Humans
*Metabolic Syndrome/microbiology/prevention & control/diet therapy/therapy
*Gastrointestinal Microbiome/physiology
Exercise
*Precision Medicine/methods
Comorbidity
Diet

@article {pmid41599892,
year = {2026},
author = {Guraka, A and Lush, M and Zouganelis, G and Waldron, J and Mekapothula, S and Masania, J and Cave, GWV and Conway, ME and Tripathi, G and Kermanizadeh, A},
title = {Investigating the Role of Diet-Manipulated Gut Bacteria in Pathogenesis of Type 2 Diabetes Mellitus-An In Vitro Approach.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020279},
pmid = {41599892},
issn = {2072-6643},
support = {NA//University of Derby/ ; NA//Animal Free Research UK/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/microbiology/etiology/metabolism ; Humans ; Feces/microbiology ; Insulin/metabolism ; Diet, High-Fat/adverse effects ; Dietary Fiber ; Cell Line, Tumor ; *Limosilactobacillus fermentum/metabolism/isolation & purification ; *Diet ; Bacteroides/metabolism/isolation & purification ; Insulin Resistance ; Glucose/metabolism ; Insulin Secretion ; Male ; },
abstract = {Background: The human gut microbiome is highly complex, and its composition is strongly influenced by dietary patterns. Alterations in microbiome structure have been associated with a range of diseases, including type 2 diabetes mellitus. However, the underlying mechanisms for this remain poorly understood. In this study, a novel in vitro approach was utilized to investigate the interplay between gut bacteria, dietary metabolites, and metabolic dysfunction. Methods: Two representative gut bacterial species-Bacteroides thetaiotaomicron and Lactobacillus fermentum-were isolated from human faecal samples and subjected to controlled dietary manipulation to mimic eubiotic and dysbiotic conditions. Metabolites produced under these conditions were extracted, characterized, and quantified. To assess the functional impact of these metabolites, we utilized the INS-1 832/3 insulinoma cell line, evaluating insulin sensitivity through glucose-stimulated insulin secretion and ERK1/2 activation. Results: Our findings demonstrate that metabolites derived from high-carbohydrate/high-fat diets exacerbate metabolic dysfunction, whereas those generated under high-fibre conditions significantly enhance insulin secretion and glucose-dependent ERK1/2 activation in co-culture compared to monocultures. Conclusions: This work systematically disentangles the complex interactions between gut microbiota, diet, and disease, providing mechanistic insights into how microbial metabolites contribute to the onset of metabolic disorders.},
}

*Gastrointestinal Microbiome/physiology
*Diabetes Mellitus, Type 2/microbiology/etiology/metabolism
Humans
Feces/microbiology
Insulin/metabolism
Diet, High-Fat/adverse effects
Dietary Fiber
Cell Line, Tumor
*Limosilactobacillus fermentum/metabolism/isolation & purification
*Diet
Bacteroides/metabolism/isolation & purification
Insulin Resistance
Glucose/metabolism
Insulin Secretion
Male

@article {pmid41599868,
year = {2026},
author = {Allegretti, JR and Kassam, Z and Kelly, CR and Grinspan, A and El-Nachef, N and Van Den Elzen, C and Jäger, R and Feuerstadt, P},
title = {A Randomized, Placebo-Controlled Trial Evaluating Multi-Species Synbiotic Supplementation for Bloating, Gas, and Abdominal Discomfort.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020255},
pmid = {41599868},
issn = {2072-6643},
support = {N/A//Seed Health Inc./ ; },
mesh = {Humans ; *Synbiotics/administration & dosage ; Double-Blind Method ; Male ; Female ; *Abdominal Pain/therapy ; Adult ; Middle Aged ; *Flatulence/therapy ; Quality of Life ; *Dietary Supplements ; Probiotics/administration & dosage ; Gases ; Treatment Outcome ; Plant Extracts/administration & dosage ; Young Adult ; },
abstract = {Background: Bloating, gas, and abdominal discomfort are common in healthy individuals but lack effective interventions. Probiotics can alleviate some gastrointestinal (GI) symptoms; however, evidence for their impact on bloating, gas and abdominal discomfort in otherwise healthy populations remains limited. Mechanistic studies suggest that synbiotics may influence the underlying mechanisms of bloating, including increased gas production, impaired gut motility, and visceral hypersensitivity, but there is a paucity of data from large trials evaluating clinical outcomes. Accordingly, we evaluated the effects of a multi-species synbiotic on GI symptoms. Methods: In a randomized, double-blind, placebo-controlled, decentralized trial, participants (n = 350) with self-reported bloating/indigestion received either a multi-species synbiotic (53.6 billion AFU multi-species probiotic and 400 mg pomegranate extract; DS-01) or placebo daily for 6 weeks. Outcomes included GI quality-of-life (DQLQ), bloating and gas (PROMIS-GI 13a), abdominal discomfort (PROMIS-GI 5a), constipation, regularity, mood-related symptoms, and safety. Results: The multi-species synbiotic improved GI quality-of-life compared to placebo (0.80 vs. 1.20; p < 0.05) at Week 6. Bloating and gas were reduced in the synbiotic arm compared to placebo (16.0 vs. 21.0; p < 0.01), with more participants reporting never/rarely bloating (72.3% vs. 55.9%; p < 0.001). Abdominal discomfort also decreased (8.0 vs. 10.0; p < 0.01). Additionally, there was a statistically significant improvement in constipation symptoms and regularity in the synbiotic arm relative to placebo. Conclusions: Daily supplementation with this multi-species synbiotic significantly improved GI quality-of-life, bloating, gas, abdominal discomfort, and bowel habits. This is the first synbiotic to demonstrate meaningful improvements in bloating and gas in a generally healthy, diverse, real-world population.},
}

