@article {pmid41757954,
year = {2026},
author = {Ke, Y and Sun, Y and Wu, J and Ye, L and Zhu, Z},
title = {Association of vaginal microbiome, cytokines, and spontaneous preterm birth among Chinese women: a nested case-control study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0260725},
doi = {10.1128/spectrum.02607-25},
pmid = {41757954},
issn = {2165-0497},
abstract = {An imbalance of the vaginal microbiome and dysregulation of cytokines are associated with spontaneous preterm birth (sPTB). To date, the relationship between the vaginal microbiome, cytokines, and sPTB remains unclear in the Chinese population. Herein, we conducted a nested case-control study using data from a prospective cohort of 749 Chinese women with a singleton pregnancy who were enrolled between 16 and 28 weeks of pregnancy. Cases consisted of individuals experiencing sPTB (n = 38), while controls were selected randomly at a 4:1 ratio to cases (n = 152). Compared to the term group, the sPTB group exhibited significantly increased abundance of vaginal Aerococcus christensenii, Gardnerella swidsinskii, and Lactobacillus iners, along with elevated levels of interleukin (IL)-1β, IL-6, and IL-12p70 in vaginal fluid (P < 0.05). Least absolute shrinkage and selection operator (LASSO) regression identified L. iners, G. swidsinskii, and IL-6 as significant risk factors for sPTB, with adjusted odds ratios (ORs) (95% CI) of 1.57 (1.06-2.34), 1.45 (1.03-2.05), and 2.05 (1.43-2.93), respectively. Finally, a logistic regression model for sPTB was established incorporating L. iners, G. swidsinskii, and IL-6, which yielded an area under the receiver operating characteristic curve (AUC) of 0.73. These findings suggest that alterations in the vaginal microbiome and cytokine levels may contribute to sPTB in the Chinese population.IMPORTANCEPreterm birth (PTB) is the leading cause of death in children under 5 years of age, of which about 70% were spontaneous ones (sPTB); while genitourinary infections are implicated in 25-40% of sPTB cases. Previous studies have revealed some features of vaginal microbiome and cytokines related to sPTB: increased richness and diversity, increased levels of Lactobacillus iners, BV-associated bacteria, low abundance of L. crispatus, and high levels of pro-inflammatory cytokines. However, there were also some inconsistent findings, and little is known in the Chinese population. This study confirmed the correlations between vaginal microbiome, cytokines, and sPTB in Chinese pregnant women. Specifically, elevated vaginal L. iners, G. swidsinskii, and IL-6 levels were significantly associated factors, which may help to identify women at high risk of sPTB.},
}

@article {pmid41757945,
year = {2026},
author = {Surve, SV and Valls, RA and Barrack, KE and Gwilt, LL and Gardner, TB and O'Toole, GA},
title = {The regional landscape of the human colon culturome in health and cystic fibrosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0312625},
doi = {10.1128/spectrum.03126-25},
pmid = {41757945},
issn = {2165-0497},
abstract = {UNLABELLED: Cystic fibrosis (CF) alters gut physiology, yet its impact on microbial communities across colonic regions (ascending, transverse, descending colon) and microhabitats (lumen, mucosa) remains incompletely understood. Here, we applied culturomics to characterize gut microbiota in a small cohort of 32 individuals (22 non-CF, 10 CF). Persons with CF (pwCF) exhibited significantly higher viable bacterial loads than non-CF individuals, particularly in mucosal samples. Anaerobes predominated overall, with relative enrichment of aerobes in the mucosa of pwCF. Alpha diversity was reduced in mucosal samples and aerobic cultures for pwCF, whereas beta diversity was influenced by all the tested variables except the colonic region. Phylum-level analyses revealed enrichment of Proteobacteria and depletion of Actinobacteria, Bacteroidota, and Firmicutes in samples from pwCF, consistent with stool analysis. Random forest models identified selected oral-associated microbes as key predictive taxa and accurately classified polyp status within this cohort. Whole-genome sequencing of Bacteroides fragilis (n = 21) and Escherichia coli (n = 15) isolates, representing a subset of 109 gut bacterial genomes sequenced from this cohort, revealed minimal genomic variation across colonic regions and sample types, indicating intra-individual strain stability. The understandings from this pilot culturome study, after future validation, may help in developing targeted microbial therapeutic approaches to address the gut dysbiosis of CF.

IMPORTANCE: This pilot study of a small cohort represents the first culturome analysis of the cystic fibrosis colon. Our preliminary findings demonstrate that cystic fibrosis (CF)-associated gut dysbiosis is spatially specific, with mucosal bacterial communities showing pronounced alterations while luminal communities show comparatively subtle phylum-specific shifts. This spatial specificity suggests the mucosal microenvironment as a potential therapeutic target and indicates that interventions focused solely on luminal bacteria may be insufficient. The promising predictive accuracy of culturome-based machine learning models in this small cohort suggests these viable bacterial signatures could serve as biomarkers for CF management pending larger validation studies. Additionally, our initial observations of CFTR modulator effects on gut microbial communities provide insight for future studies optimizing combination therapies.},
}

@article {pmid41757889,
year = {2026},
author = {El Hafi, B and Jean-Pierre, F and Taub, L and Hampton, TH and O'Toole, GA},
title = {Streptococcus sanguinis antagonizes Prevotella melaninogenica in the context of the cystic fibrosis respiratory microbiome.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0000526},
doi = {10.1128/jb.00005-26},
pmid = {41757889},
issn = {1098-5530},
abstract = {The latest generation of cystic fibrosis transmembrane conductance regulator-targeted modulator therapy, Elexacaftor/Tezacaftor/Ivacaftor (ETI), has significantly improved the clinical outcomes of persons with cystic fibrosis (pwCF) but does not appear to completely eliminate CF respiratory microbial colonization. Here, we analyzed over 4,200 publicly available respiratory microbiomes spanning pre- and post-ETI treatment periods and further stratified by age and type of sample. Our analyses reveal that despite reshaping of community composition by ETI, classical CF pathogens such as Pseudomonas and Staphylococcus spp. persist in sputum and sinonasal samples, while Streptococcus spp. drastically increase in prevalence and relative abundance post-ETI treatment. Obligate anaerobes such as Prevotella spp., Fusobacterium spp., Porphyromonas spp., and Veillonella spp. were readily detected post-ETI. We observed changes in the sputum samples from pwCF post-ETI, with an increase in the relative abundance of Streptococcus spp. and prevalence of Prevotella and a decline in Pseudomonas spp. Analysis of co-occurrence networks revealed mostly positive correlations between the different genera pre- and post-ETI; however, these correlations were reduced in number following ETI treatment, suggesting a disruption of community connectivity. To test one of the hypotheses raised by the computational analyses, we experimentally investigated the relationship between Streptococcus sanguinis and Prevotella melaninogenica in a CF sputum-like medium. Our data suggest that S. sanguinis uses reactive nitrogen species, and likely other factors, to antagonize P. melaninogenica, while Pseudomonas aeruginosa protects P. melaninogenica in CF-like culture conditions. Our findings implicate polymicrobial interactions, rather than individual species abundance, in determining microbial persistence and adaptation within the CF airway post-ETI.IMPORTANCEThe introduction of the latest cystic fibrosis transmembrane conductance regulator (CFTR)-targeted Elexacaftor/Tezacaftor/Ivacaftor (ETI) therapy represents a major therapeutic advance for persons with cystic fibrosis (pwCF); however, this therapy does not completely negate respiratory infections and colonization. We leverage large-scale publicly available microbiome data to demonstrate that while ETI therapy alters the respiratory microbial landscape, canonically prevalent and abundant CF pathogens persist in many pwCF and likely maintain ecological relevance through adaptive interactions with other taxa. Our in vitro findings also reveal that Streptococcus sanguinis can antagonize Prevotella melaninogenica, and that Pseudomonas aeruginosa can provide selective protection to quell this antagonism. These insights highlight the need to consider microbial interactions and community dynamics when evaluating long-term responses to CFTR modulators.},
}

@article {pmid41757865,
year = {2026},
author = {Hu, X and Shi, Z and Gao, Y and Zheng, H and Lin, L and Chen, JP and Chen, Y and Zhang, CX and Li, Y},
title = {Characterization of the dynamic microbiome evolution across thrips species.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70265},
pmid = {41757865},
issn = {1744-7917},
support = {2023J06040//Natural Science Foundation of Fujian Province/ ; //Ningbo Yongjiang grant/ ; 32472657//National Natural Science Foundation of China/ ; 32570491//National Natural Science Foundation of China/ ; },
abstract = {The insect microbiome profoundly influences host physiology and ecology, yet its composition and evolutionary dynamics in thrips remain poorly understood. Here, we present a systematic characterization of thrips-associated microbiomes through integrated metagenomic and culture-based approaches. Our analysis reveals that thrips microbiomes are dominated by both intracellular symbionts (e.g., Wolbachia and Spiroplasma) and extracellular taxa (e.g., Serratia, Pantoea, and Acinetobacter), with species-specific compositions exhibiting frequent gains and losses of bacterial lineages. We demonstrate that thrips microbiomes exhibit low interspecific microbial sharing, forming host-specific bacterial communities with minimal overlap between species. To address methodological challenges in microbiome research, we developed a dual-sequencing framework combining short-read sequencing (for comprehensive taxonomic detection) and long-read sequencing (for genomic verification), enabling the reconstruction of high-quality metagenome-assembled genomes that validated short-read findings. Furthermore, we isolated and sequenced the complete genomes of two dominant extracellular symbionts-Pantoea dispersa and Serratia marcescens-and performed pan-genome analyses. These revealed small core gene sets and expansive accessory genomes, including host-specific functional genes (e.g., hydrolases and neurotoxic N-acetyltransferases) likely involved in host adaptation. Our study provides a foundational genomic resource and a robust analytical pipeline for dissecting thrips microbiome evolution, with implications for understanding insect-microbe interactions and symbiont-mediated adaptations.},
}

@article {pmid41757862,
year = {2026},
author = {Zhang, Y and Zhang, R and Wang, G and Liu, Y},
title = {Antibiotic-Mediated Microbiota Depletion Suggests an Association Between Gastric Juice Dysbacteriosis and Abnormal Bile Acid Metabolism in Chronic Atrophic Gastritis Rats.},
journal = {Biomedical chromatography : BMC},
volume = {40},
number = {4},
pages = {e70404},
doi = {10.1002/bmc.70404},
pmid = {41757862},
issn = {1099-0801},
support = {82374025//National Natural Science Foundation of China/ ; 82073988//National Natural Science Foundation of China/ ; 202403021221327//Fundamental Research Program of Shanxi Province/ ; zyytd2024020//Traditional Chinese Medicine Innovation Team of Shanxi Province/ ; },
abstract = {Current research on chronic atrophic gastritis (CAG) has primarily focused on intestinal flora, while the role of gastric juice microecology remains poorly understood. This study investigated whether alterations in gastric juice microbiota and bile acid (BA) profiles are associated with CAG under microbiota perturbation. A CAG rat model was designed by a multifactor modeling method, and an antibiotic cocktail (Abx) was administered to deplete gastrointestinal microbiota. Full-length 16S rRNA gene sequencing and LC-MS technology were conducted to characterize microbial composition and metabolite profiles in gastric juice. An integrated strategy combining microbiome and metabolome data was employed to validate associations between microbiota and metabolites. CAG rats exhibited elevated proinflammatory cytokines and lipopolysaccharide (LPS) levels in gastric juice, accompanied by dysbacteriosis and aberrant BA profiles. After antibiotic treatment, LPS level and bile salt hydrolase (BSH) activity were reduced, along with the lower abundances of LPS-producing bacteria and multiple BA levels. Correlation analysis demonstrated a positive association between deoxycholic acid (DCA) and LPS-producing bacteria (Escherichia coli). These findings revealed that gastric juice dysbacteriosis and abnormal BA metabolism were relevant to the inflammatory status of CAG. This study provided multi-omics evidence supporting a potential involvement of gastric juice microecological imbalance in CAG progression.},
}

@article {pmid41757733,
year = {2026},
author = {Rau, SR and Kalkuhl, A and van Esch, E and Hahn, C and Nolte, T and Hempel, K},
title = {NPY2R Agonist-Induced Gastric Effects Leading to Intestinal Dysbiosis and Secondary Intestinal Pathology in CD1 Mice.},
journal = {Toxicologic pathology},
volume = {54},
number = {2},
pages = {167-180},
doi = {10.1177/01926233251392878},
pmid = {41757733},
issn = {1533-1601},
abstract = {Obesity research has identified several drug targets, including the neuropeptide Y receptor 2 (NPY2R), which causes anorexigenic effects and delays gastric emptying. Test Peptide, an NPY2R agonist, was tested for toxicity in CD1 mice. Following unexpected mortality in a 4-week study, a 4-day study was conducted to determine the cause. The examination included clinical observations, pathology, and microbiome analysis of jejunal samples. Histopathologic lesions were primarily observed in animals showing clinical signs of toxicity ("responders"), including vacuolation of gastric parietal cells, inflammation, ulcers, and bacterial overgrowth in the small intestine. Occasionally, vacuolation of parietal cells was noted in clinically asymptomatic animals ("non-responders") terminated after 4 days, but not in nonresponders treated for 4 weeks. Microbiome analysis revealed in responders a significantly increased abundance of pathogenic bacteria like Shigella and a significant decrease in probiotic bacteria like Lactobacillus. The altered intestinal microflora resulted in overt dysbiosis, leading to intestinal inflammation, sepsis, and death. The intestinal microbiome appears to be an important factor determining differences in the interindividual susceptibility of mice to Test Peptide treatment. The human relevance of these murine findings is considered low, owing to substantial anatomical and physiological gastrointestinal differences, and the absence of comparable observations in nonhuman primates.},
}

@article {pmid41757159,
year = {2026},
author = {Zhang, L and Ding, Z and Yi, N},
title = {BCGLMs: Bayesian modeling for disease prediction using compositional microbiome features.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag041},
pmid = {41757159},
issn = {2635-0041},
abstract = {MOTIVATION: BCGLMs is a freely available R package that provides functions for setting up and fitting Bayesian compositional models for continuous, binary, ordinal and survival responses. It also includes models with random effects to capture sample-related accumulated small effects, improving prediction accuracy. The package includes tools for summarizing results from fitted models both numerically and graphically. Built on top of the widely used brms package, BCGLMs enable users to incorporate phylogenetic relationships between microbiome taxa into the modeling framework. Overall, BCGLMs package offers a flexible and powerful set of tools for analyzing compositional microbiome data.

The package is publicly available via GitHub https://github.com/Li-Zhang28/BCGLMs.},
}

@article {pmid41757098,
year = {2026},
author = {Duan, L and Baumgartner, WA and Wanyama, JW and Okyere, L and Alvarado, DA and Minhas, BF and Gaulke, CA},
title = {Sex-stratified Gut Microbiome Disruption is Associated with Altered Hepatic Gene Expression during Acute Azoxystrobin Exposure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.18.706612},
pmid = {41757098},
issn = {2692-8205},
abstract = {UNLABELLED: Azoxystrobin is a widely used fungicide that has been associated with to reproductive, neurological, and developmental defects. This chemical also disrupts gut microbial communities; however, if these perturbations contribute to the harms associated with exposure to azoxystrobin, this remains unclear. In this study, we investigated the effects of acute exposure to a series of concentrations (5-500 mg/kg) of azoxystrobin on the host and gut microbiota in zebrafish. Fecal amplicon and shotgun metagenomic sequencing was integrated with liver gene expression to quantify associations between microbiome disruption azoxystrobin toxicity in the host. Azoxystrobin exposure resulted in significant alteration in microbiome composition and functional potential in a dose- and sex-dependent manner. Microbial communities in exposed animals exhibited an increased abundance of xenobiotic metabolism pathways and decreased bacterial motility and lipopolysaccharide biosynthesis pathway metabolism. At the host level, histopathology identified increased biliary proliferation, most evident in medium- and high-dose fish. We also observed hepatic transcriptional changes consistent with a stress response, including altered redox-associated genes and reduced expression of lipid and small-molecule metabolic genes, with sex-stratified differences. Importantly, alterations in host transcriptional programming correlated with the compositional changes in exposed microbiota. Together, these results suggest concurrent impacts of azoxystrobin on gut microbiota and the liver implicate the microbiome as a potential contributor to changes in liver gene expression during exposure.

