@article {pmid41765966,
year = {2026},
author = {Kroon, MAGM and Wortelboer, K and Davids, M and Swart, EL and van Tellingen, O and Nieuwdorp, M and D'Haens, GRAM and van Laarhoven, HWM and de Boer, NKH and Kemper, EM},
title = {Effect of curcumin on the gut microbiota of patients with ulcerative colitis, Crohn's disease and healthy participants.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41765966},
issn = {2045-2322},
abstract = {UNLABELLED: Curcumin exhibits anti-inflammatory properties, but clinical evidence is limited, in part because of its low systemic bioavailability. Nevertheless, its limited absorption may favor local activity in the gut, where it could influence inflammatory bowel disease via microbiota modulation. This study assesses the impact of curcumin on gut microbiota diversity, as well as clinical and biochemical parameters in patients with ulcerative colitis, and Crohn’s disease in remission and healthy individuals. In a single-center, open-label, single-arm study, 29 male participants aged 18–65 were included. Participants received 3 g of curcumin twice daily for 8 weeks. Blood, urine, and fecal samples were collected at baseline, 4 weeks, and 8 weeks. Clinical and biochemical parameters, along with curcumin plasma, urine, and fecal concentrations, were assessed. Microbiome diversity was analysed using 16 S rRNA amplicon sequencing. The study was registered in the Dutch Clinical Trial Register with ID NL8770. Twenty-nine participants completed the study. Curcumin was well tolerated with stable clinical scores (SSCAI ≤ 2, HBI ≤ 5). Plasma levels were near the lower limit of quantification, while fecal levels were markedly higher. No significant changes in alpha-diversity were found. A temporary shift in beta-diversity appeared at 4 weeks but reversed by week 8. Curcumin caused only transient microbiota changes and slight alterations in taxa abundance, suggesting limited potential for sustained microbiota modulation in IBD management. Clinical trial registration: The study was registered in the Dutch Clinical Trial Register with ID NL8770.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42095-w.},
}

@article {pmid41776697,
year = {2026},
author = {Shi, X and Chen, F and Dai, M and Tang, Y and Wang, J and Lin, Y and Shi, M and Lan, T and Liu, H and Jin, X and Xiao, L and Kristiansen, K and Li, X},
title = {Comprehensive catalog of gut microbial genomes in Asian elephants: insights from shotgun metagenomics.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41776697},
issn = {2524-4671},
abstract = {BACKGROUND: The gut microbiota plays a crucial role in metabolism, immune regulation, and ecological adaptation of mammals. Although significant advancements have been made in shotgun metagenomic sequencing and the emergence of algorithms for generation of metagenome-assembled genomes (MAGs), a comprehensive investigation of the gut microbiota at the species level of wild mammals, among these the Asian elephant (Elephas maximus), is still lacking.

RESULTS: Here, based on a total of 82 fresh fecal samples collected from Asian elephants residing in distinct regions of the Yunnan Province, we established a comprehensive genome catalog containing 1421 species-level genome bins (SGBs) and a gene catalog comprising 44,596,628 non-redundant genes covering the gut microbiota composition of representative Asian elephant populations. At the species level, 1368 bacteria and 53 archaea were identified, and more than 93% of the SGBs remained unclassified, indicating that there are a large number of potential new species in the Asian elephant gut microbiota. At the functional level, carbohydrate hydrolases, biosynthetic gene clusters, and metabolic pathways dominated the gut microbiome of Asian elephants. Lifestyle and migration affected the composition and functional potential of the gut microbiota of Asian elephants. A northward migration was accompanied by an increase in gut microbiota diversity, an increase in the abundance of the phylum Bacteroidota, and a decrease in the presence of potentially pathogenic genera. In contrast, a southward migration of elephant herds was accompanied by exposure to unfavorable environments, with changes in gut microbiota including increased xenobiotic degradation and metabolic capacity.

CONCLUSIONS: We constructed comprehensive catalogs of gut microbial genes and genomes representative for Asian elephant populations, providing a valuable data resource for future research. Our study elucidates migration and lifestyle may modulate the composition and functionality of the gut microbiota in Asian elephants, offering critical insights for monitoring their health and enhancing conservation strategies for wild populations.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00533-0.},
}

@article {pmid41943414,
year = {2026},
author = {Yan, D and Zuo, P and Lin, M and Li, S},
title = {The Changes of Microbiome Attached on Clear Aligners after Drinking Coca-Cola.},
journal = {Polish journal of microbiology},
volume = {75},
number = {1},
pages = {109-118},
pmid = {41943414},
issn = {2544-4646},
mesh = {Humans ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; Male ; Adult ; *Carbonated Beverages/microbiology ; },
abstract = {This study aimed to investigate the changes in the microbiome on the inner surface of clear aligners following the consumption of Coca-Cola. The pH value and bacterial composition on the inner surface of clear aligners were assessed over five wearing cycles in three groups of subjects: those with a normal diet (Group A), those who drank Coca-Cola while wearing the aligners (Group C), and those who drank Coca-Cola after removing the aligners (Group B). Microbial analysis was performed using 16S rRNA gene sequencing and operational taxonomic unit (OTU) abundance profiling. The pH of the fluid inside the aligners significantly decreased immediately after Coca-Cola consumption (0 hour) in Groups B and C (p < 0.05). Group B exhibited the most pronounced decline in pH and alpha diversity at 12 hours, along with the highest beta diversity among the groups (p < 0.05). In Group A, the relative abundances of the phylum Actinobacteria was highest at 0 hour, Bacteroidetes at 12 hours, and class Actinobacteria, Gammaproteobacteria, and species Haemophilus influenzae peaked at 24 hours; conversely, Neisseria subflava showed the lowest abundance compared to Groups B and C (p < 0.05). Compared to Group C, Group B demonstrated higher levels of phylum Fusobacteria at 4 hours and 12 hours, and lower Actinobacteria abundance at 8 hours (p < 0.05). Consumption of Coca-Cola induces unfavorable changes in the microbiome on the inner surface of clear aligners. Notably, drinking Coca-Cola without wearing the aligners resulted in a lower pH and greater microbial imbalance, especially at 12 hours post-consumption.},
}

Humans
*Bacteria/classification/genetics/isolation & purification
*Microbiota
RNA, Ribosomal, 16S/genetics
Hydrogen-Ion Concentration
Male
Adult
*Carbonated Beverages/microbiology

@article {pmid41943415,
year = {2026},
author = {Zhou, B and Liu, J and Li, L and Yu, J and Sun, X and Wang, J and Shang, S},
title = {Comparative Analysis of Rhizosphere Bacteria of Phragmites australis and Suaeda salsa (L.) Pall. on Chenier Islands.},
journal = {Polish journal of microbiology},
volume = {75},
number = {1},
pages = {55-74},
pmid = {41943415},
issn = {2544-4646},
mesh = {*Rhizosphere ; *Chenopodiaceae/microbiology ; *Poaceae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; Microbiota ; Phylogeny ; Islands ; },
abstract = {The Chenier Islands are depositional areas within intertidal zones, characterized by unique soil textures and distinctive environmental conditions that shape specific vegetation distribution patterns. However, the adaptive mechanisms of Phragmites australis (common reed) and Suaeda salsa (L.) Pall. (common seepweed) two prevalent plant species in this region-in saline stress environments, as well as the composition and functional characteristics of their rhizosphere bacterial communities, remain largely unclear. In this study, rhizosphere soil samples were collected from common reed and common seepweed. DNA was extracted and subjected to high-throughput sequencing to analyze the composition and predictive functional profiles of the rhizosphere microbial communities. The results indicated that no significant differences were observed in the alpha diversity indices (Chao1, ACE, Simpson, and Shannon), indicating similar microbial species richness and evenness in the rhizospheres of common reed and common seepweed. Taxonomic analysis at the phylum level showed that the dominant bacterial phyla shared by both plants were Proteobacteria, Bacteroidota, Chloroflexota, and Actinomycetota. Notably, Acidobacteriota and Cyanobacteria were uniquely enriched in the common reed and common seepweed rhizospheres, respectively. At the genus level, the microbial communities of both plants were largely composed of unclassified taxa and minor groups, with Zeaxanthinibacter being the only cultivable dominant genus identified. Principal Coordinates Analysis (PCoA) explained 75.02% of the total β-diversity variance, and the clear separation of samples along the first coordinate axis revealed visually distinct community structures between the two plants. PERMANOVA further confirmed that plant species significantly influenced microbial community assembly, with a moderate explanatory strength (R[2] = 0.205, p = 0.008). Integrated results from LEfSe, PICRUSt2, and FAPROTAX analyses demonstrated that common seepweed rhizospheres were enriched with 19 photosynthesis-related biomarkers, suggesting a stronger photoautotrophic potential compared to common reed. In contrast, the common reed rhizosphere retained only two oligotrophic degraders Acidobacteriota and Chloroflexota. Although PICRUSt2 predictions indicated high overlap in core metabolic pathways between the two plants, FAPROTAX profiling revealed markedly divergent energy-acquisition strategies. Specifically, the common seepweed microbiome exhibited a "photoautotrophy nitrogen fixation" coupling strategy, whereas common reed relied predominantly on a "chemoheterotrophy nitrate reduction" pathway, reflecting niche partitioning in the saline environment. It should be noted that functional predictions derived from PICRUSt2 and FAPROTAX are computational inferences rather than empirical measurements, and thus mechanistic interpretations should be treated with caution. This study identifies a rhizosphere bacterial community assembly pattern characterized by "structural differentiation but functional convergence" offering valuable insights into microbial-mediated plant adaptation to saline stress.},
}

*Rhizosphere
*Chenopodiaceae/microbiology
*Poaceae/microbiology
*Bacteria/classification/genetics/isolation & purification
*Soil Microbiology
Microbiota
Phylogeny
Islands

@article {pmid41943876,
year = {2026},
author = {Šunić, I and Šarac, J and Havaš Auguštin, D and Pozdniakova, S and Ferguson, RMW and Jergović, M and Visentin, D and Borràs, S and Archer, E and Henderson, DK and Vitko, S and Ašić, A and Bošnjaković, A and Maglica, Ž and Viegas, C and Novokmet, N and Karlović, N and Marjanović, D and Muszyński, A and Liu, Y and Karisola, P and Alenius, H and Krych, L and Lovrić, M},
title = {The Indoor Microbiome: Sampling, Analysis and Emerging Trends.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70272},
pmid = {41943876},
issn = {1758-2229},
support = {101057497//European Union's Horizon Europe research and innovation programme/ ; 101057779//European Union's Horizon Europe research and innovation programme/ ; 101056883//the European Union/ ; 22.00324//Swiss State Secretariat for Education, Research and Innovation/ ; 10040524//United Kingdom Research and Innovation/ ; APP2017786//Australian National Health and Medical Research Council/ ; APP2008813//Australian National Health and Medical Research Council/ ; 101057693//European Union's Call on Environment and Health (HORIZON-HLTH-2021-ENVHLTH-02)/ ; /AMS_/Academy of Medical Sciences/United Kingdom ; },
mesh = {*Microbiota ; *Fungi/isolation & purification/genetics/classification ; *Air Pollution, Indoor/analysis ; *Bacteria/genetics/classification/isolation & purification ; *Air Microbiology ; Humans ; Dust/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Indoor spaces contain diverse microbial communities that shape human health. These microorganisms are particularly relevant to respiratory diseases, including asthma and allergies. Despite growing recognition of the importance of indoor microbial exposures, research in this field is slowed by differences in methods. These inconsistencies make it difficult to compare results and draw conclusions. This systematic review analyses 106 studies published between 2000 and 2025 that investigated indoor microbiomes in dust, air, and other matrices across homes, schools, and other built environments. We assessed sampling strategies, DNA extraction protocols, sequencing technologies, and bioinformatic pipelines, identifying trends, inconsistencies, and areas requiring harmonisation. Passive sampling, particularly dust collection, was the most common approach, while Illumina-based 16S rRNA and ITS amplicon sequencing dominated molecular analyses. However, variations in targeted gene regions, extraction kits, and analytical tools limited cross-study comparability. Ecological findings revealed consistent detection of bacterial taxa such as Staphylococcus, Streptococcus, and Corynebacterium, and fungal taxa including Cladosporium, Aspergillus, and Penicillium, with diversity shaped by building characteristics, ventilation, humidity, occupancy, and presence of pets. This review highlights the need for standardised protocols in indoor microbiome research to facilitate reproducibility, enable meta-analyses, and inform health-related guidelines for indoor environments.},
}

*Microbiota
*Fungi/isolation & purification/genetics/classification
*Air Pollution, Indoor/analysis
*Bacteria/genetics/classification/isolation & purification
*Air Microbiology
Humans
Dust/analysis
RNA, Ribosomal, 16S/genetics

@article {pmid41943884,
year = {2026},
author = {Fonseca, LRS and Feijó, M and Vaz, CV and Pereira, BJ and Laurentino, S and Palmeira-de-Oliveira, A and Socorro, S},
title = {Urologic Bacteriome: The Hero or the Villain in Prostate Cancer Onset, Progression, and Treatment?.},
journal = {Medicinal research reviews},
volume = {},
number = {},
pages = {},
doi = {10.1002/med.70042},
pmid = {41943884},
issn = {1098-1128},
support = {MOD.PD.NAC.015.01//Liga Portuguesa Contra a Cancro (LPCC) Bolsa LPCC/Gillette-Cancro da Próstata/ ; 2021.07634//Fundação para a Ciência e a Tecnologia/ ; 2021.07367//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {Prostate cancer (PCa) is the second most frequently diagnosed cancer in men worldwide and the fifth leading cause of cancer-related mortality, presenting urgent unmet clinical needs in diagnosis and treatment. The recognition of the microbiome as a key factor in human health has prompted numerous studies, revealing an exciting new approach to cancer diagnosis and therapy. The bacteriome is the component of the microbiome that is most metabolically active and influenceable by internal and external factors, which is pivotal in the development of cancer. Initial studies exploring the link between the microbiome and PCa focused primarily on the gut bacteriome, which has been implicated in the onset and progression of the disease, as well as in resistance to therapy. Further research has demonstrated that the urologic bacteriome also plays a crucial role in the development of PCa, serving as an important factor for diagnosis and treatment. This review synthesizes current knowledge concerning the significance of the urologic bacteriome in PCa onset, progression, diagnosis/prognosis, and therapy. It also explores the impact of the bacterial metabolome in PCa, emphasizing the importance of this undervalued dimension of the bacteriome. Overall, the review provides a comprehensive analysis of how bacteria and their bioactive metabolites contribute to PCa, highlighting their clinical and therapeutic relevance. It also identifies the existing knowledge gaps, paving the way for the development of new approaches that could enhance PCa diagnosis and treatment.},
}

@article {pmid41944002,
year = {2026},
author = {Liu, Y and Yang, Y and Zhu, L and Peng, W},
title = {Beyond Weight: Systems Biology and Precision Medicine Redefine Obesity as a Multidimensional Disease.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70724},
pmid = {41944002},
issn = {1463-1326},
support = {2025ZZTS0829//Central South University Graduate Student Independent Exploration and Innovation Project/ ; 82374552//the National Natural Science Foundation of China/ ; 20240304076//Support Plan for High-level Health and Medical Talents in Hunan Province/ ; 825B20009//National Natural Science Foundation of China for PhD Students/ ; 2024JJ2086//Hunan Provincial Natural Science Foundation for Distinguished Young Scholars/ ; },
abstract = {BACKGROUND: Traditional weight-centered models do not fully capture the biological complexity of obesity. Systems biology offers a new framework by integrating molecular, cellular, clinical, and environmental information to reframe obesity as a heterogeneous, multidimensional disease.

AIMS: This review aims to reframe obesity as a heterogeneous, multidimensional disease by integrating molecular, cellular, clinical, and environmental information through the lens of systems biology.

MATERIALS AND METHODS: This article summarizes findings from recent studies employing systems biology approaches, including single-cell transcriptomics, metabolomics, epigenomics, microbiome profiling, and computational modeling.

RESULTS: These approaches have revealed marked heterogeneity in adipose remodeling, inflammatory tone, mitochondrial stress, and inter-organ communication. Such insights help explain why individuals with similar body mass index (BMI) can differ substantially in insulin resistance, organ-specific vulnerability, and treatment response.

DISCUSSION: This review focuses on obesity-relevant mechanisms, including adipose tissue heterogeneity, immunometabolic dysfunction, immune aging, and obesity-related multi-system injury. We also discuss emerging precision obesity care strategies such as biomarker-guided subtyping, cell-specific targeting, microbiome-directed intervention, and artificial intelligence-assisted prediction.

CONCLUSION: Together, these advances support a shift from BMI-based classification alone toward mechanism-informed obesity prevention and treatment.},
}

@article {pmid41944101,
year = {2026},
author = {Sohel, M and Aktar, S and Khatun, S and Hamidu, S and Nity, NU and Kumar, S and Hossain, MS and Sarker, MR and Das, SR and Dey, BR and Hasan, AMW and Islam, K and Islam, F and Al Mamun, A},
title = {A Narrative Review on Unravelling Bacterial-Mediated Carcinogenesis and Possible Alternative Treatment Strategies.},
journal = {BioMed research international},
volume = {2026},
number = {1},
pages = {e6359088},
pmid = {41944101},
issn = {2314-6141},
mesh = {Humans ; *Carcinogenesis/pathology ; *Neoplasms/microbiology/pathology/therapy ; Animals ; *Bacteria/pathogenicity ; *Bacterial Infections/complications/microbiology ; Signal Transduction ; Cytokines/metabolism ; Apoptosis ; },
abstract = {The potential roles of chemical, physical, and viral factors in cancer development are well documented. Similarly, bacterial carcinogenesis has been reported previously, though not extensively. Therefore, we aimed to provide comprehensive, mechanistic evidence on the pathogenesis of bacteria-induced carcinogenesis and possible treatments to halt cancer progression. Infections by bacteria, including Salmonella typhi, Fusobacterium spp., Chlamydia pneumoniae, Staphylococcus aureus, Helicobacter pylori, and Mycobacterium tuberculosis, have been reported as the most common carcinogenic bacteria in humans. These bacteria can produce toxins and carcinogenic metabolites those promote the development of cancer in a variety of ways, including by changing the dynamics of the cell cycle, triggering signaling pathways in the cell, such as NF-κB, MAPK, PI3K-PKB/Akt, and JAK/STAT, and activating anti-apoptosis activities by increasing Bcl-2 and decreasing BAX, and caspases expression along with suppressing p53 and pRb tumor suppressor proteins. Moreover, inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interferon-gamma (INF-γ), interleukin-1β (IL-1β), IL-4, IL-6, IL-10, IL-1, IL-17, IL-23, and other inflammatory cytokines are a few of the factors that promote chronic inflammation and initiate carcinogenesis. In addition, bacterial infection can generate free radicals that induce DNA damage, thereby promoting carcinogenesis. Following these mechanisms, bacteria can cause a wide range of cancers, such as breast, colon, pancreas, stomach, lung, gallbladder, and oral carcinoma. Fortunately, supplementation with active natural phytochemicals and nano-based strategies may counteract bacterial infection-induced carcinogenesis by regulating several cellular proteins, including those that control the cell cycle, induce apoptosis, promote metastasis, interact with growth factor receptors and tyrosine kinases, and function as antioxidants. Therefore, this narrative review aims to provide a consolidated mechanistic overview of bacterial infection-induced carcinogenesis and to highlight emerging phytochemical and nanotechnology strategies as potential therapeutic approaches. Additionally, phytochemical-based interventions and nanotechnology strategies are discussed as potential alternative therapeutic approaches to counteract bacteria-induced carcinogenesis.},
}

Humans
*Carcinogenesis/pathology
*Neoplasms/microbiology/pathology/therapy
Animals
*Bacteria/pathogenicity
*Bacterial Infections/complications/microbiology
Signal Transduction
Cytokines/metabolism
Apoptosis

@article {pmid41944109,
year = {2026},
author = {Saini, O and Kaur, A and Haneef, M and Kosey, S},
title = {Pathophysiological Role of the Gut Brain Axis in Parkinson's Disease: From Microbial Metabolites and Intestinal Permeability to Central Neuroinflammation.},
journal = {Current neurovascular research},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115672026468149260326045511},
pmid = {41944109},
issn = {1875-5739},
abstract = {INTRODUCTION: Parkinson's Disease (PD) is the second most prevalent neurodegenerative disorder, affecting over 8.5 million individuals worldwide, with its incidence expected to rise. It is characterized by dopaminergic neuronal loss in the substantia nigra pars compacta and pathological aggregation of α-synuclein into Lewy bodies, leading to motor and non-motor symptoms. Increasing evidence implicates the Gut-Brain Axis (GBA) in PD pathophysiology.

METHODS: This review synthesizes findings from human and animal studies investigating the role of gut microbiota, gut permeability, microbial metabolites, and gastrointestinal dysfunction in the development and progression of PD.

RESULTS: Gut microbiota dysbiosis is associated with altered production of short-chain fatty acids, tryptophan metabolites, and neurotransmitter precursors, contributing to neuroinflammation, increased intestinal permeability, and α-synuclein misfolding. Gastrointestinal symptoms such as constipation, dysphagia, and gastroparesis often precede motor symptoms by decades, highlighting the gut as a potential origin of pathology. Therapeutic strategies targeting the microbiome, including Mediterranean and ketogenic diets, probiotics, prebiotics, postbiotics, and experimental phage therapy, have demonstrated promising preliminary outcomes.

DISCUSSION: Despite encouraging results, inconsistencies in methodology, mechanistic uncertainties, and the lack of longitudinal and individualized studies limit current understanding. Standardization and precision-based approaches are required to clarify causality and therapeutic efficacy.

