@article {pmid41666920,
year = {2026},
author = {da Silva, AC and Lapkin, J and Yin, Q and Muller, E and Almeida, A},
title = {Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.01.013},
pmid = {41666920},
issn = {1934-6069},
abstract = {The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. Here, we analyze 11,115 human gut metagenomes from 39 countries, 13 noncommunicable diseases, and healthy individuals to understand the clinical relevance of the uncultured microbiome worldwide. We identify 317 species linked to distinct clinical states, noting an overrepresentation of uncultured bacteria in healthy subjects. The genus CAG-170 emerged as the strongest health-associated lineage across multiple diseases and geographies, standing as the most central taxon based on ecological networks of healthy populations. We find that CAG-170 is temporally stable, with its abundance and subspecies diversity negatively correlated with gut imbalance over time. Functional predictions show CAG-170 species have greater vitamin B12 biosynthesis capacity and cross-feeding potential, providing important biological insights into this elusive genus. Our findings shed light on the underexplored role of uncultured gut species in health and disease.},
}

@article {pmid41666857,
year = {2026},
author = {Kumar, A and Gantenbein, B},
title = {A Commentary on "The Gut-Disc Axis: Unraveling the Microbiome's Role in Lumbar Disc Herniation".},
journal = {Neurospine},
volume = {23},
number = {1},
pages = {29-30},
doi = {10.14245/ns.26520126.0063},
pmid = {41666857},
issn = {2586-6583},
support = {//iPSpine project/ ; //Marie Skłodowska Curie International Training Network/ ; //three Swiss National Science Foundation projects/ ; //Spark/ ; },
}

@article {pmid41666856,
year = {2026},
author = {Ambrosio, L and Schol, J and Sima, S and Ruiz-Fernandez, C and Chen, V and Russo, F and Han, IH and Sakai, D and Vadalà, G and Denaro, V and Diwan, AD and , },
title = {The Gut-Disc Axis: Unraveling the Microbiome's Role in Lumbar Disc Herniation.},
journal = {Neurospine},
volume = {23},
number = {1},
pages = {3-28},
doi = {10.14245/ns.2551584.792},
pmid = {41666856},
issn = {2586-6583},
support = {//AO Spine/ ; //AO Spine Knowledge Forum Degenerative/ ; },
abstract = {Lumbar disc herniation (LDH) is one of the most common causes of low back and leg pain. While mechanical and degenerative factors have long been considered the main contributors, persistent or recurrent symptoms in many patients suggest additional biological mechanisms. Recent research has highlighted the microbiome as a potential modulator of inflammation, immune response, and pain sensitization, introducing the "gut-spine axis" concept. This scoping review summarizes the current evidence on the role of both gut and local disc microbiota in LDH. A systematic search of PubMed/MEDLINE and Scopus was conducted up to June 2025, following PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines. Twenty-six studies were included, encompassing preclinical and clinical investigations. Animal models showed that LDH may alter gut microbial composition and that microbiome-targeted interventions can reduce inflammation, neuroinflammatory signaling, and pain sensitivity. In human studies, low-virulence bacteria, particularly Cutibacterium acnes, were frequently detected in surgically excised intervertebral discs, although results were inconsistent due to methodological heterogeneity and potential contamination. Some studies reported associations between bacterial colonization and Modic changes, disc height loss, or chronic pain. Additionally, genetic and metabolomic data suggest that gut dysbiosis and related microbial metabolites may influence systemic immune and metabolic pathways implicated in disc degeneration and pain perception. Overall, the current evidence suggests the biological plausibility of microbiome involvement in LDH pathophysiology, acting through both systemic and local mechanisms. However, the available data remain preliminary, and no mechanistic study has confirmed the observed correlations to date. Further standardized, contamination-aware studies are required to clarify causality and explore microbiome-targeted therapeutic strategies.},
}

@article {pmid41666847,
year = {2026},
author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K},
title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110114},
doi = {10.1016/j.envint.2026.110114},
pmid = {41666847},
issn = {1873-6750},
abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.},
}

@article {pmid41666743,
year = {2026},
author = {Tong, J and Zhang, W and Yu, F and Liu, R and Yan, Y and Li, Y},
title = {Flow regime specific regulation shapes microbial-mediated nitrogen cycling of plain tidal river network.},
journal = {Water research},
volume = {294},
number = {},
pages = {125510},
doi = {10.1016/j.watres.2026.125510},
pmid = {41666743},
issn = {1879-2448},
abstract = {Inter-basin water diversion projects are critical for mitigating regional water scarcity yet impose complex ecological pressures on recipient river networks. Understanding their microbial impacts is essential to optimize sluice operations and minimize ecosystem disruption. As pivotal regulators of biogeochemical cycles and ecological health, microbial communities in plain tidal networks remain poorly characterized under diversion-induced hydrodynamic shifts. This study integrated intensive field sampling across water and sediment sites in the lower tidal plain river network with a calibrated one-dimensional MIKE 11 hydrodynamic model, stratifying sampling points into low, medium, and high flow-velocity regimes. Results indicate a positive correlation between hydrological regime stability and microbial community stability. While community composition reorganizes along the flow gradient, microbial diversity and core taxa abundance remain resilient. Co-occurrence network analysis reveals that intermediate flow variability maximizes network connectivity and modular cohesion, whereas extreme hydrological conditions fragment network structures. Landscape modeling further identifies high-discharge variability zones as distinct "hotspots" for denitrification and organic matter processing, while hydrologically stable reaches act as "functional shadows" (coldspots). Structural equation modeling confirms that hydrological regulation operates not merely through direct physical forcing but via a "resource-diversity-function" cascade, indirectly driving biogeochemical cycles by modulating nutrient fluxes and reshaping microbial diversity. Consequently, this study recommends shifting management strategies toward maintaining intermediate flow variability to reinforce the robustness and self-purification capacity of riverine ecological networks.},
}

@article {pmid41666736,
year = {2026},
author = {Xu, A and Liu, Z and Gao, D and Gong, X and Wang, C and Huang, Z and Zhan, X and Liang, H},
title = {Core microbial community assembly driving greenhouse gas mitigation in tidal flow constructed wetlands treating polluted surface water.},
journal = {Journal of environmental management},
volume = {401},
number = {},
pages = {128864},
doi = {10.1016/j.jenvman.2026.128864},
pmid = {41666736},
issn = {1095-8630},
abstract = {The limited understanding of microbial assembly mechanisms in tidal flow constructed wetlands (TFCW) hinders the steering of microbiome for the pollutant removal and greenhouse gas (GHG) mitigation. In this study, TFCW with different flooding and draining (F/D) durations (TFCW1: 22 h/2 h; TFCW2: 21 h/3 h; TFCW3: 20 h/4 h; TFCW4: 19 h/5 h) were established to investigate nitrogen removal, GHG mitigation and microbial metabolic mechanisms for treating polluted surface water. A moderately shortened flooding period (20 h/4 h) reconfigured the core microbiome, resulting in an 90% total nitrogen removal and a 107 mg CO2-eq/m[2]/h global warming potential. This regime intensified habitat heterogeneity, fostering a complex and stable co-occurrence network. Structurally, this ecological restructuring enriched keystone taxa such as Nitrospira, Thauera, Candidatus Brocadia, facilitating nitrogen synergistic transformation. The structured microbial cooperation suppressed nitrous oxide production by promoting the complete reduction of nitrogen intermediates, while the draining period facilitated methane oxidation. Our findings elucidate a core ecological strategy whereby microbial communities adapt to hydraulic regime by restructuring interactions to maintain ecosystem functionality. Collectively, these findings offer guidance for the integrated optimization of GHG control in constructed wetlands.},
}

@article {pmid41666555,
year = {2026},
author = {Arisha, R and Sengupta, S and Dewangan, HK and Saeedan, AS and Ansari, MN and Rashid, S},
title = {The future of PCOS management: Disease modification through regenerative, metabolic, and digital therapeutics.},
journal = {Pathology, research and practice},
volume = {280},
number = {},
pages = {156397},
doi = {10.1016/j.prp.2026.156397},
pmid = {41666555},
issn = {1618-0631},
abstract = {Polycystic ovary syndrome (PCOS) represents the leading endocrine problem affecting women of reproductive age, leading to serious complications related to reproduction, metabolism, and psychosocial aspects. Nonetheless, due to the heterogeneous nature and complex pathophysiology associated with PCOS, this condition remains uncaptured or undertreated as it often gets diagnosed at an advanced age due to its prevalence. The pathophysiology associated with PCOS involves the combination of genetic factors, resistance, neuroendocrine imbalance, as well as environmental factors that contribute towards hyperandrogenism, ovulation defects, and metabolic disorders as well. Hence, a comprehensive literature survey was conducted using PubMed, Scopus, Web of Science, and Google Scholar, prioritizing international clinical guidelines, meta-analyses, randomized controlled trials, systematic reviews, and high-quality preclinical studies that covered publications from 2015 to 2025, with the search terms being keywords specific to the disease. At present, the treatments such as lifestyle correction, combined oral pills, and anti-insulin therapies along with anti-androgen drugs only have symptomatic roles with no impact on the underlying mechanism associated with PCOS. However, new therapeutic modalities have been proposed from the past few years that is addressed by this narrative review, including mesenchymal stem cell-based therapies, microbiome therapies, as well as second-generation pharmacotherapies such as GLP-1 agonists and SGLT2 inhibitors. This is being complemented by equal developments in artificial intelligence and the learning process. However, there is work that needs to be done in relation to harmonizing the criteria for diagnosis and the long-term safety and accessibility of effective treatments. Moving forward, the focus should be placed on phenotype-based, precision, and multidisciplinary treatments of PCOS, along with emphasizing the necessity of sturdy clinical validation before worldwide adoption.},
}

@article {pmid41666549,
year = {2026},
author = {Kang, X and Zhao, Z and Zhu, X and Ju, F},
title = {Uncovering plasticizer-degrading potential in landfill microbiomes with curated PzDE-HMM database and multi-scale validation from isolates to synthetic consortia.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141398},
doi = {10.1016/j.jhazmat.2026.141398},
pmid = {41666549},
issn = {1873-3336},
abstract = {Plasticizers are widely used additives that leach from plastic products and accumulate in landfills, yet the microbial functions supporting their degradation remain poorly resolved. Here, we combined curated functional annotation, substrate-driven enrichment, and isolate-level validation to dissect plasticizer degradation in landfill microbiomes. A plasticizer-degrading enzyme (PzDE) hidden Markov model database (PzDE-HMM) was assembled from 49 experimentally validated enzyme families. It was applied to metagenomes from five landfill niches, identifying 2219 candidate plasticizer-degrading genes, which is 3.6- and 19-fold more than those identified by KofamScan- and BLASTp-based annotation methods, respectively. Enrichment with three legacy phthalates (DEHP, DIDP, DBP) and three non-phthalate plasticizers (DOTP, DOA, ATBC) drove pronounced shifts in landfill microbial communities and functional gene repertoires, revealing coexisting broad-spectrum and substrate-specific degraders. Culture-based isolation from enriched media yielded 51 strains, and three representative isolates showed concordance between PzDE-HMM-predicted gene repertoires, substrate breadth, and degradation ability. Synthetic consortia assembled from these strains exhibited complementary degradation capacities and achieved higher removal of several plasticizers than the best single strains, illustrating how complementary gene sets can be combined to enhance multi-substrate degradation. Together, PzDE-HMM annotation workflow and this multilevel prediction-enrichment-isolate-consortium framework uncover the plasticizer-degrading and bioremediation potential of landfill microbiomes and provide a reusable resource and workflow for future plasticizer-focused microbiome studies.},
}

@article {pmid41666295,
year = {2026},
author = {Werneburg, GT and Gross, MD and Hettel, DR and Lyon, M and Jeong, SH and McSweeney, S and Knorr, JM and Adler, A and Dang, T and Orji, P and Ramanujan, S and Goldman, HB and Vasavada, SP and Miller, AW},
title = {Urinary Microbiome and Metabolome Differentiate Overactive Bladder from the Physiological State, and Reflect Recent Antibiotic Use and Treatment Response.},
journal = {The Journal of urology},
volume = {},
number = {},
pages = {101097JU0000000000004990},
doi = {10.1097/JU.0000000000004990},
pmid = {41666295},
issn = {1527-3792},
abstract = {OBJECTIVE: To characterize and compare the bacterial urinary microbiome in individuals with and without overactive bladder (OAB), and secondarily compare its composition by phenotype, comorbidities, recent antibiotic exposure, and therapeutic response.

MATERIAL AND METHODS: We isolated DNA and metabolites from the urine of females without urologic diagnoses, and with OAB. Bacterial profiles were generated with 16S rRNA sequencing and metabolite profiles were generated with untargeted metabolomics. Alpha- and beta-diversity, relative abundance, and microbe-metabolite co-occurrence interaction networks were identified by OAB status and patient characteristics.

RESULTS: One hundred fifty-two participants were included, and bacteria were identified in all urine samples. Bacilliota was the most abundant phylum and Lactobacillus, Escherichia, and Prevotella the most abundant genera in individuals without urologic conditions. Megasphaera and Scardovia were the primary genera more abundant in individuals without OAB than those with OAB (each: log2-fold change [FC] -3.7 p<0.001). Escherichia (log2-FC 5.9), Enterococcus (log2-FC 3.5), and Proteus (log2-FC 3.1) were the primary genera significantly more abundant in the urine of individuals with OAB than those without (p<0.001). Beta diversity differed between individuals with and without OAB and by diabetes mellitus status (p<0.05). Relative abundance of bacterial genera differed by OAB phenotype, diabetes mellitus status, recent antibiotic exposure, and response to OAB treatment (p<0.05). Microbe-metabolite interaction networks demonstrated central microbes and metabolites in the healthy and OAB states.

CONCLUSIONS: The study provides new understanding regarding the physiological bacterial composition of urine, as well as that in the context of OAB. Further, microbiota differed by patient phenotype, comorbidities, recent antibiotic exposure, and therapeutic response. The results inform strategies of microbiological modulation to augment existing therapeutic strategies.},
}

@article {pmid41666179,
year = {2026},
author = {Gentilini, F and Ogundipe, TG and Turba, ME and Romagnoli, N and Lambertini, C and Pollera, C and Cremonesi, P and Stancampiano, L},
title = {Beyond the host: Unveiling the independent microbiome of equine gastrointestinal nematodes.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0339596},
pmid = {41666179},
issn = {1932-6203},
mesh = {Animals ; Horses/parasitology/microbiology ; *Nematoda/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Nematode Infections/veterinary/parasitology ; Feces/microbiology/parasitology ; *Horse Diseases/parasitology/microbiology ; Host-Parasite Interactions ; Bacteria/genetics/classification ; },
abstract = {Gastrointestinal nematode infections significantly impact equine health and welfare, with rising anthelmintic resistance demanding alternative control strategies. Emerging evidence suggests that parasitic nematodes harbour distinct microbiomes, potentially influencing host-parasite dynamics and parasite survival. This study aimed to characterize and compare the microbiomes of equine gastrointestinal nematodes and their hosts, focusing on differences in composition, diversity, and core microbiota structure across different intestinal sites, nematode subfamilies, and sexes. Faecal and nematode samples were collected from equids (Equus caballus and Equus asinus) at slaughterhouses. DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were amplified and sequenced using the Illumina iSeq 100 platform. Bioinformatic analyses were performed with QIIME2 and MicrobiomeAnalyst, and statistical comparisons employed PERMANOVA, LEfSe, and alpha and beta diversity metrics. Nematodes exhibited a distinct microbiome dominated by Firmicutes, Proteobacteria, Bacteroidota, Verrucomicrobiota, and Actinobacteriota, differing significantly from the faecal microbiota. Alpha diversity analyses revealed lower richness in nematodes, while beta diversity indicated distinct community structures (p = 0.007). Microbial composition varied by gastrointestinal site, nematode subfamily, and sex. Proteobacteria were consistently enriched in nematodes, particularly in the caecum. Core microbiome analysis identified exclusive nematode-associated taxa such as Fusobacterium, Mesorhizobium, and Mycoplasma. Equine gastrointestinal nematodes harbour independent and structured microbiomes, distinct from those of their hosts. These findings underscore the ecological specialization of nematodes and highlight the potential of targeting parasite-associated microbiota for novel control strategies.},
}

Animals
Horses/parasitology/microbiology
*Nematoda/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Female
Male
RNA, Ribosomal, 16S/genetics
*Nematode Infections/veterinary/parasitology
Feces/microbiology/parasitology
*Horse Diseases/parasitology/microbiology
Host-Parasite Interactions
Bacteria/genetics/classification

@article {pmid41666176,
year = {2026},
author = {Ren, S and Wu, Q and Li, T and Jiang, L and Xiao, X},
title = {The predictive value of a multivariable model based on vaginal Lactobacillus relative abundance and microecological features at 24 weeks gestation and before delivery in spontaneous preterm birth: A Prospective cohort study.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0339775},
pmid = {41666176},
issn = {1932-6203},
mesh = {Female ; Humans ; *Premature Birth/microbiology/diagnosis ; Pregnancy ; *Vagina/microbiology ; Adult ; Prospective Studies ; *Lactobacillus/isolation & purification ; Risk Factors ; Gestational Age ; },
abstract = {BACKGROUND: Vaginal microecological imbalance, particularly reduced Lactobacillus dominance, is a significant risk factor for spontaneous preterm birth (sPTB).However, the predictive value of microbial composition, pathogen colonization, and vaginal inflammation biomarkers at different pregnancy stages remains unclear. This study aims to evaluate the predictive potential of vaginal microecology at 24 weeks of gestation and before delivery for spontaneous preterm birth.

METHODS: This was a prospective multicenter cohort study. Vaginal swabs were collected at 24 weeks of gestation and before delivery to assess Lactobacillus relative abundance(LRA), pathogen colonization, and biochemical markers (pH, hydrogen peroxide, leukocyte esterase, and sialidase). Multivariable logistic regression models, ROC curves, and Kaplan-Meier survival analysis were used to identify predictors of spontaneous preterm birth.

RESULTS: At 24 weeks of gestation, the preterm group showed significantly lower Lactobacillus relative abundance, higher AV and Nugent scores, and higher vaginal pH. Logistic regression revealed that an increase in Lactobacillus relative abundance(LRA) was negatively associated with sPTB (OR = 0.97, 95% CI = 0.96-0.98, P < 0.001), while higher parity (OR = 2.28, 95% CI = 1.56-3.32, P < 0.001) and a history of late miscarriage/preterm birth (OR = 6.96, 95% CI = 2.77-17.47, P < 0.001) increased the risk. Lactobacillus relative abundance(LRA) below 57.5% was linked to increased preterm birth risk in univariate analysis, but this was no longer significant after multivariable adjustment. Parity, late miscarriage/preterm birth history, vaginal pH > 4.5, and GBS positivity remained independent risk factors (AUC = 0.775). Kaplan-Meier survival analysis showed that women with LRA > 72.5% at 24 weeks and LRA > 57.5% before delivery had significantly higher term delivery probabilities (log-rank P < 0.001).

CONCLUSION: At 24 weeks, reduced vaginal LRA is an independent predictor of spontaneous preterm birth. Early vaginal microbiome assessment, combined with clinical features, can help identify high-risk pregnant women and improve outcomes.},
}

Female
Humans
*Premature Birth/microbiology/diagnosis
Pregnancy
*Vagina/microbiology
Adult
Prospective Studies
*Lactobacillus/isolation & purification
Risk Factors
Gestational Age

@article {pmid41666032,
year = {2026},
author = {Raghunath, R and Alvarez, MA and Bhattarai, S and Pujari, A and Solorzano Castillo, C and Arioglu-Tunçil, S and Wang, Y and Tunçil, YE and Lindemann, SR},
title = {Predicting Fiber Specificity on Gut Microbiome Modulation.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-053124-092050},
pmid = {41666032},
issn = {1941-1421},
abstract = {Dietary fibers are crucial in shaping gut microbial composition and functionality. Physical complexity and chemical interactions between fibers and the gut environment lead to diverse and specialized responses that involve entire food webs of gut bacteria; however, there is comparatively less emphasis on understanding ecological dynamics to predict these outcomes. These responses may potentially promote either a broader (less specific) or narrower (more specific) group of gut bacterial taxa, which may vary across individuals. This review examines fiber specificity at the organismal and community levels by exploring mechanistic interactions among dietary fibers and gut bacteria. We discuss the interplay of exogenous and endogenous factors and the structure-function relationships influencing fiber specificity. We establish a mathematical framework to describe specificity in fiber-microbiome interactions based on directionality, magnitude, and stochasticity of fiber-microbiome ecological responses. Finally, we identify research gaps to enhance fiber-microbiota predictions, with implications for strategies aimed at optimizing fiber design.},
}

@article {pmid41665880,
year = {2026},
author = {Bischoff, NS and Undas, AK and van Bemmel, G and Briedé, JJ and Van Breda, SG and Verhoeven, J and Verbuggen, S and Venema, K and Sijm, DTHM and de Kok, TM},
title = {Food Additive Titanium Dioxide (E171) Alters Gut Microbial Metabolic Activity and Butyrate Production in the TIM-2 In Vitro Colon Model.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag042},
pmid = {41665880},
issn = {1365-2672},
abstract = {AIMS: ood-grade titanium dioxide (E171) is widely used as a food additive, yet concerns persist regarding potential gastrointestinal effects, possibly mediated by interactions with the gut microbiome. This study aimed to investigate the physicochemical behavior of E171 under different digestive contexts and to assess its effects on gut microbial composition and metabolic activity.

METHODS AND RESULTS: The dynamic in vitro colon model TIM-2 was used to expose human fecal microbiota to E171 under fasted (aqueous suspension; E171-aq) and fed (yogurt matrix; E171-yog) conditions. Particle size distribution, reactive oxygen species formation, microbiome composition (16S rRNA gene sequencing), and short-chain fatty acid production were analyzed. Larger aggregates were observed under fasted conditions (mean diameter ~210 nm), whereas digestion in yogurt produced smaller aggregates (mean diameter ~167 nm) and a higher nanoparticle fraction, reaching up to 20%. No ROS production was detected following fermentation. Both E171-aq and E171-yog significantly increased butyrate levels, indicating altered microbial metabolic activity. Microbiome profiling revealed compositional shifts, including a decreased relative abundance of Blautia and an increased relative abundance of Lachnospiraceae, taxa associated with inflammatory and metabolic responses.

CONCLUSIONS: E171 undergoes distinct physicochemical transformations depending on the digestive context, with enhanced nanoparticle formation under fed conditions. E171 exposure also modulates gut microbiome composition and function, notably by stimulating butyrate production.},
}

@article {pmid41665694,
year = {2026},
author = {Hill, CM and Malen, RC and Reedy, AM and Kahsai, O and Curtis, K and Ma, N and Randolph, TW and Ma, J and Thomas, CE and Ogino, S and Potter, JD and Buchanan, DD and Newcomb, PA and Hullar, MAJ and Phipps, AI},
title = {Associations of epidemiologic risk factors with Fusobacterium nucleatum and bacterial alpha diversity in the colorectal tumor-associated microbiota.},
journal = {Cancer causes & control : CCC},
volume = {37},
number = {3},
pages = {45},
pmid = {41665694},
issn = {1573-7225},
support = {T32CA094880/CA/NCI NIH HHS/United States ; R01CA076366/CA/NCI NIH HHS/United States ; R01CA217970/CA/NCI NIH HHS/United States ; C10674/A27140//Cancer Research UK Grand Challenge Award/ ; CRP-24-1185864-01-PROF//American Cancer Society/ ; U01CA167551/RC/CCR NIH HHS/United States ; },
mesh = {Humans ; Female ; *Fusobacterium nucleatum/isolation & purification/genetics ; Male ; *Colorectal Neoplasms/microbiology/epidemiology ; Risk Factors ; Middle Aged ; Aged ; *Fusobacterium Infections/epidemiology/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Adult ; Microbiota ; },
abstract = {BACKGROUND: Aspects of the gut microbiome, including presence of specific bacterial species and overall community structure, have been linked to the etiology and prognosis of colorectal cancer (CRC). Less is known about the epidemiologic risk factors that are associated with the composition of the microbiota in invasive colorectal tumors.