IMPORTANCE: Widespread fungicide use contaminates ecosystems worldwide, but the biological pathways underlying their effects on humans and other animals are not well understood. Using zebrafish (Danio rerio), we found that short-term exposure to the fungicide azoxystrobin was associated with changes in the gut microbiome, liver gene activity, and liver changes. Exposure produced dose- and sex-dependent shifts in microbial communities, including changes in predicted microbial functions involved in chemical metabolism, bacterial motility and defense. Compositional changes in the microbiome correlated with gene-expression changes consistent with stress and altered metabolism in exposed fish, suggesting that exposure induced disruption may contribute to exposure impact to the host. These results highlight a potential role for the microbiome in mediation of the impacts of azoxystrobin on host physiology. As such microbial based interventions could be a viable strategy to mitigate exposure impacts on health.},
}

@article {pmid41757095,
year = {2026},
author = {Wang, F and Holmes, AJ and Browne, GV and He, X and Bockmann, MR and Davis, KM and Hughes, TE and Adler, CJ},
title = {Ecological and evolutionary dynamics of the oral microbiome across childhood.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.13.705642},
pmid = {41757095},
issn = {2692-8205},
abstract = {Childhood represents a critical period for oral microbiome development, yet evolutionary trajectories and the relative roles of host and environment remain unclear. Using a large longitudinal metagenomic dataset of 920 samples from a twin cohort spanning the first decade of life, we characterised microbial shifts and population dynamics of key bacterial groups. Microbiome diversity was initially reduced and highly heterogeneous and became increasingly complex and convergent with age. Microbial community state was associated with developmental age, environment and in late childhood was surprisingly strongly associated with host genotype. Strain-level analyses revealed species-specific temporal patterns of genetic variation particularly within Streptococcus , reflecting adaptive responses to host and environmental pressures. Fusobacterium exhibited consistently high replication rates, indicating sustained growth dynamics. Phylogenetic reconstruction further revealed host and niche specific genomic diversification of Saccharibacteria lineages. These findings establish childhood as a decisive period of oral microbial evolution and highlight the role of host-microbiome and epithelial interactions in shaping community structure, providing guidance for oral management strategies that promote lifelong oral health.},
}

@article {pmid41757041,
year = {2026},
author = {Tschang, MA and Vuong, RD and Eilers, B and Chac, D and Waalkes, A and Penewit, K and Easton, A and Schuessler, B and Daniels, R and Weil, AA and Salipante, SJ and Gibbons, SM and Schindler, AG},
title = {If you give a mouse a poopsicle: a novel fecal microbiota transplant method for exploring the role of the gut microbiome in stress-related outcomes in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.16.705192},
pmid = {41757041},
issn = {2692-8205},
abstract = {The microbiome-gut-brain axis is a mediator of stress-related disorders. The number of preclinical studies exploring the potential causal mechanism of this connection using fecal microbiota transplantation (FMT) is growing. However, the most common method for delivering fecal transplants in rodent models is still oral gavage, which creates an adverse experience that may confound stress-related outcomes. Here, we establish an alternative methodology for FMT that decreases stress induced by traditional experimental procedures. We first used preference and anxiety behavior assays to identify antibiotic therapies having maximal tolerability and minimal anxiolytic properties. We then collected feces from donor mice and homogenized them with a microbe-stabilizing buffer to create a slurry, which was frozen into pellets ("poopsicles") for subsequent FMT. Recipient mice voluntarily consumed the pellets, and blood was collected to compare corticosterone levels relative to traditional gavage FMT. Plasma corticosterone levels were found to be significantly lower in mice receiving FMT via pellets compared to oral gavage. Furthermore, relative to gavage FMT, microbial signatures of mice receiving FMT via pellets were more similar to those of the donor pellets at one week following final FMT and were sustained for up to six weeks, as assessed by comparing Bray-Curtis beta-diversity distances. Together, these results establish effective antibiotic and FMT methods that minimize treatment-induced stress, while effectively transplanting fecal microbes between murine conspecifics.},
}

@article {pmid41757006,
year = {2026},
author = {Tran, HN and Kirven, KJ and Davenport, ER},
title = {SCiMS: Sex Calling in Metagenomic Sequences.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.17.705110},
pmid = {41757006},
issn = {2692-8205},
abstract = {BACKGROUND: Host sex is a critical determinant of microbial community structure, influenced by hormonal profiles, physiology, and sex-stratified behaviors. Despite its importance, sex metadata is frequently missing or mislabeled in microbiome studies. Existing genomic sex-calling tools often fail in low-host-biomass samples (e.g., stool) because they require high read depths to achieve reliability.

RESULTS: Here, we present SCiMS (Sex Calling in Metagenomic Sequences), a bioinformatic tool that leverages host-derived DNA within metagenomic datasets to accurately predict host sex, even at low host coverage. SCiMS uses sex-chromosome read density ratios within a Bayesian classifier to provide high-accuracy sex calls. In simulations, SCiMS achieves >85% accuracy with as few as 450 host reads. When applied to 1,339 samples from the Human Microbiome Project, SCiMS outperforms existing tools, showing higher accuracy and more balanced precision-recall tradeoffs across body sites. SCiMS also generalizes effectively to non-human hosts, achieving 100% accuracy in a murine dataset and outperforming alternatives in a chicken dataset with a ZW sex determination system.

CONCLUSIONS: SCiMS provides an accurate, scalable, and cross-species generalizable solution for host sex classification in metagenomic datasets, even when host DNA is minimal. By enabling the recovery of missing sex metadata, it serves as a quality-control tool for ensuring the integrity of analyses in microbiome research. SCiMS is freely available at http://github.com/davenport-lab/SCiMS .},
}

@article {pmid41756980,
year = {2026},
author = {Park, H and Shen, X and Perelman, D and Berry, P and Lu, Y and Battersby, R and Rose, SMS and Celli, A and Bejikian, C and Snyder, M},
title = {Insulin resistance modifies longitudinal multi-omics responses to habitual diet.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.17.706440},
pmid = {41756980},
issn = {2692-8205},
abstract = {How habitual diet influences the gut microbiome and plasma metabolome across insulin resistance states remains unclear. We conducted year-long multi-omics profiling of 71 deeply phenotyped adults, integrating repeated assessments of diet, metabolome, gut microbiome, clinical laboratory measures, and inflammatory markers. Using gold-standard insulin suppression tests and machine learning-derived dietary patterns, we examined how dietary patterns relate to metabolic and microbial landscapes by insulin resistance status. Insulin-sensitive individuals exhibited stronger and more numerous diet-omics associations than insulin-resistant individuals, identifying metabolic flexibility as a central determinant of dietary responsiveness. Parabacteroides emerged as a candidate microbial mediator between refined carbohydrate-rich dietary patterns and host metabolic signatures. Integrated into a cardiovascular risk prediction model, diet, metabolites, microbial taxa, and immune markers each contributed to 10-year atherosclerotic cardiovascular disease risk. These findings show that inter-individual variation in cardiometabolic risk partly reflects differences in molecular responsiveness to habitual diet, informing precision nutrition and cardiovascular prevention.},
}

@article {pmid41756930,
year = {2026},
author = {Yuan, L and Qin, Y and West-Roberts, J and Anantharaman, K and Wang, H and Zou, Y and Duan, Y and Camargo, AP and Koonin, EV and Chen, L},
title = {A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.21.707213},
pmid = {41756930},
issn = {2692-8205},
abstract = {Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.},
}

@article {pmid41748722,
year = {2026},
author = {Hanz, U and Mueller, B and Bart, MC and Busch, K and Reichart, GJ and Rapp, HT and de Goeij, JM and Mienis, F},
title = {Unveiling in situ oxygen, carbon and nutrient cycling of a sponge-driven biological hotspot in the arctic.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41748722},
issn = {2045-2322},
abstract = {UNLABELLED: Deep-sea sponge grounds are habitat-forming benthic communities characterized by high biomass and structural complexity. Despite their ecological significance, their role for the deep-sea environment remains poorly understood and their functioning is often inferred from ex situ studies. We hypothesized that deep-sea sponge grounds exhibit substantially higher respiration and nutrient turnover than surrounding soft sediments, making them hotspots of carbon and nutrient cycling in the deep sea. Integrated respiration and nutrient cycling were quantified in a sponge ground on the summit of an Arctic seamount (Schulz Bank, ~ 580 m depth). We used in-situ incubation chambers measuring oxygen consumption, prokaryotic cell removal, and inorganic nutrient fluxes. Respiration rates ranged from 0.13 to 0.93 mmol O2 m[-2] h[-1], which is comparable to cold-water coral reefs and up to 7–21 times higher than reported for soft sediments of the Arctic deep sea. This indicates a high organic carbon demand exceeding surface-derived supply, suggesting the uptake of additional food resources. All incubations showed net release of ammonium, phosphate, nitrite and nitrate, with fluxes correlating with sponge biomass. Our results demonstrate that deep-sea sponge grounds function as hotspots of carbon and nutrient cycling and suggest distinct functional contributions of sponge groups and their microbiome.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41798-4.},
}

@article {pmid41756883,
year = {2026},
author = {Wirbel, J and Saber, W and Martens, MJ and Peled, JU and Andermann, TM and Fei, T and Brooks, EF and Doyle, B and Pincus, NB and Jenq, RR and Bar, M and Bolaños-Meade, J and Bratrude, B and Chhabra, S and Choi, SW and Clark, W and Das, S and Elmariah, H and Gooptu, M and Holtan, SG and Jones, RJ and Levine, JE and Logan, BR and Al Malki, MM and Murthy, HS and Rashidi, A and Rezvani, AR and Riches, ML and Runaas, L and Sandhu, K and Spahn, A and Sung, AD and van den Brink, MRM and Horowitz, MM and Hamadani, M and Kean, LS and Perales, MA and Bhatt, AS},
title = {Differential effects of two common GVHD prophylaxis regimens on the gut microbiome: Results from the BMT CTN 1801 study.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.19.706769},
pmid = {41756883},
issn = {2692-8205},
abstract = {Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment for many hematological malignancies, but graft-versus-host disease (GVHD) is a common complication. Low gut microbiome diversity is associated with higher GVHD risk and shorter survival in multiple studies. Recently, the BMT CTN 1703 clinical trial demonstrated superiority of a GVHD-prophylaxis regimen including post-transplant cyclophosphamide (PTCy) compared to the standard prophylaxis (tacrolimus and methotrexate, Tac/MTX) in terms of GVHD-free, relapse-free survival at one year among reduced intensity conditioning allo-HCT recipients. However, the effect of PTCy on the gut microbiome and its association with clinical outcome have not been described. Here, we report on a companion randomized clinical controlled trial (BMT CTN 1801), which collected 2575 longitudinal stool samples from 304 study participants. Samples were obtained up to weekly up to day 84 post allo-HCT and at less frequent intervals thereafter, up to 2 years. Microbiome diversity and absolute microbial load were lower in the PTCy group compared to the Tac/MTX group on days 14-28 post-HCT. However, diversity at the timepoint closest to neutrophil engraftment was not significantly associated with non-relapse mortality after one year or other clinical outcomes, contrary to expectations from previous studies. Microbial domination events, when a single species exceeds 30% relative abundance, were comparable across treatment arms and reflected both pathogen blooms as well as less severe disruptions of the microbial community. Clostridium scindens and secondary bile acid metabolism pathways were less prevalent in the PTCy arm than in the Tac/MTX arm post-HCT, yet presence of secondary bile acid metabolism pathways was associated with a lower risk of chronic GVHD. Given that PTCy was associated with a greater disruption of the microbiome as measured by diversity, absolute microbial abundance, and bile acid metabolism capability, but better clinical outcomes overall, these data suggest that the importance of the microbiome in modulating the host immune systems after allo-HCT is specific to different types of GVHD prophylaxis.},
}

@article {pmid41756881,
year = {2026},
author = {Krieger, M and Kerns, KA and Palmer, EA and McLean, JS and Kreth, J and Yardimci, GG and Merritt, JL},
title = {Paired oral clinical specimens reveal the underlying ecology supporting the emergence of inflammophilic microbiome communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.20.706901},
pmid = {41756881},
issn = {2692-8205},
abstract = {BACKGROUND: Inflammatory oral diseases are associated with reproducible shifts from commensal-dominated microbiota toward pathobiont-enriched communities, yet the ecological mechanisms underlying the emergence of inflammophiles remain poorly understood. This study aims to investigate if host-derived inflammatory environments act as selective pressures that restructure microbial metabolism and community organization during disease progression.

METHODS: We performed 16S rRNA gene sequencing of patient-matched pediatric dental plaque and odontogenic abscess specimens to capture microbial community transitions across an inflammatory ecological gradient. Community ecology modeling and inferred metagenomic analyses were used to identify taxa and functional programs associated with commensal and inflammophilic states.

RESULTS: Patient-matched comparisons revealed a reproducible ecological selection gradient linking inflammatory environments to expansion of metabolically specialized inflammophiles and depletion of carbohydrate-utilizing commensals. Commensal-dominated plaque communities exhibited anabolic, carbohydrate-centered metabolic capacity, whereas abscess microbiota were enriched for catabolic metabolism, amino acid fermentation, and antimicrobial resistance, consistent with adaptation to inflammation-driven nutrient landscapes and immune pressure.

CONCLUSIONS: These findings support a model in which host inflammation drives ecological restructuring of the oral microbiome toward metabolically adapted inflammophilic communities. Defining the metabolic requirements and selective pressures governing these transitions provides a framework for microbiome-directed therapeutic strategies aimed at restoring ecological stability during inflammatory dysbiosis.},
}

@article {pmid41756820,
year = {2026},
author = {Trang, KT and Gulick, DA and Truell, J and Tian, J and Bodkhe, R and Hiseni, P and Gravdal, K and Kirubakaran, TG and Casén, C and Singh, R and Ziegler, TR and Reimer, RA and Kraft, CS},
title = {Diet-Microbiome Analysis in a Healthy Cohort Reveals Potential Role of Intestinal Microbiota in Metabolism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.17.706416},
pmid = {41756820},
issn = {2692-8205},
abstract = {UNLABELLED: Both preclinical and clinical studies have revealed the indisputable importance of intestinal bacterial community composition in pathogenesis of various disease states, from obesity to neurodegeneration. Diet remains one of the most important factors shaping human intestinal microbiota composition. In this study, we investigated diet-microbiome interactions in a healthy cohort of 88 participants from Atlanta and Calgary. We examine microbial composition (16S rRNA sequencing) with dietary records using Spearman Correlation tests with Benjamini-Hochberg multiple hypothesis correction to make community-level comparisons between dietary scores and microbial diversity index scores. Predictive models were used for molecular-level comparisons between microbial gene pathways and molecules. Among generalized dietary and microbial indices, we identified a negative association between dietary whole grain consumption and a microbial dysbiosis score. Comparisons between dietary food groups and bacterial family abundance reveal significant associations between dairy consumption and Lactobacillaceae abundance, dietary unsaturated to saturated fatty acid ratio and Clostridia Cluster Family XIII, salt intake and Lachnospiraceae , and consumption of 'greens and beans' and Veillonellaceae . Predictive models of microbial gene pathways and molecules reveal significant positive associations between several dietary fatty acids and microbial short-chain fatty acid fermentation pathways, and between dietary lignans and archaeal methanogenesis pathways. Overall, these associations may inform future explorations on specific dietary interventions to impact the gut microbiome.

IMPORTANCE: In this study, we compare dietary records and composition of intestinal microbes in a cohort of 88 participants. We identified associations between dietary consumption of dairy and the presence of dairy-consuming bacteria called Lactobacteriaceae and between consumption of dietary fats and the presence of fat-consuming bacteria called Clostridia . Using predictive analysis, we identify specific fatty acids associated with specific biochemical pathways found in Clostridia that might underlie these associations, in addition to an association between archaeal microbes and dietary consumption of estrogen-binding molecules called lignans, which are commonly found in whole grains and vegetables. Overall, our study generates useful associations between diet and intestinal microbes that can be tested in experiments that may help scientists use diet to control intestinal microbes in order to improve human health.},
}

@article {pmid41756623,
year = {2026},
author = {Szilagyi, A and Galiatsatos, P and Margolese, N},
title = {There may be a differential mechanistic impact on colorectal cancer of lactose-containing foods between lactase persistent and lactase non-persistent populations.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1671166},
pmid = {41756623},
issn = {2296-861X},
abstract = {It is generally suggested that milk and milk products reduce the risk of colorectal cancer (CRC). While there is some controversy over specific sites affected throughout the colon and the benefits of specific dairy foods (DFs), there is a general consensus that calcium intake is the main mechanism of the cancer-reducing effects. This opinion may be sidelined by several other mechanisms. There is also a potentially important compensatory mechanism in populations with adult genetic lactase deficiency. The microbiome changes occur through a process of adaptation to continued lactose consumption. The bacterial blooms consist largely of Bifidobacterial species. These bacteria may exert anti-neoplastic effects and also increase the capacity of persons with adapted lactase insufficiency to consume dairy products. Bacterial metabolism thus provides a second pathway for lactose digestion. Since the use of Mendelian randomization (MR) accuracy disallow two different pathways for the genetic variable, this process constitutes a horizontal pleiotropy. This narrative review using articles from PubMed and Google Scholar will discuss different nutrients and mechanisms in milk and milk products that are involved in anti-neoplastic effects. The impact of adult lactase deficiency and continued dairy consumption on the microbiome, and its contribution to colorectal cancer reduction, is highlighted. The conclusions from this review are that calcium has multifaceted mechanisms of anti-carcinogenesis, but other nutrients, such as conjugated linoleic acid (CLA), lactoferrin, and folate in the dairy matrix, could also contribute. In lactase non-persistent (LNP) populations adapted to dairy foods, a bifidogenic bloom in the microbiome may add additional anti-neoplastic effects and /or increase dairy food consumption. We argue that predictions of colon cancer effects from dairy foods may be inaccurate, and that evaluating both populations together may confound outcomes.},
}

@article {pmid41756428,
year = {2026},
author = {Li, J and Bu, E and Lian, A and Li, Y and Tao, C},
title = {Polarity-Aware Knowledge Graph Reveals Diet-Microbiome-Health Mechanisms with Relevance to Muscle, Immune and Metabolic Aging.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8771108/v1},
pmid = {41756428},
issn = {2693-5015},
abstract = {Diet profoundly influences gut microbial composition and metabolism, yet mechanistic pathways linking dietary exposures to human health remain fragmented across the literature. To systematically organize and integrate this evidence, we constructed an evidence-weighted Diet-Microbiome-Health Knowledge Graph (DMH-KG) from 1,309 curated PubMed abstracts (2023-2025), using a standardized schema spanning 11 entity categories and 12 relationship types with explicit polarity labels. Entities and relationships were identified through manual annotation, yielding 10,270 entity mentions and 4,866 relationships. Expert-guided consolidation of synonymous and lexically variant terms, along with pruning of disconnected concepts, resulted in 4,766 unique entities connected by 4,772 polarity-weighted edges. To prioritize robust biological signals, a composite edge-weighting function was applied, integrating both relationship frequency and polarity. Network analysis revealed a modular small-world structure centered on microbial and inflammatory mediators. High-confidence pathways emerged, including the probiotic-SCFA-immunity axis (34 supporting documents) and the high-fat diet-LPS-endotoxemia cascade (8 documents), both of which are central to age-related immune modulation and metabolic health. Quantitative validation against five KEGG and Reactome pathways demonstrated high biological fidelity: the DMH-KG recovered all reference diet-microbiome-outcome edges for Butanoate metabolism and Secondary Bile Acid biosynthesis (100% coverage) and achieved a mean pathway-level entity coverage of 92.0%, measured as the proportion of predefined pathway components represented in the graph. A comparative pilot study further demonstrated that DMH-KG augmentation improves mechanistic specificity inference across Diet-Microbiome-Health interactions. These features position the DMH-KG as a scalable platform for mechanistic inference across Diet-Microbiome-Health interactions, with direct relevance to immune regulation, muscle health, metabolic aging, and chronic disease prevention. The framework preserves evidence provenance, relationship polarity, and biological direction, supporting both discovery science and AI-driven nutritional reasoning.},
}

@article {pmid41756197,
year = {2026},
author = {Li, F and Anyaso-Samuel, S and Yano, Y and Chang, VC and Hua, X and Wan, Y and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Liao, LM and Huang, WY and Freedman, ND and Beane Freeman, LE and Sandler, DP and Abnet, CC and Sinha, R and Shi, J and Loftfield, E and Vogtmann, E},
title = {Association between diet quality and the oral microbiome in three US cohort studies.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2635238},
pmid = {41756197},
issn = {2000-2297},
abstract = {BACKGROUND: The oral microbiome has been associated with overall health, but the contribution of dietary habits to oral microbial composition is not well understood.