Humans
*Synbiotics/administration & dosage
Double-Blind Method
Male
Female
*Abdominal Pain/therapy
Adult
Middle Aged
*Flatulence/therapy
Quality of Life
*Dietary Supplements
Probiotics/administration & dosage
Gases
Treatment Outcome
Plant Extracts/administration & dosage
Young Adult

@article {pmid41599863,
year = {2026},
author = {Baek, HI and Kwon, SY and Noh, HJ and Park, SJ},
title = {Efficacy and Safety of CKDB-322, a Combination of Lactiplantibacillus plantarum Q180 and Phaeodactylum tricornutum, for Reducing Body Fat and Abdominal Adiposity in Overweight Adults.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020250},
pmid = {41599863},
issn = {2072-6643},
support = {20020268//Ministry of Trade, Industry and Energy/ ; 2025-RISE-13-WSU//Ministry of Education/ ; },
mesh = {Humans ; Female ; Male ; Adult ; Middle Aged ; Double-Blind Method ; *Probiotics/administration & dosage/adverse effects/therapeutic use ; *Overweight/therapy ; *Lactiplantibacillus plantarum ; *Adiposity ; *Abdominal Fat ; Aged ; Young Adult ; *Obesity, Abdominal/therapy ; *Diatoms ; Body Mass Index ; Treatment Outcome ; Adipose Tissue ; Waist Circumference ; },
abstract = {BACKGROUND: CKDB-322, a combination of Lactiplantibacillus plantarum Q180 and Phaeodactylum tricornutum, has shown anti-obesity potential in preclinical models, although human evidence is still limited. This randomized, double-blind, placebo-controlled, 12-week trial evaluated the efficacy and safety of CKDB-322 in overweight adults.

METHODS: Participants were aged 19-65 years; had a body mass index (BMI) of 25-30 kg/m[2], and a waist circumference of ≥90 cm for men or ≥85 cm for women. They were randomly assigned to receive either CKDB-322, which provided 1.0 × 10[9] CFU of L. plantarum Q180 and 200 mg of P. tricornutum daily (n = 50), or a placebo (n = 50).

RESULTS: CKDB-322 supplementation resulted in statistically significant reductions in body fat mass and body fat percentage, as measured by dual-energy X-ray absorptiometry (DEXA), compared to the placebo group (p < 0.05). Computed tomography (CT) analyses also revealed significant reductions in abdominal fat area in the CKDB-322 group (p < 0.05). Additional improvements were observed in body weight and anthropometric parameters. Among metabolic biomarkers, serum triglycerides and leptin levels decreased significantly in the CKDB-322 group compared to the placebo. Exploratory microbiome analyses indicated an increase in the relative abundance of Lactobacillus, suggesting potential modulation of the gut-adipose axis. CKDB-322 was well tolerated, with no clinically significant adverse events or laboratory abnormalities.

CONCLUSIONS: Collectively, CKDB-322 demonstrated a favorable safety profile and produced statistically significant improvements in multiple adiposity-related outcomes, including reductions in body fat mass, abdominal adiposity, and key anthropometric measures, supporting its potential as a functional ingredient for body fat reduction and metabolic health.},
}

Humans
Female
Male
Adult
Middle Aged
Double-Blind Method
*Probiotics/administration & dosage/adverse effects/therapeutic use
*Overweight/therapy
*Lactiplantibacillus plantarum
*Adiposity
*Abdominal Fat
Aged
Young Adult
*Obesity, Abdominal/therapy
*Diatoms
Body Mass Index
Treatment Outcome
Adipose Tissue
Waist Circumference

@article {pmid41599842,
year = {2026},
author = {Adibi, S},
title = {A Conceptual Digital Health Framework for Longevity Optimization: Inflammation-Centered Approach Integrating Microbiome and Lifestyle Data-A Review and Proposed Platform.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020231},
pmid = {41599842},
issn = {2072-6643},
mesh = {Humans ; *Longevity ; *Inflammation ; Diet, Mediterranean ; *Life Style ; *Gastrointestinal Microbiome ; Biomarkers/blood ; Aged, 80 and over ; C-Reactive Protein/metabolism ; Male ; Artificial Intelligence ; Digital Health ; },
abstract = {Chronic low-grade inflammation, or "inflammaging," represents a central mechanism linking dietary patterns, gut microbiome composition, and biological aging. Evidence from Blue Zone populations and Mediterranean diet studies demonstrates that specific nutritional interventions are associated with up to 23% lower all-cause mortality, with analyses suggesting that part of this association may be mediated by measurable improvements in inflammatory biomarkers. This paper synthesizes published evidence from Mediterranean diet trials, centenarian microbiome studies, and digital health platforms to propose a comprehensive digital health framework that integrates quarterly inflammation and microbiome monitoring with continuous lifestyle tracking to deliver personalized longevity interventions. This paper introduces the Longevity-Inflammation Index (L-II), a composite score combining high-sensitivity C-reactive protein, interleukin-6, tumor necrosis factor-alpha, and microbiome-derived markers, with scoring algorithms derived from centenarian population studies. The proposed platform leverages artificial intelligence to generate evidence-based recommendations adapted from centenarian and Mediterranean dietary patterns. Published evidence from multiple randomized controlled trials demonstrates that Mediterranean dietary interventions reduce hs-CRP by 18-32%, increase microbiome diversity by 6-28%, and improve metabolic markers including HOMA-IR and TG/HDL ratios. Digital health platforms demonstrate sustained engagement rates of 58-84% at 12 months, with dietary logging frequencies of 4-6 days per week. Cost-effectiveness analyses of dietary interventions show incremental cost-effectiveness ratios of USD 2100-4800 per quality-adjusted life year gained. This inflammation-centered digital health framework offers a scalable approach for translating longevity research into practical interventions for healthy aging, with validation studies needed to confirm the integrated platform's efficacy and real-world implementation feasibility.},
}

