@article {pmid41515076,
year = {2026},
author = {Cano-Serrano, S and Castelán-Sánchez, HG and Oyaregui-Cabrera, H and Hernández, LG and Pérez-Pérez, MC and Santoyo, G and Orozco-Mosqueda, MDC},
title = {Assessment of Bacterial Diversity and Rhizospheric Community Shifts in Maize (Zea mays L.) Grown in Soils with Contrasting Productivity Levels.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010130},
pmid = {41515076},
issn = {2223-7747},
support = {2024-2025//CIC-UMSNH/ ; },
abstract = {The resident microbiota in agricultural soils strongly influences crop health and productivity. In this study, we evaluated the prokaryotic diversity of two clay soils with similar physicochemical characteristics but contrasting levels of maize (Zea mays L.) and wheat (Triticum aestivum L.) production using 16S rRNA gene sequencing. Yield records showed significant differences in grain production over five consecutive years. When comparing prokaryotic alpha diversity between the "non-productive" and "productive" soils, no major differences were found, and the abundance of ammonia-oxidizing archaea (AOA) and bacterial genera such as Arthrobacter, Neobacillus, and Microvirga remained consistent across soils. Analysis of the top 20 genera showing the greatest abundance shifts by compartment (bulk soil vs. rhizosphere) revealed that genera such as Priestia, Neobacillus, Sporosarcina, and Pontibacter decreased in the rhizosphere of the non-productive soil, while in the productive soil, these genera remained unchanged. In the non-productive soil, genera such as Flavisobacter decreased in abundance in the rhizosphere, whereas Arthrobacter increased. Principal coordinates analysis (PCoA) showed no clear clustering by compartment (bulk vs. rhizosphere), but two distinct clusters emerged when grouping by soil type (productive vs. non-productive). Interaction networks varied by soil type: non-productive soils showed positive Candidatus-Bacillus and negative Massilia links, while productive soils were dominated by Flavisolibacter and negative Pontibacter. Across soils, Rhizobium-Bradyrhizobium associations were positive, whereas Neobacillus and Priestia were negative. These findings highlight that a few potential beneficial microbiota and their interactions may be key drivers of soil productivity, representing targets for microbiome-based agricultural management.},
}

@article {pmid41515075,
year = {2026},
author = {Seemakram, W and Suebrasri, T and Chankaew, S and Boonlue, S},
title = {Influence of Arbuscular Mycorrhizal Fungi on Soybean Growth and Yield: A Metabarcoding Approach.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010131},
pmid = {41515075},
issn = {2223-7747},
support = {grant number B13F680065//the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; },
abstract = {This study evaluated the efficiency of arbuscular mycorrhizal fungi (AMF) in promoting the growth, yield, protein, and phytochemical contents of Glycine max cv. Morkhor 60. A completely randomized pot experiment was conducted for 90 days in non-sterile soil with nine replications. Three AMF species were tested and compared with two non-mycorrhizal controls, with and without NPK fertilizer. All AMF treatments enhanced plant growth, photosynthetic rate, and water-use efficiency compared with the unfertilized control. Inoculation with Acaulospora dilatata KKU-SK202 produced the highest pod number and increased 100-seed weight by 27.00% and 4.13% over the non-inoculated and NPK treatments, respectively. Gigaspora margarita KKU-SK210 yielded the highest total protein and phenolic contents, while A. dilatata KKU-SK401 showed the highest antioxidant activity (72.09%). Metabarcoding analysis revealed that AMF inoculation reduced root colonization by pathogenic fungi, with G. margarita KKU-SK210 and A. dilatata KKU-SK202 being the most effective. These results suggest that AMF inoculation can enhance soybean productivity and seed quality while reducing chemical fertilizer dependency and pathogenic fungal incidence.},
}

@article {pmid41515021,
year = {2025},
author = {Teng, Y and Yin, C and Xu, F and Chen, J and Wu, Q and Ye, M and Liu, Y and Zhu, K},
title = {Citrus Genotype Modulates Rhizosphere Microbiome Structure and Function Under Drought Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010077},
pmid = {41515021},
issn = {2223-7747},
support = {KJQN202303518//Science and Technology Research of Chongqing Municipal Education Commission/ ; sxzybs-202201//Research Initiation Project for Doctor Recruitment of Chongqing Three Gorges Vocational College/ ; 32201766//National Natural Science Foundation of China/ ; },
abstract = {Drought stress substantially impairs citrus growth and alters the rhizosphere microbial composition; however, the role of these microbial communities in plant drought tolerance remains poorly understood. This study investigated the rhizosphere microbial structure, soil enzymatic activities, and physicochemical properties of drought-tolerant (DR) and drought-sensitive (DS) citrus varieties under drought stress conditions. High-throughput sequencing revealed that drought significantly altered microbial community composition, reducing the bacterial Shannon diversity by about 15% and enriching Gram-negative, stress-tolerant, and potentially pathogenic bacteria, as well as plant pathogenic fungi (upregulated 25.4% in DS), while reducing undefined saprotrophs (downregulated from 76.2 to 54.0% in DS). Notably, the DR variety exhibited a more stable and complex bacterial network, with 23.5% more edges and a higher proportion of positive correlations (54.3%), higher enrichment of beneficial fungi like Penicillium and Trichoderma, and unique recruitment of mycorrhizal fungi (up to 10.2%), which were nearly absent in DS. Furthermore, soil catalase and urease activities decreased under drought stress conditions. In contrast, acid phosphatase activity increased by up to 40% in DR. Correlation analyses indicated that these microbial shifts were closely associated with changes in soil nutrient availability. Our findings demonstrated that the drought-tolerant citrus variety modulates its rhizosphere microbiome towards a more cooperative and resilient state, highlighting the critical role of host-specific microbial recruitment in enhancing plant adaptation to drought stress for sustainable agriculture.},
}

@article {pmid41514971,
year = {2025},
author = {Wang, Q and Huang, J and Zhang, Y and Li, Z and Wei, L and Yin, X and Zhang, X and Zhou, Y},
title = {Long-Term Excess Nitrogen Fertilizer Reduces Sorghum Yield by Affecting Soil Bacterial Community.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010025},
pmid = {41514971},
issn = {2223-7747},
support = {the Natural Science Foundation of Chongqing (CSTB2024NSCQ-MSX0836) the Chongqing Research Institute Performance Incentive Guide Project (cstc2022jxjl80016, cqaas2020jxjl03) the Chongqing Technology Innovation and Application Development Project (cstc2019j//The research was supported by the Natural Science Foundation of Chongqing (CSTB2024NSCQ-MSX0836), the Chongqing Research Institute Performance Incentive Guide Project (cstc2022jxjl80016, cqaas2020jxjl03), and the Chongqing Technology Innovation and Ap-pli/ ; },
abstract = {The application of nitrogen (N) fertilizer is one of the most important measures to affect crop yield and soil bacterial communities. In this study, the four rates of N (namely N0F 0 kg N ha[-1], N1F 90 kg N ha[-1], N2F 180 kg N ha[-1], and N3F 270 kg N ha[-1]) along with a control (no fertilization, CK) were evaluated for their influence on sorghum yield, soil chemical properties, bacterial community, and diversity. The results showed that the yield-increasing effect was reduced by the higher dose of N input. Compared with N0F, sorghum yield increased by 58.8% in N1F and 68.2% in N2F but decreased by 8.1% in N3F relative to N2F. The soil pH decreased significantly with increasing N application. Compared with CK or N0F, N3F treatment increased the available P content by up to 18.6% or 32.2% but decreased the alkaline hydrolysis N, available K, organic matter, and total N contents by 8.4% or 23.8%, 5.5% or 10.6%, 8.4% or 28.8%, and 11.1% or 39.6%, respectively. In addition, different fertilization treatments altered the soil bacterial communities. Excess N fertilizer led to a decrease in bacterial abundance, and compared with N0F, the absolute abundance of bacteria increased by 18.7% in N1F, while it decreased by 31.8% in N3F. The predominant phyla, including Acidobacteria, Proteobacteria, and Chloroflexi, in the microbiome shift under different N application levels. The redundancy analysis (RDA) and Pearson's correlation analyses indicated that the soil properties, especially soil pH, available P, total P, total N, and organic matter, were the key environmental factors that defined the bacterial community in the ecosystem. Within the scope of the present experiment, N application at 90 kg N ha[-1] (N1F) optimized soil bacterial community abundance in sorghum-cultivated soil, while N2F (180 kg N ha[-1]) achieved the highest sorghum yield, suggesting a trade-off between optimizing the soil microbiome and maximizing crop yield under long-term fertilization.},
}

@article {pmid41514963,
year = {2025},
author = {Yoshioka, H and Morota, G and Iwata, H},
title = {Reciprocal BLUP: A Predictability-Guided Multi-Omics Framework for Plant Phenotype Prediction.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/plants15010017},
pmid = {41514963},
issn = {2223-7747},
support = {JP23KJ0506//Japan Society for the Promotion of Science/ ; JP22K21352//Japan Society for the Promotion of Science/ ; JPMJCR16O2//Japan Science and Technology Agency/ ; JPMJAN23D1//Japan Science and Technology Agency/ ; },
abstract = {Sustainable improvement of crop performance requires integrative approaches that link genomic variation to phenotypic expression through intermediate molecular pathways. Here, we present Reciprocal Best Linear Unbiased Prediction (Reciprocal BLUP), a predictability-guided multi-omics framework that quantifies the cross-layer relationships among the genome, metabolome, and microbiome to enhance phenotype prediction. Using a panel of 198 soybean accessions grown under well-watered and drought conditions, we first evaluated four direction-specific prediction models (genome → microbiome, genome → metabolome, metabolome → microbiome, and microbiome → metabolome) to estimate the predictability of individual omics features. We evaluated whether subsets of features with high cross-omics predictability improved phenotype prediction. These cross-layer models identify features that play physiologically meaningful roles within multi-omics systems, enabling the prioritization of variables that capture coherent biological signals enriched with phenotype-relevant information. Consequently, metabolome features were highly predictable from microbiome data, whereas microbiome predictability from metabolomic data was weaker and more environmentally dependent, revealing an asymmetric relationship between these layers. In the subsequent phenotype prediction analysis, the model incorporating predictability-based feature selection substantially outperformed models using randomly selected features and achieved prediction accuracies comparable to those of the full-feature model. Under drought conditions, the phenotype prediction models based on metabolomic or microbiomic kernels (MetBLUP or MicroBLUP) outperformed the genomic baseline (GBLUP) for several biomass-related traits, indicating that the environment-responsive omics layers captured phenotypic variations that were not explained by additive genetic effects. Our results highlight the hierarchical interactions among genomic, metabolic, and microbial systems, with the metabolome functioning as an integrative mediator linking the genotype, environment, and microbiome composition. The Reciprocal BLUP framework provides a biologically interpretable and practical approach for integrating multi-omics data, improving phenotype prediction, and guiding omics-based feature selection in plant breeding.},
}

@article {pmid41514871,
year = {2025},
author = {Brajdic, L and Reed, EK and Pearson, HB and Brown, HL},
title = {Cutibacterium acnes: An Emerging Prostate Cancer Pathogen.},
journal = {Biology},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/biology15010030},
pmid = {41514871},
issn = {2079-7737},
support = {A27894/CRUK_/Cancer Research UK/United Kingdom ; 02-456679//Applied Microbiology International/ ; },
abstract = {Cutibacterium acnes (C. acnes) has emerged as a potential contributor to prostate cancer (PCa) pathogenesis, yet the mechanistic basis remains unclear. This review explores the prevalence, persistence and mechanistic impact of C. acnes within the prostate to help decipher the functional consequence and diagnostic value of a C. acnes infection in this setting. We examine the evidence supporting C. acnes colonisation of both premalignant and malignant tissue, and critically evaluate how prostate tumour physiology, particularly hypoxia and low pH, may facilitate microbial persistence. Emerging data suggest that C. acnes modulates inflammatory and immune pathways, influencing macrophage activation, cytokine production, and the regulation of immune checkpoints. Additionally, we discuss studies demonstrating its involvement in DNA damage, host cell metabolism, and extracellular matrix remodelling. The identification of C. acnes in urinary and gut microbiomes, alongside the presence of its genomic DNA in extracellular vesicles in circulation indicate broad diagnostic potential. While discrepancies in methodology have hampered a consensus, recent genomic and functional studies provide new avenues to distinguish contamination from true pathogenicity. Ultimately, future research exploring whether C. acnes is a biomarker, bystander, or bona fide driver of PCa, and its potential role in personalised diagnostics are crucial to advance the field and unravel the predictive and therapeutic value of C. acnes. Clarifying this relationship will advance our understanding of microbiome-cancer dynamics and could help inform innovative early detection and screening strategies that improve patient care.},
}

@article {pmid41514803,
year = {2025},
author = {Zhu, Y and Chai, Y and Chen, S and Qian, W and Si, H and Li, Z},
title = {Distinct Rumen Microbial Features and Host Metabolic Responses in Three Cervid Species.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010116},
pmid = {41514803},
issn = {2076-2615},
support = {2023YFD1302000//National Key Research and Development Program of China/ ; U24A20434//National Natural Science Foundation of China/ ; 20240101012JJ//Natural Science Foundation of Jilin Province/ ; },
abstract = {Rumen microbiota is pivotal for nutrient metabolism and physiological adaptation in ruminants. This study investigated the rumen microbial community, fermentation parameters, and serum biochemistry of three Cervid species-Sika deer (Cervus nippon), Reindeer (Rangifer tarandus), and Milu deer (Elaphurus davidianus) (n = 5/group)-fed an identical diet. Using 16S rRNA sequencing and biochemical analyses, we found that while Bacteroidota, Firmicutes, and Proteobacteria were dominant phyla across species. Sika deer and Milu deer exhibited significantly higher microbial diversity and abundance of carbohydrate-digesting genera (e.g., Butyrivibrio, Saccharofermentans), and pathways of carbohydrate digestion and absorption, starch and sucrose metabolism compared to Reindeer. Conversely, Reindeer showed increased abundances of Lachnospiraceae ND3007 and butyrate metabolism pathway, and significantly elevated rumen volatile fatty acid concentrations, particularly acetate and butyrate. Serum profiling revealed that Milu deer had significantly higher lipid levels (CHO, TG, LDL-C) but lower total protein and AST levels compared to other species. Notably, WGCNA linked these blood lipid traits to host genes enriched in PI3K-Akt, MAPK, and bile secretion pathways. These findings demonstrate distinct species-specific rumen fermentation patterns and host metabolic adaptations, suggesting a coordinated regulation between the rumen microbiome and host genetics in Cervid.},
}

@article {pmid41514762,
year = {2025},
author = {Wei, M and Wang, S and Lin, F and Han, S and Zhang, T and Kuang, Y and Tong, G},
title = {A Hypothesis of Gut-Liver Mediated Heterosis: Multi-Omics Insights into Hybrid Taimen Immunometabolism (Hucho taimen ♀ × Brachymystax lenok ♂).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010074},
pmid = {41514762},
issn = {2076-2615},
support = {2023YFD2400405//the National Key Research and Development Program of China/ ; NO.HSY2024Q09//the Central Public-interest Scientific Institution Basal Research Fund (HIRFRI)/ ; NO. 2023TD59//the Central Public-interest Scientific Institution Basal Research Fund (HIRFRI)/ ; },
abstract = {This study investigated the molecular and microbial factors behind the higher disease resistance of hybrid taimen by combining gut microbiome profiling with host transcriptomic analysis of intestinal and liver tissues. Both hybrid taimen and H. taimen were raised under the same recirculating aquaculture system (RAS) conditions. After recording survival rates following three enteritis outbreaks, samples of intestinal contents and tissues were collected from both groups. The gut microbiota was analyzed using full-length 16S rRNA sequencing in PacBio, and host gene expression was assessed with Illumina RNA-seq. Functional predictions were made using PICRUSt2 and Gene Set Enrichment Analysis (GSEA). Results showed that hybrids had significantly higher survival rates after enteritis (p < 0.05). Although microbial alpha diversity was similar, beta diversity revealed slight compositional differences. Hybrids showed higher levels of Hapalosiphon and Tepidimicrobium, microbes associated with antimicrobial compounds and the metabolism of short-chain fatty acids (SCFAs). Functional predictions indicated enrichment in selenocompound metabolism and ansamycin biosynthesis in hybrids. Transcriptomic analysis identified 4233 differentially expressed genes (DEGs) in the intestine and 3980 in the liver. In hybrids, intestinal tissues exhibited increased expression of immune pathways, including complement activation, lysosomal activity, and the transforming growth factor-beta (TGF-β) signaling pathway. Liver tissues demonstrated higher expression of genes related to cholesterol synthesis, fatty acid degradation, and the peroxisome proliferator-activated receptor (PPAR) signaling pathway. qRT-PCR validated the expression patterns of 20 selected DEGs. These findings tentatively suggest that the elevated disease resistance of hybrid taimen may be linked, at least in part, to a combination of microbial taxa inferred to produce antimicrobial metabolites and short-chain fatty acids, as well as an apparent intensification of intestinal immune and barrier-related gene expression, and hepatic pathways that possibly support energy supply and steroid-based immunity. However, this multi-omics data set is only correlational. We still do not know whether a single strain or a few host genes are enough to produce the resistant phenotype. Gnotobiotic trials, microbiota transplants, and targeted metabolomics will be necessary to turn these interesting associations into solid evidence.},
}

@article {pmid41514732,
year = {2025},
author = {Zhou, Y and Wu, Y and Ma, C and Ruan, X and Cha, M and Zhou, Y and Li, T and Sun, W and Liu, H},
title = {Comparative Profiling of the Fecal Bacteriome, Mycobiome, and Protist Community in Wild Versus Captive (Cervus canadensis).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010044},
pmid = {41514732},
issn = {2076-2615},
support = {2022YFDZ0072//The 2022 Inner Mongolia Autonomous Region Key R&D and Achievement Transformation Project (Science and Technology Support for Northeast Revitalization), titled "Innovation and Promotion of Application of Deer Source Probiotic Preparation"/ ; 2023RC-Industry-Research-Institute-7//The Hohhot Science and Technology Innovation Project/ ; },
abstract = {Diet and living environments exert a profound influence on gut microbiota composition. This study presents the first comprehensive characterization of fecal bacteria, fungi, and protozoa in wild (WA) (n = 10) and captive (DA) (n = 11) wapiti (Cervus canadensis) in China. Results reveal distinct microbial profiles between the two groups. In wild wapiti, Escherichia-Shigella and UCG-005 were the dominant bacterial genera, while Succinivibrio and Treponema predominated in captive individuals. Among fungi, Agaricus and Preussia were most abundant in wild wapiti, whereas Xeromyces was identified in captive ones. For protozoa, Heteromita was the primary genus in wild wapiti, while Heteromita, Entamoeba, and Eimeria were the main genera in captive wapiti. Functional predictions further underscored these differences. In wild wapiti, bacterial and fungal functions were primarily associated with carbon metabolism and the pyruvate cycle, with mutualistic interactions prevailing among bacteria, fungi, and protozoa. Conversely, captive wapiti exhibited functional profiles centered on lipopolysaccharide and amino acid metabolism, also characterized by mutualistic coexistence among microbial communities. These findings highlight the significant impact of dietary composition on the gut microbiome. In summary, wild wapiti appear to possess a superior capacity for plant fiber utilization. These findings provide valuable data for the health management of farmed wapiti and their adaptability in natural habitats.},
}

@article {pmid41514731,
year = {2025},
author = {Fu, D and Mao, K and Zang, Y and Qu, M and Qiu, Q and Zhao, X and Ouyang, K and Li, Y},
title = {Effects of Rumen-Protected β-Alanine on Growth Performance, Rumen Microbiome, and Serum Metabolome of Beef Cattle.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/ani16010043},
pmid = {41514731},
issn = {2076-2615},
support = {No. 3230810//National Natural Science Foundation of China/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; },
abstract = {β-alanine has been shown to significantly improve nitrogen utilization efficiency in beef cattle, but its impact on growth performance remains unclear. This study involved 36 healthy 18-month-old Simmental crossbred bulls with similar weights (627 ± 41 kg). The cattle were divided into two groups, with each group comprising six replicates of three animals. While the control group received the basal diet, the treatment group was administered an additional 96 g/d/cattle rumen-protected β-alanine (RP-β-Ala). The study was conducted over a 35-day period, which included an initial 7 days for adaptation. At the end of the trial, body weight was recorded, and samples were collected. Results show that RP-β-Ala enhanced average daily gain (p = 0.065) and crude protein (CP) digestibility (p = 0.065) and reduced gain-to-feed ratio (p = 0.078). Analysis of rumen microbiota revealed that RP-β-Ala positively modulated the rumen microbiota by enriching beneficial genera such as Prevotella, Treponema, and Selenomonas. This enrichment increased volatile fatty acid production and nitrogen utilization efficiency, as evidenced by elevated ruminal ammonia-N and microbial CP levels, along with decreased serum urea nitrogen. Metabolomics identified key alterations in arachidonic acid metabolism, specifically the upregulation of metabolites 14,15-DiHETrE and prostaglandin D2, and enhanced antioxidative capability indicated by increased serum total antioxidant capacity (T-AOC). Concurrently, RP-β-Ala reduced serum TNF-α levels. This reduction was achieved by suppressing harmful bacteria like Thermoactinomyces and Saccharopolyspora, along with inhibiting their polyamine synthesis, specifically spermine and spermidine. Collectively, these effects alleviated oxidative stress and inflammation. These findings demonstrate that RP-β-Ala enhances beef cattle growth through improved energy supply and antioxidant capacity.},
}