OBJECTIVE: We evaluated the association between diet quality (Healthy Eating Index [HEI] 2015) and the oral microbiome in the Agricultural Health Study, NIH-AARP Diet and Health Study, and Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial within 5,546 participants.

METHODS: Individual HEI components were scored from FFQ data and summed. Alpha and beta diversity and genus-level presence and relative abundance were estimated. The proportion of variability in the beta diversity matrices explained by diet quality and other covariates were calculated. Linear, logistic, and zero-inflated negative binomial regression models with adjustment for confounders were used and cohort-specific estimates were meta-analyzed.

RESULTS: Age explained the largest variability in beta diversity (Bray-Curtis), followed by smoking, education, and the HEI component for added sugar. Although overall diet quality was not associated with alpha diversity overall, the added sugar component was consistently inversely associated with alpha diversity. At the genus-level, most of the identified associations were with added sugar.

CONCLUSIONS: Consumption of added sugars was consistently associated with oral microbial diversity and specific genera.},
}

@article {pmid41756132,
year = {2026},
author = {Bamrung, V and Sitthicharoenchai, P},
title = {The evolving story of Streptococcus gallolyticus: classification, pathogenesis, role in human and animal disease, and laboratory diagnostics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1765252},
pmid = {41756132},
issn = {1664-302X},
abstract = {Streptococcus gallolyticus, formerly known as S. bovis, belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC). Besides being a part of the gut microbiome, this organism has gained interest due to its association with infective endocarditis and its strong correlation with colorectal cancer in humans. In veterinary medicine, systemic infection caused by S. gallolyticus has been reported in various animal populations, including porcine, ruminant, and avian species. Despite its clinical importance in humans and animals, two key challenges persist: the limited understanding of the pathogenesis due to its ubiquitous nature and inconsistencies in diagnostic laboratory reporting of the bacteria in SBSEC. This review summarizes the taxonomic characterization of the SBSEC, its clinical manifestations across species, current understanding of the bacterial pathogenesis, and the laboratory diagnostic assays used for its detection. We will further discuss the importance of SBSEC speciation and subspeciation, highlighting their distinct clinical implications and potential impact on human and animal health.},
}

@article {pmid41756131,
year = {2026},
author = {Liu, Z and Deng, W and Xu, W and Ye, L and Rao, Z},
title = {Probiotic supplementation modulates the gut microbiome and improves clinical outcomes in pediatric refractory asthma.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1756436},
pmid = {41756131},
issn = {1664-302X},
abstract = {BACKGROUND: Refractory asthma in children remains a clinical challenge despite conventional therapies, with emerging evidence linking gut microbiome dysbiosis to persistent inflammation via the gut-lung axis. This study investigated whether multi-strain probiotic supplementation could improve asthma control and restore microbial balance when added to standard treatment.

METHODS: This prospective randomized controlled trial enrolled 88 children aged 4-8 years with refractory asthma. Participants were allocated into two groups (n = 44 each): a conventional treatment group (bronchodilators and glucocorticoids) and a combination treatment group, which received conventional therapy plus a multi-strain probiotic (Bifidobacterium, Lactobacillus acidophilus, Streptococcus thermophilus) for 4 months. Primary outcomes were asthma control level, Asthma Control Test (ACT) scores, and pulmonary function (FEV₁, FVC, PEF). Secondary outcomes included gut microbiota changes, assessed by 16S rRNA gene sequencing.

RESULTS: Combination therapy achieved complete asthma control in 68.18% of patients versus 36.36% with conventional therapy (Z = 2.415, p < 0.05). Post-treatment ACT scores were higher in the combination group (22.45 ± 1.20 vs. 19.78 ± 1.45; p < 0.05), with superior improvements in FEV1 (2.65 ± 0.10 L vs. 2.30 ± 0.08 L; p < 0.001), FVC (3.10 ± 0.18 L vs. 2.80 ± 0.15 L; p < 0.001), and PEF (4.00 ± 0.25 L/s vs. 3.50 ± 0.20 L/s; p < 0.001). Symptoms resolved faster with combination therapy (e.g., cough: 5.60 ± 1.50 vs. 10.45 ± 2.30 days; p < 0.05). Microbiome analysis showed increased alpha diversity (e.g., Shannon index: p < 0.05) and beneficial shifts in the combination group, including higher Bifidobacterium (25.00 ± 15.31% vs. 0.98 ± 1.92%; p < 0.001) and reduced Bacteroides, with distinct beta diversity clustering (PERMANOVA p < 0.05).

CONCLUSION: Adjunctive multi-strain probiotics enhance clinical outcomes and gut microbiome health in pediatric refractory asthma, supporting microbiome-targeted therapies via the gut-lung axis. Larger, double-blind randomized controlled trials are warranted to confirm long-term benefits.},
}

@article {pmid41756119,
year = {2026},
author = {Cai, L and Sun, J and Li, H and Wang, C and Zhang, M and Shao, Q and Wang, Z},
title = {A novel internal reference microorganism-based method reveals wild-enriched Penicillium for enhancing growth and disease resistance in Fritillaria thunbergii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1746815},
pmid = {41756119},
issn = {1664-302X},
abstract = {INTRODUCTION: Fritillaria thunbergii Miq. is an important traditional Chinese medicinal herb, but bulb rot disease causes severe losses during its cultivation. Screening and reintroducing beneficial microorganisms from the wild rhizosphere is an effective strategy to increase disease resistance in cultivated plants. However, the absolute quantitative characteristics of microorganisms cannot be reflected by traditional methods based on relative abundance analysis due to compositional bias.

METHODS: In this study, we identified Clavatospora as a host-specific internal reference microorganism (IRM) and established an IRM-based relative abundance differential microorganism analysis (IRMRADMA) method.

RESULTS: Application of this method revealed that wild F. thunbergii possesses greater potential than cultivated plants for mining beneficial rhizosphere microorganisms. Specifically, Penicillium was identified as a key wild-enriched genus. Subsequently, two strains, Penicillium korosum and Penicillium aculeatum, were isolated from the rhizosphere of wild F. thunbergii. Functional tests confirmed that these strains demonstrated dual functions in disease suppression and plant growth promotion by solubilizing phosphate, producing siderophores, antagonizing pathogens, and upregulating defenserelated genes.

CONCLUSION: This study established the IRM-RADMA method and identified key Penicillium strains from the wild Fritillaria thunbergii rhizosphere. Their confirmed dual functions in growth promotion and disease suppression validate the 'plant microbiome rewilding' strategy, offering a new paradigm for the biological control of F. thunbergii diseases.},
}

@article {pmid41755783,
year = {2026},
author = {Kim, KS and Cho, JY and Park, YC and Hong, JH and Jung, JG and Sunwoo, J},
title = {Exploring LEPR-Linked Metabolic Diversity through Gut Microbiome-Metabolome Network Analysis in Non-Obese Adults.},
journal = {Biomolecules & therapeutics},
volume = {34},
number = {2},
pages = {448-460},
doi = {10.4062/biomolther.2025.161},
pmid = {41755783},
issn = {1976-9148},
abstract = {Genetic variation in the leptin receptor (LEPR) gene has been implicated in metabolic regulation, while the gut microbiome and circulating metabolites are increasingly recognized as mediators of host metabolic phenotype. However, the systems-level interactions among LEPR genotypes, gut microbial composition, and serum metabolomic profiles remain poorly understood, particularly in healthy individuals. We conducted a cross-sectional study involving 37 healthy Korean adults. Three LEPR single nucleotide polymorphisms (rs1137101, rs1173100, rs790419) were genotyped. Untargeted metabolomics of fasting serum was performed using gas chromatography-time-of-flight mass spectrometry, and gut microbiome composition was profiled by 16S rRNA gene sequencing. Statistical analysis included principal component analysis, Mann-Whitney U tests, and Spearman correlations. Network analysis integrating microbiome, metabolomic, and clinical phenotype data was conducted using Cytoscape. A total of 54 serum metabolites were identified. LEPR genotypes, particularly rs1137101 and rs1173100, were associated with differences in metabolites such as pimelic acid, malonic acid, and 2,4-dihydroxybutyric acid. Firmicutes negatively correlated with saturated fatty acids and organic acids, whereas Actinobacteria positively correlated with cholesterol and amino acids. Network analysis revealed indole-3-acetate and cholesterol as central nodes linking microbial taxa with body mass index and leptin levels. However, no direct molecular pathways connecting leptin or its receptor were identified. LEPR genetic variation is associated with distinct serum metabolomic patterns and microbiome-host networks in healthy adults. Although no direct leptin signaling links were found, network-level associations suggest indirect genetic influences on metabolic states through microbiome-metabolome interactions. These findings advance understanding of personalized metabolic regulation and gene-microbiome interplay.},
}

@article {pmid41755580,
year = {2026},
author = {Mendoza, ADG and Nuncio-Mora, L and Sánchez, V and Gonzalez, V and Nicolini, H},
title = {Dysbiosis in the Family nucleus of Children Diagnosed With Autism Spectrumin Mexico City.},
journal = {Actas espanolas de psiquiatria},
volume = {54},
number = {1},
pages = {121-127},
pmid = {41755580},
issn = {1578-2735},
abstract = {BACKGROUND: The relationship between the gut microbiome and Autism Spectrum Disorder (ASD) has been the subject of growing interest in scientific research. Research into the relationship between the gut microbiome and ASD has gained relevance in recent years as recent studies have identified significant differences in the gut microbiome abundance and composition in ASD children compared to neurotypical ones. However, little is known about the microbiome interplay, changes and relationship in parents and children with ASD, considering that they share a consistent environment. Charactering the microbiota of trio-type families with a child diagnosed with autism.

METHODS: The hypervariable region of the 16s ribosomal gene was sequenced from stool samples from adolescents with ASD and their parents. The analysis was performed using various software programs, including QIIME2 and DADA2.

RESULTS: In this paper, we discuss this relationship in three families, and observed that the gut microbiome of the offspring with ASD is more similar to the mother's than the father's microbiome.

CONCLUSIONS: These observations could lead to the understanding of the potential heritability of the disorder through parental connectedness of the gut microbiome and eventually to the development of interventions aimed at modulating the gut microbiota to improve symptoms associated with ASD.},
}

@article {pmid41755545,
year = {2026},
author = {Song, Z and Song, C and Yi, X and Shao, Y and Zhang, Y},
title = {Targeting the transferrin receptor in breast cancer: nanotechnology-based drug delivery strategies.},
journal = {Nanomedicine (London, England)},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/17435889.2026.2628237},
pmid = {41755545},
issn = {1748-6963},
abstract = {Breast cancer remains a leading cause of cancer-related morbidity and mortality worldwide, with treatment efficacy often limited by systemic toxicity, poor tumor selectivity, and multidrug resistance. Nanotechnology-based drug delivery systems offer a promising strategy to enhance therapeutic precision, particularly through active targeting of tumor-associated receptors. The transferrin receptor (TfR), which is frequently overexpressed in breast cancer cells, has emerged as an attractive target due to its role in receptor-mediated endocytosis. This review critically summarizes recent advances in transferrin-functionalized nanocarriers for breast cancer therapy, including liposomal, polymeric, dendrimeric, metallic, and hybrid platforms. Key design parameters influencing cellular uptake, biodistribution, and therapeutic efficacy - such as particle size, surface charge, ligand density, and release behavior - are discussed. We highlight progress in multifunctional and stimuli-responsive systems designed to overcome tumor microenvironment barriers and multidrug resistance. In addition, emerging evidence on the role of the gut microbiota in modulating breast cancer progression and treatment response is examined, with a focus on its potential impact on targeted nanomedicine efficacy. Finally, current translational challenges and future directions, including personalized and microbiome-informed nanotherapeutic strategies, are outlined. Literature was identified through systematic searches of PubMed, Web of Science, Scopus, and Google Scholar from January 2005 to March 2025.},
}

@article {pmid41755503,
year = {2026},
author = {Li, J and Will, I and Silva, LM and Travers-Cook, TJ and Blackwood, PE and King, KC},
title = {Integrating the Microbiome Into Infection Ecology and Evolution in Wild Animals.},
journal = {Molecular ecology},
volume = {35},
number = {5},
pages = {e70281},
pmid = {41755503},
issn = {1365-294X},
support = {//Canada Excellence Research Chairs, Government of Canada/ ; },
abstract = {Parasites are a ubiquitous force in nature threatening wildlife populations and ecosystems. Interactions between hosts and their parasites are impacted by host-associated microbiomes, which are essential for host development, physiology and immunity. We synthesise current understanding of the ecological interactions between host microbiomes and parasites, ranging from competitive to facilitative, and explore their potential evolutionary consequences for parasite virulence and transmission in the wild. We highlight recent mechanistic insights that support integrating a microbiome perspective into wildlife parasitology, with examples across diverse animal taxa including amphibians, bats, insects and corals, particularly within the context of climate change. Adopting such a holistic approach can open new avenues whereby host microbial shifts can be used to predict and mitigate infectious diseases in wild populations. Finally, we propose a conceptual framework to guide future research on microbiome-parasite-host interactions, aiming to better reflect natural ecological complexities and advance both fundamental understanding and conservation applications.},
}

@article {pmid41755380,
year = {2026},
author = {Lee, Y and Mustakim, KR and Eo, MY and Cho, YJ and Kim, SM},
title = {Peri-implantitis as a potential risk factor for peri-implant oral malignancy.},
journal = {Journal of the Korean Association of Oral and Maxillofacial Surgeons},
volume = {52},
number = {1},
pages = {27-33},
doi = {10.5125/jkaoms.2026.52.1.27},
pmid = {41755380},
issn = {2234-7550},
abstract = {Peri-implant oral malignancy (PIOM) refers to malignant tumors arising around dental implants and is an increasingly reported complication of implant therapy. PIOM may follow distinct pathophysiological mechanisms, including chronic peri-implant inflammation and implant-related factors that contribute to carcinogenesis. This current review aims to explore the potential role of peri-implantitis (PI) as a risk factor for PIOM, discussing the proposed pathogenic mechanisms, histological findings, and clinical implications. A comprehensive literature search was conducted in PubMed, Scopus, and Web of Science databases. Relevant case reports, clinical studies, and reviews on the keywords "PIOM" and "PI" published from 2019 up to 2025 were included and qualitatively analyzed. Clinicopathologic characteristics are summarized as location and morphology, disease progression, histopathology, and degree of differentiation, and pathophysiological hypotheses involve inflammatory and electrochemical pathways, epithelial barrier dysfunction, molecular alterations, microbiome dysbiosis, and immune dysregulation. Current evidence remains limited and primarily anecdotal. Several studies suggest that chronic inflammation, titanium particle exposure, corrosion byproducts, and sustained tissue damage in peri-implant tissues may contribute to oncogenesis. While a direct causal link between PI and PIOM remains unproven, chronic peri-implant inflammation may contribute to malignancy development in predisposed individuals. Clinicians should consider a biopsy when peri-implant lesions exhibit atypical features, promptly.},
}