Humans
*Longevity
*Inflammation
Diet, Mediterranean
*Life Style
*Gastrointestinal Microbiome
Biomarkers/blood
Aged, 80 and over
C-Reactive Protein/metabolism
Male
Artificial Intelligence
Digital Health

@article {pmid41599822,
year = {2026},
author = {De Beul, E and Heyse, J and Jurgelewicz, M and Baudot, A and Vu, LD and Van den Abbeele, P},
title = {N-Acetylglucosamine and Immunoglobulin Strengthen Gut Barrier Integrity via Complementary Microbiome Modulation.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020210},
pmid = {41599822},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Acetylglucosamine/pharmacology ; Adult ; Animals ; Caco-2 Cells ; *Immunoglobulins/pharmacology ; Fatty Acids, Volatile/metabolism ; *Intestinal Mucosa/drug effects/microbiology/metabolism ; Cattle ; Male ; Female ; Coculture Techniques ; },
abstract = {Background: Gut barrier dysfunction and altered gut microbial metabolism are emerging signatures of chronic gut disorders. Considering growing interest in combining structurally and mechanistically distinct bioactives, we investigated the individual and combined effects of serum-derived bovine immunoglobulin (SBI) and N-acetylglucosamine (NAG) on the gut microbiome and barrier integrity. Methods: The validated ex vivo SIFR[®] (Systemic Intestinal Fermentation Research) technology, using microbiota from healthy adults (n = 6), was combined with a co-culture of epithelial/immune (Caco-2/THP-1) cells. Results: While SBI and NAG already significantly improved gut barrier integrity (TEER, transepithelial electrical resistance, +21% and +29%, respectively), the strongest effect was observed for SBI_NAG (+36%). This potent combined effect related to the observation that SBI and NAG each induced distinct, complementary shifts in microbial composition and metabolite output. SBI most selectively increased propionate (~Bacteroidota families) and health-associated indole derivatives (e.g., indole-3-propionic acid), while NAG most specifically boosted acetate and butyrate (~Bifidobacteriaceae, Ruminococcaceae, and Lachnospiraceae). The combination of SBI_NAG displayed effects of the individual ingredients, thus, for instance, enhancing all three short-chain fatty acids (SCFA) and elevating microbial diversity (CMS, community modulation score). Conclusions: Overall, SBI and NAG exert complementary, metabolically balanced effects on the gut microbiota, supporting combined use, particularly in individuals with gut barrier impairment or dysbiosis linked to lifestyle or early-stage gastrointestinal disorders.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Acetylglucosamine/pharmacology
Adult
Animals
Caco-2 Cells
*Immunoglobulins/pharmacology
Fatty Acids, Volatile/metabolism
*Intestinal Mucosa/drug effects/microbiology/metabolism
Cattle
Male
Female
Coculture Techniques

@article {pmid41599794,
year = {2026},
author = {Al Hazaimeh, R and Shackelford, L and Boateng, J},
title = {Effects of Mixed Fruits and Berries on Ameliorating Gut Microbiota and Hepatic Alterations Induced by Cafeteria Diet.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020181},
pmid = {41599794},
issn = {2072-6643},
support = {ALAX-012-0918//USDA/NIFA Capacity-Building Grant/ ; ALAX-12-2017//USDA/NIFA Evans-Allen/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Male ; Rats, Sprague-Dawley ; *Fruit ; *Liver/pathology/metabolism ; Rats ; Dysbiosis ; *Fatty Liver/etiology/prevention & control ; Disease Models, Animal ; Metabolic Syndrome/etiology ; *Diet/adverse effects ; },
abstract = {Background/Objectives: The study investigated the potential of mixed fruits and berries (MFB) as a dietary intervention to mitigate cafeteria (CAF) diet-induced gut microbiome dysbiosis and hepatic dysfunction associated with metabolic syndrome and steatohepatitis (MASH) in an adolescent rat model. Methods: Forty-eight adolescent male Sprague-Dawley rats (n = 3 cages per group (two rats per cage)) were divided into eight experimental groups, where NC received the normal AIN-93G basal diet, PC received the CAF diet and normal AIN-93G basal diet, T1 and T2 received MFB supplementation (3% and 6% levels) without CAF exposure, P1 and P2 received a MFB (3% and 6% levels) supplementation initiated at the onset of CAF feeding, and I1 and I2 received MFB supplementation initiated 2 weeks after CAF feeding. After 6 weeks, cecal 16S rRNA, hepatic histopathology, Oil Red O staining, and metabolic dysfunction-associated steatotic liver disease (MASLD)-related biomarkers (liver enzymes, alanine aminotransferase (ALT), and aspartate aminotransferase (AST)) were analyzed. Results: AST: ALT ratio was the highest in the PC group (3.63, p < 0.05) compared to the MFB groups. Oil Red O staining showed lower hepatic lipid accumulation, and histological analysis demonstrated a marked reduction in portal inflammatory cell infiltration in MFB. Alpha diversity (Simpson Index) decreased in PC (Kruskal-Wallis, p = 0.043). CAF increased Lactobacillus johnsonii (+75%, p < 0.05), while reducing L. murinus and L. intestinalis (~90%, p < 0.05). MFB supplementation restored Bifidobacterium Pseudolongum and increased Akkermansia muciniphila levels in the P2, I1, and I2 groups (~20-fold, p < 0.05). Bacteroides dorei was present in all groups except the PC group. These bacteria presented a positive correlation with key SCFAs. Conclusions: The results from this study indicated that MFB supplementation modulated gut microbiota composition and enhanced SCFA production, thereby strengthening intestinal barrier integrity and reducing gut-derived inflammation. Collectively, these effects attenuated hepatic lipid accumulation and inflammation, highlighting the potential of MFB to restore gut-liver axis homeostasis disrupted by CAF-induced dysbiosis in adolescent rats.},
}