@article {pmid41514654,
year = {2025},
author = {Liu, KYP and Huang, A and Pepin, C and Shen, Y and Tsang, P and Poh, CF},
title = {Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.},
journal = {Cancers},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/cancers18010145},
pmid = {41514654},
issn = {2072-6694},
abstract = {The oral microbiome has become an emerging focus of oral cancer research, with growing evidence linking microbial communities to disease development, progression, and prognosis. However, there is limited consensus on optimal sampling strategies, storage methods, and analytical approaches. This narrative review critically evaluates current strategies for sampling, preservation, DNA extraction, sequencing, and data analysis in oral microbiome research related to oral cancer. We compared commonly used sampling methods, including saliva, oral rinse, swab, brush, and tissue biopsy, and reviewed preservation conditions, extraction kits, sequencing platforms, and analytical pipelines reported in recent oral microbiome studies. Sampling approaches affect microbial yield and site specificity. Saliva and oral rinse samples are convenient and noninvasive but may dilute lesion-specific microbial signals, whereas lesion-directed swabbing or brushing yields greater microbial biomass and biological relevance. Preservation media and storage temperature significantly influence microbial stability, and DNA extraction methods vary in their ability to remove host DNA. Although 16S rRNA gene sequencing remains the most common approach, shotgun metagenomics offers higher resolution and function insights but is still limited by clinical applicability. Differences in data pre- and post-processing models and normalization strategies further contribute to inconsistent microbial profiles. Given that oral mucosal sites differ markedly in structure and microenvironment, careful consideration is required to ensure that collected samples accurately represent the biological question being addressed. Methodological consistency across all workflow stages-from collection to analysis-is essential to generate reproducible, high-quality data and to enable reliable translation of oral microbiome research into clinical applications for cancer detection and risk assessment. Together, these insights provide a framework to guide future study design and support the development of clinically applicable microbiome-based biomarkers.},
}

@article {pmid41514614,
year = {2025},
author = {Peddireddi, RSS and Kuchana, SK and Kode, R and Khammammettu, S and Koppanatham, A and Mattigiri, S and Gobburi, H and Alahari, SK},
title = {Role of Gut Microbiome in Oncogenesis and Oncotherapies.},
journal = {Cancers},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/cancers18010099},
pmid = {41514614},
issn = {2072-6694},
abstract = {The gut microbiome has emerged as a key regulator of human health, influencing not only metabolism and immunity but also the development and treatment of cancer. Mounting evidence suggests that microbial dysbiosis contributes to oncogenesis by driving chronic inflammation, producing genotoxic metabolites, altering bile acid metabolism, and disrupting epithelial barrier integrity. At the same time, the gut microbiome significantly modulates the host response to oncotherapies including chemotherapy, radiotherapy, and especially immunotherapy, where microbial diversity and specific taxa determine treatment efficacy and toxicity. This review synthesizes current evidence on the role of the gut microbiome in both oncogenesis and oncotherapies, focusing on thirteen cancers with the strongest and most clinically relevant microbiome associations, colorectal cancer, gastric cancer, hepatocellular carcinoma, gallbladder cancer, esophageal cancer, pancreatic cancer, oral squamous cell carcinoma, cervical cancer, prostate cancer, breast cancer, lung cancer, brain cancer, and melanoma. These cancers were selected based on robust mechanistic data linking microbial alterations to tumor initiation, progression, and therapy modulation, as well as their global health burden and translational potential. In addition, we have provided mechanistic insights or clinical correlations between the microbiome and cancer outcomes. Across cancers, common microbial mechanisms included pro-inflammatory signaling (e.g., NF-κB and STAT3 pathways), DNA damage from bacterial toxins (e.g., colibactin, nitrosating species), and metabolite-driven tumor promotion (e.g., secondary bile acids, trimethylamine N-oxide). Conversely, beneficial commensals such as Faecalibacterium prausnitzii and Akkermansia muciniphila supported antitumor immunity and improved responses to immune checkpoint inhibitors. In conclusion, the gut microbiome functions as both a driver of malignancy and a modifiable determinant of therapeutic success. Integrating microbiome profiling and modulation strategies such as dietary interventions, probiotics, and fecal microbiota transplantation into oncology practice may pave the way for personalized and more effective cancer care.},
}

@article {pmid41514613,
year = {2025},
author = {Leonov, G and Starodubova, A and Makhnach, O and Goldshtein, D and Salikhova, D},
title = {Intratumoral Microbiome: Impact on Cancer Progression and Cellular Immunotherapy.},
journal = {Cancers},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/cancers18010100},
pmid = {41514613},
issn = {2072-6694},
support = {КBК: 075 0110 47 2 U8 70440 621. Scientific topic code: FSSF-2025-0004.//This research was funded by Ministry of Education and Science, grant number КBК: 075 0110 47 2 U8 70440 621. Scientific topic code: FSSF-2025-0004./ ; },
abstract = {The intratumoral microbiota, comprising bacteria, fungi, and viruses within the tumor microenvironment, actively influences carcinogenesis. Key mechanisms include the induction of host DNA damage, modulation of critical oncogenic signaling pathways such as WNT-β-catenin, NF-κB, and PI3K, and the orchestration of inflammatory processes. The microbiome's interaction with the host immune system is complex and bidirectional. On one hand, specific microbes can foster a pro-tumorigenic niche by suppressing the activity of cytotoxic T cells and natural killer (NK) cells or by promoting the accumulation of immunosuppressive cell types like tumor-associated macrophages (TAMs). On the other hand, microbial components can serve as neoantigens for T cell recognition or produce metabolites that reprogram the immune landscape to enhance anti-tumor responses. The composition of this microbiome is emerging as a crucial factor influencing the outcomes of immunotherapies. Prospective investigations in cancer immunotherapy ought to prioritize mechanistic inquiry employing integrative multi-omics methodologies. The execution of meticulously designed clinical trials for the validation of microbial biomarkers, and the systematic, evidence-based development of microbiome-targeted therapeutic interventions aimed at enhancing antitumor immune responses.},
}

@article {pmid41514460,
year = {2026},
author = {Vander Elst, N},
title = {Clinical implementation of endolysins targeting gram-positive bacteria points toward a combination strategy with standard-of-care antibiotics: a selective review.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-025-03655-4},
pmid = {41514460},
issn = {2047-783X},
abstract = {Endolysins, which are peptidoglycan hydrolases derived from bacteriophages, are expected to innovate antimicrobial treatment. More specifically, several endolysins that target gram-positive bacteria are currently being evaluated in clinical trials, reflecting increasing interest in their therapeutic application. Research involving endolysins has expanded exponentially over the last 20 years, which has resulted in a substantial diversification. With most of the field having focused on endolysin discovery, biochemical characterization and applying protein engineering strategies, it remains unclear whether endolysins should eventually be implemented as stand-alone antimicrobials or alongside standard-of-care antibiotics, an ambiguity that is also reflected in the endolysins that are currently being evaluated in clinical trials. This selective review, inspired by a selection of preclinical studies in which endolysin monotherapy had inconsistent outcomes, concludes that endolysins hold their greatest therapeutic potential when used in combination with standard-of-care antibiotics, except in cases, where therapy is limited to a local or topical application only. In the latter, antibiotic supplementation can negatively impact the microbiome that is essential to maintain, for example, skin, ear, eye, nasopharyngeal, gut and vaginal homeostasis. By combining endolysins with antibiotics that preferably target the bacterial cell wall or membrane, such as β-lactams, as well as lipo- and glycopeptides, synergistic or additive effects can be exploited that substantially reduce minimal inhibitory concentrations, restoring antibiotic susceptibility in otherwise resistant bacteria. Overall, this selective review asserts that endolysins may be best implemented alongside standard-of-care antibiotics, as this may lead to more consistent and reliable clinical outcomes, particularly in systemic infections.},
}

@article {pmid41514445,
year = {2026},
author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C},
title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02318-0},
pmid = {41514445},
issn = {2049-2618},
support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.

RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.

CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.},
}

@article {pmid41514433,
year = {2026},
author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02309-1},
pmid = {41514433},
issn = {2049-2618},
support = {2023YFD1801100//National Key R&D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&D Program of Ningxia Hui Autonomous Region/ ; },
abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.

RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen α-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.

CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through α-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.},
}

@article {pmid41514203,
year = {2026},
author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S},
title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04678-x},
pmid = {41514203},
issn = {1471-2180},
abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.},
}

@article {pmid41514163,
year = {2026},
author = {Cullen, JT and Lawlor, PG and Cormican, P and Gardiner, GE},
title = {Profiling the bacteriome of a diet fed in meal or pelleted form, delivered as dry, wet/dry or liquid feed and its impact on the fecal and intestinal bacteriome of grow-finisher pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf461},
pmid = {41514163},
issn = {1525-3163},
abstract = {Research is limited on how feed-associated microbes impact the intestinal bacteriome, growth and feed efficiency of pigs. The aims of this study were to; (1) profile the bacteriome of a meal or pelleted diet, delivered as dry, wet/dry or liquid feed using 16S rRNA gene sequencing; (2) determine its impact on the fecal and intestinal bacteriome of grow-finisher pigs; (3) investigate if differentially abundant bacterial taxa are correlated with growth parameters of these pigs. The experiment was a 2 x 3 factorial arrangement, with two factors for feed form (meal, pellets) and three factors for feed delivery (dry, liquid, wet/dry). It involved 216 Danavil Duroc x (Large White x Landrace) pigs penned in same sex pen groups of 6 pigs of similar weight (average ∼33.3 kg). Pen groups were blocked by sex and weight before being randomly assigned to 1 of 6 wheat-barley-soya-based dietary treatments in a completely randomised block design: (1) Dry meal; (2) Dry pellets; (3) Liquid meal; (4) Liquid pellets; (5) Wet/dry meal; (6) Wet/dry pellets. Diets were fed on an ad-libitum basis for 64 days. Liquid feed was prepared at a water: feed ratio of 2.5:1 (fresh matter basis). Dry feed was sampled from silos and bags and liquid feed from mixing tanks and troughs. Bacterial richness was lower in the dry pellets compared to meal (P ≤ 0.05). The liquid feed bacteriome was more diverse than that of dry feed (P ≤ 0.001). Weissella and Leuconostoc had higher relative abundance (RA) in residual-trough sampled liquid feed compared to mixing tank and fresh trough-sampled feed. The ileal bacteriome was more diverse (P ≤ 0.01) in meal-fed than pellet-fed pigs, with higher RA of Megasphaera and Mitsuokella, while Streptococcus and Escherichia-Shigella had greater RA in pellet-fed pigs (P ≤ 0.01). Lactobacillus was enriched in the intestinal digesta of liquid meal-fed pigs (P ≤ 0.05), corresponding with its predominance in this diet. Liquid meal-, liquid pellet- and wet/dry pellet-fed pigs had the highest average daily gain (P < 0.001). Feed conversion efficiency (FCE) was better in dry pellet-fed compared to liquid-fed pigs (P < 0.001). Leuconostoc (associated with feed fermentation) was most abundant in the feces and ileal digesta of liquid-fed pigs and correlated with poorer FCE (P ≤ 0.05). The same Leuconostoc found in liquid feed were also detected in the digesta and feces of liquid-fed pigs, implicating feed bacteria as a potential cause of the poorer FCE of liquid-fed pigs.},
}

@article {pmid41514147,
year = {2026},
author = {Guo, X and Dai, H and Jia, Z and Peng, Y and Lu, L and Su, Y and Li, J and Li, Q and Huang, Z and Wang, Y and Qi, F and Li, D and Lv, X and Liang, Y and Ma, B},
title = {Reactive oxygen species in the rhizosphere orchestrate the recruitment of beneficial bacteria.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {41514147},
issn = {1460-2075},
support = {42090060,42277283//the National Natural Science Foundation of China/ ; 2024SSYS0104,2021C02064-7 and 2024ZD1000603//Key Research and Development Program of Zhejiang Province (Key R&D plan of Zhejiang Province)/ ; 2024M762854//| Postdoctoral Research Foundation of China (China Postdoctoral Research Foundation)/ ; },
abstract = {Respiratory burst oxidase homolog D (RBOHD)-dependent reactive oxygen species (ROS) in Arabidopsis are well known to suppress pathogen colonization, but their influence on beneficial microbes remains unclear. Here, we found that the beneficial rhizobacterium Pseudomonas anguilliseptica was significantly less enriched in the rhizosphere of rbohD mutants than in that of wild-type plants. Conversely, elevated rhizosphere ROS levels, either triggered by pretreatment with pathogenic Dickeya solani bacteria or caused by mutations in ROS scavenging genes (e.g., in apx1 and cat2 mutants), promoted the rhizosphere recruitment of P. anguilliseptica. This promoting effect was abolished by catalase treatment. In situ microfluidic chemotaxis assays further revealed that P. anguilliseptica exhibits a chemotactic response to low concentrations of hydrogen peroxide (≤ 500 nM), accompanied by upregulated expression of chemotaxis- and motility-related genes. Notably, inoculation of P. anguilliseptica effectively suppressed D. solani-induced disease symptoms, and this protective effect was attenuated by catalase treatment. Collectively, these findings reveal a previously unrecognized role of ROS in recruitment beneficial microbiota to enhance plant growth and suppress disease symptoms.},
}

@article {pmid41513966,
year = {2026},
author = {Grübbel, H and Ly-Sauerbrey, Y and Arndt, F and Pavletić, B and Leuko, S and Rinderknecht, F},
title = {Short-time thermal inactivation of surrogates of the public transport microbiome with a low-cost thermoresistometer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35087-3},
pmid = {41513966},
issn = {2045-2322},
abstract = {In this study, the thermal inactivation of the bacterial genera Staphylococcus, Enterococcus and Burkholderia, which can be found in public transportation environments, as well as the bacteriophage MS2 as a surrogate for potential viral pathogens are investigated. To quantify the thermal inactivation characteristic, an automated and inexpensive thermoresistometer is constructed and set up, which enables the microorganisms to be exposed to short-term thermal shocks. The time dependent temperature curves were measured to account for heat-up and cooling times. Afterwards, the microorganisms were exposed to temperatures in the range of [Formula: see text] to [Formula: see text] for durations of 2 s up to 10 s and the thermal inactivation of the respective microorganisms was measured by counting colony forming units (CFU) and plague forming units (PFU). The data was visualized and fitted to an analytical thermodynamic model based on a first-order reaction and the Arrhenius equation to predict thermal inactivation times. This study reports the first measured thermal inactivation values for E. viikkiensis and B. lata, which have not been studied before. The results for MS2 and S. capitis show significantly shorter inactivation times than previous experiments. After exposure to [Formula: see text] for 2 s there was no measurable survival of all tested microorganisms. The semi-automated test setup used allows for consistent measurements and can be adapted by other research groups.},
}

@article {pmid41513795,
year = {2026},
author = {Wadia, R},
title = {Microbiome signatures in cancer.},
journal = {British dental journal},
volume = {240},
number = {1},
pages = {42},
doi = {10.1038/s41415-025-9491-8},
pmid = {41513795},
issn = {1476-5373},
}

@article {pmid41513699,
year = {2026},
author = {Veerus, L and Subrahmanian, A and Blaser, MJ},
title = {The testobolome in microbial testosterone metabolism and human health.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {9},
pmid = {41513699},
issn = {2055-5008},
support = {NIH U01AI22245/NH/NIH HHS/United States ; },
mesh = {*Testosterone/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism/classification/genetics ; },
abstract = {We propose the term testobolome, analogous to the estrobolome, to describe gut bacteria that metabolize testosterone. Testosterone undergoes microbial transformations similar to estrogens, potentially influencing host hormone homeostasis and health. This review defines the testobolome, identifies its known members, and explores mechanisms that are shared or distinct from the estrobolome. We outline a framework for future research into microbiome-mediated steroid metabolism, including its role in aging and hormone-driven diseases.},
}

*Testosterone/metabolism
Humans
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism/classification/genetics

@article {pmid41513667,
year = {2026},
author = {Azizan, N and Al-Maleki, AR and Rofiee, MS and Karajacob, AS and Loke, MF and Goh, JPE and Kallarakkal, TG and Wan Harun, WHA and Vaithilingam, RD and Teh, LK and Salleh, MZ and Tay, ST},
title = {Metabolomic profiling reveals alterations in Candida pathophysiology and host interactions during primary oral candidiasis and following antifungal treatment.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1089},
pmid = {41513667},
issn = {2045-2322},
support = {DP KPT FRGS/1/2019/SKK11/UM/01/1//Ministry of Higher Education, Malaysia/ ; },
mesh = {Humans ; *Antifungal Agents/therapeutic use/pharmacology ; *Candidiasis, Oral/drug therapy/metabolism/microbiology/physiopathology ; *Metabolomics/methods ; Female ; Male ; Middle Aged ; Adult ; *Metabolome ; Aged ; *Candida/drug effects/pathogenicity/metabolism ; *Host-Pathogen Interactions ; },
abstract = {Comparative metabolomics may shed light on host immunity and biology in oral candidiasis (oral thrush). Untargeted metabolomic analyses were performed on oral rinses collected from 26 primary oral candidiasis patients (OT), 12 patients after antifungal treatment (AT), and 12 unaffected individuals (C). Host immune modulation metabolites against oral candidiasis, Candida virulence and antifungal properties were identified. The upregulation of C17 sphinganine, L-leucine, monoacylglycerol, phosphatidylethanolamine, and spermine, in OT and AT groups, highlights the role of host immunity in Candida clearance. The altered sphingolipid levels suggest disrupted membrane integrity and immune function, while dysregulated amino acid, purine, and glutathione metabolism reflect oxidative stress and inflammation. Antifungal metabolites, specifically dichloroacetate, 1-monopalmitin, and undecane-2-one, were significantly upregulated in the OT group; conversely, fatty acids (palmitic amide, linoleamide, stearamide, and pentadecanal) were downregulated. Metabolomic similarities between oral candidiasis and xerostomia were evident, with shared markers such as L-valine, L-leucine, D-proline and 4-hydroxyphenylpyruvic acid. Increases in lipid metabolites, carboxylic acids, and amino acids, particularly L-leucine and hypoxanthine in patients upon resolution of oral candidiasis following antifungal treatment suggests fungal clearance, immune activation and recovery from oxidative stress. Some metabolites identified in oral candidiasis patients have reported roles in oral carcinogenesis, however, the findings remain observational and warrant further validation. Our results demonstrate that oral candidiasis is associated with distinct metabolomic alterations compared with healthy controls, and that antifungal therapy reshapes the oral metabolic profiles via complex host-microbiome-fungal metabolic pathways. The identification of oral candidiasis-associated metabolites also highlights their potential as non-invasive biomarkers and therapeutic targets for oral healthcare.},
}

Humans
*Antifungal Agents/therapeutic use/pharmacology
*Candidiasis, Oral/drug therapy/metabolism/microbiology/physiopathology
*Metabolomics/methods
Female
Male
Middle Aged
Adult
*Metabolome
Aged
*Candida/drug effects/pathogenicity/metabolism
*Host-Pathogen Interactions

@article {pmid41513661,
year = {2026},
author = {Meyer, AR and Tan, JP and Mihaila, MP and Neugebauer, M and Nyström, L and Bokulich, NA},
title = {Shipped and shifted: modeling collection-induced bias in microbiome multi-omics using a tractable fermentation system.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00909-1},
pmid = {41513661},
issn = {2055-5008},
support = {101060247//HORIZON EUROPE European Research Council/ ; 101060247//HORIZON EUROPE European Research Council/ ; 22.00210//Swiss State Secretariat for Education, Research and Innovation (SERI)/ ; 22.00210//Swiss State Secretariat for Education, Research and Innovation (SERI)/ ; },
abstract = {Large-scale, decentralized microbiome sampling surveys and citizen science initiatives often require periods of storage at ambient temperature, potentially altering sample composition during collection and transport. We developed a generalizable framework to quantify and model these biases using sourdough as a tractable fermentation system, with samples subjected to controlled storage conditions (4 °C, 17 °C, 30 °C, regularly sampled up to 28 days). Machine-learning models paired with multi-omics profiling-including microbiome, targeted and untargeted metabolome profiling, and cultivation-revealed temperature-dependent shifts in bacterial community structure and metabolic profiles, while fungal communities remained stable. Storage induced ecological restructuring, marked by reduced network modularity and increased centrality of dominant taxa at higher temperatures. Notably, storage duration and temperature were strongly encoded in the multi-omics data, with temperature exerting a more pronounced influence than time. 24 of the top 25 predictors of storage condition were metabolites, underscoring functional layers as both sensitive to and informative of environmental exposure. These findings demonstrate that even short-term ambient storage (<2 days) can substantially reshape microbiome, metabolome, and biochemical profiles, posing risks to data comparability in decentralized studies and emphasizing the need to recognize and address such biases. Critically, the high predictability of storage history offers a path toward bias detection and correction- particularly when standardized collection protocols are infeasible, as is common in decentralized sampling contexts. Our approach enables robust quantification and modeling of such storage effects across multi-omics datasets, unlocking more accurate interpretation of large-scale microbiome surveys.},
}

@article {pmid41513603,
year = {2026},
author = {Liu, P and Yang, Z and Yin, Q and Jin, X and Dong, Y and Luo, Y and Tao, B and Xu, X and Cheng, Y and Yang, B},
title = {A community screening tool for neuropsychiatric symptoms in the elderly: integrating cortisol, microbiome, and social factors with machine learning.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-025-03797-3},
pmid = {41513603},
issn = {2158-3188},
abstract = {Neuropsychiatric symptoms (NPS) are early indicators of cognitive decline due to neurodegenerative diseases, and their timely detection is of the utmost importance. We aimed to develop and validate methods for large-scale NPS screening among elderly individuals and explore underlying metabolic mechanisms. This observational, cross-section study involved 138 and 200 participants in the modeling and external validation cohorts, respectively, chosen from community healthcare centers in Chongqing, China. Data collection involved demographic questionnaires, saliva samples for oral microbiome analysis, and assays for other biomarkers (IL-6, IL-1β, TNF-α, Cath-B and cortisol). EXtreme gradient boosting(XGBoost), support vector machine(SVM), and logistic regression(LR) were developed with RFE and LASSO. The models were primarily evaluated using AUROC and F1 scores. The best model was interpreted using SHAP values, while the LR model was transformed into a nomogram. Additionally, BioCyc function pathway analysis was used to predict the functional shift of biomarkers. The genus-augmented XGBoost model achieved the highest performance, with an AUROC of 0.936 and an F1 score of 0.864, outperforming other models. The LR model was converted into a nomogram to facilitate NPS-risk assessment in community settings. The external validation confirmed the strong predictive power (AUROC = 0.986, F1 score = 0.944). Enrichment and correlation analyses revealed cortisol and microbial interactions with pathways such as the pentose phosphate pathway and enterobacterial common antigen biosynthesis. The XGBoost-augmented model and nomogram offer promising tools for community-based NPS screening, while enrichment analysis provides insights into biological mechanisms.},
}

@article {pmid41513411,
year = {2026},
author = {Cristoferi, L and D'Amato, D and Maino, C and Bernasconi, D and Dinelli, ME and Malandrin, SMI and Facciotti, F and Festa, MM and Gerussi, A and Rossi, E and Malinverno, F and Tettamanti, P and Cazzaniga, ME and Corso, R and Ippolito, D and Galimberti, S and Invernizzi, P and Carbone, M},
title = {Prospective, randomised, placebo-controlled, phase 2 clinical trial assessing the efficacy and safety of oral vancomycin in patients with primary sclerosing cholangitis with/out inflammatory bowel disease in Italy: study protocol of VanC-IT trial.},
journal = {BMJ open},
volume = {16},
number = {1},
pages = {e106630},
doi = {10.1136/bmjopen-2025-106630},
pmid = {41513411},
issn = {2044-6055},
mesh = {Humans ; *Cholangitis, Sclerosing/drug therapy/complications ; *Inflammatory Bowel Diseases/complications/drug therapy ; Italy ; Adult ; Adolescent ; Middle Aged ; Prospective Studies ; *Vancomycin/administration & dosage/therapeutic use/adverse effects ; Administration, Oral ; *Anti-Bacterial Agents/administration & dosage/therapeutic use/adverse effects ; Young Adult ; Aged ; Female ; Male ; Randomized Controlled Trials as Topic ; Clinical Trials, Phase II as Topic ; Treatment Outcome ; },
abstract = {BACKGROUND: Primary sclerosing cholangitis (PSC) is the classical hepatobiliary manifestation of inflammatory bowel disease (IBD). No therapy currently halts disease progression. The strong gut-liver axis implicated in PSC pathogenesis supports the investigation of microbiome-targeted treatments. Oral vancomycin (OV), an antibiotic with potential immunomodulatory properties, has shown encouraging results in improving clinical symptoms and liver biochemistry in PSC. However, prospective data on its safety and efficacy remain limited.