@article {pmid41754858,
year = {2026},
author = {Bertin, L and Facchin, S and Barberio, B and Maniero, D and Lorenzon, G and Cesaroni, F and Zanconato, M and Romanelli, G and Francini-Pesenti, F and Busetto, L and Cananzi, M and Gaio, P and Bosa, L and Zingone, F and Gianolio, L and Damas, OM and Savarino, EV},
title = {Diet and Gut Microbiota in Inflammatory Bowel Disease: A Clinical and Nutritional Perspective.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {2},
pages = {},
pmid = {41754858},
issn = {1424-8247},
abstract = {Inflammatory bowel diseases, comprising Crohn's disease and ulcerative colitis, represent chronic inflammatory disorders with rising global incidence, underscoring the pivotal role of modifiable environmental factors in disease pathogenesis. Diet and intestinal microbiota have emerged as critical bidirectional therapeutic targets through complex interactions with host immune responses. Epidemiological evidence demonstrates that healthy and high fiber diets reduce disease risk, while ultra-processed foods and inflammatory dietary patterns increase susceptibility. Therapeutic nutritional interventions, including exclusive enteral nutrition, the Crohn's Disease Exclusion Diet combined with partial enteral nutrition, and the Mediterranean diet can induce and maintain clinical remission while promoting favorable microbiome modifications characterized by the enrichment of butyrate-producing taxa such as Faecalibacterium prausnitzii and Roseburia species, alongside a reduction in pathogenic Proteobacteria. Micronutrient deficiencies affect up to 78% of patients through malabsorption, chronic blood losses, dietary restrictions, and drug-nutrient interactions. Nutritional status significantly impacts surgical outcomes, with preoperative malnutrition and sarcopenia associated with increased postoperative complications, and it reciprocally influences biologic therapy response. Integration of personalized, microbiome-informed dietary strategies as complementary components of comprehensive treatment plans represents a promising therapeutic frontier, requiring multidisciplinary collaboration, rigorous clinical trials with standardized microbiome analyses, and precision nutrition algorithms accounting for disease phenotype, baseline microbial composition, and individual patient characteristics to optimize outcomes and improve quality of life.},
}

@article {pmid41754809,
year = {2026},
author = {Krakowska, A and Skiba-Kurek, I and Zontek-Wilkowska, J and Koczurkiewicz-Adamczyk, P and Muszyńska, B and Skalski, T},
title = {The Use of Biomass from In Vitro Fungal Cultures as a Bioactive Ingredient with Antimicrobial Activity in Hydrogel Dressings.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {2},
pages = {},
pmid = {41754809},
issn = {1424-8247},
support = {NCN 2024/08/X/NZ7/01059//National Science Centre/ ; },
abstract = {Background/Objectives: Chronic wounds represent a significant clinical burden and require multimodal treatment strategies targeting inflammation, infection, moisture balance, and tissue remodeling, as defined by the TIME framework. This study aimed to evaluate the therapeutic potential of innovative hydrogel dressings enriched with fungal biomass, designed to exploit natural bioactive compounds-such as antimicrobial peptides and proteolytic enzymes-to enhance wound healing while maintaining high biocompatibility. Methods: Hydrogel dressings incorporating selected fungal biomasses were fabricated and characterized for physicochemical and biological performance. Key material properties relevant to wound care, including hydrophilicity and porosity, were analyzed to assess exudate management capacity and maintenance of a moist wound environment. Antimicrobial activity was tested against common wound pathogens, and species-pathogen interactions were evaluated using generalized linear modeling. In vitro biocompatibility was assessed using human keratinocytes and compared with conventional silver nanoparticle-based dressings. Results: The developed hydrogels demonstrated properties suitable for clinical application, including superhydrophilicity and high porosity, supporting effective exudate control and moisture retention. Significant broad-spectrum antimicrobial activity was observed, particularly against Staphylococcus aureus and Pseudomonas aeruginosa, with effects dependent on fungal species. Statistical modeling revealed highly significant interactions between fungal species and pathogens in inhibition zones (p < 0.001). Hydrogels containing Pleurotus ostreatus and Agaricus bisporus showed broad activity against Escherichia coli, P. aeruginosa, and S. aureus, whereas Enterococcus faecalis exhibited resistance. Fungal biomass-based dressings displayed superior keratinocyte biocompatibility compared to silver nanoparticle controls. Conclusions: Fungal biomass-reinforced hydrogels offer a promising, safer, multifunctional alternative for infected chronic wound management, supporting both antimicrobial action and tissue regeneration.},
}

@article {pmid41754522,
year = {2026},
author = {Atkins, H and Stegman, N and Putonti, C},
title = {Diverse Temperate Coliphages of the Urinary Tract.},
journal = {Viruses},
volume = {18},
number = {2},
pages = {},
pmid = {41754522},
issn = {1999-4915},
support = {1R15AI171873-05/NH/NIH HHS/United States ; },
abstract = {While Escherichia coli can be found in the bladders of females without lower urinary tract symptoms, its presence is often associated with urinary tract infections (UTIs). The genomic plasticity of E. coli, including urogenital strains, is largely shaped by the integration of prophages. Although genomic and metagenomic analyses of urinary E. coli and the urinary microbiome suggest that prophages are abundant, many represent uncharacterized species. Sequence analysis suggests that these prophages represent temperate phages. This study aimed to fill this gap, isolating and characterizing temperate phages from urinary E. coli strains. We assessed phage host range across a panel of urinary isolates, providing a critical first step for future work investigating their putative role in shaping E. coli populations within the urinary community. In total, 20 temperate urinary phages were evaluated. Phage morphology and genic content of these phages were determined via transmission electron microscopy (TEM) and whole-genome sequencing, respectively. Together, these analyses provide insight into the diversity, infectivity, and genomic composition of temperate coliphages from the female urinary tract.},
}

@article {pmid41754473,
year = {2026},
author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A},
title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754473},
issn = {2076-0817},
abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.},
}

@article {pmid41754458,
year = {2026},
author = {Anderson, JG and Scarsella, E and Soltero-Rivera, M and Goldschmidt, S and Rojas, CA and Ganz, HH},
title = {First Description of Oral Microbiota in Domestic Cats Affected by Oral Squamous Cell Carcinoma.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754458},
issn = {2076-0817},
support = {annual grant 2022//Foundation for Veterinary Dentistry/ ; 5K12-CA138464//National Cancer Institute/National Institutes of Health/ ; UL1 TR001860/TR/NCATS NIH HHS/United States ; },
abstract = {Oral squamous cell carcinoma (OSCC) accounts for the majority of feline oral neoplasms and carries a poor prognosis; however, the oral microbiome in affected cats remains poorly characterized. This study aimed to preliminarily describe the oral bacterial communities of cats with OSCC and compare them with those of clinically healthy cats using DNA amplicon sequencing. Oral swabs were collected from cats with OSCC, including tumor surfaces, tumor cut surfaces, and clinically normal mucosa distant from the tumor (n = 20 total samples), and from the gingival margin of healthy cats (n = 12). DNA was extracted and full-length 16S rRNA gene sequencing was performed to assess microbial composition and diversity. Cats with OSCC exhibited significant alterations in oral microbiota compared with healthy controls, including reduced alpha diversity, distinct beta-diversity clustering, and consistent taxonomic shifts. Healthy cats displayed a relatively conserved core microbiome dominated by Porphyromonas spp., Bacteroides, Pasteurellaceae, Helcococcus, and Moraxella. In contrast, OSCC-associated samples showed increased relative abundances of anaerobic and disease-associated taxa, including Filifactor villosus, Bacteroides pyogenes, Odoribacter denticanis, Porphyromonas circumdentaria, and members of the Pasteurellaceae. These findings provide the first description of the oral microbiota associated with feline OSCC and demonstrate exploratory microbial differences between health and disease.},
}

@article {pmid41754428,
year = {2026},
author = {Ugwu, CE and Akinsulie, OC and Ayandokun, TF and Ajibade, FA and Shahzad, S and Aliyu, VA and Oladoye, MJ and Idris, I and Obasi, KO and Edeh, JK and Olojede, AA and Ukauwa, CB and Adeyemi, MI and Ugwu, CC and Ugorji, LC},
title = {Mechanisms and Therapeutic Potential of Nutritional Immunity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754428},
issn = {2076-0817},
abstract = {Nutritional immunity is a major facet of host defense, wherein the host immune system strategically limits pathogen access to critical nutrients, including iron, zinc, vitamins, lipids, and amino acids, to repress microbial proliferation and virulence. This review provides a comprehensive synthesis of the molecular mechanisms that power nutrient immunity, including metal homeostasis, nutrient competition, transporter modulation, hormonal regulation, and direct antimicrobial actions. We examine nutrient-specific strategies employed by the host, such as iron-withholding mechanisms, vitamin deprivation, and copper-mediated toxicity. We also explore how diverse pathogens, including extracellular, intracellular, and eukaryotic pathogens, adapt to these hostile nutritional landscapes through siderophore diversification, regulatory integration, and metabolic rewiring. Comparative genomic analyses reveal convergent evolution in nutrient acquisition systems, illuminating the dynamic arms race between host restriction and microbial evasion. We examine the immunological mechanisms that regulate nutritional immunity. Further, we discuss the translational potential of nutritional immunity, cutting across nutrient-based therapies, host-directed interventions, and emerging diagnostic biomarkers. Finally, we suggest future directions that synergize nutritional immunity with microbiome ecology, global malnutrition, and personalized medicine. By elucidating the interconnection between metabolism and immunity, this review highlights the therapeutic promise of starving or toxifying the pathogen to save the host.},
}

@article {pmid41754400,
year = {2026},
author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M},
title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754400},
issn = {2076-0817},
abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.},
}

@article {pmid41754336,
year = {2026},
author = {Haidri, I and Ullah, Q and Qasim, M and Amir, MA and Haider, W and Nguyen, HH and Promwee, A},
title = {Microbiome-Mediated Cd Stabilization in Chilli Pepper: Roles of Capsaicinoids and Cultivar Genetics Under Environmental Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
pmid = {41754336},
issn = {2223-7747},
support = {WU-CIA0 5205/2025//Walailak University under the international research collaboration scheme/ ; },
abstract = {Chilli pepper agroecosystems (Capsicum annuum L.) are increasingly threatened by cadmium (Cd) contamination, with emerging climatic stressors such as drought further exacerbating risks to food safety and crop productivity. This review synthesizes current evidence on microbiome-mediated Cd phytostabilisation in chilli pepper, with a particular focus on the roles of capsaicinoids and cultivar-specific genetic regulation in shaping rhizosphere microbial communities. Existing studies demonstrate that capsaicinoid-rich cultivars selectively recruit specialized rhizosphere microbes, enhancing root-level Cd sequestration and achieving Cd retention efficiencies of approximately 40-55%, thereby substantially restricting Cd translocation to edible fruit tissues. Multi-strain plant growth-promoting rhizobacteria (PGPR) consortia, especially when combined with structured organic amendments, have been reported to reduce fruit Cd and nickel (Ni) accumulation by more than 87% in contaminated soils. These responses are regulated by pungency-associated genetic loci, including Pun1 (pungency locus 1) and Pun4 (pungency locus 4) genes, which influence secondary metabolism and microbial assembly under metal stress conditions. The review highlights key knowledge gaps regarding the long-term stability of engineered rhizobiomes, the in situ dynamics of the Capsicum volatilome as a microbial recruitment signal, and the interactive effects of Cd contamination and drought in field environments. Overall, this synthesis provides a mechanistic framework for deploying high-pungency cultivars and microbiome-based strategies to improve Cd phytostabilisation, with important implications for sustainable chilli production in drought-prone, metal-contaminated agroecosystems.},
}

@article {pmid41754214,
year = {2026},
author = {Churin, AA and Sokolyanskaya, LO and Lukina, AP and Karnachuk, OV},
title = {Current Concepts in Probiotic Safety and Efficacy.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040696},
pmid = {41754214},
issn = {2072-6643},
support = {25-24-00493//Russian Science Foundation/ ; },
abstract = {Background/Objectives: Advances in molecular biology, genetics, and microbiome research have significantly expanded our understanding of probiotic microorganisms and their interactions with human health, stimulating the development of both traditional and next-generation probiotic products. Although probiotics are widely used and generally considered safe for healthy individuals, accumulating evidence indicates that their safety profile varies significantly depending on the strain, dose, host, and context, with rare but clinically significant adverse events reported in vulnerable populations. Methods: This review summarizes current knowledge on the efficacy and safety of probiotics, analyzes limitations in clinical safety reporting, and compares regulatory frameworks governing the use of probiotics as dietary supplements, medicinal products, and live biotherapeutics. Particular attention is given to new genomic and computational approaches to safety assessment. Conclusions: Overall, the review emphasizes the need for coordinated regulation, rigorous clinical evidence, and integrated, modern safety assessment strategies to support the responsible expansion of probiotic use.},
}

@article {pmid41754202,
year = {2026},
author = {Reytor-González, C and Sarno, G and Montalvan, M and Verde, L and Annunziata, G and Barrea, L and Muscogiuri, G and Simancas-Racines, D},
title = {Obesity, Bariatric Surgery, and Cancer Risk: Nutritional Perspectives and Long-Term Clinical Implications.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040685},
pmid = {41754202},
issn = {2072-6643},
abstract = {Obesity is recognized as a causal risk factor for the development of multiple cancers, with risk magnitude varying by tumor site, sex, life stage, and adipose tissue distribution. This narrative review synthesizes recent epidemiological evidence linking excess body fatness with cancer incidence and mortality and integrates the biological mechanisms that explain this association. Chronic low-grade inflammation, insulin resistance with compensatory hyperinsulinemia, dysregulation of adipose-derived hormones and sex steroids, impairment of anti-tumor immune responses, alterations in the gut microbiota, and remodeling of the tumor microenvironment collectively create conditions that favor tumor initiation and progression. Bariatric surgery is the most effective clinical intervention for achieving substantial and sustained weight loss in individuals with severe obesity, and growing evidence indicates that it is associated with a reduction in overall cancer risk and cancer-related mortality, particularly for malignancies strongly linked to obesity. However, the extent of this benefit differs by surgical technique and remains less consistent for colorectal cancer. Beyond metabolic improvements, bariatric surgery produces long-term changes in nutritional physiology that may also influence oncologic outcomes. Persistent deficiencies of micronutrients such as iron, folate, vitamin B12, vitamin D, and calcium can affect DNA synthesis, methylation, oxidative balance, and cellular repair. Altered protein and energy intake may contribute to loss of lean mass and reduced metabolic resilience, while changes in alcohol absorption and metabolism can increase systemic exposure to ethanol and its carcinogenic metabolites. In addition, bariatric surgery induces sustained remodeling of the gut microbiome and bile acid metabolism, which may further modulate tumorigenic signaling. Overall, the oncological impact of bariatric surgery reflects a balance between metabolic improvement and long-term nutritional management, underscoring the need for structured follow-up and targeted nutritional strategies to optimize cancer risk reduction.},
}

@article {pmid41754199,
year = {2026},
author = {Arabi, T and Akbar, A and Yaqinuddin, A and Khan, MI and Arora, I},
title = {Cross-Cultural Nutritional Epigenomics: Diet and Microbiome Interactions Shaping Type 2 Diabetes in Arab and Western Populations.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040681},
pmid = {41754199},
issn = {2072-6643},
abstract = {In the Middle East and North Africa (MENA) region, the prevalence of Type 2 Diabetes (T2D) is 17-18%, substantially higher than the ~9-10% reported in Western populations, with some Gulf states approaching 25% in adults. Historically, Arab diets, characterized by high fiber intake from whole grains, legumes, and fermented dairy products, have contrasted markedly with the Western dietary pattern increasingly prevalent among urbanized Arab populations. These nutritional shifts have been associated with changes in gut microbial composition, including lower representation of short-chain fatty acid-producing bacteria and higher abundance of dysbiosis-associated taxa. Concurrently, diet-derived compounds and microbial metabolites have been associated with changes in DNA methylation, histone modifications, and non-coding RNA expression. Epigenome-wide association studies revealed both shared and population-specific methylation signatures in patients with T2D. However, integrated multi-omics studies remain limited in Arab populations, where the disease burden is highest. This review integrates emerging evidence on diet-linked epigenetic alterations, microbiome-associated metabolic pathways, and their intersection in potentially contributing to T2D risk and progression. Given the heterogeneity of T2D across populations, there is a pressing need for culturally contextualized precision medicine frameworks that integrate population-specific diet-microbiome-epigenome dynamics rather than extrapolating findings across populations. Additionally, this review synthesizes evidence that dietary patterns are associated with T2D-relevant pathways through the diet-microbiome-epigenome axis, with emphasis on Arab/MENA populations and Western comparator cohorts.},
}