CONCLUSION: Advancing knowledge of the gut-brain axis in PD presents valuable opportunities for early biomarkers and microbiota-targeted interventions, offering novel strategies to delay disease progression and improve patient quality of life.},
}

@article {pmid41944570,
year = {2026},
author = {Ostner, J and Li, H and Müller, CL},
title = {Score Matching for Differential Abundance Testing of Compositional High-Throughput Sequencing Data.},
journal = {Statistics in medicine},
volume = {45},
number = {8-9},
pages = {e70534},
pmid = {41944570},
issn = {1097-0258},
support = {ZT-I-PF-5-138//Helmholtz-Gemeinschaft/ ; R01GM123056/NH/NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods/statistics & numerical data ; Computer Simulation ; *Models, Statistical ; Humans ; Single-Cell Analysis ; },
abstract = {The class of a-b power interaction models, proposed by [1], provides a general framework for modeling sparse compositional data with pairwise feature interactions. This class includes many distributions as special cases and enables modeling of zero entries through power transformations, making it particularly suitable for modern high-throughput sequencing data with excess zeros, including single-cell RNA-Seq and microbial amplicon data. Here, we present an extension of this class of models that allows inclusion of covariate information, thus enabling accurate characterization of covariate dependencies in heterogeneous populations. Combining this model with a tailored differential abundance (DA) test leads to a novel DA testing scheme, cosmoDA, that can reduce the false positive detection rate caused by correlated features. cosmoDA uses penalized generalized score matching for parsimonious model fitting. We show on simulated benchmarks that cosmoDA can accurately estimate feature interactions in the presence of population heterogeneity and significantly reduces the false discovery rate when testing for differential abundance of correlated features. Using single-cell and amplicon data, we illustrate cosmoDA's ability to estimate data-adaptive Box-Cox-type data transformations and assess the impact of zero replacement and power transformations on downstream differential abundance results. cosmoDA is available at https://github.com/bio-datascience/cosmoDA.},
}

*High-Throughput Nucleotide Sequencing/methods/statistics & numerical data
Computer Simulation
*Models, Statistical
Humans
Single-Cell Analysis

@article {pmid41944618,
year = {2026},
author = {Fróis-Martins, R and Mertens, S and Tran, VDT and Maufrais, C and d'Enfert, C and Sanglard, D and LeibundGut-Landmann, S},
title = {Manipulation of regulators of morphogenesis is not sufficient to render a Candida albicans colonizer strain pathogenic.},
journal = {mBio},
volume = {},
number = {},
pages = {e0041526},
doi = {10.1128/mbio.00415-26},
pmid = {41944618},
issn = {2150-7511},
abstract = {As a member of the microbiome, Candida albicans colonizes the oral cavity and other mucosal surfaces of the human body. While commensalism is tightly controlled by the host immune system, the fungal determinants enabling the fungus to colonize the host mucosa without causing tissue damage and inflammation remain less clear. In search of genetic determinants that may underlie the commensal lifestyle of the low-damage-inducing C. albicans isolate 101, we identified a small sequence duplication in one allele of the Brg1 hyphal morphogenesis regulator gene, resulting in a truncated loss-of-function allele (BRG1[TRUNC]). Replacing BRG1[TRUNC] by the full-length allele (BRG1[FL]) resulted in a modest increase in filamentation but did not alter the phenotype of the fungus in the oral mucosa of experimentally colonized mice. Analysis of a spontaneous hyperfilamentous variant of the BRG1[FL]/BRG1[FL] derivative of C. albicans strain 101 identified a Glu-to-Lys change at position 1541 in the Cyr1 adenylate cyclase (CYR1[E1541K]). While the CYR1[E1541K] mutation led to greatly increased filamentation, expression of hyphae-associated genes, and host cell damage when tested in vitro, it was insufficient to render C. albicans strain 101 more pathogenic in the oral mucosa in vivo, irrespective of the BRG1 status. Together, this highlights that the low-damage-inducing nature of strain 101 cannot be overcome by manipulating BRG1 and CYR1, two genes with known roles in C. albicans virulence.IMPORTANCEDuring homeostasis, the fungus Candida albicans establishes mutualistic interactions with its human host. It can, however, also adopt a pathogenic state and cause infections with diverse clinical manifestations that pose a significant challenge for diagnosis and therapy. Understanding the fungal determinants that underlie C. albicans colonization under steady-state conditions may thus provide new avenues for modulating the fungus-host interaction in candidiasis patients to restore homeostasis. Here, we report gene variants in key regulators of C. albicans morphogenesis and virulence that distinguish strains with distinct capacity to drive inflammation and cause disease. Gene-exchange mutants provided evidence for the impact of a BRG1 loss-of-function allele and a CYR1 gain-of-function mutation toward in vitro biomarkers of fungal pathogenicity. However, in vivo in an experimental model of C. albicans oral colonization, none of these gene variants individually or in combination was sufficient to change the pathogenic state of the fungus. These findings indicate that C. albicans mucosal colonization is regulated by a complex gene network rather than by single genetic determinants.},
}

@article {pmid41944629,
year = {2026},
author = {Poopalarajah, R and Jha, AR},
title = {Human lifestyle-associated factors modulate the gut resistome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0145825},
doi = {10.1128/msystems.01458-25},
pmid = {41944629},
issn = {2379-5077},
abstract = {Antimicrobial resistance poses a serious threat to global public health in the 21st century. The human gut is a major reservoir of antimicrobial resistance genes and is strongly shaped by lifestyle factors linked to urbanization. Antibiotic use is widely known as a main driver of gut antimicrobial resistance; however, lifestyle encompasses other host and environmental determinants that also profoundly impact the gut resistome. These factors restructure gut microbiome composition and diversity, which, in turn, shape the abundance, persistence, and mobility of ARGs within the gut ecosystem. Lifestyle transitions along the urbanization gradient illustrate how antibiotic use, subsistence strategies, diet, agriculturally linked environmental exposures, host health, and global patterns of ARG distribution influence gut microbial diversity and ARG prevalence. Frequent antibiotic use in urban settings disrupts gut homeostasis and promotes resistome expansion. Transitions from traditional subsistence strategies to industrialized food systems are associated with dietary changes, such as reduced fiber intake, contributing to lower gut microbial diversity and increased ARG burden. Agrarian practices involving close human and livestock contact and antimicrobial use in animal husbandry facilitate ARG dissemination through the food chain. Host physiological factors and environmental exposures across diverse geographic regions additionally influence gut microbiome resilience and resistome composition. Integrating microbial community structure with ARG profiles provides insight into how lifestyle factors shape the gut resistome and influence ARG emergence and spread.},
}

@article {pmid41944651,
year = {2026},
author = {Morrison, JM and Steuart, R and Russell, CJ},
title = {Pediatric tracheostomy-associated respiratory infections: an evolving paradigm.},
journal = {Current opinion in pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOP.0000000000001559},
pmid = {41944651},
issn = {1531-698X},
abstract = {PURPOSE OF REVIEW: Children with tracheostomy frequently experience tracheostomy-associated infections (TRAINs) such as pneumonia and tracheitis. This review will summarize current evidence regarding the diagnosis, treatment, and prevention of TRAINs.

RECENT FINDINGS: Recent evidence highlights limitations of respiratory culture testing in the face of a diverse, dynamic bacterial community within the airways of children with tracheostomy, challenging the notion that a positive bacterial culture is sufficient for diagnosing bacterial TRAIN. For this reason, recent consensus guidelines recommend against the routine obtainment of respiratory cultures for TRAIN diagnosis in the absence of specific clinical symptoms. Additional evidence for microbiome shifts and host inflammation as diagnostic tools may help identify those who will benefit from antibiotic treatment. Recent findings support selective anaerobic coverage when aspiration is suspected and suggest shorter antibiotic courses may be effective. Cycled inhaled tobramycin shows potential for reducing TRAIN frequency and related hospitalizations.

SUMMARY: With recent advances in TRAIN pathobiology, diagnosis, treatment, and prevention of TRAINs is undergoing a paradigm shift. Future translational research will define the airway microbiome during TRAINs and during wellness and its impact on host inflammation. Antibiotic clinical trials are needed to optimize treatment and prevention of TRAINs.},
}

@article {pmid41944793,
year = {2026},
author = {Kumar, J and Hartzell, C and Abelson, E and Mano, KJ and Chidambaran, V},
title = {Prevalence, Expression, Assessment, Mechanisms, and Management of Pain in Autistic Children: A Scoping Review.},
journal = {A&A practice},
volume = {20},
number = {4},
pages = {e02178},
doi = {10.1213/XAA.0000000000002178},
pmid = {41944793},
issn = {2575-3126},
mesh = {Humans ; Child ; *Pain Management/methods ; *Autism Spectrum Disorder/complications/epidemiology ; Prevalence ; Adolescent ; Child, Preschool ; Pain Measurement ; *Pain/epidemiology ; *Chronic Pain/epidemiology/therapy ; },
abstract = {Autism spectrum disorder is a neurodivergent condition affecting communication, social interaction, and behavior, and is characterized by sensory-processing abnormalities. There is a high incidence of chronic pain in autistic children, and pain can also be a presenting symptom of autism. With improved identification of autism in children, it is increasingly important to understand the implications for pain management. This scoping review describes and summarizes existing literature on pain prevalence, mechanisms, expression, and assessment challenges, as well as acute and chronic pain management in autistic children. A systematic search strategy of MEDLINE, PsycINFO, SCOPUS, and Web of Science was utilized to identify major findings of qualitative, quantitative, observational studies, and reviews reporting on pain in pediatric patients (3-18 years) with concomitant autistic symptomatology. We identified 260 eligible articles, of which 85 were included for review. Our findings challenge earlier assumptions that autistic children are not sensitive to pain. Rather, they react differently to pain than nonautistic peers, have comorbidities that increase pain risk, and are hypersensitive to painful stimuli. Altered sensory-processing, genetic mechanisms, and brain-gut microbiome interactions have been suggested as mechanisms for higher pain sensitivity. The combination of altered pain expression and lack of proper pain assessment tools in this population can lead to unnecessary testing or delays in diagnosis and management. Management of pain requires parental engagement, multidisciplinary coordination, and tailored interventions unique to the individual's responses.},
}

Humans
Child
*Pain Management/methods
*Autism Spectrum Disorder/complications/epidemiology
Prevalence
Adolescent
Child, Preschool
Pain Measurement
*Pain/epidemiology
*Chronic Pain/epidemiology/therapy

@article {pmid41944837,
year = {2026},
author = {Weirauch, T and Vehreschild, MJGT},
title = {[Modulation of the gut microbiome for the eradication of multidrug-resistant pathogens: current approaches and perspectives].},
journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz},
volume = {},
number = {},
pages = {},
pmid = {41944837},
issn = {1437-1588},
abstract = {The global rise in antibiotic resistance represents one of the greatest threats facing modern medicine. Colonization of the gastrointestinal tract with multidrug-resistant organisms is considered a critical risk factor for nosocomial infections across various patient populations. In this context, targeted decolonization strategies are moving into the focus of clinical research. For a long time, non-absorbable antibiotics were considered a promising approach for local eradication; however, the evidence generated on this question does not suggest sufficient clinical efficacy of this approach. Alternative strategies, such as fecal microbiota transplantation, have shown encouraging results in case reports and small-scale studies for the decolonization of multidrug-resistant organisms. Live biotherapeutic products and certain probiotics are also being explored as potential options for microbiome modulation and reduction of antimicrobial resistance. However, the current evidence base remains heterogeneous, and robust randomized controlled trials are largely lacking. This article aims to provide an overview on the current understanding of gastrointestinal colonization with multidrug-resistant organisms and to discuss the clinical relevance of non-absorbable antibiotics as well as the potential role of microbiome-based therapies in the context of the global antibiotic resistance crisis.},
}

@article {pmid41944841,
year = {2026},
author = {Tom, A and Kurian, PS and Philip, S and Mathew, D and Vijayaraghavan, R and Sumbula, V and Varkey, ME},
title = {Exploratory profiling of microbial communities associated with tapping panel dryness in Hevea brasiliensis.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41944841},
issn = {1432-072X},
}

@article {pmid41945577,
year = {2026},
author = {Faridoun, A and Carvalho, R and Smith, J and Gibb, A and Jain, L and Zhang, A and Sran, A and Redmond, J and Malik, MZ and Gibson, M and Haider, A and Rekhi, U and Bhagirath, A and Rock, LD and Altabtbaei, K},
title = {FAVABEAN and FALAPhyl: Open-source pipelines for scalable 16s rRNA microbiome data processing and visualization.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0331145},
pmid = {41945577},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Humans ; *Software ; Phylogeny ; *Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {Reproducible and scalable analysis of 16S rRNA amplicon sequencing data remains a persistent challenge in microbiome research due to the complexity of available tools, incompatibilities between platforms, and the need for extensive bioinformatics expertise. We developed two containerized workflows-FAVABEAN (Fast Amplicon Variant Annotation, Binning, Error-correction And ANalysis) and FALAPhyl (Forays into Automating Laborious Analyses of Phylogeny)-to address these challenges. FAVABEAN and FALAPhyl are Snakemake-based pipelines designed for flexible execution across local, cluster, and cloud environments. FAVABEAN automates preprocessing, ASV inference, and taxonomic assignment using DADA2 and FIGARO, integration of taxonomic knowledge when samples are sequenced with multiple primers using SMURF. FALAPhyl supports downstream analysis including alpha/beta diversity, network analysis, and differential abundance testing, with integrated provenance tracking. We validated both pipelines using three case studies involving oral microbiome datasets. In Case Study 1, we compared oral microbiota across family members and niches, showing primer-dependent variability in ASV-based similarity and minimal reseeding from familial sources after prophylaxis. Case Study 2 analyzed dental aerosol samples, revealing no significant microbial differences between pre-, intra-, and post-procedure air. Case Study 3, a randomized trial of a nitrate mouthrinse, demonstrated no significant microbiome shifts, highlighting oral microbial stability. FALAPhyl's integration of DAtest enabled empirical evaluation of multiple statistical tests, aiding robust differential abundance inference. FAVABEAN and FALAPhyl offer a reproducible, automated solution for 16S rRNA amplicon data analysis. Their modular design, containerization, and provenance tracking enhance accessibility and scientific rigor in microbiome research.},
}

*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Humans
*Software
Phylogeny
*Computational Biology/methods
Bacteria/genetics/classification

@article {pmid41946252,
year = {2026},
author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP},
title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {141985},
doi = {10.1016/j.jhazmat.2026.141985},
pmid = {41946252},
issn = {1873-3336},
abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.},
}

@article {pmid41946778,
year = {2026},
author = {Nazir, I and Perez, D and Vargas, SJR and Ur Rehman, S and Arora, D and Chandra, M and Thimmapuram, J and Ebner, P},
title = {Assessing the impact of phage therapy on growth performance, microbiome and phage specific immune response in chickens.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45338-y},
pmid = {41946778},
issn = {2045-2322},
}

@article {pmid41946922,
year = {2026},
author = {Ding, Y and Zhang, Z and Wang, K and Jiang, C},
title = {The microbiome regulates host metabolic health and diseases through microbial enzymes.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {41946922},
issn = {1759-5053},
abstract = {The microbiome is widely involved in host metabolism, with many omics studies suggesting that it is important for metabolic health. Although studies in this area have made great strides in furthering our understanding of the role of the microbiome in health and disease, key challenges still hinder the safe clinical application of gut microbiota-targeted therapies. These limitations include a lack of confirmation of causality between the gut microbiota and host health, insights into the molecular mechanisms by which the gut microbiota functions to affect host health, and the development of therapeutic strategies that accurately regulate the function of the gut microbiota towards specific microbial enzyme targets without affecting its overall composition and viability. Microbial enzymes with various functions and activities have attracted the attention of many researchers in the past few years, especially microbiota-host isozymes, which are enzymes in the microbiome and the host that share a similar function. Such isozymes, as well as microbial-specific enzymes involved in basic biological processes of the gut microbiota, metabolism of nutrients, and synthesis of active metabolites and interactions in microbial-host communities, are the key mediators of gut microbiota-host crosstalk and have received much attention. In this Review, we provide a holistic understanding of the multifaceted role of gut microbial enzymes, including providing guidance for their discovery, while highlighting the great potential of gut microbial enzyme-oriented therapies for precision medicine.},
}

@article {pmid41947036,
year = {2026},
author = {Ali, S and Patel, AJ and Lehman, PC and Fitzjerrells, RL and Kasi, PM and Mangalam, AK},
title = {The distinct roles of Negativicoccus and Fusobacterium in proximal- and late-onset colorectal cancer.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655193},
doi = {10.1080/19490976.2026.2655193},
pmid = {41947036},
issn = {1949-0984},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology ; Female ; Male ; Feces/microbiology ; Middle Aged ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Aged ; DNA, Ribosomal/chemistry/genetics ; *Fusobacterium/isolation & purification/genetics ; Anal Canal/microbiology ; DNA, Bacterial/genetics/chemistry ; *Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; Adult ; },
abstract = {Despite the emerging role of the gut microbiome in colorectal cancer (CRC), its significance in early-onset CRC (EOCRC, < 50 y) versus late-onset CRC (LOCRC) and the molecular differences between proximal and distal CRC remain poorly understood. To circumvent the logistical and patient compliance challenges of stool collection, we explored the utility of anal swabs as a convenient alternative for characterizing gut microbiome signatures in CRC. We profiled the CRC microbiome using anal swabs (n = 76) and stool samples (n = 33) by 16S rRNA sequencing. Diversity indices were compared using Wilcoxon tests, compositional differences assessed by PERMANOVA, and correlations were performed in paired samples. Correlation analysis revealed strong associations between microbial phyla (Bacteroidetes, R = 0.86, p = 4.7 × 10[-6]; Firmicutes, R = 0.65, p = 3.4 × 10[-3]; Verrucomicrobiota, R = 0.81, p = 4.8 × 10[-5]; and Fusobacterium, R = 0.80, p = 7.3 × 10[-5]) and major genera (Bacteroides, R = 0.88, p = 1.7 × 10[-5]; Fusobacetrium, R = 0.75, p = 1.5 × 10[-3]; Blautia, R = 0.77, p = 8.5 × 10[-4]; and Bifidobacterium, R = 0.81, p = 3.3 × 10[-4]) across sample types, validating the use of anal swabs. However, Actinobacteriota and Prevotella were not correlated, likely reflecting the perianal skin-associated microbiota and underscoring the need for validation against stool or mucosal biopsies. Importantly, anal swabs revealed associations between Negativicoccus and proximal CRC (p = 0.047) and between the Fusobacteriota phylum and LOCRC (p = 0.042), suggesting subtype-specific CRC subtypes. In mechanistic studies, using the mucous-secreting HT-29 MTX cell line, we observed that Negativicoccus was associated with activation the RAS/MAPK pathway, upregulated c-MYC, KRAS, MAPK1, and Cyclin D1 (p < 0.05) and increased proinflammatory cytokines (IL-8) (p < 0.05), thereby increasing cell proliferation. In contrast, Fusobacterium modulates the WNT/β-catenin pathway, increasing β-catenin and AXIN1 (p < 0.05), promoting cell migration (p < 0.05), and extracellular matrix (ECM) remodeling. These findings highlight distinct microbial contributions to CRC pathogenesis, with Negativicoccus influencing proliferation and inflammation, whereas Fusobacterium promotes migration and invasion. Understanding these pathways offers potential for harnessing the gut microbiome's diagnostic and therapeutic power in CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology
Female
Male
Feces/microbiology
Middle Aged
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Aged
DNA, Ribosomal/chemistry/genetics
*Fusobacterium/isolation & purification/genetics
Anal Canal/microbiology
DNA, Bacterial/genetics/chemistry
*Bacteria/classification/genetics/isolation & purification
Sequence Analysis, DNA
Adult

@article {pmid41947046,
year = {2026},
author = {Wieser, NV and Admiraal, I and Weiss, R and Ghiboub, M and Davids, M and Lefèvre, A and Emond, P and Powell, EA and Sim, K and Kroll, JS and de Jonge, WJ and Sovran, B and Kinross, JM},
title = {Fecal tryptophan metabolism predicts the development of infant eczema: a prospective longitudinal study.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655171},
doi = {10.1080/19490976.2026.2655171},
pmid = {41947046},
issn = {1949-0984},
mesh = {Humans ; *Tryptophan/metabolism ; Infant ; *Feces/microbiology/chemistry ; Prospective Studies ; Longitudinal Studies ; Male ; Female ; *Eczema/microbiology/diagnosis/metabolism ; Gastrointestinal Microbiome ; Infant, Newborn ; Metabolomics ; Biomarkers/analysis ; Bifidobacterium/metabolism/genetics ; Bacteria/classification/metabolism/genetics/isolation & purification ; Indoles/metabolism ; RNA, Ribosomal, 16S/genetics ; Metabolome ; United Kingdom ; },
abstract = {Early-life microbial metabolism of tryptophan plays a critical role in immune modulation and may influence susceptibility to inflammatory disorders such as eczema. However, longitudinal human data linking microbial tryptophan metabolism to eczema onset are limited. We conducted a prospective cohort study of 40 term-born UK infants, followed from birth to 24 months, stratified by early-onset (infants developing eczema <12 months, n = 12) or late-onset (infants developing eczema ≥12 months, n = 7) doctor-diagnosed eczema. Fecal samples underwent targeted tryptophan LC-MS metabolomics and 16S rRNA sequencing. Tryptophan metabolomics revealed dynamic changes in tryptophan metabolites that were associated with disease status compared to healthy infants. Infants with early-onset eczema (<12 months) exhibited elevated tryptophan and tryptamine levels at 6 months, while those with late-onset eczema (≥12 months) showed reduced indole-3-lactic acid (ILA) levels prior to diagnosis at 9 months. 16S and metabolomics correlations highlighted a metabolic shift in Bifidobacterium from ILA, a metabolite that predominated fecal metabolome during early infancy but decreases by 12 months, coinciding with increased indole-3-aldehyde (I3AD) metabolism by Bifidobacterium. Receiver operating characteristic (ROC) curve analysis identified a small panel of early predictive indole-pathway markers, including tryptophan and the indole/indole-3-sulfate (I3S), I3S/ILA, and tryptophan/ILA ratios, discriminating both early- and late-onset eczema development. Our findings reveal distinct, time-dependent disruptions in microbial tryptophan cometabolism associated with eczema onset. ILA may serve as a biomarker for the diagnosis of infantile eczema. Further validation studies to establish its clinical utility are now required.},
}

Humans
*Tryptophan/metabolism
Infant
*Feces/microbiology/chemistry
Prospective Studies
Longitudinal Studies
Male
Female
*Eczema/microbiology/diagnosis/metabolism
Gastrointestinal Microbiome
Infant, Newborn
Metabolomics
Biomarkers/analysis
Bifidobacterium/metabolism/genetics
Bacteria/classification/metabolism/genetics/isolation & purification
Indoles/metabolism
RNA, Ribosomal, 16S/genetics
Metabolome
United Kingdom

@article {pmid41947175,
year = {2026},
author = {Xiao, Q and Wen, Z and Zhan, H and Zhao, H and Jiao, Y and Huang, D and Li, H and Chen, C},
title = {Si-Ni-San alleviates depression-like behavior via regulating the gut microbiota-tryptophan metabolism-AhR/NF-κB pathway axis.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {41947175},
issn = {1749-8546},
support = {82405203//the National Nature Science Foundation of China/ ; 20242BAB20451//Jiangxi Provincial Natural Science Foundation/ ; 202610094//The Science and Technology Program of Jiangxi Provincial Health Commission/ ; ZZ17-ND-12//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; ZZ17-YQ-054//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; PY-2025004B//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; JSYL2025001//The Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; },
abstract = {BACKGROUND: Si-Ni-San (SNS), a classic herbal formula from the Treatise on Cold Damage Diseases, is used to treat depression by relieving "liver qi stagnation". However, the underlying mechanism remains unclear.