METHODS AND ANALYSIS: Oral Vancomycin for primary sclerosing Cholangitis in ITaly (VanC-IT) is a phase II, dose-finding, randomised, placebo-controlled, trial designed to evaluate the efficacy and safety of OV in patients with PSC, with or without underlying IBD. Adults and adolescents aged 15-75 years will be enrolled following a 10-week screening and run-in period and randomised in a 1:1:1 ratio to receive either placebo, OV 750 mg/day or OV 1500 mg/day for 24 weeks. Randomisation will be stratified by baseline liver stiffness (< or ≥14.4 kPa). Participants will be followed at 4 and 12 weeks post-treatment. The primary efficacy outcome is the change in serum alkaline phosphatase at 24 weeks. Key secondary outcomes will assess the safety, the impact of OV on liver biochemistry, PSC risk scores, circulating and imaging markers of liver disease, IBD activity, quality of life and incidence of PSC-related clinical events. Key translational aims include sequencing of the faecal microbiota, metabolomic profiling of serum and stool samples and immunological profiling of serum associated with OV treatment.

ETHICS AND DISSEMINATION: The protocol has been approved by the Ethics Committee CE Brianza on 10 February 2023, number 4017. Trial registration number NCT05876182. Participants will be required to provide written informed consent. The results of this trial will be disseminated through national and international presentations and peer-reviewed publications.

TRIAL REGISTRATION NUMBER: NCT05876182.},
}

Humans
*Cholangitis, Sclerosing/drug therapy/complications
*Inflammatory Bowel Diseases/complications/drug therapy
Italy
Adult
Adolescent
Middle Aged
Prospective Studies
*Vancomycin/administration & dosage/therapeutic use/adverse effects
Administration, Oral
*Anti-Bacterial Agents/administration & dosage/therapeutic use/adverse effects
Young Adult
Aged
Female
Male
Randomized Controlled Trials as Topic
Clinical Trials, Phase II as Topic
Treatment Outcome

@article {pmid41513029,
year = {2026},
author = {Cross, CB and Bowen, JM and Leifert, WR and Beale, DJ and Francois, M and Joshi, R and Fosh, BG and Coller, JK and Tuke, J and Bareham, M and Cosier, DJ and To, LH and Ryan, FJ and Wardill, HR},
title = {Pre-treatment Gut Microbiome and Salivary Metabolome Signatures Associate with Chemotherapy-Induced Cognitive Decline in Women with Breast Cancer: A Prospective Pilot Study.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {218234},
doi = {10.1016/j.canlet.2025.218234},
pmid = {41513029},
issn = {1872-7980},
}

@article {pmid41512948,
year = {2026},
author = {Masso, ZF and Ebrahim Mullah, HB and Thiba, A and Dinat, S and Nweke Supervisor, EE and Norton, GR and Woodiwiss, AJ and Cromarty, AD and Candy, GP},
title = {Identification of multiple cardiotonic steroids in faecal material of untreated humans and rat strains.},
journal = {Steroids},
volume = {},
number = {},
pages = {109747},
doi = {10.1016/j.steroids.2026.109747},
pmid = {41512948},
issn = {1878-5867},
abstract = {UNLABELLED: Endogenous cardiotonic steroid (CTS) concentrations are raised in cardiovascular diseases. CTSs undergo gastro-hepatobiliary recirculation, with the gut being an important route of elimination, yet the presence of CTSs in faecal material is seldom reported. This study investigated methods to extract and identify the presence of CTSs in faecal material of rats and humans without prior treatment.

METHODS: Freeze-dried faecal material from different untreated rat strains was extracted using various solvents, with separation and identification of CTSs using HPLC/MS. Preliminary results were obtained from human faecal material.

RESULTS: Multiple CTSs were identified in faecal material, with marinobufagenin (MBG) predominant. Telocinobufagin was only detected in certain rat strains, whereas the extraction methods used did not recover ouabain. MBG and digoxin were elevated in Dahl salt sensitive rats fed supplementary salt. Bufalin was present in most spontaneously hypertensive rats (SHRs) but was not detectable in Wistar Kyoto rats (WKY). Conversely, digitoxin was detected in most WKYs but only few SHRs. Levels of digitoxin and bufalin remained relatively constant over 24 days in untreated rats. Solvent selection was critical in determining the CTSs extracted from human faecal material.

CONCLUSIONS: Multiple CTSs were detected in faecal material of untreated rats and humans Steroids varied between rat strains and aligned with phenotype. Extraction requires further solvent optimisation and the use of tandem MS/MS is essential to reliably detect the profile of CTSs present. Analysis of CTSs present in readily available faecal material will enable studies to determine relationships between CTSs, the microbiome and disease progression.},
}

@article {pmid41512779,
year = {2026},
author = {Sawangproh, W and Phaenark, C and Paejaroen, P},
title = {Microplastic pollution in annelids: A systematic review of species-specific impacts, toxicity pathways, and ecological risks.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119686},
doi = {10.1016/j.ecoenv.2026.119686},
pmid = {41512779},
issn = {1090-2414},
abstract = {Microplastic (MP) pollution has emerged as a pervasive environmental stressor affecting terrestrial, freshwater, and marine ecosystems, with sediment-associated particles posing risks due to their persistence, bioavailability, and interactions with organisms and co-occurring contaminants. Annelids, including oligochaetes and polychaetes, are key ecosystem engineers that regulate sediment structure, nutrient cycling, and organic matter decomposition, making them highly relevant for evaluating the ecological risks of MP and nanoplastic (NP; <1 µm) contamination. Here, we synthesize peer-reviewed studies published up to 30 March 2025 to assess species-specific responses, toxicity pathways, and ecological implications of MP and NP exposure across terrestrial, freshwater, and marine annelids. By integrating evidence within a feeding-guild framework, we show that annelid responses are strongly trait-dependent rather than uniform. Deposit feeders and detritivores, such as Arenicola marina, Lumbriculus variegatus, Eisenia fetida, and Enchytraeus crypticus, frequently exhibit oxidative stress, altered energy allocation, gut microbiome disruption, and reproductive impairment. In contrast, filter feeders, including Sabella spallanzanii, often function as particle sinks with limited direct physiological effects, while carnivorous species, such as Hermodice carunculata, facilitate trophic transfer of MPs. Particle characteristics, particularly small size (<100 µm), irregular morphology, polymer type (notably polyethylene and polystyrene), and chemical aging, emerge as consistent determinants of adverse outcomes. Conversely, survival and population-level effects are often absent under short-term or environmentally realistic exposures, indicating compensatory physiological responses and limitations of standard toxicity endpoints. Overall, this review demonstrates that annelids act not only as sensitive sentinels of plastic contamination but also as active regulators of MP fate and ecological risk in sediment-based ecosystems.},
}

@article {pmid41512666,
year = {2026},
author = {Liu, JB and Li, S and Sun, GZ and Lin, ZX and Miao, ZM},
title = {Gut microbiota modulation by novel synbiotic improves production performance and ovarian function in aged laying hens via gut-ovary axis.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106394},
doi = {10.1016/j.psj.2026.106394},
pmid = {41512666},
issn = {1525-3171},
abstract = {The management of oxidative stress and ovarian dysfunction associated with aged laying hens, which is highly involved in gut microbiota, has been suggested as a feasible approach to improve production performance. Here, we investigated the effects of a novel synbiotic (Bacillus amyloliquefaciens + inulin, BAI), a gut microbiota regulator, on the improvement of production performance in aged laying hens, and dissected the underlying mechanisms using multi-omics analysis. Our findings showed that, compared to the control, high-dosage BAI supplementation significantly improved production performance; enhanced intestinal health, evidenced by the increase of villus height (p < 0.01), the expression of gut barrier-related genes (Claudin-1 and Claudin-2) (all p < 0.001), and immune levels (SIgA and IFN-γ) (all p < 0.01); meliorated ovarian function, confirmed by reduced oxidative stress (p < 0.001) and pathological lesions, as well as increased follicle numbers (p < 0.01 or p < 0.001), serum contents of reproductive hormone (estrogen, luteinizing hormone, and follicle-stimulating hormone) (p < 0.05 or p < 0.001), and the mRNA levels of yolk precursor synthesis-associated genes (APOVLDL-Ⅱ, VTG-Ⅱ, and VLDLR) (all p < 0.001). The 16S rRNA sequencing showed that BAI augmented the relative amount of Lactobacillus, Akkermansia, and Bacteroides and other short-chain fatty acids (SCFAs)-producers. Blood metabolome analysis demonstrated that the predominant metabolites changed by BAI were principally involved in SCFA metabolism, steroid hormone biosynthesis, steroid biosynthesis, and intestinal immune network for IgA production. Ovarian transcriptome analysis indicated that BAI significantly inhibited pathways of ferroptosis and peroxisome, confirmed by RT-qPCR. Furthermore, fecal microbiota transplantation (FMT) from BAI-treated aged hens improved production performance, ovarian function, and oxidative stress status in antibiotic-administrated hens. In sum, our study uncovers that BAI improves production performance and ovarian dysfunction via gut microbiota in aged laying hens. Thus, modulating gut microbiome is an effective approach to laying rate reduction of aged hens.},
}

@article {pmid41512635,
year = {2025},
author = {Li, N and Zhu, Z and Wu, S and Gong, D and Day, R and Vijayakumar, V and Yu, X and Chen, Q and Feng, Y and Wang, Q and Hu, Z and Li, J and Du, J and Xu, C and Li, W and Chen, L and Hu, J and Li, X},
title = {Effects of a novel synbiotic intervention on abdominal visceral fat reductions and gut microbiota in overweight and obese adults: A randomized, double-blind, placebo-controlled trial.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {57},
number = {},
pages = {106560},
doi = {10.1016/j.clnu.2025.106560},
pmid = {41512635},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: Emerging evidence highlight the gut microbiome as an important regulator of metabolic health, with probiotics and prebiotics demonstrating exciting potential for their role in health promotion. This study aims to investigate a novel synbiotic formulation comprising four probiotic strains (Bifidobacterium animalis subsp. lactis CECT 8145, and three Lacticaseibacillus rhamnosus strains), prebiotics (inulin, fructooligosaccharides), and Chrysanthemum morifolium extract. We hypothesized that this intervention would improve metabolic health parameters, particularly visceral adiposity.

METHODS: In a 12-week, double-blind, randomized, placebo-controlled, parallel-group trial with a 6-week post-intervention follow-up, 112 participants (BMI: 24.0-34.9 kg/m[2]) received daily synbiotic or a matched placebo. Changes in visceral adipose tissue (VAT) area, serving as the primary endpoint, were quantified by dual-energy X-ray absorptiometry (DXA). Secondary outcomes included analysis of blood biochemical parameters, body composition, and fecal microbiota characterization.

RESULTS: Compared with placebo, synbiotic supplementation significantly reduced VAT area from baseline to week 12 (p = 0.048). In subgroup analyses by gender and BMI, the effect was more pronounced in men than in women (p = 0.051) and was highly significant in individuals with 24 ≤ BMI <28 (p = 0.003). However, subcutaneous adipose tissue (SAT) increased in the 24 ≤ BMI <28 subgroup (p = 0.027). Although no significant changes occurred in blood biochemistry, BMI, or waist circumference, the synbiotic group showed a trend toward greater total body fat reduction between weeks 12-18 (p = 0.077). Microbiota analysis revealed transient enrichment of B. animalis subsp. lactis (ASV110) and L. rhamnosus (ASV473), which dissipated by week 18.

CONCLUSIONS: This synbiotic formulation reduced visceral fat, a key driver of metabolic dysfunction, and modulated adipose distribution, particularly in men and overweight (24 ≤ BMI <28) individuals. These results support its use as a functional food for visceral adiposity management.

TRIAL REGISTRATION: This study was registered on the website of www.chictr.org.cn, number ChiCTR2400088457.},
}

@article {pmid41512573,
year = {2025},
author = {Henson, CC and Green, K and Slater, R and McLaughlin, J and Hann, M and Barraclough, L and Burden, S and Gillespie, L and Ward, T and Probert, C},
title = {Feasibility Study Exploring the Effect of Pelvic Radiotherapy on the Intestinal Microbiome and Metabolome to Improve the Detection and Management of Gastrointestinal Toxicity.},
journal = {Clinical oncology (Royal College of Radiologists (Great Britain))},
volume = {50},
number = {},
pages = {103994},
doi = {10.1016/j.clon.2025.103994},
pmid = {41512573},
issn = {1433-2981},
abstract = {AIMS: Eighty percent patients develop gastrointestinal (GI) symptoms during pelvic radiotherapy. The triggering event is a known enabling identification of pathophysiological changes. The focus of this study was feasibility (identification, recruitment, and retention), however, exploratory microbiome and metabolome analyses were performed.

MATERIALS AND METHODS: Patients undergoing pelvic radiotherapy underwent faecal sampling (baseline, week 4, and 6 months), with assessment of GI toxicity using the Imflammatory Bowel Disease Questionnaire (IBDQ) bowel (IBDQB) subset. Participants were split into 2 groups based on IBDQB at week-4. Exploratory analysis was performed to identify differences in metabolome (gas chromatography-mass spectrometry) and microbiome (16s rRNA sequencing).

RESULTS: Two hundred twenty-seven patients were screened, 69 were approached, and 17 were recruited over 18 months (mean age: 61.6 ± 15.3 years; 14 female; 1 withdrawal). Metabolome analysis showed lower heptanal and octanal in baseline samples of patients with higher GI toxicity; lower (methyltrisulfanyl)methane in week-4 samples of patients with higher GI toxicity; and higher butanoic acid and benzaldehyde in month 6 samples in patients with higher GI toxicity. Whole-group microbiome analysis showed a trend towards decreased alpha diversity at 4 weeks; no differences in beta diversity; and a trend towards increase in Lachnoclostridium and decrease in Ruminococcaceae Incertae sedis at week 4. Microbiome analysis split by GI toxicity showed lower alpha diversity for the high GI toxicity group (each timepoint); no significant difference in beta diversity between groups; more genera differentially abundant between the GI toxicity groups at 4 weeks, than at other timepoints.

CONCLUSION: Recruitment was lower than anticipated. Attrition was low. Exploratory analysis suggests heptanal and octanal may have a role as a biomarker for GI toxicity, and lower alpha diversity may predict GI toxicity, with Lachnoclostridium and Ruminococcaceae Incertae sedis as bacteria of interest.},
}

@article {pmid41512536,
year = {2026},
author = {Xu, J and Fang, J and Wu, R and Wang, Y and Zhang, C and Wang, X and Qiu, T},
title = {Exploring the genomic features and plant growth-promoting properties of Enterobacter vonholyi Y16 isolated from maize rhizosphere.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128437},
doi = {10.1016/j.micres.2026.128437},
pmid = {41512536},
issn = {1618-0623},
abstract = {Maize yields rely heavily on chemical fertilizers, yet over half of the applied nitrogen remains unutilized, and excessive use harms soil, highlighting the need for sustainable alternatives. Plant growth-promoting rhizobacteria (PGPR) enhance plant growth and stress resistance, providing sustainable agricultural solutions. Here, we isolated Enterobacter vonholyi Y16 from the maize rhizosphere, and demonstrated multiple plant growth-promoting traits, including phosphate solubilization, potassium solubilization, siderophore secretion, and indole-3-acetic acid biosynthesis. An integrated approach combining rhizosphere microbiome profiling with plant transcriptomics was employed to elucidate the mechanisms of gene expression changes underlying PGPR-induced maize growth promotion. Inoculation with Y16 significantly increased primary root length in Arabidopsis thaliana by 16.7 %, and enhanced maize plant height, stem diameter, fresh shoot weight, and fresh root weight by 18.41 %, 22.32 %, 48.41 %, and 62.31 %, respectively. Strain Y16 successfully colonized the rhizosphere and influenced bacterial community composition under sterile soil conditions. Transcriptomic analysis revealed Y16-mediated regulation of key pathways, including plant hormone signaling, mitogen-activated protein kinase signaling, phenylpropanoid biosynthesis, and starch and sucrose metabolism. Notably, auxin-responsive genes were upregulated, correlating with Y16 abundance. These findings provide theoretical evidence for the molecular mechanisms of plant growth promotion by PGPR and offer insights for advancing sustainable agricultural development.},
}

@article {pmid41512232,
year = {2025},
author = {Kang, JW and Vemuganti, V and Jonaitis, EM and Johnson, SC and Asthana, S and Carlsson, CM and Chin, NA and Engelman, CD and Ulland, TK and Rey, FE and Bendlin, BB},
title = {Biomarkers.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21 Suppl 2},
number = {},
pages = {e105650},
doi = {10.1002/alz70856_105650},
pmid = {41512232},
issn = {1552-5279},
mesh = {Humans ; Male ; Female ; *Biomarkers/blood ; Aged ; *Alzheimer Disease/diagnosis ; Neuropsychological Tests ; *Imidazoles/blood ; Executive Function/physiology ; Middle Aged ; Aged, 80 and over ; Gastrointestinal Microbiome/physiology ; },
abstract = {BACKGROUND: Among the various modifiable risk factors for AD development, the gut microbiome stands out as a potential therapeutic target, offering opportunities for intervention in the very early stages to potentially prevent disease onset. Notably, specific gut microbial metabolites may critically modulate metabolic and neuroimmune mechanisms shared with type 2 diabetes (T2D) and atherosclerosis-conditions that increase the risk of neurovascular and neurodegenerative disorders. Among these metabolites, imidazole propionate (ImP), a gut bacteria-derived metabolite of histidine, has garnered attention for its potential to cross the blood-brain barrier and exacerbate neurodegenerative processes.

METHOD: Participants included in the analysis were from Wisconsin ADRC and Wisconsin Registry for Alzheimer's Prevention (WRAP) studies. ImP was determined using the Metabolon platform. Three composite tests for measuring executive functions, along with assessments of two other cognitive domains-immediate learning and delayed recall-were used to compute the global composite scores for the three-test version of the Preclinical Alzheimer's Cognitive Composite (PACC3). The PACC3 scores were derived using three distinct measures of executive functions-Animal Naming Test (PACC3-AN, n = 859), Category Fluency Test (PACC3-CFL, n = 1118), and Trail-Making Test B (PACC3-TRLB, n = 1116)-and subsequently transformed into z-scores. Ordinary Least Squares (OLS) multiple linear regression approach was used to evaluate the relationship between levels of ImP and cognitive scores while accounting for covariates such as age and sex in the analysis.

RESULT: Lower cognitive performance was associated with higher levels of plasma ImP while controlling for age and sex, even in cognitively normal individuals before the onset of detectable cognitive symptoms.