Animals
*Gastrointestinal Microbiome
Male
Rats, Sprague-Dawley
*Fruit
*Liver/pathology/metabolism
Rats
Dysbiosis
*Fatty Liver/etiology/prevention & control
Disease Models, Animal
Metabolic Syndrome/etiology
*Diet/adverse effects

@article {pmid41599773,
year = {2026},
author = {Mucci, B and Palazzolo, E and Ruberti, F and Ientile, L and Natale, M and Esposito, S},
title = {Advances in the Management of Pediatric Inflammatory Bowel Disease: From Biologics to Small Molecules.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010176},
pmid = {41599773},
issn = {1424-8247},
abstract = {Background: The management of pediatric inflammatory bowel disease (PIBD) has evolved significantly over the past two decades, transitioning from corticosteroids and immunomodulators to biologic and small-molecule therapies. These advances have aimed not only to control inflammation but also to promote mucosal healing, improve growth, and enhance long-term quality of life. Objectives: This narrative review summarizes current evidence on the efficacy, safety, and clinical applications of biologic and novel small-molecule therapies in PIBD, highlighting emerging trends in personalized and precision-based management. Methods: A literature search was performed across PubMed, Embase, and the Cochrane Library, focusing on studies published within the last five years. Additional data were retrieved from key guidelines and position papers issued by ECCO-ESPGHAN, SIGENP, the FDA, and the EMA. Results: Anti-tumor necrosis factor (TNF) agents such as infliximab and adalimumab remain first-line biologics with proven efficacy in remission induction and maintenance. Newer biologics-vedolizumab, ustekinumab, risankizumab, and mirikizumab-offer alternatives for anti-TNF-refractory cases, showing encouraging short-term results and favorable safety profiles. Although many are approved only for adults with limited pediatric evidence, emerging small molecules-including Janus kinase (JAK) inhibitors (tofacitinib, upadacitinib) and sphingosine-1-phosphate (S1P) modulators (etrasimod)-provide oral, rapidly acting, and non-immunogenic treatment options for refractory disease. Furthermore, the gut microbiome is increasingly recognized as an emerging therapeutic target in PIBD, with growing evidence that host-microbiome interactions can influence both the efficacy and safety of biologics and small-molecule therapies. Conclusions: While biologics and small molecules have transformed PIBD management, challenges remain, including high treatment costs, limited pediatric trial data, and variable access worldwide. Future directions include multicenter pediatric studies, integration of pharmacogenomics, and biomarker-guided precision medicine to optimize early, individualized treatment and improve long-term outcomes.},
}

@article {pmid41599753,
year = {2026},
author = {Jin, Y and Wang, L and Lin, R and He, J and Liu, D and Liu, Y and Deng, Y},
title = {Synergistic Effects of Plant Polysaccharides and Probiotics: A Novel Dietary Approach for Parkinson's Disease Intervention.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010157},
pmid = {41599753},
issn = {1424-8247},
support = {Grant Nos. 82003985, 81973712, and 82004030//the National Natural Science Foundation of China/ ; Grant No. 20230204019YY//the Jilin Province Science and Technology Development Plant/ ; Grant No. 2023C027-3//the Jilin Provincial Development and Reform Commission Project/ ; Grant Nos, S202410199012, S202410199095X, andS202510199023//the Undergraduate Innovation and Entrepreneurship Proiects/ ; },
abstract = {Parkinson's disease (PD), the second most common neurodegenerative disorder globally, relies primarily on dopamine replacement therapy for conventional treatment. This approach fails to reverse core pathological processes and is associated with long-term side effects. Recent research on the microbiota-gut-brain axis (MGBA) has revealed that PD pathology may originate in the gut, forming a vicious cycle from the gut to brain through α-synuclein propagation, gut dysbiosis, intestinal barrier disruption, and neuroinflammation. This offers a novel perspective for managing PD through dietary interventions that modulate the gut microbiome. However, single probiotic or prebiotic interventions show limited efficacy. This review systematically introduces the novel concept of "synbiotics combining medicinal plant polysaccharides with probiotics," aiming to integrate traditional "medicinal food" wisdom with modern microbiome science. The article systematically elucidates the pathological mechanisms of MGBA dysfunction in PD and the intervention mechanisms of probiotics and emphasizes the structural and functional advantages of medicinal plant polysaccharide as superior prebiotics. The core section delves into the multifaceted synergistic mechanisms between these two components: enhancing probiotic colonization and vitality, optimizing microbial metabolic output, synergistically reinforcing the intestinal and blood-brain barriers, and jointly regulating immune and neuroinflammation. This approach targets the MGBA to achieve multi-level intervention for PD.},
}