METHODS: Using tumor and paired normal colorectal tissue samples from a subset of participants in the population-based Seattle Colon Cancer Family Registry, we compared the presence of Fusobacterium nucleatum (F. nucleatum) (n = 898) measured via droplet digital PCR and alpha diversity (Shannon index) (n = 611) measured via 16S rRNA gene sequencing in colorectal tissue across demographics, health behaviors, and neighborhood socioeconomic status (nSES).

RESULTS: Normalized counts of F. nucleatum were consistently higher in tumor tissue than in patient-matched normal tissue across all risk factors, while alpha diversity was lower. Female sex was associated with high presence and enrichment of F. nucleatum in tumor tissue (odds ratio [OR] 1.61; 95% confidence interval [CI] 1.02, 2.54 and OR 1.58, 95% CI 1.10, 2.27, respectively). Relative to those aged 40-49 years, the youngest age group (< 40 years) had lower alpha diversity in tumor tissue (OR for highest vs. lowest tertile: 0.33; 95% 0.13, 0.83). Other factors, including diet, were not related to F. nucleatum presence or tumor tissue alpha diversity.

CONCLUSION: By uncovering epidemiologic risk factors for F. nucleatum presence and bacterial diversity in the intratumoral microbiota, this work informs our understanding of associations of the gut microbiota with CRC etiology and outcomes.},
}

Humans
Female
*Fusobacterium nucleatum/isolation & purification/genetics
Male
*Colorectal Neoplasms/microbiology/epidemiology
Risk Factors
Middle Aged
Aged
*Fusobacterium Infections/epidemiology/microbiology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Adult
Microbiota

@article {pmid41665368,
year = {2026},
author = {Flörl, L and Cabrera, PM and Moccia, MD and Plüss, S and Bokulich, NA},
title = {HighALPS: ultra-high-throughput marker-gene amplicon library preparation and sequencing on the Illumina NextSeq and NovaSeq Platforms.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002326},
doi = {10.1128/msystems.00023-26},
pmid = {41665368},
issn = {2379-5077},
abstract = {Microbiome research using amplicon sequencing of microbial marker genes has surged over the past decade, propelled by protocols for highly multiplexed sequencing with barcoded primer constructs. Newer Illumina platforms like the NovaSeq and NextSeq series significantly outperform older sequencers in terms of reads, output, and runtime. However, these platforms are more prone to index-hopping, which limits the application of protocols designed for older platforms such as the Earth Microbiome Project protocols; hence, there is a need to adapt these established protocols. Here, we present an ultra-high-throughput amplicon library preparation and sequencing protocol (HighALPS) incorporating the capabilities of these newer sequencing platforms, designed for both 16S rRNA gene and fungal internal transcribed spacer domain sequencing. Our results demonstrate good run performance across different sequencing platforms and flow cells, with successful sequencing of mock communities, validating the protocol's effectiveness. The HighALPS library preparation method offers a robust, cost-effective, and ultra-high-throughput solution for microbiome research, compatible with the latest sequencing technologies. This protocol allows multiplexing thousands of samples in a single run at a read depth of tens of millions of sequences per sample.IMPORTANCEMarker gene amplicon sequencing on Illumina devices remains the most commonly used technology to profile microbial communities. Yet, most library preparation protocols are not adapted to harness the capabilities and deal with the caveats of the latest Illumina sequencing platforms, which highly outperform older platforms in terms of speed, quality, and output. Here, we present an ultra-high-throughput, cost-effective, and robust library preparation protocol (HighALPS) optimized to fully leverage the capabilities of the latest Illumina sequencing platforms. The combinatorial unique dual index strategy effectively combats miss-assignment of reads due to index-hopping, which is more prevalent in newer platforms. The HighALPS protocol incorporates technological (e.g., novel sequencing chemistry and lab automation platforms) as well as bioinformatics advances (e.g., denoising algorithms which make triplicate amplifications unnecessary) of the last few years to optimize and streamline library preparation for bacterial and fungal communities.},
}

@article {pmid41665365,
year = {2026},
author = {Anwyl, GA and Jimenez, NR and Hurwitz, B and Herbst-Kralovetz, MM},
title = {Draft genome sequence of endometrial Alloscardovia omnicolens strain Y28 identified in endometrial cancer.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0124425},
doi = {10.1128/mra.01244-25},
pmid = {41665365},
issn = {2576-098X},
abstract = {We report a 1.8 Mb draft genome of Alloscardovia omnicolens Y28 isolated from a patient with endometrial cancer.},
}

@article {pmid41665359,
year = {2026},
author = {Passarelli, GV and Whang, SN and Gilbert, NM and Hu, J},
title = {The vaginal microbiome, papillomavirus infection, and cervical cancer: established associations in search of model systems and mechanistic answers.},
journal = {mBio},
volume = {},
number = {},
pages = {e0267725},
doi = {10.1128/mbio.02677-25},
pmid = {41665359},
issn = {2150-7511},
abstract = {High-risk human papillomavirus (HPV) infection is the causative factor for approximately 5% of all human cancers and the leading cause of cervical cancer. High-risk HPV-associated cervical cancer still claims more than 340,000 women's lives globally each year despite the availability of prophylactic HPV vaccines. Currently, there is no medical treatment for HPV infections and associated lesions except invasive surgical procedures. For more than a decade, numerous studies have demonstrated a correlation between certain community state types (CSTs) of the vaginal microbiome and HPV-associated infection and cancer. This review aims to provide a general overview of the most recent studies on this topic, focusing primarily on clinical data linking a Lactobacillus-depleted vaginal microbiome (i.e., bacterial vaginosis and CST-IV) and HPV but also describing the limited mechanistic findings in the field. Finally, a novel mouse model addressing the causative effect of the vaginal microbiome on papillomavirus-associated disease progression and cancer development is proposed.},
}

@article {pmid41665353,
year = {2026},
author = {Talma, K and Sipe, J and Bossa, N and Stiffler, W and Hankinson, E and Gunsch, C and Wiesner, M},
title = {Material matters: a framework for integrating surface properties into built environment microbiome research.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0203625},
doi = {10.1128/aem.02036-25},
pmid = {41665353},
issn = {1098-5336},
abstract = {The built environment (BE), where we spend the majority of our time, contains a variety of surfaces with distinct properties. Our understanding of how these surfaces shape the microbiome of the BE (MoBE) is underdeveloped and limits the ability to develop a bioinformed microbial management framework. Lab-scale studies have shown the impact of surface properties (roughness, wettability, porosity) on microbial communities, but studies sampling the BE microbiome have often overlooked this metadata. A keyword search of the literature found that only 31% of studies that sampled the indoor microbiome reported material information, which did not include any material characterization data. We have used the kitchen as a case study to illustrate the complexity of the microbial community and material surfaces that are present in the BE. We also describe how the use of BE spaces, such as cleaning, can impact both the materials and microbial community. We propose an interdisciplinary approach to studying the MoBE, incorporating techniques from material characterization into environmental microbiological sampling to elucidate the role of materials and their surface properties on the MoBE. Utilizing this interdisciplinary approach, a bioinformed framework can be developed for managing healthy MoBEs-one that improves occupant health by incorporating material science into microbial risk assessment and design strategies.},
}

@article {pmid41665079,
year = {2026},
author = {Chen, C and Zhang, Y and Yin, G and Sun, D and Li, Y and Hou, L and Liu, M},
title = {Warming Modulates Microplastic Impacts on Coastal Nitrogen Cycling by Synergistically Amplifying Sediment Hypoxia and Restructuring the Denitrifying Microbiome.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08930},
pmid = {41665079},
issn = {1520-5851},
abstract = {Global warming and microplastics (MPs) pollution are emerging stressors that threaten coastal ecosystems, yet their combined impacts on biogeochemical cycles remain poorly resolved. Here, we integrated a factorial microcosm experiment with stable isotope tracing and molecular techniques to disentangle how warming and MPs jointly regulate nitrogen (N) cycling in coastal sediments. We demonstrate that warming and MPs interacted nonadditively to reshape nitrification, denitrification, and associated nitrous oxide (N2O) production dynamics. Warming reversed the stimulatory effect of polyethylene (PE) on nitrification, turning it inhibitory, and amplified the suppressive impact of poly(butylene adipate-co-terephthalate) (PBAT), primarily through synergistic intensification of anoxic stress. In contrast, warming strengthened PE-driven stimulation of denitrification and mitigated PBAT-induced inhibition, likely due to the selective enrichment of nirS- and nosZ-harboring denitrifiers. Moreover, warming overturned the stimulatory effects of both PE and PBAT on N2O production, shifting toward inhibition through nitrifier denitrification, as substantiated by dual-isotope ([15]N-[18]O) tracing and genomic evidence. Collectively, these findings provide novel mechanistic insights into how warming interacts with MPs to reconfigure sedimentary N cycling, with broad implications for predicting the responses and evolution of coastal ecosystems under accelerating global change.},
}

@article {pmid41665004,
year = {2026},
author = {Wang, P and Wang, C and Wang, Y},
title = {Nucleotide salvage, genome instability, and potential therapeutic applications.},
journal = {Nucleic acids research},
volume = {54},
number = {4},
pages = {},
pmid = {41665004},
issn = {1362-4962},
support = {R35 ES031707/NH/NIH HHS/United States ; },
mesh = {*Genomic Instability ; Humans ; DNA Replication/genetics ; *Nucleotides/metabolism ; Animals ; Neoplasms/genetics/metabolism ; Mutagenesis ; Epigenesis, Genetic ; },
abstract = {Nucleotide salvage is crucial for maintaining DNA replication when de novo nucleotide synthesis is limited, but this metabolic flexibility poses potential threats to genome stability. Salvage kinases phosphorylate nucleosides broadly, allowing for oxidized and alkylated 2'-deoxynucleosides as well as posttranscriptionally modified ribonucleosides to enter the 2'-deoxynucleoside triphosphate (dNTP) pool. The ensuing contamination of the dNTP pool and the subsequent incorporation of modified nucleotides into genomic DNA promote mutagenesis, induce replication stress, elicit double-strand breaks, and disrupt epigenetic signaling. Although only a small subset of modified nucleosides have been assessed for salvage and genomic incorporation, the scope of salvageable substrates is probably much wider, with significant implications in mutational burden, chromatin instability, and epigenetic regulation. This overlooked aspect of genome instability is especially relevant in biological contexts of high salvage activity or elevated nucleoside damage, including chronic inflammation, cancer, aging, and dietary/microbiome exposures. Emerging evidence links salvage metabolism to tumor progression, where incorporation of salvage-derived nucleotides may contribute to unexplainable mutational signatures detected in cancers, such as gastrointestinal cancer. Recognizing salvage as a hidden source of mutagenesis reshapes our understanding of genome instability and provides potential opportunities for disease prevention, diagnosis, and therapeutic intervention.},
}

*Genomic Instability
Humans
DNA Replication/genetics
*Nucleotides/metabolism
Animals
Neoplasms/genetics/metabolism
Mutagenesis
Epigenesis, Genetic

@article {pmid41664846,
year = {2026},
author = {Stolf, CS and Paz, HES and Paraluppi, MC and Miguel, MMV and Santamaria, MP and Monteiro, MF and Amgarten, DE and Franco, RRA and Branco-de-Almeida, LS and Shaddox, LM and Casarin, RCV},
title = {Molar-Incisor and Generalized Grade C Periodontitis: Distinct Microbiome-Immune Interactions Suggest Divergent Pathogenesis.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70077},
pmid = {41664846},
issn = {1600-0765},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2021/14430-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; R01DE019456/DE/NIDCR NIH HHS/United States ; },
abstract = {AIM: Molar-Incisor (PerioC-MIP) and Generalized (PerioC-G) Grade C Periodontitis could have distinctive etiopathogenesis behind their unique clinical patterns. Thus, this study aimed to distinguish these two phenotypes by analyzing the subgingival metagenomic profile and the inflammatory markers levels.

METHODS: In this cross-sectional comparative study, Gingival Crevicular Fluid (GCF) and Subgingival Biofilm (SB) were collected from 18 PerioC-MIP North Americans and 14 periodontally healthy controls (HC) from the same location (HC-MIP) and 20 PerioC-G Brazilians and 20 controls (HC-G). From GCF, immunoenzymatic analysis was performed. SB functional and taxonomic bacterial content was determined using shotgun metagenomics sequencing.

RESULTS: Taxonomic results showed significantly different alpha- and beta-diversity profiles between disease groups (p < 0.05). Aggregatibacter actinomycetemcomitans and Streptococcus sanguinis were associated with PerioC-MIP; levels of Tannerella forsythia, Filifactor alocis, Porphyromonas gingivalis, Fretibacterium fastidiosum, and Treponema denticola were significantly enriched at PerioC-G (p < 0.05). PerioC-G had the function for flagellar assembly enriched, while PerioC-MIP SB was associated with biofilm formation of Escherichia coli. Different GCF inflammatory marker levels for each pattern resulted in PerioC-G presenting higher levels of IL-1β, IL-6, and IL-10 than PerioC-MIP (p < 0.05).

CONCLUSION: PerioC-G and PerioC-MIP presented different taxonomical profiles and GCF cytokine levels, raising the hypothesis that they may represent two different stages/susceptibility patterns of Periodontitis Grade C.},
}

@article {pmid41664751,
year = {2026},
author = {Rams, TE and Gupta, CS},
title = {Povidone-Iodine Antimicrobial Activity In Vitro Against Periodontal Bacterial Pathogens.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e101128},
pmid = {41664751},
issn = {2168-8184},
abstract = {Background Povidone-iodine (PV-I) is known to be active in vitro against periodontal bacterial pathogens, but previous studies most often used ≥5-minute contact times for PV-I testing and/or evaluated laboratory reference strains of bacterial species. This study further examined the antimicrobial effects of PV-I by using a 60-second in vitro treatment time for 10% and 5% PV-I on freshly recovered clinical isolates of subgingival biofilm bacteria from severe human periodontitis lesions. Methods Subgingival biofilm samples from 22 adults with severe periodontitis were mixed in vitro with 10% PV-I, 5% PV-I, or no PV-I (n = 22 samples per group), with residual PV-I neutralized after 60 seconds with sodium thiosulfate. The samples were then inoculated onto enriched Brucella blood agar (EBBA), with samples not treated with PV-I additionally plated onto EBBA supplemented with breakpoint concentrations of either amoxicillin, clindamycin, doxycycline, or metronidazole to detect antibiotic-resistant test species. After 7 days of anaerobic incubation, total viable microbial counts and selected red/orange complex periodontal pathogens (Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia/nigrescens, Parvimonas micra, Campylobacter rectus, Fusobacterium nucleatum, and Streptococcus constellatus) were phenotypically identified and quantitated on the EBBA plates, with additional cultivable isolates from PV-I-treated samples identified using matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry. Results Subgingival biofilm samples treated in vitro for 60 seconds with 10% or 5% PV-I yielded significantly lower mean total viable microbial counts (60-68% less) and significantly lower mean total cultivable proportions of red/orange complex periodontal pathogens (0.5%-0.7%) than samples not exposed to PV-I (14.8%) (P < 0.001), with no statistically significant differences between 10% and 5% PV-I in vitro treatments. All evaluated red/orange complex periodontal pathogens were culture-negative in 21 (95.5%) and 19 (86.4%) of the 22 subgingival biofilm samples after 10% and 5% PV-I in vitro treatment, respectively. Antibiotic-resistant and antibiotic-susceptible red/orange complex periodontal pathogens were similarly sensitive in vitro to 10% and 5% PV-I. Streptococcus species, particularly Streptococcus oralis, were the most prevalent cultivable isolates in subgingival samples treated in vitro with 10% or 5% PV-I for 60 seconds. Conclusions Both 10% and 5% PV-I significantly suppressed total viable microbial counts and red/orange complex periodontal pathogens, but not periodontal health-associated Streptococcus species, during 60 seconds of in vitro treatment on subgingival biofilm samples from patients with severe periodontitis, with no statistically significant differences in the antimicrobial activity of the two PV-I concentrations. These in vitro PV-I susceptibility findings with freshly isolated subgingival biofilm bacteria further support the clinical use of PV-I in periodontal therapy as an adjunct to mechanical root debridement in altering a pathogenic subgingival microbiome toward one compatible with periodontal health.},
}

@article {pmid41664705,
year = {2026},
author = {Ding, Z and Luo, Z and Zhang, L and Zhang, S and Zhang, R and Qiu, Z and Huang, C},
title = {State-of-the-Art Strategies for Circular RNA in Cancers: Opportunity and Challenge.},
journal = {MedComm},
volume = {7},
number = {2},
pages = {e70608},
pmid = {41664705},
issn = {2688-2663},
abstract = {Circular RNAs (circRNAs) are characterized by their covalently closed structure, remarkable stability, and precise spatiotemporal regulation, evolving from once-overlooked transcriptional byproducts to pivotal molecular regulators. In addition to their well-established function as microRNA sponges, circRNAs serve as protein scaffolds, transcriptional modulators, and even templates for functional peptide synthesis. This review synthesizes recent breakthroughs across the entire circRNA life cycle, encompassing biogenesis, degradation, nucleocytoplasmic transport, and extracellular vesicle-mediated secretion, while systematically analyzing their multifaceted involvement in tumorigenesis, immune evasion, metastatic dissemination, programmed cell death, and tumor-microbiome crosstalk. We highlight their exceptional potential as liquid biopsy biomarkers and critically assess translational applications in circRNA-based vaccines, targeted delivery platforms, and engineered cell therapies like CAR-T. Emerging artificial intelligence approaches that accelerate circRNA discovery, functional characterization, and therapeutic design are also discussed. Addressing current challenges in standardization and delivery methodologies, we propose future directions for incorporating circRNAs and their encoded proteins into precision oncology and next-generation immunotherapies. Together, these advances position circRNAs as a transformative paradigm with the potential to revolutionize cancer diagnostics, targeted therapeutics, and RNA vaccine development.},
}

@article {pmid41664381,
year = {2026},
author = {Li, C and Liu, J and Liu, J and Zhang, S and Zhang, J and Yang, B and Liu, Y and Du, S and Han, X and Zhang, L},
title = {Root exudate-microbe interactions mediated by Oceanobacillus picturae and stachyose promote cadmium tolerance in Perilla frutescens.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70183},
pmid = {41664381},
issn = {1744-7909},
abstract = {Cadmium (Cd) is a toxic heavy metal that poses serious risks to human health and the ecological environment. Perilla frutescens (L.) Britt. has important medicinal and culinary value, yet its seedlings are highly sensitive to cadmium exposure. Carbohydrates, which mediate key aspects of plant-microbe interactions, play an essential role in recruiting rhizosphere microbiota. In this study, we examined how inoculation with Oceanobacillus picturae alleviates cadmium toxicity by secreting carbohydrate metabolites that reshape the rhizosphere microbial community of perilla. Inoculation markedly reduced cadmium-induced root damage, increasing fresh and dry plant weights by 2.3-fold and 1.1-fold, and enhancing root length by 14% compared with the control. In addition, root exudate profiles showed clear changes following inoculation. Metabolomic analyses revealed that stachyose was a key exudate enriched under stress conditions and acted synergistically with Azospirillum brasilense and Acinetobacter pittii to enhance perilla growth and cadmium tolerance. These findings demonstrate that perilla recruits specific plant growth-promoting rhizobacteria through stachyose-mediated chemical signaling in response to cadmium stress. This work advances our understanding of plant-microbe interactions under heavy metal stress and provides a foundation for microbiome-based phytoremediation technologies. It also offers practical value for developing sustainable agricultural practices and supporting ecological conservation.},
}

@article {pmid41664220,
year = {2026},
author = {Wienholts, K and van Helsdingen, CPM and Wood, HM and Talboom, K and de Wilt, JHW and Bottomley, D and Young, C and Quirke, P and Derikx, JPM and Tanis, PJ and Hompes, R},
title = {The perioperative microbiome of patients undergoing rectal cancer surgery: A pilot study.},
journal = {Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland},
volume = {28},
number = {2},
pages = {e70397},
pmid = {41664220},
issn = {1463-1318},
support = {12314//KWF Kankerbestrijding/ ; //B. Braun Surgical, S.A.U./ ; //Stryker European Operations B.V./ ; C10674/A27140/CRUK_/Cancer Research UK/United Kingdom ; NIHR203331//National Institute for Health and Care Research/ ; },
mesh = {Humans ; Pilot Projects ; *Rectal Neoplasms/surgery/microbiology ; *Gastrointestinal Microbiome/genetics/drug effects ; Male ; Middle Aged ; Female ; Aged ; Feces/microbiology ; Perioperative Period ; Anastomotic Leak/microbiology ; Proctectomy ; Ileostomy ; RNA, Ribosomal, 16S ; Enterococcus/isolation & purification ; Anti-Bacterial Agents/administration & dosage ; Streptococcus/isolation & purification ; },
abstract = {AIM: The gut microbiome plays a crucial role in health and disease, and its involvement in postoperative complications like anastomotic leakage (AL) is of growing interest. Despite substantial preclinical evidence linking microbiome alterations to surgical outcomes, human studies are scarce, particularly those exploring the perioperative dynamics of the gut microbiome beyond a single time point. This descriptive, hypothesis-generating pilot study aims to elucidate the perioperative changes in the faecal microbiome of patients undergoing rectal cancer surgery.

METHOD: Seventeen patients from Amsterdam University Medical Centers participated in the IMARI-study and the IntAct-trial between April 2020 and April 2022. All patients in these studies underwent rectal resection for malignancy with a primary anastomosis, with or without a diverting ileostomy. Samples collected included preoperative stool, intraoperative anastomotic colonic tissue and swab and postoperative stool. Bacterial DNA was extracted and analysed using 16S rRNA gene sequencing.

RESULTS: An increase in Enterococcus and Streptococcus was observed postoperatively compared to preoperative and intraoperative samples. Postoperative samples showed a significant decrease in alpha diversity compared to preoperative and intraoperative samples. Beta diversity analysis revealed distinct clustering of postoperative stool and ileostomy samples. Preoperative oral antibiotics significantly altered the intraoperative microbiome composition and reduced postoperative alpha diversity.