CONCLUSION: Despite the modest associations, the significance of predictors suggests these factors warrant further exploration in understanding their combined contribution to ImP levels and broader neurodegenerative mechanisms.},
}

Humans
Male
Female
*Biomarkers/blood
Aged
*Alzheimer Disease/diagnosis
Neuropsychological Tests
*Imidazoles/blood
Executive Function/physiology
Middle Aged
Aged, 80 and over
Gastrointestinal Microbiome/physiology

@article {pmid41511994,
year = {2026},
author = {Mullowney, MW and Moran, A and Hernandez, A and McMillin, M and Rose, AR and Moran, D and Little, J and Nguyen, AB and Patel, BK and Lehmann, CJ and Odenwald, MA and Pamer, EG and Yeo, KJ and Sidebottom, AM},
title = {Fecal butyrate and deoxycholic acid quantitation for rapid assessment of the gut microbiome.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0337727},
pmid = {41511994},
issn = {1932-6203},
mesh = {*Deoxycholic Acid/analysis ; Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; Chromatography, High Pressure Liquid ; *Butyrates/analysis ; Mass Spectrometry ; },
abstract = {The intestinal microbiome is composed of myriad microbial species with impacts on host health that are mediated by the production of metabolites. While loss of bacterial species and beneficial metabolites from the fecal microbiome is associated with development of a range of diseases and medical complications, there are currently no clinical diagnostic tests that rapidly identify individuals with microbiome deficiencies. This method aims to rapidly quantify fecal concentrations of butyrate and deoxycholic acid, as depletion of these two metabolites are associated with adverse clinical outcomes and result from the loss of a subset of health-associated bacterial species. We present a rapid diagnostic screen based on 3-nitrophenylhydrazine derivatization and ultrahigh-performance liquid chromatography-mass spectrometry that measures fecal butyrate and deoxycholic acid concentrations as markers of microbiome function. A matrix-matched calibration curve was developed using a simulated fecal mixture to optimize accuracy and facilitate adherence to clinical laboratory regulations. The assay resulted in an analytical measurement range from 4.30-3030 µM (LLOQ = 3.71 µM) for butyrate and from 0.9-64.9 µM (LLOQ = 0.7 µM) for deoxycholic acid. Precision evaluation demonstrated a coefficient of variation <15% at all quality control levels tested. The rapid liquid chromatography-mass spectrometry screen can be performed in under an hour from extraction to provision of quantitative results, enabling the rapid identification of patients with defective microbiome function.},
}

*Deoxycholic Acid/analysis
Humans
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome
Chromatography, High Pressure Liquid
*Butyrates/analysis
Mass Spectrometry

@article {pmid41511948,
year = {2026},
author = {Cazals, A and Gebhardt-Henrich, S and Berger, Q and Rossignol, MN and Jardet, D and Toscano, MJ and Zerjal, T},
title = {Exploring the relationships between the gut microbiome composition and movement patterns of laying hens in a multitier cage-free housing system.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0340059},
pmid = {41511948},
issn = {1932-6203},
mesh = {Animals ; *Chickens/microbiology/physiology ; *Gastrointestinal Microbiome ; Female ; RNA, Ribosomal, 16S/genetics ; *Housing, Animal ; Bacteria/genetics/classification ; Cecum/microbiology ; *Behavior, Animal ; },
abstract = {In this study we investigated the relation between caecal microbiota composition and movement patterns in laying hens. We used hens from Pure line matings of Hendrix Genetics to continuously monitor the movement of individuals in a connected three-tier aviary throughout the laying period, from 18 to 60 weeks of age. The aviary contained three vertical tiers: a top-level, mid-level, and lower-level. In addition, the aviary had a floor littered and an attached wintergarden which was accessible from approximately 21 WOA onwards. Differences in the hens' use of space were observed including: differences in the number of visits and time spent in the wintergarden and litter areas. Microbiota characterization, using 16S rRNA gene sequencing from 237 samples, revealed an association (P < 0.05) between microbiome composition and the number of visits to the litter. We observed differences (adjusted P-value < 0.05) between hens that frequently visited the litter (>30 times/day) and those that visited the litter less often (<10 times/day) in five bacterial families and seven genera. Notably, hens classified as visiting the litter less often, showed an increased abundance of Coriobacteriales, Peptococcales, Oribacterium and Lachnoclostridium taxa. Overall, this study offers new insights on the potential role of the microbiota in hen movement patterns.},
}

Animals
*Chickens/microbiology/physiology
*Gastrointestinal Microbiome
Female
RNA, Ribosomal, 16S/genetics
*Housing, Animal
Bacteria/genetics/classification
Cecum/microbiology
*Behavior, Animal

@article {pmid41511880,
year = {2026},
author = {Gawron, J and Czech, M and Rückert, T and Holzmüller, V and Andreev, G and Burk, AC and Hartmann, A and Chatterjee, S and Andrieux, G and Marquard, FE and Baur, AS and Stell, AV and Krausz, M and Braun, LM and Osswald, N and Melchinger, W and Wertheimer, T and Proano-Vasco, AI and Maas-Bauer, K and Schmitt-Graeff, A and Boerries, M and Köhler, N and Ayuk, FA and Schell, C and Quante, M and Zeiser, R},
title = {Gastrin for the treatment of acute graft-versus-host disease of the stomach.},
journal = {Blood},
volume = {},
number = {},
pages = {},
doi = {10.1182/blood.2025031080},
pmid = {41511880},
issn = {1528-0020},
abstract = {Acute graft-versus-host disease (aGVHD) is a major cause of death after allogeneic hematopoietic cell transplantation (allo-HCT) and patients with steroid-refractory aGVHD have a dismal prognosis. We have previously shown that the enteroendocrine hormone glucagon-like peptide-2 (GLP-2) has tissue regenerative activity in the lower GI in mice and patients with steroid-refractory aGVHD. Here we explored the tissue protective effect of the enteroendocrine hormone gastrin for aGVHD of the stomach. We observed that aGVHD caused a loss of gastrin-producing G-cells and parietal cells (PCs) and an increase of pH in the stomach, while allogeneic T cells infiltrated the stomach wall. Pentagastrin treatment of aGVHD mice rescued the loss of PCs, normalized the pH in the stomach, increased stomach stem cell marker expression and abundance of LGR5+ cells, and changes in the stomach microbiome. Gastrin also increased the viability of stomach and small intestine organoids in vitro. Gast-/- mice experienced more severe aGVHD in the intestine and liver compared to WT mice, which was rescued by pentagastrin-treatment. In patients developing aGVHD, low gastrin levels in stomach biopsies were connected to reduced survival. Moreover, gastrin expression in the stomach correlated with aGVHD severity and tissue damage scores in independent patient cohorts. This study delineates the protective role of gastrin in aGVHD of the stomach in mice and patients and provides a rationale for therapeutic use of pentagastrin in a clinical trial for patients with aGVHD.},
}

@article {pmid41511735,
year = {2026},
author = {Balkrishna, A and Agarwal, U and Saxena, S and Sharma, G and Arya, V},
title = {Toward an Integrated Therapeutic Approach for Familial Hypercholesterolemia.},
journal = {Current medical science},
volume = {},
number = {},
pages = {},
pmid = {41511735},
issn = {2523-899X},
support = {F. No. Ad-35013/4/2022-KPMG-NMCG//Ministry of AYUSH, Government of India/ ; },
abstract = {Familial hypercholesterolemia (FH) is a heritable condition that disrupts the body's ability to clear low-density lipoprotein cholesterol (LDL-C), commonly known as "bad cholesterol" from the bloodstream. This leads to persistently elevated LDL levels from birth, significantly increasing the risk of premature atherosclerosis and cardiovascular events, such as heart attack and stroke. This occurs due to variations in genes such as low-density lipoprotein receptor (LDLR), apolipoprotein B (APOB), and proprotein convertase subtilisin/kexin type 9 (PCSK9). The treatments that are available for FH include pharmacological interventions, microbiome-based treatments, molecular approaches, nanotechnology methods, surgical procedures, nutraceuticals, herbal therapy, yoga and physical fitness methods, along with lifestyle management. This review discusses the adverse effects associated with various conventional treatment methods for hypercholesterolemia and the need for a safe and effective approach for the treatment of this genetic condition. An integrated approach combining pharmacological, molecular, and lifestyle interventions has emerged as a pragmatic solution. Yoga and fitness-based therapies positively impact lipid profiles, offering non-pharmacological and holistic adjunctive options. This comprehensive approach addresses the multifaceted aspects of FH management, considering genetic factors, socioeconomic considerations, and individualized patient needs.},
}

@article {pmid41511706,
year = {2026},
author = {Shekar, P and Pradeep, S and Shivamallu, C and Prashant, A and Vishwanath, P},
title = {Immune-microbiota crosstalk in colorectal cancer: mechanistic pathways, biomarkers, and translational therapeutics.},
journal = {Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico},
volume = {},
number = {},
pages = {},
pmid = {41511706},
issn = {1699-3055},
abstract = {Colorectal cancer (CRC) is caused by a complex interaction between genetic, environmental, and microbial risk factors, and intestinal microbiota has critical roles in inflammation, immunology, and epithelial integrity. Pathobionts from the intestines (Fusobacterium nucleatum, Bacteroides fragilis, and E. coli that produce colibactin) promote DNA damage, immunity protection from cancer therapy, and resistance to chemotherapy treatments. The beneficial commensals and metabolites of intestinal microbes (namely butyrate) increase the mucosal immune response and inhibit tumor-specific signaling mechanisms. Microbe controlled changes of populations of myeloid, lymphoid, and regulatory cells dictate the state of the tumor-immune system and provide actionable checkpoints and biomarkers for cancer therapy. An enormous variety of clinical interventions based on the gut microbiota (probiotics, prebiotics, and fecal microbiota transfer) and diagnostic approaches is currently being developed. Translational issues are difficult due to the interindividual variability and regulatory complexity of tumors. Research needs include standardizing multi-omics data from multidisciplinary teams and mechanistic validation in organoid and gnotobiotic models as well as prediction algorithms to optimize the microbiome-based medicine for individual patients. Targeting the immune-microbiota axis may provide new therapeutic strategies in the diagnosis, prognosis, and therapy of CRC.},
}

@article {pmid41511412,
year = {2026},
author = {Jeong, J and Baines, KJ and Maleki Vareki, S},
title = {Microbial-Derived Metabolites and Their Impact on Cancer Immunotherapy.},
journal = {Cancer immunology research},
volume = {},
number = {},
pages = {OF1-OF11},
doi = {10.1158/2326-6066.CIR-25-1018},
pmid = {41511412},
issn = {2326-6074},
support = {//Weston Family Foundation (WFF)/ ; //Lotte and John Hecht Memorial Foundation (LJHMF)/ ; //Ontario Institute for Cancer Research (OICR)/ ; },
abstract = {The gut microbiome has emerged as a modulator of both cancer progression and patient responses to therapies like immune checkpoint inhibitors (ICI). Recent evidence highlights microbially derived metabolites as key regulators of immune response and tumor microenvironment dynamics. This review explores the role of four prominent classes of bacterial metabolites-inosine, indole, bile acids, and short-chain fatty acids-in shaping antitumor immunity and modulating ICI efficacy. Each of these metabolites and their derivatives demonstrate complex and context-dependent effects on immune cells. The duality of exerting both pro- and anti-inflammatory effects underscores the therapeutic potential and challenges of metabolite-targeted interventions. By examining current preclinical findings and ongoing clinical trials, we identify promising avenues for enhancing immunotherapy through microbiome modulation and call for further mechanistic insights to inform precision treatment strategies.},
}

@article {pmid41511307,
year = {2025},
author = {Kang, S and Jeong, DY and Seo, J and Daily, JW and Park, S},
title = {Microbiota-Mediated Bile Acid Metabolism as a Mechanistic Framework for Precision Nutrition in Gastrointestinal and Metabolic Diseases.},
journal = {Cells},
volume = {15},
number = {1},
pages = {},
pmid = {41511307},
issn = {2073-4409},
support = {RS-2023-00208567//National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT/ ; },
mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/physiology ; *Metabolic Diseases/metabolism/microbiology ; *Gastrointestinal Diseases/microbiology/metabolism ; Animals ; *Precision Medicine ; },
abstract = {Gut microbiota play a central role in shaping bile acid (BA) metabolism through community-specific capacities for deconjugation, dehydroxylation, and other transformation reactions. Distinct microbiome compositional patterns-often referred to as enterotype-like clusters-correspond to reproducible functional profiles that generate unique BA metabolic signatures with relevance for metabolic and gastrointestinal health. This narrative review synthesizes current evidence describing the interplay between microbial composition, BA metabolism, and metabolic dysfunction. A structured literature search was conducted in PubMed, Web of Science, EMBASE, and Scopus using predefined keywords related to bile acids, microbiome composition, metabolic disorders, and enterotypes. Studies were screened for human clinical relevance and mechanistic insights into BA-microbiome interactions. Across the evidence base, Bacteroides-, Prevotella-, and Ruminococcus-associated community types consistently demonstrate different BA transformation capacities that influence secondary BA production and downstream host signaling through FXR and TGR5. These differences are linked to variation in metabolic dysfunction-associated steatotic liver disease, obesity, type 2 diabetes, inflammatory bowel disease, and colorectal cancer. Host genetic variations in BA synthesis, transport, and signaling further modify these microbiome-BA interactions, contributing to the heterogeneity of dietary intervention responses. Overall, the literature supports a model in which microbiome-derived BA profiles act as metabolic phenotypes that shape host lipid and glucose homeostasis, inflammation, and gut-liver axis integrity. Emerging clinical applications include microbiome-stratified dietary strategies, targeted probiotics with defined BA-modifying functions, and therapeutic approaches that align BA-modulating interventions with an individual's microbial metabolic capacity. Establishing integrated biomarker platforms combining microbiome clustering with BA profiling will be essential for advancing precision nutrition and personalized management of metabolic and gastrointestinal diseases.},
}

Humans
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome/physiology
*Metabolic Diseases/metabolism/microbiology
*Gastrointestinal Diseases/microbiology/metabolism
Animals
*Precision Medicine

@article {pmid41511192,
year = {2026},
author = {Shi, C and Li, L and Sun, XL and Liu, S and Zhou, Y},
title = {Polystyrene Microplastics Disrupt Vertical Transmission of the Breast Milk Microbiome, Impairing Early-Life Gut Colonization and Immune Development in Offspring.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {1},
pages = {e71448},
doi = {10.1096/fj.202503819R},
pmid = {41511192},
issn = {1530-6860},
support = {2025GY068//Public Welfare Application Research Project of Huzhou Science and Technology Bureau (CN)/ ; 2025C02106//Key Research and Development Program of Zhejiang Province (Key R&D plan of Zhejiang Province)/ ; },
mesh = {Female ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Pregnancy ; *Polystyrenes/toxicity ; Maternal Exposure/adverse effects ; Mice ; *Prenatal Exposure Delayed Effects ; *Milk/microbiology ; *Milk, Human/microbiology ; },
abstract = {Microplastics, as a class of emerging contaminants (ECs), have been found to accumulate in mammary tissue, and their potential transgenerational risks to offspring health have garnered widespread attention. Here, we investigated whether maternal microplastic exposure may alter the breast milk microbiome, thereby disrupting early intestinal microbiota colonization in offspring and affecting their immune development. Pregnant and lactating dams were exposed to two concentrations of polystyrene microplastics (PS-MPs, 10 and 40 mg/L) via drinking water. Our results showed that maternal PS-MPs exposure disrupted early gut microbiota colonization in offspring, manifested as imbalances in both maternal milk microbiota and offspring gut microbiota. Beneficial bacterial abundance decreased (e.g., Ligilactobacillus), while potentially harmful bacteria increased (e.g., Escherichia-Shigella). Concurrently, offspring from the exposed group exhibited excessive weight gain and impaired immune development, characterized by significantly reduced serum interleukin-6 (IL-6) levels, decreased splenic T-cell proportions, and compromised intestinal barrier integrity. Further analysis indicated that these outcomes were associated with alterations in milk microbiome structure and short-chain fatty acids (SCFAs) concentrations. Collectively, this study reveals the potential for maternal exposure to PS-MPs to impair offspring gut microbiota colonization and immune development by reshaping breast milk microbiota, suggesting the potential hazards of PS-MPs to maternal and infant health.},
}

Female
Animals
*Gastrointestinal Microbiome/drug effects
*Microplastics/toxicity
Pregnancy
*Polystyrenes/toxicity
Maternal Exposure/adverse effects
Mice
*Prenatal Exposure Delayed Effects
*Milk/microbiology
*Milk, Human/microbiology

@article {pmid41511110,
year = {2026},
author = {Gallardo Molina, P and Choi, BI and Vanek, M and Khan, MH and Tomasek, K and Kwant, AN and Dijkstra, P and de Vos, MGJ and Wolfe, AJ},
title = {SimUrine: a novel, fully defined artificial urinary medium for enhanced microbiological research of urinary bacteria.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0155925},
doi = {10.1128/aem.01559-25},
pmid = {41511110},
issn = {1098-5336},
abstract = {UNLABELLED: Urinary tract infections represent one of the most prevalent bacterial diseases, yet current diagnostic and research methodologies are hampered by inadequate culture media that fail to replicate the bladder biochemical environment. Conventional artificial urine formulations contain undefined components, lack essential nutrients, or inadequately support urinary microbiome (urobiome) growth. To address these limitations, we developed SimUrine, a fully defined synthetic urine medium that aims to replicate human bladder chemistry while supporting diverse microbial growth requirements. SimUrine was systematically developed through iterative optimization of multi-purpose artificial urine, incorporating defined concentrations of carbon sources, vitamins, trace elements, and amino acids within physiologically relevant ranges. The modular design enables component substitution without complete reformulation, facilitating customization for culturomics, antimicrobial susceptibility testing, and microbial ecology studies, while reducing batch-to-batch variability associated with authentic urine. Performance evaluation demonstrated SimUrine's capability to support the growth of fastidious urobiome members, including Lactobacillus species, Aerococcus urinae, and Corynebacterium riegelii, which fail to proliferate in conventional minimal media. Physicochemical characterization confirmed that SimUrine formulation exhibits properties within normal human urine ranges for density, conductivity, osmolarity, and viscosity, ensuring physiological relevance. Clinical applications revealed reduced antibiotic susceptibility compared to standard media, suggesting a more accurate representation of in vivo conditions. Co-culture experiments using Escherichia coli and Enterococcus faecalis demonstrated previously unobserved microbial interactions, highlighting SimUrine's utility for investigating urobiome dynamics. SimUrine represents a significant advancement in urobiome research methodology, providing a standardized, reproducible platform for investigating the urobiome under physiologically relevant conditions, potentially improving fundamental understanding and clinical diagnostic approaches.

IMPORTANCE: Urinary tract infections (UTIs) affect millions globally, yet current research and diagnostic methods rely on inadequate culture media that fail to replicate the bladder's unique biochemical environment. This fundamental limitation has hindered accurate UTI research and potentially compromised clinical treatment decisions. SimUrine addresses this critical gap as the first fully defined synthetic urine medium that mimics human bladder chemistry while supporting the growth of diverse urinary microbes. The breakthrough enables the cultivation of urobiome organisms in a minimal medium that resembles natural conditions, revealing novel microbial interactions that influence urinary health. Crucially, SimUrine demonstrates different antimicrobial susceptibility patterns compared to standard clinical media, suggesting current testing protocols may inaccurately predict treatment outcomes. This standardized, reproducible platform eliminates the variability of authentic urine samples while maintaining physiological relevance, potentially transforming urobiome research methodology and providing a new tool for the study of UTIs worldwide.},
}

@article {pmid41511078,
year = {2026},
author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P},
title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41511078},
issn = {2057-5858},
mesh = {*Feces/microbiology/virology ; Animals ; *Marsupialia/microbiology/virology/classification ; Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Viruses/genetics/classification ; },
abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.},
}

*Feces/microbiology/virology
Animals
*Marsupialia/microbiology/virology/classification
Phylogeny
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Viruses/genetics/classification

@article {pmid41510789,
year = {2026},
author = {Samy, A and Hassan, HMA and Elsherif, HMR},
title = {Synergistic roles of citric and formic acids and their salts on broiler health and performance.},
journal = {British poultry science},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/00071668.2025.2606833},
pmid = {41510789},
issn = {1466-1799},
abstract = {1. Organic acids have shown promise as safe and natural growth enhancers when added to broiler diets. 2. The current study aimed to assess how adding organic acids and their salts (OA+S) affected the intestinal microbiota, growth performance, antioxidant status and blood biochemical markers in broiler chickens.Four groups, each consisting of 90 chicks divided into six replicates (15 chicks per replicate), were randomly selected from 360 one-day-old chicks with similar initial body weights. 3. Birds fed a basal diet and received either: T1 (no addition; CTRL), T2 (1.5 g/kg feed formic acid + sodium formate, FFA), T3 (1.5 g/kg citric acid + sodium citrate, CCA) or T4 (0.75 g/kg each of FFA and CCA, MIX).Broilers fed MIX had the best BWG and FCR (p ≤ 0.05).4. All treatments significantly (p ≤ 0.05) improved performance compared to the control group. Antioxidant enzyme concentrations were higher in broiler chicks administered a combination of OA and their salts (FFA and CCA) relative to CTRL. 5. The levels of creatinine, aspartate aminotransferase (AST) and alanine aminotransferase (ALT) were not affected (p > 0.05) among all groups.6. The addition of FFA significantly elevated thyroid hormone levels (p ≤ 0.05); however, they remained within the normal range. 7. Feeding MIX enhanced immune responses to avian influenza H5, H9 and Newcastle disease ND titre compared to birds fed CTRL. 8. Lactobacillus spp. and total bacterial counts were higher in the FFA supplemented group than in CTRL.9. Broilers fed FFA had enhanced growth, better antioxidant status, improved gut microbiome and improved serum biochemical indicators, making it a safe and effective alternative to conventional antimicrobial growth promoters.},
}

@article {pmid41510741,
year = {2026},
author = {Xu, H and Huang, J and Guan, H and Wang, D and Yang, S},
title = {Citrus Flavanones as Neuroprotective Agents: Mechanisms and Dietary Relevance in Ischemic Stroke.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14131},
pmid = {41510741},
issn = {1520-5118},
abstract = {Neuroprotection is pivotal in ischemic stroke management. Citrus flavanones, abundant in citrus fruits and their derived products, demonstrate significant neuroprotective potential, yet a comprehensive review of their roles in ischemic stroke is lacking. This review clarifies their mechanisms and applications for ischemic stroke prevention/treatment. Profiles of citrus flavanones in different dietary sources are summarized, and the dietary relevance of the concentrations used in preclinical studies is critically discussed. Citrus flavanones exert protection through diverse mechanisms, including antioxidation, anti-inflammation, mitochondrial protection, autophagy modulation, apoptosis inhibition, endoplasmic reticulum stress suppression, and blood-brain barrier (BBB) preservation, with angiogenesis promotion also suggested. They interact with the central nervous system either directly by crossing the BBB or indirectly via the microbiome-gut-brain axis. This review offers valuable insights to guide future research and the development of citrus-flavanone-based functional foods or therapeutics for ischemic stroke.},
}

@article {pmid41510663,
year = {2026},
author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y},
title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09250},
pmid = {41510663},
issn = {1520-5118},
abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.},
}

@article {pmid41510046,
year = {2025},
author = {Saiedi, E and Shapouri, R and Haghi, F and Zeighami, H},
title = {Comparative analysis of gut microbiota composition in the fecal samples from type 2 diabetes mellitus patients and healthy individuals: a case control study.},
journal = {Iranian journal of microbiology},
volume = {17},
number = {6},
pages = {875-884},
pmid = {41510046},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Insulin resistance and elevated blood glucose levels are the hallmarks of Type 2 Diabetes Mellitus (T2DM), a chronic metabolic condition. Emerging research suggests that gut microbiota may play a causal role in T2DM. This study compares T2DM patients' gut microbiota to healthy controls, focusing on Lactobacillus, Bifidobacterium, Akkermansia muciniphila, Prevotella, Bacteroidetes, and Firmicutes.