@article {pmid41754197,
year = {2026},
author = {Zhu, A and Bonja Geleto, F and Mohammed Ali, M and Ashenafi, H and Erko, B and Taye, B},
title = {Household Food Insecurity Alters Gut Microbiome Composition and Enriches Sutterella in Ethiopian Schoolchildren.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040680},
pmid = {41754197},
issn = {2072-6643},
support = {Picker ISI//Colgate University/ ; },
abstract = {Background: Household food insecurity (HFI) adversely affects child development by restricting caloric intake, dietary diversity, and food quality. Since diet is a key factor influencing the gut microbiome, HFI may negatively impact health by altering microbial communities. However, direct evidence linking HFI to changes in the gut microbiome is limited. Therefore, we investigated the effects of HFI as a composite variable and used individual HFI assessment questions as specific proxies for dietary deprivation on the gut microbiome in a group of Ethiopian schoolchildren. Methods: Fecal samples were collected from 57 school-aged children in Ethiopia, and microbial profiles were established using 16S rRNA amplicon paired-end sequencing. Food insecurity was assessed using the Household Food Insecurity Access Scale (HFIAS). Results: We observed no significant differences in alpha diversity across food security status (Wilcoxon p > 0.05). However, beta diversity analysis revealed a significant shift in microbiome composition between food-secure and food-insecure individuals (Bray-Curtis dissimilarity; PERMANOVA, p < 0.05). Further analyses of individual HFIAS questions as specific proxies for dietary deprivation showed that limited dietary variety, consumption of disliked foods, and reduced meal size were each associated with significant changes in microbial compositions (PERMANOVA; all q < 0.05). Differential abundance analyses consistently identified Sutterella as significantly more abundant among food-insecure participants (composite model q = 0.11; component-specific models q < 0.05). Additionally, a microbial feature-based machine learning model accurately predicted food security status (AUC = 0.81), with Sutterella emerging as the top predictive feature. Conclusions: Our findings suggest that food insecurity metrics are associated with alterations in gut microbial composition. The consistent enrichment of Sutterella in food-insecure children in this study suggests the need for future mechanistic studies to explore its role in mediating the effects of food insecurity.},
}

@article {pmid41754196,
year = {2026},
author = {Qiu, Y and Laguna, JC and Alegret, M and Vilà, L},
title = {A Global Perspective on Metabolic Dysfunction-Associated Steatotic Liver Disease: From Molecular Mechanisms to Therapeutic Strategy Innovation.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040679},
pmid = {41754196},
issn = {2072-6643},
support = {PID2023-146140OB-I00//MICIU/AEI/10.13039/501100011033 and FEDER, UE/ ; 2021SGR-00345//Generalitat de Catalunya/ ; 202406910009//China Scholarship Council/ ; },
abstract = {Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is a prevalent global health issue driven by metabolic syndrome, with cardiovascular disease being the leading cause of mortality. This review synthesizes current knowledge on its multifactorial pathogenesis, the impact of sexual dimorphism, and key experimental models. The progression of MASLD involves interconnected pathways including dysregulated de novo lipogenesis, insulin resistance, mitochondrial dysfunction, gut dysbiosis, ferroptosis, and genetic and epigenetic predispositions. These mechanisms not only promote hepatic injury but also accelerate atherosclerosis. Notably, MASLD exhibits significant sexual dimorphism, influenced by physiological differences, sex hormones, genetic factors, and the microbiome. The study of these complex processes relies mostly on dietary-induced animal models, particularly in rats, which effectively recapitulate features of the human disease. Given the multifaceted nature of MASLD, the therapeutic focus is shifting from monotherapies to combination or dual-target strategies. To enable this transition, refinement of preclinical models is essential to better understand and target this complex disorder.},
}

@article {pmid41754185,
year = {2026},
author = {Alessa, H and Quinn, ME and Alhomidan, L and Ross, C and Kainadas, S and Brownson, E and MacDonald, J and Seenan, JP and Nichols, B and Koutsos, A and Gerasimidis, K},
title = {In Vitro Effects of Twelve Food Additives on Gut Microbiome and Its Fibre Fermentation Capacity in Adults with Crohn's Disease in Remission and Healthy Controls.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040668},
pmid = {41754185},
issn = {2072-6643},
support = {N/A//The Ministry of Education in Saudi Arabia, and Imam Abdulrahman Bin Faisal University in Dammam, Saudi Arabia, funded Hanoof Alessa's PhD/ ; },
abstract = {Background/Objectives: Animal studies have shown that food additives may adversely affect the gut microbiome. However, the effect of food additives on the microbiome in adults with Crohn's disease (CD) remains less explored. This study investigated the impact of food additives on gut microbiome and fibre fermentation capacity in adults with CD and healthy controls (HCs) using in vitro faecal fermentations. Methods: Faeces from 6 HCs and 6 patients with CD in clinical remission (Harvey Bradshaw Index < 5) were used for in vitro fermentation of a fibre mix with one of 12 food additives (calcium propionate, carboxymethylcellulose, carrageenan kappa, cinnamaldehyde, maltodextrin, polysorbate-80, potassium sorbate, sodium benzoate, sodium sulphite, titanium dioxide, turmeric, and xanthan gum). Short-chain fatty acids (SCFAs) were measured using gas chromatography, the microbiome was profiled with 16S rRNA amplicon sequencing and total bacterial load was measured with qPCR. Results: Maltodextrin increased acetate production in both groups. In HCs, turmeric increased acetate and butyrate production, sodium sulphite reduced acetate production, and maltodextrin reduced butyrate production. Microbiome Shannon α-diversity increased with titanium dioxide (both groups), and with carrageenan kappa only in patients with CD. In both groups, the addition of maltodextrin and polysorbate-80 induced significant shifts in microbiome structure (β-diversity). Significant shifts were seen with maltodextrin (HC: R[2] = 6.8%, p = 0.001; CD: R[2] = 5.1%, p = 0.004) and sodium sulphite (HC: R[2] = 6.9%, p = 0.001). Maltodextrin significantly decreased the estimated absolute abundance of Escherichia-Shigella in patients CD; sodium benzoate, potassium sorbate, and calcium propionate did so in HCs. Faecalibacterium decreased in the presence of polysorbate-80 in the HC and CD groups, as well as in the presence of maltodextrin in the CD group. Total bacterial load decreased with polysorbate-80, potassium sorbate, maltodextrin and calcium propionate in both groups. Xanthan gum decreased total bacterial load in HCs. Conclusion: Certain food additives significantly affected fibre fermentation capacity and microbiome structure, with only modest differences observed according to participants' health status.},
}

@article {pmid41754156,
year = {2026},
author = {Carvalho, PA and Paciência, I and Moreira, A and de Castro Mendes, F},
title = {Air Pollution, Asthma and Diet: From Mechanisms to Prevention Strategies.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040639},
pmid = {41754156},
issn = {2072-6643},
abstract = {BACKGROUND/OBJECTIVES: Air pollution is a major environmental determinant of asthma morbidity and lung function impairment across the life course. Both outdoor and indoor exposures contribute to asthma development and exacerbations, impaired lung function growth, and accelerated decline, with heightened susceptibility during pregnancy and childhood. In this narrative review, we aimed to: (i) synthesize evidence on outdoor and indoor air pollution in asthma and lung function decline; (ii) describe key modulators of pollution-related risk; (iii) evaluate diet and supplementation as effect modifiers; and (iv) outline strategies and recommendations to mitigate pollution-related asthma burden.

METHODS: A narrative synthesis was conducted based on a comprehensive PubMed literature search through 2025, integrating evidence from observational and interventional studies evaluating habitual diet and nutritional supplementation as potential modifiers of the respiratory effects of indoor and outdoor air pollution.

RESULTS: We synthesized human observational and interventional studies associating outdoor and indoor air pollution with asthma and lung function outcomes, highlighted major susceptibility modulators and mechanistic pathways, and appraised emerging evidence that habitual diet and nutritional supplementation might modify pollutant-related respiratory effects. Mechanistic evidence supported dietary modulation through redox buffering, epithelial-immune pathways, lipid-mediated inflammatory balance, and microbiome-immune crosstalk. However, human evidence remained heterogeneous across pollutants, settings, dietary metrics, and endpoints.

CONCLUSIONS: Emissions reduction at source remained the cornerstone of prevention. Effective mitigation should be multi-level and equity-focused, combining structural air-quality improvements with pollution-aware asthma care and feasible household practices. Diet should be framed as a supportive, food-first resilience strategy, improving overall diet quality, fat quality, and fiber intake rather than a substitute for emissions reduction or guideline-based asthma management.},
}

@article {pmid41754155,
year = {2026},
author = {He, J and Shan, L and Yu, L and Yu, L and Jiang, X and Shen, Y and Du, Z and Yu, R and Zhao, C and Du, X and Wang, H and Yang, R and Fang, C},
title = {Structural Insights and Metabolic Profiles of Oxidized Green Coffee Extract, and Its Impact on Obesity and Gut Microbiota in High-Fat Diet-Fed Mice.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040638},
pmid = {41754155},
issn = {2072-6643},
support = {Yunnan Internstion Joint Laboratory of Green Health Food (China & Thailand) (202203AP140011)//Chongye Fang/ ; },
abstract = {Background: Obesity is a severe chronic disease impacting health, closely linked to intestinal microbiota. Gut microbiome significantly contributes to obesity and metabolic issues. This study aims to explore the structural characterization of two coffee extracts and their effects on gut microbiota disturbances caused by a high-fat diet (HFD). Methods: Male C57BL/6J mice were divided into four groups-normal diet (ND), high-fat diet (HFD), HFD supplemented with unroasted coffee extract (UC), and HFD supplemented with oxidized green coffee extract (GCE). Results: Structural characterization revealed that both extracts are polymeric phenolic compounds rich in hydroxyl and carboxyl groups. Full-target metabolomic analysis revealed significant metabolic differences between the extracts, with 499 differential metabolites identified: a total of 247 metabolites were upregulated and 252 were downregulated in GCE compared to UC. Supplementation with GCE reduced body weight gain and adipose tissue accumulation, improved dyslipidemia and insulin sensitivity, and enhanced hepatic antioxidant capacity in high-fat model mice. Gut microbial analysis showed that GCE significantly (p < 0.05) increased the growth of beneficial bacteria such as Prevotella, Butyricimonas, and Parabacteroides. Conclusions: Oxidized green coffee extract has the effect of lowering lipids and increasing intestinal beneficial bacteria.},
}

@article {pmid41754142,
year = {2026},
author = {Moitra, P and Madan, J and Shah, K and Mandavkar, P and Joshi, R and Kalita, S and Udipi, SA},
title = {Almond Supplementation Improves Acne Lesions and Skin Microbial Diversity in Adults with Mild to Moderate Acne Vulgaris.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040625},
pmid = {41754142},
issn = {2072-6643},
support = {SH-22-Udipi-NR-01//Almond Board of California/ ; },
abstract = {OBJECTIVES: This randomized, controlled, parallel-group study was conducted to evaluate the effectiveness of daily almond consumption on acne lesion counts, skin hydration, sebum production, and skin microflora composition in 18-35-year-old young adults with acne vulgaris in Mumbai, India.

METHODS: A defined amount of whole, unsalted almonds with skin (60 g) was provided to the experimental group (n = 36). The control group (n = 38) received isocaloric cereal-pulse-based snack varieties. The primary endpoints were changes in inflammatory, non-inflammatory, and total acne lesion counts after 20 weeks of supplementation. Secondary endpoints included changes in facial sebum, hydration levels, skin morphology and microflora, and selected biochemical parameters.

RESULTS: At week 20, the almond group showed greater reductions in total lesion counts (-22.2% vs. -9.8%), inflammatory lesion counts (-8.3% vs. +12%), and non-inflammatory lesion counts (-26.1% vs. -20.4%) than controls. Objective lesion volume, area, and height measures for both single and clustered acne decreased in the almond group (p ≤ 0.001). Microbial diversity increased, with the Shannon index (2.6 to 3.4 (p = 0.039) and the Chao1 richness index (266.9 → 835.2; p < 0.001) showing improvements at endline. Moreover, significant post-intervention changes in the psychosocial outcomes, such as the acne-related quality of life scores (p < 0.001) and anxiety symptoms (p = 0.016), were observed in the almond group.

CONCLUSIONS: Daily almond consumption reduced acne lesion count and improved skin microbial diversity and acne-specific quality of life, highlighting its potential to complement standard acne treatments and support skin health.},
}

@article {pmid41754141,
year = {2026},
author = {Kou, R and Pan, C and Xing, X and Wang, J and Morrin, ST and Buck, RH and Li, X and Mao, Y and Wang, S},
title = {Long-Term Associations of Early-Life Human Milk Oligosaccharide Intake with Allergic Disease Development and Gut Microbiota Profiles in 5-Year-Old Children.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040624},
pmid = {41754141},
issn = {2072-6643},
abstract = {Background: Based on our extensive cohort study, the Maternal Nutrition and Infant Investigation (MUAI), this research investigated the associations between human milk oligosaccharide (HMO) intake during the postnatal period and allergic disease development and gut microbiome composition in early childhood through long-term follow-up. Methods: Human breast milk (HBM) samples at five lactation stages and fecal samples of infants and young children were collected. Children aged 5 years included in this study were categorized into allergic and non-allergic groups via standardized allergen testing. Results: The findings indicated that higher HMO intake levels across five distinct lactation periods may be linked to a reduced incidence of allergies in children. The consumption of six major structurally representative HMOs was significantly associated with alterations in the gut microbiota profiles of young children. Moreover, there were notable differences in gut microbiota composition between allergic and non-allergic children. Specifically, beneficial bacteria such as Bifidobacterium, Akkermansia, and Ruminococcus were significantly enriched, in addition to the levels of metabolite propionic acid, a beneficial short-chain fatty acid, which were notably higher in the non-allergic group. To further validate the relationship between Bifidobacterium abundance and early HMO intake, the analysis revealed that a differential strain biomarker, Bifidobacterium adolescentis (B. adolescentis), exhibited significant correlations with specific HMOs at different lactation stages, particularly showing a strong positive correlation with 2'-fucosyllactose (2'-FL) content. Conclusions: These findings suggest that early-life HMO intake is associated with long-term differences in allergic outcomes, potentially through modulation of gut microbiota composition, particularly the enrichment of B. adolescentis.},
}

@article {pmid41754137,
year = {2026},
author = {Guo, Y and Wang, Q and Guo, H and Zhang, H and Wu, L and Li, X and Bian, X and Li, J and Ma, R},
title = {From Microbiota to Defense: The Preventive Effect and Mechanism of Total Flavonoids from Sea Buckthorn Leaves in DSS-Induced Colitis.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040620},
pmid = {41754137},
issn = {2072-6643},
support = {zyytd2024038//the Shanxi Health Committee/ ; 202203021221259//the Natural Science Foundation of Shanxi Province/ ; },
abstract = {OBJECTIVES: The main purpose of this study was to evaluate the potential preventive effect of Total Flavonoids from Sea Buckthorn Leaves (Fla) on dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) in mice from an integrated perspective of "gut microbiota-host interaction," and to elucidate its regulatory mechanism within the microbiota-metabolite-barrier-immune axis.

METHODS: A DSS-induced UC mouse model was established, and mice were randomly assigned into normal control, model, mesalazine, and Fla low, middle, and high-dose groups. Disease severity, colonic barrier integrity, inflammatory cytokines, gut microbiota composition, and short-chain fatty acid levels were evaluated using histopathological, molecular biological, and metabolomic analyses.

RESULT: Fla significantly ameliorated colonic damage and other pathological symptoms. It enhanced intestinal barrier integrity by upregulating ZO-1, E-cadherin, and MUC2 expression and suppressed inflammation by reducing TNF-α and IL-6 levels. Furthermore, Fla reshaped gut microbiota, increasing beneficial Akkermansia abundance, and elevated short-chain fatty acid (SCFA) production, with the most pronounced effects observed at the middle dose.

CONCLUSIONS: In summary, in this preventive model, Fla synergistically enhances intestinal barrier function and suppresses excessive local inflammatory responses by reshaping the gut microbiota and promoting SCFA production, ultimately alleviating UC. This study provides scientific evidence for the high-value utilization of sea buckthorn leaves (a by-product) and offers new insights for developing microbiome-based preventive strategies for UC.},
}

@article {pmid41754113,
year = {2026},
author = {Kang, S and Sim, H and O'Keeffe, S and Park, JO and Seo, W and Koh, JS and Lee, MW and Song, IC and Lee, HJ and Jo, DY and Kang, YE and Yi, HS and Ryu, H},
title = {Stage-Dependent Metabolic Responses to Oral Nutritional Supplementation in Cancer Cachexia: A Single-Arm Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040597},
pmid = {41754113},
issn = {2072-6643},
abstract = {BACKGROUND/OBJECTIVES: Cancer cachexia is a multifactorial syndrome characterized by involuntary weight loss and muscle wasting, leading to impaired quality of life and poor clinical outcomes. Although oral nutritional supplements (ONS) are recommended to support inadequate oral intake during chemotherapy, their effects on underlying metabolic alterations and gut microbiome composition, particularly across different stages of cachexia remain unclear. This single-arm pilot study aimed to evaluate the feasibility and metabolic effects of an 8-week ONS intervention in patients with cancer cachexia undergoing chemotherapy.

METHODS: This study was conducted at the Chungnam National University Hospital, Daejeon, Republic of Korea between January 2023 and October 2023. The primary endpoints were feasibility outcomes, including adherence, tolerability, attrition rate, and ONS-related adverse events. Secondary outcomes included body composition, physical performance, biochemical markers, quality of life, plasma GDF-15 levels, serum metabolomics, and gut microbiome composition. Assessment of secondary outcomes and multi-omics profiling was performed at baseline and after 8 weeks. Patients were stratified into severe and non-severe cachexia groups and analyzed.

RESULTS: A total of 10 patients (median age 65 years, range 42-76) participated. Primary cancer types included cholangiocarcinoma (n = 4), colorectal (n = 4), and gallbladder cancer (n = 2). Adherence was 82%, with excellent tolerability and no ONS-related adverse events. Body composition, quality of life, and gut microbiome showed no significant changes. Hand-grip strength and walking-speed were slightly improved after 8 weeks intervention (p = 0.014 for hand-grip strength; p = 0.021 for walking-speed, Wilcoxon signed-rank test) in overall cohort. Metabolomics identified 10 metabolites, predominantly fatty acids, with significant between-group differential responses (p < 0.05, Mann-Whitney U test). Non-severe cachexia patients showed reductions in circulating fatty acids following ONS, consistent with attenuated lipolysis and reduced endogenous fat mobilization, whereas severe cachexia patients demonstrated increases, suggesting limited metabolic responsiveness to nutritional intervention. Fatty acid metabolism emerged as the predominant discriminatory pathway.