CONCLUSION: This pilot study reveals significant perioperative shifts in the gut microbiome of rectal cancer patients. These findings underscore the importance of considering microbiome dynamics perioperatively when designing and interpreting studies that correlate the microbiome with clinical outcomes. However, the conclusions should be viewed as preliminary and require confirmation in larger studies, including causal relation, to postoperative outcomes.},
}

Humans
Pilot Projects
*Rectal Neoplasms/surgery/microbiology
*Gastrointestinal Microbiome/genetics/drug effects
Male
Middle Aged
Female
Aged
Feces/microbiology
Perioperative Period
Anastomotic Leak/microbiology
Proctectomy
Ileostomy
RNA, Ribosomal, 16S
Enterococcus/isolation & purification
Anti-Bacterial Agents/administration & dosage
Streptococcus/isolation & purification

@article {pmid41664134,
year = {2026},
author = {Huang, L and Yang, X and Pan, C and Zhang, W and Li, Y and Zhang, R and Li, H and Li, Y and Zhuo, Y and Jiang, X and Che, L and Lin, Y and Xu, S and Fang, Z and Feng, B and Wu, D and Hua, L},
title = {Effects of nicotinamide riboside supplementation during late gestation and lactation on sow performance, milk metabolome, and gut microbiome.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {26},
pmid = {41664134},
issn = {1674-9782},
support = {2023YFD1300804//Key Technologies Research and Development Program of China/ ; 32472948//National Natural Science Foundation of China/ ; CARS-35//Earmarked Fund for China Agriculture Research System/ ; },
abstract = {BACKGROUND: Nicotinamide riboside (NR) supplementation has been demonstrated efficacy in enhancing female reproductive outcomes, but its regulatory role in sow performance and gut microbiome remains undefined. This study systematically evaluated the impacts of dietary NR supplementation during late gestation and lactation on sow performance and gut microbiome remodeling. A total of 280 sows were randomized assigned to one of four groups: a control group fed basal diet or one of three groups receiving NR-supplemented diets (2, 4, or 8 g/d; n = 70/group). Sow reproductive performance, blood metabolic parameters, milk metabolome, and fecal 16S rRNA sequencing were measured.

RESULTS: Maternal NR supplementation linearly shortened farrowing duration (P < 0.01) and tended to decrease the incidence of intrauterine growth restriction and the number of late gestation mummies (P < 0.1), while concurrently increasing the within-litter uniformity (P = 0.1). Litter weaning weight and average daily gain increased quadratically with NR dosage (P < 0.05). NR supplementation orchestrated plasma metabolite regulation (triglycerides and total cholesterol; P < 0.05), enhanced antioxidant biomarkers (T-AOC, GSH-Px, T-SOD; P < 0.05), and reduced inflammatory cytokines (TNF-α; P < 0.05) across gestation and lactation. Milk yield, colostrum/milk dry matter, crude protein, and crude fat were increased (P < 0.05), together with higher levels of NAD[+] metabolites (NAD⁺, NR, nicotinamide) and beneficial bioactive factors (milk polar lipids, 3-aminosalicylic acid, fenugreekine; P < 0.05). Gut microbiota analyses at lactation day 14 revealed NR-enriched beneficial taxa (Bifidobacterium, Ruminococcus, Lachnospiraceae, Subdoligranulum, Clostridium butyricum, Succiniclasticum) across sow-offspring dyads, which was associated with the activation of microbial NAD⁺ enzymes (NadR/NAMPT; P < 0.05) and enhancement of systemic short-chain fatty acid flux, notably an increase in plasma butyrate acid (P < 0.05).

CONCLUSION: Maternal supplementation of NR during late gestation and lactation increases sow performance and promotes gut NAD[+] metabolic-associated microbiome remodeling. These findings propose maternal NR intervention as a novel strategy to enhance mammary lactogenesis and lactation metabolism in swine production, with potential applications for therapeutic strategies for lactation insufficiency.},
}

@article {pmid41664082,
year = {2026},
author = {Shi, K and Mou, D and Luo, X and Yang, Q},
title = {Bile acid profiles reflect metabolic adaptability to rapid weight loss in boxers.},
journal = {BMC sports science, medicine & rehabilitation},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13102-025-01462-2},
pmid = {41664082},
issn = {2052-1847},
support = {2025D01B143//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; KY2024095//Basic operating funds for public welfare research institutions in the Xinjiang Uyghur Autonomous Region/ ; },
abstract = {PURPOSE: This exploratory pilot study investigated serum bile acids (BAs) as metabolic regulators in boxers, focusing on their dynamic responses to rapid weight loss (RWL) and recovery across different training levels. A developmental control group of young athletes served as a physiological reference.

METHODS: Serum samples from 13 male boxers (5 elite, 8 national-level) and 10 young athletes were collected at baseline, post-RWL, and after 24 h recovery. Targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) quantified 82 BA species. Multivariate (OPLS-DA), univariate, and KEGG pathway analyses assessed phase- and level-dependent differences.

RESULTS: Elite boxers showed higher baseline concentrations of conjugated and regulatory BAs (e.g., taurolithocholic acid [TLCA], glycohyocholic acid [GHCA]) and faster post-RWL restoration of BA balance. Non-elite athletes exhibited stronger shifts toward unconjugated secondary BAs (e.g., deoxycholic acid [DCA], lithocholic acid [LCA]) and incomplete recovery. Compared with young athletes, trained boxers displayed enhanced BA conjugation and FXR/TGR5-linked regulation. KEGG analysis indicated RWL-related disturbances in bile secretion and peroxisomal pathways, while elite profiles reflected greater hepatic-intestinal resilience.

CONCLUSION: BA composition may serve as a biochemical marker of metabolic adaptability in combat athletes. Elite boxers maintained tighter BA homeostasis through weight cycles, whereas non-elite athletes exhibited transient hepatic stress. Findings are preliminary and should be interpreted cautiously due to small subgroup sizes and unstandardized diet and microbiome control.},
}

@article {pmid41663986,
year = {2026},
author = {Petrosyan, K and Thijs, S and Krucon, T and Piwowarczyk, R and Wiśniewska, K and Kaca, W and Vangronsveld, J},
title = {Seed endophytic bacteria are involved in metal adaptation of Orobanche lutea: community dynamics and plant growth promotion traits.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08304-4},
pmid = {41663986},
issn = {1471-2229},
support = {BOF21BL12//Hasselt University grant BOF-BILA/ ; BOF24KV09//Special Research Fund (BOF - Incoming Mobility)/ ; SUPB.RN.25.231//Kochanowski University in Kielce grant/ ; RID/SP/0015/2024/01//Poland Minister of Science/ ; 08M03VGRJ//Hasselt University Methusalem project/ ; },
}

@article {pmid41663943,
year = {2026},
author = {Li, M and Yang, R and Bai, Q and Yang, Z and Huang, T and Qiao, Y and Yang, B and Chen, J and Lin, W},
title = {Manipulating root-associated microbiomes to boost drought resistance in dryland winter wheat with Streptomyces pactum Act12.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04812-3},
pmid = {41663943},
issn = {1471-2180},
support = {32401443//National Natural Science Foundation of China/ ; 2025CYJSTX02-16//the earmarked fund for Modern Agro-industry Technology Research System of Shanxi Province/ ; },
}

@article {pmid41663939,
year = {2026},
author = {Li, G and Liu, X and Han, M and Qin, X and Li, P},
title = {Rhizosphere bacterial characteristics reveal the invasive advantage of Sphagneticola trilobata compared to the greening grass Axonopus compressus.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04817-y},
pmid = {41663939},
issn = {1471-2180},
support = {ZDYF2025XDNY122//Key Research and Development Project of Hainan Province/ ; },
}

@article {pmid41663924,
year = {2026},
author = {Li, B and Shi, X and Yao, X and Yan, Y and Wu, K and Zhang, C and Ren, Y},
title = {Association of the residual feed intake (RFI) with the rumen microbiota composition and metabolism in Dorper-Hu crossbred lambs.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04788-0},
pmid = {41663924},
issn = {1471-2180},
support = {2020BQ53//The Science and Technology Innovation Program of Shanxi Agricultural University/ ; SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; Modern Agro-industry Technology Research System in Shanxi Province//Modern Agro-industry Technology Research System in Shanxi Province/ ; },
}

@article {pmid41663923,
year = {2026},
author = {Tao, L and Zhao, T and Xu, Y and Chen, W and Zhu, X and Hao, Y and Zhu, L and Jiao, N and Cao, M and Pu, X and Zhu, R},
title = {Integrative multi-cohort analysis identifies urinary microbiota as non-invasive biomarkers of bladder cancer.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04829-8},
pmid = {41663923},
issn = {1471-2180},
support = {32470098//National Natural Science Foundation of China/ ; 92251307//National Natural Science Foundation of China/ ; BJJY2024098//Shanghai Oriental Talents Program/ ; },
}

@article {pmid41663851,
year = {2026},
author = {Guo, R and Li, Y and Tang, C and Zhao, Y and Wang, M and Qiao, G and Klosterman, SJ and Wang, Y},
title = {The bark latent fungus Botryosphaeria dothidea exacerbates branch dieback following the infection with Verticillium dahliae.},
journal = {Stress biology},
volume = {6},
number = {1},
pages = {13},
pmid = {41663851},
issn = {2731-0450},
support = {32130071//National Natural Science Foundation of China/ ; },
abstract = {Verticillium wilt, caused by the soilborne fungus Verticillium dahliae, has resulted in high mortality of Cotinus coggygria (smoke tree) in China. Symptoms of this disease are complex, many infected smoke trees exhibit wilting or dieback on some branches but no other branches. Whether other microbial taxa act synergistically to contribute to symptom development is unknown. Here, we investigated the microbial community assembly features associated with different branches of smoke trees with or without Verticillium wilt symptoms and established linkages between symptomatic branches and putative keystone taxa. Amplicon data analyses revealed that V. dahliae significantly affected the microbiota structure within tree branches. Microbial network connectivity indicated that Verticillium wilt destabilized the network, and fungal communities were more sensitive to Verticillium wilt than the bacterial communities. Based on taxonomic level information, the fungus Botryosphaeria dothidea was significantly enriched in diseased branches and positively correlated with the abundance of V. dahliae. Through microbial isolations, pathogen co-inoculations, histopathological assays, and RNA-seq analyses, the results indicated that plants infected with V. dahliae showed significantly increased susceptibility to B. dothidea and downregulated expression of defense-related genes. Overall, the results revealed that Verticillium wilt provokes changes in the structure of the smoke tree microbiome and that these changes likely influence symptom development in some but not all tree branches. The synergistic interplay between the commensal fungus B. dothidea and the soil-borne fungus V. dahliae promotes wilt progression in smoke trees, offering new insights into developing effective control strategies through fungicides plus enhancing host vigor.},
}

@article {pmid41663651,
year = {2026},
author = {Weng, Y and Han, Y and Wang, L and Zafar, MH and Wu, Q and Zhang, W and Wang, H},
title = {Cornus officinalis extract modulates rumen microbiome and growth of lambs fed a high-concentrate diet.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02017-5},
pmid = {41663651},
issn = {2191-0855},
support = {NO. 31872988//National Natural Science Foundation of China/ ; 2024YFD300204//National Key Research and Development Program of China/ ; },
}

@article {pmid41663543,
year = {2026},
author = {},
title = {Culturing microbiome therapeutics with big data.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41663543},
issn = {1546-1696},
}

@article {pmid41663351,
year = {2026},
author = {Wang, Y and Tang, Y and Huang, Q and An, J and Zhou, Y and Yang, H and Song, F and Zhang, X and Huang, C},
title = {Engineered Lactobacillus reuteri for scavenging reactive oxygen species and modulating oral microflora in periodontitis therapy.},
journal = {International journal of oral science},
volume = {18},
number = {1},
pages = {16},
pmid = {41663351},
issn = {2049-3169},
support = {82471018//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82271010//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82301154//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Limosilactobacillus reuteri/genetics/metabolism ; *Periodontitis/microbiology/therapy ; *Reactive Oxygen Species/metabolism ; *Probiotics/therapeutic use ; Oxidative Stress ; Animals ; Humans ; Hyaluronic Acid/chemistry ; Bacterial Adhesion ; *Microbiota ; },
abstract = {The onset and progression of periodontitis are closely associated with subgingival dysbiosis and excessive localized oxidative stress. While some oral probiotics exhibit certain inhibitory effects on periodontitis-related pathogens, they often struggle to effectively colonize and antagonize these pathogens due to the complex oxidative stress at the site of periodontitis. In this study, we engineer Lactobacillus reuteri with a reactive oxygen species (ROS)-responsive adhesive polymer (phenylboric acid-dopamine-hyaluronic acid) (LR@PDH). In the periodontitis microenvironment, this polymer can consume ROS and then expose the phenolic hydroxyl group of dopamine, promoting the selective adhesion and colonization of Lactobacillus reuteri at the site of inflammation to antagonize pathogens. The results show that, compared to conventional probiotic therapy, inflammation-responsive adhesive Lactobacillus reuteri effectively alleviates local oxidative stress, reduces the abundance of pathogenic bacteria in the subgingival microbiome, and inhibits the progression of periodontitis. Additionally, its good biocompatibility and safety highlight its potential as a therapeutic approach for clinical treatment of periodontitis.},
}

*Limosilactobacillus reuteri/genetics/metabolism
*Periodontitis/microbiology/therapy
*Reactive Oxygen Species/metabolism
*Probiotics/therapeutic use
Oxidative Stress
Animals
Humans
Hyaluronic Acid/chemistry
Bacterial Adhesion
*Microbiota

@article {pmid41663154,
year = {2026},
author = {Yang, Y and Yang, R and Chen, Y and He, C and Zhang, Y and He, J and Zhang, J and Wang, H and Liang, J and Deng, Z and Teng, L},
title = {Acinetobacter baumannii promotes gastric cancer metastasis via NA-mediated NAD metabolism reprogramming and glycolytic activation.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336161},
pmid = {41663154},
issn = {1468-3288},
abstract = {BACKGROUND: Gastric cancer (GC) is one of the most common malignancies worldwide and it is the third leading cause of cancer-related death in China. While Helicobacter pylori is a known GC pathogen, its abundance declines in tumours and the role of other bacteria in GC metastasis remains unclear.

OBJECTIVE: We aim to investigate the mechanisms of other bacteria influencing GC progression and metastasis.

DESIGN: Integrated intratumoural microbiome-metabolome analysis identified GC-associated microbes and metabolites. We then demonstrated the pro-metastatic role of Acinetobacter baumannii (A. baumannii, Ab) and its metabolite nicotinic acid (NA) using genetic, molecular and in vivo approaches.

RESULTS: The abundance of A. baumannii was significantly increased in GC tissues, correlating with advanced tumour stage and intratumoural NA levels. Fluorescence in situ hybridisation confirmed its colonisation in GC tumours. In co-culture systems, A. baumannii increased NA levels, enhancing nicotinamide adenine dinucleotide (NAD) metabolism and increasing 1-Methylnicotinamide accumulation in tumour cells. Mutagenesis of the bacterial NA synthase gene pncA confirmed that A. baumannii excreted an NA-dependent pro-metastasis effect. Mechanically, A. baumannii promotes GC metastasis by reprogramming tumour cell glucose metabolism, reducing oxidative phosphorylation while enhancing glycolysis and activating the hypoxia-inducible factor-1 pathway in GC cells through metabolites both in vivo and in vitro.

CONCLUSIONS: This study elucidates the role of A. baumannii in enhancing NAD metabolism in GC cells through NA synthesis, consequently promoting GC metastasis. These findings establish a microbiota-metabolism axis as a mechanistic foundation for developing targeted therapeutic strategies against GC metastasis.},
}

@article {pmid41662940,
year = {2026},
author = {Wang, P and Li, M and Zhou, Y and Su, D and Zhao, C and Liu, W and Li, Z and Guo, S and Sun, M},
title = {Soil microbiome drives soil multifunctionality across slope positions in a mountain tea plantation ecosystem.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123994},
doi = {10.1016/j.envres.2026.123994},
pmid = {41662940},
issn = {1096-0953},
abstract = {Slope position, a key topographic factor, exerts a strong influence on terrestrial ecosystem multifunctionality. However, the contribution of soil microbiomes to driving soil multifunctionality (SMF) along slope positions remains poorly understood. Here, the changes in soil properties, microbial characteristics, and SMF induced by slope position, as well as the relationships between microbial indices and SMF were investigated. The results demonstrated that most soil parameters, such as soil organic carbon, microbial biomass carbon and β-1, 4-glucosidase enzyme activity, were the highest in the middle slope (MS), being 1.77 to 1.90 times that of the top slope (TS). SMF peaked at the MS (0.76), whereas the lowest value (-0.81) was recorded at the TS. Bacterial alpha diversity was greatest at the MS, while fungal diversity was highest at the foot of the slope (FS). Microbial community structure varied significantly among slope positions and showed strong correlations with SMF and multiple soil factors, such as pH and soil organic carbon. Co-occurrence network analysis indicated a decline in bacterial network complexity from 0.53 to 0.25, while fungal network complexity increased from 0.31 to 0.73 with the rising of slope position. Random forest analysis identified fungal and bacterial community compositions as the most important microbial predictors of SMF. Collectively, these findings reveal the slope-microbiome dynamics in sustaining SMF under topographic variation, highlighting microbe-based soil management for enhanced ecosystem functioning in mountainous landscapes.},
}

@article {pmid41662935,
year = {2026},
author = {Otaru, S and Carpenter, DO},
title = {Glyphosate Exposure and Metabolic Syndrome: A Scoping Review of Epidemiological and Mechanistic Evidence.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123992},
doi = {10.1016/j.envres.2026.123992},
pmid = {41662935},
issn = {1096-0953},
abstract = {BACKGROUND: Glyphosate, the active ingredient in many widely used herbicides, is a pervasive environmental contaminant due to extensive agricultural and residential use. Initially deemed safe, emerging evidence suggests chronic glyphosate exposure may impair metabolic health. This scoping review maps the evidence linking glyphosate exposure with metabolic syndrome (MetS), type 2 diabetes (T2DM), and related outcomes, integrating findings from human, animal, and cellular studies.

METHODS: We reviewed studies published from 2004 in PubMed and Google Scholar that examined glyphosate exposure in relation to metabolic outcomes. Thirteen epidemiological (cross-sectional and cohort) and 25 experimental (animal or in vitro) studies were included. Key data were extracted and synthesized narratively.

RESULTS: Most human studies, primarily cross-sectional analyses of U.S. NHANES data, reported positive associations between glyphosate biomarkers and metabolic risk factors. Higher exposure was consistently linked to elevated liver enzymes, insulin resistance, hyperglycemia, and increased odds of MetS. Two longitudinal studies supported these associations, while one occupational cohort found an inverse association with T2DM. Experimental models demonstrated that glyphosate induces hepatic steatosis, inflammation, oxidative stress, and mitochondrial dysfunction, disrupts glucose metabolism and insulin signaling, alters the gut microbiome, and modulates endocrine and epigenetic pathways, supporting its role as a metabolic disruptor.

CONCLUSION: While predominantly cross-sectional human data limit causal inference, the convergence of epidemiological associations and mechanistic findings indicate that glyphosate may be an environmental risk factor for metabolic syndrome and related conditions. Given its widespread use, even modest metabolic effects warrant further investigation through longitudinal studies with robust exposure assessment.},
}

@article {pmid41662519,
year = {2026},
author = {Shobu, K and Takai, M and Tanino, H and Fukuda, Y and Inoue, T},
title = {Structural and mechanistic diversity of glycogen phosphorylases from gut bacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {7},
pages = {e2518513123},
doi = {10.1073/pnas.2518513123},
pmid = {41662519},
issn = {1091-6490},
support = {22K05442//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H02557//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23ama121003 JP25ama121003 JP24ama121004//Japan Agency for Medical Research and Development (AMED)/ ; 25K08921//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 25K02216//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Gastrointestinal Microbiome ; Cryoelectron Microscopy ; Crystallography, X-Ray ; *Glycogen Phosphorylase/metabolism/chemistry/genetics ; Escherichia coli/enzymology ; Catalytic Domain ; Adenosine Monophosphate/metabolism ; Models, Molecular ; *Bacterial Proteins/metabolism/chemistry/genetics ; Protein Multimerization ; Protein Conformation ; },
abstract = {Glycogen phosphorylase (GP) plays a central role in glycogen metabolism. While the structure and regulation of mammalian GPs have been extensively studied, the corresponding mechanisms in gut bacterial GPs remain poorly understood. Here, we investigate GPs from Escherichia coli (EcGP), Segatella copri (ScGP), and Dorea longicatena (DlGP), which represent three phylogenetic clades of GPs, using enzymatic assays, cryo-electron microscopy (cryo-EM), and X-ray crystallography. We find that ScGP forms a unique pentamer that undergoes adenosine monophosphate (AMP)-dependent assembly into a dimer-of-pentamer, which inhibits activity by restricting substrate access to the catalytic site. EcGP exists in equilibrium among monomers, dimers, and tetramers, with AMP promoting tetramer dissociation and enhancing catalytic efficiency. In contrast, DlGP remains predominantly monomeric and is unresponsive to AMP. These findings uncover structural and regulatory diversity among gut bacterial GPs. Notably, the oligomeric states of GPs modulate substrate accessibility and enzyme activation, suggesting a distinct mode of allosteric regulation beyond the canonical T-to-R transition model. Because bacterial GPs contribute to the generation of glucose, their regulation may influence the composition of gut-derived metabolites that affect host glucose homeostasis and insulin sensitivity. Our study provides mechanistic insight into the structural and functional diversity of gut bacterial GPs and lays a foundation for future exploration of microbiome-mediated metabolic interactions.},
}

*Gastrointestinal Microbiome
Cryoelectron Microscopy
Crystallography, X-Ray
*Glycogen Phosphorylase/metabolism/chemistry/genetics
Escherichia coli/enzymology
Catalytic Domain
Adenosine Monophosphate/metabolism
Models, Molecular
*Bacterial Proteins/metabolism/chemistry/genetics
Protein Multimerization
Protein Conformation

@article {pmid41662488,
year = {2026},
author = {Su, J and Zhang, S and Liang, L and Bai, H and Bai, M and He, H and Wang, Y and Liu, H and Liang, X and Sun, Y and Wu, H},
title = {Bacteria and Fungi Synergistically Reprogram Flavonoid Metabolites in the Pericarp of Citrus Reticulata 'Chachi' During Storage.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e00267},
doi = {10.1002/advs.202500267},
pmid = {41662488},
issn = {2198-3844},
support = {2022SDZG07//Open Competition Program of Ten Major Directions of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province/ ; 2020B020221001//Key Realm R&D Program of Guangdong Province/ ; 2060302//Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resources/ ; },
abstract = {The mature pericarp of Citrus reticulata ' Chachi ' (PCRC) is a traditional Chinese medicine known for its enhanced efficacy through long-term storage and processing. However, the specific mechanisms underlying these enhancements remain unclear. This study employed widely targeted metabolomics, microbial amplicon sequencing, and fermentation assays to investigate the microbiome 's influence on PCRC 's flavonoid profile over 0-19 years of storage. Correlation analysis revealed that the accumulation of polymethoxyflavones (PMFs) was closely linked to specific bacterial and fungal communities. Solid-state fermentation showed that Bacillus subtilis N18-1 enhanced the content of certain PMFs, while Aspergillus tubingensis P21-1 reduced them. Liquid-state assays confirmed that A. tubingensis P21-1 converted nobiletin to 3 ' -demethylnobiletin, and B. subtilis N18-1 further converted this to tangeretin. Combined with genome sequencing and molecular docking, four candidate genes were identified. The catalytic activity verification assays demonstrated that At21-68 and At21-21 catalyze the conversion of nobiletin to 3 '-demethylnobiletin, while Bs18-51 and Bs18-84 catalyze the conversion of 3 ' -demethylnobiletin to tangeretin. These findings highlight the synergistic molecular mechanism by which microorganisms modulate PMFs during PCRC aging, providing insights for optimizing medicinal plant aging through microbial biotransformation.},
}

@article {pmid41662332,
year = {2026},
author = {Vettiatil, D and Soorajkumar, A and Dubin, RA and Pedrosa, EM and Schornagel, A and Lambert, JS and Costa, IP and McDonald, J and Swagemakers, SMA and van der Spek, PJ and Frankovich, J and Cunningham, JL and Lachman, HM},
title = {Ultrarare Variants in DNA Damage Repair and Mitochondrial Genes in Pediatric Acute-Onset Neuropsychiatric Syndrome and Acute Behavioral Regression in Neurodevelopmental Disorders.},
journal = {Developmental neuroscience},
volume = {},
number = {},
pages = {1-28},
doi = {10.1159/000550301},
pmid = {41662332},
issn = {1421-9859},
abstract = {INTRODUCTION: We recently identified variants in 10 genes that are members of either the p53 pathway or Fanconi Anemia Complex (FAC), regulators of the DNA repair (DNA damage response; DDR) in 17 cases with Pediatric Acute-Onset Neuropsychiatry Syndrome (PANS) or regression in autism spectrum disorder (ASD) and other neurodevelopmental disorders (NDD). We aimed to identify additional cases with genetic vulnerabilities in DDR and related pathways.