MATERIALS AND METHODS: This case-control research involved 50 T2DM patients and 50 healthy controls, aged 39-75. Quantitative real-time PCR (qPCR) employing 16S rRNA gene primers was used to detect and quantify bacterial diversity in fecal samples. Statistical analyses were performed to compare the microbiota composition between groups.

RESULTS: The gut microbiome of patients with Type 2 Diabetes Mellitus differed significantly from that of healthy controls. In T2DM patients, Lactobacillus spp. and the Firmicutes phylum had higher relative fold differences, while A. muciniphila had lower abundance. No substantial alterations were seen in Bifidobacterium spp., Prevotella, or Bacteroidetes. T2DM patients had more Lactobacillus spp. and Firmicutes and less A. muciniphila in their gut microbiome.

CONCLUSION: While gut microbiota is linked to T2DM, this study analyzes the bacterial composition to identify taxa that change significantly. Further research is essential to unravel the complex relationships between gut microbiota and T2DM pathogenesis, particularly through species-level analysis and genomic studies to identify the primary associated clades.},
}

@article {pmid41510045,
year = {2025},
author = {Maneesha, S and Arman, B and Kirti, D and Preethi, B and Rinku, C and Teenus, J and Raman, K and Raja, S and Anmol, K and Minal, BT},
title = {Preliminary investigation of changes in pathogen presence in the vaginal microbiome in association with age.},
journal = {Iranian journal of microbiology},
volume = {17},
number = {6},
pages = {901-911},
pmid = {41510045},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: The vaginal microbiome represents a dynamic ecosystem that undergoes significant transformations throughout a woman's lifespan, influenced by hormonal fluctuations and physiological changes. Interpreting pathogen distribution and developing suitable therapeutic care techniques for women's reproductive health depends on an understanding of these age-related patterns. This study aims to thoroughly describe age-related changes in the makeup of the vaginal microbiome and the distribution of pathogenic species.

MATERIALS AND METHODS: Vaginal swab samples were collected from 29 subjects, categorized into different age groups (A: 15-30 years, B: 31-40 years, C: 41-50 years, and D: 51-60 years old females). Microbiome DNA was extracted from the collected vaginal swabs and shotgun next generation sequencing was performed. Post-sequencing, data was analysed using in-house pipeline followed by statistical analysis using R programming.

RESULTS: The results showed that microbial diversity varied significantly with age. Group C displayed the most severe pathogenic burden; Group A had the highest overall species diversity with 350 bacterial species. Group D displayed the greatest overall relative abundance levels of microorganisms, primarily due to Lactobacillus rhamnosus dominance.

CONCLUSION: This study shows that the composition of the vaginal microbiome changes fundamentally over the course of a woman's life, with each stage bringing with it its own set of microbial signatures, pathogenic risks, and therapeutic prospects.},
}

@article {pmid41510033,
year = {2025},
author = {Ghaderi, F and Hajebrahimi, Z and Fateh, A and Sotoodehnejadnematalahi, F and Ahmadi Badi, S and Vaezijoze, S and Siadat, SD},
title = {Tight junctions expression is affected by active, inactive, and derivatives of Akkermansia muciniphila.},
journal = {Iranian journal of microbiology},
volume = {17},
number = {6},
pages = {885-892},
pmid = {41510033},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Tight junctions (TJs) in the gastrointestinal tract are comprised of various junctional proteins including Occludin and Zonula Occludens (ZO-1) that have a critical role in epithelial barrier function. Gut microbiota and their derived metabolites can maintain and regulate gut epithelial barrier integrity.

MATERIALS AND METHODS: In the present study, the effects of active, heat-inactivated, cell-free supernatant, and outer membrane vesicles (OMVs) of Akkermansia muciniphila were evaluated on the expression of occludin and ZO-1 genes in Caco-2 cell line by quantitative real-time PCR.

RESULTS: Data have shown that both forms of the active (metabolically active, growing, and dividing state), and heat inactivated (by exposure to 56°C for 20 minutes) forms of the bacteria and the cell-free supernatant could affect the expression of occludin and ZO-1 genes (P < 0.05). OMVs significantly increased the expression of the occludin gene but had no effects on the expression of ZO-1.

CONCLUSION: Akkermansia muciniphila and its derived metabolites might have the potential to be used in the pharmaceutical and medicinal fields as probiotic, paraprobiotic and postbiotic agents to prevent metabolic and inflammatory diseases; Although, further research is needed to understand their interactions within the complex gut microbiome and to evaluate potential side effects or risks associated with their use.},
}

@article {pmid41509984,
year = {2026},
author = {Tenea, GN and Flores, C},
title = {Post-harvest microbiome dynamics and their impact on the safety and quality of Lupinus mutabilis sweet (Chocho).},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100536},
pmid = {41509984},
issn = {2666-5174},
abstract = {Chocho (Lupinus mutabilis Sweet), a traditional Andean legume, undergoes diverse post-harvest handling and processing steps that can influence its microbial composition and physicochemical properties. To understand how these factors shape food safety and consumer health, we characterized the chocho microbiome across the farm-to-table chain, including field-dried grains (Group C), open-market ready-to-eat products (Group A), and supermarket grains (Group K). Bacterial and fungal communities were profiled using 16S rRNA and ITS amplicon sequencing, and moisture, pH, titratable acidity, and total alkaloids were quantified and correlated with microbial patterns. High-depth 16S rRNA sequencing (60,000-140,000 reads/sample) showed the highest bacterial diversity in Group A (Shannon = 5.23), followed by Group K (4.69) and Group C (4.08). Richness and evenness differed significantly (p < 0.05) among groups, and beta-diversity analyses (Bray-Curtis, Jaccard, UniFrac) revealed clear clustering by grain source (PERMANOVA, p ≤ 0.005). Market grains were enriched in handling-associated genera such as Pseudomonas, Flavobacterium, and Enterococcus, whereas field grains contained soil-associated taxa including Paenibacillus and Arthrobacter. Fungal profiling showed the greatest richness and phylogenetic diversity in local-producer samples, with supermarket grains displaying lower but more even communities. Xerophilic Wallemia dominated dry grains, whereas moisture-exposed market grains were enriched in spoilage yeasts (Debaryomyces, Candida, Rhodotorula). Physicochemical traits varied widely: moisture (3.7-8.7%), titratable acidity (0.09-0.59%), pH (4.9-6.2), and alkaloids (<0.5% in processed grains vs. 5-7% in field samples). PCA explained 90.6% of the variance, with alkaloids strongly correlating with acidity (r = 0.94). Several processed samples exceeded national alkaloid limits (<0.02%), indicating incomplete debittering. These findings demonstrate that environmental exposure and handling strongly influence the microbial and toxicological safety of chocho along its supply chain.},
}

@article {pmid41509630,
year = {2026},
author = {Hill, K and LaFollette, A and Kirby, TO and Negrete, S and Babcock, D and Felton, K and Kohl, H and Sharma, K and Castillo, A and Roullet, JB and Gibson, KM and Ochoa-Repáraz, J},
title = {Impact of a GABA-Producing Lactococcus lactis on Microbiota and Mycobiota During CNS Inflammatory Demyelination.},
journal = {FASEB bioAdvances},
volume = {8},
number = {1},
pages = {e70085},
pmid = {41509630},
issn = {2573-9832},
abstract = {Gut microbes are key regulators of immune homeostasis. Their composition fluctuates over time and between individuals and is also influenced by disease. We and others have reported changes in gut bacterial composition following induction of experimental autoimmune encephalomyelitis (EAE), a well-established model for multiple sclerosis (MS). Specifically, we observed reductions in the abundance of bacteria capable of producing gamma-aminobutyric acid (GABA). Because GABA regulates immune cell function, we genetically engineered a Lactococcus lactis strain to overproduce GABA (P8s-GAD L. lactis) and hypothesized that this strain would have protective activity in EAE. To test this hypothesis, a suspension of P8s-GAD L. lactis was administered by gavage to C57BL/6 Envigo (Env) and Jackson Laboratories (Jax) mice at the time of EAE induction. Controls included mice treated with unmodified L. lactis (P-L. lactis) and mice treated with sterile bacterial medium. P8s-GAD L. lactis was clinically protective in Env mice but not in Jax mice. To understand the lack of protection in Jax mice, we examined the effects of treatments on intestinal micro- and mycobiota using 16S rRNA and IST sequencing, and samples were collected at disease induction, 14 days after, and at the end of the experiment (day 28). We also examined the impact of treatments on the brain, using whole-brain proteomics (day 28). Despite the lack of disease protection, P8s-GAD L. lactis significantly modified the gut microbiome by affecting broad taxonomic composition, as quantified by beta-diversity changes over time, and the CNS protein profile, including an increase in Gabra6 expression, the alpha-6 subunit of the GABA type A (GABARA) receptor. These changes, combined with reduced EAE severity observed in Env mice, suggest that GABA-producing bacteria could be considered for the treatment of neuroinflammatory conditions. The study also highlights the importance of controlling the mouse source in probiotic and microbiota research within experimental models of immune-mediated diseases.},
}

@article {pmid41509585,
year = {2026},
author = {Kang, NK and Kang, MJ and Keum, GB and An, C and Park, EJ and Bae, EK},
title = {Soil Chemistry and Microbial Community Patterns Across Tricholoma matsutake Fairy-Ring Developmental Stages in Yeongju, South Korea.},
journal = {Mycobiology},
volume = {54},
number = {1},
pages = {78-88},
pmid = {41509585},
issn = {1229-8093},
abstract = {This study investigates how shiro developmental stages, soil physicochemical properties, and seasonal variation shape fungal and bacterial communities associated with Tricholoma matsutake in a Pinus densiflora forest in Yeongju, South Korea. Seasonal soil samples from past, present, and future shiro zones were analyzed using ITS and 16S rRNA metabarcoding together with soil chemical measurements. Shiro-driven spatial heterogeneity, rather than seasonality, was the dominant factor structuring microbial communities. Fungal assemblages differed significantly among shiro stages, with exchangeable potassium (K[+]) emerging as the primary driver and a strong predictor of T. matsutake abundance. Elevated K[+] in active shiro zones corresponded to reduced fungal diversity, suggesting competitive exclusion by dominant ectomycorrhizal taxa. In contrast, bacterial communities were shaped mainly by water-soluble iron (Fe), shifting from Acidobacteria-rich assemblages in past zones to Proteobacteria in active zones. The enrichment of siderophore-associated taxa suggests a potential role of Fe acquisition processes, broadly consistent with mechanisms proposed in the mycorrhiza helper bacteria hypothesis, though not directly tested here. Overall, T. matsutake development generates nutrient-specific biogeochemical gradients-K[+] for fungi and Fe for bacteria-that reorganize soil microbial communities. These findings underscore tightly linked biotic-abiotic interactions in shiro ecology and highlight microbial and chemical features that may serve as indicators of shiro activity.},
}

@article {pmid41509546,
year = {2026},
author = {Steriade, C},
title = {The Gut Feeling Behind Autoimmune Encephalitis.},
journal = {Epilepsy currents},
volume = {},
number = {},
pages = {15357597251412104},
pmid = {41509546},
issn = {1535-7597},
abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.

METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.

RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.

SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.},
}

@article {pmid41509542,
year = {2025},
author = {Fang, Y and Cai, Y and Chen, X and Lin, Z},
title = {Exercise intervention regulates gut microbiota to improve type 2 diabetes: a narrative review of the mechanisms.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1698112},
pmid = {41509542},
issn = {2296-861X},
abstract = {BACKGROUND: The gut microbiota is increasingly recognized as a key factor in the pathogenesis of type 2 diabetes mellitus (T2DM). Concurrently, exercise intervention has emerged as a promising non-pharmacological strategy for T2DM management, potentially mediated through gut microbiome modulation.

METHODS: This narrative review searched Web of Science, PubMed, and Embase for literature published from 1992 to the present, ultimately including 58 relevant publications. The focus was on elucidating the physiological mechanisms by which exercise modulates gut microbiota to ameliorate T2DM.

RESULTS: Our synthesis indicates that exercise training beneficially alters gut microbiota composition and function, which in turn enhances systemic insulin sensitivity and improves metabolic disturbances in T2DM. These improvements are mediated through multiple pathways, including bile acid metabolism, short-chain fatty acid production, lipopolysaccharide reduction, and branched chain amino acid catabolism. The effects of exercise on the gut microbiome are influenced by factors such as exercise intensity, duration, and type, suggesting the need for individualized regimens.

CONCLUSION: Exercise intervention improves T2DM by modulating gut microbiota via several mechanistic pathways. Future research should prioritize personalized exercise prescriptions, larger sample sizes, integrated multi-omics approaches, and exploration of combined interventions with diet or medication to optimize T2DM prevention and treatment.},
}

@article {pmid41509497,
year = {2025},
author = {Shen, Z and Eckert, J and Saffery, R and Allen, KJ and Walsh, A and , and Deming, C and Chen, Q and Laky, K and Li, JM and Chatman, L and , and Kong, HH and Perrett, KP and Segre, JA and Frischmeyer-Guerrerio, PA},
title = {Skin microbiome composition and function in the development of atopic diseases during infancy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.22.696050},
pmid = {41509497},
issn = {2692-8205},
abstract = {BACKGROUND: Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While FLG null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome.

OBJECTIVE: To determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.

METHODS: We analyzed >1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with FLG mutation status.

RESULTS: Within AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased Staphylococcus hominis and Lactococcus species, along with increased Dermacoccus nishinomiyaensis and Malassezia slooffiae . At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers exhibited additional microbial shifts, including reduced Streptococcus species and increased Malassezia slooffiae . Strain-level analyses revealed mother-infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity.

CONCLUSIONS: Infant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.},
}

@article {pmid41509494,
year = {2025},
author = {Zhang, A and Horai, R and Jittayasothorn, Y and Badger, JH and Wu, Z and Gupta, A and Arunkumar, S and Murphy, CE and Shi, G and Nagarajan, V and McCulloch, JA and Kodati, S and Sen, HN and Lee, JW and Jacobs, JP and Xu, X and Mattapallil, MJ and Peng, Z and Xu, B and Palmer, RJ and Majdalani, N and Honda, K and O'hUigin, C and Caspi, RR},
title = {Gut microbial interaction networks control autoimmunity to neuroretina.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.04.691931},
pmid = {41509494},
issn = {2692-8205},
abstract = {The gut microbiome influences the development of immune-mediated inflammatory diseases. One such condition is autoimmune uveitis, a sight-threatening ocular inflammation driven by retina-specific T cells [1] . Using a model of spontaneous experimental autoimmune uveitis (sEAU) we showed that gut commensals provide innate and adaptive immune stimuli that trigger the disease [2] . Here we report that uveitis-promoting microbes are present in human gut flora and that colonization of germ-free (GF) mice with commensal flora from healthy human donors was sufficient to provoke disease. Severity of sEAU correlated with expansion of Akkermansia and contraction of short-chain fatty acid (SCFA)-producing Firmicutes, as well as decreased SCFA levels and a dominant gut Th1 effector response. Mechanistic gain-of-function experiments, enriching GF sEAU mice with Akkermansia, reproduced these microbiome, metabolite and immune phenotype shifts, and exacerbated disease. We propose that Akkermansia promotes autoimmunity by outcompeting SCFA-producers and enhancing Th1-type responses. Notably, an inverse correlation between Akkermansia (Verrucomicrobia) and Firmicutes was also present in fecal microbiome of patients with uveitis, multiple sclerosis and Crohn's disease. These findings reveal a stereotypic gut microbial interaction network that regulates systemic immune balance, and may represent an ecologically conserved mechanism through which the gut microbiome modulates autoimmune and inflammatory diseases.},
}

@article {pmid41509481,
year = {2026},
author = {Hallberg, ZF and Alvarez-Aponte, ZI and Gaudinier, AC and Taga, ME},
title = {Quenching corrinoid-based interactions in a model bacterial coculture.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41509481},
issn = {2692-8205},
abstract = {Microbial community structure is driven, in part, by the metabolic interdependencies of resident microbes. Thus, manipulating specific metabolic interactions represents one attractive way to both understand how microbial communities perform complex functions and alter them for therapeutic or environmental effects. However, it is not yet possible to control the availability of those metabolites produced by some members of the community that are required by others. Here, we report the development of a metabolite 'quenching' strategy that disrupts a specific metabolic interaction involving corrinoids, the vitamin B 12 family of cofactors, by applying a high-affinity corrinoid-binding protein, BtuG, to bacteria engaged corrinoid cross-feeding. Using a model coculture composed of Sinorhizobium meliloti , a bacterium that produces a corrinoid (cobalamin), and an Escherichia coli strain engineered to be corrinoid-dependent, we demonstrate corrinoid quenching by sequestration of extracellular corrinoid and show that BtuG specifically blocks corrinoid-dependent growth. We use this tool to calculate the amount of cobalamin released by S. meliloti cells and find that the cobalamin release rate is dependent on the growth phase of the producer, increasing to a maximum of approximately 40 cobalamin molecules per minute per cell in late exponential phase. This work establishes a strategy to selectively block microbial interactions that may be more broadly applied to dissecting community structure and function. We expect that applying high-affinity 'molecular sponges' to quench nutrient sharing will allow for the identification of key nutrients that structure microbial communities and empower precision microbiome manipulation strategies.},
}

@article {pmid41509386,
year = {2025},
author = {Balogun, IO and Mancuso, CP and Lieberman, TD},
title = {High Precision Binary Trait Association on Phylogenetic Trees.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.24.696407},
pmid = {41509386},
issn = {2692-8205},
abstract = {UNLABELLED: Traditional methods for identifying associations between genomic features and traits, or between pairs of genomic traits, struggle when applied to bacterial genomes. While several microbial GWAS (mGWAS) methods have been developed to account for the fact that genome-wide linkage in bacteria creates strong evolutionary-induced associations, these methods have high false discovery rates or lack statistical power, have poor performance on negative interactions, and face computational limits at the scale required for pangenome-wide study of gene-gene interactions. Here, we present SimPhyNI, a computationally optimized framework for efficient and rigorous mGWAS studies. SimPhyNI builds null co-occurrence distributions by independently simulating traits using phylogenetically-informed parameters, novelly including time to first event. The constrained variation in these simulations, combined with log odds ratio scoring for comparing across traits, robustly identifies both positive and negative associations. Using synthetic datasets mimicking both gene-gene and gene-trait associations, we demonstrate that SimPhyNI achieves high precision and recall for both positive and negative interactions. We demonstrate SimPhyNI's utility by detecting interactions between phage defense systems in E. coli and gene-gene interactions across the entire E. coli pangenome (>9 million tests). Though developed here for binary traits, SimPhyNI's design supports extension to multi-state and continuous traits using generalized models of stochastic simulation. SimPhyNI's performance and scalability enable genome-wide discovery of genetic interactions that drive microbial function, ecology, and disease.

DATA SUMMARY: SimPhyNI is publicly available at https://github.com/jpeyemi/SimPhyNI , and code for related benchmarking, validation, and biological analyses are available at doi.org/10.5061/dryad.9kd51c5xt. The neighbor-joining phylogenetic tree and phage defense system annotations used in this study were obtained from Wu et al. (2024). A representative set of Escherichia coli genomes and the corresponding maximum-likelihood phylogenetic tree were downloaded from the PanX database (https://pangenome.org/Escherichia_coli).