PURPOSE OF THE RESEARCH: This study aimed to investigate the mechanism by which SNS alleviates depression-like behavior, specifically focusing on its role in modulating gut microbiota and host tryptophan metabolism.

METHODS: A depression model was induced in mice by chronic unpredictable mild stress (CUMS). The antidepressant effects of SNS were evaluated through behavioral tests. Integrated untargeted and targeted metabolomics, alongside 16S rRNA sequencing, were utilized to identify potential gut-brain signaling molecules. Molecular interactions between the gut-brain signaling molecule and its target were validated by surface plasmon resonance (SPR) and molecular docking. Key protein expression was measured via Western blot and ELISA. Finally, the function of gut microbiome-derived indole-3-acetic acid (IAA) as a key gut-brain signaling molecule was confirmed by oral supplementation experiments.

RESULTS: SNS significantly alleviated CUMS-induced depression-like behaviors. Multi-omics analysis revealed that SNS reversed tryptophan metabolic disorders and elevated gut microbiome-derived IAA levels in both the colon and prefrontal cortex, which was attributed to the enrichment of Lactobacillus. Further investigations confirmed that IAA directly binds to and activates the aryl hydrocarbon receptor (AhR), thereby inhibiting NF-κB pathway-mediated neuroinflammation. Moreover, oral supplementation with IAA replicated the antidepressant effects of SNS and suppressed CUMS-induced neuroinflammation via the AhR/NF-κB signaling pathway.

CONCLUSION: SNS alleviates depression-like behavior by modulating gut microbiota-mediated tryptophan metabolism to enhance IAA production, thereby activating central AhR signaling and suppressing NF-κB-mediated neuroinflammation.},
}

@article {pmid41947210,
year = {2026},
author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J},
title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02403-y},
pmid = {41947210},
issn = {2049-2618},
support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; },
abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.

RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.

CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.},
}

@article {pmid41947241,
year = {2026},
author = {Wang, Z and Li, LK and Zhou, NN and Wang, T and Wang, YX and Qiao, F and Du, ZY and Zhang, ML},
title = {Microbiota-gut-muscle axis shapes fish muscle texture by regulating collagen synthesis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02400-1},
pmid = {41947241},
issn = {2049-2618},
support = {2022YFD2400800//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Increasing studies have emphasized the communication network between the gut microbiome and host organs, revealing that such interactions significantly influence host physiological performances. However, whether a gut-muscle axis exists to regulate muscle quality in animal production is unknown.

RESULTS: In two independent cohorts, the muscle hardness of tilapia subjected to a long-term faba bean diet exhibited significant inter-individual variation. RNA-Seq analyses of the high-hardness (H) and low-hardness (L) groups pointed to collagen-based extracellular matrix as a possible factor driving muscle hardness development. Transplantation of gut microbiota from the H donor resulted in enhanced collagen synthesis in gnotobiotic zebrafish. Muscular collagen deposition was featured with an increased abundance of gut Cetobacterium. Gnotobiotic models colonized with live C. somerae exhibited enhanced collagen synthesis. Integrated analyses of microbiome function, bacterial genome, and metabolic profiles identified acetate as a key effector of C. somerae. Acetate incubation upregulated collagen I expression in TGF-β-activated fibroblasts in an acetylation-dependent manner. Mechanistically, acetate promoted the acetylation of SMAD2/3, enhancing its nuclear transport and stability, which ultimately increased collagen expression. An acetate-supplemented feeding experiment corroborated these findings.

CONCLUSION: The comprehensive results provided evidences that gut microbes regulated tilapia muscle texture through SMAD2/3 acetylation-driven collagen synthesis. This study expands our understanding of the multifaceted role of the gut-muscle axis in muscle physiology. Furthermore, our findings highlight that targeting gut microbiota and the downstream collagen synthesis pathway could be promising for manipulating muscle quality in animal production. Video Abstract.},
}

@article {pmid41947254,
year = {2026},
author = {Passmore, JS and Nieves Delgado, A and Happel, AU},
title = {Ethical design as a prerequisite for translational microbiome science.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41947254},
issn = {2049-2618},
support = {INV-037612/GATES/Gates Foundation/United States ; VI.Vidi.221F.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; K43TW012864/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Translational Research, Biomedical/ethics ; *Translational Science, Biomedical/ethics ; Research Design ; },
abstract = {Human microbiome research is expanding globally, yet remains dominated by samples, institutions, and leadership from the Global North. This imbalance undermines scientific validity, as microbiomes are shaped by socio-ecological context and temporal dynamics, and risks producing diagnostics and therapeutics that are not applicable across diverse populations. In this comment, we engage with van Daele et al.'s framework of co-laboration and argue for ethical, interdisciplinary, and locally led research models that center community participation, context-rich metadata, and equitable authorship. We outline structural requirements-governance tools, funding mechanisms, and accountability systems-needed to ensure these frameworks are implemented and advance both scientific integrity and global health equity. Video Abstract.},
}

Humans
*Microbiota
*Translational Research, Biomedical/ethics
*Translational Science, Biomedical/ethics
Research Design

@article {pmid41947255,
year = {2026},
author = {Van Daele, W and Tito Tadeo, RY and Perera, J and Tshokey, T and Iversen, PO and Jayasinghe, S and Raffaetà, R and Wangmo, N and Fjeld, HE and R, SC and Thoradeniya, T and Raes, J},
title = {Toward ethical human microbiome research: improving health through radical interdisciplinary and intercultural co-laboration.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41947255},
issn = {2049-2618},
support = {Project no. 324158//Norwegian Research Council/ ; grant G0B7320N//Fonds Wetenschappelijk Onderzoek/ ; GA n. 949742 ERC-HealthXCross//European Union's Horizon 2020 Research and Innovation Programme/ ; },
mesh = {Humans ; *Microbiota ; *Biomedical Research/ethics ; Global Health ; Europe ; North America ; },
abstract = {As human microbiome research is globalizing, it raises ethical concerns regarding the European and North American dominance in the field, which may reproduce a colonial bias and perpetuate inequities in global health research and outcomes. We suggest disentangling this ethical quandary into three main concerns: 1) scientific bias toward European and North American populations; 2) limited meaningful community inclusion, participation, and ownership, and 3) scant significant inclusion of diverse global researchers. We then formulate three recommendations for their resolution, deploying co-laboration-joint labor of diverse partners in generating synergies between diverse disciplines, cultures, and knowledges around shared concerns-and co-laborative science-a form of citizen science based on such synergies between diverse partners-to guide meaningful inclusive, participatory, and ethical human microbiome research. To conclude, we promote a programmatic list for putting co-laborative ethical science into practice, benefiting global communities, individuals, and researchers alike and decolonizing and improving health worldwide.},
}

Humans
*Microbiota
*Biomedical Research/ethics
Global Health
Europe
North America

@article {pmid41947543,
year = {2026},
author = {Samyn, M and Gasparetto, M},
title = {Is it time to consider oral vancomycin treatment for the management of pediatric inflammatory bowel disease irrespective of the presence of primary sclerosing cholangitis?.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70431},
pmid = {41947543},
issn = {1536-4801},
support = {//None/ ; },
}

@article {pmid41947788,
year = {2026},
author = {Gorczyca, K and Kimber-Trojnar, Ż and Kozioł, MM and Leszczyńska-Gorzelak, B},
title = {Association of culture-detected vaginal microbiota and body composition parameters with gestational diabetes outcomes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1776505},
pmid = {41947788},
issn = {2235-2988},
mesh = {Humans ; Female ; Pregnancy ; Cross-Sectional Studies ; Adult ; *Diabetes, Gestational/microbiology/epidemiology ; *Vagina/microbiology ; *Body Composition ; *Microbiota ; Candida albicans/isolation & purification ; Life Style ; Streptococcus agalactiae/isolation & purification ; Poland/epidemiology ; Young Adult ; },
abstract = {OBJECTIVE: To evaluate associations between culture-detected vaginal microbial colonization, body composition parameters, and lifestyle factors in women with gestational diabetes (GD).

DESIGN: Cross-sectional observational study.

SETTING: Tertiary university hospital, Department of Obstetrics and Perinatology, Lublin, Poland.

POPULATION: One hundred pregnant women, including 47 with GD and 53 healthy controls.

METHODS: Anthropometric measurements, bioelectrical impedance analysis (BIA), and vaginal culture-based microbiological assessment were performed. Dietary habits, lifestyle behaviours, and supplement use were evaluated using a validated questionnaire. BIA assessed hydration status and body composition, including total body water, extracellular and intracellular water, lean tissue mass, and body cell mass.

MAIN OUTCOME MEASURES: Prevalence of selected vaginal microorganisms (Candida albicans, Streptococcus agalactiae), body composition indices, and lifestyle factors.

RESULTS: Women with GD had significantly higher BMI during pregnancy, greater lean tissue mass and body cell mass, and increased total and extracellular water compared with controls (all p < 0.05). Vaginal swabs showed a higher prevalence of Candida albicans (27.7% vs. 5.7%) and Streptococcus agalactiae (23.4% vs. 0%) in the GD group. Women with GD more frequently reported alcohol and coffee consumption before pregnancy and were less likely to use folic acid or probiotic supplements. Due to multiple comparisons, some findings may reflect type I error and should be interpreted cautiously.

CONCLUSIONS: GD was associated with a higher prevalence of selected culture-detected vaginal microorganisms, as well as differences in body composition and health-related behaviours. These findings highlight potential interactions between metabolic status, microbial colonization, and lifestyle factors in pregnancy. Given the cross-sectional design, causality cannot be inferred, and comprehensive microbiome studies are needed to confirm broader ecological changes.},
}

Humans
Female
Pregnancy
Cross-Sectional Studies
Adult
*Diabetes, Gestational/microbiology/epidemiology
*Vagina/microbiology
*Body Composition
*Microbiota
Candida albicans/isolation & purification
Life Style
Streptococcus agalactiae/isolation & purification
Poland/epidemiology
Young Adult

@article {pmid41947790,
year = {2026},
author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X},
title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1744020},
pmid = {41947790},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Mycobiome ; *Constipation/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Adult ; Dysbiosis/microbiology ; Viruses/classification/genetics/isolation & purification ; Metagenome ; Chronic Disease ; Aged ; },
abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.

METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.

RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable α-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.

CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Virome
*Mycobiome
*Constipation/microbiology/virology
Metagenomics
Feces/microbiology/virology
Female
*Bacteria/classification/genetics/isolation & purification
Male
Middle Aged
*Fungi/classification/genetics/isolation & purification
Adult
Dysbiosis/microbiology
Viruses/classification/genetics/isolation & purification
Metagenome
Chronic Disease
Aged

@article {pmid41948035,
year = {2026},
author = {Li, Y and Wang, B and Lan, C and Dai, P and Zhao, L and Zhang, M and Fang, Q},
title = {Differential responses of crop pollen microbial communities to insect visitation and host identity: fungi are more sensitive than bacteria.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1789970},
pmid = {41948035},
issn = {1664-302X},
abstract = {INTRODUCTION: In the pollination process, pollen serves not only as a key vehicle for plant reproductive success but also as an important ecological interface for microbial transmission and selection. However, how insect visitation and host plant identity jointly affect the assembly of pollen microbial communities in agroecosystems remains poorly understood.

METHODS: Here, we employed bagging and open-pollination treatments combined with high-throughput sequencing to investigate the effects of insect visitation and host plant identity on the structure, composition, diversity, interspecific interactions, and core taxa of pollen microbial communities in crops.

RESULTS: Results showed that insect visitation and host plant identity jointly and significantly influenced the structure of pollen bacterial asnd fungal communities and altered their taxonomic composition, diversity, and interaction patterns, with these effects being mainly evident in cross-pollinated plants and more pronounced in fungal than in bacterial communities. Further analyses revealed that insect visitation increased network connectivity while reducing modularity (0.046) in bacterial communities of cross-pollinated plants, whereas their fungal network exhibited reduced connectivity and increased modularity (0.787). In cross-pollinated plants, fungal core taxa dominated the fungal communities (>87%), while bacterial core taxa contributed relatively little to overall community.

DICUSSION/CONCLUSION: Overall, insect visitation and host plant identity jointly shape pollen microbial communities, but bacterial and fungal communities exhibit distinct response patterns, with bacterial communities being relatively stable and fungal communities being more sensitive. This study highlights the key roles of insect visitation and host plant identity in pollen microbiome assembly and provides a theoretical basis for understanding crop pollination ecology and plant-pollinator-microbe interactions.},
}

@article {pmid41948039,
year = {2026},
author = {Wang, W and Liao, X and Liu, J and Liu, B and Zhou, C and Liang, P},
title = {Elevated postoperative IL-1β induces disorder of intestinal microenvironment and alteration of gut microbiota.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1744636},
pmid = {41948039},
issn = {1664-302X},
abstract = {INTRODUCTION: Previous research hinted at the importance of postoperative gut dysbiosis prevention, but the mechanisms remained unclear, posing a challenge for prevention and therapy. This study aims to investigate the characteristics of postoperative dysbiosis and the underlying mechanisms.

METHODS: The clinical cohort investigated the perioperative change of gut microbiota in patients undergoing thoracoscopy and its relationship with peripheral inflammatory indicators. Gut microbiome was characterized by 16S rRNA gene sequencing and Bugbase phenotype analysis. In the laboratory study, a mouse model of surgery/anesthesia stress was established to further investigate the potentially underlying mechanisms.

RESULTS: Microbiome analysis revealed a decrease in alpha diversity and a shift from obligate anaerobes to aerobes/facultative anaerobes after thoracoscopy. Postoperative IL-1β was negatively correlated with obligate anaerobe abundance and positively correlated with facultative anaerobe abundance. Higher facultative anaerobe abundance was associated with increased risk of postoperative complications and longer hospital stays. In the mouse model, surgery and rIL-1β intervention mirrored the oxygen phenotype changes in clinical cohort, and the colonic epithelium exhibited decreased ATP levels and hypoxic staining scores, with increased lactic acid. Downregulating postoperative IL-1β with IL-1β siRNA mitigated colonic hypoxic environment impairment and gut microbiota oxygen phenotype changes induced by surgery/anesthesia stress.

CONCLUSION: Postoperative gut dysbiosis involves a phenotypic shift of the gut microbiota from anaerobes toward aerobes and facultative anaerobes. This shift may be driven by an IL-1β-colonic epithelial oxygen metabolism-colonic oxygen environment-gut microbiota regulatory axis, offering potential insights for early risk stratification of severe postoperative complications and strategies to improve postoperative recovery.},
}

@article {pmid41948040,
year = {2026},
author = {Mo, X and Liu, Y and Huang, Z and Yu, H and Huang, J and Wu, Z and Tan, M and Fan, H and Ma, F and Zeng, B},
title = {Soil N and P nutrient metabolism affected by fungal community in larch plantation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1658803},
pmid = {41948040},
issn = {1664-302X},
abstract = {INTRODUCTION: The time-response mechanism of soil nitrogen (N) and phosphorus (P) nutrients across different stand ages remains intricate and inadequately quantified, particularly unclear is the effects of rhizosphere soil microbial communities, which serve as crucial drivers on soil N and P nutrients. This study delved into the effects of soil fungal community on the shifts of soil physicochemical properties and their correlations between N-P distribution within rhizosphere of Larix kaempferi (Japanese larch) with different tree stands.

METHODS: This study investigated the responses of soil nitrogen (N) and phosphorus (P) along a stand age gradient (young: <20 years; mid-aged: 20-30 years; near-mature: 30-40 years; mature: >40 years) in Larix kaempferi forests, with a focus on the associations between rhizosphere microbial communities and soil nutrient dynamics. By covering key developmental stages of forest succession, we examined age-related changes in rhizosphere soil N and P concentrations, soil physicochemical properties, and fungal community structure.

RESULTS: The results showed that fungal community structure gradually diversified from young to near-mature forests and became more stable in the mature forest stage. Differences in forest age were associated with changes in the availability and distribution of soil N and P nutrients, accompanied by shifts in the relative abundance of microbial functional genes related to N and P cycling. In particular, the abundance of P cycling-related functional genes showed patterns consistent with soil N and P variations, while N fixation-related functional genes exhibited the highest abundance in the middle-aged forest stage.

DISCUSSION: Overall, variations in stand development along the forest age gradient were closely linked to changes in soil nutrient distribution and rhizosphere microbial biomass, highlighting the potential role of rhizosphere microbial communities in soil N and P cycling in larch plantation ecosystems.},
}

@article {pmid41948042,
year = {2026},
author = {Dresel, FC and Gourlay, CW},
title = {Investigating the pH dependent antifungal effects of butyrate on Candida albicans.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1793162},
pmid = {41948042},
issn = {1664-302X},
abstract = {INTRODUCTION: Candida species are common members of the human gastrointestinal microbiome but are also associated with a range of diseases when microbial community balance is disrupted. Short-chain fatty acids produced by gut bacteria, particularly butyrate, play important roles in host-microbiome interactions and are increasingly explored as therapeutic modulators of microbial composition. Butyrate is present both as a microbial metabolite and dietary component and has been reported to influence Candida abundance within the gut. However, the antifungal activity of sodium butyrate (NaB) against Candida albicans under physiologically relevant gut pH conditions remains poorly understood.

METHODS: We examined the effects of NaB on C. albicans growth and physiology under pH conditions representative of the gastrointestinal environment. Growth, hyphal transition, respiration and biofilm formation were assessed in the presence of NaB at neutral pH. Parallel experiments at acidic pH (pH 4.0) evaluated fungicidal activity and associated cellular responses, including mitochondrial membrane potential, reactive oxygen species (ROS) accumulation, and intracellular calcium homeostasis. Histone deacetylase inhibitory activity of NaB was also assessed to determine its early cellular effects.

RESULTS: NaB displayed rapid histone deacetylase inhibitor activity in C. albicans and significantly inhibited growth, hyphal morphogenesis, respiration, and biofilm formation at neutral pH. In contrast, under acidic conditions (pH 4.0) NaB exhibited fungicidal activity. This lethal effect was associated with mitochondrial depolarisation, elevated ROS levels, and disruption of intracellular calcium regulation. Further analyses indicated that oxidative stress and loss of calcium homeostasis are key contributors to NaB-induced cell death under acidic conditions.