METHODS: Whole exome sequencing (WES) and whole genome sequencing (WGS) data from 32 individuals were filtered and analyzed to identify ultrarare pathogenic or likely pathogenic variants.

RESULTS: Variants affecting DDR were found in 14 cases diagnosed with PANS or regression (CUX1, USP45, PARP14, UVSSA, EP300, TREX1, SAMHD1, STK19, MYTl1, TEP1, PIDD1, ADNP, FANCD2, and RAD54L). The CUX1 variant is de novo, as are two cases who had mutations in genes that affect mitochondrial functions that are connected directly or indirectly to mitophagy (PRKN and POLG), which can trigger the same innate immune pathways when disrupted as abnormal DDR. We also found pathogenic or likely pathogenic secondary mutations in several genes that are primarily expressed in the gut that have been implicated in gut microbiome homeostasis (e.g., LGALS4, DUOX2, CCR9).

CONCLUSION: These findings align with previous genetic findings and strengthen the hypothesis that abnormal DDR and mitochondrial dysfunction underly pathogenic processes in neuropsychiatric decompensation. The potential involvement of genetic variants in gut microbiome homeostasis is a novel aspect of our study. Functional characterization of the downstream impact of DDR deficits may point to novel treatment strategies.},
}

@article {pmid41661845,
year = {2025},
author = {Arana Håkanson, C and Stiger, F and Brusselaers, N and Engstrand Lilja, H},
title = {Childhood appendectomy and subsequent psychiatric illness.},
journal = {PLOS mental health},
volume = {2},
number = {1},
pages = {e0000219},
pmid = {41661845},
issn = {2837-8156},
abstract = {AIM: The appendix is considered a reservoir for the gut microbiome to restore the gut microbiota after disruptions. Therefore, removal of the appendix because of appendicitis, might result in long-term disruption of the microbiome with related health consequences. The aims of the study were to explore if there is an association between childhood appendectomy, the risk of psychiatric illness and healthcare consumption later in life.

METHODS: Individuals (N = 752) who underwent childhood appendectomy in a tertiary paediatric surgical department in Sweden were included, individually-matched to 5 non-exposed individuals (N = 3760). Data on psychiatric diagnoses, healthcare visits, and use of psychiatric drugs were collected from population-based registers. Stratified Cox and Poisson regression analyses were used, adjusted for antibiotics, proton pump inhibitors and non-steroidal anti-inflammatory drugs.

RESULTS: Median age at appendectomy was 11 (2-16) years and median follow-up time 15.5 (6-21) years. The risk of psychiatric illness in general (HR 1.19; 95% CI 1.04-1.37; p-value 0.013) and affective disorders (HR 1.20, 95% CI 1.01-1.42; p-value 0.038) was higher among those with appendectomy. Out- (IRR 1.20; 95% CI 1.18-1.23; p-value <0.001) and in-patient visits (IRR 1.19, 95% CI 1.10-1.28; p-value <0.001) were more common among those with appendectomy.

CONCLUSION: Childhood appendectomy was associated with an increased risk of psychiatric illness and healthcare consumption.},
}

@article {pmid41661350,
year = {2026},
author = {Uğur Aydin, Z and Korucu, H and Bulak Yeliz, S and Demirkaya, K and Can Demirdöğen, B},
title = {A clinical next-generation sequencing study on the microbial profiles of asymptomatic apical periodontitis in type 2 diabetic and systemically healthy individuals following adjuvant antimicrobial photodynamic therapy.},
journal = {Clinical oral investigations},
volume = {30},
number = {2},
pages = {75},
pmid = {41661350},
issn = {1436-3771},
abstract = {OBJECTIVES: The aim was to evaluate the effect of type 2 diabetes mellitus on the root canal microbiota and its response to antimicrobial photodynamic therapy (aPDT) combined with chemomechanical preparation in asymptomatic apical periodontitis (AP), by next-generation sequencing.

MATERIALS AND METHODS: A total of 22 teeth with a single root and single canal, diagnosed with asymptomatic AP, were included in this study: 11 teeth from patients with T2D (T2D group) and 11 from systemically healthy individuals (Control group). Root canal samples were collected before root canal treatment and after aPDT combined with chemomechanical preparation. Following chemomechanical preparation, canals were incubated with methylene blue for 5 min and photoactivated with a 630 nm LED for 60 s. Root canal samples were collected at two time points—before treatment (Control.Pre, T2D.Pre) and after treatment (Control.aPDT, T2D.aPDT). Following propidium monoazide (PMA) treatment, genomic DNA was isolated using a silica column method and quantified fluorometrically. The V3–V4 regions of the 16S rRNA gene were amplified and sequenced using the Illumina MiSeq platform. Data were processed in QIIME2 with DADA2 for denoising and classified taxonomically using Human Oral Microbiome Database (HOMD). Diversity analyses and statistical evaluations (PERMANOVA and multivariable association analysis using MaAsLin3; FDR-corrected) were performed in R.

RESULTS: A total of 44 root canal samples (Control.Pre, Control.aPDT, T2D.Pre, T2D.aPDT; n = 11) were analyzed via 16S rRNA V3–V4 sequencing, yielding 4.6 million high-quality reads and 2,745 Amplicon Sequence Variants (ASVs). Alpha diversity did not differ between pre and post disinfection procedure samples in healthy individuals (p > 0.05), whereas a significant reduction in observed ASV richness was detected in the T2D group after the disinfection procedures (p < 0.05). The number of ASVs shared between pre and post disinfection procedure samples was lower in the T2D group than in controls. Beta diversity based on unweighted UniFrac distances showed significant shifts after the disinfection procedures in both groups (p < 0.05), while weighted UniFrac analyses showed no significant differences (p > 0.05). Taxonomic analysis revealed a post disinfection increase in oxygen tolerant taxa and a reduction in obligate anaerobes in both groups, with more pronounced changes in the T2D group.

CONCLUSIONS: Following chemomechanical preparation and aPDT, a pronounced restructuring of the root canal microbiota was observed in both healthy individuals and individuals with T2D. In individuals with T2D, the post-disinfection period was characterized by reduced alpha diversity and a lower number of shared ASVs, indicating more limited microbial continuity.

CLINICAL RELEVANCE: The reduced microbial stability observed in individuals with diabetes suggests that systemic metabolic status may affect microbial responses to chemomechanical disinfection combined with aPDT.},
}

@article {pmid41661346,
year = {2026},
author = {Kaja, E and Grupińska, J and Budzyń, M and Ciomborowska-Basheer, J and Szwed, A and Makałowska, I and Papadovasilakis, Z and Formanowicz, D},
title = {Disease- and chemotherapy-associated salivary microbiome changes in breast cancer patients.},
journal = {Breast cancer research and treatment},
volume = {216},
number = {1},
pages = {2},
pmid = {41661346},
issn = {1573-7217},
mesh = {Humans ; Female ; *Saliva/microbiology ; *Breast Neoplasms/drug therapy/microbiology/pathology ; *Microbiota/drug effects/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/chemically induced/microbiology ; Adult ; Neoadjuvant Therapy/adverse effects ; Aged ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; },
abstract = {PURPOSE: The microbiome of the saliva can be influenced by various factors, including systemic diseases and chemotherapy. Oral dysbiosis manifests as altered bacterial composition and abundance, which often correlates with increased local and systemic inflammation. The aim of the study was to investigate the dysbiosis in the saliva of breast cancer (BC) patients before and during neoadjuvant chemotherapy (NAC).

METHODS: Saliva samples were collected from 50 breast cancer patients at three timepoints (before, during, and after NAC). Saliva from 10 healthy women was used as control samples. Full-length gene 16S rRNA sequencing and analysis were performed using the Microbiome Analyst platform, R and JADBIO AutomatedML platform to compare the abundances of bacterial taxa.

RESULTS: Alpha and beta diversity measures differed between breast cancer patients and healthy controls. In addition, eight bacterial genera differed significantly between breast cancer patients and controls, including Porphyromonas, Campylobacter, Oribacterium, Veillonella, and Alloprevotella. Longitudinal analysis revealed significant decrease of bacterial diversity in the course of neoadjuvant chemotherapy as well as significant change in the prevalence of a few low-abundant genera.

CONCLUSIONS: The obtained results confirm BC-related and NAC-related dysbiosis in saliva, which emphasizes the potential of saliva as a diagnostic and prognostic tool in patients with breast cancer.},
}

Humans
Female
*Saliva/microbiology
*Breast Neoplasms/drug therapy/microbiology/pathology
*Microbiota/drug effects/genetics
Middle Aged
RNA, Ribosomal, 16S/genetics
*Dysbiosis/chemically induced/microbiology
Adult
Neoadjuvant Therapy/adverse effects
Aged
Bacteria/genetics/classification/isolation & purification
Case-Control Studies

@article {pmid41661278,
year = {2026},
author = {Zhang, H and Zhai, C and Hu, H and Qian, G and Mao, M},
title = {A metagenomic study of the gut microbiome in patients with type 2 diabetes mellitus and myocardial infarction.},
journal = {Acta diabetologica},
volume = {},
number = {},
pages = {},
pmid = {41661278},
issn = {1432-5233},
support = {XFCX-DMYH//Jiaxing Institute of Arteriosclerotic Disease/ ; },
abstract = {OBJECTIVE: This study aimed to investigate gut microbiota composition and metabolic functions in patients with type 2 diabetes mellitus (DM) complicated by myocardial infarction (MI) and to explore potential mechanisms linking the gut microbiome to MI development.

METHODS: Sixty patients with DM complicated by MI and 52 patients with DM alone were initially recruited. After quality control, 29 DM + MI patients and 33 DM patients were included in the final analysis. Gut microbial profiles were characterized using shotgun metagenomic sequencing and bioinformatics analyses. Microbial diversity, composition, and gene functions were compared between groups based on KEGG, COG, and CAZy annotations.

RESULTS: Overall microbial diversity and metabolic profiles were comparable between the two groups; however, significant differences were observed in specific taxa and functional genes. Taxa enriched in the DM + MI group included Bacteroidales, Prevotellaceae, and Lachnospiraceae. In total, 510 KEGG orthology (KO) units and 21 pathways-including ABC transporters, quorum sensing, and general metabolic pathways-differed significantly between groups. Carbohydrate transport and metabolism, as well as glycoside hydrolase activity, represented the most enriched functional categories. Random forest models based on selected microbial species, KO units, and KEGG pathways achieved areas under the curve (AUCs) of 0.868, 0.885, and 0.820, respectively.

CONCLUSION: Patients with DM complicated by MI exhibit distinct gut microbial compositions and functional gene signatures compared with patients with DM alone. These microbiome-based markers may contribute to early risk stratification and provide potential targets for microbiota-focused interventions to mitigate MI risk in patients with diabetes.},
}

@article {pmid41661275,
year = {2026},
author = {Chakraborty, P and Basu, M and Mukhopadhyay, P and Chowdhury, R and Ghosh, S},
title = {Study of oral microbiome by next generation sequencing in T1DM adolescents with periodontal disease.},
journal = {Acta diabetologica},
volume = {},
number = {},
pages = {},
pmid = {41661275},
issn = {1432-5233},
support = {(Memo No: 94 (Sanc.) /ST/ P/S&T/9G-2/2016//Department of Science and Technology, Government of West Bengal/ ; WB-RSSDI/3/2016//RSSDl West Bengal/ ; },
abstract = {BACKGROUND: Periodontal disease (PD) is common in type 1 diabetes mellitus (T1DM); however, studies related to oral microbiome in PD in type 1 diabetes is limited.

METHODS: In this cross-sectional study,60 participants were enrolled in three groups. T1DM with PD (DMPD, n = 20), T1DM without periodontal disease (DM, n = 20)), and siblings without diabetes but with PD (PD, n = 20)). All the participants underwent comprehensive periodontal examination. Gingival plaque samples were collected for DNA isolation and next-generation sequencing to quantify microbiological abundance.

RESULTS: In total, 3294 operational taxonomic units were identified and analysed. Significant difference was observed across the groups, notably Prevotella, Megasphaera, Dialister, and Camphylobacter, Aggregatibacter, and Corynebacterium showed difference in abundance. Prevotella was found to have a very high and statistically significant abundance in DMPD. Prevotella, Veillonella, and Selenomonas were significantly higher in the poorly controlled glycemic group. Subjects with severe Gingival Index (GI) exhibit higher abundance of Capnocytophaga, Neisseria and Rothia compared to those with non-severe GI.

CONCLUSION: The Oral microbiome composition of individuals with T1DM varied significantly in the presence of periodontal disease. The oral microbiome also varies according to glycemic status of T1DM and severity of PD. The markedly increased abundance of certain phyla and genera in subjects with PD and diabetes suggests a role for the relevant microbiota in the development of periodontal infection in T1DM subjects.},
}

@article {pmid41661179,
year = {2026},
author = {Bhattacharjee, D and Millman, LC and Seesengood, ML and Martineau, LM and Seekatz, AM},
title = {Genomic insights into the functional and metabolic versatility of gut microbiome Anaerostipes species.},
journal = {Microbial genomics},
volume = {12},
number = {2},
pages = {},
pmid = {41661179},
issn = {2057-5858},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Feces/microbiology ; Genome, Bacterial ; Phylogeny ; Genomics ; *Eubacteriales/genetics/metabolism ; Butyrates/metabolism ; },
abstract = {Members of the class Clostridia, a polyphyletic group of pathogenic and beneficial Gram-positive, spore-forming anaerobes in the Bacillota (Firmicutes) phylum, are prevalent in the human gut. While this class includes select pathogens known to cause disease, many species are associated with beneficial functions, such as providing colonization resistance against pathogens. Despite a demonstrated value in maintaining Clostridial populations in the gut, functional strain diversity of most commensal Clostridial species remains understudied. Here, we isolated and characterized Clostridial isolates, focusing on the genomic diversity of Anaerostipes, a prevalent butyrate-producing genus within the gut microbiota. We conducted a genomic comparison across 21 Anaerostipes strains isolated from healthy human faecal samples (n=5) and publicly available genomes (n=105). Whole genome comparisons across the Anaerostipes genus demonstrated 12 species bins, clustering into three major functionally distinct clusters correlating with host origin. One cluster (representing mostly Anaerostipes caccae genomes) was distinguished by possessing a complete vitamin B12 biosynthesis pathway. Variability in genomic and phenotypic carbohydrate metabolism was demonstrated within dominant species of the human microbiota (Anaerostipes hadrus, A. caccae and Anaerostipes hominis). Collectively, these data indicate genomic metabolic variance across Anaerostipes species that may influence coexistence within the gut environment and variably influence health.},
}

*Gastrointestinal Microbiome/genetics
Humans
Feces/microbiology
Genome, Bacterial
Phylogeny
Genomics
*Eubacteriales/genetics/metabolism
Butyrates/metabolism

@article {pmid41661138,
year = {2026},
author = {Bäcker, M and Doekes, HM and Garza, DR and Meijer, J and van Vliet, S and Allen, RJ and Hogeweg, P and Dutilh, BE and van Dijk, B},
title = {Spatial structure: Shaping the ecology and evolution of microbial communities.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf067},
pmid = {41661138},
issn = {1574-6976},
abstract = {Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interaction ranges and steep nutrient gradients underlie cross-feeding, quorum sensing, and niche construction, generating spatial patterns that influence microbial behavior, community assembly, and stability. Here, we review theoretical and experimental evidence for how spatial organization drives eco-evolutionary processes, including founder effects during colonization, allele surfing during range expansion, emergent patterns that facilitate multilevel selection, and the exploration of rare epistatic genotypes. While the ecological and evolutionary consequences of spatial structure at the microscale are becoming clearer, linking these processes across scales to predict community- and ecosystem-level outcomes remains a major challenge. Addressing spatial interactions explicitly in microbiome research will be key. Recent advances in computational modeling, cultivation approaches, and omics now offer unprecedented opportunities to meet this challenge, providing fresh insights into how spatial structure governs the organization and dynamics of the microbial world across scales.},
}

@article {pmid41661098,
year = {2026},
author = {Michita, RT and Jimenez, N and Herbst-Kralovetz, MM and Mysorekar, IU},
title = {Underexplored maternal microbiomes: immune, metabolic, and microbial pathways shaping pregnancy outcomes.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0060825},
doi = {10.1128/iai.00608-25},
pmid = {41661098},
issn = {1098-5522},
abstract = {Maternal microbial ecosystems play critical roles in shaping reproductive physiology and pregnancy outcomes. During the pre-conception and prenatal periods, these communities modulate maternal physiology by regulating immune tolerance, nutrient metabolism, and susceptibility to pregnancy complications such as preterm birth, hypertensive disorders, and gestational diabetes. While the gut microbiota has been extensively studied, the roles of cervicovaginal, urinary, respiratory, oral, and upper reproductive tract microbiomes remain less clear. In this minireview, we synthesize current knowledge on these underexplored maternal microbiomes, with an emphasis on the cervicovaginal and urinary microbiota and their interactions with the placenta and fetus. We discuss cross-niche microbial signaling, the role of environmental and social determinants in shaping these ecosystems, and mechanisms by which microbes or their products influence host physiology without direct colonization. We also consider the translational potential of microbiota-based interventions to safely improve pregnancy outcomes. Finally, we identify major knowledge gaps and research priorities necessary to advance a more integrated understanding of maternal microbial influences on reproductive and neonatal health. Our synthesis reframes the maternal microbiome as a coordinated, multi-site network that modulates systemic immune and metabolic pathways critical for reproductive success. Understanding these connections will open new avenues for predicting, preventing, and treating pregnancy-related disorders through precision microbiome science.},
}

@article {pmid41661001,
year = {2026},
author = {Ou, T and Gao, H and Xiong, Y and Jiang, K and Qiu, C and Lin, K and Liu, X and Xie, J},
title = {Pseudomonas koreensis HLG18 improves mulberry waterlogging resilience in riparian zone by synergistically modulating endophytic microbiome and metabolic profiles.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0295925},
doi = {10.1128/spectrum.02959-25},
pmid = {41661001},
issn = {2165-0497},
abstract = {Endophytes play essential roles in protecting plants against abiotic stresses. However, whether and how they enhance waterlogging resilience in mulberry through changes in host-associated microbiota and metabolites remains unclear. Here, an endophytic bacterium strain HLG18, with plant growth promotion potential, was selected and identified as Pseudomonas koreensis HLG18. Genome analysis revealed that it possessed multiple genes involved in phytohormone biosynthesis, mineral dissolution, and stress adaptation. Greenhouse experiments consistently indicated that P. koreensis HLG18 significantly stimulated mulberry growth under waterlogging stress, accompanied by enhanced antioxidant enzyme activities and osmoprotectants. Amplicon sequencing revealed distinct endospheric microbiome profiles following HLG18 treatment, with notable changes in genera, such as Rhizorhapis, Bacillus, Caulobacter, and Rhodococcus. Meanwhile, soil potassium, phosphorus, and iron levels also differed. Correlation analyses indicated that the relative abundances of Rhizorhapis, Bacillus, Caulobacter, and Rhodococcus were significantly associated with soil properties and mulberry performance. Concurrently, metabolomic profiling revealed distinct metabolic signatures between treatments, including higher levels of stress-related metabolites (e.g., L-arginine, L-isoleucine) and differences in key metabolic pathways, such as tryptophan and purine metabolism. Overall, this study uncovers that P. koreensis HLG18 is linked to altered microenvironmental features and host metabolic patterns under waterlogging, providing new insights into endophyte-assisted plant stress adaptation.IMPORTANCEWaterlogging severely threatens the riparian zone of the Three Gorges Reservoir in China, causing extensive plant mortality and hindering restoration efforts. Mulberry is a promising candidate for ecological restoration, yet its growth is severely constrained under such conditions. Endophytes have emerged as key mediators of plant stress tolerance; however, their potential role in supporting mulberry adaptation to waterlogging in riparian zones remains largely unexplored. Our results show that the endophytic bacterium Pseudomonas koreensis HLG18 significantly promotes mulberry growth and enhances waterlogging tolerance. HLG18 inoculation is associated with distinct shifts in the host's endophytic microbiome, soil properties, and metabolite profiles, suggesting potential links to mulberry performance under waterlogging. Our findings highlight the potential of endophytes as bioinoculants to enhance mulberry waterlogging tolerance for ecological restoration in fragile riparian ecosystems and provide a valuable reference for harnessing beneficial microbial resources in sustainable agriculture under waterlogged conditions.},
}

@article {pmid41660981,
year = {2026},
author = {Li, M and Feng, Y and Cao, X and Li, N and Chen, X and Bai, Z and Fei, Z and Lu, Z and Zhang, H and Zhou, D},
title = {Comparable efficacy and mechanisms of sterile soil ingestion versus low hygiene exposure in DSS-induced colitis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0241525},
doi = {10.1128/aem.02415-25},
pmid = {41660981},
issn = {1098-5336},
abstract = {Accumulating evidence suggests that exposure to low-hygiene environments (LHE) can alleviate chronic diseases by modulating the gut microbiota. Soil has been identified as a key factor in shaping microbial communities within the LHE. Furthermore, influenced by cultural customs and traditions, the practice of soil ingestion persists in many regions worldwide, serving both nutritional and medicinal purposes. However, whether soil confers efficacy comparable to that of LHE exposure or which intervention demonstrates better efficacy remains unexplored. This study compared the interventional effects and underlying mechanisms of sterile soil ingestion versus LHE exposure in dextran sulfate sodium (DSS)-induced chronic ulcerative colitis (UC) mice. Our results demonstrated that UC mice exhibited significant gut dysbiosis, characterized by reduced microbial diversity and disruption of microbial network structure. Both LHE exposure and soil ingestion markedly reshaped the gut microbial ecosystem, exhibiting highly similar regulatory patterns in microbial composition. LHE exposure increased fecal acetic acid concentrations, while soil ingestion elevated butyric acid levels. Moreover, both interventions effectively alleviated UC clinical symptoms, restored intestinal barrier integrity, and downregulated pro-inflammatory cytokine levels. In summary, sterile soil ingestion and LHE exposure exert comparable protective effects in UC mice. Given its operational simplicity and feasibility, sterile soil represents a promising translation and application. These findings support the potential of sterile soil as a practical therapeutic approach for alleviating UC-related gut ecological disruption in modern urban settings.IMPORTANCEUrbanization and excessive hygiene have reduced human exposure to soil and environmental microorganisms, contributing to the rising incidence of immune-related disorders such as inflammatory bowel disease. This study demonstrates that sterile soil ingestion and low-hygiene environment exposure comparably reshape the gut microbiota, enhance short-chain fatty acid production, and alleviate colitis in mice. These findings highlight sterile soil as a practical and controllable intervention to mimic the protective benefits observed in traditional, microbe-rich environments. Given the challenges of accessing low-hygiene settings in modern urban life, sterile soil represents a feasible therapeutic approach to alleviate gut dysbiosis and inflammation, with broad implications for microbiome-based therapeutics in industrialized societies.},
}