IMPACT STATEMENT: Understanding how bacterial genes associate with traits and with one another is essential for predicting disease outcomes, antibiotic resistance, and future evolution. However, identifying these interactions is challenging because shared ancestry creates false correlations. SimPhyNI overcomes this through an ancestry-informed statistical simulation process, achieving near-zero false positive rates while maintaining computational efficiency for large scale analyses. This efficiency enables systematic mapping of gene-gene interaction networks across large datasets containing thousands of genes and genomes. As microbial genomic datasets continue to expand, SimPhyNI's scalability and precision will accelerate discovery of the mechanistic principles underlying infectious disease, microbiome function, and microbial evolution and ecology.},
}

@article {pmid41509298,
year = {2025},
author = {Sharma, A and Panzetta, ME and Overly, M and Yang, H and Ernst, RK and Valdivia, RH},
title = {Multi-omic comparative analysis of members of the Akkermansia genus reveals species-specific adaptations to growth in mucin.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.30.696933},
pmid = {41509298},
issn = {2692-8205},
abstract = {Akkermansia muciniphila is a commensal, mucophilic anaerobic bacterium that influences human host physiology. Although additional prominent Akkermansia species have been identified in humans, their responses to mucin-rich environments remain poorly understood. We conducted a comparative analysis of four representative human isolates: A. muciniphila, A. biwaensis, A. massiliensis, and A. durhamii, focusing on proteins involved in mucin degradation, cell-surface components, and species-specific secreted metabolites during growth in mucin. Our results reveal unique adaptations of A. muciniphila to exploit mucin-rich environments, including higher expression of key mucin-degrading proteins during growth in mucin compared to other Akkermansia species. We also demonstrate that A. muciniphila expresses a significantly greater number of secreted PEPCTERM proteins, which contribute to host colonization. The expression of pili-associated proteins varied across species, with non- muciniphila species producing more predicted pili, suggesting the ability to colonize additional niches. Lastly, we find that small peptides previously linked to host and microbiome modulation in the GI tract are over-represented in the metabolomes of non- muciniphila species. Conversely, A. muciniphila produces more hydroxylated fatty acids, indicating potential mechanisms for modulating host health. These findings highlight genetic and regulatory mechanisms that may explain A. muciniphila 's dominance in the human gut.},
}

@article {pmid41509238,
year = {2025},
author = {Shrestha, A and Eline, Y and Sundstrom, K and Van Leuven, JT},
title = {Hive-associated bacteria improve honeybee survival during Paenibacillus larvae infection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.24.696342},
pmid = {41509238},
issn = {2692-8205},
abstract = {Honeybees (Apis mellifera L.) are the most common pollinators of crops. Honeybee larvae are susceptible to Paenibacillus larvae , a spore-forming Gram-positive bacterium that causes American Foulbrood (AFB), one of the most destructive brood diseases worldwide. Existing antibiotic treatments are undesirable due to increasing pathogen resistance and their residual accumulation in bee products. Consequently, there is increasing interest in biological agents and natural strategies for AFB control. However, most studies remain limited to in vitro or in vivo experiments and rarely evaluate impacts on adult bees. In this study, we systematically investigated hive-associated bacteria for their potential to enhance larval survival during P. larvae infection. Bacteria isolated from AFB-infected combs were sequenced and screened for antagonistic activity. Several Bacillus species-including B. zhangzhouensis , B. subtilis , B. amyloliquefaciens , B. licheniformis , and B. mojavensis -inhibited one or more P. larvae strains. Notably, the lysate of B. licheniformis suppressed all tested strains; Further characterization revealed that its main antibacterial component consists of heat-stable proteins between 30-50 kDa. Two Bacillus strains were selected for larval infection assays using laboratory-reared honeybee larvae: both significantly improved survival by 42% and 71%, respectively. To evaluate potential effects on adult bees, newly emerged workers were caged and fed B. licheniformis ASx lysate. Their survival differed from that of untreated controls but remained comparable to the Terra-Pro-fed bees, a Terramycin-based AFB treatment, and their gut microbiome remained similar to that of untreated controls. Overall, our findings suggest that hive-associated Bacillus species offer promising, low-impact candidates for AFB disease management.},
}

@article {pmid41509197,
year = {2026},
author = {Ke, Z and Lin, L and Long, Y and Zhang, W and Guo, J and Yuan, L},
title = {Dihydroquercetin Attenuates Silica-Induced Pulmonary Fibrosis by Modulating the Gut Microbiota and the Serum Metabolites in Mice.},
journal = {Food science & nutrition},
volume = {14},
number = {1},
pages = {e71389},
pmid = {41509197},
issn = {2048-7177},
abstract = {Dihydroquercetin (DHQ), a crucial dihydroflavone found in nature, demonstrates notable antioxidant, anti-inflammatory, and antifibrotic effects. Nevertheless, the impact on the gut microbiome and metabolites associated with silicosis remains unclear. Hence, the objective of this research was to examine how DHQ impacts silicosis and the associated mechanisms through analyzing gut microbiota with 16S rRNA sequencing and conducting serum metabolomic analysis. The findings of our study showed that administering DHQ significantly attenuated the level of inflammation and fibrosis in the lung tissues of C57BL/6 mice exposed to silica. Furthermore, DHQ clearly raised the amount of Muribaculaceae, while diminishing the amount of Lactobacillus. DHQ treatment significantly decreased the sphingomyelin, arachidonic acid and its metabolites. Significantly, the correlation analysis showed that the influence of DHQ on the arachidonic acid metabolism, steroid hormone biosynthesis, and sphingolipid signaling pathways were linked to changes in the levels of Muribaculaceae and Lactobacillus in the gut microflora. In summary, our research demonstrated that DHQ can attenuated inflammation and lung fibrosis caused by silica exposure in the C57BL/6 mice, potentially by modulating the gut microbiota and serum metabolites.},
}

@article {pmid41509044,
year = {2026},
author = {El-Hadedy, DE and Chen, T and Cai, KQ and Klein-Szanto, AJ and Mu, A and Campbell, KS and Whelan, KA and Al-Hebshi, NN},
title = {Vendor-specific microbiomes influence oral cancer development and its response to Streptococcus mitis intervention in mice.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2611642},
pmid = {41509044},
issn = {2000-2297},
abstract = {BACKGROUND: We previously demonstrated that Streptococcus mitis exhibits anticancer properties in vitro. Here, we sought to validate these findings in vivo. Because mice from different vendors harbor distinct microbiomes that can influence disease susceptibility and experimental outcomes, we also examined whether vendor-specific oral and gut microbiomes affect oral carcinogenesis and response to S. mitis intervention.

MATERIALS AND METHODS: Oral carcinogenesis was induced using 4-NQO in C57BL/6 mice from Jackson Laboratory and Taconic Biosciences (n = 32 per vendor). Mice were randomized to biweekly oral swabbing with S. mitis or vehicle for 28 weeks. Oral and fecal microbiomes were profiled at baseline and week 8. At week 32, tongues were evaluated for tumor development.

RESULTS: Oral and gut microbiomes differed significantly between vendors. 4-NQO exposure induced marked microbial shifts and partial convergence of microbiome profiles. Jackson mice developed a significantly higher squamous cell carcinoma (SCC) burden. Several microbial taxa were associated with SCC, notably Clostridium, which was enriched in oral and fecal samples from Jackson mice. S. mitis reduced SCC burden in both cohorts and was accompanied by decreased Clostridium abundance.

CONCLUSIONS: These data support S. mitis as a potential anticancer agent and underscore the importance of microbiome context in preclinical cancer models.},
}

@article {pmid41509043,
year = {2026},
author = {Zhou, Z and Zhuang, Z and Ding, Y and Jiang, Y and Chen, S and Zhang, Q and Que, H and Lin, J and Deng, H and Wang, Y},
title = {Oral microbiome diversity and all-cause mortality in hypertensive adults: findings from a nationally representative cohort.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2609456},
pmid = {41509043},
issn = {2000-2297},
abstract = {BACKGROUND: Oral microbiome diversity has been associated with general health. However, its association with long-term outcomes in hypertensive individuals remains unclear.

OBJECTIVES: This study aimed to investigate whether oral microbiome diversity is associated with all-cause mortality in hypertensive individuals.

DESIGN: Data from 2,669 hypertensive individuals in the National Health and Nutrition Examination Survey (NHANES, 2009-2012) were analyzed. Oral microbiome diversity was assessed using four alpha-diversity metrics: the Simpson index, Shannon-Weiner index, Faith's Phylogenetic Diversity, and observed amplicon sequence variants (ASVs). Weighted multivariable Cox proportional hazards regression and interaction analyses were conducted.

RESULTS: During a mean follow-up of 8.61 years, 268 all-cause deaths occurred. Higher oral microbiome diversity assessed by the Simpson index (hazard ratio [HR] = 0.38; 95% confidence interval [CI], 0.20-0.75; P trend < 0.01) and Shannon-Weiner index (HR = 0.47; 95% CI, 0.25-0.88; P trend < 0.05), was significantly associated with reduction in all-cause mortality risk. A potential interaction between sex and oral microbiome diversity on mortality risk was observed.

CONCLUSIONS: Higher oral microbiome diversity is an independent protective factor for survival in patients with hypertension, with potential sex-specific differences in this association. These findings suggest that enhancing oral microbiome diversity may potentially help promote overall health in individuals with hypertension.},
}

@article {pmid41509038,
year = {2026},
author = {Xu, T and Wei, Z and Zeng, Q and Feng, Q and Zhi, M},
title = {Unveiling potential driver taxa in subgingival plaque and their roles in mediating periodontitis progression.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2609452},
pmid = {41509038},
issn = {2000-2297},
abstract = {BACKGROUND: Periodontitis progression is accompanied by a succession of the oral microbiome. However, the dynamic microbial transitions that link different disease stages and contribute to disease progression remain incompletely understood.

OBJECTIVE: This study aims to identify microbial taxa that may serve as potential drivers underlying increasing severity of periodontitis.

DESIGN: Subgingival sample 16S rRNA gene sequencing data were reprocessed for quality control and taxonomic annotation. MaAsLin2 was used to identify microbial differences between groups, and co-occurrence networks were built based on the differential taxa. NetMoss algorithm was applied to identify key microbes driving the transition from health to periodontitis. Correlation and mediation analyses were used to assess the associations between these driver taxa and periodontal clinical indicators.

RESULTS: Putative novel pathogens (e.g. Filifactor alocis, Slackia exigua) were markedly enriched in periodontitis, whereas potential protective taxa (e.g. Haemophilus and Rothia) had higher relative abundance in the health group. The microbial co-occurrence networks in the periodontitis groups were progressively disrupted, characterized by reduced network robustness and heightened vulnerability in the Stage III and IV groups. The driver taxa probably influenced the severity of periodontitis through modulation of periodontal clinical indicators, with positive or negative correlations observed between these taxa and periodontal clinical indicators.

CONCLUSIONS: Capnocytophaga, Paludibacter, Dialister pneumosintes, Eubacterium minutum and Phocaeicola abscessus are proposed as key driver taxa across different periodontal health conditions, and exhibited significant correlations with periodontal clinical indicators.},
}

@article {pmid41509037,
year = {2026},
author = {Anshory, M and Strepis, N and Hays, JP and Rosandy, MG and Prawesti, AR and Iskandar, A and Wulanda, IA and Setyowatie, L and David, NI and Malem, NR and Kalim, H and Nijsten, TE and Nouwen, JL and Thio, HB},
title = {Transition of oral microbiome profile in HIV-infected Indonesian patients: the role of antiretroviral therapy.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2609445},
pmid = {41509037},
issn = {2000-2297},
abstract = {BACKGROUND: HIV infection alters host immunity, including the oral environment, leading to microbial imbalance and increased risk of opportunistic infections. Although antiretroviral therapy (ART) improves immune function, its effect on the oral microbiome remains unclear, particularly in Indonesia. This study investigated oral microbiome composition in people living with HIV and its associations with ART status, age, and sex.

METHODS: In this cross-sectional study, oral rinse samples from 245 adults (115 HIV-on-ART, 15 HIV-ART-naïve, and 115 HIV-negative controls) were analysed using 16S rRNA gene sequencing. Alpha and beta diversity metrics, differential abundance (ANCOM-BC2), and multivariable associations (PERMANOVA) were assessed.

RESULTS: The oral microbiome differed significantly between HIV-positive groups and controls (PERMANOVA p = 0.001, R² = 1.8%). HIV-ART-naïve individuals exhibited the highest alpha diversity and enrichment of pro-inflammatory genera, including Fusobacterium, Alloprevotella, and Staphylococcus. ART-treated individuals displayed a partial shift toward the control profile but retained persistent depletion of bacteria such as Filifactor and (Eubacterium) saphenum. Multivariate analysis identified HIV status, age, and sex as independent contributors to microbial variation.

CONCLUSION: HIV infection is associated with a distinct oral dysbiosis characterised by an increase in opportunistic pathogens and reduction in commensal bacteria. HIV-on-ART individuals show a transitional shift towards the HIV-negative oral microbiome profiles. Our findings suggest that biological and/or demographic factors coupled to oral microbiome profiles may facilitate targeted interventions in the personalised management of oral health for individuals living with HIV.},
}

@article {pmid41508690,
year = {2026},
author = {Jo, M and An, S and Kim, KT and Kim, DS and Kim, H and Kim, KH and Kim, S and Lee, YH and Chi, WJ and Park, SY},
title = {A multifunctional Streptomyces murinus bioinoculant integrates immune priming and microbiome restructuring for sustainable control of Sclerotinia minor in Brassica rapa.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70544},
pmid = {41508690},
issn = {1526-4998},
support = {//National Institute of Biological Resources/ ; },
abstract = {BACKGROUND: Harnessing beneficial soil microbes provides an eco-friendly alternative to pesticides for sustainable crop protection. Members of the genus Streptomyces combine broad antagonistic activity with plant immune priming and growth promotion, yet their ecological roles and field reliability remain insufficiently understood. We investigated the soil actinobacterium Streptomyces murinus JS029 in the Brassica rapa-Sclerotinia minor pathosystem to elucidate its mechanisms of pathogen suppression, plant immune activation and rhizosphere microbiome modulation, and to develop a field-deployable formulation.

RESULTS: Streptomyces murinus JS029 secreted chitinase, cellulase and protease and produced the polyene macrolides pentamycin and filipin I, which are known to disrupt fungal cell walls and plasma membranes. Plants exposed to Streptomyces murinus JS029 exhibited strong activation of salicylic acid, jasmonic acid and ethylene signalling pathways and were associated with enhanced biomass and strong protection against Sclerotinia minor. A barley-based solid formulation ensured reproducible field efficacy, reducing disease by approximately 70-80%. Rhizosphere sequencing revealed increased fungal richness and distinct bacterial-fungal compositional shifts, indicating functional reassembly of the soil microbiome. Genome analysis and ultraviolet (UV) mutagenesis linked antifungal activity to a polyene biosynthetic gene cluster.

CONCLUSION: Streptomyces murinus JS029 integrates direct antagonism, immune priming and microbiome restructuring to support disease-suppressive soils. These findings provide mechanistic insights and a practical framework for deploying multifunctional Streptomyces bioinoculants as sustainable alternatives to chemical fungicides in integrated pest management systems. © 2026 Society of Chemical Industry.},
}

@article {pmid41508656,
year = {2026},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {6},
number = {1},
pages = {70-76},
doi = {10.1158/2767-9764.CRC-25-0445},
pmid = {41508656},
issn = {2767-9764},
support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; },
mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Prospective Studies ; Male ; Female ; *Specimen Handling/methods ; Middle Aged ; Australia ; Aged ; Occult Blood ; Adult ; *Neoplasms/microbiology ; Surveys and Questionnaires ; Metagenomics/methods ; },
abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.

SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.},
}

Humans
Pilot Projects
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
Prospective Studies
Male
Female
*Specimen Handling/methods
Middle Aged
Australia
Aged
Occult Blood
Adult
*Neoplasms/microbiology
Surveys and Questionnaires
Metagenomics/methods

@article {pmid41508600,
year = {2026},
author = {Black, TC and Demas, GE and Wellman, CL and Cusick, JA},
title = {Getting Over It: Maternal Stress and Gut Microbiome Manipulations Do Not Affect Rates of Offspring Habituation During Long Bouts of Stress.},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.70057},
pmid = {41508600},
issn = {2471-5646},
support = {T32HD049336//National Institutes of Health (NIH)/ ; IOS-1656414//National Institutes of Health (NIH)/ ; //UVU Honor's Tuition Scholarship/ ; //UVU SAC and URSCA Dissemination Grants/ ; },
abstract = {Conspecific competitive interactions occur in a variety of contexts, including for resources and territory. These competitive interactions can vary in frequency and duration. The amount of aggression displayed and whether individuals alter their aggressive response during longer competitive bouts may be impacted by individual differences in stress response and behavior. The maternal environment, including maternal stress and the maternal microbiome, can have sex-specific, developmental effects on offspring's physiology and aggressive behavior. We tested whether the maternal environment affects changes to offspring aggressive behavior during long competitive bouts in Siberian hamsters (Phodopus sungorus). We exposed pregnant females to one of four treatments (social stressor, microbiome manipulation, combined social stress and microbiome manipulation, or no treatment) for ten days. Using a resident-intruder behavioral paradigm, adolescent offspring were exposed to a same-sex intruder for 15 min. We assessed differences in offspring behavioral responses during the first and last 5 min of the competitive interaction. All offspring displayed less aggression during the last 5 min compared to the first 5 min, regardless of maternal treatment. Regardless of maternal treatment, both female and male offspring reduced social behavior towards the intruder, while increasing non-social and decreasing anxiety like behavior across the 15-min trial. Our results are consistent with habituation towards an intruder and indicate that early development does not affect habituation during aggression with a conspecific, further confirming the complexity and highly conserved mechanisms involved in habituation.},
}

@article {pmid41508594,
year = {2026},
author = {Zhao, W and Zhang, Y and Ma, H and Sun, P and Zhang, Y},
title = {Characterization of the follicular fluid microbiome in endometriosis patients undergoing in vitro fertilization.},
journal = {Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology},
volume = {42},
number = {1},
pages = {2612148},
doi = {10.1080/09513590.2025.2612148},
pmid = {41508594},
issn = {1473-0766},
mesh = {Humans ; Female ; *Follicular Fluid/microbiology ; *Endometriosis/microbiology/complications ; *Fertilization in Vitro ; Adult ; *Microbiota/genetics ; Pregnancy ; *Infertility, Female/microbiology/therapy/etiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Pregnancy Rate ; },
abstract = {BACKGROUND: Endometriosis (EMs) is a common gynecological disorder associated with infertility. EMs patients often require assisted reproductive technology (ART) but exhibit lower success rates. This study aimed to characterize the follicular fluid microbiome in EMs patients undergoing in vitro fertilization (IVF) and provide insights into mechanisms underlying lower pregnancy rates.

METHODS: Follicular fluid samples were collected from EMs patients and control subjectsundergoing IVF. Microbial DNA was subjected to 16S rRNA gene sequencing. Bioinformatic analyses, including alpha and beta diversity analysis, microbial composition profiling and biomarker identification, were performed.

RESULTS: The follicular fluid microbiome in EMs patients exhibited altered alpha and beta diversity compared to controls. Distinct microbial compositions were observed at various taxonomic levels. Differentially abundant taxa were identified as potential biomarkers for EMs. Microbial profiles were associated with clinical parameters such as oocyte quality and fertilization rates. Models based on microbial profiles were constructed to elucidate the relationship between EMs and IVF outcomes. Functional predictions suggested alterations in metabolic pathways in the follicular fluid microbiome of EMs patients.

CONCLUSIONS: This study revealed significant alterations in the follicular fluid microbiome of EMs patients, providing a basis for further research into the role of the microbiome in EMs-related infertility.},
}

Humans
Female
*Follicular Fluid/microbiology
*Endometriosis/microbiology/complications
*Fertilization in Vitro
Adult
*Microbiota/genetics
Pregnancy
*Infertility, Female/microbiology/therapy/etiology
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Pregnancy Rate

@article {pmid41508551,
year = {2026},
author = {Winn, M and Karra, P and Benson, R and Pauleck, S and Chaiyakunapruk, N and Khaing, W and Veettil, SK and McFarland, MM and Casucci, T and Xu, Y and Hu-Lieskovan, S and Litchman, M and Playdon, M and Hardikar, S},
title = {Metabolic Syndrome and Obesity-related cancer Risk and Survival: An Umbrella Review of Systematic Reviews With Meta-analysis of Observational Studies.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70073},
doi = {10.1111/obr.70073},
pmid = {41508551},
issn = {1467-789X},
support = {NCIF30CA278348/CA/NCI NIH HHS/United States ; NCIK07CA222060/CA/NCI NIH HHS/United States ; NCIR00CA218694/CA/NCI NIH HHS/United States ; NCIK00CA2644000/CA/NCI NIH HHS/United States ; NCIF99CA264400/CA/NCI NIH HHS/United States ; T32DK091317/DK/NIDDK NIH HHS/United States ; },
abstract = {INTRODUCTION: Metabolic syndrome (MetS) may be associated with obesity-related cancer (ORC) owing to shared risk factors like physical inactivity, insulin resistance, gut microbiome dysfunction, and inflammation. We conducted an umbrella review of systematic reviews with meta-analysis to synthesize the evidence on the association between MetS and ORC risk and survival.

METHODS: Searches in five databases (Medline, Embase, CINAHL, Cochrane Library, and Scopus) retrieved 2524 systematic reviews with meta-analyses (SRMAs), which underwent title and abstract screening (2524), full-text review (41), and data extraction for included SRMAs (21). Summary effects and 95% confidence intervals were re-estimated using random-effects models. Methodological quality, certainty of evidence, and publication bias were assessed using the AMSTAR 2, modified Ioannidis criteria, and Egger's test, respectively.

RESULTS: A total of 25 associations between MetS and ORC risk and five between MetS and survival were evaluated. Overall, 10 associations evaluating MetS and ORC risk were highly suggestive (four) or suggestive (six), while the rest were classified as weak (seven) or nonsignificant (eight). One association was suggestive for MetS and ORC survival, while the rest were classified as weak (three) or nonsignificant (one). The Egger's and excess significance tests were significant for 8(32%) associations between MetS and ORC risk and 3(60%) associations between MetS and ORC survival.

CONCLUSION: This umbrella review suggests metabolic syndrome increases the risk of several obesity-related cancers and worsens colorectal cancer survival. Despite study variability, consistent associations across diverse populations highlight the urgency of prevention and management strategies targeting metabolic dysfunction to reduce cancer burden. Summary In this umbrella review, highly suggestive and suggestive evidence supports associations between MetS and the risk and survival of several obesity-related cancers. However, a better understanding of the relationship between metabolic syndrome and obesity-related cancers is still needed to provide appropriate clinical care, design optimal interventions, and prevent subsequent increases in the risks of cancer, morbidity, and mortality.},
}

@article {pmid41508485,
year = {2026},
author = {Wang, X and Qiu, M and Shao, Y and Tu, Z and Liu, J},
title = {Mechanism of high-fat diet exacerbating α-lactalbumin-induced allergic responses: Microbiome and metabolomic insights.},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {118064},
doi = {10.1016/j.foodres.2025.118064},
pmid = {41508485},
issn = {1873-7145},
mesh = {Animals ; *Lactalbumin/immunology/adverse effects ; *Diet, High-Fat/adverse effects ; *Metabolomics ; Mice ; *Food Hypersensitivity/microbiology/metabolism/immunology/etiology ; *Gastrointestinal Microbiome ; Immunoglobulin E/blood ; Male ; Mice, Inbred C57BL ; Histidine/metabolism ; Staphylococcus ; Cytokines/metabolism ; Immunoglobulin G/blood ; *Microbiota ; },
abstract = {High-fat diet (HFD) is a key contributor in exacerbating food allergy, but there is little in-depth research on the mechanisms by which HFD affects allergic responses induced by α-lactalbumin (ALA). The mechanism of HFD exacerbating ALA-induced allergic responses (H-ALA) was studied via microbiome and metabolomics. HFD induced alterations in body weight and temperature in ALA-sensitized mice, while exacerbating allergic responses by increasing ALA-specific IgG/IgE levels and disrupting Th1/Th2 cytokine balance. In H-ALA, 16S rRNA gene sequencing revealed that Staphylococcus and Bilophila were the dominant genera, and untargeted metabolomics demonstrated an upregulation of histidine accompanied by reduced indole-3-acetic acid. Correlation analysis and subsequent mechanistic validation suggested that HFD might exacerbate ALA-induced allergic responses through promoting the expansion of Staphylococcus and elevating histidine levels. These findings will provide a theoretical foundation for the prevention and intervention of HFD-exacerbated food allergy.},
}

Animals
*Lactalbumin/immunology/adverse effects
*Diet, High-Fat/adverse effects
*Metabolomics
Mice
*Food Hypersensitivity/microbiology/metabolism/immunology/etiology
*Gastrointestinal Microbiome
Immunoglobulin E/blood
Male
Mice, Inbred C57BL
Histidine/metabolism
Staphylococcus
Cytokines/metabolism
Immunoglobulin G/blood
*Microbiota

@article {pmid41507958,
year = {2026},
author = {Ramadan, YN and Alatawi, MN and Albalawi, AS and Hetta, HF},
title = {Bacterial contributions to cancer development: mechanisms, dysbiosis, and cross-cancer associations.},
journal = {Infectious agents and cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13027-025-00722-7},
pmid = {41507958},
issn = {1750-9378},
}

@article {pmid41507781,
year = {2026},
author = {Vlasblom, AA and Patel, S and Lawlor, PG and Claesson, MJ and Crespo-Piazuelo, D and Eckenberger, J and Huseyin, CE and Elend, C and Wagenaar, JA and Zomer, AL and Duim, B},
title = {Targeted isolation of bacteria with potential to competitively exclude Staphylococcus aureus in the upper respiratory tract of pigs.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04613-0},
pmid = {41507781},
issn = {1471-2180},
support = {50-52900-98-043//JPIAMR (JPIAMR-2017-1-B/ ; },
abstract = {BACKGROUND: Considering global antimicrobial resistance (AMR) prevalence, alternative or complementary strategies to antimicrobial use, are of interest. Livestock- associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is of particular interest as despite significant AMU reduction, LA-MRSA prevalence in pig husbandry has not decreased. To develop such strategy, we performed targeted isolation of bacterial species with potential antagonism against LA-MRSA in pig farms.