DISCUSSION: These findings reveal a strong pH dependence in the antifungal activity of butyrate against C. albicans. While NaB acts primarily as a physiological inhibitor of growth and virulence traits at neutral pH, acidic conditions convert its activity to a fungicidal mechanism driven by mitochondrial dysfunction, oxidative stress, and calcium dysregulation. This pH-dependent behaviour has implications for understanding microbiome-derived metabolites in fungal ecology within the gut and highlights the potential of butyrate-based strategies to modulate C. albicans overgrowth.},
}

@article {pmid41948045,
year = {2026},
author = {Dong, Y and Du, B and Xie, C and Zhang, S and Pang, Q and Zhang, D},
title = {Potassium sorbate induces developmental and microbiome changes in Drosophila melanogaster with attenuated trans-generational toxicity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783630},
pmid = {41948045},
issn = {1664-302X},
abstract = {Potassium sorbate (PS) is a widely used antimicrobial additive employed as a preservative in food, cosmetics, and animal feed. Early childhood represents a critical developmental window characterized by rapid growth, immune system maturation, gut microbiota establishment, and physiological homeostasis development, which may be particularly vulnerable to chemical exposures (during which chemical exposures may exert heightened impacts). Nevertheless, the effects of PS on childhood development and gut microbiota remain poorly understood, and its potential trans-generational effects have yet to be elucidated. In this study, we employed Drosophila melanogaster, an established model for studying evolutionarily conserved aspects of development, metabolism, and host-microbiota interactions, to systematically evaluate PS toxicity across multiple parameters: developmental dynamics, gut microbiota composition, gene regulation in adulthood, and trans-generational effects. Our findings demonstrate a dose-dependent biphasic response: while low-dose PS exposure (25 mg/L) accelerated larval pupation and adult emergence, suggesting a potential growth-promoting effect, high-dose exposure (≥ 500 mg/L) significantly delayed development and reduced adult lifespan (observed in females at 1,000 and males at 500-1,000 mg/L). Notably, trans-generational analysis revealed persistent developmental delays in the F1 generation, with offspring of 1,000 mg/L-exposed parents showing prolonged larval pupation time despite normal adult emergence timelines, indicative of partial developmental recovery. Mechanistically, high-dose PS disrupted endocrine signaling and altered expression of key developmental pathway regulators (EcR, InR, TOR, and E74B). These transcriptional changes were largely reversible in offspring, further supporting a similar gradually wash out recovery. While gut microbiota remained stable in exposed parents, offspring of 1,000 mg/L-exposed flies had significant microbiome alterations, highlighting clear trans-generational dysbiosis. This study provides new evidence that PS exposure during a sensitive developmental period in D. melanogaster can perturb development and gut microbial homeostasis across generations, offering insights relevant to understanding how early-life chemical exposures might influence conserved biological processes in higher organisms.},
}

@article {pmid41948046,
year = {2026},
author = {Liu, R and Liu, J and Li, Z and Wang, Z and Ding, J and Yuan, J and Yao, B and Dong, X and Dai, W and Huang, Z and Zhang, CS and Zhang, W and Zheng, Y},
title = {The composting microbiome and a multifunctional Bacillus tequilensis JZF3 with straw degradation and pathogen inhibition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768200},
pmid = {41948046},
issn = {1664-302X},
abstract = {Aerobic composting is a sustainable approach for converting organic waste into bio-fertilizer, where microorganisms play a central role in the degradation of recalcitrant lignocellulose. This study employed high-throughput sequencing to analyze the dynamic changes in bacterial and fungal communities during composting using distillers' grains, oil cake and cattle manure as raw materials. The results revealed pronounced successional changes in both microbial community structure and predicted function over time. Specifically, Firmicutes and Ascomycota were the dominant bacterial and fungal phyla, respectively, with the genus Bacillus maintaining high abundance throughout the process. The predicted functional profile indicated a shift in bacterial functions from initial xenobiotic biodegradation to core metabolic processes (such as energy and carbohydrate metabolism) in later stages. A total of 97 bacterial strains belonging to 38 species were isolated from different composting samples, with four strains (Bacillus licheniformis JZF8, B. altitudinis JZF2, B. tequilensis JZF3, and B. siamensis FJ3-3) showing strong cellulase, ligninase and protease activities. Among them, strain JZF3 not only exhibited these enzymatic activities and significant antagonistic activity against plant pathogens, but also was a dominant culturable species within the compost community. Furthermore, strain JZF3 was able to directly degrade rice straw without chemical pretreatment, achieving a degradation rate of 22.5%. The resulting degradation products also significantly promoted the growth of tobacco seedlings. This study identifies B. tequilensis JZF3 as a multifunctional agent that combines straw degradation with pathogen suppression and plant growth promotion, offering a novel strategy for synergizing agricultural waste recycling with disease control.},
}

@article {pmid41948248,
year = {2026},
author = {Padmavathy, K and Maakhni, E and Biswas, PS and Sheikh, F and Chhabra, T and Das, B},
title = {Oral-Systemic Interactions in Modern Healthcare: A Systematic Review of the Interrelationship Between Dental Pathologies and Systemic Diseases.},
journal = {Cureus},
volume = {18},
number = {3},
pages = {e104813},
pmid = {41948248},
issn = {2168-8184},
abstract = {Periodontitis is a prevalent chronic inflammatory disease characterised by destruction of the supporting structures of the teeth, and increasing evidence indicates that periodontal inflammation and oral microbial dysbiosis contribute to systemic diseases through inflammatory, immune, and vascular mechanisms. This systematic review examined associations between periodontitis and cardiovascular, metabolic, autoimmune, neurological, and inflammatory outcomes in adult populations. Studies published from 2015 onward were identified using a structured literature search, including cohort studies, randomised controlled trials, case-control studies, cross-sectional analyses, Mendelian randomisation studies, and microbiome-based investigations. Due to heterogeneity in study designs and outcomes, qualitative synthesis was performed. Eleven studies met the inclusion criteria, demonstrating consistent associations between periodontitis and increased risk of hypertension, atrial fibrillation, rheumatoid arthritis, dementia, and elevated systemic inflammatory markers. Quantitative findings showed higher blood pressure, increased C-reactive protein levels, greater autoantibody positivity, enhanced inflammasome activity, and reduced oral microbiome diversity in individuals with periodontal disease. Periodontal therapy improved periodontal health and systemic inflammation, although cardiometabolic improvements were modest or inconsistent. The evidence supports periodontitis as a chronic inflammatory condition with significant systemic consequences, mediated by inflammatory, immune, and endothelial pathways, underscoring the importance of integrating periodontal health into disease prevention and management strategies in modern healthcare.},
}

@article {pmid41948280,
year = {2026},
author = {Algindan, Y and AboAlsamh, H and Ahmad, S},
title = {Professional perspectives on PN among registered dietitians in Saudi Arabia: a mixed-methods assessment.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1695919},
pmid = {41948280},
issn = {2296-861X},
abstract = {BACKGROUND: The clinical implementation of personalized nutrition (PN) remains limited, despite growing interest. Healthcare professionals' readiness for adoption must be better understood.

OBJECTIVE: The aim of this study is to explore registered dietitians' perceptions, attitudes, and readiness regarding PN and multi-omics approaches in Saudi Arabia.

METHOD: A mixed-methods survey of 88 registered dietitians in Saudi Arabia provided quantitative and qualitative data on personalized nutrition technology (PNT) adoption patterns and barriers, analysed using the Consolidated Framework for Implementation Research (CFIR) to identify implementation barriers and facilitators.

RESULTS: PNT adoption was low (16%). Work experience, but not education level, had a relatively greater correlation with perceived usefulness of PNT (r = 0.280, p = 0.007). Genomics, metabolomics, and microbiome testing demonstrated strong correlations with PNT usefulness (r = 0.321-0.571, p ≤ 0.004). Qualitative findings identified knowledge gaps as the primary challenge and emphasized education as the key facilitator.

CONCLUSION: While Saudi dietitians have positive attitudes toward PN, they face significant implementation barriers at both an organizational and educational levels. For PN integration to be achieved within the Kingdom's healthcare system, policy, academic, and institutional interventions are required to enhance organizational support, professional training gaps, and interprofessional collaboration frameworks.},
}

@article {pmid41948282,
year = {2026},
author = {Verstegen, REM and de Bruijn, MJW and Garssen, J and Folkerts, G and Kostadinova, AI and Hendriks, RW and Willemsen, LEM},
title = {Dietary fructo-oligosaccharides dose-dependently modulate the microbiome and suppress type 2 lung inflammation in a murine model of house dust mite-induced allergic asthma.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1705988},
pmid = {41948282},
issn = {2296-861X},
abstract = {INTRODUCTION: A balanced microbiome is crucial for local and systemic immune regulation. Dietary fibers can support the intestinal microbiome, protecting the host from allergic diseases, including asthma. The effects of fibers depend on their type, dose, and disease context. Here, we investigated the preventative effects of four doses of fructooligosaccharides (FOS) in a murine model for house dust mite (HDM)-induced allergic asthma.

METHODS: BALB/c mice received a diet containing 1%, 2.5%, 5%, or 10% FOS (w/w) both prior to and during sensitization and challenges with HDM. Bronchoalveolar lavage fluid (BALF), lung tissue, serum, and cecum content were collected at the endpoint. Fecal microbiome composition was analyzed, and levels of short-chain fatty acids (SCFAs) were measured in cecum content, serum, and lung samples.

RESULTS: HDM-allergic mice showed eosinophilic airway inflammation and increased pulmonary type 2 inflammation, while cecal SCFA levels were lower compared to sham mice. Serum acetate concentrations showed a similar decline (p = 0.092). The 10% FOS diet did not prevent allergic sensitization or eosinophilic airway inflammation; however, it significantly reduced the proportions of T helper 2 (Th2) cells and the Th2/Th1 ratio in the lungs, decreased concentrations of chemokine (C-C motif) ligand 2 (CCL22) and interleukin (IL-13) in the BALF, and inhibited IL-13 production upon ex vivo HDM restimulation of lung cells. The 2.5% and 5% FOS diets also decreased Th2 cell frequency in the lungs. High doses of FOS increased the abundance of fecal Prevotellaceae, while reducing fecal Oscillospiraceae and Lactobacillaceae. These microbial shifts were correlated with protective effects against type 2 inflammation. In HDM-allergic mice, fecal Prevotellaceae abundance correlated positively with serum acetate concentrations, which were correlated with type protective effects. In allergic mice, the 2.5% and 5% FOS doses were associated with increased abundance of fecal Muribaculaceae and Bacteroidaceae, respectively, along with elevated cecal SCFA concentrations. In addition, the 5% FOS dose increased the relative abundance of fecal Lachnospiraceae, which correlated negatively with serum acetate levels and type prevention.

DISCUSSION: Dietary FOS modulated the gut microbiome and attenuated pulmonary type 2 immune responses in a dose-dependent manner. These findings underscore the importance of fiber dosing for precision nutrition strategies in allergy management.},
}

@article {pmid41948296,
year = {2026},
author = {Asad, S and Gu, P and Jiang, F and Liu, J and Chen, M and Karunarathna, SC and Atiq, M and Younas, M and Yapa, PN and Kan, X and Zhang, J},
title = {Pseudomonas parafulva SAPEU-1 as a keystone modulator: reshaping citrus phyllosphere microbiome to suppress citrus canker.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1771742},
pmid = {41948296},
issn = {1664-462X},
abstract = {INTRODUCTION: Citrus canker disease, caused by the pathogen Xanthomonas citri subsp. citri (Xcc) poses a substantial challenge for citrus production due to the limited efficacy of chemical control and increasing pathogen resistance.

METHODS: In this study, we isolated an endophytic bacterial strain, Endophyte S2, from the phyllosphere of citrus plants in Yunnan Province, China. We evaluated its efficacy both as a biocontrol agent and as a modulator of the citrus leaf microbiome.

RESULTS AND DISCUSSION: In vitro antagonism assays revealed that Endophyte S2 achieved the highest inhibition rate (68.2%) against Xcc among all tested isolates. Molecular identification based on 16S rRNA gene sequencing classified S2 as Pseudomonas parafulva SAPEU-01. In greenhouse trials, citrus plants with Xcc infestation were treated with SAPEU-01, and phyllosphere samples were collected before treatment and one month after, and analyzed by Illumina MiSeq sequencing. Post-treatment, α-diversity (richness and evenness) increased significantly, and β-diversity (PCoA, Bray-Curtis) showed a clear separation of microbial community structure, with reduced intra-group variability. Taxonomic shifts included the enrichment of Proteobacteria (particularly Pseudomonadaceae and Sphingomonadaceae), as well as genera such as Pseudomonas, Sphingomonas, and Methylobacterium, concomitant with a marked decline in Xanthomonadaceae (including X. citri) and opportunistic taxa such as Escherichia coli O157:H7 and Klebsiella aerogenes. Beneficial taxa, including Leuconostoc tardus, Sphingomonas, and Curtobacterium luteum, also increased. These results suggest Pseudomonas parafulva SAPEU-01 not only suppresses the pathogen but also restructures the phyllosphere microbiome toward greater stability and potential resilience.},
}

@article {pmid41948323,
year = {2026},
author = {Chao, K and Ding, Y and Ji, W and Wang, D and Liang, Q and Sun, S and Li, L and Yang, H and Zhao, J},
title = {Indole-3-acetic acid derived from Blautia protects against sepsis-induced acute lung injury.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1707493},
pmid = {41948323},
issn = {1664-3224},
mesh = {Animals ; *Sepsis/complications/microbiology/immunology ; Rats ; *Acute Lung Injury/etiology/prevention & control/microbiology/immunology/metabolism ; Male ; Humans ; Gastrointestinal Microbiome/drug effects ; *Indoleacetic Acids/pharmacology/metabolism ; Disease Models, Animal ; Female ; CD8-Positive T-Lymphocytes/immunology ; Middle Aged ; Rats, Sprague-Dawley ; Aged ; },
abstract = {OBJECTIVES: Sepsis-induced acute lung injury (SI-ALI) significantly contributes to sepsis mortality, with CD8[+] T cell depletion being a critical pathogenic factor. While Blautia, a gut commensal bacterium with established probiotic benefits in diverse diseases, its role in SI-ALI pathogenesis remains undefined. Here, we investigated the therapeutic potential of Blautia in lethal SI-ALI.

METHODS: Gut microbiome profiling was performed in SI-ALI patients and healthy controls to identify disease-associated microbial alterations. A cecal ligation and puncture (CLP) rat model of sepsis was used to validate microbiota changes and evaluate the therapeutic effects of Blautia supplementation. Untargeted metabolomic analysis was conducted to identify key metabolites associated with Blautia. Functional studies were performed to assess lung injury, immune responses, CD8[+] T cell abundance, and survival following Blautia or metabolite administration.

RESULTS: Gut microbiome analysis identified significant Blautia depletion in SI-ALI patients compared to healthy controls. This pathogenic alteration was faithfully reproduced in cecal ligation and puncture (CLP) -modeled septic rats, in which Blautia supplementation attenuated lung injury, enhanced systemic immune responses,and improved survival. Untargeted metabolomic profiling identified indole-3-acetic acid (IAA) as a key Blautia-derived metabolite. Administration of IAA alone recapitulated the protective effects of Blautia, significantly ameliorating SI-ALI. Crucially, both interventions restored CD8[+] T cell populations and augmented their functional responses. Clinical analysis revealed that elevated Blautia abundance in sepsis patients inversely correlated with pulmonary injury severity and positively associated with augmented CD8[+] T cell effector functions.

DISCUSSION: Our findings establish that Blautia and Blautia-derived IAA mitigates SI-ALI by counteracting CD8[+] T cell depletion and dysfunction, highlighting a novel and promising mechanism-based therapeutic strategy for life-threatening sepsis.},
}

Animals
*Sepsis/complications/microbiology/immunology
Rats
*Acute Lung Injury/etiology/prevention & control/microbiology/immunology/metabolism
Male
Humans
Gastrointestinal Microbiome/drug effects
*Indoleacetic Acids/pharmacology/metabolism
Disease Models, Animal
Female
CD8-Positive T-Lymphocytes/immunology
Middle Aged
Rats, Sprague-Dawley
Aged

@article {pmid41948342,
year = {2026},
author = {Gao, KP and Dou, JR and Ma, BB and Ma, TB and Li, N and Qian, AD and Shan, XF and Sun, WW and Zhang, L and Zhang, D and Wang, CF and Zhang, DX},
title = {Engineered Lactobacillus casei targets the IgT-pIgR axis to confer mucosal protection against Aeromonas veronii in snakehead (Channa argus).},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1759765},
pmid = {41948342},
issn = {1664-3224},
mesh = {Animals ; *Lacticaseibacillus casei/genetics/immunology ; *Aeromonas veronii/immunology ; *Fish Diseases/immunology/microbiology/prevention & control ; *Gram-Negative Bacterial Infections/immunology/prevention & control/veterinary/microbiology ; *Immunity, Mucosal ; Probiotics/administration & dosage ; *Bacterial Outer Membrane Proteins/immunology/genetics ; Bacterial Vaccines/immunology ; *Fish Proteins/immunology/genetics ; *Fishes/immunology/microbiology ; },
abstract = {INTRODUCTION: Aeromonas veronii remains a pervasive aquatic pathogen precipitating catastrophic economic depletion and threats to global food security. Conventional therapeutic modalities are constrained by inadequate stability, prohibitive costs, and biosafety risks.

METHODS: To address such challenges, an engineered Lactobacillus casei strain was developed to constitutively express the A. veronii outer membrane protein OmpAI through a tandem promoter system to ensure optimized antigen delivery.

RESULTS: Anal intubation with engineered L. casei in Channa argus stimulated compartmentalized mucosal immunity, evidenced by a six-fold elevation in hindgut IgT transcripts, significant infiltration of IgT[+] B cells, and pIgR mediated transcytosis, synchronized with systemic IgM activation. The probiotic treament accelerated pathogen clearance, improved survival rates to 42.9% compared to 12.5% in control group, and reorganized the commensal microbiome through a specific enrichment of beneficial Firmicutes.

DISCUSSION: This study elucidated a novel engineered-probiotic mucosal vaccination strategy for teleosts, providing a noninvasive, mucosal targeted immunoprophylactic strategy to decrease antibiotic dependency in aquaculture.},
}

Animals
*Lacticaseibacillus casei/genetics/immunology
*Aeromonas veronii/immunology
*Fish Diseases/immunology/microbiology/prevention & control
*Gram-Negative Bacterial Infections/immunology/prevention & control/veterinary/microbiology
*Immunity, Mucosal
Probiotics/administration & dosage
*Bacterial Outer Membrane Proteins/immunology/genetics
Bacterial Vaccines/immunology
*Fish Proteins/immunology/genetics
*Fishes/immunology/microbiology

@article {pmid41948584,
year = {2026},
author = {Yu, J and Liu, X},
title = {Gut microbiota and sepsis: mechanisms, clinical correlations, and therapeutic prospects.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1793041},
pmid = {41948584},
issn = {2296-858X},
abstract = {Sepsis is a life-threatening organ dysfunction triggered by a dysregulated host response to infection. According to the Global Burden of Disease Study, this condition affects over 50 million people annually and causes approximately 5.3 million deaths, with fatality rates varying significantly across populations and healthcare settings, ranging from about 20% to 50%, representing a major challenge in critical care medicine. In recent years, the gut microbiota, as the largest microbial ecosystem in the human body, has increasingly demonstrated a central role. It is not only essential for maintaining intestinal barrier integrity, immune homeostasis, and metabolic balance but also actively participates in the pathogenesis, progression, and outcomes of sepsis through modulating immune responses, influencing the production of key metabolites, and mediating gut-organ axes. This article systematically reviews the characteristics of sepsis-induced gut microbiota dysbiosis, delves into the molecular mechanisms by which dysbiosis drives immune disorders, metabolic disturbances, and multi-organ injury, evaluates the clinical potential and current limitations of microbiome-associated biomarkers, and summarizes recent advances and controversies in microbiota-targeted therapeutic strategies, including probiotics, fecal microbiota transplantation, precision nutrition, and antibiotic stewardship. This review aims to analyze the shortcomings and translational challenges in current research, providing a theoretical basis and forward-looking perspective for developing precise microbiome-based individualized management strategies for sepsis.},
}

@article {pmid41948629,
year = {2026},
author = {Osei-Poku, P and Wilson, MB and Shardow, ALK and Abakah, A and Amewu, EKA and Kyerewaa, CA and Larbi, A and Kwarteng, A},
title = {Tetracycline Resistance Pattern Among Lymphatic Filariasis-Hyperendemic Communities in Southern Ghana: A Mixed-Method Approach.},
journal = {Health science reports},
volume = {9},
number = {4},
pages = {e72242},
pmid = {41948629},
issn = {2398-8835},
abstract = {BACKGROUND AND AIM: Tetracyclines continue to serve as a cost-effective and essential treatment for common infections, particularly in resource-limited regions such as lymphatic filariasis (LF)-hyperendemic communities. The growing use of tetracycline-based antibiotics by symptomatic filarial lymphedema patients, likely influenced by the demonstrated benefits of anti-Wolbachia therapy, especially following doxycycline trials, underlines the necessity for vigilant monitoring of tetracycline resistance patterns. This study evaluated patients' antibiotic knowledge, attitude and practice in LF-endemic communities, and the resistance profiles of tetracycline-class antibiotics to assess the clinical impact of resistance on current anti-Wolbachia treatments.

METHODS: This cross-sectional study in Ghana's Ahanta West District enrolled 71 filarial lymphedema patients from four LF-hyperendemic communities. Structured questionnaires evaluated KAP on antibiotic use and resistance, complemented by microbiological analysis of wound swabs from 28 patients to profile the wound microbiome and assess tetracycline resistance.

RESULTS: Mean antibiotic knowledge (1.8 ± 1.0), attitude (1.4 ± 1.1), and practice (1.9 ± 1.1) scores were low, yielding a combined KAP score of 5.0 ± 1.9 (31.2% ± 11.9%) with no significant correlation to the educational level of patients. the facilities survey, the primary healthcare facilities in the area stocked at least one tetracycline-class antibiotic (specifically tetracycline and/or doxycycline). Microbiological testing identified 68 distinct bacterial isolates (20 genera, 36 species; dominated by S. sciuri, S. aureus). Varied tetracycline resistance observed: doxycycline (35.3%), tetracycline (26.5%), and minocycline (17.6%), with nine (13.2%) isolates resistant to all three. High-resolution melting analysis detected tet(M) gene in 34.1% (14) of isolates with Tm variation (69.27°C-73.06°C), suggesting variants.

CONCLUSION: Multifaceted strategies are essential to curb tetracycline resistance and overuse. These include culturally adapted education to enhance antibiotic stewardship among patients and providers, optimized wound care protocols addressing polymicrobial infections through improved hygiene and tailored regimens, and ongoing resistance surveillance to track trends while promoting therapeutic alternatives.},
}

@article {pmid41948819,
year = {2026},
author = {Cheng, L and Cai, J and Auster, A and Cho, S and Keir, M and Rhee, H and Kapili, B and Shalon, D and Ning, M},
title = {Translational Modeling of Gut Microbiome-Mediated Drug Metabolism: A Case Example of Sulfasalazine.},
journal = {CPT: pharmacometrics & systems pharmacology},
volume = {15},
number = {4},
pages = {e70246},
doi = {10.1002/psp4.70246},
pmid = {41948819},
issn = {2163-8306},
mesh = {Humans ; *Sulfasalazine/pharmacokinetics/administration & dosage ; *Gastrointestinal Microbiome/physiology ; *Models, Biological ; Feces/microbiology ; Sulfapyridine/pharmacokinetics/metabolism ; Male ; Mesalamine/pharmacokinetics/metabolism ; Adult ; *Anti-Inflammatory Agents, Non-Steroidal/pharmacokinetics ; Female ; },
abstract = {The gut microbiome can contribute to drug metabolism and significantly influence pharmacokinetic (PK) behavior. Sulfasalazine is well-known to be metabolized by gut bacterial azoreductases into sulfapyridine and mesalamine. Despite in vitro and in vivo evidence of the gut microbiome's role in drug metabolism, quantitative predictions of its impact on drug PK are lacking. To address this gap, we used sulfasalazine and its metabolites as a case example to build a translational modeling framework to predict the extent of gut microbiome-mediated drug metabolism and subsequent PK of the metabolites. First, sulfasalazine conversion kinetics was measured in vitro using pooled human fecal homogenate incubation. In vitro Vmax was 650.5 and 200.9 pmol/min/mg feces, and Km was 3648 and 1605 μM for sulfapyridine and mesalamine formation, respectively. Based on colon and feces bacterial counts from nine healthy humans, a ratio of 0.47 was used to scale in vitro fecal Vmax to the colon level. Second, physiologically-based pharmacokinetic (PBPK) models for sulfasalazine, sulfapyridine, and mesalamine were built in Simcyp and verified to predict their oral PK when dosed directly. Lastly, sulfapyridine or mesalamine PK after dosing sulfasalazine was predicted by linking the parent and metabolite PBPK models with colon luminal metabolism kinetics. The observed sulfapyridine and mesalamine PK after dosing sulfasalazine were predicted with weighted average fold-errors of 1.21, 1.22, and 1.05 for Cmax, Tmax, and AUC, respectively. Overall, this in vitro to in vivo translation and modeling framework provides valuable insights for quantitatively predicting the in vivo impact of gut microbiome-mediated drug metabolism.},
}

Humans
*Sulfasalazine/pharmacokinetics/administration & dosage
*Gastrointestinal Microbiome/physiology
*Models, Biological
Feces/microbiology
Sulfapyridine/pharmacokinetics/metabolism
Male
Mesalamine/pharmacokinetics/metabolism
Adult
*Anti-Inflammatory Agents, Non-Steroidal/pharmacokinetics
Female

@article {pmid41948926,
year = {2026},
author = {Garg, I and Singh, N and Rawat, S and Negi, T and Chaurasia, U and Gupta, P},
title = {Decoding the Skin Micro-Immune Milieu, Homeostasis, and Keratinocyte Trafficking in Psoriatic Disease.},
journal = {Immunological investigations},
volume = {},
number = {},
pages = {1-31},
doi = {10.1080/08820139.2026.2651752},
pmid = {41948926},
issn = {1532-4311},
abstract = {INTRODUCTION: The skin, acting as a complex interface between the immune system and microbiome, maintains balance through coordinated interactions among the epidermal barrier, microbiome, and immune responses. Psoriasis, a chronic autoimmune and inflammatory disorder, disrupts this balance by altering keratinocyte growth, immune signaling, and microbial diversity.