@article {pmid41660969,
year = {2026},
author = {Bautista, J and Bazantes-Rodríguez, E and Cedeño, H and Anrango-Flores, C and Carrera-Cruz, F and Cisneros-Nieto, Z and López-Cortés, A},
title = {Reprogramming human health through the microbiome and precision medicine.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/1040841X.2026.2629269},
pmid = {41660969},
issn = {1549-7828},
abstract = {The human microbiome, comprising trillions of microorganisms across multiple body sites, is increasingly recognized as a key contributor to host immunity, metabolism, and neurobiology, influencing development and disease susceptibility throughout life. Rather than acting in isolation, microbial communities operate within a complex host-environment system shaped by genetics, diet, lifestyle, and medical exposures. Conceptually, the microbiome can be understood as part of a host-microbe meta-organism and, from a translational perspective, as a dynamic and potentially modifiable organ system. While short-term perturbations such as antibiotics may transiently disrupt microbial ecosystems, persistent maladaptive configurations, commonly termed dysbiosis, are associated with metabolic disease, chronic inflammation, neurodevelopmental disorders, and cancer, although causality remains context dependent. This review synthesizes the functional roles of beneficial microbes and their metabolites, the mechanistic and clinical implications of dysbiosis, and immune pathways shaped by microbial signals. We further discuss emerging therapeutic strategies, including dietary modulation, probiotics, engineered microbial consortia, postbiotics, and fecal microbiota transplantation, enabled by multi-omics technologies, organoid models, and computational frameworks. Key challenges include defining context-specific microbial health, ensuring durable engraftment, and addressing regulatory and ethical considerations. Framing the microbiome as a dynamic component of host physiology provides a foundation for microbiome-guided precision and preventive medicine.},
}

@article {pmid41660849,
year = {2026},
author = {Zhang, Y and Wen, H and Tang, X and Yao, Y},
title = {Integrative analysis of immune and microbial subtypes predicts immunotherapy response in stomach adenocarcinoma.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0215125},
doi = {10.1128/spectrum.02151-25},
pmid = {41660849},
issn = {2165-0497},
abstract = {The tumor immune microenvironment and intratumoral microbiota play critical roles in cancer progression and immunotherapy response, yet their integrated functions in stomach adenocarcinoma (STAD) are not well understood. This study conducted a multi-omics analysis of transcriptomic and microbiome data from 348 patients with STAD. Using the ImmuCellAI algorithm, immune cell infiltration (ICI) was estimated, and non-negative matrix factorization classified samples into three immune subtypes (INC-1, INC-2, and INC-3). Differential expression analysis identified immune-related signature genes enriched in immune signaling pathways. Tumor mutational burden, microsatellite instability, immune checkpoint gene expression, and drug sensitivity were compared across subtypes. Microbiome clustering identified three subtypes (MC-1, MC-2, and MC-3), with associations to immune infiltration and microbial composition. The immune subtypes showed distinct patterns of ICI, clinical stage, and gene expression, with differentially expressed genes enriched in immune and tumor-related pathways. Microbiome subtypes exhibited unique diversity metrics and associations with the immune microenvironment. Integration of immune and microbial data improved immune checkpoint blockade (ICB) prediction, with genera like Staphylococcus and Ralstonia correlating with immune genes such as CD22, VIPR2, and FLT3. These findings provide insights into ICB response and support more precise immunotherapy strategies for STAD.IMPORTANCEDeciphering the interactions between the tumor immune microenvironment and the intratumoral microbiota is crucial for advancing precision immunotherapy in stomach adenocarcinoma (STAD). In this study, we present an integrative multi-omics framework that stratifies patients into distinct immune and microbial subtypes, uncovering their associations with immunogenomic profiles, immune cell infiltration patterns, and clinical features. Notably, we identify specific microbial genera correlated with immune-related gene expression and immune checkpoint blockade responsiveness. These findings provide novel insights into the immune-microbiome axis in STAD and underscore the potential of integrative multi-omics approaches to enhance patient stratification and guide more effective immunotherapeutic strategies.},
}

@article {pmid41660769,
year = {2026},
author = {Tahara, T and Shimogama, T and Shijimaya, T and Yamazaki, J and Nakamura, N and Takahashi, Y and Naganuma, M},
title = {Interaction of host genetic factor and gastric microbiome in DNA methylation induction.},
journal = {Epigenomics},
volume = {},
number = {},
pages = {1-3},
doi = {10.1080/17501911.2026.2627274},
pmid = {41660769},
issn = {1750-192X},
}

@article {pmid41660430,
year = {2026},
author = {Dong, X and Chen, X and Xu, Y and Zeng, D and Li, P},
title = {Gut microbiota composition and systemic immune-inflammatory marker correlations in infertile women with endometriosis: a pilot case-control study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1720894},
pmid = {41660430},
issn = {2235-2988},
mesh = {Humans ; Female ; *Endometriosis/microbiology/immunology/complications ; Case-Control Studies ; *Gastrointestinal Microbiome ; Pilot Projects ; Adult ; RNA, Ribosomal, 16S/genetics ; *Biomarkers/blood ; Feces/microbiology ; *Infertility, Female/microbiology/immunology ; *Bacteria/classification/genetics/isolation & purification ; Inflammation ; DNA, Bacterial/genetics/chemistry ; },
abstract = {BACKGROUND: The specific gut microbial signatures and their correlation with immune-inflammatory markers in infertile women with endometriosis remain underexplored.To investigate the differences in gut microbiota and their associations with biochemical immune markers in infertile women with endometriosis compared to controls.

METHODS: This case-control study enrolled 32 infertile women with endometriosis and 13 control women with male-factor infertility. Fecal samples were collected for 16S rRNA sequencing to profile the gut microbiota, and serum samples were obtained to measure inflammation-related biomarkers. Bioinformatics analyses were applied to compare gut microbial community structures and to examine correlations between differentially abundant bacteria and immune markers.

RESULTS: The endometriosis group exhibited significant enrichment of Lachnospira, Bacilli, Lactobacillales, Parasutterella, Enterococcus, and Veillonella. Comparative analysis revealed significantly altered abundances of multiple taxa, including Lachnospira, Parasutterella, Alistipes, Enterococcus, Veillonella, Streptococcus, Desulfovibrionaceae, Ruminococcaceae, Bilophila, and Peptoniphilus (all P < 0.05). Several inter-species correlations were identified among these bacteria. Importantly, specific microbiota were correlated with immune markers: Streptococcus and Veillonella were positively correlated with macrophage migration inhibitory factor (MIF); Bilophila and Enterococcus were positively correlated with TNF-α and IL-6; Veillonella was positively correlated with TNF-α; Desulfovibrionaceae was negatively correlated with TNF-α and IL-6; and Parasutterella was negatively correlated with CA125.

CONCLUSION: In this exploratory investigation, specific gut microbial signatures were observed in infertile patients with endometriosis, showing correlations with select systemic immune-inflammatory biomarkers. These initial observations point to a possible association between gut microbiota imbalance and the inflammatory aspects of endometriosis-associated infertility. Consequently, microbial modulation merits further investigation as a potential strategy to alleviate inflammation and potentially enhance reproductive outcomes.},
}

Humans
Female
*Endometriosis/microbiology/immunology/complications
Case-Control Studies
*Gastrointestinal Microbiome
Pilot Projects
Adult
RNA, Ribosomal, 16S/genetics
*Biomarkers/blood
Feces/microbiology
*Infertility, Female/microbiology/immunology
*Bacteria/classification/genetics/isolation & purification
Inflammation
DNA, Bacterial/genetics/chemistry

@article {pmid41660426,
year = {2026},
author = {Wang, S and Yang, Y and Lei, L and Wan, R and Su, Z and Liu, Y and Tang, H and Hu, G and Li, C and Li, C and Meng, J and Yang, K},
title = {SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1754671},
pmid = {41660426},
issn = {2235-2988},
mesh = {*Androgens/biosynthesis/metabolism ; *Databases, Genetic ; Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Transketolase/genetics/metabolism ; *Clostridium/genetics/enzymology/metabolism ; *Microbiota ; Prostatic Neoplasms ; },
abstract = {Androgens are critical for the growth of prostate cells, as well as prostate tumor cells. For prostate cancer patients under Androgen Deprivation Therapy (ADT) such as castration treatment, investigating the potential for androgen production by gut microbes is crucial. In microbe species, the side chain cleavage activity of steroid-17, 20-desmolase (SSTD) is responsible for 11-oxy-androgens production by biotransformation from cortisol, as well as from other endogenous steroids and pharmaceutical glucocorticoids. The side-chain cleavage product of prednisone could significantly promote the proliferation of prostate cancer cells. The SSTD is a complex formed by N-terminal and C-terminal transketolases encoded by desA and desB genes, whose activity has been well-characterized in Clostridium scindens ATCC 35704. While a void still existed in evaluating the androgen producing potential by gut microbiota owing to relatively low abundance of SSTD-carrying species and the lack of professional gene database. Meanwhile, mining SSTD encoding genes in explosion sequencing data has become computationally expensive and time-consuming using comprehensive database. Here, a professional database consisted of SSTD-coding genes, named SSTDhunter, was constructed using a large-scale genomic analysis along with homologous genes as background. These SSTD-coding genes were reconstruction through comprehensive characteristics consisted of operon structures, sequence identities, phylogenetic topologies and comparative analysis. To reduce false positives, protein sequences of homologous genes tktA, which encode component of sugar transketolase, were also included in SSTDhunter database as background noise. SSTDhunter is for rapid investigation of SSTD-coding genes in massive metagenomic data, which is freely available at http://www.orgene.net/SSTDhunter/.},
}

*Androgens/biosynthesis/metabolism
*Databases, Genetic
Humans
*Gastrointestinal Microbiome/genetics
Male
Transketolase/genetics/metabolism
*Clostridium/genetics/enzymology/metabolism
*Microbiota
Prostatic Neoplasms

@article {pmid41660425,
year = {2026},
author = {Ni, H and Zhu, J and Chen, Y and Zheng, Y and Chen, B and Dong, C and Zhang, S and Xu, Y and Jiang, Y},
title = {Clinical characteristics and prognostic impact of streptococcal colonization in critically ill patients with severe pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1647511},
pmid = {41660425},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Critical Illness ; Retrospective Studies ; Prognosis ; Middle Aged ; Aged ; *Streptococcal Infections/microbiology/mortality ; Intensive Care Units ; *Streptococcus/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/microbiology ; *Pneumonia, Bacterial/microbiology/mortality ; },
abstract = {BACKGROUND: Streptococcus species are predominant commensal residents of the respiratory tract in healthy individuals and contribute to immune and metabolic regulation. However, the association between streptococcal colonization and clinical outcomes in patients with severe pneumonia remains undercharacterized. This study aimed to explore the clinical characteristics and the impact of streptococcal colonization on the prognosis of critically ill patients with pneumonia.

METHOD: We conducted a multicenter, retrospective, observational cohort study of critically ill pneumonia patients admitted to 12 intensive care units (ICUs) between January 2019 and December 2023 who underwent metagenomic next-generation sequencing (mNGS). Patients were stratified into Streptococcus-colonized and non-colonized groups based on bronchoalveolar lavage fluid (BALF) mNGS results, conventional microbiological testing (CMT), and clinical assessments. Propensity score matching (PSM) was utilized to minimize baseline confounding variables. Using nearest-neighbor matching at a 1:2 ratio, baseline characteristics were balanced between groups post-matching. The primary endpoint was 28-day all-cause mortality.

RESULTS: A total of 1,897 patients were enrolled in this study. Among them, 21 patients under 18 years of age, 139 patients lost to follow-up within 28 days, and 4 patients with confirmed streptococcal infection were excluded. Finally, 1,733 patients met the inclusion criteria. The cohort had a mean age of 65 years, with the majority being males (1,213/1,733, 70%). Among these, 148 (8.5%) were classified as Streptococcus-colonized, and 1,585 (91.5%) were Streptococcus-colonization-negative. No significant difference in 28-day all-cause mortality was observed between the colonized and non-colonized groups (35.81% vs. 38.51%, p=0.578). Patients with Streptococcus colonization had a significantly shorter median length of stay (LOS) (17 days, interquartile range [IQR] 11-30) than those without colonization (22 days, IQR 12-33; P = 0.044). Similarly, their median intensive care unit (ICU) LOS (11 days, IQR 7-16) was also significantly shorter than that of non-colonized patients (14 days, IQR 8-25; P = 0.003). Multivariable Cox regression analysis further demonstrated that Streptococcus colonization was not an independent risk factor for 28-day mortality (HR = 1.10, 95% CI: 0.79-1.51, p=0.579).

CONCLUSION: Our findings suggest a potential role for Streptococcus colonization in improving clinical outcomes in severe pneumonia. The presence or absence of Streptococcus colonization may influence short-term prognostic benefits in critically ill pneumonia patients. Further research is needed to clarify the clinical significance and potential mechanisms of Streptococcus colonization.},
}

Humans
Male
Female
Critical Illness
Retrospective Studies
Prognosis
Middle Aged
Aged
*Streptococcal Infections/microbiology/mortality
Intensive Care Units
*Streptococcus/genetics/isolation & purification
Bronchoalveolar Lavage Fluid/microbiology
*Pneumonia, Bacterial/microbiology/mortality

@article {pmid41660022,
year = {2026},
author = {Shaji, A and Ramachandran, AK and Chandrasekaran, N and Savarimalai, KC and Adhira, R},
title = {A cross-sectional metagenomic analysis of the microbial ecology in symptomatic apical periodontitis - An in vivo study.},
journal = {Journal of conservative dentistry and endodontics},
volume = {29},
number = {1},
pages = {60-64},
pmid = {41660022},
issn = {2950-4708},
abstract = {BACKGROUND: Symptomatic apical periodontitis (SAP) is a painful inflammatory disease driven by root canal infection. A detailed understanding of its microbial ecology, compared to a noninfectious baseline, is needed.

AIMS: This study aimed to characterize the microbial ecology of SAP using 16S ribosomal (RNA) 16S rRNA metagenomic sequencing and compare it to control teeth undergoing root canal treatment after trauma.

MATERIALS AND METHODS: This cross-sectional study included 10 patients with SAP and 10 control patients. Pulpal samples were collected aseptically. Microbial DNA was extracted, and the full-length 16S rRNA gene was sequenced through Oxford Nanopore Technology. Analysis was performed using QIIME2.

STATISTICAL ANALYSIS USED: Microbial abundances and diversity indices were compared using an independent samples t-test or Mann-Whitney U-test (P < 0.05 significant).

RESULTS: The SAP microbiome was dysbiotic and enriched in anaerobes. Veillonella parvula was highly abundant in SAP (mean 13.1%) but absent in controls. Species like Dialister pneumosintes and Prevotella melaninogenica were found almost exclusively in SAP. Commensals including Faecalibacterium prausnitzii were significantly reduced.

CONCLUSION: SAP is associated with a distinct microbial signature defined by the enrichment of anaerobic pathobionts and a loss of commensals, revealing a polymicrobial, dysbiotic community.},
}

@article {pmid41660005,
year = {2026},
author = {Wicaksono, WA and Zukancic, E and Zlatnar, M and Suwanto, A and Berg, G},
title = {Traditional fermented foods of Indonesia harbour functionally redundant but phylogenetically diverse taxa.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag005},
pmid = {41660005},
issn = {2633-6685},
abstract = {Fermented foods represent complex microbial ecosystems that contribute to food quality, functionality, and potential health benefits, yet many traditional fermented foods remain poorly characterized. The aim of this study was to study microbial diversity, and functional potential of underexplored traditional Indonesian fermented food. The fermented products displayed substantial variation in bacterial richness, ranging from 65 to 614 bacterial amplicon sequence variants across samples. The microbial communities were dominated by bacterial taxa affiliated with the orders Bacillales and Lactobacillales, alongside fungal taxa from the order Mucorales. The plant-based products i.e. tape ketan and tape singkong had a higher bacterial abundance but lower diversity than animal-based terasi. We found significant correlations between bacterial and fungal communities dominated by positive cooccurrence patterns and highly complex networks especially in terasi. Each food product was characterized by a unique functional profile of genes linked to beneficial metabolic functions (biosynthesis of bacteriocins, short-chain fatty acids, and vitamins) but tape ketan samples demonstrated the highest diversity and abundance of them. Metagenome assembled genomes reflect a high diversity of health beneficial properties as well as substrate-specific degradation capabilities. Traditional Indonesian fermented foods harbour functionally redundant but phylogenetically diverse taxa offering a potential source for probiotic traits and functional food development.},
}

@article {pmid41659981,
year = {2025},
author = {Santangelo, A and Corsello, A and Villano, G and Diana, MC and Striano, P},
title = {Climate change, gut microbiome, and epilepsy-New paradigms beyond the gut-brain axis.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1726561},
pmid = {41659981},
issn = {1664-2295},
}

@article {pmid41659959,
year = {2025},
author = {Abdelmegeid, M and Zeineldin, M and Seboussi, R and Mohamadin, M and Alharthi, AS and Mansour, N and Okasha, LA and Elolimy, AA and Saliu, EM},
title = {Metagenomic analysis of the camel rumen archaeome and its functional potential.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1738018},
pmid = {41659959},
issn = {2297-1769},
abstract = {The camel rumen harbors a unique and underexplored archaeal community that plays a critical role in methanogenesis and ruminal fermentation. This study aimed to characterize the taxonomic composition and functional potential of the camel rumen archaeome using whole-genome shotgun metagenomic sequencing. Across the seven healthy racing camel rumen samples, the archaeal community was dominated by Euryarchaeota (50.1 ± 0.02%) and the Methanomada group (49.7 ± 0.03%), with Methanobacteriaceae and Methanobrevibacter representing the predominant family and genus, respectively. Species-level analysis revealed Methanobrevibacter sp. YE315 and Methanobrevibacter millerae as the most abundant archaeal species across all samples. Alpha-diversity analyses indicated a diverse and evenly distributed archaeal population in the camel rumen. Beta-diversity based on Bray-Curtis and Jaccard dissimilarities demonstrated strong similarity among samples, highlighting a conserved archaeal community structure across individuals. Core microbiome assessment (≥ 80% occurrence) identified seven dominant Methanobrevibacter species as the stable core archaeome. Functional profiling revealed a consistent metabolic repertoire dominated by methanogenesis (PWY-5209), amino acid biosynthesis, and nucleotide metabolism pathways. Functional alpha-diversity metrics and beta-diversity clustering highlighted low inter-sample variability and a stable functional architecture. Overall, the camel rumen archaeome exhibited a stable and conserved community composition and functional architecture, underscoring its central role in hydrogen utilization and methane production within the rumen ecosystem. Although based on a small number of animals from a single location and therefore descriptive in nature, this study provides a comprehensive metagenomic overview of the taxonomic and functional profiles of the camel rumen archaeal community.},
}

@article {pmid41659872,
year = {2026},
author = {Zhou, W and Zhang, S and Wang, C},
title = {Gut microbial alterations associated with the exacerbation of experimental autoimmune uveitis in PGRN-deficient mice.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1641755},
pmid = {41659872},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Uveitis/immunology/microbiology/genetics ; *Progranulins/deficiency/genetics ; Mice ; *Autoimmune Diseases/immunology/microbiology/genetics ; Disease Models, Animal ; Mice, Inbred C57BL ; Mice, Knockout ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: Progranulin (PGRN) has been shown to play a protective role in the development of a variety of immune-mediated diseases, and the gut microbiome has been implicated in the pathogenesis of autoimmune diseases. In this study, we investigate the changes in the gut microbiota and their association with the severity of experimental autoimmune uveitis (EAU) in PGRN-deficient mice.

METHODS: WT and PGRN-deficient C57BL/6 mice were used to induce EAU using interphotoreceptor-binding protein peptide. Gastrointestinal (GI) contents collected from both groups of induced EAU were subjected to 16S rRNA gene sequencing analysis.

RESULTS: PGRN-deficient mice developed exacerbated EAU compared to wild-type (WT) mice. The microbial richness of the GI contents in PGRN-deficient EAU mice was significantly lower than in WT mice. The PGRN-deficient EAU mice showed a significantly reduced microbial abundance in five phyla, namely, Cyanobacteria, Epsilonbacteraeota, Firmicutes, Nitrospirae, and Patescibacteria, and a significantly increased abundance in the other four phyla, namely, Deferribacteres, Proteobacteria, Spirochaetes, and Tenericutes. More importantly, a newly emerged phylum named Chlamydiae was detected in the gut microbial community of PGRN-deficient EAU mice. The histopathological scores were significantly negatively correlated with gut microbial abundance and significantly positively correlated with chlamydial abundance.

CONCLUSION: Our results showed that PGRN plays a protective role in EAU, and the significant changes in the gut microbiome may be associated with the exacerbation of inflammation in the PGRN-deficient EAU mice.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Uveitis/immunology/microbiology/genetics
*Progranulins/deficiency/genetics
Mice
*Autoimmune Diseases/immunology/microbiology/genetics
Disease Models, Animal
Mice, Inbred C57BL
Mice, Knockout
RNA, Ribosomal, 16S/genetics

@article {pmid41659810,
year = {2025},
author = {Shi, L and Yu, Y and Ma, Z and Jiang, W},
title = {Gut microbiota, liver disease, and perioperative anesthesia: interactions, risks, and therapeutic opportunities.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1759076},
pmid = {41659810},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Liver Diseases/microbiology/therapy ; Dysbiosis ; *Anesthesia/adverse effects/methods ; Anesthetics/adverse effects ; Perioperative Care ; Animals ; },
abstract = {Liver disease is increasingly common worldwide and poses significant challenges during anesthesia and surgery. Growing evidence demonstrates that the gut microbiome plays an essential role in hepatic inflammation, metabolic imbalance, immune dysfunction, and the progression of conditions such as metabolic associated steatotic liver disease, alcohol related liver injury, and cirrhosis. This review summarizes the concept of the gut-liver-anesthesia axis, which describes how disturbances in the intestinal microbiome shape perioperative risk. Importantly, this framework conceptualizes the gut-liver-anesthesia axis as a unified perioperative risk model, integrating microbial dysbiosis, hepatic vulnerability, and anesthetic exposure into a single pathophysiological continuum. Patients with advanced liver disease frequently exhibit reduced microbial diversity, impaired intestinal barrier function, disordered bile acid signaling, and heightened systemic inflammation. These alterations increase susceptibility to infection, kidney injury, hemodynamic instability, and neurocognitive complications including hepatic encephalopathy and postoperative delirium. Anesthetic agents can further disrupt the gut ecosystem by weakening mucosal integrity and facilitating bacterial translocation, while the microbiome itself influences drug metabolism and clearance, leading to unpredictable anesthetic responses. Understanding this bidirectional interaction highlights opportunities for microbiome focused perioperative strategies. Approaches such as probiotic based preparation, opioid sparing anesthesia, regional techniques, early enteral feeding, and targeted microbial restoration may improve postoperative outcomes in patients with liver disease.},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology
*Liver Diseases/microbiology/therapy
Dysbiosis
*Anesthesia/adverse effects/methods
Anesthetics/adverse effects
Perioperative Care
Animals

@article {pmid41659802,
year = {2025},
author = {Zeng, D and Zhang, T and Zhu, Y and Feng, J and Ye, Z and Zhao, J and Huang, P and Zhang, L and Liu, T},
title = {Effects of modified fasting therapy on tongue coating and gut microbiome in overweight and obese adults: a controlled clinical trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1686416},
pmid = {41659802},
issn = {2296-861X},
abstract = {INTRODUCTION: Caloric restriction facilitates weight loss and metabolic improvement, in part by altering the gut microbiota. However, its influence via the tongue coating microbiota and gut microbiota remains largely unexplored.