RESULTS: Duplicate piglet nasal swabs from three European countries (Germany, Ireland and The Netherlands) were taken longitudinally from birth up to 10 weeks, one for amplicon sequencing and qPCR, and the other was cryopreserved for culturing. We identified potential probiotic species by anticorrelation analysis of bacterial abundance from amplicon sequencing data with quantitative S. aureus estimates from qPCR data from the samples. A literature-screen was performed on the species identified, to determine their probiotic potential. Following this, 1302 isolates were grown from selected cryopreserved swabs and identified using MALDI-TOF and additional 16S rRNA gene sequencing to isolate the anticorrelating species. Ninety-five isolates of interest were screened for absence of tetracycline resistance and hemolytic activity and whole genome sequencing was conducted to verify their taxonomy and to assess their AMR and virulence gene profile. Additional phenotypic antimicrobial resistance testing selected three different Lactococcus lactis strains. During an in vitro challenge using spent medium, all three strains demonstrated inhibition against two S. aureus strains.

CONCLUSIONS: Our study, using an anticorrelation based targeted approach, identified three L. lactis strains with weak negative correlation with S. aureus, suitable for in vivo safety and efficacy testing in pigs. These L. lactis strains may have the ability to be used safely to reduce LA-MRSA carriage in the nasal passages of pigs but further in vivo testing is necessary to confirm this potential.},
}

@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04664-3},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.

STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.

RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.

CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}

@article {pmid41507771,
year = {2026},
author = {Agorsor, IDK and Khadka, P and Danna, CH},
title = {The Arabidopsis UMAMIT30 transporter contributes to amino acid root exudation.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07930-8},
pmid = {41507771},
issn = {1471-2229},
support = {SG00409//University of Virginia 4-VA grant/ ; IOS-1943120//National Science Foundation CAREER Award/ ; },
abstract = {BACKGROUND: Root exudation is an important trait that enables plants to shape their interactions with soil-borne organisms. Amino acids present in root exudates play important roles in bacterial chemotaxis, bacterial metabolism, and root colonization, contributing to plant nutrition and health. Notwithstanding the importance of amino acids in shaping the rhizosphere microbiome, the identities of the plant amino acid transporters that mediate their root exudation have remained elusive.

RESULTS: Here, we report that the Arabidopsis UMAMIT30 transporter, robustly expressed in root and shoot tissues, significantly contributes to amino acid root exudation. umamit30 loss-of-function mutants were compromised for amino acid root exudation as shown by the low concentration of amino acids, particularly glutamine, recovered from root exudates compared to wild-type plants. Amino acid quantification, as well as uptake and secretion assessments using radiolabelled glutamine, revealed that the shoots of umamit30 accumulate amino acids and have a reduced capacity to secrete glutamine, impacting root exudation.

CONCLUSIONS: Our results identify UMAMIT30 as a broadly specific amino acid exporter strongly expressed in Arabidopsis vasculature. Loss-of-function mutants displayed reduced amino acid levels in root exudates, with significant drops in glutamine and asparagine among others, yet exhibited no detectable growth defects under our growth conditions. UMAMIT30 disruption led to elevated shoot amino acid content and reduced glutamine efflux from shoots, suggesting a role in phloem uploading as an upstream step necessary for root exudation. Despite decreased levels of root-exuded amino acids, the plant growth-promotion conferred by the soil-borne beneficial bacterium Pseudomonas simiae WCS417r remained unmodified in umamit30 mutants.},
}

@article {pmid41507594,
year = {2026},
author = {Gandham, A and Prokopidis, K and Glavas, C and Scott, D and Lorentzon, M},
title = {Impact of probiotic, prebiotic, and synbiotic supplementation on the gut microbiome in older adults with sarcopenia, obesity, and sarcopenic obesity.},
journal = {Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA},
volume = {},
number = {},
pages = {},
pmid = {41507594},
issn = {1433-2965},
abstract = {Gut microbiome plays an important role in several metabolic, immune, and inflammatory pathways; however, there is limited evidence for its role in body composition and musculoskeletal health. Sarcopenia, defined as a loss of skeletal muscle mass and function, and obesity, can co-exist in a condition known as sarcopenic obesity. This condition is highly prevalent among older adults, hence increasing the risk of negative health implications such as metabolic dysfunction, chronic inflammation, reduced physical performance, and poor quality of life. These age-related conditions are closely associated with alterations to the gut microbiome, including microbial profiles and a reduction in beneficial metabolites such as short-chain fatty acids (SCFAs). Probiotic, prebiotic, and synbiotic interventions are therefore emerging as promising strategies to improve the gut microbiome by enhancing microbial diversity and restoring microbial communities. This review utilizes current evidence on the impact of these interventions on gut microbiota composition, inflammatory and metabolic biomarkers, body composition, and functional outcomes in older adults with sarcopenia, obesity, and sarcopenic obesity. Probiotics, containing live beneficial microorganisms, have shown potential in enhancing SCFA production, reducing inflammation, and improving insulin sensitivity. Prebiotics are non-digestible fibers that selectively activate the growth of beneficial gut bacteria, further supporting gut health by proliferating the growth of SCFA-producing bacteria. Synbiotics, a combination of probiotics and prebiotics, provide a synergistic approach to gut health, accounting for the microbial composition and functional capability. Recent studies have demonstrated that probiotics, prebiotics, and synbiotics may reduce inflammation and improve muscle mass and strength among older adults with sarcopenia, obesity, and sarcopenic obesity. These interventions have the potential in mitigating obesity-related metabolic dysfunction and inflammation, particularly in individuals with sarcopenic obesity. Although, preclinical studies in mice exhibit beneficial effects, clinical studies in older adults remain limited, with heterogeneity of study design, intervention types, and outcome measures. This review highlights the need for robust, well-designed clinical trials to understand the mechanistic and molecular pathways through which probiotic, prebiotic, and synbiotic supplementation may modulate the gut microbiome and improve musculoskeletal health among older adults. These interventions may provide innovative, non-invasive therapeutic strategies for managing sarcopenia, obesity, and sarcopenic obesity, ultimately contributing to healthier aging and improved quality of life of older adults. This review also underscores the potential of microbiome-targeted interventions for aging populations, highlighting the need for further research.},
}

@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41507585},
issn = {2058-5276},
support = {BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}

@article {pmid41507362,
year = {2026},
author = {Elettrico, L and Piacenti, G and Levra Levron, C and Ansai, O and Croce, A and Duval, C and Proserpio, V and Donati, G},
title = {Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.},
journal = {Cell death and differentiation},
volume = {},
number = {},
pages = {},
pmid = {41507362},
issn = {1476-5403},
support = {IG2023 - Id.21640//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; postdoc fellowship//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; MFAG 2023 - Id.29203//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; postdoc fellowship//Fondazione Umberto Veronesi (Umberto Veronesi Foundation)/ ; },
abstract = {Skin homeostasis depends on interactions between epithelial cells and the microbiome mediated by molecular and biochemical factors. Perturbations of this interplay are linked to inflammatory disorders, including wound healing and cancer. While research has mainly illuminated shifts in microbial community composition, novel computational approaches are starting to reveal the host-microbe functional interactome in the cutaneous ecosystem. In this review, we specifically focus on known molecular and metabolic mechanisms linking skin epithelial cells and microorganisms in health and disease. Additionally, we summarise computational tools available to investigate these interactions integrating omics data. Furthermore, we present potential applications of this functional crosstalk to advance therapies targeting skin pathologies. Finally, we propose a comparative interactomics approach to envision the existence of ecological memories in the skin ecosystem, in parallel with the one described in the gut, hypothesising a link between epithelial and microbial memories in barrier tissues.},
}

@article {pmid41507168,
year = {2026},
author = {Lan, J and Wang, J and Huang, S and Li, C and Deng, Z and Hao, Z and Ma, Y},
title = {Neuropeptide SP protects against colitis and linked anxiety-like behavior through the putative roles of gut microbiota and metabolite inositol.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {295},
pmid = {41507168},
issn = {2041-1723},
support = {31772686//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Microglia/metabolism/drug effects ; *Colitis/chemically induced/metabolism/microbiology/prevention & control ; Mice ; *Inositol/metabolism ; Male ; *Anxiety/metabolism ; NF-kappa B/metabolism ; Mice, Inbred C57BL ; *Substance P/pharmacology/metabolism ; Dextran Sulfate ; Hippocampus/metabolism/drug effects/pathology ; Astrocytes/metabolism/drug effects ; Disease Models, Animal ; Signal Transduction ; },
abstract = {The gut-brain axis links gut inflammation to psychiatric symptoms in inflammatory bowel disease (IBD), but the underlying mechanisms remain unclear. We demonstrate that neuropeptide substance P (SP) alleviated intestinal injury and behavioral disorders induced by dextran sodium sulfate in mice. SP mitigated hippocampal neuroinflammation and inhibited microglial activation and astrocyte loss. Furthermore, SP improved gut microbiome dysregulation, and its protective effects depended on the putative roles of microbiota. Notably, through modulating microbiota, SP dampened the NF-κB pathway in microglia, and increased GABAergic/Ca[2+] signaling within astrocytes. SP elevated the microbiota-derived metabolite inositol. Supplementing inositol mimicked SP's benefits and activated GABAergic signaling, while the inositol inhibitor reversed SP's neuroprotective impacts, highlighting inositol's indispensable role. Collectively, SP exerts beneficial effects via microbiota's putative roles and inositol, involving the suppression of microglial NF-κB pathway while enhancing astrocytic GABAergic/Ca[2+] signaling. Our findings underscore SP's potential as a therapeutic intervention for these disorders in IBD.},
}

Animals
*Gastrointestinal Microbiome/drug effects/physiology
Microglia/metabolism/drug effects
*Colitis/chemically induced/metabolism/microbiology/prevention & control
Mice
*Inositol/metabolism
Male
*Anxiety/metabolism
NF-kappa B/metabolism
Mice, Inbred C57BL
*Substance P/pharmacology/metabolism
Dextran Sulfate
Hippocampus/metabolism/drug effects/pathology
Astrocytes/metabolism/drug effects
Disease Models, Animal
Signal Transduction

@article {pmid41506609,
year = {2026},
author = {Wang, W and Zhang, K and Liu, Z and Liu, X and Wang, X},
title = {Effects of Polyethylene Microplastics and Cadmium Co-contamination on the Soybean-Soil System:Integrated Metabolic and rhizosphere Microbial Mechanisms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127643},
doi = {10.1016/j.envpol.2026.127643},
pmid = {41506609},
issn = {1873-6424},
abstract = {The coexistence of microplastics (MPs) and heavy metals in agricultural soils presents complex and poorly understood ecological risks. While previous studies have examined the individual effects of these pollutants, the interactive mechanisms governing their combined impact on plant-soil systems, particularly through integrated metabolic and microbial pathways remain unclear. This study investigated the effects of polyethylene microplastics (PE-MPs) and cadmium (Cd) co-exposure on soybean-soil systems. Under moderate Cd exposure (20 mg/kg), specific PE-MPs concentrations (1% and 5%) enhanced Cd accumulation in soybean roots, whereas this trend reversed under high Cd levels (50 mg/kg). Co-exposure maintained stable shoot growth through activation of stress-response pathways (β-alanine, porphyrin, and pantothenate metabolism). Rhizosphere microbiome analysis revealed that 5% and 10% PE-MPs reduced the abundance of Sphingomonas and Bradyrhizobium in Cd-contaminated soil and suppressed nitrogen-cycling functionality. Integrated metabolite-microbe network analysis identified malonyldaidzin as a potential mediator linking soybean leaf metabolism with rhizobacterial interactions, associated with root Cd accumulation. These findings demonstrate that PE-MPs fundamentally alter Cd behavior through tripartite plant-metabolite-microbe interactions, thereby highlighting the need to incorporate MPs effects into ecological risk assessments of heavy metal contamination in agricultural ecosystems.},
}

@article {pmid41506211,
year = {2026},
author = {Zhao, N and Zhang, Z and Ding, H and Guillemot, T and Wang, D and Wang, H},
title = {Electron transfer versatility of a Geobacter sp. links PAH degradation with multi-electron acceptor respiration, including crystalline magnetite.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {141052},
doi = {10.1016/j.jhazmat.2026.141052},
pmid = {41506211},
issn = {1873-3336},
abstract = {Anaerobic degradation of polycyclic aromatic hydrocarbons (PAHs) is often constrained by the availability and accessibility of terminal electron acceptors in anoxic, metal-rich environments. Here we characterize a Geobacter sp. (strain GeoA) that couples phenanthrene oxidation to respiration with nitrate, Mn(IV), Fe(III)-citrate, sulfate, Cr(VI), and crystalline magnetite. Phenanthrene removal (initial 280 μM) proceeded fastest with Mn(IV) and nitrate (about 96 % within 5-7 d), followed by Fe(III)-citrate (about 95 % in 20 d), sulfate (about 95 % in 24 d), and Cr(VI) (about 61 % in 56 d, concomitant with complete reduction of 2.1 mM Cr(VI)). While previous studies mainly focused on amorphous or poorly crystalline Fe(III) minerals, the role of highly crystalline magnetite as an active electron sink has remained unclear. In this study, GeoA reduced ∼35 % of supplied magnetite (20 mM Fe(III) basis) and exhibited an acetate:Fe(III) stoichiometry (∼1:8) consistent with dissimilatory reduction. XPS and AQDS enhancement assays, together with upregulation of pilA and the flavin exporter yeeO, indicate that both direct and shuttle-facilitated extracellular electron transfer contribute to crystalline iron oxide reduction. Metabolite profiling with [13]C-bicarbonate labelling, together with genomic evidence, supports a carboxylation-initiated route for anaerobic phenanthrene activation. An analysis of Earth Microbiome Project datasets shows Geobacter predominance among dissimilatory iron-reducing genera in soils and sediments, consistent with ecological adaptation to solid-phase electron acceptors. These findings expand the known respiratory flexibility and bio-remediation potential of PAH-degrading bacteria and provide the first mechanistic evidence of PAH oxidation coupled to magnetite reduction by a single pure strain, highlighting crystalline magnetite as a relevant electron sink in PAH-metal co-contaminated anoxic environments.},
}

@article {pmid41505994,
year = {2026},
author = {Zhao, S and Xu, H and Liu, R and Wang, J and Zhi, B and Fu, X and Cao, X and Ma, X and Shao, Z},
title = {Biodegradation and disintegration of expanded polystyrene by sphaeromatid isopods Sphaeroma via their gut bacteria.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119207},
doi = {10.1016/j.marpolbul.2025.119207},
pmid = {41505994},
issn = {1879-3363},
abstract = {Wood-boring isopods have been documented inhabiting the plastic floats of expanded polystyrene (EPS), which is extensively utilized in mariculture as buoyant material. However, little is known about their role in the plastic fragmentation and degradation. This report confirmed that globally distributed Sphaeroma gnawed and ingested EPS foam, and digested it via their gut microbiome. After 7 days of exposure, each Sphaeroma consumed 4.4 ± 0.2 mg EPS, ingested 50 microbeads and egested 2.5 ± 0.7 × 10[3] microplastics. Analyses using μFTIR, GPC, and GC-MS revealed polystyrene (PS) degradation in the gut of Sphaeroma. High throughput 16S rRNA sequencing revealed that Exiguobacterium spp. and Brevibacterium spp. were associated with PS diets in the gut microbiome of Sphaeroma, suggesting their potential key role in vivo. Further characterizations of PS weight loss, changes in chemical and thermal properties, and identification of metabolic intermediates confirmed that PS can be degraded by five gut bacteria from the above two genera. Antibiotic bioassay confirmed that gut microbes are essential for the EPS depolymerization in Sphaeroma by. All these results demonstrate that the gut microbiome contributes to EPS digestion in the host. Together, these results found marine isopods in coastal negatively influenced the environmental fats of the plastic fate, by fragmenting plastics and generating microplastics, via their PS-degrading gut microbiota.},
}

@article {pmid41505190,
year = {2026},
author = {McGarrity-Yoder, M and Cope, EK and Wayment, HA and Rodriguez-Pla, A and Crane, TE},
title = {Biopsychosocial Determinants, Diet Quality, Gastrointestinal Health, and Disease Activity in Adults With Rheumatoid Arthritis: Cross-Sectional Descriptive Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e79889},
doi = {10.2196/79889},
pmid = {41505190},
issn = {1929-0748},
mesh = {Humans ; Cross-Sectional Studies ; *Arthritis, Rheumatoid/psychology/physiopathology ; Adult ; Female ; Male ; Arizona ; *Diet ; Middle Aged ; *Gastrointestinal Tract/physiopathology ; Aged ; Surveys and Questionnaires ; },
abstract = {BACKGROUND: Rheumatoid arthritis (RA) causes pain, fatigue, joint deformity, disability, and an increased risk for serious sequelae, often despite treatment, in 1.3 million Americans. RA is affected by numerous biopsychosocial determinants, which greatly complicate treatment, including altered efficacy.

OBJECTIVE: The purpose of this study is to examine associations between individual biopsychosocial determinants, diet quality, gastrointestinal (GI) health, and disease activity in adults with RA.

METHODS: This cross-sectional, descriptive study has been approved by the Northern Arizona University Internal Review Board (# 2111208-12). We will include 96 adults with RA recruited from across Arizona using social media and community events (through the Arthritis Foundation) and various primary care and rheumatology practices in Flagstaff and the greater Phoenix metro area. Individual biopsychosocial factors will be measured with a demographic survey and direct measures. The Arizona Food Frequency Questionnaire will measure dietary intake for the past 6 months, and Healthy Eating Index-2020 scores will be calculated from these data. The Automated Self-Administered 24-hour diet recall will measure recent dietary intake. Fecal analyses for gut microbiome diversity and composition and fecal calprotectin will measure current GI health. Disease activity will be measured by the Health Assessment Questionnaire-Disability Index and pain scale, Disease Activity Score of 28 Joints, and hematology results (C-reactive protein and erythrocyte sedimentation rate). In addition to descriptive statistics, hierarchical linear regression will examine hypothesized associations between diet quality, GI health, and disease activity. We hypothesize that individual biopsychosocial determinants will be associated with diet quality, which will be indirectly associated with disease activity through gut microbiome diversity and level of GI inflammation in adults with RA.

RESULTS: This study was funded in February 2024. As of December 19, 2025, a total of 80 individuals have been recruited. Data analysis has not yet commenced at the time of manuscript submission. Study results are expected to be published in fall 2026.

CONCLUSIONS: RA is a complicated disease that impacts millions. Few individuals reach sustained remission, even while following provider recommendations. A better understanding of the various factors that impact this complicated disease has the potential to support changes in research and care that will improve the lives of people with RA. The knowledge gained in this study will provide a foundation to inform future interventional research targeting diet quality to support GI health and decrease RA disease activity. Further, the details of this research plan provide methodological resources for other RA researchers, and research results have the potential to improve communication between rheumatology providers and patients.