RESULTS AND DISCUSSION: The psoriatic environment exhibits dysbiosis, with reduced α-diversity and increased β-diversity, thereby worsening lesions. Beneficial microbes like Staphylococcus epidermidis provide protection, while opportunistic pathogens such as Staphylococcus aureus, Streptococcus pyogenes, Malassezia, Candida albicans, and HPV can trigger psoriatic outbreaks. Keratinocytes, essential to disease development and progression, interact actively with immune cells, fibroblasts, and Langerhans cells through cytokines, chemokines, and extracellular vesicles, influencing cell movement and inflammation. Changes in pathways like GLUT-1-mediated glucose metabolism and PI3K/Akt/mTOR signaling promote epidermal overgrowth, new blood vessel formation, and immune imbalance. Oxidative stress and mitochondrial dysfunction also weaken skin homeostasis. The skin's lymphoid tissue (SALT) and inducible SALT are crucial for immune surveillance and autoimmunity but become hyperactive in psoriasis.

CONCLUSION: Understanding the complex network linking the skin microbiome, immune system, and keratinocyte behavior is essential for developing advanced treatments. Combining immunology, molecular biology, and drug delivery science, using molecular docking, in-silico modeling, and nanotherapy, offers promising options for targeted psoriasis therapy.},
}

@article {pmid41949018,
year = {2026},
author = {Grabska, M and Gorecki, A and Pye, HV and Adriaenssens, EM and Grzesiuk, M},
title = {Phage Cocktail Designed for Wastewater Bioremediation Has Limited Effect on Crustacean Filtrator Microbiome Diversity and Health.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70329},
pmid = {41949018},
issn = {1758-2229},
support = {UMO-2021/03/Y/NZ9/00141 under the frame work of JPIAMR-ACTIONGA no. 963864//National Science Centre/ ; MR/W031205/1/MRC_/Medical Research Council/United Kingdom ; BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13631/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13633/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13634/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13635/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13636/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Bacteriophages/physiology ; *Microbiota ; *Wastewater/microbiology/virology ; *Daphnia/microbiology/virology/growth & development ; RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; Bacteria/genetics/classification/virology ; Klebsiella pneumoniae/virology ; Pseudomonas aeruginosa/virology ; Enterobacter/virology ; Female ; Biodiversity ; },
abstract = {In this study we investigated the impact of a phage cocktail on Daphnia magna microbiome and the life-history parameters. A mixture of four phages able to infect strains of Klebsiella pneumoniae, Enterobacter sp. and Pseudomonas aeruginosa was tested on three D. magna clones. The host-associated microbiome composition in both the examined variants and the control was analysed using 16S rRNA amplicon sequencing. Additionally, the survival, growth rate, age, size at the first reproduction, and neonate per female were assessed. The analysis revealed minor shifts in microbial composition following phage exposure. Nevertheless, results showed that the phage cocktail increased microbiome diversity. None of the life-history parameters studied were affected by the presence of the phage cocktail, and no adverse effects were observed. The results indicated that under laboratory conditions the phage cocktail is safe for D. magna and its microbiome.},
}

Animals
*Bacteriophages/physiology
*Microbiota
*Wastewater/microbiology/virology
*Daphnia/microbiology/virology/growth & development
RNA, Ribosomal, 16S/genetics
Biodegradation, Environmental
Bacteria/genetics/classification/virology
Klebsiella pneumoniae/virology
Pseudomonas aeruginosa/virology
Enterobacter/virology
Female
Biodiversity

@article {pmid41949064,
year = {2026},
author = {Chongtham, C and Biswas, T and Kumari, N and Kar, R and Jyotsna, and S, J and Pant, A and S Patil, V and Arimbasseri, GA},
title = {The JNK2-microbiome axis modulates gut barrier integrity through microbial acetate.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2651962},
doi = {10.1080/19490976.2026.2651962},
pmid = {41949064},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Acetates/metabolism ; *Intestinal Mucosa/microbiology/metabolism ; Mice, Inbred C57BL ; Milk ; *Mitogen-Activated Protein Kinase 9/metabolism/genetics ; Female ; Weaning ; Dextran Sulfate ; Male ; Diet, High-Fat ; },
abstract = {BACKGROUND: Weaning involves a nutritional shift from fat-rich milk to carbohydrate-based solid food, reshaping metabolism, microbiota, and gut immune tolerance. While dairy remains a component of the human diet beyond weaning, the impact of continued milk supplementation on gut epithelial homeostasis remains poorly understood.

RESULT: Here, using a mouse model, we show that continued milk-based feeding post-weaning promotes intestinal barrier function by enriching the commensal bacterium Dubosiella newyorkensis, which produces acetate to activate epithelial JNK2 signaling. This pathway enhances barrier integrity and suppresses inflammation induced by mild dextran sodium sulfate (DSS) treatment. In contrast, feeding a lard-based high-fat diet or transient pharmacologic inhibition of JNK2 induces epithelial P38 activation, resulting in barrier disruption and inflammation. Importantly, the beneficial effects of milk were observed only if they were initiated during the weaning period, when the microbiome is in a metastable transitional state. Initiation of the same intervention two weeks after weaning led to P38 activation and inflammatory responses.

CONCLUSION: Our findings show that immediate post-weaning milk supplementation preserves a beneficial gut microbiome, marked by the persistence of D. newyorkensis and enhanced gut barrier integrity. Even a one-week delay eliminates this protective effect, emphasizing the critical timing of post-weaning nutritional intervention for maintaining intestinal health.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
*Acetates/metabolism
*Intestinal Mucosa/microbiology/metabolism
Mice, Inbred C57BL
Milk
*Mitogen-Activated Protein Kinase 9/metabolism/genetics
Female
Weaning
Dextran Sulfate
Male
Diet, High-Fat

@article {pmid41949254,
year = {2026},
author = {Du, J and Sun, Y and Yu, D and Lu, S and Yu, S and Wang, M and Zhou, G and Xu, S and Zhang, L and Zhu, Y and Zhou, L},
title = {Oral liposomal co-delivery of ultrasmall ceria and 5-aminosalicylic acid alleviates DSS colitis via ROS scavenging and microbiome remodeling.},
journal = {Journal of materials chemistry. B},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6tb00173d},
pmid = {41949254},
issn = {2050-7518},
abstract = {Inflammatory bowel disease (IBD) is a refractory gastrointestinal disorder characterized by sustained intestinal inflammation, mucosal barrier dysfunction, and gut dysbiosis. Excess reactive oxygen species (ROS) is a key driver of these pathological processes. Although CeO2-based nanozymes can scavenge ROS, their clinical application is limited by poor aqueous stability. Here, we developed an oral nanozyme by co-encapsulating ultrasmall CeO2 nanoparticles and the clinical drug 5-aminosalicylic acid (5-ASA) within liposomes. The resulting formulation (CeLA) exhibited excellent colloidal stability and robust ROS-scavenging activity and provided marked cytoprotection against oxidative stress in vitro. In a dextran sulfate sodium (DSS)-induced colitis model, CeLA alleviated clinical symptoms, restored intestinal barrier integrity, and suppressed pro-inflammatory cytokine expression. Notably, CeLA also reshaped the dysbiotic gut microbiome by reducing pro-inflammatory bacterial taxa. This multifunctional nanozyme integrates antioxidant, anti-inflammatory, and microbiome-modulating effects, offering a promising therapeutic strategy for IBD.},
}

@article {pmid41949255,
year = {2026},
author = {Wang, W and Guan, R and Wang, Q and Xiong, L and He, A and Bai, L and Li, Z and Lu, C and Zhang, S and Zhao, C and Yin, Y and Li, J and Wang, Y and Jiang, G},
title = {Traditional Fermentation Amplifies PFAS Bioaccessibility: Defining Fermented Fish Products as an Unrecognized Source of Dietary Exposure.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15723},
pmid = {41949255},
issn = {1520-5851},
abstract = {Per- and polyfluoroalkyl substances (PFAS), as a class of persistent organic pollutants, are well-characterized environmental and human health threats; however, their behavior in food systems, particularly during fermentation, remains poorly understood. Here, we show that traditional fermentation significantly enhances the PFAS bioaccessibility. Through a 300 day model fermentation system, we observed near-complete release of several major PFAS congeners. While microbial transformation of the PFAS precursor of N-ethyl perfluorooctane sulfonamide (N-EtFOSA) was observed, persistent congeners of perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) remained unaffected during microbiome restructuring. We demonstrate that matrix degradation and microbial activity synergistically modify the PFAS binding states. In silico modeling reveals a shift in bioaccessibility determinants from specific binding to partitioning behavior, establishing that fermentation liberates PFAS via two key pathways: microbial degradation of structural components, releasing bound contaminants and altered PFAS partitioning during digestion. Our findings establish fermentation as a previously unrecognized amplifier of dietary PFAS exposure, with substantial implications for food safety and public health, especially in populations with high consumption of traditionally fermented products.},
}

@article {pmid41949309,
year = {2026},
author = {Yang, P and Wu, Z and Zhang, S and Yan, L and Yan, Y and Zhou, F and Ren, X and Li, Y and Gu, S and Gao, S and Zhang, Z and Zhang, Y and Zhu, H and Li, H and Zhang, Z},
title = {Predicting dairy cattle PL via longitudinal rumen microbiome dynamics using machine learning approaches.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0296925},
doi = {10.1128/spectrum.02969-25},
pmid = {41949309},
issn = {2165-0497},
abstract = {Aging is a spontaneous biological process involving intricate regulatory mechanisms over time. Studies in mice and humans indicate that the gut microbiota is closely linked to the aging process and plays an important role in it. However, the relationship between the rumen microbiota and aging in dairy cows remains unclear. In this study, we characterized rumen microbial differences across different parities in 341 dairy cows using 16S rRNA amplicon sequencing and identified microbial markers associated with productive lifespan (PL) and farm profitability through machine learning analysis. Our findings reveal that as parity increases, the rumen microbiota undergoes systematic succession: alpha diversity indices significantly decrease, microbial interactions weaken, the abundance of Proteobacteria increases, while the abundance of Bacteroidetes decreases in higher-parity cows. By integrating machine learning with 16S sequencing, we identified characteristic microbial markers predictive of PL and farm profitability. Specifically, the support vector regression model achieved a predictive performance with an area under the curve (AUC) of 0.788 and identified eight key genera associated with the PL of dairy cows. Meanwhile, the random forest (RFTEST) model attained an AUC of 0.763 and selected eight key microorganisms linked to the economic benefits of the farm, with fivefold cross-validation confirming the reliability of RFTEST. Combined with SHapley Additive exPlanations (SHAP) analysis, the genus-level taxa Eubacterium_hallii_group and Prevotella_7 can serve as indicator strains for PL and farm profitability in dairy cows. Therefore, alterations in the rumen microbiota may serve as a key driver of aging in dairy cows. This study aims to provide insights for improving PL and farm profitability through the modulation of rumen microbiota.IMPORTANCEIn the dairy industry, longevity is a critical economic trait that directly impacts overall farm profitability. Although dairy cows have a natural lifespan of approximately 20 years-with optimal productivity often extending beyond the fifth parity-their average PL is only about 2.7 parities. Identifying factors influencing PL is therefore crucial. Given the vital role of the rumen microbiota in regulating dairy performance, milk fat/protein synthesis, and other key physiological processes, elucidating its correlation with PL is essential for developing probiotic interventions to enhance longevity. Furthermore, early detection of aging-associated microbial signatures could facilitate proactive adjustments to feeding strategies. Notably, this is the first study to link parity-driven microbiome succession with PL prediction in dairy cattle. Consequently, by identifying microbial molecular markers linked to PL and potential probiotic targets, this study highlights promising opportunities to improve dairy cow health and advance sustainable dairy farming practices.},
}

@article {pmid41949699,
year = {2026},
author = {Shen, H and Zhang, L and Ma, X and Yin, Y and Wang, J and Tan, B},
title = {Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41949699},
issn = {1869-1889},
abstract = {The human microbiome is a dynamic ecosystem that profoundly influences host physiology through complex molecular interactions. Advances in high-throughput profiling now enable multi-omics measurements at scale, yet integration remains difficult due to biological complexity, technical variability, sparsity, and small cohorts. This review targets bioinformatics practitioners and clinical microbiology researchers applying machine learning to host-microbiome studies. Here, we survey state-of-the-art methods for integrating heterogeneous data types and highlight algorithmic innovations for high dimensionality and small cohorts. We also examine approaches for interpretability that translate mechanistic insight into clinically actionable models. Finally, we outline a standardized benchmarking framework emphasizing open data, rigorous evaluation, and biologically informed architectures. By synthesizing multi-omics measurements with advanced analytics, we chart a pathway toward personalized, microbiome-based therapies while deepening our understanding of host-microbiome crosstalk.},
}

@article {pmid41950008,
year = {2026},
author = {Mifflin, KA and Kigerl, KA and Hudson, LC and Guan, Z and Popovich, PG},
title = {Protocol for performing traumatic spinal cord injury surgery on mice in germ-free isolators and assessing injury recovery and pathophysiology.},
journal = {STAR protocols},
volume = {7},
number = {2},
pages = {104488},
doi = {10.1016/j.xpro.2026.104488},
pmid = {41950008},
issn = {2666-1667},
abstract = {An altered gut microbiome affects recovery from traumatic spinal cord injury (SCI). Here, we present a protocol for performing SCI survival surgery on mice in germ-free isolators. Specifically, we describe steps for colonization, preparing surgical tools, performing surgery, and post-surgical care. We then outline procedures for behavioral assessment, followed by collecting and processing tissue to assess injury recovery and pathophysiology. This protocol can be easily adapted to study the gut microbiome's influence on other forms of central nervous system injury.},
}

@article {pmid41950061,
year = {2026},
author = {Dayman, NA and Patel, D and Wisniewska, A and Fletcher, E and Ahmed, MI and Modha, D and Barer, MR and Gaillard, EA},
title = {Face mask sampling for the detection of microbes in expelled aerosols and the impact of airway clearance on microbial yield in children with cystic fibrosis: a feasibility trial.},
journal = {Journal of medical microbiology},
volume = {75},
number = {4},
pages = {},
doi = {10.1099/jmm.0.002150},
pmid = {41950061},
issn = {1473-5644},
mesh = {Humans ; *Cystic Fibrosis/microbiology ; Child ; Male ; Female ; Adolescent ; Child, Preschool ; *Masks/microbiology ; Prospective Studies ; Cross-Sectional Studies ; Feasibility Studies ; Infant ; Sputum/microbiology ; *Bacteria/isolation & purification/classification ; Specimen Handling/methods ; Pseudomonas aeruginosa/isolation & purification ; Aerosols ; *Respiratory Tract Infections/microbiology/diagnosis ; },
abstract = {Background. Early identification of pulmonary exacerbations is vital for the management of cystic fibrosis (CF). Non-invasive airway sampling in preschool children can be inaccurate. Face mask sampling (FMS) is a novel non-invasive approach that can be used to assess microbial airway pathogens in patients with CF.Methods. Prospective cross-sectional study in children with CF. Children wore a suitably sized face mask fitted with two strips of a polyvinyl alcohol sampling matrix for a period of 15 min. Routine microbiology sampling using cough swab, sputum and/or bronchoalveolar lavage was completed following FMS. Children then completed their routine airway clearance with their physiotherapist. Following this, a separate face mask was worn for a further 15 min, after which further routine microbiology sampling (cough swab or sputum) was completed. The face masks were stored at room temperature before transfer and processing in the laboratory to quantify bacterial burden and identify key pathogens such as Mycobacterium abscessus and Pseudomonas aeruginosa.Results. Eleven children (six male, median age 12 years, range 1-16 years), from the Leicester CF cohort were included. All patients tolerated the FMS. Nine face mask samples from 11 participants isolated respiratory pathogens, including M. abscessus (n=3). P. aeruginosa was not detected on face mask samples. There was a trend towards an increase in microbial yield (prGen16s) following airway clearance (n=5), but this did not reach statistical significance.Conclusions. FMS systems are feasible for children and young people with CF. They may provide an effective method to detect exhaled lower airway pathogens including non-tuberculous mycobacteria. The effect of physiotherapy on the exhaled microbiome needs to be explored further.},
}

Humans
*Cystic Fibrosis/microbiology
Child
Male
Female
Adolescent
Child, Preschool
*Masks/microbiology
Prospective Studies
Cross-Sectional Studies
Feasibility Studies
Infant
Sputum/microbiology
*Bacteria/isolation & purification/classification
Specimen Handling/methods
Pseudomonas aeruginosa/isolation & purification
Aerosols
*Respiratory Tract Infections/microbiology/diagnosis

@article {pmid41950213,
year = {2026},
author = {Babbo, CC and van Rensburg, J and Mellet, J and Velaphi, SC and Nakwa, FL and Masemola, MYK and Kali, GTJ and Foden, CJ and Oosthuizen-Vosloo, S and Chellan, V and Mosuwe, O and Mistry, P and Buyens, ARM and Barmania, F and Pillay, S and Ballot, DE and Coetzee, M and Horn, AR and Wright, C and Schubertand, PT and Pepper, MS},
title = {Protocol: A multi-factorial, multi-centre study, for biomarker identification in healthy controls for comparison to babies with moderate-severe NESHIE.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0346798},
pmid = {41950213},
issn = {1932-6203},
mesh = {Humans ; Infant, Newborn ; *Biomarkers/blood/analysis/metabolism ; *Hypoxia-Ischemia, Brain/genetics/metabolism/diagnosis ; Female ; Male ; DNA Methylation ; Case-Control Studies ; },
abstract = {Neonatal encephalopathy suspected to be hypoxic-ischaemic encephalopathy (NESHIE) remains a leading cause of neonatal mortality and long-term neurodevelopmental impairment, particularly in low- and middle-income countries. While therapeutic hypothermia reduces mortality in moderate to severe cases, a significant proportion of affected infants continue to experience adverse neurological outcomes. This multi-centre observational study aims to elucidate the clinical and biological mechanisms underlying NESHIE by conducting a comprehensive comparative analysis of neonates with moderate to severe NESHIE and healthy term controls. Participants with NESHIE were previously recruited under an existing approved protocol (University of Pretoria ethics reference: 481/2017), and healthy neonates will be newly enrolled. The study will integrate clinical and molecular data to: (1) identify clinical risk factors associated with NESHIE; (2) perform whole genome sequencing to detect relevant genetic variants; (3) analyse DNA methylation patterns via bisulfite sequencing; (4) assess gene expression using bulk and single-cell RNA sequencing (RNA-seq); (5) characterise proteomic and metabolomic profiles through liquid chromatography-mass spectrometry of dried blood spot samples; (6) examine the placental microbiome; and (7) evaluate placental histopathological differences between groups. By offering a multi-dimensional view of the molecular and microbial landscape of NESHIE in a South African cohort, this study aims to enhance understanding of the disease pathogenesis. Ultimately, the findings may support the development of biomarkers for early diagnosis, improve risk stratification, and guide novel therapeutic strategies for affected neonates. The study has received National Health Research Database (NHRD) registration under GP_202411_053 (Gauteng) and WC_202411_026 (Western Cape), with ethics approvals granted by the University of Pretoria (184/2024), University of the Witwatersrand (250406B), and Stellenbosch University (N24/12/154_RECIP_UP184/2024) as well as their respective tertiary academic hospitals.},
}

Humans
Infant, Newborn
*Biomarkers/blood/analysis/metabolism
*Hypoxia-Ischemia, Brain/genetics/metabolism/diagnosis
Female
Male
DNA Methylation
Case-Control Studies

@article {pmid41950528,
year = {2026},
author = {Federico, VA and Cliffel, DE and Gaddy, JA and Townsend, SD},
title = {Shaping of the Infant Gut Microbiome by Milk Oligosaccharides.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051024-062915},
pmid = {41950528},
issn = {1545-4509},
abstract = {The gut microbiome governs aspects of human growth and development. While human milk's primary purpose is metabolism, it also provides nonnutritious biologics and macromolecules. This mixture includes the human milk oligosaccharides (HMOs), which are indigestible and survive the low pH of the stomach and small intestine, reaching the large intestine intact. Here, HMOs serve as prebiotics for beneficial bacteria, providing a competitive growth advantage over potential pathogens. Upon metabolizing HMOs, commensals generate short-chain fatty acids and metabolites that enhance the gut community. Therefore, HMOs work to develop and sustain the gut microbial community as a living therapeutic that prevents illness from potential microbial pathogens and modulates development of the infant gut. The goal of this targeted review is to characterize the roles HMOs play in governing bacterial and viral members of the infant gut microbiome, describing how HMOs both define a healthy microbiota and prevent microbial dysbiosis.},
}

@article {pmid41950533,
year = {2026},
author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X},
title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128511},
doi = {10.1016/j.micres.2026.128511},
pmid = {41950533},
issn = {1618-0623},
abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.},
}