METHODS: To address this gap, we conducted a single-center, prospective, controlled study from 23 April to 5 July 2021, enrolling 48 participants with a body mass index (BMI) ≥ 24 kg/m[2]. Participants were assigned to either a 7-day modified fasting group (550 kcal/day, n = 35) or a control group (n = 13) based on their personal preference.

RESULTS: In the fasting group, body weight decreased by 4.0 ± 1.6 kg (p < 0.01), BMI decreased by 1.51 ± 0.58 (p < 0.01), significantly, accompanied by marked improvements in blood glucose and lipid profiles (p < 0.05). 16S rRNA sequencing of tongue coating and fecal samples revealed distinct microbial alterations between groups. In the tongue microbiota, Haemophilus was reduced, while Prevotella and Actinomyces were enriched, along with suppression of nucleotide synthesis and glycolysis pathways. In the gut microbiota, Bacteroides decreased, and Clostridia increased, with significant upregulation of gluconeogenesis and branched-chain amino acid biosynthesis pathways (p < 0.05). Notably, specific taxa such as Haemophilus and Granulicatella were positively correlated with body weight and BMI (r > 0.4, p < 0.05).

DISCUSSION: These findings suggest that MFT improves metabolic outcomes by reshaping the taxonomic composition and possible functional capabilities of the tongue coating and gut microbiota in overweight and obese individuals. However, these findings should be interpreted in the context of the limitations of the study, including its non-randomized design and the preliminary nature of the gut microbiome analysis due to a small sample size.

CLINICAL TRIAL REGISTRATION: http://www.chictr.org.cn/, identifier ChiCTR2100047532.},
}

@article {pmid41659745,
year = {2025},
author = {Xu, Q and Lv, T},
title = {New Highlights: The Microbiome of Bronchoalveolar Lavage Fluid Predicts the Prognosis of Lung Cancer.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {5},
pages = {630-632},
pmid = {41659745},
issn = {2730-5848},
}

@article {pmid41659628,
year = {2026},
author = {Della Libera, K and Adamowicz, EM and Muehlbauer, A and Priya, S and Alazizi, A and Luca, F and Blekhman, R},
title = {Metabolic modeling and functional genomics reveal taxa and host gene interactions in colorectal cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.26.700635},
pmid = {41659628},
issn = {2692-8205},
abstract = {Colorectal cancer (CRC) is associated with changes in the microbial communities in the tumor microenvironment. Although metabolic reprogramming is an important feature of host cells in CRC, little is known about metabolic changes in the tumor-associated microbiota and how these microbial metabolic alterations can contribute to disease. Here, we investigated metabolic host-microbiome interactions in CRC using complementary computational and experimental approaches. Using patient-specific in silico metabolic models across three independent datasets, we discovered that Fusobacterium , a cancer-promoting taxon, consistently grows faster in tumor-associated versus normal tissue-associated microbiomes. This finding prompted us to investigate whether host metabolic changes drive these microbial growth advantages. By integrating our metabolic predictions with host transcriptomics data, we identified correlations between tumor gene expression and the growth of CRC-associated taxa (including Porphyromonadaceae , Blautia , and Streptococcus), as well as associations between host genes and microbial metabolism of dietary components (including choline, amino acids, and starch). To test whether these correlations reflect causal relationships, we simulated spent medium experiments in silico , demonstrating that Blautia preferentially grows on metabolites produced by tumor versus normal host cells. We further validated the direct impact of microbes on host metabolism using an in vitro system, where colon cancer cells exposed to human microbiomes showed gene expression changes in response to specific taxa including Bilophila , Anaerotruncus , and Escherichia . Together, these findings reveal a metabolic dialogue between host and microbiome in CRC, where tumor metabolic reprogramming creates a favorable environment for pathogenic microbes, which in turn may reinforce tumorigenic processes through metabolic crosstalk.},
}

@article {pmid41659521,
year = {2026},
author = {Zhou, Z and Nguyen, KL and Chen, S and Wang, Y and Li, M and Biachi, D and Ge, W and Kuo, S and Gharieb, S and Tung, E and Parmar, R and Ji, J and Khorana, R and Hetta, A and Cann, I and Mackie, R and Lau, G and Yang, J and Mei, W},
title = {Bacteroides intestinalis -Driven Arabinoxylan Fermentation Mitigates Inflammatory and Metabolic Dysfunction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.28.702158},
pmid = {41659521},
issn = {2692-8205},
abstract = {Insufficient dietary fiber intake is strongly associated with gut microbiome dysfunction and an increased risk of noncommunicable diseases. Synergistic synbiotics, which pair defined microbial strains with their preferred carbohydrate substrates, offer a promising strategy to restore these functions. However, the rational design of such interventions remains challenging by insufficient understanding of microbial fiber-degrading capacities and the host-relevant bioactivities of fermentation-derived metabolites. Here, we identify human colonic commensal Bacteroides intestinalis (B . intestinalis) as a key microbial mediator of dietary fiber-driven metabolic, immune, and neuronal benefits. We demonstrate that the synergistic interaction between B . intestinalis and its preferred substrate, insoluble wheat arabinoxylan abundant in dietary fiber, enhances the production of anti-diabetic and anti-steatotic bile acid species, hyocholic acid and hyodeoxycholic acid, anti-inflammatory, antioxidant phenolic compounds, and a spectrum of neuroactive compounds. These metabolic effects are accompanied by coordinated transcriptional remodeling in the colon and spleen implicating pathways governing circadian rhythm regulation, lipid metabolism, and immune defense. Importantly, these beneficial effects are preserved in conventionally raised mice with established high fat diet-induced obesity, where BI and inWAX improve glucose tolerance. Our findings uncover a mechanistic framework linking B . intestinalis -mediated fiber fermentation to gut-liver-brain crosstalk and establish a rational foundation for precision synbiotic design.},
}

@article {pmid41659429,
year = {2026},
author = {Vallecillo-Zuniga, ML and Akeefe, A and Brown, DG and Wahlig, TA and Marchetti, M and Heiner, T and Davis, KL and Nieznanski, C and Flynn, A and Leung, DT},
title = {Longitudinal Changes in Nasal and Oral Microbiome and Antimicrobial Resistance Gene Profiles in Response to Human Fecal Microbiota Transplantation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.27.701854},
pmid = {41659429},
issn = {2692-8205},
abstract = {The gut-lung axis describes interactions between intestinal and respiratory mucosal systems through microbial, metabolic, and immune pathways, but the systemic impact of gut-targeted therapies on upper respiratory tract (URT) communities remains underexplored. We conducted a longitudinal study in adult patients undergoing fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infection (CDI) alongside healthy controls. Fecal, nasal, and oral samples were collected at baseline (Day 0) and on Days 14 and 56 following FMT. Shotgun metagenomic sequencing was performed to quantify microbial diversity, taxonomic composition, and the abundance of antimicrobial resistance genes (ARGs). FMT was associated with increased gut diversity and decreased levels of key intestinal taxa commonly considered pathobionts, including Klebsiella spp., Escherichia spp., Shigella spp., and Klebsiella pneumoniae . At the phylum level, fecal Bacteroidota increased, while Mucoromycota decreased following treatment. Post-FMT nasal microbiome changes included reduced richness and diversity, expansion of Moraxella , and decreases in taxa linked with respiratory colonization, including Staphylococcus aureus and Streptococcus pneumoniae . By Day 56, nasal communities partially recovered toward healthy profiles. Baseline nasal ARG abundance decreased following FMT, particularly among β-lactam, aminoglycoside, and fluoroquinolone resistance genes, and remained comparable to healthy controls by Day 56. In contrast, the oral microbiome and oral resistome remained largely stable, with only minor fluctuations, and no consistent increases in respiratory pathobiont-associated taxa. In summary, FMT was associated with broader effects beyond the gut, including changes in the URT microbial ecology and antimicrobial resistance profiles. Together, these findings are consistent evidence of gut-lung microbial interactions, linking intestinal dynamics with respiratory microbial composition and antimicrobial resistance patterns.},
}

@article {pmid41659373,
year = {2026},
author = {Farhan, M and Pan, J and Zhao, J and Yang, H and Zhang, S},
title = {Aphid adaptation to plant secondary metabolites: adaptive mechanism of resistance evolution and future prospects.},
journal = {Horticulture research},
volume = {13},
number = {1},
pages = {uhaf269},
pmid = {41659373},
issn = {2662-6810},
abstract = {Aphids are demonstrated to be voracious phloem feeders, among the most damaging insect pests, due to their capacity to decrease crop production and vector plant viruses. Plant secondary metabolites (PSMs) comprise an essential element of plant protection, which in most cases deters and affects aphid performance. Nonetheless, aphids have developed various resistance mechanisms to counteract these chemicals. This review provides an extensive overview of the biological and molecular adaptations that aphids employ to counteract PSMs, including enzymatic detoxification, antioxidant defense, sequestration, behavioral response shifts, suppression of plant defense mechanisms by symbionts, and manipulation of host signaling pathways by effector proteins. We also described the suppression of the defense pathways by aphid-associated viruses, which further complicates plant-aphid interactions. Although significant insights have been gained about each of the individual mechanisms, research gaps remain, particularly in the functional confirmation of detox genes, the communication interactions of the symbionts, and whether sequestration could play an ecological role across species. Intensive efforts involving molecular-based breeding of horticultural crops, as well as traditional breeding with wild relatives highly endowed with aphid-resistant PSM traits, should be employed in the future to provide sustainable crop protection. New technologies in crop genomics, the identification of effectors, and microbiome research promise the development of resistant cultivars that are not only resistant to aphids but also prevent the spread of disease by their vectors. Together, all this knowledge has the potential to produce high-yielding crops that are resistant to aphids and to implement sustainable farming practices.},
}

@article {pmid41659330,
year = {2025},
author = {Wu, H and Wei, G and Huang, S and Wan, L and Xu, Q and Huang, C},
title = {The gut-brain axis mediates precocious puberty induced by environmentally relevant low-dose endocrine-disrupting chemical mixtures.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1728811},
pmid = {41659330},
issn = {1664-2392},
mesh = {*Endocrine Disruptors/toxicity/adverse effects ; *Puberty, Precocious/chemically induced ; Humans ; Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Brain/drug effects ; Dysbiosis/chemically induced ; *Brain-Gut Axis/drug effects ; },
abstract = {BACKGROUND: The global rise in precocious puberty (PP) is increasingly linked to exposure to endocrine-disrupting chemicals (EDCs). However, the mechanisms by which environmentally relevant, low-dose mixtures of EDCs influence PP remain inadequately explained by direct endocrine disruption.

OBJECTIVE: This systematic review evaluates a novel hypothesis: that disruption of the gut-brain axis (GBA) serves as a pivotal mechanism in EDC mixture-induced PP.

METHODS: We synthesized evidence from 87 studies (45 human, 32 animal, 10 in vitro) following PRISMA 2020 guidelines. An exploratory Random Forest analysis was employed to identify key mediators and estimate the relative contribution of the GBA pathway.

RESULTS: Perinatal exposure to low-dose EDC mixtures consistently induced gut dysbiosis, characterized by reduced microbial diversity (Shannon Δ = -1.8), a 40% decrease in Lactobacillus, and a 1.5-fold increase in Bacteroides. This dysbiosis was linked to impaired production of butyrate (↓50%) and secondary bile acids, increased intestinal permeability (FITC-dextran ↑80%), and systemic inflammation (IL-6 ↑1.8-fold). Fecal microbiota transplantation from PP donors into germ-free mice recapitulated early pubertal onset, supporting a causal role for gut microbiota. Exploratory modeling suggested that mediators within the GBA pathway could be associated with a large share (approximately 68%) of the model-internal variance explanation for PP risk at low experimental doses (≤1 μg/kg/day), indicating its potential prominence over direct endocrine disruption in this analysis. Significant synergistic effects (Synergy Index > 2.3) were observed under mixture exposures.

CONCLUSION: This review identifies the GBA as a critical and previously underappreciated mechanism for low-dose EDC mixture-induced precocious puberty in a dose-dependent manner. Our findings underscore the need for regulatory paradigms and future research to integrate this pathway when assessing the risks of complex, real-world chemical mixtures.},
}

*Endocrine Disruptors/toxicity/adverse effects
*Puberty, Precocious/chemically induced
Humans
Animals
*Gastrointestinal Microbiome/drug effects
Female
*Brain/drug effects
Dysbiosis/chemically induced
*Brain-Gut Axis/drug effects

@article {pmid41659075,
year = {2026},
author = {Duggar, M and Sun, Y and Leardini, D and Jia, Q and Muratore, E and Dallas, RH and Ferrolino, J and Cherian, A and Cesaro, S and Faraci, M and Fraczkiewicz, J and Ussowicz, M and Englund, JA and Hakim, H and Hayden, RT and Klein, EJ and Wolf, J and Maron, G and Tang, L and Masetti, R and Margolis, EB},
title = {Pre-HCT Resistome Disruption Predicts ESBL Gene Expansion in Pediatric Transplant Recipients: A Prospective Multi-Center Study.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.20.26344466},
pmid = {41659075},
abstract = {BACKGROUND: Infections are the leading cause of non-relapse mortality in pediatric hematopoietic cell transplant (HCT) recipients. Up to 90% of bacteremias in these patients originate from gut microbiome organisms. However, selection for resistance genes, such as Extended-spectrum β-lactamase (ESBL), in these patient's gut microbiomes remains poorly understood.

METHODS: Stools were prospectively collected from pediatric HCT recipients at multiple centers (n=133 patients, five centers) on the day of HCT, the day of neutrophil engraftment, and 30 days post-HCT. Bacterial DNA was isolated and sent for shotgun metagenomic sequencing. Antibiotic resistance genes were identified using the MEGARes database. Associations between ESBL gene abundance changes and antibiotic exposure were examined using univariate and Inverse Probability of Treatment Weighting linear regression models with covariate balancing propensity scores.

RESULTS: Pre-existing gut resistome disruption at the time of HCT showed a stronger correlation with ESBL gene expansion than post-transplant antibiotic exposure. Specifically, patients with greater baseline resistome distance from healthy children showed increased ESBL genes during the neutropenic period. Post-transplant β-lactam exposure (total or ESBL-cleavable) did not correlate with increases in ESBL genes in already-colonized patients. However, aminoglycosides and anaerobic active antibiotics were associated with acquisition of new ESBL organisms during the neutropenic period, while pre-existing microbiome disruption primarily drove selection of resistant bacteria already present.

CONCLUSIONS: These findings indicate that antibiotic stewardship before HCT, in addition to reducing the use of anaerobic active antibiotics during early transplant, may be necessary to prevent ESBL-related infections in pediatric transplant recipients.

LAY SUMMARY: Infections are the leading cause of death after HCT, and recently the role of the gut microbiome in harboring dangerous bacteria has been highlighted. This study aims to understand multidrug resistant bacteria changes in the gut microbiome early after HCT.},
}

@article {pmid41658751,
year = {2026},
author = {De, A and Sarveswari, KN and Tolat, S and Hameed, S and Bhat, S and Jain, S and Swami, OC},
title = {Oryza Ceramax in Dermatologic Care: A Multi-pathway Approach to Skin Hydration and Barrier Repair.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e100886},
pmid = {41658751},
issn = {2168-8184},
abstract = {Environmental stressors, including climate change, pollution, and lifestyle factors, can disrupt the skin barrier, leading to dryness and exacerbating conditions such as atopic dermatitis (AD), acne, and psoriasis. Effective barrier repair requires maintaining hydration and lipid balance, particularly the ceramide-cholesterol-fatty acid ratio of 3:1:1, which is recommended by dermatological societies for optimal skin restoration. Although traditional moisturizers provide hydration through occlusives, humectants, and emollients, they often do not achieve sustained barrier repair or adequate intracellular hydration. Next-generation moisturizers are designed with bioactive ingredients that aim to both hydrate and support barrier repair by reducing inflammation, modulating the microbiome, and promoting skin homeostasis. Oryza Ceramax (Alaina Healthcare; Alembic Pharmaceuticals Pvt. Ltd., Vadodara, India), a next-generation moisturizer incorporating a 3:1:1 ceramide-cholesterol-fatty acid ratio, includes aquaporin (AQP) boosters, naturally sourced betaine, saffron extract, hyaluronic acid, and other bioactive components that resemble the skin's natural lipid composition. Clinical evidence supports the efficacy of ceramide-dominant formulations in improving hydration and reducing transepidermal water loss (TEWL), with studies reporting TEWL reductions of approximately 10% and hydration improvement lasting up to 72 hours. Oryza Ceramax is formulated to align with dermatologic recommendations for use in dry or impaired skin and is free from parabens, alcohol, mineral oil, and soap (PAMS-free). Its formulation characteristics are consistent with evidence-based principles for skin barrier protection and hydration maintenance. This narrative review examines the science underlying multi-pathway approaches to skin barrier repair and hydration, using Oryza Ceramax as an example of a ceramide- and AQP-based formulation. The findings highlight emerging strategies in moisturizer design but also emphasize the need for independent, well-controlled clinical studies to validate these observations.},
}

@article {pmid41658674,
year = {2026},
author = {Ajmera, K and Patel, O and Shah, N},
title = {Artificial Intelligence in Gastroenterology: Beyond Diagnostics and Toward Lifestyle and Dietary Interventions For Gastrointestinal Disorders.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e100976},
pmid = {41658674},
issn = {2168-8184},
abstract = {Gastrointestinal (GI) diseases such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), celiac disease, liver cirrhosis, and functional gastroesophageal reflux disorder (GERD) are often associated with a substantial increase in various symptoms, including pain, a reduced quality of life, and the need for medical attention. Dietary and lifestyle changes remain the backbone of treatment for many of these diseases, but they are not always implemented due to obstacles such as low adherence, a lack of customization, inadequate health insurance, and difficulty in accessing expert advice. Artificial intelligence (AI) has demonstrated significant potential in gastroenterology, particularly in diagnostics such as endoscopy and imaging. However, its therapeutic applications, especially in providing diet and lifestyle support, remain in early stages. To bridge this gap, this narrative review examines the potential of AI to deliver culturally responsive, scalable, and personalized dietary guidance to this patient population. The significance of this approach cannot be overstated, particularly for patients from diverse racial backgrounds and for those who lack access to medical treatment. AI offers a solution that utilizes natural language processing (NLP), predictive analytics, and real-time patient support, thereby helping to improve adherence, personalize advice, and extend treatment beyond the clinic. One option is to integrate digital medicines, microbiome data, wearables, and AI-driven systems to ensure proactive management of GI problems through continuous monitoring. When AI is developed in an ethical manner that protects data and emphasizes integrity, it can gradually transform the dietary management of GI disorders. AI could help improve GI health by encouraging a more proactive and personalized approach to treatment, increasing patient independence, and reducing unnecessary physician visits.},
}

@article {pmid41658610,
year = {2026},
author = {Bautista, J and Bedón-Galarza, R and Martínez-Hidalgo, F and Masache-Cruz, M and Benítez-Núñez, M and Valencia-Arroyo, C and López-Cortés, A},
title = {Decoding the microbial blueprint of pancreatic cancer.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1737582},
pmid = {41658610},
issn = {2296-858X},
abstract = {Pancreatic cancer (PC) represents one of the most formidable challenges in oncology, characterized by its asymptomatic onset, delayed clinical detection, and dismal prognosis. Among pancreatic neoplasms, pancreatic ductal adenocarcinoma (PDAC) accounts for over 90% of cases and remains the most aggressive form, driven by late diagnosis, intrinsic chemoresistance, and a profoundly immunosuppressive tumor microenvironment. Recent advances have reframed the human microbiome not as a passive bystander but as an active architect of pancreatic tumor biology. This review delineates the mechanistic axes through which microbial ecosystems orchestrate PDAC progression across four key anatomical niches-gastrointestinal, oral, urogenital, and intrapancreatic. We elucidate how microbial dysbiosis fosters oncogenesis through immune evasion, metabolic reprogramming, and chronic inflammation, implicating specific taxa such as Fusobacterium nucleatum, Malassezia spp., and Porphyromonas gingivalis in immune suppression and chemoresistance. Microbial enzymatic inactivation of gemcitabine and modulation of cytokine networks further underscore the microbiome's pivotal role in therapeutic failure. Conversely, commensal and probiotic species may potentiate immunosurveillance and enhance treatment efficacy. This review also explores microbiota-derived biomarkers for early detection and the translational promise of microbiome-targeted interventions, including fecal microbiota transplantation, probiotics, and selective antibiotics. By decoding the microbial blueprint of PC, we propose a paradigm in which the microbiome emerges as both a biomarker and a therapeutic axis, offering novel avenues for precision oncology. Furthermore, this integrative synthesis emphasizes the multi-omic, immunometabolic, and therapeutic dimensions of the pancreatic cancer-microbiome interface, where metagenomic, transcriptomic, metabolomic, and immunomic layers converge to shape tumor evolution and therapeutic response, advancing the vision of microbiome-informed precision oncology.},
}

@article {pmid41658268,
year = {2026},
author = {Tashkandy, NR},
title = {Alterations in gut microbial metabolic pathways following bariatric surgery assessed by 16S rRNA gene sequencing.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e2},
pmid = {41658268},
issn = {2632-2897},
abstract = {Researchers have studied gut microbiota changes following bariatric surgery (BS), but not gut diversity and function in patients who fail to reduce weight. Stool samples were collected from three groups of women: 15 women who did not lose weight after BS ("Yes" group), 9 overweight women without surgery, and 8 slim women ("No" group). 16S ribosomal RNA gene sequencing and PICRUSt2 were used for the analysis. The surgery and control groups had equal alpha and beta diversity, perhaps due to the high proportion of overweight participants (n = 24). All groupings were dominated by Bacteroidota and Bacillota. Barnesiellaceae decreased with BS, although Streptococcaceae remained frequent in overweight people. The iron supplementation group had High abundance of Atopobiaceae and Prevotellaceae. Barnesiellaceae abundance was considerably lower in both surgical groups (with and without iron supplementation) than in the no-iron and no-surgery groups. The ornithine degradation and haem biosynthesis routes use different metabolites than the glycine super system. Finally, the "Yes" group significantly upregulated PWY0-1241, PWY-5177, and PWY-5855 signaling pathways. In conclusion, gut bacteria and metabolic functions may predict weight loss after surgery better than diversity markers. The requirement for orthogonal validation assays is suggested by pathway analysis outperforming diversity metrics.},
}

@article {pmid41658015,
year = {2026},
author = {Liao, S and Yang, H and Song, L and Shi, L and Lan, Z and Zhao, W and Bao, Z and Hu, Q and Tang, X and Zhuang, S and Wang, H and Zhong, S},
title = {Impact of obstructive sleep apnea on gut microbiome of patients with symptomatic intracranial atherosclerotic stenosis.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1713733},
pmid = {41658015},
issn = {1663-4365},
abstract = {INTRODUCTION: Obstructive sleep apnea syndrome (OSAS) is positively associated with increased risks of ischemic stroke. Patients with stroke exhibit remarkable gut microbiota dysbiosis. However, the impact of OSAS on gut microbiota of patients with symptomatic intracranial atherosclerotic stenosis (sICAS), one of the most common causes of stroke, remains unknown.