@article {pmid41599684,
year = {2026},
author = {Bangeppagari, M and Jagadish, P and Srinivasa, A and Choi, W and Tiwari, P},
title = {Natamycin in Food and Ophthalmology: Knowledge Gaps and Emerging Insights from Zebrafish Models.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010086},
pmid = {41599684},
issn = {1424-8247},
abstract = {Natamycin, a polyene macrolide antifungal, has long been used as a food preservative and is the only Food and Drug Administration (FDA)-approved topical treatment for fungal keratitis. While its safety is supported by specific ergosterol interaction and minimal systemic absorption, current research mainly focuses on short-term effects, often overlooking long-term, developmental, and microbiome-related impacts. In food applications, questions remain about cumulative exposure and potential disruptions to gut microbiota. For ophthalmology, advanced delivery methods like nanocarriers and hydrogels enhance drug penetration but may alter pharmacokinetics and pose formulation challenges. Regulatory approvals have historically depended on established safe use and limited toxicological data, emphasizing the need for more systematic evaluations. Zebrafish (Danio rerio) represent a promising yet underutilized model for addressing significant gaps in research, particularly in the realms of microbiome studies, ocular health, developmental processes, and multigenerational effects. When paired with omics technologies, zebrafish facilitate comprehensive system-level mapping of drug-induced outcomes. This review consolidates existing evidence and positions zebrafish as a vital translational link between in vitro assays, mammalian models, and clinical practice. Additionally, it proposes a framework to ensure the effective and scientifically supported use of natamycin in both food and medicinal applications.},
}

@article {pmid41599664,
year = {2025},
author = {Hwang, JH and Choi, YK},
title = {Herbal and Natural Products for Antibiotic-Associated Diarrhea: A Systematic Review of Animal Studies Focusing on Molecular Microbiome and Barrier Outcomes.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010064},
pmid = {41599664},
issn = {1424-8247},
support = {NRF-2022R1A2C1013518//National Research Foundation of Korea/ ; },
abstract = {Background/Objectives: Antibiotic-associated diarrhea (AAD) arises from antibiotic-induced disruption of microbial diversity, metabolic activity, epithelial integrity, and mucosal immunity. Probiotics are widely used but often show limited efficacy under antibiotic pressure. Herbal and natural products (HNPs) may provide multi-target benefits by modulating microbiota-dependent and host-directed pathways. This review synthesized animal studies evaluating HNP or HNP-probiotic combination (HNP-C) therapies using molecular microbiome endpoints. Methods: Following PRISMA 2020 guidelines, controlled in vivo studies assessing HNP or HNP-C interventions for AAD were searched in Pubmed, EMBASE, Web of Science, Scopus, and CNKI through November 2025. Eligible studies reported microbial diversity, taxonomic shifts, short-chain fatty acids (SCFAs), barrier markers, or immune responses. Risk of bias was assessed using the SYRCLE tool. Due to heterogeneity, findings were narratively synthesized. Results: Twenty-seven studies met inclusion criteria (21 HNP, 6 HNP-C). HNP monotherapies consistently improved α-diversity, shifted β-diversity toward healthy controls, restored SCFA-producing taxa, and increased SCFA levels. They also enhanced tight junction proteins and reduced inflammatory cytokines. HNP-C interventions demonstrated more comprehensive microbial, epithelial, and immune recovery; however, only two studies included direct comparisons among HNP-only, probiotic-only, and combination groups. In these, HNP-C showed greater improvements than individual components, suggesting complementary or potentially complementary or additive effects. Other HNP-C studies were limited by absent comparator arms. Conclusions: HNPs appear to support recovery of microbial diversity, metabolic function, epithelial barrier integrity, and immune regulation by engaging microbiota-dependent and host-mediated mechanisms. HNP-C strategies may offer complementary benefits, although rigorously controlled comparative studies and clinical validation remain needed.},
}

@article {pmid41599644,
year = {2025},
author = {Machado, EP and Junkert, AM and Lazo, REL and Fernandes, IDC and Tonin, FS and Ferreira, LM and Borba, HHL and Pontarolo, R},
title = {Mapping the Vaginal Metabolic Profile in Dysbiosis, Persistent Human Papillomavirus Infection, and Cervical Intraepithelial Neoplasia: A Scoping Review.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010042},
pmid = {41599644},
issn = {1424-8247},
abstract = {Background/Objectives: This scoping review aimed to map evidence on metabolic alterations in the vaginal environment associated with dysbiosis, transient and persistent human papillomavirus (HPV) infection, and cervical dysplasia, highlighting potential metabolic and protein biomarkers for early detection of cervical cancer. Methods: Systematic searches were conducted in PubMed, Scopus, and Web of Science, following the JBI methodology and PRISMA-ScR guidelines. Studies jointly evaluating vaginal metabolites and proteins in women with HPV and cervical intraepithelial neoplasia (CIN) in the context of dysbiosis were included. Results: After duplicate removal, 196 records were screened, and 41 studies were selected-mostly cross-sectional observational designs-published between 2006 and 2025, predominantly by Chinese research groups. Lactobacillus spp. predominated in HPV-negative women, while HPV infection was associated with a dysbiotic environment enriched with anaerobes such as Gardnerella vaginalis, Atopobium vaginae, Prevotella, and Sneathia. Of 389 metabolic and protein markers associated with HPV infection and CIN, 44 underwent ROC analysis, with prolineaminopeptidase, 5'-O-methylmelledonal, and calonectin showing high diagnostic performance (AUC > 0.90). Conclusions: These results suggest vaginal microbiome and metabolic profiles may represent promising biomarkers for persistent HPV infection. Further, longitudinal studies with larger samples are needed for clinical validation.},
}