CONCLUSIONS: This study showed the feasibility of integrating ONS with multi-omics profiling. Our findings suggest that metabolic alterations might precede clinically detectable changes, potentially providing a rationale for early intervention. Specifically, certain fatty acids were identified as candidate biomarkers that warrant further validation in larger cohorts.},
}

@article {pmid41754110,
year = {2026},
author = {Singh, N and Hosein, E and Virkud, YV and Keet, C and Kulis, M},
title = {The Gut Microbiome in the IgE-Mediated Food-Allergic Patient-A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040593},
pmid = {41754110},
issn = {2072-6643},
abstract = {Food allergies (FA) are a major public health concern in both children and adults. Immunoglobulin E (IgE)-mediated FA is characterized by allergic reactions driven by allergen-specific IgE and the subsequent degranulation of mast cells and basophils. Current FA management primarily involves avoidance of allergen-containing food, and more recently, therapies such as oral immunotherapy (OIT), sublingual immunotherapy (SLIT), and the anti-IgE biologic omalizumab. However, these interventions are not curative. The gut microbiome has been implicated in the development and regulation of oral tolerance to food antigens. This narrative review explores the role of probiotics, fecal microbiota transplantation (FMT), dietary interventions, and the interaction between the microbiome and OIT as potential strategies to manage established FA. We also explore barriers to their proliferation as part of regular clinical care. We conclude that future research should (1) address how the microbiome interacts with immunotherapies other than OIT, (2) explore the role of novel microbiome-based treatments like FMT as potential adjuvants to existing food allergy therapeutics, and (3) focus on developing standardized protocols and endpoints for microbiome-based therapeutics.},
}

@article {pmid41754097,
year = {2026},
author = {Hansen, B and Alvanou, E and Pavlou, MAS and Wilmes, P and Schneider, JG},
title = {Fasting and Nutrition as Promising Treatment Strategies for Women with Rheumatoid Arthritis in Transitional Hormonal Stages.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040580},
pmid = {41754097},
issn = {2072-6643},
support = {PRIDE/11823097//Luxembourg National Research Fund/ ; },
abstract = {Rheumatoid arthritis (RA) is a systemic and chronic autoimmune disease affecting about 1% of the global population, with a higher prevalence in women. Its treatment has been improved greatly over the past 30 years but there is no definitive cure available, and another unmet need exists for transitional hormonal stages such as pregnancy or menopause, which spurs the need to research new therapy options. In recent years, dietary interventions, particularly fasting and plant-based nutrition, have gained attention for their potential to alleviate RA symptoms. Fasting has been shown to reduce systemic inflammation, promote autophagy, and modulate immune cell activity, possibly leading to decreased joint pain and swelling. Nutritional strategies, such as anti-inflammatory and plant-based diets, have been shown to impact the gut microbiome and potentially support weight management, improve metabolic health, and reduce oxidative stress, all of which might contribute to better RA disease outcomes. Although the precise mechanisms remain under investigation, these approaches offer promising complementary strategies for enhancing RA management and improving patients' quality of life. This review explores the preventive and therapeutic potential of fasting and nutrition in RA, and their possible application in the context of hormonal fluctuations and transitional stages during a women's life.},
}

@article {pmid41754082,
year = {2026},
author = {Smółka, L and Strugała, M and Blady, K and Pomianowski, B and Kursa, K and Stanek, A},
title = {Pathogenetic Gut Microbiota in Aortic Diseases: Evidence and Mechanisms Across Aneurysm, Dissection, and Inflammatory Aortopathies.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040565},
pmid = {41754082},
issn = {2072-6643},
abstract = {Aortic diseases, including abdominal aortic aneurysm (AAA), thoracic aortic aneurysm (TAA), aortic dissection (AD), and Takayasu arteritis (TAK), are characterized by vascular remodeling and chronic immune-inflammatory activation, with AD often representing an acute complication of long-standing aortic wall vulnerability. Increasing evidence suggests that gut dysbiosis, impaired intestinal barrier integrity, and microbiota-derived metabolites may contribute to aortic wall injury. We synthesized current evidence linking the gut microbiome to aortic diseases and explored potential translational implications. PubMed, Scopus, and Web of Science were searched for microbiome-related studies on AAA, TAA, AD, and TAK published up to December 2025. Human observational and interventional studies were integrated with relevant experimental research. The strongest evidence was identified for AAA, where multiple cohorts report gut dysbiosis and reduced microbial diversity. Translational studies have detected bacterial DNA and microbial products in blood, aneurysm wall, or intraluminal thrombus, consistent with barrier-related microbial signaling and vascular inflammation, although these low-biomass findings do not establish microbial viability or causality. Microbiota-derived mediators-including trimethylamine-N-oxide, lipopolysaccharides, short-chain fatty acids, and bile acid derivatives-interact with pathways involved in cytokine signaling, oxidative stress, innate immune activation, and extracellular matrix degradation. Evidence for TAA and AD remains limited and suggests mainly modifier effects, whereas early studies in TAK indicate disease-associated microbiome and metabolite alterations. Mendelian randomization analyses have explored genetically proxied microbiome-AAA associations; however, results are heterogeneous, and causal inference remains provisional. Overall, the gut microbiome emerges as a plausible modifier of aortic disease, with the greatest translational relevance in AAA, highlighting the need for longitudinal multi-compartment studies and targeted interventions with aortic endpoints.},
}

@article {pmid41754081,
year = {2026},
author = {Grammatiki, M and Tsekmekidou, X and Koufakis, T and Kotsa, K},
title = {Nutritional Interventions in Type 1 Diabetes: Boosting Residual GLP-1 Responses-Is It an Option?.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040564},
pmid = {41754081},
issn = {2072-6643},
abstract = {Type 1 diabetes (T1D) is characterized by autoimmune beta-cell destruction and lifelong insulin dependence, yet early-stage disease (Stages 1-2) retains residual beta-cell function that may still respond to incretin signaling. Incretin hormones-mainly glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP)-enhance postprandial insulin secretion and suppress glucagon, and GLP-1 also exhibits beta-cell protective effects in preclinical models. Although the incretin effect is markedly reduced in established T1D, intestinal GLP-1 secretion is largely preserved, creating a mechanistic rationale for strategies that increase endogenous GLP-1 during the "residual function" window. This narrative review summarizes dietary and lifestyle interventions that may enhance endogenous GLP-1 responses and discusses their potential role as adjuncts to insulin therapy, particularly when combined with emerging beta-cell-preserving immunomodulatory approaches that may prolong early disease stages. Mechanistically, high-fiber diets may increase GLP-1 via microbiota-derived short-chain fatty acids acting on L-cell receptors; low-glycemic index carbohydrates may favor distal nutrient delivery and a GLP-1-dominant incretin profile; and Mediterranean dietary patterns may promote GLP-1 secretion through unsaturated fatty acids, fiber, and polyphenols, including potential DPP-4-modulating effects. This narrative review examines nutrition and lifestyle interventions modulating residual incretins to elongate early T1D stages and enhance glycemic control as insulin adjuncts, per Nutrients' Special Issue. Available evidence is strongest in non-T1D populations, with limited T1D-specific trials, highlighting the need for stage-targeted studies incorporating GLP-1 dynamics, C-peptide, glycemic variability, and microbiome outcomes.},
}

@article {pmid41754080,
year = {2026},
author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F},
title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040563},
pmid = {41754080},
issn = {2072-6643},
support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; },
abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.},
}

@article {pmid41754077,
year = {2026},
author = {Ashkanani, G and Rob, M and Yousef, M and Ashkanani, A and Al-Najjar, YA and Laws, S and Chaari, A},
title = {The Effects of Microbiome Modulating Therapies on Inflammatory Markers in Autoimmune Disease: A Systematic Review and Meta-Analysis.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/nu18040560},
pmid = {41754077},
issn = {2072-6643},
abstract = {BACKGROUND: Autoimmune diseases (ADs) are a growing global health burden, driven by chronic inflammation and immune dysregulation. The gut-immune axis plays a central role in their pathogenesis, with dysbiosis linked to several conditions. This has prompted investigation into nutraceuticals such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation as adjunctive therapies.

METHODS: We conducted a systematic review and meta-analysis following PRISMA guidelines, searching PubMed, Embase, and Web of Science for randomized controlled trials evaluating these interventions in autoimmune diseases.

RESULTS: Twenty-eight randomized control trials (RCTs) involving 2002 patients across 11 countries met inclusion criteria. Across the included RCTs, pooled analyses demonstrated significant reductions in c-reactive protein (CRP) (SMD -0.67, 95% CI -1.00 to -0.33; I[2] = 80.8%) and Tumor necrosis factor-alpha (TNF-α) (SMD -1.81, 95% CI -2.67 to -0.94; I[2] = 96%), a significant increase in Interleukin-10 (IL-10) (SMD 2.65, 95% CI 0.64 to 4.66; I[2] = 98%), and no overall significant effect on Interleukin-6 (IL-6) (SMD -0.89, 95% CI -1.99 to 0.22; p = 0.12). The strongest evidence of benefit was observed in rheumatoid arthritis, multiple sclerosis, and inflammatory bowel disease. Pooled effects are limited by extreme between-study heterogeneity (I[2] 80-98%), leaving interpretation as exploratory rather than definitive. More limited or inconsistent findings were reported for systemic lupus erythematosus, hypothyroidism, axial spondylarthritis, and juvenile idiopathic arthritis. Heterogeneity in study design, probiotic strain selection, dosage, and treatment duration limited comparability across trials.

CONCLUSIONS: Overall, microbiome-targeted nutraceuticals appear promising for attenuating systemic inflammation in select autoimmune conditions, but results remain mixed. Larger, rigorously designed RCTs with standardized endpoints are needed to clarify efficacy, identify optimal formulations, and define patient populations most likely to benefit.},
}

@article {pmid41753774,
year = {2026},
author = {Dobrzyński, J and Naziębło, A and Kulkova, I and Szpytma, M and Antosik, A and Sitarek-Andrzejczyk, M and Wróbel, B},
title = {Paenibacillus-Pseudomonas Consortium Improves Barley Performance with Minimal Impact on Native Rhizobacterial Community.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020488},
pmid = {41753774},
issn = {2076-2607},
abstract = {The intensive use of mineral nitrogen fertilizers in cereal production contributes to environmental degradation, highlighting the need for more sustainable crop management strategies. Plant growth-promoting bacteria (PGPB) offer a promising alternative; however, their effects on native rhizosphere communities remain underexplored, particularly in barley. This study evaluates the impact of a bacterial consortium composed of Paenibacillus sp. Z15 and Pseudomonas sp. KR227 on barley growth, yield, and rhizosphere bacteria under field conditions in temperate climate (2025). Plant biometric traits, photosynthetic pigment content, and soil properties were measured, and rhizobacterial communities were analyzed using 16S rRNA gene (V3-V4) sequencing. The PGPB consortium significantly increased early root biomass (120%), shoot height (7.8%), and grain yield (15.5%), while no significant effects were observed on soil chemistry or photosynthetic pigments. Sequencing revealed no major changes in alpha or beta diversity; however, transient shifts in the relative abundance of specific taxa were detected relatively shortly after inoculation and mostly disappeared by harvest. These findings indicate that the Paenibacillus-Pseudomonas consortium can enhance barley performance without disrupting native rhizobacterial communities. Overall, the results support the potential of PGPB as a sustainable agronomic tool and provide new insights into PGPB-microbiome interactions in barley under field conditions.},
}

@article {pmid41753768,
year = {2026},
author = {Frantz, CM and Crump, BC and Carpenter, S and Firth, E and Orellana, MV and Light, B and Junge, K},
title = {Microbial Ecology of Rotten Sea Ice: Implications for Arctic Carbon Cycling with Global Warming.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020482},
pmid = {41753768},
issn = {2076-2607},
support = {1656026//USA National Science Foundation/ ; PLR-1304228//USA National Science Foundation/ ; },
abstract = {"Rotten" sea ice, ice in an advanced stage of melt, represents an important but understudied habitat in the rapidly changing Arctic. As Arctic warming accelerates, this late-season ice type will become more prevalent, yet little is known about its microbial inhabitants or their roles in Arctic marine biogeochemical cycles. We examined microbial communities (prokaryote and algal abundance, 16S and 18S rRNA gene and transcript sequencing) and biogeochemical properties of rotten sea ice and earlier-season ice near Utqiaġvik, Alaska, USA. Rotten ice was comparatively warm, isothermal, and largely drained of brine, with extensive, interconnected pore networks linked to melt ponds above and seawater below. Unlike earlier-season ice, fluids saturating rotten ice were vertically homogeneous in pH, dissolved inorganic carbon, prokaryote and phytoplankton abundance, and microbial community composition. However, particulate carbon and nitrogen exhibited strong vertical gradients, with the highest concentrations near the surface. Microbial communities in rotten ice were significantly different from those in earlier-season ice and varied between individual floes. These findings indicate that rotten ice constitutes a distinct microbial habitat and may serve as an important source of nutrient-rich particulate matter in the future Arctic Ocean during the summer melt season.},
}

@article {pmid41753757,
year = {2026},
author = {Zhou, J and Zhu, B and Bing, Z and Wang, T and Zhao, Y},
title = {The Gut-Liver Axis in MASLD: From Host-Microbiome Crosstalk to Precision Therapeutics.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020471},
pmid = {41753757},
issn = {2076-2607},
support = {T2341015//National Natural Science Foundation of China/ ; 32271182//National Natural Science Foundation of China/ ; 8257103456//National Natural Science Foundation of China/ ; 2024300382//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is an emerging global health challenge with limited effective therapeutic options. The gut microbiota, at the interface of host metabolism and immunity, acts as a critical disease modifier via the gut-liver axis. This review goes beyond cataloging its associations and synthesizes how intrinsic and extrinsic factors sculpt a permissive microbial ecosystem. These factors likely converge to establish a state of "metabolic dysbiosis", fueling MASLD progression through three core mechanisms: compromised intestinal barrier integrity with immune activation, dysregulation of key microbial metabolite axes, and direct hepatic insult from gut-derived products. Next, we evaluate the translational landscape through a mechanism-informed precision framework, with an emphasis on how microbiome-based interventions could be aligned with non-invasive biomarkers increasingly used for MASLD risk stratification and treatment monitoring. By integrating evidence across scales, this review aims to frame a roadmap from microbiome correlations to causality-driven, personalized therapeutic strategies for MASLD.},
}

@article {pmid41753756,
year = {2026},
author = {Cano, RJ and García Menéndez, G},
title = {Why Clinical Trials of Microbiome-Targeted Interventions Often Fail to Support Health Claims: A Commentary on Probiotics and Translational Design.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020470},
pmid = {41753756},
issn = {2076-2607},
abstract = {The rapid expansion of probiotics and other microbiome-modulating interventions has been accompanied by a growing number of human clinical trials. However, despite frequent reports of statistically significant microbiome changes, relatively few studies generate evidence that convincingly supports health claims or translates into reproducible, clinically meaningful outcomes. This gap is often attributed to the inherent complexity and inter-individual variability of the gut microbiome; however, recurring shortcomings in trial design and interpretation likely play an equally important role. In this Commentary, we examine common failure modes that weaken the clinical validation of microbiome-mediated interventions. These include overreliance on descriptive microbiome metrics (e.g., alpha diversity and taxonomic shifts) as surrogate endpoints, misalignment between prespecified endpoints and the claims ultimately advanced, and excessive dependence on symptom-only outcomes in settings characterized by substantial placebo responsiveness. We further highlight how inadequate control of key confounders-particularly diet, antibiotic exposure, and concomitant medications-combined with endpoint overload and underpowered study designs, can obscure true biological signal and increase the risk of irreproducible findings. We argue that stronger evidence emerges when the microbiome is treated as a mechanistic mediator rather than a clinical endpoint. Trials are most interpretable when intended claims are prospectively defined, linked to explicit biological mechanisms, and evaluated using a hierarchy of endpoints that prioritizes host-relevant outcomes and objective biomarkers, with microbiome measures integrated to support mechanistic plausibility. Adoption of staged development pathways disciplined statistical planning, and transparent management of confounding variables can further improve reproducibility and clinical relevance.},
}

@article {pmid41753753,
year = {2026},
author = {Lerner, A and Lieber, AD and Nelson-Dooley, C and Leu, A and Perro, M and Koch, G and Benzvi, C and Smith, J},
title = {Genetically Modified Microorganisms: Risks and Regulatory Considerations for Human and Environmental Health.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020467},
pmid = {41753753},
issn = {2076-2607},
abstract = {Advances in affordable genetic engineering have accelerated the creation and large-scale environmental release of genetically modified microorganisms (GMMs). While beneficial applications exist, GMMs may present unique, long-term risks to human and environmental health. Unlike static chemicals, GMMs are biologically active, self-replicating entities capable of rapid mutation and global dispersal. Current regulatory frameworks place responsibility on each country to regulate GMMs, without a clear, coordinated international policy. This review details critical risk scenarios, including horizontal gene transfer to native species and the possible disruption of vital human microbiomes (gut, oral, and infant), which could increase resistance to degradation, promote traits that expand a microbe's range of hosts or ecological niches, and enhance the production of novel metabolites with unexpected biological activity. In soil, GMMs may support the emergence of "super bugs" or destabilize carbon sequestration cycles, potentially impacting climate resilience. Engineered microbial enzymes in the food supply may also act as environmental drivers of autoimmunity. Given the limited understanding of microbial ecology, we propose a decision-based biosafety workflow emphasizing pre-release risk assessment and continuous post-release monitoring. We urge national and international regulators to adopt the precautionary principle to better protect human health and the environment from the potential negative outcomes of GMMs.},
}