METHODS: This study included patients with sICAS, the severity of OSAS was defined by the apnea-hypopnea index (AHI). AHI < 5 was considered no sleep apnea, AHI 5-15 was defined as mild OSAS, AHI 15-30 as moderate OSAS, and AHI > 30 as severe OSAS. Fecal samples were collected and subjected to 16 s rRNA gene sequencing. PICRUSt2 was used to predict the functional properties of the bacterial communities.

RESULTS: In total, 99 sICAS patients were included, with No-OSAS (N = 22), Mild (N = 25), Moderate (N = 30), and Severe (N = 22). Patients with OSAS exhibited significantly altered gut microbiota composition compared to those without sleep apnea, characterized by increased abundances of pathogens such as Escherichia-Shigella and decreased abundances of beneficial microbes such as short-chain fatty acids-producing bacteria Blautia. Importantly, these microbes were significantly associated with AHI. Several microbial metabolic pathways such as Peptidoglycan biosynthesis, C5-branched dibasic acid metabolism, and Pantothenate and CoA biosynthesis were downregulated with OSAS.

CONCLUSION: OSAS is associated with gut dysbiosis and altered microbial metabolic functions in patients with sICAS.},
}

@article {pmid41658004,
year = {2025},
author = {Qiu, S and Zheng, B and Pan, J and Yu, S and Qian, J and Tung, TH and Shen, B},
title = {Difference analysis of intestinal microbiota in patients in the intensive care unit using different sampling methods: a systematic review and meta-analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1723862},
pmid = {41658004},
issn = {1664-302X},
abstract = {BACKGROUND: The normal intestinal microbiota undergoes rapid and notable changes in patients in the intensive care unit (ICU) because of factors such as host physiological stress, changes in gastrointestinal function, and antibiotic exposure. Different specimen types are used for intestinal microbial analysis because of sampling difficulties. Therefore, this study conducted a meta-analysis to investigate changes in the intestinal microbiota of patients admitted to the ICU and whether using different specimen types affects microbiota analysis.

METHODS: A systematic review was conducted encompassing studies published in electronic databases up to May 1, 2024. We included 11 studies that compared the abundance and diversity of the gut microbiota between ICU patients and healthy cohorts (HC). A standardized mean difference (SMD) meta-analysis using random effects models was performed to quantify microbial differences, including an assessment of various sampling methods.

RESULTS: After ICU admission, the intestinal microbiota of patients differed significantly from that of the normal population, showing lower diversity and richness. A significant difference in beta diversity was also observed. Specifically, the relative abundances of Proteobacteria and Fusobacteria were elevated in ICU patients, while Firmicutes abundance was diminished. Crucially, the comparison of stool versus rectal swab specimens demonstrated no significant difference in the measured alpha diversity of the gut microbiota.

CONCLUSION: The early intestinal microbiota of patients in the ICU differed from that of healthy individuals. A comprehensive understanding of the early changes in the intestinal microbiota of patients in the ICU can help formulate prevention and treatment strategies. Furthermore, using feces and swab samples for analysis did not significantly affect the diversity of the intestinal microecology. Therefore, rectal swabs may be an attractive method for sampling the gut microbiota and metabolome.

PROSPERO Registration number is CRD42022385146 (Available from: https://www.crd.york.ac.uk/PROSPERO/view/CRD42022385146).},
}

@article {pmid41658001,
year = {2025},
author = {Ruiz-Aymá, G and Romero-Arguelles, R and Rios-Del Toro, EE and Juarez-Gaspar, A and Olalla-Kerstupp, A and Loredo-Tovias, M and González-Rojas, JI and Villarreal-Treviño, L and Guzmán-Velasco, A and Gomez-Govea, MA},
title = {Postbiotic metabolites present in the supernatants of Lysinibacillus xylanilyticus and Bacillus cereus promote the germination and growth of Hibiscus sabdariffa and Prosopis juliflora.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1741549},
pmid = {41658001},
issn = {1664-302X},
abstract = {INTRODUCTION: The search for sustainable agricultural strategies has highlighted the importance of plant-microbe interactions within soil ecosystems. In particular, extracellular metabolites produced by soil bacteria represent a promising, yet underexplored, source of bioactive compounds capable of modulating plant germination and early development.

METHODS: This study evaluated the biostimulant potential of extracellular metabolites present in bacterial cell-free supernatants on the germination and early growth of Hibiscus sabdariffa and Prosopis juliflora under controlled laboratory conditions. Two native bacterial strains isolated from soils of Nuevo León, Mexico, were identified as Lysinibacillus xylanilyticus and Bacillus cereus using MALDI-TOF mass spectrometry. Supernatants obtained after cultivation in Luria-Bertani (LB) medium were applied directly to seeds, and germination and growth parameters were recorded. Phytochemical screening of the supernatants was also performed.

RESULTS: The L. xylanilyticus supernatant significantly enhanced seed germination (96.66 ± 5.77%; p < 0.0001) and promoted early growth in both plant species, increasing shoot length, leaf width, and fresh biomass. In contrast, the B. cereus supernatant inhibited H. sabdariffa germination (30 ± 10%; p = 0.0146) and showed limited effects on P. juliflora. Notably, a 50:50 mixture of both supernatants completely inhibited H. sabdariffa germination while significantly stimulating P. juliflora germination (90 ± 10%; p = 0.0130). Phytochemical analysis revealed low concentrations of carbohydrates and coumarins, suggesting that the observed effects were likely mediated by other, unidentified bioactive metabolites.

DISCUSSION: These findings demonstrate that extracellular metabolites produced by soil-derived bacteria exert species-specific and measurable biological effects on seed germination and early plant growth. The contrasting responses observed between plant species and supernatant combinations underscore the complexity of plant-microbe chemical interactions. Overall, this study highlights the potential of bacterial extracellular metabolites as microbiome-based tools for sustainable agriculture and ecological restoration.},
}

@article {pmid41657993,
year = {2025},
author = {Zhu, L and Zhang, H and Tang, M and Yang, X and Chen, Y},
title = {Parents-child multiple sites of microbial and metabolic signatures in autism spectrum disorder.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745874},
pmid = {41657993},
issn = {1664-302X},
abstract = {INTRODUCTION: To investigate the horizontal transmission of oral-gut microbiota in autism spectrum disorder (ASD) families and its potential implications for ASD pathogenesis.

METHODS: The research employed a paired cohort design using family cohorts (23 ASD children/17 parents vs. 18 Non-ASD children/16 parents), conducting integrated microbiome and metabolomic analyses of oral and fecal samples.

RESULTS: The findings revealed that ASD families exhibited significantly increased oral microbial species diversity alongside substantial alterations in gut microbiota composition, particularly demonstrating a lower Firmicutes/Bacteroidetes ratio (3.60/2.97) compared to Non-ASD families (5.59/5.35). Specific microbial changes included notable enrichment of Prevotella_9 in ASD gut microbiota. Metabolomic profiling identified significant disruptions in multiple metabolic pathways, including impaired L-rhamnose degradation and glutathione metabolism. The study observed coordinated oral-gut axis alterations through synchronized changes in Caulobacter and Serratia abundances, suggesting a distinct dysbiotic pattern along this microbial continuum. Additional metabolic findings demonstrated reduced levels of fecal glutamine and Ala-Gly in ASD children, with glycylproline exhibiting high predictive value for family typing (AUC = 0.91). Integrative analysis further revealed significant correlations between Holdemanella and various lipid metabolites.

DISCUSSION: It indicates that ASD families display characteristic oral-gut microbiota interactions accompanied by metabolic abnormalities, potentially reflecting familial microbial transmission patterns that may contribute to ASD pathophysiology.},
}

@article {pmid41657979,
year = {2025},
author = {Lin, S and Shi, E and Zhang, Y and Wang, X and Tian, Z and Han, J and Li, Q},
title = {Gut microbiota, circulating metabolites, and pancreatic cancer risk: a multi-method causal inference study with cross-population validation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1730313},
pmid = {41657979},
issn = {1664-302X},
abstract = {Pancreatic cancer (PC) is a lethal malignancy with limited early detection strategies and poor therapeutic response. Emerging evidence implicates the gut microbiota in carcinogenesis, yet whether microbial alterations are causal or secondary remains uncertain. In this study, we integrated cross-sectional 16S rDNA sequencing, two-sample Mendelian randomization (MR), and mediation analysis to investigate the causal role of gut microbiota in PC risk. We profiled fecal microbiota in a Beijing-based cohort of 26 newly diagnosed PC patients and 9 healthy controls, revealing significant dysbiosis characterized by reduced microbial diversity, depletion of butyrate-producing genera (e.g., Faecalibacterium), and enrichment of pro-inflammatory taxa such as Olsenella. Using European GWAS summary data, MR analysis identified 17 gut microbial taxa causally associated with PC risk, including Olsenella and Pauljensenia sp000411415. Notably, higher abundance of Pauljensenia sp000411415 was associated with increased PC risk, an effect partially mediated by reduced circulating levels of octanoylcarnitine (C8) and glutarylcarnitine (C5-DC)-metabolites independently linked to lower PC risk. Population-matched MR in East Asian cohorts validated several causal associations, enhancing ancestral relevance. Our findings support a causal role for specific gut microbes in pancreatic carcinogenesis and highlight a Pauljensenia-acylcarnitine axis whereby microbial suppression of protective metabolites may contribute to disease development. This integrative approach bridges microbial dysbiosis with functional mechanisms, offering novel insights for microbiome-informed strategies in PC prevention and early detection.},
}

@article {pmid41657915,
year = {2026},
author = {Till, JM and Brock, OD and Ahern, PP},
title = {Striking a balance: how the gut microbiome shapes the fate of intestinal CD4+ T cells.},
journal = {Discovery immunology},
volume = {5},
number = {1},
pages = {kyaf020},
pmid = {41657915},
issn = {2754-2483},
abstract = {The induction of immune tolerance, a state of immunologic hyporesponsiveness to an antigen, is essential to prevent the destructive potential of the immune system in response to harmless or beneficial agents. Early efforts to understand tolerance focused on model stimuli, self-antigens, transplanted organs, and the growing fetus. Through co-evolution, the microbiome and the host immune system have developed strategies that promote immunological tolerance to the microbiome. This dialogue ensures the maintenance of mutualistic interactions that provide a stable habitat for the microbiome which in turn confers numerous physiological benefits to the host. Despite the gut microbiome being a potent inducer of immune tolerance, the mechanisms through which specific members shaped immune function remained largely ignored for decades. The growing appreciation for the immunomodulatory capacity of the microbiome has led to a massive expansion of efforts to define how the balance between tolerance and inflammation is induced and maintained at mucosal sites like the intestine. While the ensuing research uncovered myriad fundamental insights into the concerted host and microbial functions promoting host-microbiome mutualism, inducing tolerance to clinically relevant antigens remains a major challenge in the development of tolerogenic therapies. Here, we trace the interaction between intestinal CD4+ T cells and the microbiome, from antigen uptake through to the development of a polarized collection of CD4+ T cells, whose functions are essential for immunological tolerance, and highlight the knowledge gaps that limit efforts to leverage these interactions for clinical benefit.},
}

@article {pmid41657902,
year = {2026},
author = {Wang, N and Fan, J and Geng, X and Zhang, S and Pan, Z and Jin, C and Chen, Y and Wu, N},
title = {Odoribacter splanchnicus inhibits toxin production in Clostridioides difficile: insights from clinical correlation and in vitro validation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741232},
pmid = {41657902},
issn = {1664-302X},
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated diarrhea. Although gut microbiota dysbiosis is central to CDI, the specific commensal species that confer protection are not well defined.

METHODS: We performed 16S rRNA sequencing on fecal samples from a clinical cohort of 30 CDI patients, 30 non-CDI diarrhea patients, 27 asymptomatic C. difficile carriers, and 30 healthy controls. To functionally validate the clinical finding, an in vitro anaerobic co-culture system was established between the Odoribacter splanchnicus type strain and C. difficile. Toxin protein levels in the supernatant were quantified by ELISA at multiple time points (24, 48, and 72 h). Sporulation was assessed via ethanol resistance assays, and the expression of toxin genes (tcdA/tcdB) was measured by quantitative PCR (qPCR).

RESULTS: Clinical analysis revealed a significant negative correlation between the abundance of Odoribacter splanchnicus and CDI severity. In vitro, a high initial ratio of O. splanchnicus significantly suppressed C. difficile toxin production during the stationary phase, without inhibiting bacterial growth. This reduction in vitro levels was accompanied by a concurrent increase in sporulation and was preceded by a downregulation of tcdB gene expression.

CONCLUSION: This work positions O. splanchnicus as a highly promising candidate for the development of next-generation, defined microbial therapeutics and provides a mechanistic foundation for future anti-virulence approaches to combat CDI.},
}

@article {pmid41657896,
year = {2026},
author = {Wicaksono, WA and Thorsen, J and Stokholm, J and Berg, G},
title = {Metagenomic analysis of the nasopharyngeal microbiomes and resistomes in asthma, COVID-19 infected, and healthy individuals.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1729707},
pmid = {41657896},
issn = {1664-302X},
abstract = {INTRODUCTION: The nasopharyngeal microbiome presents an important environmental human interface and a window in the fight against chronic diseases like asthma, respiratory infections, and antimicrobial resistance. To identify the microbial structure and function, we designed a pilot study with individuals with asthma, COVID-19 infection, and healthy controls.

METHODS: We compare the microbial and resistome profiles of healthy individuals, patients with asthma, and patients with PCR-confirmed COVID-19 using shotgun metagenome sequencing. Additionally, metagenome-assembled genomes were generated to assess the virulence potential of the bacteria identified in the nasopharynx.

RESULTS: We found different patterns in microbial diversity, richness, and structure between individuals with asthma and those who are healthy, but not for those with COVID-19. Our results revealed unexpected insights into the quite diverse nasopharynx resistome encompassing 23 distinct drug classes, mainly based on antibiotic efflux (63.9%) and antibiotic inactivation (24.6%), regardless of the disease state. The majority of the antimicrobial resistance genes (ARGs) confer resistance to multidrug (45%), followed by those genes that confer resistance to aminoglycosides, tetracyclines, polymyxin, beta-lactam, and macrolide-lincosamide-streptogramin. A high proportion of ARGs was associated with various Pseudomonas species, which was confirmed by analysing metagenome-assembled genomes. Pseudomonas brenneri exhibited the highest number of ARGs and virulence factors, indicating notable pathogenic potential.

CONCLUSION: The study reveals distinct bacterial community compositions in healthy individuals and individuals with asthma. Pseudomonadales, particularly Pseudomonas species, contribute to the nasopharyngeal resistome. No association was found between nasopharyngeal resistome profiles and asthma development. Future research may explore airway microbial functions' influence on asthma development.},
}

@article {pmid41657853,
year = {2026},
author = {Ayivi-Tosuh, SM and Dofuor, AK and Yamoah, JAA and Gayi, BK and Aiduenu, AF and Akomea, A and Anovunga, SA and Ekloh, W and Basing, LA},
title = {Gut-Microbiome Interactions: Characterization, Therapeutic Implications and Machine Learning.},
journal = {Sage open pathology},
volume = {19},
number = {},
pages = {30502098251415109},
pmid = {41657853},
issn = {3050-2098},
abstract = {The gut microbiome is vital in maintaining overall health, yet its complexity and dynamic interactions are still not fully understood. This diverse microbial community comprises bacteria, viruses, fungi, and archaea, contributing to metabolism, immune regulation, and disease susceptibility. However, imbalances in the gut microbiome (dysbiosis), have been linked to various diseases, underscoring the importance of understanding microbial interactions within the gut ecosystem. This review explores these interactions, focusing on biochemical and molecular mechanisms that shape microbial behavior and function. Additionally, it examines the therapeutic potential of the gut microbiome, particularly its involvement in disease progression, prevention, and treatment. The role of medicinal plants in influencing gut microbial composition is also discussed, given their potential to support microbiome health. Lastly, it highlights the integration of machine learning in microbiome research, offering new insights into microbial interactions, predictive disease modeling, and personalized medicine. By addressing these key areas, this review aims to deepen our understanding of gut-microbiome dynamics and their implications for human health and disease management.},
}

@article {pmid41657562,
year = {2025},
author = {Zhang, S and Song, X and Wen, Y and Wang, G},
title = {Chronic constipation and the brain-gut-microbiome axis: the role of 5-HT signaling and Traditional Chinese Medicine in pathophysiology and treatment.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1706411},
pmid = {41657562},
issn = {2296-858X},
abstract = {Chronic constipation (CC) is a prevalent functional gastrointestinal disorder involving complex interactions among the brain-gut-microbiome axis, with 5-hydroxytryptamine (5-HT) as a key signaling node. Aberrations in 5-HT synthesis, release, receptor expression, or reuptake disrupt gastrointestinal motility, contributing to CC pathogenesis. Traditional Chinese Medicine (TCM), including herbal compounds, monomers, acupuncture, and tuina, exerts therapeutic effects by modulating the 5-HT signaling pathway. Animal studies demonstrate that TCM interventions regulate gut microbiota, promote 5-HT production via metabolites like short-chain fatty acids (SCFAs) and bile acids, and target receptors (e.g., 5-HT3R, 5-HT4R) to enhance intestinal motility. Clinical trials validate TCM's efficacy in normalizing 5-HT levels and improving symptoms, with advantages in safety and holistic regulation. However, important gaps remain, including incomplete understanding of upstream and downstream 5-HT signaling mechanisms, paradoxical 5-HT expression, and limited investigation of comorbid emotional disorders. Future studies should explore how TCM interventions modulate the gut microbiota-5-HT axis and inflammation-related pathways to provide novel insights into CC management.},
}

@article {pmid41657545,
year = {2025},
author = {Jebril, N and Chabuk, S and Al-Sabary, A and Al-Mansouri, N and Al-Jobouri, W and Al-Saidi, S},
title = {Endospore-forming Bacillus subtilis isolated from third molar exudates and its association with cardiovascular disease: a retrospective cohort study.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1726295},
pmid = {41657545},
issn = {2673-4842},
abstract = {BACKGROUND: Various techniques have been previously modified to reduce early postoperative complications following third molar extraction. Given the influence of the oral microbiome, increasingly resistant bacteria have been linked to systemic diseases such as cardiovascular disease (CVD).

OBJECTIVE: In this study, we aimed to identify the spore-forming bacterium Bacillus subtilis isolated from third molar exudates and to investigate its potential association with CVD.

METHODS: In Iraq, dental hospitals don't keep thorough medical records for each patient. This lack of documentation makes it tough to carry out hospital-based research. Therefore, by collecting exudates from third molars, we conducted a retrospective cohort study of the population undergoing third molar exudate removal in a private dental clinic as an alternative setting to compare cardiovascular outcomes between individuals with cardiovascular disease and controls. Based on clinical assessments, body mass index, LDL cholesterol, C-reactive protein, systolic blood pressure, diastolic blood pressure, hypertension, and smoking status were measured. The study was conducted on 40 men, comprising 20 patients with diagnosed cardiovascular disease and 20 controls. Light and transmission electron microscopy were used to perform a phenotypic evaluation of the bacterial isolates (spore formation, biofilm production). Biofilm formation was assessed using Congo red agar, crystal violet staining, and scanning electron microscopy (SEM). In addition, systolic and diastolic blood pressure (SBP and DBP) values were obtained to further assess cardiovascular risk.

RESULTS: The number of B. subtilis isolates was higher in the CVD group than in the control group (non-CVD) and demonstrated significantly greater biofilm-forming ability (OD600 = 1.45 ± 0.22 vs 0.85 ± 0.19, p < 0.01). TEM confirmed dense endospore architecture from patients with CVD, while SEM revealed extensive extracellular matrix formation within CVD biofilms. Patients with oral colonization by B. subtilis showed a significantly higher prevalence of CVD (32.6%) compared to those without colonization (12.6%, p = 0.008). The presence of biofilm-positive B. subtilis strains was independently associated with CVD (OR 2.91; 95% CI, 1.23-6.83). Spore-forming B. subtilis isolates from third molars of patients with CVD demonstrated enhanced biofilm formation and sporulation phenotypes. A moderate positive correlation (r = 0.48) was also observed between B. subtilis presence and SBP and DBP. These findings suggest that these bacterial characteristics are potentially the cause of systemic inflammation and represent a potential microbial link to CVD.