@article {pmid41599414,
year = {2026},
author = {Buendia-Corona, RE and Velasco Dey, MF and Valencia Robles, L and Hernández-Biviano, HJ and Hermosillo-Abundis, C and Castro-Pastrana, LI},
title = {Computational Identification of Blood-Brain Barrier-Permeant Microbiome Metabolites with Binding Affinity to Neurotransmitter Receptors in Neurodevelopmental Disorders.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {2},
pages = {},
doi = {10.3390/molecules31020366},
pmid = {41599414},
issn = {1420-3049},
support = {CVU 921738//SECIHTI/ ; },
mesh = {*Blood-Brain Barrier/metabolism ; Humans ; *Neurodevelopmental Disorders/metabolism/microbiology ; Molecular Docking Simulation ; *Receptors, Neurotransmitter/metabolism/chemistry ; *Gastrointestinal Microbiome ; },
abstract = {The gut microbiome produces thousands of metabolites with potential to modulate central nervous system function through peripheral or direct neural mechanisms. Tourette syndrome, attention-deficit/hyperactivity disorder, and autism spectrum disorder exhibit shared neurotransmitter dysregulation and microbiome alterations, yet mechanistic links between microbial metabolites and receptor-mediated neuromodulation remain unclear. We screened 27,642 microbiome SMILES metabolites for blood-brain barrier permeability using rule-based SwissADME classification and a PyTorch 2.0 neural network trained on 7807 experimental compounds (test accuracy 86.2%, AUC 0.912). SwissADME identified 1696 BBB-crossing metabolites following Lipinski's criteria, while PyTorch classified 2484 metabolites with expanded physicochemical diversity. Following 3D conformational optimization (from SMILES) and curation based on ≤32 rotatable bonds, molecular docking was performed against five neurotransmitter receptors representing ionotropic (GABRA2, GRIA2, GRIN2B) and metabotropic (DRD4, HTR1A) receptor classes. The top 50 ligands across five receptors demonstrated method-specific BBB classification (44% SwissADME-only, 44% PyTorch-only, 12% overlap), validating complementary prediction approaches. Fungal metabolites from Ascomycota dominated high-affinity top ligands (66%) and menaquinone MK-7 showed broad phylogenetic conservation (71.4% of phylum). Our results establish detailed receptor-metabolite interaction maps, with fungal metabolites dominating high-affinity ligands, challenging the prevailing bacterial focus of the microbiome and providing a foundation for precision medicine and a framework for developing microbiome-targeted therapeutics to address clinical needs in neurodevelopmental disorders.},
}

*Blood-Brain Barrier/metabolism
Humans
*Neurodevelopmental Disorders/metabolism/microbiology
Molecular Docking Simulation
*Receptors, Neurotransmitter/metabolism/chemistry
*Gastrointestinal Microbiome

@article {pmid41599407,
year = {2026},
author = {Cevallos-Fernández, E and Beltrán-Sinchiguano, E and Jácome, B and Quintana, T and Rivera, N},
title = {Fermented Plant-Based Foods and Postbiotics for Glycemic Control-Microbial Biotransformation of Phytochemicals.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {2},
pages = {},
doi = {10.3390/molecules31020360},
pmid = {41599407},
issn = {1420-3049},
mesh = {Humans ; *Phytochemicals/metabolism/pharmacology ; Animals ; *Fermented Foods ; *Glycemic Control ; Biotransformation ; Fermentation ; Gastrointestinal Microbiome ; },
abstract = {Plant-based fermented foods are increasingly promoted for glycemic control, yet their mechanisms and clinical impact remain incompletely defined. This narrative review synthesizes mechanistic, preclinical, and human data for key matrices-kimchi and other fermented vegetables, tempeh/miso/natto, and related legume ferments, kombucha and fermented teas, plant-based kefir, and cereal/pulse sourdoughs. Across these systems, microbial β-glucosidases, esterases, tannases, and phenolic-acid decarboxylases remodel polyphenols toward more bioaccessible aglycones and phenolic acids, while lactic and acetic fermentations generate organic acids, exopolysaccharides, bacterial cellulose, γ-polyglutamic acid, γ-aminobutyric acid, and bioactive peptides. We map these postbiotic signatures onto proximal mechanisms-α-amylase/α-glucosidase inhibition, viscosity-driven slowing of starch digestion, gastric emptying and incretin signaling, intestinal-barrier reinforcement, and microbiota-dependent short-chain-fatty-acid and bile-acid pathways-and their downstream effects on AMPK/Nrf2 signaling and the gut-liver axis. Animal models consistently show improved glucose tolerance, insulin sensitivity, and hepatic steatosis under fermented vs. non-fermented diets. In humans, however, glycemic effects are modest and highly context-dependent: The most robust signal is early postprandial attenuation with γ-PGA-rich natto, strongly acidified or low-glycemic sourdough breads, and selected kombucha formulations, particularly in individuals with impaired glucose regulation. We identify major sources of heterogeneity (starters, process parameters, substrates, background diet) and safety considerations (sodium, ethanol, gastrointestinal symptoms) and propose minimum reporting standards and trial designs integrating metabolomics, microbiome, and host-omics. Overall, plant-based ferments appear best positioned as adjuncts within cardiometabolic dietary patterns and as candidates for "purpose-built" postbiotic products targeting early glycemic excursions and broader metabolic risk.},
}

Humans
*Phytochemicals/metabolism/pharmacology
Animals
*Fermented Foods
*Glycemic Control
Biotransformation
Fermentation
Gastrointestinal Microbiome