@article {pmid41753743,
year = {2026},
author = {Zhao, P and Shi, B and Zhou, X and Zhao, Z and Hu, J and Zhang, X},
title = {Dietary Energy Levels Impact on Skin Microbiota and Metabolites of Yaks.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020457},
pmid = {41753743},
issn = {2076-2607},
support = {32302720//the National Natural Science Foundation of China/ ; GAU-KYQD-2022-18//the Gansu Agricultural University Public Recruitment Doctoral Research Start-up Fund/ ; },
abstract = {The study aims to investigate the skin microbiome composition of Yaks and the effects of different dietary nutrient levels on the skin microbiome diversity and metabolites. A total of 19 healthy Tianzhu White Yaks at two age stages (2.5 and 4.5 years old) were selected and fed either a high-energy diet (n = 9) or a low-energy diet (n = 10). After 90 days of feeding, skin microbiota and skin tissue metabolites were detected using 16S rRNA sequencing and LC-MS/MS untargeted metabolomics, respectively. The results showed: (1) the phyla Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidetes exhibited relatively high abundances in the skin of yaks, and the total abundance of these four phyla reached as high as 99.3%. Alpha diversity analysis indicated that the alpha diversity index of yak skin microbiota was significantly higher (p < 0.05) in the low-energy nutritional level group than in the high-energy nutritional level group in yaks of both 2.5 and 4.5 years of age. Principal coordinate analysis (PCoA) revealed a distinct separation of all skin microbiota samples into two clusters: the high-energy (H) and low-energy (L) groups. (2) A total of 114 differentially expressed metabolites were screened across both groups, significantly enriched (p < 0.05) in pathways including synaptic vesicle trafficking and glycerophospholipid metabolism; (3) Correlation analysis between microbiota and metabolites revealed significant positive correlations (p < 0.01) between Psychrobacter and choline, and between Corynebacterium and palmitic acid. In conclusion, A low-energy diet increases skin microbial diversity, which is beneficial for maintaining community stability; In contrast, a high-energy diet enriches bacterial genera such as Corynebacterium and Psychrobacter, enhancing functions related to antibacterial activity and barrier protection.},
}

@article {pmid41753733,
year = {2026},
author = {Ihuț, A and Răducu, C and Ranta, M and Andrecan, A and Uiuiu, P},
title = {Gut Microbiome Health in Farm Animals and Fish: Implications for Human Health and the Risk of Gastrointestinal Diseases.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020447},
pmid = {41753733},
issn = {2076-2607},
abstract = {The gut microbiome is central to immune, metabolic, and gastrointestinal health across species. Dysbiosis disrupts microbial communities and is linked to inflammatory bowel disease, celiac disease, and other immune-mediated gastrointestinal disorders. This review addresses the central question of how diet- and environment-driven gut dysbiosis in farm animals and fish is transmitted through the food chain to influence human gastrointestinal health within a One Health framework. This review synthesizes recent evidence within the One Health framework, focusing on how diet- and environment-induced dysbiosis in farm animals and fish can influence human gastrointestinal health via the food chain. We highlight mechanisms of immune modulation, alterations in food products, and the risks of pathogen transmission and antimicrobial resistance. An important limitation of the current body of evidence is the lack of studies that comprehensively trace the proposed axis from animal gut dysbiosis to human health outcomes. Emerging interventions, including precision nutrition, probiotics, and microbiota-targeted therapies, show potential for restoring microbial balance, though translating these findings into clinical practice remains challenging. By integrating human, veterinary, and environmental perspectives, this work proposes a novel cross-species microbiome-diet-immune framework to guide future research and interventions, advancing One Health strategies for disease prevention, antimicrobial resistance mitigation, and sustainable gastrointestinal health.},
}

@article {pmid41753726,
year = {2026},
author = {Kundnani, NR and Sharma, A and Levai, MC and Marin-Bancila, L and Georgescu, D and Botas, L and Chiriac, SD and Valcovici, M and Popa, MD},
title = {Early-Life β-Lactam Exposure and the Developing Microbiome: Clinical Relevance and Controversies.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020440},
pmid = {41753726},
issn = {2076-2607},
abstract = {Antibiotic-induced dysbiosis has been increasingly implicated in a range of pediatric outcomes, yet the concept remains variably defined and often inconsistently applied. The purpose of this review is to provide an overview and critical evaluation of the available data regarding the effects of early-life exposure to β-lactam antibiotics on the developing microbiome. We conducted a narrative review of experimental and epidemiological studies examining β-lactam exposure during pregnancy, the perinatal period, and early childhood was conducted. β-lactams induce reproducible alterations in microbial composition, diversity, and metabolic function, including decreases in Bifidobacterium and Lactobacillus and a relative increase in Enterobacteriaceae and other facultative anaerobes, especially in early life. Reduced microbial diversity and changed short-chain fatty acid-producing taxa often accompany these compositional changes. However, associations with immune, metabolic, and neurodevelopmental outcomes are heterogeneous and frequently confounded by indication host-related factors. Evidence for causality in humans remains limited despite strong mechanistic support from animal models. Current data support cautious interpretation, even though β-lactam-associated microbiome perturbations may contribute to disease susceptibility during vulnerable developmental windows. While mechanistic and longitudinal evidence continues to develop, antibiotic stewardship focused on appropriate indication and duration is still crucial.},
}

@article {pmid41753701,
year = {2026},
author = {Zhao, J and Du, F and Zhu, J and Liu, G and Zhou, X and Zhang, Y and Rong, X},
title = {Bacterial Community Structure and FEAST Source Tracking of Endophytes in Vernonia anthelmintica (L.) Willd. from Southern Xinjiang, China.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020414},
pmid = {41753701},
issn = {2076-2607},
abstract = {Using 16S rRNA gene amplicon sequencing and FEAST microbial source tracking, this study characterized the bacterial communities in tissues (roots, stems, leaves, seeds) and associated soils (rhizosphere and bulk soil) of Vernonia anthelmintica, an important Uyghur medicinal plant endemic to arid southern Xinjiang. We found significantly higher bacterial diversity in soil than in plant tissues, with Pseudomonadota-dominated plant-associated communities and Actinobacteria co-dominating in soils. Bacterial community structures varied across plant compartments, with soil communities exhibiting greater stability and broader niche breadth. Critically, FEAST source tracking revealed that rhizosphere soil contributed 23.8%, 13.4%, 17.9%, and 10.8% of the bacterial communities in roots, stems, leaves, and seeds, respectively, identifying soil as the primary source of endophytic bacteria. These findings highlight the pivotal role of arid-region soil microbial diversity in shaping the unique endophytic microbiome of V. anthelmintica, providing a scientific basis for conserving soil microbial health to support its standardized cultivation and sustainable utilization in Uyghur medicine.},
}

@article {pmid41753691,
year = {2026},
author = {Liu, B and Lu, T and Yao, T and Zhao, X and Yang, L},
title = {Developmental Stage-Driven Niche Differentiation and Assembly of Rhizosphere and Endophytic Bacterial Communities in Helianthus annuus Under Saline-Alkaline Stress.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020404},
pmid = {41753691},
issn = {2076-2607},
support = {2024LHMS04006//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; BR251306//Inner Mongolia Autonomous Region Direct University Basic Research Grant/ ; RZ2400001775//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; U23A2054//Joint Funds of the National Natural Science Foundation of China/ ; 2025KYPT0100; 2023YFHH0028//the Science and Technology Program of Inner Mongolia Autonomous Region/ ; 2025//Ecological Restoration of Degraded Grassland and High-Quality Development of Grassland Animal Husbandry/ ; },
abstract = {Soil salinization severely constrains agricultural productivity, while root-associated microbiota contribute to plant adaptation to saline-alkali stress. However, developmental assembly dynamics of rhizosphere and root endosphere bacterial communities remain insufficiently characterized in irrigation-driven saline-alkali agroecosystems such as the Hetao Plain of northern China. Here, Helianthus annuus plants were sampled at seedling, squaring, and flowering stages, and rhizosphere and root microbiota were analyzed using high-throughput amplicon sequencing integrated with soil physicochemical measurements, beta nearest taxon index-based community assembly inference, and co-occurrence network analysis. The rhizosphere maintained higher diversity, broader taxonomic heterogeneity, and persistently complex interaction networks, whereas the root endosphere exhibited progressive diversity reduction and compositional convergence during plant development. Developmental progression drove contrasting successional trajectories, with increasing rhizosphere complexity and endophytic convergence toward a Proteobacteria-dominated core, particularly Pseudomonas. Beta nearest taxon index analysis indicated mixed stochastic and dispersal-related processes in the rhizosphere but drift-dominated assembly in late-stage roots. Functional predictions revealed enhanced nitrogen-related metabolic potential during flowering, coinciding with enrichment and network centrality of Pseudomonas. These findings demonstrate stage-dependent spatial reorganization of sunflower root microbiomes under saline-alkali stress and provide a framework for identifying functionally relevant microbial groups for targeted microbiome-based agricultural management.},
}

@article {pmid41753678,
year = {2026},
author = {Zhao, Q and Li, B and Liang, C and Wei, J and Ma, J and Qin, W},
title = {Fertility-Associated Soil Chemistry Predominantly Influence Gut Microbiota Diversity in Goitered Gazelles of the Qaidam Basin, China.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020391},
pmid = {41753678},
issn = {2076-2607},
support = {32160316//National Natural Science Foundation of China/ ; },
abstract = {This study focused on the links between soil physicochemical properties and the gut microbiota of goitered gazelles (Gazella subgutturosa) in the hyper-arid Qaidam Basin. By integrating 16S rRNA gene sequencing, soil physicochemical analysis (11 soil indicators), and microbial source tracking (FEAST) on samples of feces (n = 58), soil (n = 35), and water (n = 35) collected from six typical regions. We systematically revealed the mechanisms by which soil properties influence the gut microbiome of wildlife in an arid desert ecosystem based on source tracking and Multiple Regression on distance Matrices (MRM) analysis. The results showed that soil total phosphorus (TP) was significantly positively correlated with the α-diversity of gut microbiota (coefficient = 0.4/0.23/0.332; p < 0.05), while soil organic carbon (SOC) was significantly negatively correlated (coefficient = -0.44/-0.436; p < 0.05), indicating that soil nutrients indirectly predict host microbial diversity by regulating vegetation productivity and forage quality. β-diversity analysis further demonstrated that spatial heterogeneity in soil pH (coefficient = 0.3083; p < 0.05) and TP (coefficient = 0.227; p < 0.05) significantly drove the structural differentiation of gut microbial communities. Source-tracking results based on FEAST revealed significant regional differences in the proportional contribution of environmental microorganisms to the gut microbiota, with individuals in resource-poor habitats (ALK region) exhibiting higher input from soil microbes (8.0672% ± 6.9291%; p < 0.05). In conclusion, this study clarifies the ecological mechanism by which soil physicochemical properties regulate the diversity and composition of herbivore gut microbiota through a "soil-plant-food-gut microbiota" cascading pathway, providing important empirical evidence for understanding animal-microbe-environment interactions and adaptive evolution in extreme environments.},
}

@article {pmid41753674,
year = {2026},
author = {Ece, G and Aktaş, A and Koyuncu Özyurt, Ö and Demirbakan, H and Alışkan, HE and Sağlık, İ and Zorbozan, O and Çetin Duran, A and Uğur, AR and Öcal, D and Uzunoğlu, E and Kaya, E and Mutlu Sarıgüzel, F and Bayındır, F and Yetkin, G and Altındiş, M and Yenice Aktaş, S and Kula Atik, T},
title = {Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020387},
pmid = {41753674},
issn = {2076-2607},
abstract = {The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice.},
}

@article {pmid41753673,
year = {2026},
author = {Petalas, K and Konstantinou, GN},
title = {Chronic Rhinosinusitis at the Interface of Type 2 Inflammation, Epithelial Barrier Dysfunction, and Microbiome Dysbiosis.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020386},
pmid = {41753673},
issn = {2076-2607},
abstract = {Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disease of the nasal and paranasal sinus mucosa with substantial impact on quality of life. Although atopy and/or allergic rhinitis frequently coexist with CRS, often alongside type 2-skewed inflammation, the extent to which allergic mechanisms define a discrete CRS entity remains debated, in part due to inconsistent operational definitions and overlapping clinical phenotypes. In parallel, culture-independent sequencing studies have reframed CRS as a disorder of host-microbe interactions, with many cohorts reporting reduced sinonasal microbial diversity, enrichment of potentially pathogen taxa (including Staphylococcus aureus), and biofilm-associated community states. However, causality and directionality remain uncertain. In this narrative review, we synthesize evidence at the interface of epithelial barrier dysfunction, type 2 cytokine networks (IL-4/IL-13/IL-5), and microbiome dysbiosis, highlighting where data are consistent across studies versus where findings are heterogeneous or predominantly associative. We discuss representative allergy-associated CRS prototypes such as allergic fungal rhinosinusitis and central compartment atopic disease as clinical models to interrogate these interactions, while distinguishing them from non-IgE-mediated type 2 entities such as aspirin-exacerbated respiratory disease. We also summarize current data linking atopy to sinonasal microbial signatures and discuss emerging microbiome-directed interventions (topical probiotics, bacteriophages, and microbiota transfer concepts) alongside biologics and precision anti-inflammatory therapies. Finally, we highlight key knowledge gaps, including the limited endotype-resolved and longitudinal studies, variable allergic phenotyping in microbiome research, and the need for standardized definitions and biomarker-driven stratification to clarify clinical utility and to guide mechanism-informed therapeutic trials.},
}

@article {pmid41753667,
year = {2026},
author = {Li, Y and Vigil, J and Pradhan, R and Zhu, J and Libault, M},
title = {Integrating Single-Cell and Spatial Multi-Omics to Decode Plant-Microbe Interactions at Cellular Resolution.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020380},
pmid = {41753667},
issn = {2076-2607},
support = {2414183//National Science Foundation (NSF)/ ; 2425989//National Science Foundation (NSF)/ ; 2022-67013-36144//USDA National Institute of Food and Agriculture (USDA-NIFA)/ ; },
abstract = {Understanding the intimate interactions between plants and their microbiota at the cellular level is essential for unlocking the full potential of plant holobionts in agricultural systems. Traditional bulk and microbial community-level sequencing approaches reveal broad community patterns but fail to resolve how distinct plant cell types interact with or regulate microbial colonization, as well as the diverse antagonistic and synergistic interactions and responses existing between various microbial populations. Recent advances in single-cell and spatial multi-omics have transformed our understanding of plant cell identities as well as gene regulatory programs and their dynamic regulation in response to environmental stresses and plant development. In this review, we highlight the single-cell discoveries that uncover the plant cell-type-specific microbial perception, immune activation, and symbiotic differentiation, particularly in roots, nodules, and leaves. We further discuss how integrating transcriptomic, epigenomic, and spatial data can reconstruct multilayered interaction networks that connect plant cell-type-specific regulatory states with microbial spatial niches and inter-kingdom signaling (e.g., ligand-receptor and metabolite exchange), providing a foundation for developing new strategies to engineer crop-microbiome interactions to support sustainable agriculture. We conclude by outlining key methodological challenges and future research priorities that point toward building a fully integrated cellular interactome of the plant holobiont.},
}

@article {pmid41753654,
year = {2026},
author = {Hodzhev, Y and Zhelyazkova, V and Toshkova, N and Barashkova, AS and Tsafarova, B and Panaiotov, S and Stoev, P},
title = {Evaluation of the Bacterial Diversity in the World's Deepest Cave-Veryovkina, Arabika Massif, Western Caucasus.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020368},
pmid = {41753654},
issn = {2076-2607},
support = {KP-06-N-51/9-2021//Bulgarian Science Fund/ ; BG16RFPR002-1.014-0017//Procedure BG16RFPR002-1.014 "Sustainable development of Centers of Excellence and Centers of Competence, including specific infrastructures or their associations of the NRRI", Program "Research, Innovation and Digitalization for Smart Transformation 202/ ; },
abstract = {Veryovkina Cave is the world's deepest known cave (2212 m deep). It is located in the Arabika Massif of Gagra Mountain in the Western Caucasus. Its microbiome remains unknown because of difficulties in access. Ten sediment samples were collected at vertical depths ranging from 300 m to 2204 m; they varied by substrate type, moisture content, and visitor accessibility. Total microbial DNA was isolated, and 16S ribosomal gene metabarcoding was applied for taxonomic identification. Seven samples showed reliable content, whereas three samples indicated no recoverable reads. Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant phyla in total. Depth stratification of microbiota showed that (1) shallow wet clays were dominated by Acidimicrobia and Actinobacteria; (2) mid-depth wet clays showed the highest abundance of Nitrospira, Betaproteobacteria, and Vicinamibacter; and (3) deep, dry substrates were dominated by Thermoleophilia and Rubrobacteria. Multivariate analyses showed that substrate type and moisture tended to explain more variation in microbial abundance than depth or human activity. We demonstrate the presence of distinct ecological niches within the cave ecosystem, which emphasizes the role of local conditions in shaping microbial diversity.},
}