@article {pmid41950535,
year = {2026},
author = {Adeniji, A and Liu, Q and Huang, X and Lu, X and Li, S and Guo, R},
title = {Correlation between root exudate composition and beneficial bacteria underlies Fusarium wilt resistance in cucumber.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128512},
doi = {10.1016/j.micres.2026.128512},
pmid = {41950535},
issn = {1618-0623},
abstract = {Rhizosphere microbes regulated by root exudates play important roles in promoting plant growth and suppressing soil-borne diseases. However, their functions in monoculture systems are not well studied. Here, we integrated metabolomic and microbiome analyses to compare root exudate profiles and rhizosphere communities of Fusarium oxysporum f. sp. cucumerinum (Foc) resistant (CL11) and susceptible (ZN6) cultivars grown in naturally infested, continuous-cropping soil. The asymptomatic, resistant cultivar CL11 (CL11H) exhibited a metabolic signature enriched in defensive compounds (ganoderic acid I and L-isoleucine) and harbored a beneficial bacterial community dominated by Streptomyces, Cellvibrio, and Ensifer. While the asymptomatic susceptible cultivar ZN6 (ZN6H) showed elevated levels of primary metabolites (methylmalonic and succinic acids) and an enrichment in the relative abundance of Amycolatopsis and Flavobacterium. Upon symptom development, susceptible symptomatic ZN6 (ZN6D) mounted a "cry-for-help" response, accumulating L-tryptophan and citric acid, which correlated with recruitment of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. Conversely, resistant symptomatic CL11 (CL11D) deployed a metabolic profile (L-3-cyanoalanine, 4-hydroxybenzoyl glucose, D-fructose), which enriched Bacillus and Cellvibrio. Exogenous application of citric acid, L-isoleucine, L-tryptophan, hexadecanedioic acid, and succinic acid to susceptible ZN6 plants significantly suppressed wilt disease. These metabolites restructured the rhizosphere bacterial communities, demonstrated by enrichments of Pseudomonas, Burkholderia-Caballeronia-Paraburkholderia, and Comamonadaceae by L-tryptophan, as well as Pseudomonas and Bacillus promoted by L-isoleucine and citric acid, respectively. Moreover, succinic acid suppressed disease through microbiome-mediated mechanisms despite its in vitro positive effect on Foc growth. These findings demonstrate that root exudates are linked to cultivar-specific disease outcomes, and that target metabolite application can suppress Fusarium wilt through microbiome-mediated mechanisms or a combined antifungal mode.},
}

@article {pmid41950737,
year = {2026},
author = {Jung, Y and Yeo, S and Kim, RH and Seo, CH and Joo, SY and Shin, JH and Cho, YS},
title = {Response to antihistamines in post-burn pruritus is associated with gut microbiota composition and function: A prospective cohort study with a nested case-control analysis.},
journal = {Burns : journal of the International Society for Burn Injuries},
volume = {52},
number = {5},
pages = {108005},
doi = {10.1016/j.burns.2026.108005},
pmid = {41950737},
issn = {1879-1409},
abstract = {Post-burn pruritus (PBP) is a common complication following burn injuries, with substantial interindividual variability in response to antihistamine treatment. While altered gut microbial communities have been observed in patients with histamine intolerance, no studies have examined the relationship between gut microbiota and antihistamine responsiveness in burn patients. Therefore, we hypothesized that the gut microbiome composition differs according to antihistamine responsiveness in patients with PBP. A total of 56 male burn patients categorized into no-pruritus, antihistamine-responsive (HR), and antihistamine-nonresponsive (HNR) groups. Fecal samples were collected at baseline and after 8 weeks of antihistamine treatment. Microbial composition was analyzed using 16S rRNA gene sequencing, and functional prediction was conducted with PICRUSt2. Overall microbial diversity did not differ significantly between groups; however, distinct taxonomic and functional features were identified. The HR group was characterized by enrichment of Sutterella and showed a temporal increase in microbial diversity and Bifidobacterium abundance after 8 weeks of treatment, accompanied by enrichment of redox-related microbial functions. In contrast, the HNR group showed increased Akkermansia and Acidaminococcus with reduced antioxidant defenses and activation of non-histaminergic pruritic pathways. This study is the first to suggest that gut microbiota composition and function are associated with antihistamine responsiveness in patients with PBP. Distinct microbial signatures and functional pathways were identified among non-pruritic individuals, antihistamine responders, and non-responders. Our findings indicate a potential involvement of gut microbes in the pathophysiology of PBP and highlight the possibility of microbiota-targeted therapeutic strategies.},
}

@article {pmid41938779,
year = {2026},
author = {Luttenschlager, H and Noel, G and Alabi, T and Carpentier, J and Francis, F and Megido, RC},
title = {Microbial drivers of Black Soldier Fly biowaste valorization: from microbiome functions to scalable insect-microbe systems.},
journal = {AIMS microbiology},
volume = {12},
number = {1},
pages = {126-149},
pmid = {41938779},
issn = {2471-1888},
abstract = {Biowaste and agro-industrial co-products continue to increase with population growth and rising living standards, calling for scalable valorization strategies that go beyond simple mineralization. The black soldier fly (BSF) has emerged as a practical bioconversion platform capable of channeling biodegradable organic waste into high-value proteins, lipids, and chitin. In parallel, microbial interventions are increasingly recognized as key levers for substrate conditioning, process stabilization, and performance optimization in BSF-based systems. In this review, we adopted a function-first perspective to examine how microbial processes shape and connect three major biological valorization routes: aerobic composting, anaerobic digestion (AD), and BSF bioconversion. Rather than focus on taxonomic inventories, we synthesized evidence on microbial functions that matter in practice, including extracellular hydrolysis of complex polymers, regulation of short-chain fatty acids, detoxification and pathogen suppression, and process stabilization. We further reviewed microbe-assisted strategies, such as lactic pre-fermentation, directed acidogenesis, and probiotic or defined consortia and their effects on waste reduction, conversion efficiency, product quality, and sanitary safety. Finally, we translated these microbial mechanisms into scalable design principles for configuring and operating integrated insect-microbe systems, highlighting how microbial functions underpin reproducible, enterprise-ready performance across composting, AD, and BSF-integrated workflows.},
}

@article {pmid41938782,
year = {2026},
author = {Mataragka, A and Ringø, E and Papastathis, AK},
title = {Climate-driven restructuring of sediment microbiomes and ecosystem functions in aquaculture systems.},
journal = {AIMS microbiology},
volume = {12},
number = {1},
pages = {150-172},
pmid = {41938782},
issn = {2471-1888},
abstract = {Aquaculture expansion is occurring under accelerating climatic pressure. Warming, marine heatwaves, deoxygenation, salinity fluctuation, and intensified nutrient loading act simultaneously in aquaculture sediments, altering redox gradients and substrate fluxes that structure microbial communities. These stressors strengthen deterministic environmental filtering, reorganize interaction networks toward reduced-state dominance, and redistribute functional investment within sediment microbiomes; the biogeochemical engines regulating nutrient cycling, water quality, and disease dynamics. Such restructuring is associated with altered nitrogen processing, modified greenhouse gas fluxes, sulfide accumulation, enhanced pathogen performance, and enrichment of antimicrobial resistance determinants, with direct implications for production stability and disease risk. Evidence is synthesized to integrate quantified environmental forcing, ecological assembly mechanisms, and molecular functional responses into a unified framework linking microbial restructuring to ecosystem performance and operational resilience. Structural and functional microbial indicators suitable for early detection of redox compression and functional destabilization are evaluated, alongside resilience-oriented strategies spanning ecological design, microbiome management, engineering control, and adaptive monitoring. Despite substantial empirical progress, major gaps remain in resolving compound-stressor interactions, temporal reversibility, cross-system threshold comparability, and predictive modeling of microbial assembly under multi-driver forcing. Addressing these gaps is essential for developing mechanistically grounded, climate-resilient aquaculture systems.},
}

@article {pmid41938867,
year = {2026},
author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R},
title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779554},
pmid = {41938867},
issn = {2235-2988},
mesh = {Female ; Humans ; Phylogeny ; *Candidiasis, Vulvovaginal/virology/microbiology ; Genome, Viral ; Vagina/virology/microbiology ; Metagenomics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Adult ; *Double Stranded RNA Viruses/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.

METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.

RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.

DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.},
}

Female
Humans
Phylogeny
*Candidiasis, Vulvovaginal/virology/microbiology
Genome, Viral
Vagina/virology/microbiology
Metagenomics
Capsid Proteins/genetics
RNA, Viral/genetics
RNA-Dependent RNA Polymerase/genetics
Adult
*Double Stranded RNA Viruses/genetics/isolation & purification/classification

@article {pmid41939093,
year = {2026},
author = {},
title = {Gut microbiome metaproteomics for colorectal cancer risk stratification: moving from taxonomic signatures to functional protein biomarkers: Retraction.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {4},
pages = {2724},
pmid = {41939093},
issn = {2049-0801},
abstract = {[This retracts the article DOI: 10.1097/MS9.0000000000004567.].},
}

@article {pmid41939102,
year = {2026},
author = {Mohan, A and Sultany, A and Fatima, SB and Hasan, ZW and Butt, MD and Alkhazender, AHJ and Lal, PM and Aminpoor, H and Karimi, H and Kumar, V and Tejwaney, U and Kumar, S},
title = {Association between atrial fibrillation and gastrointestinal bleeding: pathophysiology, risk stratification, and management - a narrative review.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {4},
pages = {2566-2573},
pmid = {41939102},
issn = {2049-0801},
abstract = {Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, significantly increasing the risk of thromboembolic events, necessitating anticoagulation therapy. However, anticoagulation, particularly with novel oral anticoagulants, elevates the risk of gastrointestinal bleeding (GIB), creating a clinical dilemma in managing AF patients. This narrative review explores the pathophysiology linking AF and GIB, emphasizing the hypercoagulable state in AF and the mucosal damage caused by anticoagulants. Epidemiological data reveal that GIB incidence in AF patients ranges from 1.32% to 5.4% annually, with risk factors including older age, prior GIB, and concomitant antiplatelet use. Risk stratification tools such as CHA2DS2-VASc and HAS-BLED aid in balancing thromboembolic and bleeding risks, though their predictive performance remains modest. Comparative studies highlight that rivaroxaban carries a higher GIB risk, while apixaban offers a safer profile. Management strategies include proton pump inhibitors for prophylaxis, endoscopic interventions for acute bleeding, and individualized decisions on resuming anticoagulation post-GIB, typically within 7-30 days. Emerging research on the gut microbiome's role in AF pathogenesis suggests potential novel therapeutic avenues. A multidisciplinary approach involving cardiologists, gastroenterologists, and hematologists is essential to optimize outcomes. Future directions include developing safer anticoagulants, refining risk prediction models, and exploring microbiome-targeted therapies.},
}

@article {pmid41939187,
year = {2026},
author = {Zhang, H and Wu, ZH and Sun, XM and Sun, C and Chang, J and Yuan, L},
title = {Gender-specific and dose-dependent responses to L-se-methylselenocysteine are mediated by the gut microbiota-metabolite axis: implications for intestinal homeostasis and safe clinical application.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1803630},
pmid = {41939187},
issn = {2296-861X},
abstract = {INTRODUCTION: L-Se-methylselenocysteine is a prominent naturally occurring organic selenium compound with notable health benefits and validated efficacy in managing various diseases. However, its impacts on intestinal microecology and the role of the gut microbiota-metabolite axis in mediating host health outcomes remain unclear.

METHODS: Sprague-Dawley rats were subjected to a 90-day chronic toxicity study, combined with integrated intestinal microbiome and metabolome analysis, to explore L-Se-methylselenocysteine's effects and underlying mechanisms.

RESULTS: L-Se-methylselenocysteine at doses of 0.25-0.75 mg/kg bw/ day enhanced gut microbiota biodiversity, enriched probiotic abundance, ameliorated hematological and serum biochemical indices, and promoted synthesis of beneficial metabolites via modulating the gut microbiota-metabolite axis. Notably, high-dose L-Se-methylselenocysteine (2.25 mg/kg bw/day) induced irreversible hepatosplenic injury in female rats but not males, with gender-specific responses mediated by the axis.

DISCUSSION: L-Se-methylselenocysteine confers intestinal health benefits through the gut microbiota-metabolite axis, while defining a safe dosage range. This study provides a solid scientific basis for the rational application of L-Se-methylselenocysteine as a selenium supplement.},
}

@article {pmid41939240,
year = {2026},
author = {Barrera-Suarez, MA and Zhao, CY and Karnatovskaia, LV and Sung, J},
title = {Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2650247},
pmid = {41939240},
issn = {2993-3935},
abstract = {Diet-gut microbiome interactions drive substantial inter-individual variability in metabolic responses to food, a fact that challenges the efficacy of uniform dietary recommendations. To address this complexity, advances in multi-omics profiling, dietary assessment technologies, and host clinical phenotyping now generate high-resolution multimodal datasets. However, managing these vast amounts of data necessitates the integration of artificial intelligence (AI) and machine learning (ML) approaches. In this review, we first delineate the multimodal data landscape and its associated computational workflows. These range from the initial preprocessing of heterogeneous inputs (filtering, normalization, dimensionality reduction) to ML modeling strategies designed to address high dimensionality, sparsity, and compositionality through feature engineering and regularization. We then summarize core ML applications, including the classification of habitual dietary patterns from microbiome signatures, prediction of postprandial metabolic responses, responder stratification, and in silico simulation of dietary perturbations. Furthermore, recent randomized controlled trials demonstrate the tangible clinical potential of AI-guided personalization. Next, we highlight composite microbiome health metrics and diet-specific indices, such as GMWI2 and DI-GM. These tools are essential because they condense high-dimensional taxonomic profiles into interpretable wellness scores for monitoring diet-induced shifts. We subsequently examine genome-scale metabolic models and microbiome "digital twins" that mechanistically link dietary substrates to community metabolism and host-relevant metabolites. We also discuss emerging hybrid AI-mechanistic frameworks that enhance interpretability, biological plausibility, and scalability. Finally, we outline translational priorities-including the development of diverse longitudinal cohorts, standardized benchmarking, and clinically trustworthy AI-that are required to realize equitable, microbiome-informed precision nutrition.},
}

@article {pmid41939241,
year = {2026},
author = {Pereira, FC and El Aidy, S},
title = {Drug-microbiome interactions: What we know and why predictive translation remains elusive.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2649166},
pmid = {41939241},
issn = {2993-3935},
abstract = {Medication-induced alterations of the gut microbiome influence drug efficacy, toxicity, and long-term outcomes. Despite extensive evidence for drug-microbe interactions, predictive translation into clinical practice remains limited. Generalization from shifts in taxonomic profiles, mechanistic studies or isolated enzymatic assays is challenging because microbial activity is highly context-dependent. Drug-microbiome interactions are shaped by host factors including pH, transit time, nutrient and cofactor availability, and spatial organization along the gastrointestinal tract. Here, we argue that predictive translation requires measuring functional outputs, site-specific activity, ecological interactions, and host-contextual modulation, rather than static microbial properties.},
}

@article {pmid41939697,
year = {2026},
author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M},
title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786817},
pmid = {41939697},
issn = {1664-302X},
abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.},
}

@article {pmid41939699,
year = {2026},
author = {Zeng, H and Gao, Z and Wang, Z and Li, K and Xu, B and Yan, Z and Gu, Y and Du, W and Ding, H and Wang, J},
title = {Temporal succession and assembly of marine bacterial communities in Maxwell Bay, Antarctica during summer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1748960},
pmid = {41939699},
issn = {1664-302X},
abstract = {INTRODUCTION: In recent years, ecological feedbacks driven by climate change have become increasingly prominent. The polar amplification effect has made Antarctic ecosystems pivotal indicators for reflecting global climatic impacts. As core drivers of biogeochemical cycling, marine microbes play a central role. Therefore, deciphering their temporal dynamics and assembly mechanisms is crucial for projecting the trajectories of polar ecosystems. However, the intrinsic ecological processes regulating microbial summer succession, particularly the relative contribution of deterministic processes, remain insufficiently quantified.

METHODS: In the present study, Maxwell Bay, Antarctica-a coastal marine region heavily influenced by glacial melt-was selected as the model system. Surface seawater samples were collected sequentially during the 2022 austral summer, followed by 16S rRNA gene amplicon sequencing and phylogenetic null model analysis.

RESULTS: Our results revealed a distinct shift in the assembly mechanisms of bacterial communities. In January, community structure was shaped jointly by stochastic and deterministic processes, with stochastic processes contributing a greater proportion to assembly. This state transitioned to the predominance of deterministic homogeneous selection (84.68%) in February. Mantel tests, followed by linear regression analyses, confirmed that this phylogenetic transition was driven by shifting environmental factors. Specifically, water temperature served as the primary influencing factor in January, whereas silicate and nitrate concentrations emerged as the key factors in February. Subsequent partial least squares path modeling (PLS-PM) and redundancy analysis (RDA) further validated these findings, demonstrating that the identified environmental variables collectively explained more than 50% of the observed variation in community structure. Notably, nitrate drawdown was significantly correlated with the increased relative abundances of dominant bacterial genera in February.

DISCUSSION: By quantifying the relative roles of deterministic and stochastic processes in microbial community assembly, this study demonstrates that environmental selection is the dominant factor mediating microbial responses to polar warming. These findings provide a mechanistic foundation for the development of predictive models for future marine biogeochemical cycles in polar regions.},
}

@article {pmid41939702,
year = {2026},
author = {Shi, Y and Chu, H and He, R and Ma, W and Liang, Q and Li, Z and Gao, Y and Luo, C},
title = {Harnessing rhizosphere microbes: the synergistic roles of PGPR and AMF in sustainable tomato production under stress.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1746930},
pmid = {41939702},
issn = {1664-302X},
abstract = {Tomato (Lycopersicon esculentum L.) is among the most economically important vegetable crops worldwide, yet its production is severely constrained by multiple biotic and abiotic stresses, including pathogens, pests, drought, salinity, and heavy metal toxicity. Amid intensifying climate change and increasing demands for sustainable agriculture, plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) have emerged as key beneficial rhizospheric microorganisms with significant potential for enhancing plant stress tolerance and promoting growth. PGPR directly promote the growth of tomato plants through biological nitrogen fixation, solubilization of phosphate and potassium, siderophore-mediated iron uptake, and the production of phytohormones. Indirectly, PGPR suppress pathogens, activate induced systemic resistance (ISR), reinforce cell walls, enhance the activities of antioxidant enzymes, and regulate the accumulation of osmolytes. AMF form symbiotic associations with the roots of tomato plants, enhancing nutrient and water absorption via extraradical mycelial networks, improving phosphorus and nitrogen uptake, modulating abscisic acid (ABA), jasmonic acid (JA), and strigolactone signaling pathways, activating mycorrhiza-induced resistance (MIR), and enhancing photosynthetic efficiency and water-use efficiency under stress. The co-inoculation of PGPR and AMF yields synergistic effects by facilitating mutual colonization, optimizing nutrient bioavailability, coordinately strengthening antioxidant and osmotic regulation systems, and reinforcing systemic defense responses, thereby conferring more robust and efficient stress tolerance than single inoculations. Despite significant advances, key challenges persist in elucidating tripartite molecular crosstalk, maintaining stability during field applications, and developing tailored microbial consortia. This review synthesizes the individual and synergistic mechanisms through which PGPR and AMF enhance the resilience of tomato plants to biotic and abiotic stresses, offering valuable insights for engineering microbial communities to enhance stress resistance in crops.},
}

@article {pmid41939703,
year = {2026},
author = {Liao, HY and Ren, YS and Li, J and Huang, HT and Li, ZL and Zeng, Y and Zhu, DH},
title = {Geographical variation of Ceracris kiangsu gut microbiota and its association with environmental factors.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1752887},
pmid = {41939703},
issn = {1664-302X},
abstract = {The yellow-spined bamboo locust (Ceracris kiangsu) is one of the most destructive forest pests in China, causing severe damage to bamboo forests across multiple provinces. Understanding the relationship between its gut microbiota and environmental factors is crucial for revealing its ecological adaptability and migration potential. This study used 16S rRNA high-throughput sequencing to analyze gut bacterial communities of C. kiangsu from six geographically distinct populations in China. The results showed that Firmicutes and Proteobacteria were the dominant phyla, while bacterial diversity and composition varied significantly among populations. Precipitation and sunshine duration were identified as the main environmental factors most strongly associated with microbial community structure. These findings suggest that environmental conditions are strongly associated with variation in the gut microbiota of C. kiangsu, potentially affecting its adaptability and outbreak dynamics. This research provides new insights into the ecological mechanisms underlying pest distribution and offers a microbiome-based foundation for developing sustainable control strategies to reduce the agricultural and forestry losses caused by this species.},
}

@article {pmid41939705,
year = {2026},
author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP},
title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768977},
pmid = {41939705},
issn = {1664-302X},
abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.},
}

@article {pmid41939710,
year = {2026},
author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J},
title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741638},
pmid = {41939710},
issn = {1664-302X},
abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.},
}

@article {pmid41939716,
year = {2026},
author = {Zhang, B and Zhao, J and Zhuang, L and Liu, Y and Meng, P and Wang, S and Liu, Y and Zhang, T and Xu, J and Qin, W},
title = {Peat promotes production of the edible mushroom Oudemansiella raphanipes by regulating casing soil microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1774800},
pmid = {41939716},
issn = {1664-302X},
abstract = {INTRODUCTION: As an exotic edible mushroom, Oudemansiella raphanipes has attracted extensive attention for efficient cultivation. Peat-amended casing soil is known to increase its productivity, while the underlying mechanisms remain unclear.

METHODS: In this study, high-throughput 16S rRNA gene sequencing was performed to characterize bacterial communities in casing soils with five peat proportions.

RESULTS: Results showed that peat proportion had a significant effect on O. raphanipes yield, with the 70% peat treatment achieving the maximum yield of 279.21 g per cultivation bag, 38.12% higher than the control without peat. Casing soil with 70% peat harbored higher bacterial richness, enriched beneficial taxa such as Paenisporosarcina, enhanced chemoheterotrophy and nitrogen fixation functions, and more deterministic community assembly compared with other treatments. The bacterial ecological network in casing soil with 70% peat also showed the highest average connectivity, shortest average path length, and strongest robustness. Further, soil physical properties had a greater influence on bacterial community structure in the casing soil than chemical properties. Soil density, available phosphorus and potassium significantly influenced the bacterial community in the 70% peat group.