@article {pmid41599227,
year = {2026},
author = {Cordero, C and Caballero-Román, A and Martínez-Ruiz, S and Olivo-Martínez, Y and Baldoma, L and Badia, J},
title = {Extracellular Vesicles from Probiotic and Beneficial Escherichia coli Strains Exert Multifaceted Protective Effects Against Rotavirus Infection in Intestinal Epithelial Cells.},
journal = {Pharmaceutics},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/pharmaceutics18010120},
pmid = {41599227},
issn = {1999-4923},
support = {PID2019-107327RB-100//MCIU(MICCIN)/AEI/ ; PID2022-137192OB-I00//MICIU/AEI/10.13039/501100011033/ ; },
abstract = {Background/Objectives: Rotavirus remains a major cause of severe acute gastroenteritis in infants worldwide. The suboptimal efficacy of current vaccines underscores the need for alternative microbiome-based interventions, including postbiotics. Extracellular vesicles (EVs) from probiotic and commensal E. coli strains have been shown to mitigate diarrhea and enhance immune responses in a suckling-rat model of rotavirus infection. Here, we investigate the regulatory mechanisms activated by EVs in rotavirus-infected enterocytes. Methods: Polarized Caco-2 monolayers were used as a model of mature enterocytes. Cells were pre-incubated with EVs from the probiotic E. coli Nissle 1917 (EcN) or the commensal EcoR12 strain before rotavirus infection. Intracellular Ca[2+] concentration, ROS levels, and the expression of immune- and barrier-related genes and proteins were assessed at multiple time points post-infection. Results: EVs from both strains exerted broad protective effects against rotavirus-induced cellular dysregulation, with several responses being strain-specific. EVs interfered with viral replication by counteracting host cellular processes essential for rotavirus propagation. Specifically, EV treatment significantly reduced rotavirus-induced intracellular Ca[2+] mobilization, ROS production, and COX-2 expression. In addition, both EV types reduced virus-induced mucin secretion and preserved tight junction organization, thereby limiting viral access to basolateral coreceptors. Additionally, EVs enhanced innate antiviral defenses via distinct, strain-dependent pathways: EcN EVs amplified IL-8-mediated responses, whereas EcoR12 EVs preserved the expression of interferon-related signaling genes. Conclusions: EVs from EcN and EcoR12 act through multiple complementary mechanisms to restrict rotavirus replication, spread, and immune evasion. These findings support their potential as effective postbiotic candidates for preventing or treating rotavirus infection.},
}

@article {pmid41599184,
year = {2026},
author = {Caturano, A and Nilo, D and Nilo, R and Sircana, MC and Erul, E and Zielińska, K and Russo, V and Santonastaso, E and Sasso, FC},
title = {Old Drug, New Science: Metformin and the Future of Pharmaceutics.},
journal = {Pharmaceutics},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/pharmaceutics18010077},
pmid = {41599184},
issn = {1999-4923},
abstract = {Metformin, a 60-year-old biguanide and cornerstone of type 2 diabetes therapy, continues to challenge and inspire modern pharmaceutical science. Despite its chemical simplicity, metformin displays highly complex pharmacokinetic and pharmacodynamic behavior driven by transporter dependence, luminal activity, and formulation-sensitive exposure. Originally regarded as limited by low permeability and incomplete absorption, metformin has emerged as a paradigm for gut-targeted therapy, controlled- and delayed-release systems, and personalized pharmaceutics. Growing evidence has repositioned the intestine, rather than systemic plasma exposure, as a major site of action, highlighting the central role of organic cation transporters and multidrug efflux systems in determining efficacy, variability, and gastrointestinal tolerability. Beyond metabolic control, insights into transporter regulation, pharmacogenetics, microbiome interactions, and manufacturing quality have expanded metformin's relevance as a model compound for contemporary drug development. Advances in formulation design, quality-by-design manufacturing, and regulatory control have further reinforced its clinical robustness, while repurposing efforts in oncology, immunometabolism, and regenerative medicine underscore its translational potential. This review integrates mechanistic pharmacology, formulation science, and clinical translation to position metformin not merely as an antidiabetic agent, but as a didactic model illustrating the evolution of pharmaceutics from molecule-centered design to system-oriented, precision-driven therapy.},
}

@article {pmid41599092,
year = {2026},
author = {Sinhalage, K and Polizel, GHG and Karrow, NA and Schenkel, FS and Cánovas, Á},
title = {Sheep Genetic Resistance to Gastrointestinal Nematode Infections: Current Insights from Transcriptomics and Other OMICs Technologies-A Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010106},
pmid = {41599092},
issn = {2076-0817},
support = {0//Ontario Ministry of Agriculture, Food and Agribusiness (OMAFA), the Ontario Agri-Food Innovation Alliance/ ; 0//Agricultural Research and Innovation Ontario (ARIO)/ ; 0//Ontario Sheep Farmers/ ; 0//the Natural Sciences and Engineering Research Council of Canada (NSERC; Ottawa, Ontario, Canada) and the NSERC - Discovery Grant Established Researchers/ ; 0//Food from Thought, University of Guelph/ ; },
mesh = {Animals ; Sheep ; *Sheep Diseases/parasitology/genetics/immunology ; *Nematode Infections/veterinary/genetics/parasitology/immunology ; *Disease Resistance/genetics ; Transcriptome ; Nematoda ; Genomics/methods ; *Gastrointestinal Diseases/veterinary/genetics/parasitology/immunology ; Host-Parasite Interactions/genetics ; Proteomics ; Gene Expression Profiling ; },
abstract = {Gastrointestinal nematode (GIN) infections are the most prevalent parasitic diseases in grazing sheep worldwide, causing significant productivity losses, high mortality and, as a result, economic losses and emerging animal welfare concerns. Conventional control strategies, primarily relying on anthelmintic treatments, face limitations due to rising drug resistance and environmental concerns, underscoring the need for sustainable alternatives. Selective breeding for host genetic resistance has emerged as a promising strategy, while recent advances in transcriptomics and integrative omics research are providing deeper insights into the immune pathways and molecular and genetic mechanisms that underpin host-parasite interactions. This review summarizes current evidence on transcriptomic signatures associated with resistance and susceptibility to H. contortus and T. circumcincta GIN infections, highlighting candidate genes, functional genetic markers, key immune pathways, and regulatory networks. Furthermore, we discuss how other omics approaches, including genomics, proteomics, metabolomics, microbiome, and multi-omics integrations, provide perspectives that enhance the understanding of the complexity of the GIN resistance trait. Transcriptomic studies, particularly using RNA-Sequencing technology, have revealed differential gene expression, functional genetic variants, such as SNPs and INDELs, in expressed regions and splice junctions, and regulatory long non-coding RNAs that distinguish resistance from susceptible sheep, highlighting pathways related to Th2 immunity, antigen presentation, tissue repair, and stress signaling. Genomic analyses have identified SNPs, QTL, and candidate genes linked to immune regulation and parasite resistance. Proteomic and metabolomic profiling further elucidates breed- and tissue-specific alterations in protein abundance and metabolic pathways, while microbiome studies demonstrate distinct microbial signatures in resistant sheep, suggesting a role in modulating host immunity. In conclusion, emerging multi-omics approaches and their integration strategies provide a comprehensive framework for understanding the complex host-parasite interactions that govern GIN resistance, offering potential candidate biomarkers for genomic selection and breeding programs aimed at developing sustainable, parasite-resistant sheep populations.},
}