CONCLUSION: In countries like Iraq, researchers run into real problems when they try to study links between oral health and other diseases. There's no NHS dental system, so they can't rely on existing records for data. Therefore, this study provides a protocol for conducting investigations related to oral health through collaboration with other institutions, such as universities. With respect to the main finding of this study, spore-forming B. subtilis isolated from third molar exudates demonstrated phenotypic characteristics that may contribute to persistent oral colonization and increase systemic inflammatory risk. The observed association with cardiovascular disease warrants further investigation into oral-systemic microbial pathways.},
}

@article {pmid41657532,
year = {2026},
author = {Ashaolu, TJ and Lee, CC and Tarhan, O and Rashidinejad, A and Jafari, SM},
title = {Nexus of Whey Proteins, Gut Dysbiosis, and Colonic Health.},
journal = {Food science & nutrition},
volume = {14},
number = {2},
pages = {e71487},
pmid = {41657532},
issn = {2048-7177},
abstract = {The gut microbiota is essential for colonic health, and its imbalance (dysbiosis) is linked to conditions like inflammatory bowel disease and metabolic disorders. Whey proteins (WPs), including β-lactoglobulin, α-lactalbumin, glycomacropeptide, and lactoferrin, possess antimicrobial, immunomodulatory, and prebiotic-like properties that may help restore microbial balance. Beyond modulating the microbiome, WPs play a significant role in reinforcing intestinal barrier integrity and regulating host metabolism. This review summarizes evidence from in vitro, in vivo, and clinical studies showing WPs can enhance beneficial bacteria (e.g., Bifidobacterium, Lactobacillus) while suppressing harmful ones. Furthermore, WP supplementation has been shown to alleviate dysbiosis-related conditions such as colitis, obesity, and allergies by improving microbial diversity, enhancing short-chain fatty acid production, strengthening the mucosal barrier, and modulating immune responses. However, the effects vary depending on WP composition, processing, and individual microbiota. Despite encouraging results, knowledge gaps remain regarding optimal dosing and long-term impacts. Overall, WPs show promise as functional food components and potential therapeutic agents for promoting colonic health, metabolic homeostasis, and gut barrier function, but more research is needed to refine their clinical application.},
}

@article {pmid41657529,
year = {2026},
author = {Wang, H and Shi, Y and Wang, W and Li, X},
title = {Association of Anti-Inflammatory Dietary Adherence With Biomarkers and Gut Microbiota Related to Colorectal Cancer Risk: A Retrospective Study.},
journal = {Food science & nutrition},
volume = {14},
number = {2},
pages = {e71497},
pmid = {41657529},
issn = {2048-7177},
abstract = {Colorectal cancer is one of the most common cancers and a primary cause of death. The increased incidence in low- and middle-income nations highlights the need for better prevention. Chronic inflammation, obesity, and gut microbial dysbiosis are major risk factors for CRC, making nutritional interventions attractive. This study aims to examine the association between adherence to an anti-inflammatory diet and anthropometric, biochemical, inflammatory, molecular, and gut microbiota parameters related to colorectal cancer risk. In this retrospective analysis, anti-inflammatory diet adherents (n = 515) and non-adherents (n = 435) were compared. Hematological, hepatic, inflammatory, tumor, genetic/molecular, and gut microbiota tests were performed, and chi-square tests were used for categorical outcomes. Multiple regression was used to examine the association between adherence to an anti-inflammatory diet and the development of colorectal cancer. Multiple logistic regression analysis indicated that anti-inflammatory diets were associated with improved clinical, biochemical, and microbiome outcomes in patients with CRC. Diet adherence was associated with a lower risk of obesity, central obesity, dyslipidemia, anemia, and leukocytosis after adjusting for age, sex, BMI, smoking, and caloric intake (β = -1.90, SE = 0.26, OR = 0.15, 95% CI: 0.09-0.25). Several inflammatory markers, including CRP, IL-6, CEA, and MMP-9, decreased markedly (p < 0.001). Molecular alterations associated with CRC, including p53 mutation, Ki-67 overexpression, microsatellite instability, APC mutation, and β-catenin nuclear expression, were significantly decreased (p < 0.001). Bifidobacterium, Lactobacillus, Faecalibacterium prausnitzii, and Akkermansia muciniphila were increased, and pathogenic species decreased in the gut (ORs 2.10-2.30; Fusobacterium nucleatum, Clostridium difficile, pathogenic Escherichia coli; ORs 0.16-0.18). Anti-inflammatory diets significantly improve metabolic, inflammatory, tumor-related, and microbiome profiles in patients with CRC. Adherence to an anti-inflammatory dietary pattern is significantly associated with improved metabolic, inflammatory, molecular, and gut microbiota profiles, all of which are linked to colorectal cancer risk. These findings support anti-inflammatory dietary strategies as cost-effective and non-invasive approaches for colorectal cancer prevention and adjunctive management.},
}

@article {pmid41657399,
year = {2026},
author = {Abbondio, M and Tanca, A and Sau, R and Pira, G and Errigo, A and Manetti, R and Pes, GM and Bibbò, S and Dore, MP and Uzzau, S},
title = {A human fecal metaproteomic dataset from celiac disease patients on gluten-free diet with or without poly-autoimmunity.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112501},
pmid = {41657399},
issn = {2352-3409},
abstract = {This dataset provides the fecal metaproteome profiles of 28 celiac disease patients on a gluten-free diet, distinguished by the presence or absence of co-occurring autoimmune conditions. The resource includes raw liquid chromatography-tandem mass spectrometry (LC-MS/MS) files, database search results, protein/peptide identification outputs, and taxonomic/functional annotation outputs, along with comprehensive anthropometric, clinical, and dietary metadata for each patient. The identified proteins originate from microbial, human, and plant sources, consistent with the multi-database search strategy used. This collection is designed for reuse in meta-analyses and integrative studies exploring functional changes in the gut microbiome related to auto-immune status and dietary variables. The complete dataset is available via the ProteomeXchange Consortium with the identifier PXD069517.},
}

@article {pmid41657369,
year = {2026},
author = {Patil, LR and Shetty, VV and Patil, SG and Aithal, KR and Oli, AM and Kaulgud, R and Yenagi, VA and Dharne, M and Dastager, SG and Chandrasekran, AM and Prabhakaran, D},
title = {Influence of Yoga-based cardiac rehabilitation on gut-microbiome diversity and Gut-Heart-Brain axis (YoGH-Biome) in heart failure: a study protocol.},
journal = {BMJ open sport & exercise medicine},
volume = {12},
number = {1},
pages = {e003147},
pmid = {41657369},
issn = {2055-7647},
abstract = {Heart failure (HF) is a chronic and progressive cardiovascular condition associated with significant morbidity, mortality and healthcare burden. Increasing evidence points to a critical role of gut dysbiosis and the gut-heart-brain axis in HF pathophysiology. Altered gut microbiota may influence systemic inflammation, neurohormonal activity and cardiac function through gut-derived metabolites such as trimethylamine N-oxide (TMAO) and short-chain fatty acids (SCFAs). Yoga-based cardiac rehabilitation (Yoga-CaRe) is a cost-effective intervention that has been shown to improve quality of life, exercise capacity and cardiovascular outcomes in cardiac patients. However, the mechanism underlying its benefits remains unclear. Furthermore, its effect on gut microbiota diversity and the downstream impact on the gut-heart-brain axis in HF remains largely unexplored. This study outlines a prospective, randomised, open-label, blinded-endpoint trial investigating the effects of a 12-week Yoga-CaRe intervention versus enhanced standard care in 60 HF patients with reduced ejection fraction. Participants will be randomly assigned in a 1:1 ratio to either the Yoga-CaRe or the control group. The Yoga-CaRe group will participate in 20 supervised yoga sessions, complemented by guided daily home practice, while the control group will receive enhanced standard care. The trial will assess changes in gut microbiota composition, levels of gut-derived metabolites (TMAO and SCFAs), inflammatory biomarkers (TNF-α and high-sensitivity C reactive protein), heart rate variability, 6 min walk test (6MWT) and echocardiography. Biological samples and clinical data will be analysed using integrated bioinformatics and statistical approaches to evaluate intervention efficacy and identify potential mechanistic pathways. The YoGH-Biome study has received ethical clearance from the Institutional Ethics Committee of the SDM College of Medical Sciences and Hospital, India (SDMIEC/2025/1073). It is registered with the Clinical Trials Registry of India. Study results will be disseminated via scientific publications, conferences and stakeholder forums to inform integrative strategies for HF management. Trial registration number: CTRI/2023/12/060757.},
}

@article {pmid41657363,
year = {2026},
author = {Bujaldón, R and Montero, E and Chamorro, C and Marín, MJ and Iniesta, M and Sanz, M and Herrera, D},
title = {Subgingival microbiome and adjunctive use of probiotics in the treatment of periodontitis in patients with diabetes: a secondary analysis of a randomized clinical trial.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2624894},
pmid = {41657363},
issn = {2000-2297},
abstract = {BACKGROUND: Adjunctive therapies have been proposed to enhance periodontal outcomes by modulating the subgingival microbiome. However, the microbiological effects of probiotic supplementation in diabetic patients with periodontitis remain unclear, particularly when assessed using high-resolution sequencing methods.

AIM: To evaluate the effect of a Limosilactobacillus reuteri as an adjunct to subgingival instrumentation on the subgingival microbiome in the treatment of periodontitis in patients with diabetes.

METHODS: This was a secondary analysis of a randomized, triple-blind, placebo-controlled clinical trial. Forty patients with stage II-III periodontitis and diabetes received subgingival instrumentation and either L. reuteri lozenges (n = 19) or placebo (n = 21) for 3 months. Subgingival samples were collected at baseline, 3, and 6 months. The V3-V4 region of the 16S rRNA gene was sequenced and analyzed using QIIME2. Alpha diversity was analyzed with mixed-effects models, beta diversity with PERMANOVA, and differential abundance with linear models.

RESULTS: A total of 116 high-quality samples were included. Alpha and beta diversity metrics did not show significant differences between groups or across time points. L. reuteri was detected inconsistently in the subgingival microbiome, with low relative abundances and no sustained presence over time. No bacterial species exhibited significant changes in differential abundance between the probiotic and placebo groups over time.

CONCLUSIONS: Adjunctive L. reuteri supplementation did not significantly alter subgingival microbiome diversity or composition over 6 months.},
}

@article {pmid41656827,
year = {2026},
author = {Upadhyay, SK},
title = {Strigolactones Targeting Plant-Microbe Dialogues From Roots to Soil: Unlocking Pathways for Sustainable Agriculture.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70787},
doi = {10.1111/ppl.70787},
pmid = {41656827},
issn = {1399-3054},
mesh = {*Lactones/metabolism/pharmacology ; *Plant Roots/microbiology/metabolism ; *Plant Growth Regulators/metabolism ; *Agriculture/methods ; *Soil Microbiology ; Mycorrhizae/physiology ; Soil/chemistry ; Signal Transduction ; Plant Development ; },
abstract = {Strigolactones (SLs) are phytohormones derived from carotenoids that influence various aspects of plant growth, development, and the ability of plants to respond to environmental changes and microbial interactions. Initially categorized as shoot branching inhibitors, SLs are now recognized as crucial rhizospheric signaling molecules that govern nutrient availability, hormonal control, and microbial interactions. Despite significant progress in SL biology, a cohesive synthesis connecting SL molecular signaling, rhizosphere communication, and stress tolerance remains fragmented, hindering their practical use in sustainable agriculture. A more comprehensive understanding of their synthesis process (D27-CCD7/8-MAX1-CLA cascade), their perception (D14-MAX2-SMXL module), and the impact of SMXL7 on chromatin has revealed significant implications on physiology. To enhance plant development under stress conditions, SLs drive auxin transport, regulate ABA-dependent stress signaling, influence the antagonistic effects of cytokinins, and coordinate gibberellin activity with the circadian rhythm. SLs augment arbuscular mycorrhizal colonization, stimulate nodulation, and attract plant growth-promoting rhizobacteria through chemotactic and metabolic interactions. Using GR24 and SL-conjugated nanomaterials enhances plant resistance to drought, salt, and metal stress. Modifying SL-transporters with CRISPR improves SL signaling and fosters beneficial symbiotic associations. The study is crucial because it underscores the importance of SLs in recruiting beneficial microorganisms and facilitating microbial-hormonal interactions. This review proposes a cohesive conceptual framework that integrates receptor specificity, rhizospheric sensing, and microbial response, beyond mere descriptive synthesis. It sets distinct research targets, such as receptor-specific SL-analogues, in situ sensing techniques, and tailored SL-responsive microbial consortia, to make biostimulation more precise and assist crops in withstanding climatic stress more effectively.},
}

*Lactones/metabolism/pharmacology
*Plant Roots/microbiology/metabolism
*Plant Growth Regulators/metabolism
*Agriculture/methods
*Soil Microbiology
Mycorrhizae/physiology
Soil/chemistry
Signal Transduction
Plant Development

@article {pmid41656717,
year = {2026},
author = {Cho, G and Kim, DH and Kim, JS and Song, J and Kim, SJ},
title = {Bayesian Pairwise Compositional Lotka-Volterra Modeling Infers Potential Rhizosphere Microbial Suppressors of Ralstonia pseudosolanacearum.},
journal = {The plant pathology journal},
volume = {42},
number = {1},
pages = {50-60},
doi = {10.5423/PPJ.OA.10.2025.0143},
pmid = {41656717},
issn = {1598-2254},
support = {PJ01727501//Rural Development Administration/ ; },
abstract = {The Ralstonia solanacearum species complex (RSSC) is a major soil-borne pathogen of solanaceous crops. During a field experiment originally designed to monitor rhizosphere and episphere microbiomes in two pepper cultivars, a naturally emerging and asymptomatic Ralstonia dominance event was detected in the rhizosphere without visible wilt symptoms. This unexpected occurrence provided an opportunity to characterize asymptomatic RSSC dynamics and their microbial interactions under field conditions. Full-length 16S rRNA amplicon sequencing showed that one ASV (Sq_1) was nearly absent from the episphere but increased sharply in the rhizosphere from week 3 onward, dominating 20-80% of samples during weeks 7-10. Phylogenetic comparison with 93 historical Korean RSSC isolates placed Sq_1 within a 16S-defined lineage corresponding to pepper-associated R. pseudosolanacearum biovars 3 and 4. Sq_1 abundance accounted for a large portion of β-diversity turnover in the rhizosphere. After within-plot correlations were meta-analyzed, selected taxa were evaluated using a Bayesian pairwise compositional Lotka-Volterra (pcLV) model, which identified three taxa (Sq_272, TRA3-20; Sq_178, Bradyrhizobium; and Sq_124, Bryobacter) that consistently exerted inhibitory effects on Sq_1 per-interval growth. Supported by the longitudinal design and the high accuracy of PacBio full-length 16S sequencing, these findings highlight potential microbial suppressors of RSSC and demonstrate the utility of pcLV modeling for resolving directional interactions at the ASV level.},
}

@article {pmid41656565,
year = {2026},
author = {Akber, MA and Fang, X},
title = {Soil type and growth stage-dependent rhizosphere bacteriome of alfalfa under challenge by the fungal pathogen Rhizoctonia solani.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70620},
pmid = {41656565},
issn = {1526-4998},
support = {32171678//National Natural Science Foundation of China/ ; 23ZDNA009//Gansu Provincial Science and Technology Major Projects/ ; },
abstract = {BACKGROUND: Alfalfa (Medicago sativa) is the most important forage legume crop in China, but its productivity is severely threatened by root rot caused by Rhizoctonia solani. The use of resistant varieties is regarded as the most effective and sustainable strategy for disease management. However, the interaction between the host genotypes of alfalfa and R. solani in shaping the rhizosphere microbiome, and the role of these microbial assemblages in host resistance, remains poorly understood. This study investigated the rhizosphere bacteriome of alfalfa varieties with contrasting resistance to R. solani across different soil types and growth stages. Disease severity, plant biomass, and antioxidant enzyme activities were also evaluated.

RESULTS: Significant changes were observed in the composition and diversity of the bacterial community under infection by R. solani. The resistant variety exhibited higher activities of superoxide dismutase, peroxidase, and catalase. Pathogen inoculation was associated with a more complex and positively interconnected microbial network, indicating shifts in potential microbial associations. Notable shifts in α-diversity, Bray-Curtis β-diversity, and growth-stage-specific bacterial genera were observed between 8 and 16 weeks. In contrast, differences between soil types were less pronounced, which shows that the growth stage strongly influenced rhizosphere bacteriome structure.

CONCLUSION: These findings advance understanding of host-microbiome-pathogen interactions and provide a basis for microbiome-assisted strategies in sustainable management of root rot in alfalfa cultivation. © 2026 Society of Chemical Industry.},
}

@article {pmid41656437,
year = {2026},
author = {Pan, L and Cai, B},
title = {The core microbiome of the AMF hyphosphere: mineralization mechanisms of key soil mineral elements.},
journal = {Mycorrhiza},
volume = {36},
number = {1},
pages = {6},
pmid = {41656437},
issn = {1432-1890},
support = {No. 31972502//National Natural Science Foundation of China/ ; },
mesh = {*Mycorrhizae/metabolism/physiology ; *Microbiota ; *Soil Microbiology ; *Soil/chemistry ; Phosphorus/metabolism ; Nitrogen/metabolism ; Sulfur/metabolism ; Carbon/metabolism ; *Minerals/metabolism ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) lack the enzymatic capacity to directly mineralize many essential soil elements and therefore rely on their hyphosphere core microbiome, a microbial consortium increasingly recognized as the "second genome" of AMF. However, the definition, functional mechanisms, and ecological relevance of this core microbiome remain poorly resolved. This review addresses how hyphosphere core microorganisms regulate the mineralization of soil carbon, nitrogen, phosphorus, and sulfur. We first outline the conceptual development of the core microbiome and then, for the first time, propose a five-dimensional screening framework integrating abundance stability and universality, functional stability, dynamic responsiveness, ecological niche specificity, and community supportiveness to identify authentic core members. Using this framework, we synthesize evidence on the mechanisms by which the hyphosphere core microbiome mediates biomineralization, highlighting its role in converting organically bound nutrients into plant-available forms. By integrating the functions of hyphosphere core microorganisms across carbon, nitrogen, phosphorus, and sulfur cycles, this review provides a unified ecological perspective on how the AMF hyphosphere core microbiome drives soil nutrient turnover (Fig. 1). Overall, this framework advances understanding of hyphosphere ecology and offers practical implications for soil ecosystem restoration and sustainable agricultural management.},
}

*Mycorrhizae/metabolism/physiology
*Microbiota
*Soil Microbiology
*Soil/chemistry
Phosphorus/metabolism
Nitrogen/metabolism
Sulfur/metabolism
Carbon/metabolism
*Minerals/metabolism

@article {pmid41656241,
year = {2026},
author = {Liu, X and Qiao, Y and He, W and Chen, X and Zhou, Q and Xu, Y and Yang, Y and Li, C and Yu, J and Luo, P},
title = {Integrated multi-omics profiling reveals effects of exogenous plant growth regulators on tobacco rhizosphere under Vulpia myuros rotation.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08312-4},
pmid = {41656241},
issn = {1471-2229},
support = {110202101009 (XJ-01)//Key Science and Technology Project of China National Tobacco Corporation/ ; 110202201040 (XJ-11)//Key Science and Technology Project of China National Tobacco Corporation/ ; },
}

@article {pmid41655925,
year = {2026},
author = {Ren, J and Zhang, B and Luo, K and Zhao, Y},
title = {Exploring the role of type 3 resistant starch crystalline polymorphs in modulating gut health and alleviating inflammation in colitis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150805},
doi = {10.1016/j.ijbiomac.2026.150805},
pmid = {41655925},
issn = {1879-0003},
abstract = {Type 3 Resistant starch (RS3) has garnered increasing attention for its potential therapeutic effects in inflammatory bowel diseases (IBD), such as colitis. However, the impact of different crystalline forms of RS3 on the alleviation of colitis remains unclear. This study examined A-type and B-type crystalline RS3 microparticles (ARS and BRS) derived from debranched waxy maize starch. BRS exhibited higher crystallinity and RS content than ARS by around 8% and 11%, respectively. Treatment with ARS and BRS led to a 12.5-31.1% reduction in cytokine levels (TNF-α, IL-1β, IL-6) compared to NS, while improving colon morphology. Notably, BRS more effectively promoted Lactobacillus growth, suppressed harmful Patescibacteria, and increased SCFA levels (by 5.1 μmol/g) compared to ARS. The findings underscore the significance of RS3's crystalline structure in its anti-inflammatory potential, suggesting it as a promising strategy for colitis management and offering insights into RS's benefits for gut health.},
}

@article {pmid41655800,
year = {2026},
author = {Zhu, J and Yang, L and Fang, Z and Chen, J and Fu, R and Liu, S and Chen, M},
title = {Xin-Jia-Tong-Xie-Yao-Fang restores the intestinal barrier to alleviate irritable bowel syndrome via microbial butyrate mediated PI3K/Akt pathway suppression.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108344},
doi = {10.1016/j.micpath.2026.108344},
pmid = {41655800},
issn = {1096-1208},
abstract = {BACKGROUND: Xin-Jia-Tong-Xie-Yao-Fang (XJTXYF) is a proven prescription for managing diarrhea-predominant irritable bowel syndrome (IBS-D), which is a prevalent functional gastrointestinal disorder. However, the underlying mechanism of XJTXYF remains unclear. This study aims to explore the material basis and potential mechanisms of XJTXYF against IBS-D.

METHODS: The constituents of XJTXYF were identified by UPLC-Q-TOF-MS/MS, and potential targets and pathways were screened by network pharmacology. Changes in the intestinal microbiome and fecal butyric acid levels after XJTXYF administration were analyzed through 16S rRNA sequencing and HPLC respectively. The abdominal withdrawal reflex score, serum levels of FITC-D and the expression of intestinal epithelial tight junction proteins, as well as the activity of the PI3K/Akt pathway were assessed. In-vitro experiments involved silencing GPR109A using small interfering RNA and inducing barrier damage with LPS pre-treatment in the Caco-2 cell line. Barrier function was evaluated by FITC-D permeability and tight junction protein expressions. The activity of the PI3K/Akt pathway was determined through Western blotting analysis.

RESULTS: The major active compounds of XJTXYF identified by UPLC-Q-TOF-MS/MS include Saikosaponin C, Hesperetin, Neohesperidin, Albiflorin, Quercetin and so on. The PI3K/Akt signaling pathway was predicted by network pharmacology as a potential target of XJTXYF in treating IBS-D. Animal experiments demonstrated that XJTXYF could increase body weight, improve visceral hypersensitivity, rebalance gut flora dysbiosis and upregulate fecal butyric acid content in IBS mice. The XJTXYF also showed the abilities of intestinal barrier repairment and PI3K/Akt pathway suppression. Fecal microbiota transplantation and the positive controls (NaB and Clostridium Butyricum) verified that a causal relationship existed between gut microbiome changes and IBS-D improvement after XJTXYF treatment. In-vitro experiments revealed the role of butyrate in barrier protection via PI3K/Akt inhibition.

CONCLUSION: Overall, in this study, we revealed that XJTXYF could restore intestinal barrier function through microbial butyrate mediated PI3K/Akt inhibition and improve IBS-D symptoms.},
}

@article {pmid41655731,
year = {2026},
author = {Teng, J and Li, W and Wei, Y and Wang, C and Yun, X and Lu, Y and Chen, J and Ma, X and Zhao, Y},
title = {Gut microbiome diversity and functional profiles of Culicoides across Sanya, Ruili, and Linyi, China.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108013},
doi = {10.1016/j.actatropica.2026.108013},
pmid = {41655731},
issn = {1873-6254},
abstract = {BACKGROUND: Biting midges (Culicoides spp.) are vectors of diverse microbes such as viruses, bacteria, protozoa, and nematodes that cause diseases in both wild and domestic animals. Despite their ecological significance and role in disease transmission, the composition and underlying mechanisms shaping the gut microbiota of Culicoides remain poorly characterized.

OBJECTIVES: This study aimed to investigate the composition and functional profiles of the gut microbiota of adult Culicoides collected from three representative cities spanning tropical, subtropical, and temperate climate zones in China.

METHODS: 16S high-throughput sequencing was used to study the microbial composition and function of Culicoides in the three regions. This study further incorporated six environmental factors and seven genetic diversity indices to explore their relationships with the microbial community.

RESULTS: The findings revealed significant variations in the gut microbial composition, dominant species, and diversity of Culicoides across different climate zones. NoTable differences were observed in microbial functions related to insect growth, development, and oxidative stress, with Culicoides from the Sanya zone exhibiting a greater abundance of functions and participating in more signaling processes. Environmental factors and host genetic diversity across different habitats collectively shape the composition of the gut microbiota of Culicoides. Structural equation modeling (SEM) revealed that environmental factors exert predominantly direct selective effects on microbial community assembly, whereas host genetic diversity plays a critical indirect regulatory role. These environment-host-microbiota interactions exhibit significant spatial heterogeneity. In low-latitude regions (Sanya), environmental factors mainly manifest direct filtering effects, whereas in ecotone areas (Ruili), environmental pressures indirectly modulate microbial composition by altering host genetic adaptation.

CONCLUSIONS: Our findings revealed that Culicoides gut microbiomes exhibit distinct biogeographical divergence, characterized by environment-driven variations in microbial community structure and functional potential. Host genetic adaptation serves as a key mediator and synergistic modulator of these patterns. This tripartite environment-host-microbiome interaction demonstrates clear dependence on geographic gradient.},
}