CONCLUSION: Together, this study suggested that peat promoted O. raphanipes production by regulating the casing soil microbiome, providing a theoretical basis for optimizing practical cultivation strategies.},
}

@article {pmid41939722,
year = {2026},
author = {Ryan, SM and Brayden, DJ},
title = {Food-derived molecules as regulators of intestinal tight junctions and barrier function: mechanisms and implications.},
journal = {Frontiers in drug delivery},
volume = {6},
number = {},
pages = {1692219},
pmid = {41939722},
issn = {2674-0850},
abstract = {Controlling TJ permeability in the small intestine facilitates nutrient absorption, maintains luminal osmotic balance, and prevents the paracellular entry of pathogens. The pharmaceutical industry has leveraged the capacity of medium-chain fatty acids and their derivatives to transiently and reversibly open epithelial TJs in formulations to enable oral administration of therapeutic peptides, some of which have received regulatory approval or are progressing in advanced clinical trials. Other food-derived agent including chitosan and its analogues enhance mucoadhesion and also modulate TJ permeability in the intestine. Recently, pelargonidin, a polyphenolic pigment isolated from strawberries, has emerged as a promising food-derived TJ opener, facilitating oral insulin delivery in rat models. Conversely, other food or food-derived molecules reinforce TJ integrity while exerting antioxidant effects, thereby offering potential therapeutic benefits for conditions characterized by increased intestinal permeability including inflammatory bowel disease, sepsis, and coeliac disease. Examples of such agents include the short-chain fatty acid (SCFA), sodium butyrate, various essential and non-essential amino acids, fermented food, the trace element, zinc, and anthocyanins. The exploration of food-derived substances as modulators of intestinal epithelial TJ dynamics is still in its early stages but holds significant promise for future health applications.},
}

@article {pmid41939734,
year = {2026},
author = {Puppo, F and Carbone, RG},
title = {Microbiome in connective tissue diseases associated interstitial lung disease.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1738689},
pmid = {41939734},
issn = {2296-858X},
abstract = {Microbiome consists of a large community of bacteria, yeast, protozoa, and viruses that co-exist in symbiosis with human hosts. Changes in microbiome, named "dysbiosis," alter the interplay between microbiome and immune system triggering inflammation and contributing to the pathogenesis of connective tissue diseases (CTD). Interstitial lung diseases (ILD) are a group of pulmonary disorders characterized by lung tissue fibrosis and impaired lung function. The existence of a gut-lung axis is well demonstrated; however, it is not established whether gastrointestinal dysbiosis contributes to ILD development. ILD represent a major cause of morbidity and mortality in CTD patients. Lung microbiome changes and high microbial load are associated with worse prognosis and acute exacerbations in patients with CTD-ILD and especially in those affected by rheumatoid arthritis, systemic sclerosis and dermatomyositis. Probiotics are active microorganisms that normalize the intestinal flora and their use has been proposed as potential supportive treatment of CTD-ILD. Present knowledge of the relationships between dysbiosis and CTD-ILD development is largely incomplete and further studies are needed to validate this issue. Aim of this concise review is to report current knowledge on microbiome in CTD-ILD focusing on clinical lung aspects and therapeutic options.},
}

@article {pmid41939772,
year = {2026},
author = {Zheng, B and Shen, X and Han, N and Guo, X and Wan, S},
title = {The microbiota-gut-brain-epigenome axis as a novel therapeutic target for decoding postpartum depression.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1778348},
pmid = {41939772},
issn = {2296-858X},
abstract = {BACKGROUND: Postpartum depression (PPD) is a psychological disorder affecting approximately 10-15% of women following childbirth, with significant implications for maternal and infant well-being. While hormonal fluctuations and psychosocial factors have long been considered primary contributors, recent reports demonstrated that gut microbiome is implicated in modulating maternal mood and behavior. The bidirectional communication between the gut and brain, mediated by microbiota-gut-brain axis, along with genetic and epigenetic modifications, has gained increasing attention as a potential mechanistic pathway in PPD. However, the precise genetic and epigenetic underpinnings of this interaction remain to be elucidated.

OBJECTIVE: This review aims to explore the genetic and epigenetic landscape of postpartum depression, with a significant focus pertinent to gut microbiota role in shaping neurobiological outcomes. By integrating recent findings from genomic, epigenomic, and microbiome research, we seek to elucidate novel mechanistic insights and potential therapeutic avenues.

METHODS: A comprehensive literature search was conducted using public databases, including PubMed, Google Scholar, and NCBI, to identify relevant studies on PPD, gut microbiota, genetics, and epigenetics.

RESULTS: Gut microbiota and neuroimmune modulation: peripartum changes in gut microbiota composition have been linked to immune dysregulation, inflammation, and neurotransmitter imbalances, all of which are implicated in PPD pathophysiology. Genetics and epigenetics of PPD: Genome-wide association studies (GWAS) revealed a profound genetic risk loci associated with PPD. Additionally, DNA methylation, histone modifications, and non-coding RNAs have profound functional implications in gene expression regulation, influencing PPD susceptibility. Epigenetic influence of the gut microbiome: The gut microbiome affects epigenetic modifications, such as DNA methylation and histone acetylation, which may lead to fetal programming and maternal mental health disorders. Choline metabolism and maternal mental health: Choline, an essential nutrient involved in epigenetic regulation, influences gut microbiota composition and brain function. Dysregulation in choline metabolism is associated with higher risk of PPD. Clinical and therapeutic implications: Understanding the genetic and epigenetic mechanisms underlying PPD offers new avenues for personalized therapeutic interventions, including probiotic and prebiotic strategies, microbiome-based treatments, and targeted epigenetic therapies.

CONCLUSION: The interplay between genetics, epigenetics, and gut microbiota represents a novel and promising area of research in understanding postpartum depression. The microbiota-gut-brain axis serves as a crucial mediator in this relationship, influencing neuroimmune regulation, neurotransmitter synthesis, and epigenetic modifications. Future studies should focus on integrating multi-omics approaches to unravel the molecular complexity of PPD and develop targeted interventions aimed at restoring microbiome and epigenetic homeostasis.},
}

@article {pmid41939831,
year = {2026},
author = {Omolo, CA and Yata, VK and Janapati, YK and Dachani, SR},
title = {Editorial: Innovative therapeutic strategies for managing diabetic foot ulcers and mitigating associated complications.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1788742},
pmid = {41939831},
issn = {1663-9812},
}

@article {pmid41939871,
year = {2026},
author = {Tonk-Rügen, M and Schilling, T and Cabezas-Cruz, A and Hoelzle, LE},
title = {Microbiota-immune crosstalk in livestock: implications for tick-borne disease control.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1731518},
pmid = {41939871},
issn = {1664-3224},
mesh = {Animals ; *Livestock/immunology/microbiology ; *Tick-Borne Diseases/immunology/prevention & control/veterinary/microbiology ; *Microbiota/immunology ; Ticks/microbiology/immunology ; },
abstract = {Globally, livestock health, which impacts animal welfare and agricultural productivity, is continuously threatened by tick-borne diseases (TBDs). The growing issues of acaricide overuse in livestock, emerging resistance, and vector adaptation to climate change require novel and sustainable intervention strategies. Recent advances in microbiome research reveal how host and vector microbiota influence immune responses, particularly through natural antibodies (nAbs) that modulate vector competence and pathogen transmission. In livestock, nAbs targeting microbial glycans are heritable, measurable, and linked to health outcomes. In cattle, nAb titers to bacterial antigens are associated with mastitis risk and longevity, while in pigs, early-life nAb levels are proposed as resilience markers. Studies in poultry further demonstrate the importance of high nAb phenotypes for health and production. These findings highlight nAbs as both immunological markers and potential targets for genetic selection to improve disease resistance. Emerging interventions, such as anti-microbiota vaccines and immunobiotics, aim to modulate nAb repertoires, disrupt pathogen colonization, and enhance disease resilience. Additionally, microbial glycans serve as key targets for inducing cross-reactive immunity against TBDs. Manipulation of the livestock microbiota through diet, probiotics, and prebiotics shows promise in diversifying nAb profiles and improving robustness against infection. Despite these advances, research gaps remain, particularly in establishing causality and practical feasibility in livestock systems. This review emphasizes the need for integrative research across immunology, microbiology, and veterinary sciences to leverage microbiota-immune interactions in enhancing livestock resilience against TBDs, exploring how nAbs shaped by the gut microbiota can modulate tick microbiomes and impact pathogen transmission.},
}

Animals
*Livestock/immunology/microbiology
*Tick-Borne Diseases/immunology/prevention & control/veterinary/microbiology
*Microbiota/immunology
Ticks/microbiology/immunology

@article {pmid41939876,
year = {2026},
author = {Li, L and Zhu, G and Chen, M and Qiu, B and Li, Y and Liu, S and Gu, W and Liu, L},
title = {ARG1-polyamine axis: cell-type-specific functions in disease pathogenesis and therapeutic targeting.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1744890},
pmid = {41939876},
issn = {1664-3224},
mesh = {Humans ; *Polyamines/metabolism ; *Arginase/metabolism/antagonists & inhibitors ; Animals ; Neoplasms/metabolism ; },
abstract = {ARG1 catalyzes the conversion of L-arginine to L-ornithine, urea, polyamines, and L-proline, thereby balancing nitrogen detoxification with tissue-specific roles in proliferation and immunity. This review delineates the context-dependent functions of ARG1 across diverse cell types-including tumor cells, immune cells, endothelial cells, keratinocytes, and stem cells. In tumors, ARG1 drives immunosuppression and metabolic reprogramming but can paradoxically suppress tumorigenesis. Immune modulation via ARG1-polyamine crosstalk regulates T cell differentiation, macrophage polarization, and microbiota interactions, influencing infection and autoimmunity. Endothelial ARG1 exacerbates obesity-related vascular dysfunction, while keratinocyte ARG1 impacts wound healing and psoriasis. Emerging therapies-such as ARG1 inhibitors, engineered extracellular vesicles, and microbiome interventions-show preclinical promise in cancer, cardiovascular, and neurodegenerative diseases. By mapping ARG1's spatiotemporal metabolic networks, this work highlights its dual roles and positions ARG1 as a central player for precision medicine in complex pathologies.},
}

Humans
*Polyamines/metabolism
*Arginase/metabolism/antagonists & inhibitors
Animals
Neoplasms/metabolism

@article {pmid41939907,
year = {2026},
author = {Jayaraman, S and Mahalingam, SS and Zhu, Z and Faddoul, F and Paes da Silva, A and Asaad, R and Bhaskaran, N and Schneider, E and Taylor, T and Horne, S and Yoo, A and Zhang, L and Burgener, A and Pandiyan, P},
title = {Enrichment of Candida associated with dysbiosis contributes to mucosal CD4[+]FOXP3[+] regulatory T cell accrual and their dysfunction in aging.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1714595},
pmid = {41939907},
issn = {1664-3224},
mesh = {Humans ; *T-Lymphocytes, Regulatory/immunology/metabolism ; *Dysbiosis/immunology/microbiology ; Middle Aged ; *Aging/immunology ; *Mouth Mucosa/immunology/microbiology ; Male ; Female ; Aged ; *Candida/immunology ; Adult ; Forkhead Transcription Factors/metabolism/immunology ; },
abstract = {Age-associated T cell dysfunction is a defining feature of inflammaging and immunosenescence, the progressive decline in immune competence observed with advancing age. Here we identified the association between aging (defined as age >60) and fungal dysbiosis, notably characterized by increased colonization of Candida species in the oral mucosa. There is also a notable enrichment of other taxa related to the order Saccharomycetales in older individuals. In contrast, younger individuals exhibit a greater abundance of Cryptococcus, Yarrowia, Kluyveromyces, and various Incertae sedis lineages. Further analysis, stratified by HIV status, shows that older individuals in both healthy and HIV+ groups display significantly higher levels of Candida. Gingival tissues reveal that both healthy older group and HIV-positive group exhibit elevated levels of CD4[+]FOXP3[+] regulatory T cells (Tregs) along with increased salivary concentrations of soluble TLR-2 and IL-6 compared to younger healthy group. Importantly, the abundance of Candida is positively correlated with elevated levels of mucosal Tregs, dysfunctional Tregs (TregDys), and hyperactivated CD4[+] T cells. In vitro experiments provided mechanistic insights by further demonstrating that Candida can induce both proliferation and dysfunction of Tregs in an IL-6 dependent manner, supporting the notion that Candida plays a role in oral T cell senescence and inflammaging. Collectively, these findings underscore a direct relationship between the commensal mycobiome and Treg population, which normally promotes mucosal homeostasis but becomes susceptible to dysfunction with aging.},
}

Humans
*T-Lymphocytes, Regulatory/immunology/metabolism
*Dysbiosis/immunology/microbiology
Middle Aged
*Aging/immunology
*Mouth Mucosa/immunology/microbiology
Male
Female
Aged
*Candida/immunology
Adult
Forkhead Transcription Factors/metabolism/immunology

@article {pmid41939911,
year = {2026},
author = {Zhao, WY and Zhao, JW},
title = {Pancreatic cancer immunotherapy biomarkers: from traditional markers to multimodal integration and dynamic monitoring.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1686658},
pmid = {41939911},
issn = {1664-3224},
mesh = {Humans ; *Pancreatic Neoplasms/therapy/diagnosis/immunology ; *Biomarkers, Tumor ; *Immunotherapy/methods ; *Carcinoma, Pancreatic Ductal/therapy/immunology/diagnosis ; Animals ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains an intractable cancer marked by delayed diagnosis, rapid progression, and significant resistance to current treatments. Conventional biomarkers, such as CA19-9, have insufficient sensitivity and specificity. Meanwhile, the practical use of newer markers such as the tumor mutational burden and microsatellite instability is limited by the absence of standardized testing protocols and definitive threshold values. Circulating tumor DNA and exosomal miRNA hold promise for continuously tracking tumor dynamics and effectiveness of immunotherapy, but additional validation is necessary before their routine clinical application. Recent advancements in multiomics, nanotechnology, and artificial intelligence have opened new possibilities for more accurate and comprehensive biomarkers. For instance, Shah et al. developed shortwave-infrared-emitting nanoprobes to specifically target CD8[+] cytotoxic T cells, permitting high-sensitivity in vivo imaging in breast cancer models. Batool et al. utilized nanoplasmonic sensors to detect changes in serum programmed death-ligand 1 and cytokine levels within 1-2 weeks post-treatment, achieving picomolar sensitivity. Chang et al. combined fluorescence and photoacoustic imaging in the NanoTrackThera platform, facilitating the real-time monitoring of immunotherapy efficacy. This review highlights the evolution of PDAC biomarkers from traditional markers to multimodal integration and dynamic monitoring. The limitations of current markers and potential of emerging technologies, including metabolic reprogramming markers, epigenetic regulators, and AI-driven predictive models, are discussed. Future directions include multicenter prospective trials to validate multimodal models, standardize detection methods, and increase interdisciplinary collaboration. By integrating genomic, epigenetic, metabolic, and microbiome data, these models can better capture the complexity of PDAC, thereby improving patient outcomes through precision immunotherapy.},
}

Humans
*Pancreatic Neoplasms/therapy/diagnosis/immunology
*Biomarkers, Tumor
*Immunotherapy/methods
*Carcinoma, Pancreatic Ductal/therapy/immunology/diagnosis
Animals

@article {pmid41939913,
year = {2026},
author = {Van Doorn, J and Brooks, SR and LiCausi, F and Zhou, K and Betrapally, NS and Gubitz-Hess, E and Cougnoux, A and Dell'Orso, S and Islam, S and Colbert, RA and Navid, F},
title = {Rapamycin treatment ameliorates HLA-B27-mediated gut inflammation and alters the microbiome in experimental spondyloarthritis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1755132},
pmid = {41939913},
issn = {1664-3224},
mesh = {Animals ; *HLA-B27 Antigen/genetics/immunology ; *Sirolimus/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Rats ; Rats, Transgenic ; Disease Models, Animal ; Cytokines/metabolism/genetics ; *Spondylarthritis/drug therapy/immunology/microbiology ; Humans ; Male ; Inflammation/drug therapy ; Colon/drug effects/immunology/microbiology/pathology ; },
abstract = {OBJECTIVE: To determine whether rapamycin affects HLA-B27-mediated gut inflammation in experimental spondyloarthritis (SpA).

METHODS: HLA-B27/human β2-microglobulin transgenic (B27-Tg) rats with gut inflammation were treated with rapamycin (1.5 mg/kg intraperitoneally, 3 times a week) or vehicle for 5 weeks. Healthy age-matched wild type (WT) rats were treated in parallel. Gut inflammation was evaluated via stool scoring and histological assessment. Transcriptome and microbiome analyses were performed on colon tissue and cecal luminal contents, respectively. Bulk immune cells were isolated from the colonic lamina propria of B27-Tg and WT animals, treated with rapamycin ex vivo, and pro-inflammatory cytokine expression was measured using qPCR.

RESULTS: Rapamycin treatment reduced stool and colon histological scores in B27-Tg rats compared to vehicle-treated B27-Tg controls. Transcriptome analysis revealed that rapamycin reduced expression of key pro-inflammatory cytokines like Il17a, Il17f, Tnf, Il1a, IL1b, and Il22 in B27-Tg colon tissue compared to vehicle-treated B27-Tg controls. Ex vivo treatment of bulk immune cells isolated from B27-Tg rat colon with rapamycin reduced expression of Il17a, Il17f, Ifng, and Il22 compared to vehicle-treated cells. Rapamycin treatment decreased the abundance of cecum microbiota associated with inflammation in B27-Tg rats. Rapamycin also altered the gut microbiome in WT rats, without associated changes in the tissue transcriptome.

CONCLUSION: Our study demonstrates that rapamycin treatment substantially reduces HLA-B27-mediated gut inflammation in experimental SpA. Results from this pre-clinical model suggest further evaluation of rapamycin as a therapeutic strategy in HLA-B27 associated diseases is warranted.},
}

Animals
*HLA-B27 Antigen/genetics/immunology
*Sirolimus/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
Rats
Rats, Transgenic
Disease Models, Animal
Cytokines/metabolism/genetics
*Spondylarthritis/drug therapy/immunology/microbiology
Humans
Male
Inflammation/drug therapy
Colon/drug effects/immunology/microbiology/pathology

@article {pmid41940020,
year = {2026},
author = {Usman, S and Yan, Q and Gao, L and Deng, S and Lu, L and Pang, T and Lai, D and Jones, CS and Yi, X and Zhang, J},
title = {Inclusion of different levels of fermented elephant grass in broiler chicken diet: effects on growth, physiology, carcass traits and gut microbial community.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1767570},
pmid = {41940020},
issn = {1664-042X},
abstract = {The physiological and microbiome-modulating benefits of dietary forage in monogastrics are impeded by recalcitrant fiber and anti-nutritional factors. However, fermentation and appropriate inclusion levels may overcome these limitations. This study evaluated the effects of two fermented cultivars of elephant grass (Cenchrus purpureus cv. Guiminyin and cv. Purple) incorporated into broiler diets at different inclusion levels, with emphasis on cultivar-specific responses, growth performance, physiological status, and gut microbial composition. A total of 240 male (30-days old) Jinling earth-neck chickens were housed in four replicate pens of 12 birds each, and randomly assigned to five dietary treatments (48 birds per treatment): a control diet with no inclusion (0%), CpGui5 (5% Guiminyin inclusion), CpGui10 (10% Guiminyin inclusion), CpPur5 (5% Purple inclusion), and CpPur10 (10% Purple inclusion). CpGui5 and Control diets had statistically similar and higher final weight, total weight gain, average daily gain and feed efficiency which were higher than the other treatments (P < 0.05). On the other hand, Control, CpGui5 and CpPur5 had higher daily feed intake compared to CpGui10 and CpPur10 which had the lower daily feed intake (P < 0.05). Slaughter performance revealed significant differences (P < 0.05), with the control, CpGui5, CpPur5 and CpPur10 groups maintaining higher live weight, dressed weight, half-bore, and breast muscle rate while CpGui10 recorded the lowest values. Blood biochemical indices, including total protein, albumin, liver enzymes, and renal function markers, were unaffected by dietary treatments (P > 0.05), indicating no adverse physiological effects. Gut microbiome analysis showed stable richness (Chao1, ACE) across treatments, while diversity (Shannon, Simpson) was reduced in CpPur5 relative to other groups (P < 0.05). A shared core microbiome of 202 OTUs was detected across all treatments, alongside treatment-specific enrichment of taxa. LEfSe (Linear Discriminant Analysis Effect Size) analysis identified treatment-specific enrichment of functionally relevant bacterial genera, including Megamonas in CpGui5 and Ruminococcaceae_UCG-014 and unclassified Lachnospiraceae at higher inclusion levels (CpGui10). Overall, moderate inclusion of fermented elephant grass, especially CpGui5 supports broiler performance while maintaining physiological health and gut microbial stability, highlighting its potential as a sustainable functional feed resource for poultry production.},
}

@article {pmid41940149,
year = {2026},
author = {Etesami, H and Yadegari, AH and Otabek, U and Zahro, B and Shavakatullo, N and Tolqinjon, A},
title = {The root's hidden ally: How the rhizosheath microbiome fortifies crops against drought.},
journal = {aBIOTECH},
volume = {7},
number = {1},
pages = {100015},
pmid = {41940149},
issn = {2662-1738},
abstract = {Drought stress poses a significant threat to global agriculture, necessitating innovative strategies to enhance plant resilience. This review highlights the rhizosheath-the soil layer tightly bound to roots by mucilage and microbial biofilms-as a critical but underexplored microbial niche for sustainable drought mitigation. Unlike the vulnerable rhizosphere, the rhizosheath has a cohesive structure that acts as a protective "mini-oasis," preserving moisture and sustaining microbial activity when water is scarce. We synthesize evidence showing that resident rhizosheath bacteria, including genera such as Bacillus, Pseudomonas, and Azospirillum, enhance plant drought tolerance through multiple mechanisms: improving soil structure and water retention, modulating phytohormone levels, facilitating nutrient acquisition, and activating antioxidant and genetic defense pathways in the plant. Despite promising laboratory findings, there has been little field-scale validation of these effects. Here, we critically assess translational challenges and outline future research priorities, such as understanding plant-microbe specificity and optimizing synthetic microbial consortia. Addressing these questions will enable manipulation of the rhizosheath microbiome for development of climate-resilient crops and securing food production in water-limited environments.},
}