PRR1-10.2196/79889.},
}

Humans
Cross-Sectional Studies
*Arthritis, Rheumatoid/psychology/physiopathology
Adult
Female
Male
Arizona
*Diet
Middle Aged
*Gastrointestinal Tract/physiopathology
Aged
Surveys and Questionnaires

@article {pmid41505077,
year = {2026},
author = {Ghaemi, M and Ghaemi, A and Tavakkoli, H and Mashhadinejad, M and Kheradmand, D},
title = {The MOF-Microbiome Axis: a New Paradigm for Precision Nanomedicine.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41505077},
issn = {1867-1314},
abstract = {The gut microbiome is crucial for human health, and its imbalance, known as dysbiosis, is associated with diseases such as inflammatory bowel disease, metabolic disorders, and neurological disorders. Traditional treatments, such as probiotics and fecal microbiota transplants, often lack precision, making the emerging field of nanomedicine a promising alternative. This review introduces the "MOF-Microbiome Axis," which explores the interactions between metal-organic frameworks (MOFs), versatile, porous materials, and the gut microbiome. It focuses on designing gastrointestinal-targeted MOFs that are biocompatible and responsive to stimuli. We discuss how MOFs can serve as scaffolds, controlled-release vehicles, and metabolite scavengers, highlighting their therapeutic applications in targeted antimicrobial therapy, enhanced probiotic delivery, and immunomodulation. The review also addresses important challenges in biosafety, scalable production, and personalized treatment, suggesting future directions such as bio-hybrid systems and precision microbiome editing. Overall, the MOF-Microbiome Axis offers a new perspective on microbiome engineering and advanced therapeutic approaches.},
}

@article {pmid41504923,
year = {2026},
author = {Yousefi, F and Salehi, B and Ghorbani, N and Yaghmayee, S and Eslami, M},
title = {Integrative analysis of placental metabolic reprogramming and microbiome alterations in gestational diabetes mellitus (GDM).},
journal = {Acta diabetologica},
volume = {},
number = {},
pages = {},
pmid = {41504923},
issn = {1432-5233},
}

@article {pmid41504672,
year = {2026},
author = {Somboonna, N and Rujirawan, P and Wongsaroj, L and Promvaranon, T and Rerknimitr, P},
title = {Nail Fold Microbiome Alterations in Patients Treated With Epidermal Growth Factor Receptor Inhibitors.},
journal = {Experimental dermatology},
volume = {35},
number = {1},
pages = {e70201},
doi = {10.1111/exd.70201},
pmid = {41504672},
issn = {1600-0625},
support = {RA61/079//The Ratchadapiseksomphot Endowment Fund, Faculty of Medicine, Chulalongkorn University/ ; },
}

@article {pmid41504597,
year = {2026},
author = {Larner, W and Thölke da Silva Grego, N and Panfilio, KA},
title = {Intraspecific microbiome dynamics across the life cycle of the milkweed bug Oncopeltus fasciatus.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001583},
pmid = {41504597},
issn = {2057-5858},
mesh = {Animals ; *Heteroptera/microbiology/growth & development ; RNA, Ribosomal, 16S/genetics ; Female ; *Microbiota/genetics ; Life Cycle Stages ; *Bacteria/genetics/classification/isolation & purification ; Male ; *Hemiptera/microbiology ; Phylogeny ; },
abstract = {The microbiome is an important part of the complete nutritional and genomic profile of insects. The species-rich insect order Hemiptera (aphids, cicadas and true bugs) is highly diverse for mode of microbiome acquisition, with the conundrum that species in the seed-feeding subfamily Lygaeinae have lost obvious anatomy for housing bacteria, either in bacteriocytes or midgut crypts. Here, we characterize the microbiome of the milkweed bug Oncopeltus fasciatus as a tractable lygaeinid, using 16S rRNA gene sequencing. We assess how bacterial taxa vary between the sexes and across life history stages in a controlled environment, focusing on maternal-to-embryo transmission and distinguishing egg-stage constituents that are superficial or internal (transovarially transmitted). Among a core microbiome of 28 genera, the egg stage shows the greatest diversity, with a particular expansion of the family Comamonadaceae. We also analyse inter-individual variability in nymphs and adults and validate structured, stage-specific detection of seed material. Comparative analysis identifies Rhizobium as a notable microbiome constituent in seed-feeding Hemiptera, which we had previously shown to lack nitrogen metabolism components in the genome. Overall, we provide a nuanced assessment of bacterial abundance dynamics between individuals and across the life cycle and discuss the implications for acquisition and potential relevance as nutritional endosymbionts. This will underpin comparative investigations in seed-feeding bugs and future work in O. fasciatus on tissue-specific and diet-specific microbiome profiles, including in natural populations.},
}

Animals
*Heteroptera/microbiology/growth & development
RNA, Ribosomal, 16S/genetics
Female
*Microbiota/genetics
Life Cycle Stages
*Bacteria/genetics/classification/isolation & purification
Male
*Hemiptera/microbiology
Phylogeny

@article {pmid41504479,
year = {2026},
author = {Vompe, AD and Hamidizade, M and López, MM and O'Connor, E and Kaur, L and Hockett, KL and Bull, CT},
title = {Translational microbiomes in agriculture: microbial communities as tools to effect host and system health for improved crop production.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0170425},
doi = {10.1128/aem.01704-25},
pmid = {41504479},
issn = {1098-5336},
abstract = {The boom of microbiome research in agriculture over the past several decades allows scientists, growers, policymakers, and businesses to collaborate on a unique opportunity-deploying microbiomes and microbiome attributes for the improvement of crop production. The idea of translational microbiomes is well established in the medical field; however, this framework is relatively new to agriculture. In this review, we discuss a series of methodologies grounded in microbiome science to enhance crop health. These include diagnostic approaches (pathogen and toxin detection and the monitoring of stress-related community ecology patterns) and intervention strategies (synthetic communities, microbiome-aware crop management practices, passaging microbiomes, and exploiting the vertical and lateral transmission of microbiomes to seeds). Developing and implementing these approaches remain challenging due, in part, to a shortage of long-term in situ studies demonstrating the robustness and effectiveness of translational microbiome efforts against the background of heterogeneity and ecological complexity of agricultural systems. Moreover, the cost and availability of 'omics methods central to microbiome analysis, disparate standards for microbiome product development, and limited longstanding relationships with stakeholders have slowed down the application of microbiome-based solutions. However, the increasing cost-effectiveness of microbiome approaches in crop management makes translational microbiomes likely assets in the movement toward precision agriculture. This "personalized treatment" for plants holds promise for improved food security and environmental sustainability, by reducing commonplace synthetic amendments and promoting native microbial biodiversity.},
}

@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0305125},
doi = {10.1128/spectrum.03051-25},
pmid = {41504449},
issn = {2165-0497},
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}

@article {pmid41504323,
year = {2026},
author = {Lanzara, R and Conti, C and Zito, L and Anaclerio, F and Affaitati, GP and Giamberardino, MA and Stuppia, L and Porcelli, P},
title = {Gut Microbiota and Psychological Distress in Fibromyalgia: A Systematic Review.},
journal = {Biopsychosocial science and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1097/PSY.0000000000001463},
pmid = {41504323},
issn = {2998-8756},
abstract = {OBJECTIVE: This systematic review aimed to summarize the recent evidence of the relationship between gut microbiota and psychological distress in patients with fibromyalgia (FM).

METHODS: According to PRISMA guidelines, we conducted a systematic search of the literature on PubMed, Scopus, EBSCO, WOS, and Cochrane. The records were selected using multiple combinations of relevant search terms involving microbiota, psychological distress, and FM. Articles in English with human participants were reviewed.

RESULTS: The initial search identified 135 records, excluding duplicates, of which 10 research reports met the predefined inclusion criteria and were analyzed. Most studies (n=7) were case-control, two were randomized controlled trials, and one was observational. Most studies found an imbalance in the gut microbial communities of FM patients and a significant difference between FM patients and HC in microbiome composition/diversity or gut permeability. Intestinal dysbiosis and gut permeability were also associated with high psychological distress (emotional, cognitive, and somatic symptoms).

CONCLUSION: Alterations in the gut microbiota of FM patients seem to support the hypothesis that gut-brain axis regulation is impaired in stress-related pain conditions. Although the results are promising, further studies are needed to clarify the role of the microbiota-gut-brain axis in the pathophysiological mechanisms underlying FM.},
}

@article {pmid41504275,
year = {2026},
author = {Xu, C and Antonacci, S and Marques, FZ},
title = {The maternal microbiome influence on pregnancy success: breeding comparison of germ-free and conventionalized mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2609405},
doi = {10.1080/19490976.2025.2609405},
pmid = {41504275},
issn = {1949-0984},
mesh = {Female ; Animals ; Pregnancy ; Mice ; *Germ-Free Life ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation & purification/metabolism ; Male ; Diet ; Fertility ; Breeding ; },
abstract = {Germ-free (GF) animals, which are entirely devoid of all microorganisms, are one of the most powerful tools for studying the role of the microbiome in a phenotype, moving the microbiome field from association to causation. They allow the introduction of specific microbes or microbial communities to interrogate the causality of microbiomes in protecting against or contributing to a phenotype. Here, we report critical and underappreciated challenges in using GF models to investigate the intergenerational effects of maternal diet and microbiota on offspring health. Using 57 GF and littermate conventionalized GF dams, we observed unexpectedly high maternal (odds ratio 11.5, p < 0.0001) and offspring (odds ratio 4.12, p < 0.0001) mortality in GF animals. Remarkably, GF dams had an extremely low pregnancy and parturition (pmicrobiome < 0.0001) and a high incidence of cecal torsion (18.2%) compared to the conventionalized group, underscoring the indispensable role of the maternal microbiome in reproductive success and early development. Notably, even conventionalized GF mothers on high-fiber diets exhibited poor fertility, suggesting that microbial colonization timing and maternal microbial capacity to metabolize fiber are crucial. These findings not only reveal significant limitations in GF breeding protocols but also indicate that the maternal microbiota might influence offspring health far earlier than previously recognized, with implications for the developmental origins of health and disease research.},
}

Female
Animals
Pregnancy
Mice
*Germ-Free Life
*Gastrointestinal Microbiome
Mice, Inbred C57BL
Bacteria/classification/genetics/isolation & purification/metabolism
Male
Diet
Fertility
Breeding

@article {pmid41504254,
year = {2026},
author = {Lin, P},
title = {The importance of the microbiome in uveitis.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICU.0000000000001197},
pmid = {41504254},
issn = {1531-7021},
abstract = {PURPOSE OF REVIEW: The purpose of this review was to summarize the literature on preclinical and clinical studies demonstrating the impact of the intestinal microbiome in noninfectious uveitis.

RECENT FINDINGS: Preclinical studies using the experimental autoimmune uveitis (EAU) model have shown commensals such as Desulfovibrio and Prevotella, as well as Ruminococcaceae, associated with uveitis, which overlap with some clinical studies in uveitis patients. Interventions that target the microbiome that can be developed for the treatment of uveitis include antibiotics, fecal metabolites or metabolite agonists that are protective in uveitis, probiotics, dietary interventions, or fecal microbial transplant.

SUMMARY: There is significant data supporting the importance of the intestinal microbiome in noninfectious uveitis through enrichment or depletion of certain gut bacteria as well as their metabolites. Targeting the intestinal microbiome or their metabolites might be a viable option for the treatment of noninfectious uveitis.},
}

@article {pmid41504167,
year = {2026},
author = {Zhou, Q and Gao, X and Wu, Q and Zeng, W and Cao, W and Zhou, T and Cui, X and Chen, J and Gao, D and Zhao, H},
title = {Cross-Kingdom Synthetic Microbiota Suppresses Wheat Fusarium Crown Rot by Remodeling the Rhizosphere Microbiome and Metabolome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11786},
pmid = {41504167},
issn = {1520-5118},
abstract = {Fusarium crown rot (FCR) of wheat lacks sustainable control. We assembled a cross-kingdom synthetic microbial community (SMC) of Trichoderma harzianum T19 and five Bacillus strains and tested it in nonsterile soil challenged with Fusarium pseudograminearum. The SMC treatment significantly suppressed FCR, reducing the disease severity index by approximately 70%. Wheat growth and yield were simultaneously enhanced. In the rhizosphere, SMC improved soil health by elevating soil organic matter and nitrogen levels by over 50%, while mitigating pathogen-induced nutrient imbalances and boosting nutrient-cycling enzyme activities. Amplicon sequencing revealed that SMC suppressed pathogenic Fusarium in the rhizosphere and enriched beneficial microbes, including antagonistic fungi (Trichoderma, Chaetomium) and plant growth-promoting bacteria (Pseudomonas, Paenibacillus). Co-occurrence network analysis showed that SMC treatment restructured the rhizosphere microbial network with higher connectivity, stability, and a prevalence of positive cooperative interactions under F. pseudograminearum stress. Defense-related metabolites, such as epi-jasmonic acid, allantoin, Nβ-acetyltryptamine, and dihydrodaidzein, accumulated to higher levels with SMC. These findings demonstrate that the cross-kingdom SMC modulates soil nutrients, microbial community structure, and rhizosphere metabolites to synergistically promote wheat growth and enhance resistance to FCR.},
}

@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).

METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.

RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.

CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Hyperuricemia/microbiology
Male
Female
*Overweight/microbiology
Middle Aged
Cross-Sectional Studies
Feces/microbiology
Adult
Metagenomics
Metagenome

@article {pmid41503894,
year = {2026},
author = {Kim, HS},
title = {Do Akkermansia mutants underlie to the global metabolic disease epidemic?.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612582},
doi = {10.1080/19490976.2025.2612582},
pmid = {41503894},
issn = {1949-0984},
mesh = {Humans ; *Metabolic Diseases/epidemiology/microbiology ; *Mutation ; Anti-Bacterial Agents/pharmacology/adverse effects ; *Akkermansia/genetics/drug effects ; Gastrointestinal Microbiome/drug effects ; Epidemics ; },
abstract = {Antibiotic-induced mutations in Akkermansia muciniphila promote bacterial survival while compromising beneficial host interactions, revealing a potential new link between antibiotic-driven microbiome disruption and metabolic disease. The widespread presence of these mutants suggests that they may contribute to the increasing prevalence of metabolic disorders. If validated in diverse global human cohort studies, these mutants could serve as biomarkers of disease susceptibility and as targets for therapeutic intervention.},
}

Humans
*Metabolic Diseases/epidemiology/microbiology
*Mutation
Anti-Bacterial Agents/pharmacology/adverse effects
*Akkermansia/genetics/drug effects
Gastrointestinal Microbiome/drug effects
Epidemics

@article {pmid41503829,
year = {2026},
author = {Zhang, H and Wang, Y and Ning, B and Wang, Y and Sun, T and Xu, J},
title = {The gut microbiota-obesity axis in the pathogenesis and prognosis of breast cancer.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2611203},
doi = {10.1080/07853890.2025.2611203},
pmid = {41503829},
issn = {1365-2060},
mesh = {Humans ; *Obesity/complications/microbiology/immunology ; *Breast Neoplasms/microbiology/immunology/pathology/therapy ; *Gastrointestinal Microbiome/physiology/immunology ; Female ; *Dysbiosis/microbiology/complications/immunology ; Prognosis ; Probiotics/therapeutic use ; },
abstract = {BACKGROUND: Breast cancer (BC) remains a major global health concern, accounting for 11.7% of all cancer cases and ranking as the second leading cause of female cancer-related deaths worldwide. Increasing evidence highlights the interplay between gut microbiota (GM) dysbiosis and obesity-associated metabolic dysfunction in BC progression. This review aims to elucidate the role of GM in obese patients with BC.

METHODS: A systematic literature search was conducted in PubMed and Web of Science databases for publications from July 2015 to January 2025. Search terms combined BC, GM, obesity, dysbiosis, immunity, and microbiome. Article selection prioritized studies investigating microbial alterations in BC patients, mechanistic links between obesity and cancer progression, and GM-targeted interventions. Both original studies and authoritative reviews were included, supplemented by manual reference screening.

DISCUSSION: Obesity may trigger systemic inflammation, altered adipokine secretion, and disrupted steroid hormone metabolism via gut-derived β-glucuronidase activity, thereby exacerbating BC occurrence and recurrence. GM dysbiosis-driven metabolites such as branched-chain amino acids (BCAAs) and short-chain fatty acids (SCFAs) can activate oncogenic signaling pathways and immunosuppressive myeloid-derived suppressor cells (MDSCs), fostering tumor immune evasion. Conversely, dietary interventions, probiotics, and fecal microbiota transplantation (FMT) can alleviate dysbiosis, strengthen gut barriers, and restore anti-tumor immunity, improving chemotherapy response and reducing recurrence. However, challenges persist in deciphering BC subtype-related microbial signatures and optimizing microbiota-targeted therapies.

CONCLUSION: Future longitudinal studies are needed to clarify causal relationships, validate microbial biomarkers, and translate preclinical findings into clinical applications. Addressing the gut-breast axis may offer transformative potential for precision oncology in obesity-driven BC.},
}

Humans
*Obesity/complications/microbiology/immunology
*Breast Neoplasms/microbiology/immunology/pathology/therapy
*Gastrointestinal Microbiome/physiology/immunology
Female
*Dysbiosis/microbiology/complications/immunology
Prognosis
Probiotics/therapeutic use

@article {pmid41503825,
year = {2026},
author = {Kang, K and Kim, JY and Yim, JJ and Kim, D},
title = {Gut-lung axis and microbiome alterations in mycobacterial infections: from pathogenesis to therapeutic potential.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612428},
doi = {10.1080/19490976.2025.2612428},
pmid = {41503825},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/therapy ; *Lung/microbiology/immunology ; Animals ; Probiotics ; Fecal Microbiota Transplantation ; *Mycobacterium Infections/microbiology/therapy ; },
abstract = {Mycobacterial lung diseases, including tuberculosis (TB) and nontuberculous mycobacterial pulmonary disease (NTM-PD), are increasingly recognized as disorders influenced not only by host immunity but also by microbiota. Emerging evidence identifies the gut-lung axis (GLA) as a key bidirectional communication network linking intestinal and pulmonary homeostasis. Mycobacterial infection itself induces airway and gut dysbiosis through immune and metabolic disturbances, which is further exacerbated by prolonged antibiotic therapy. Dysbiosis within either site reciprocally affects the other via GLA, leading to reduced microbial diversity, impaired epithelial integrity, and systemic inflammation. These alterations disrupt metabolite-mediated immunoregulation and attenuate IL-22-driven epithelial defense, thereby weakening bacterial clearance and promoting chronic inflammation. Distinct microbial features, such as the depletion of beneficial SCFA-producing taxa and enrichment of pro-inflammatory anaerobes, are observed in both TB and NTM-PD. Moreover, therapy-induced microbiome remodeling influences treatment response and disease relapse. Restoring microbial balance through probiotics, prebiotics, postbiotics, dietary modulation, or fecal microbiota transplantation offers a promising adjunctive strategy. This review integrates current evidence linking microbiome dysbiosis to mycobacterial pathogenesis and highlights microbiome-targeted interventions as an emerging therapeutic frontier in pulmonary mycobacterial diseases.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/therapy
*Lung/microbiology/immunology
Animals
Probiotics
Fecal Microbiota Transplantation
*Mycobacterium Infections/microbiology/therapy

@article {pmid41503704,
year = {2026},
author = {De Palma, G and Costanzini, A and Mohan, V and Sidani, S and Saqib, Z and Pigrau, M and Lu, J and Causada Calo, N and Pinto-Sanchez, I and Verdu, EF and Marcon, M and Barbara, G and Stanghellini, V and De Giorgio, R and Collins, SM and Bercik, P},
title = {The role of gut microbiota in chronic intestinal pseudo-obstruction: exploring fecal microbiota transplantation as a treatment option.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2610597},
doi = {10.1080/19490976.2025.2610597},
pmid = {41503704},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; *Intestinal Pseudo-Obstruction/therapy/microbiology ; *Gastrointestinal Microbiome ; Animals ; Humans ; Mice ; Male ; Female ; Middle Aged ; Adult ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Chronic Disease/therapy ; Aged ; Feces/microbiology ; Disease Models, Animal ; Italy ; },
abstract = {Chronic intestinal pseudo-obstruction (CIPO) is characterized by bowel dilation and obstructive symptoms without any structural blockage. Although the microbiota is known to affect gastrointestinal function, its role in CIPO is poorly understood. We aimed to characterize the CIPO microbiota, investigate its role in disease expression and explore the therapeutic role of fecal microbiota transplantation (FMT). CIPO patients (n = 14) and healthy controls (HC, n = 12) were recruited from Italy and Canada. Microbiota profiles and functions were assessed by 16S rRNA sequencing and PICRUSt. Germ-free NIH Swiss mice were colonized with HC and CIPO microbiota, their intestinal transit and bowel distension were assessed by videofluoroscopy and computed tomography (CT), and the expression of host genes by NanoString®. The CIPO microbiota exhibited reduced microbial diversity with dominance of Proteobacteria and altered metabolic function. Mice with CIPO microbiota developed marked bowel distension and slow intestinal transit associated with altered expression of multiple genes related to immunity, the intestinal barrier and neuromuscular function. FMT from a HC improved the microbiota profile, intestinal transit and bowel distension in both CIPO mice and a selected CIPO patient, in whom a marked clinical improvement was sustained for 8 y. Thus, our findings support the use of microbiota-directed therapies to induce clinical improvement in CIPO patients.},
}

*Fecal Microbiota Transplantation
*Intestinal Pseudo-Obstruction/therapy/microbiology
*Gastrointestinal Microbiome
Animals
Humans
Mice
Male
Female
Middle Aged
Adult
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Chronic Disease/therapy
Aged
Feces/microbiology
Disease Models, Animal
Italy

@article {pmid41503689,
year = {2026},
author = {Broedlow, CA and McGaugh, A and Glynn, TR and Cherenack, EM and Miller, C and Alcaide, ML and Bauermeister, JA and Grov, C and Parisi, R and Martinez, D and Carrico, AW and Klatt, NR and Manuzak, JA},
title = {Douching Is Associated With Dysregulated Rectal Mucosal Immunity in Sexual Minority Men.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf577},
pmid = {41503689},
issn = {1537-6613},
support = {//AIDS Healthcare Foundation/ ; //IDSA GERM/ ; P30AI073961//University of Miami Center for AIDS Research/ ; T32AI007433//University of Miami Center for AIDS Research/ ; K23DA060719//University of Miami Center for AIDS Research/ ; L60DA059128//University of Miami Center for AIDS Research/ ; 1F32AI162229//University of Miami Center for AIDS Research/ ; },
abstract = {BACKGROUND: Receptive condomless anal sex (CAS) associates with elevated rectal inflammation and mucosal injury, increasing HIV acquisition risk. Although douching may amplify rectal inflammation and alter microbial communities, this has not been well characterized in sexual minority men (SMM).

METHODS: Ninety-two SMM (median age, 34.6 years) who were HIV negative and reported receptive CAS provided rectal swabs during sexually transmitted infection (STI) clinic visits. Associations among rectal douching, rectal cytokine/chemokine levels, and microbial communities, evaluated via immunoassay and 16S rRNA gene sequencing, respectively, were assessed.

RESULTS: When compared with nondouching SMM (n = 27), SMM who douched (n = 64) reported more receptive CAS partners and displayed elevations in rectal cytokine/chemokines linked to immune activation and inflammation. Lower microbial richness, evenness, and Shannon diversity in SMM who reported douching were observed. Significant associations were identified between microbial alpha diversity metrics and rectal chemokine/cytokine levels. Finally, significant correlations were observed between rectal cytokine/chemokine levels and individual microbial genera.

CONCLUSIONS: Among SMM engaging in receptive CAS, douching may identify those with amplified biobehavioral HIV and STI risk. Elucidating the mechanisms whereby douching dysregulates rectal immune function and alters rectal microbial communities could yield targets for biomedical approaches to optimize HIV/STI prevention in SMM during receptive CAS.},
}