Animals
Sheep
*Sheep Diseases/parasitology/genetics/immunology
*Nematode Infections/veterinary/genetics/parasitology/immunology
*Disease Resistance/genetics
Transcriptome
Nematoda
Genomics/methods
*Gastrointestinal Diseases/veterinary/genetics/parasitology/immunology
Host-Parasite Interactions/genetics
Proteomics
Gene Expression Profiling

@article {pmid41599047,
year = {2026},
author = {Gioula, G and Exindari, M},
title = {The Airway Microbiome as a Modulator of Influenza Virus Infection: Mechanistic Insights and Translational Perspectives-Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010063},
pmid = {41599047},
issn = {2076-0817},
mesh = {Humans ; *Influenza, Human/microbiology/virology/immunology ; *Microbiota ; Animals ; *Orthomyxoviridae ; *Respiratory System/microbiology ; },
abstract = {Outcomes of influenza virus infection vary widely across individuals, reflecting not only viral genetics and host factors but also the composition and function of the airway microbiome. Over the past few years, mechanistic work has clarified how specific commensals (for example, Staphylococcus epidermidis and Streptococcus oralis) restrict influenza replication by priming epithelial interferon-λ programs, reshaping intracellular metabolite pools (notably polyamines), dampening host protease activity, and maintaining barrier integrity; meanwhile, pathobionts (notably Staphylococcus aureus and Streptococcus pneumoniae) can enhance viral fitness via secreted proteases and neuraminidases that activate hemagglutinin and remodel sialylated glycoconjugates and mucus, setting the stage for secondary bacterial disease. Recent studies also highlight the gut-lung axis: gut microbiota-derived short-chain fatty acids (SCFAs), especially acetate, protect tight junctions and modulate antiviral immunity in influenza models. Together, these insights motivate translational strategies-from intranasal live biotherapeutics (LBPs) to metabolite sprays and decoy/dual neuraminidase approaches-that complement vaccines and antivirals. We synthesize recent evidence and outline a framework for leveraging the airway microbiome to prevent infection, blunt severity, and reduce transmission. Key priorities include strain-level resolution of commensal effects, timing/dosing windows for metabolites and LBPs, and microbiome-aware clinical pathways for anticipating and averting bacterial coinfection. Overall, the airway microbiome emerges as a tractable lever for influenza control at the site of viral entry, with several candidates moving toward clinical testing.},
}

Humans
*Influenza, Human/microbiology/virology/immunology
*Microbiota
Animals
*Orthomyxoviridae
*Respiratory System/microbiology

@article {pmid41599046,
year = {2026},
author = {Plewa, P and Graczyk, P and Figiel, K and Dach, A and Pawlik, A},
title = {Gut and Joint Microbiome and Dysbiosis: A New Perspective on the Pathogenesis and Treatment of Osteoarthritis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010062},
pmid = {41599046},
issn = {2076-0817},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Osteoarthritis/therapy/microbiology/pathology/etiology ; *Dysbiosis/microbiology/therapy ; Probiotics/therapeutic use ; Animals ; *Joints/microbiology/pathology ; },
abstract = {Osteoarthritis (OA) is one of the most common and burdensome musculoskeletal disorders and a major cause of pain, disability, and reduced quality of life worldwide. In recent years, increasing attention has been paid to extra-articular factors influencing its development and progression, opening new avenues of research into pathophysiological mechanisms and potential therapies. One of the most promising areas concerns the role of the gut-joint axis and related alterations in the gut microbiome. Numerous studies indicate that an imbalance of gut bacteria, increased intestinal permeability, and low-grade inflammation may contribute to the progression of degenerative joint processes. The mechanisms through which the microbiota influences the immune system and host metabolism are becoming increasingly well understood, including pathways involving short-chain fatty acids, tryptophan metabolites, and bile acids. Despite growing evidence linking dysbiosis to the pathogenesis of OA, effective therapeutic strategies based on microbiome modulation remain under active investigation. Among the most frequently studied approaches are probiotics, dietary interventions, and more advanced strategies such as gut microbiota transplantation and targeted modulation of microbial metabolites. However, before these methods can become part of routine treatment, extensive clinical trials and a clearer understanding of causal relationships between the microbiome and joint degeneration are required. This article summarises the current state of knowledge regarding the role of the gut microbiome in osteoarthritis, outlines key research findings, and highlights current and potential therapeutic directions.},
}

Humans
*Gastrointestinal Microbiome
*Osteoarthritis/therapy/microbiology/pathology/etiology
*Dysbiosis/microbiology/therapy
Probiotics/therapeutic use
Animals
*Joints/microbiology/pathology