@article {pmid41940156,
year = {2026},
author = {Ma, J and Qiao, J and Cao, Y and Cheng, Z},
title = {Harnessing artificial intelligence to decode the rhizosphere microbiome.},
journal = {aBIOTECH},
volume = {7},
number = {1},
pages = {100005},
pmid = {41940156},
issn = {2662-1738},
abstract = {The rhizosphere microbiome plays crucial roles in plant health by regulating nutrient cycling and enhancing stress resilience. However, due to its complexity, the rhizosphere microbiome is quite challenging to analyze using conventional approaches. Recent advances in artificial intelligence (AI) offer unprecedented opportunities to decipher intricate microbial interactions and leverage their potential for crop breeding. In this review, we assess AI methodologies derived from human microbiome studies that address foundational data challenges, including high dimensionality, compositionality, and sparsity. Next, we examine the uses of these methods for the functional prediction of microbial traits. We then shift our focus to the rhizosphere, exploring AI-driven approaches for predictive modeling of rhizosphere dynamics, integrating plant phenotypic and microbiome data, and designing synthetic microbial communities (SynComs). Finally, we discuss the major challenges and future prospects of using AI in rhizosphere microbiome research. Specifically, we propose an emerging AI paradigm that integrates complementary inside-out (hologenome-based genomic selection) and outside-in (SynCom design) strategies, powered by transformative technologies such as federated learning, large language models, digital twins, and autonomous AI agents. This review underscores the potential for AI to revolutionize microbiome science and crop improvement.},
}

@article {pmid41940273,
year = {2026},
author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X},
title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.},
journal = {Current zoology},
volume = {72},
number = {1},
pages = {14-29},
pmid = {41940273},
issn = {1674-5507},
abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.},
}

@article {pmid41940285,
year = {2025},
author = {Jeong, GH and Lim, KS},
title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.},
journal = {Journal of animal science and technology},
volume = {67},
number = {6},
pages = {1207-1214},
pmid = {41940285},
issn = {2055-0391},
abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.},
}

@article {pmid41940567,
year = {2026},
author = {De Zutter, N and Audenaert, K},
title = {Can We Breed Microbiomes to Sustain Plant Productivity?.},
journal = {Microbial biotechnology},
volume = {19},
number = {4},
pages = {e70351},
pmid = {41940567},
issn = {1751-7915},
mesh = {*Microbiota ; *Plant Breeding/methods ; *Crops, Agricultural/microbiology/genetics/growth & development ; Quantitative Trait Loci ; *Plants/microbiology/genetics ; },
abstract = {Global food systems face challenges from population growth, shifting diets and climate change. While decades of plant-centric breeding and high-input agriculture have generated high yielding crops, this strategy has unintentionally reshaped the plant associated microbiomes, often coinciding with a depletion of their functional diversity. We revisit these breeding strategies and propose extending breeding targets beyond the plant genome to include the plant microbiome. In this regard, resistance breeding shows, albeit unintended, that plant genetics shape the microbiome: by narrowing the genetic base, we have selected for highly specialised pathogenic microbiomes. This raises a key question: can we intentionally apply the same principle to select for beneficial microbiomes? To answer this question, a thorough insight into microbial community architecture, hubs and functional redundancy is key. We outline two complementary avenues: (i) rewilding to restore ancestral microbial partners and (ii) microbiome breeding guided by QTL/GWAS mapped host loci that gate microbial recruitment, immune filtering and exudate composition. This approach comprises the integration of trait-based phenotyping, multi-omics, network-informed SynCom design and field testing across environments to capture G × E × M (genotype × environment × microbiome) interactions. Treating the microbiome as a selectable, designable and heritable trait can convert small gains into durable long-lasting crop resilience.},
}

*Microbiota
*Plant Breeding/methods
*Crops, Agricultural/microbiology/genetics/growth & development
Quantitative Trait Loci
*Plants/microbiology/genetics

@article {pmid41940646,
year = {2026},
author = {Yin, X and Niu, Y and Chen, B and Zhang, H and Guo, R and Niu, C and Kang, J and Shi, H and Kong, X and Ma, W and Ma, Z and Wei, Y and Hua, Y},
title = {Screening and dynamic change study of microbial and metabolite markers for calf diarrhea based on multi-omics and machine learning.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0000526},
doi = {10.1128/msystems.00005-26},
pmid = {41940646},
issn = {2379-5077},
abstract = {UNLABELLED: Neonatal calf diarrhea is a leading cause of calf mortality and substantial economic loss in the livestock industry, yet the dynamic microbial and metabolic signatures accompanying disease onset remain poorly defined. Here, we integrated 16S rRNA high-throughput sequencing, untargeted metabolomics, and machine learning approaches to longitudinally profile fecal samples from neonatal calves at 0, 5, 10, 15, and 20 days of age. Diarrheic calves exhibited significantly reduced gut microbial α-diversity, as indicated by lower Chao1 richness and Shannon index compared with healthy counterparts. At the genus level, Tyzzerella and Fusobacterium emerged as core differential taxa associated with diarrhea and were further validated as robust biomarkers using an XGBoost predictive model. Metabolomic analysis showed that differential metabolites were mainly enriched in pathways including the phosphotransferase system. Notably, dulcitol, N-acetylmuramate, and D-fructose were highlighted as potential contributors to diarrhea, possibly through modulating intestinal osmolality and inflammatory responses. Pearson correlation analysis revealed significant associations between Tyzzerella/Fusobacterium and key metabolites, suggesting coordinated microbe-metabolite interactions during disease progression. Temporal pattern analysis identified an early-life signal: a high abundance of Escherichia-Shigella at birth may act as an important trigger for subsequent diarrhea. In addition, several metabolites displayed distinct age-dependent trajectories, indicating their potential as time-resolved metabolic biomarkers. Collectively, this study delineates dynamic shifts in the gut microbiome and metabolome during neonatal calf diarrhea, identifies Tyzzerella and Fusobacterium, together with characteristic metabolites such as dulcitol and N-acetylmuramate, as candidate biomarkers, and provides a high-performance predictive framework to support early diagnosis and targeted microbiota-based interventions.

IMPORTANCE: Neonatal calf diarrhea causes substantial early-life mortality and economic losses, yet the dynamic microbiota-metabolite alterations and early-warning biomarkers during disease onset remain poorly defined. Here, we longitudinally profiled fecal microbiota and metabolites in calves from birth to day 20 and integrated machine learning approaches to systematically characterize diarrhea-associated signatures. Diarrheic calves showed reduced α-diversity, and Tyzzerella and Fusobacterium emerged as core differential genera with predictive value validated using an XGBoost model. Differential metabolites were mainly enriched in pathways such as the phosphotransferase system (PTS), and dulcitol and N-acetylmuramate may contribute to diarrhea by modulating intestinal osmolality or inflammatory responses. Notably, a higher abundance of Escherichia-Shigella at birth was potentially associated with subsequent diarrhea risk, while L-glutamic acid, choline, and LysoPC exhibited distinct temporal trajectories. Collectively, these findings provide translational candidate biomarkers to support early warning and microbiota-targeted precision interventions for neonatal calf diarrhea.},
}

@article {pmid41940665,
year = {2026},
author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X},
title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191125},
doi = {10.1128/spectrum.01911-25},
pmid = {41940665},
issn = {2165-0497},
abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.

IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.},
}

@article {pmid41940696,
year = {2026},
author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M},
title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0190325},
doi = {10.1128/aem.01903-25},
pmid = {41940696},
issn = {1098-5336},
abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.},
}

@article {pmid41940869,
year = {2026},
author = {Sharif-Askari, Z and Atoui, K and El Zein, W and Rizk, M and Sharif Askari, E},
title = {From periodontitis to neurodegeneration: Can probiotics modulate the P. gingivalis-amyloid pathway in Alzheimer's disease?.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261432686},
doi = {10.1177/13872877261432686},
pmid = {41940869},
issn = {1875-8908},
abstract = {Alzheimer's disease (AD) is a neurodegenerative disorder characterized by the gradual destruction of cognitive and behavioral functions. Despite the continuous research efforts, there is still no cure for this disease. In recent years, researchers have investigated Porphyromonas gingivalis (P. gingivalis) as a potential cause of AD. P. gingivalis-lipopolysaccharides (LPS) and gingipains have been implicated in neuroinflammatory cascades relevant to AD. The gut-brain axis provides a pathway for microbial migration, immune activation, and regulation of the central nervous system function. Emerging evidence suggests that selected probiotics may modulate these pathways by restoring microbial balance, reinforcing epithelial barrier function, and regulating innate and adaptive immunity. Importantly, much of the evidence and mechanistic support for these effects derives from preclinical and animal studies, whereas human data remain limited to associative findings and early-stage clinical trials. Early clinical trials report modest improvements in cognitive scores and systemic inflammatory markers. Strain selection, dose, and treatment duration make direct comparisons challenging. This review integrates the literature on the links between P. gingivalis and AD, suggesting that probiotics may be used as neuroprotective agents. Taken together, current preclinical signals are consistent with the potential of probiotics as feasible adjuncts, pending confirmatory trials with standardized formulations.},
}

@article {pmid41941327,
year = {2026},
author = {Strope, TA and Easson, CG and Fiore, CL},
title = {Low Abundance Taxa Show Diverse Microbial Symbiotic Interactions With the Freshwater Sponge, Radiospongilla crateriformis, Pre and Post Gemmulation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70331},
pmid = {41941327},
issn = {1758-2229},
support = {//Appalachian State University/ ; 1924540//National Science Foundation/ ; },
mesh = {*Symbiosis ; *Porifera/microbiology/growth & development/physiology ; Animals ; *Bacteria/classification/genetics/isolation & purification ; Fresh Water/microbiology ; *Microbiota ; Flavobacterium/genetics ; Phylogeny ; },
abstract = {Freshwater sponges, most of which have a dormant stage with gemmules, are well poised for microbiome focused experiments. Here, we leveraged field collections of freshwater sponges pre-gemmule (Pre) and post-gemmule (Post) formation to compare the microbial symbiont metatranscriptome at the two developmental stages. There were no broad changes to the microbiome in composition between the two stages; however, there were significant differences in the abundance of several bacterial taxa and functional genes between Pre and Post sponge samples. For example, many Polynucleobacter spp. increased from Pre to Post samples, but no putative symbiosis factors were associated with Polynucleobacter and these may be loosely associated with the sponges. In contrast, we hypothesise that Flavobacterium spp. are facultative symbionts of freshwater sponges that begin to leave when the sponge tissue degrades, or they may decrease their metabolic activity. Functions attributed to Flavobacterium spp. such as type IX secretion system (T9SS) component and ankyrin repeat domains, all decreased in the Post samples and suggests that this group can interact with the sponge host or be free-living. These results provide a foundation for future hypothesis testing and experimental work with the microbiomes of freshwater sponges.},
}

*Symbiosis
*Porifera/microbiology/growth & development/physiology
Animals
*Bacteria/classification/genetics/isolation & purification
Fresh Water/microbiology
*Microbiota
Flavobacterium/genetics
Phylogeny

@article {pmid41941330,
year = {2026},
author = {Dunn, ES and Spalding, HL and Hill-Spanik, KM and Fullerton, H},
title = {Examining Short Temporal Changes in Intertidal Macroalgal Microbiomes at 'Ewa Beach, O'Ahu, Hawai'i: Some Hosts Varied While Others Remained Stable.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70333},
pmid = {41941330},
issn = {1758-2229},
mesh = {Hawaii ; *Microbiota ; *Seaweed/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Climate Change ; Rhodophyta/microbiology ; Seawater/microbiology ; Phaeophyceae/microbiology ; },
abstract = {Understanding the temporal variability of microbiomes is crucial for predicting dynamics within macroalgal communities under future climate change scenarios, rising temperatures, and increased marine heatwave events. Short-term variation has been observed in human- and coral-associated microbes, but these dynamics are less understood in macroalgae. Intertidal macroalgal communities are ideal systems for investigating microbiome temporal variation due to their exposure to daily fluctuations in abiotic conditions. We characterised and examined the variability in the microbiota of seven macroalgal species, with representatives from three different phyla, across five sequential low tides in May 2021 at a single intertidal bench at 'Ewa Beach, O'ahu, Hawai'i, USA. Bacterial community compositions found in two red algae, Acanthophora spicifera and Laurencia dendroidea, and one brown alga, Dictyota sandvicensis, had variable abundances of several amplicon sequence variants contributing to significant dissimilarity through time. Two green macroalgae (Avrainvillea lacerata and Halimeda discoidea) were stable over time. Temporal stability of the macroalgal microbiotas, therefore, was variable amongst macroalgal species, but may be dependent on its horizontal or vertical positioning within the intertidal zone, which can vary the level of environmental stress (e.g., temperature, light, desiccation). Additional work exploring the drivers of the temporal variability observed herein is needed.},
}

Hawaii
*Microbiota
*Seaweed/microbiology
*Bacteria/classification/genetics/isolation & purification
Climate Change
Rhodophyta/microbiology
Seawater/microbiology
Phaeophyceae/microbiology

@article {pmid41941490,
year = {2026},
author = {Ventero, MP and Herrero, R and Tyshkovska, I and Valverde-Fredet, MD and Rodríguez, JC and Rodríguez-Fernández, M and González-De-La-Aleja, P and Trigo, M and Parra, M and Aller, AI and Otero, S and Espindola-Gomez, R and Ramos, JM and León, EM and García, M and Navarrete-Lorite, MN and Llenas-García, J and Portillo, I and Jover, F and Tasias, M and Caston, JJ and Gil, C and Vinuesa-Garcia, D and Gomez-Ayerbe, C and Martínez Marcos, FJ and Merchante, N and De Lucas, EM},
title = {Dynamics of the microbiota in patients with Clostridioides difficile: Recurrence, treatment, sex, and immunosuppression.},
journal = {PLoS pathogens},
volume = {22},
number = {4},
pages = {e1014063},
doi = {10.1371/journal.ppat.1014063},
pmid = {41941490},
issn = {1553-7374},
abstract = {BACKGROUND: Alterations in the gut microbiome are central to the pathogenesis and recurrence of Clostridioides difficile infection (CDI).

OBJECTIVE: To evaluate intestinal microbiome changes during CDI and their association with recurrence, sex, age, and immunosuppression.

METHODS: Patients from the CDI-ANCRAID-SEICV cohort were consecutively enrolled. Stool samples were obtained at diagnosis (Dx), end of treatment (ET), and eight weeks post-treatment (8W) or upon recurrence. Microbiota composition was analyzed by 16S rRNA sequencing using QIIME2 and R. Outcomes were compared by demographics, immunosuppression, and treatment (vancomycin [VNC], vancomycin-bezlotuzumab [VNC-BZL], fidaxomicin [FDX]).

RESULTS: Among 143 patients, non-recurrent cases showed higher biodiversity at 8W versus diagnosis (H p = 0.002, ASVs p < 0.001), unlike recurrent cases. Diversity decreased with VNC (H p > 0.001, ASVs p < 0.001) but was preserved with FDX (H p = 0.15). Recovery of Shannon diversity was limited in women (p = 0.50) and immunocompromised patients (p = 0.31). At ET, Fusobacteria and Verrucomicrobiota were less abundant in recurrent than non-recurrent cases (0.77%, 0.53% vs 3.43%, 3.50%). FDX-treated samples showed higher Bacteroidetes (31.33%) compared to VNC (5.23%) or VNC-BZL (3.12%). Women exhibited increased Firmicutes abundance (p = 0.034).

CONCLUSIONS: Restoration of microbial diversity correlates with CDI resolution. FDX preserves gut microbiota better than VNC or VNC-BZL. Women and immunocompromised patients demonstrate impaired microbiota recovery.},
}

@article {pmid41941984,
year = {2026},
author = {Margaux, E and Elise, T and Muriel, D and Matthijs, M and Jellina, P and Arnau, VV and Jean, S and Nicky, D and Bart, B and Jeroen, R and Kaat, A},
title = {A pilot study on the role of the oxytocinergic system in gut microbiome composition in children with autism: baseline associations and effects of intranasal oxytocin.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106579},
doi = {10.1016/j.bbi.2026.106579},
pmid = {41941984},
issn = {1090-2139},
abstract = {Autistic children often experience behavioral difficulties alongside nutritional and gastro-intestinal (GI) problems, including gut dysbiosis. Recent research has highlighted important interactions between the oxytocinergic system and gut microbiome compositions, however, insights into how exogenous administration of oxytocin may influence GI health remain largely unexplored. Here, we first examined whether nutrition, GI symptoms and microbiome compositions vary in autistic versus non-autistic children, and how alterations link to clinical-behavioral difficulties and oxytocinergic signaling. Next, we examined the effect of a four-week intranasal oxytocin administration regimen on GI health/dysbiosis in autistic children enrolled in a randomized placebo-controlled trial. Compared to non-autistic children, autistic children consumed more soft drinks, and fewer vegetables and experienced abdominal pain more frequently over the past three months. Notably, epigenetic variations in the oxytocin receptor gene (OXTR) were associated with stool consistency, indicating that children with looser stools exhibited lower OXTR methylation levels, indicative of increased receptor expression. Additionally, a higher abundance of Romboutsia was associated with OXTR hypo-methylation and more anxiety-like behavior. In autistic children, the four-week oxytocin regimen had no effect on bacterial diversity but did modify stool consistency, leading to less dense stools with an overall more normal stool consistency, and an increased abundance of the potentially anti-inflammatory genus Fusicatenibacter. To conclude, this study provides novel insights into the role of the oxytocinergic system in GI symptoms and gut microbiome compositions in autistic children, and preliminary evidence suggesting a modulatory effect of exogenously administered oxytocin on these parameters.},
}

@article {pmid41941985,
year = {2026},
author = {Bettio, MK and Vidal, T and Rose, JJ and Jois, M and Flavel, M and Petrovski, S},
title = {Polyphenol-Rich Feed Material increases Anaerostipes and reduces methanogenic archaea in the horse hindgut microbiome.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {105885},
doi = {10.1016/j.jevs.2026.105885},
pmid = {41941985},
issn = {0737-0806},
abstract = {BACKGROUND: The gastrointestinal microbiota plays a critical role in horse health and performance. While sugarcane-derived polyphenols have shown microbiota-modulating properties in other species, their effects in horses remain unexplored.

AIMS/OBJECTIVES: This study investigated whether supplementation with a sugarcane-derived polyphenol feed material modulates the hindgut microbiota of healthy adult horses.

METHODS: An observational longitudinal study was conducted on six horses over 12 weeks. Faecal samples were collected at three time points: baseline (P1), during supplementation (P2), and post-supplementation (P3). Microbial composition was assessed by 16S rRNA gene sequencing targeting the V3-V4 region. Alpha and beta diversity, as well as differential abundance analyses, were performed.

RESULTS: Alpha diversity metrics (Chao1, Shannon, Simpson) showed no significant differences across time points. However, Anaerostipes increased by 105.3% during supplementation and 23.6% post-supplementation. Prevotella abundance also rose post-supplementation. Methanogenic Archaea, including Methanomassiliicoccus, decreased by 79.1% during supplementation, while members of Methanobacteriales were reduced by 61.8%. These changes partially reversed in the post-supplementation phase. Core microbiota genera remained stable throughout.

CONCLUSION: Supplementation with a sugarcane-derived polyphenol feed material modulated specific microbial taxa without disrupting overall microbial diversity. The intervention enhanced fermentative SCFA-producing bacteria and suppressed methanogenic Archaea, supporting the potential use of this feed material as a microbiome enhancer for improving hindgut health and reducing methanogenesis in horses.},
}

@article {pmid41942049,
year = {2026},
author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J},
title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.004},
pmid = {41942049},
issn = {2090-1224},
abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.

OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.

METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.

RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.

CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.},
}

@article {pmid41942109,
year = {2026},
author = {Alsarahead, RA and El-Shehabi, FS and Hijjawi, NS},
title = {Prevalence and subtype diversity of Blastocystis hominis among gastroenteritis patients in northern and central Jordan.},
journal = {Transactions of the Royal Society of Tropical Medicine and Hygiene},
volume = {},
number = {},
pages = {},
doi = {10.1093/trstmh/trag033},
pmid = {41942109},
issn = {1878-3503},
support = {49//Deanship of Scientific Research at Hashemite University/ ; //Department of Graduate Studies/ ; },
abstract = {BACKGROUND: Blastocystis hominis is a common intestinal eukaryotic organism that infects both humans and animals. Although its pathogenicity remains debated, it has been associated with diarrhoea and gastroenteritis. This study aimed to determine its prevalence and characterize its genetic subtypes (STs) in symptomatic patients presenting with gastrointestinal complaints.

METHODS: DNA was extracted from 279 stool samples collected from patients in northern and central regions of Jordan. Nested polymerase chain reaction targeting the 18S rRNA gene locus and Sanger sequencing of positive samples were used for B. hominis detection and subtype identification. Phylogenetic relationships were analysed using Unipro UGENE and MEGA software. Statistical analyses, prevalence, Pearson's χ2 test (p<0.05) were conducted using SPSS.

RESULTS: The present study found a B. hominis prevalence of 7.2% (20/279). Three subtypes were identified: ST1 35% (7/20), ST2 10% (2/20) and ST3 55% (11/20). No mixed-subtype infections were detected. A statistically significant association was observed between B. hominis infection and patient age (p<0.05), with infection rates influenced by age and not by gender. The highest prevalence, based on sequencing, was observed in the 6- to <12-y age group. The association between B. hominis infection and gender was not statistically significant.

CONCLUSIONS: The relatively low prevalence of B. hominis among patients suggests it may function more as an indicator of gut health rather than as a primary pathogen. However, confirmation of this hypothesis requires additional microbiome and longitudinal studies. The frequent detection of ST1 and ST3 aligns with previous findings that link these subtypes to clinical symptoms. Broader epidemiological studies are needed to clarify the distribution patterns and clinical significance of B. hominis in human populations.},
}