@article {pmid41753652,
year = {2026},
author = {Adeyemi, OD and Nahashon, SN},
title = {Mitigating Salmonella in Poultry Using Probiotics: Mechanisms, Challenges, and Opportunities.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020365},
pmid = {41753652},
issn = {2076-2607},
abstract = {The global poultry industry continues to face significant challenges due to Salmonella infections, which pose severe public health concerns and economic losses. Recently, the reemergence of antimicrobial resistance has led to the restriction of antibiotic use in poultry, especially as growth promoters, thus accelerating the search for sustainable alternatives. Among these, probiotics have gained attention as potential candidates for improving poultry health and mitigating Salmonella colonization in the gut. This review summarizes the key mechanisms through which probiotics exert anti-Salmonella effects, including competitive exclusion, production of antimicrobial substances, reinforcement of the intestinal barrier, and modulation of host immune responses. Commonly used probiotic strains in poultry such as Lactobacillus and Bacillus are discussed, alongside emerging candidates derived from non-poultry hosts that may offer additional functional benefits. Despite encouraging findings, the use of probiotics in poultry faces several challenges, including strain-specific efficacy, variation in results across studies, environmental influences, and regulatory limitations. Therefore, we further explore future directions that are aimed at improving probiotic application in poultry production, such as microbiome-guided strain selection, advanced delivery systems, and combination therapies. Advancing our understanding of probiotic-pathogen-host interactions will be essential for optimizing probiotic use to enhance poultry health, reduce zoonotic transmission of Salmonella, and contribute to safer and more sustainable food systems.},
}

@article {pmid41753650,
year = {2026},
author = {Wang, K and White, JF and Zhu, Z and Zhang, W and Li, X and Li, S},
title = {Desert Plant Seed Endophytes: A Reservoir of Stress-Adapted Bacillus Strains for Enhancing Wheat Salinity Tolerance.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020363},
pmid = {41753650},
issn = {2076-2607},
support = {25YFFA043//Gansu Provincial Key Research and Development Program/ ; },
abstract = {Land desertification poses a major ecological challenge and threatens agricultural productivity. This study investigated the seed endophytic microbiomes of desert plants as a potential resource for mitigating salt stress in crops. Using high-throughput sequencing, we characterized the bacterial and fungal communities within seeds of 12 desert plant species. Dominant taxa included Firmicutes (particularly Bacillus), Bacteroidota, Proteobacteria, Ascomycota, and Basidiomycota. Culturable bacteria were subsequently isolated from Haloxylon ammodendron (C.A.Mey.) Bunge (HB) and Hedysarum scoparium Fisch. & C.A.Mey. (HSA) seeds. These isolates were screened for plant growth-promoting (PGP) traits and tolerance to salt (NaCl) and alkali (NaHCO3). Selected strains, including the high indole-3-acetic acid (IAA)-producing Bacillus sp. HB-4, were used to inoculate wheat (Triticum aestivum L.) under 150 mM NaCl or 150 mM NaHCO3 stress. Inoculation with strain HB-4 significantly improved wheat growth under stress. This improvement was associated with increased chlorophyll and proline content, enhanced activities of the antioxidant enzymes catalase and peroxidase, and reduced levels of malondialdehyde, a marker of oxidative damage. Our results demonstrate that desert plant seeds harbor taxonomically distinct and functionally resilient endophytes. The successful application of a desert-adapted Bacillus strain to alleviate salt stress in wheat highlights the potential of such microbiomes as a novel source of inoculants for sustainable agriculture in saline-affected regions.},
}

@article {pmid41753637,
year = {2026},
author = {Zhao, J and Lu, Z and Wu, J and Wang, L and Huang, J and Yang, F},
title = {Microcin C7 Prevents Cyclophosphamide-Induced Immunosuppression and Intestinal Injury by Modulating T-Cell Differentiation and Gut Microbiota Composition in Mice.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020350},
pmid = {41753637},
issn = {2076-2607},
support = {2022YFC2105003//National Key Research and Development Program of China/ ; NCTIP-XD/B05//National Center of Technology Innovation for Pigs/ ; },
abstract = {Microcin C7 (McC7) is a ribosomally synthesized antimicrobial peptide that has emerged as a promising candidate due to its dual antibacterial and immunomodulatory activities. This study evaluated the preventive effect of McC7 against cyclophosphamide (CTX)-induced immunosuppression and intestinal injury. An immunosuppression model was established by intraperitoneal CTX injection in mice, which were randomly allocated into five groups (n = 15): a negative control, a CTX model group, and three McC7 treatment groups receiving dietary McC7 at 100, 200, or 400 mg/kg both before and during CTX exposure. Body weight and feed intake were monitored throughout the study. Organ indices, serum biochemical parameters, immune and antioxidant markers, and intestinal morphology were assessed. Splenic T-cell subsets were analyzed by flow cytometry, and gut microbiota composition was evaluated by 16S rRNA sequencing. McC7 supplementation significantly attenuated the CTX-induced reduction in body weight, feed intake, and organ indices, ameliorated markers of hepatic and renal injury, and restored the splenic CD4[+]/CD8[+] T-cell ratio. McC7 enhanced intestinal mucosal barrier integrity, increased the abundance of beneficial bacteria such as Candidatus Arthromitus and ASF356, and reduced the abundance of the potentially pathogenic genus Bilophila. In conclusion, our results demonstrate that McC7 alleviates CTX-induced immunosuppression by regulating T-cell differentiation, maintaining cytokine homeostasis, and modulating gut microbial composition to support intestinal health.},
}

@article {pmid41753636,
year = {2026},
author = {Ma, J and Ning, X and Li, J and Dai, S and Sun, F and Li, H and Sun, S and Ding, Y},
title = {Metabolite-Mediated Alleviation of Iron Deficiency and Growth Promotion of Malus hupehensis by Bacillus licheniformis LCDD6 in Calcareous Soil.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020349},
pmid = {41753636},
issn = {2076-2607},
support = {2022TZXD0037//Key Research and Development Program of Shandong Province/ ; },
abstract = {Calcareous soils are typically deficient in essential nutrients such as iron, phosphorus, and potassium, which frequently results in nutrient deficiency in fruit trees. Bacillus licheniformis LCDD6 markedly enhanced Malus hupehensis seedling growth and plant iron nutrition in calcareous soil. This study aimed to elucidate the mechanism underlying these beneficial effects of strain LCDD6 under iron deficiency. Transcriptomic analysis revealed that iron deficiency induced metabolic reprogramming in strain LCDD6, characterized by a significant upregulation of genes involved in the biosynthesis of the siderophore bacillibactin and plant growth hormone indoleacetic acid (IAA). Consistently, metabolomic profiling identified bacillibactin and IAA as the dominant metabolites produced under iron-deficient conditions. A 60-day pot experiment further demonstrated that the cell-free fermentation broth of strain LCDD6 significantly enhanced plant growth and rhizosphere soil enzyme activities. The crude bacillibactin extract derived from the fermentation exerted the strongest effects on plant growth and iron accumulation, whereas IAA preferentially stimulated root development and promoted plant phosphorus accumulation. Additionally, different metabolites exerted distinct and selective effects on the rhizosphere microbial community, with fungi showing stronger and more metabolite-specific responses than bacteria. The crude bacillibactin extract enriched fungal taxa, particularly Coprinellus, which showed strong positive correlations with plant growth traits and iron accumulation, while Stachybotrys, enriched under IAA treatment, was positively correlated with plant phosphorus content. Overall, strain LCDD6 promotes plant growth under iron-deficient conditions through the coordinated action of multiple metabolites, with bacillibactin as the primary contributor and IAA providing complementary effects. These findings offer mechanistic insight and a scientific basis for developing Bacillus-based biofertilizers to improve nutrient acquisition in calcareous soils.},
}

@article {pmid41753617,
year = {2026},
author = {Sekar, KPC and Schmiliver, B and Pieterick, PE and Cha, T and Patel, HA and Robinson, H and Kumar, P and Wu, DT and Jones, R and Goudy, S},
title = {Harnessing Microbiome-Mediated and Macrophage-Driven Mechanisms for Oral Wound Healing.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020330},
pmid = {41753617},
issn = {2076-2607},
abstract = {Oral mucosa healing is a complex process that involves the innate wound healing system, including the coagulation cascade, extracellular matrix remodeling, immune cell responses, and fibroblast and epithelial responses, within the context of a dynamic resident microbiome. Unlike cutaneous wounds, oral wounds heal rapidly with minimal scarring despite constant exposure to diverse microbial communities, saliva, and mechanical stress. Emerging evidence highlights the critical interplay between microbiome-mediated signaling and macrophage plasticity in shaping wound outcomes, suggesting that similar mechanisms operate within the oral cavity. Inflammation is an essential component of wound repair, and its resolution is necessary to promote tissue remodeling and functional regeneration. Macrophages play a central role in this transition through phenotype switching from a pro-inflammatory (M1) to a pro-resolving, anti-inflammatory (M2) state. This review synthesizes current understanding of the oral microbiome's influence on macrophage polarization across distinct stages of oral wound healing and examines microbial-based strategies that modulate the immune response to enhance repair. Significant knowledge gaps remain, including limited clinical translation, inter-individual variability in microbiome composition, and complete mechanistic insight into host-microbe immune interaction. Addressing these challenges enables the development of precision microbiome-based therapeutics that restore microbial balance, direct macrophage-driven regeneration, and improve outcomes in oral wounds and chronic inflammatory conditions.},
}

@article {pmid41753608,
year = {2026},
author = {Casais, V and Pereira, J and Garcia, E and Coelho, C and Figueira, D and Ares, A and Tiago, I and Costa, J},
title = {Functional Profiling of Kiwifruit Phyllosphere Bacteria: Copper Resistance and Biocontrol Potential as a Foundation for Microbiome-Informed Strategies.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020321},
pmid = {41753608},
issn = {2076-2607},
support = {UIDB/04004/2025//Fundação para a Ciência e Tecnologia/ ; Associated Laboratory TERRA LA/P/0092/2020//Fundação para a Ciência e Tecnologia/ ; Community Initiative Action 1.1 Operational Groups "I9K-InovKiwi-Development of strategies for the sustainability of the kiwifruit sector through the creation of a value-added product"//PDR2020 and co-financed by the FEADER under the Portugal 2020 Partnership Agreement/ ; IPN//Fundo de Inovação, Tecnologia e Economia Circular/ ; },
abstract = {Bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa) is a major threat to global kiwifruit production. Copper-based bactericides remain widely used, but increasing resistance highlights the urgency of developing sustainable alternatives. Understanding the functional capabilities of phyllosphere bacteria under copper pressure is critical for designing microbiome-informed management strategies. This study provides a culture-based functional inventory of bacteria associated with Actinidia chinensis var. deliciosa leaves from Portuguese orchards under long-term copper management, aiming to identify native taxa with traits relevant to plant health and resilience. A total of 1058 isolates were recovered and grouped into 261 Random Amplification of Polymorphic DNA (RAPD) clusters, representing 58 species across 29 genera. Representative strains were screened for Plant Growth-Promoting (PGP) traits (Indole-3-acetic acid (IAA), siderophore production, phosphate solubilization, ammonia production), copper tolerance, and in vitro antagonism against Psa. Copper resistance was widespread (53.3% of isolates with MIC ≥ 0.8 mM), including the first evidence of a highly copper-resistant PSA strain in Portuguese kiwifruit orchards and an exceptionally resistant non-pathogenic strain closely related to Erwinia iniecta (MIC 2.8 mM). A subset of 25 isolates combined all four PGP traits, and several also exhibited antagonism against Psa in vitro, among them Bacillus pumilus consistently supressed pathogen growth. Notably, antagonistic and multifunctional traits co-occurred in some isolates, highlighting promising candidates for integrated biocontrol strategies. Overall, the findings reveal a functionally diverse and copper-resilient collection of cultured bacteria, offering both challenges and opportunities for microbiome-based disease management. This work establishes a robust functional basis for subsequent in planta validation and the development of sustainable, microbiome-informed approaches for Psa control.},
}

@article {pmid41753597,
year = {2026},
author = {Izquierdo-Jiménez, CM and Recuero, C and Maicas, S and Del Castillo-Madrigal, I},
title = {Indigenous Olive Orchard Bacteria as Biocontrol Agents: An Integrated Culture-Dependent and Soil Microbiome Approach.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020310},
pmid = {41753597},
issn = {2076-2607},
support = {No specific grant//SEIPASA/ ; },
abstract = {Olive orchard soils are a source of microorganisms capable of inhibiting major olive pathogens. In this study, rhizobacteria were isolated and characterized based on plant growth-promoting traits, and soil 16 rRNA gene sequencing analysis was performed to analyze microbial communities at two key olive phenological stages (flowering and fruit formation). Using a culture-dependent approach, a total of 90 bacterial isolates representing distinct colony morphotypes were recovered from olive soils, with 35 during the flowering stage and 55 during the fruit formation stage, indicating a higher cultivable diversity during the latter period. We identified some bacterial strains with antagonistic activity and observed phenology-related shifts in the soil microbiome. Using differential abundance analysis, we identified bacterial taxa that were significantly enriched or depleted during olive fruit formation. Overall, this study demonstrates that olive-associated bacteria harbor antagonistic potential against olive pathogens. The use of bacteria adapted to olive agroecosystems represents a promising strategy for sustainable disease management.},
}

@article {pmid41753594,
year = {2026},
author = {Zhao, M and Chen, X and Liu, W and Li, Z and Li, W and Yang, F and Guo, Z and Li, Z and Tian, Y and Zhang, W and Zhang, G and Chen, T},
title = {Bioremediation of Saline-Alkali Soil Using a Waste Biomass-Functional Microorganism Composite Amendment and Preliminary Multi-Crop Field Validation.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020304},
pmid = {41753594},
issn = {2076-2607},
support = {25JRRA173//Natural Science Foundation of Gansu Province Project/ ; 2024ZY033//Qinghai Provincial Central Government Guide Local Science and Technology Devel-739 opment Project/ ; 2024//Undergraduate Key Teaching Reform Project of Lanzhou Jiaotong 740 University/ ; 2024//Graduate Students Key Teaching Reform Project for Graduate Students at Lan-741 zhou Jiaotong University/ ; 2025//Key Projects for Undergraduate Teaching Reform/ ; },
abstract = {Soil salinization threatens crop production; however, in multi-crop field systems, evidence for the effectiveness of waste biomass-functional microorganism composite amendments remains limited. Here, we developed a composite microbial soil conditioner (F2) using pine needles and crushed corn cobs as carriers combined with salt-tolerant strains Bacillus subtilis (K1), Azotobacter chroococcum (Y1), and Bacillus gelatinus (J3) to remediate moderately saline-alkali soil from central Gansu (pH 8.36 ± 0.18; EC 1658 ± 55.24 μS·cm[-1]). Saturation screening identified an optimal carrier ratio of pine needles:corn cobs = 1:2 and an inoculum ratio of K1:Y1:J3 = 1:2:1. In pot experiments, F2 increased soil organic matter and water-holding capacity, enhanced alkaline phosphatase, urease, and sucrase activities, and significantly reduced soil pH and EC. Maize seedling height and chlorophyll content increased by 53.87% and 38.88%, respectively. Amplicon-based microbiome profiling indicated enrichment of beneficial microbial taxa and strengthened primary metabolic functions under F2. Field validation across five crops (flax, potato, edible sunflower, sorghum, and maize) showed consistent growth and yield-related improvements. Overall, these results demonstrate that the biomass-microbe composite amendment effectively alleviates saline-alkali constraints by jointly improving soil properties, microbial functions, and crop performance.},
}

@article {pmid41753589,
year = {2026},
author = {Xia, X and Yang, S and Song, X and Hao, C and Sun, H and Xu, X and Lu, X and Li, F},
title = {The Influence of Transgenic Maize on the Endophytic Microorganisms of Eisenia fetida.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020302},
pmid = {41753589},
issn = {2076-2607},
support = {ZR2021QC207//Shandong Province Natural Science Foundation Young Project/ ; 2023ZD04062//the Biological Breeding-Major Projects/ ; CXGC2025C05//The 2025 Annual Basic Research Task of the Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; },
abstract = {To evaluate the comprehensive ecological risks associated with transgenic plant residues, this study examined their impact on Eisenia fetida and their endogenous microorganisms. The results indicated that transgenic plant residues did not influence the survival or weight of E. fetida, but they significantly altered the microbial community structure at specific time points. Specifically, the diversity and structure of the fungal community exhibited significant changes on the 14th and 28th days after treatment. In contrast, the bacterial response was delayed, with 22 biomarkers, including Caproiciproducens, Lachnoclostridium, and Enterococcus, being specifically enriched on the 21st day. This study confirmed that transgenic plant residues can temporally reshape the microecology within E. fetida. The practical significance of this research lies in highlighting the importance of incorporating the microbiome into safety assessment frameworks, thereby providing a scientific foundation for developing more forward-looking ecological risk assessment standards.},
}

@article {pmid41753582,
year = {2026},
author = {Pickup, RW and Ooi, PB and Agrawal, G and Atkinson, PM and Sanderson, J and Ali, RAR},
title = {Crohn's Disease in Malaysia: Could Application of the Precautionary Principle Reduce Future Incidence?.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020295},
pmid = {41753582},
issn = {2076-2607},
support = {STR-FCRI-LIVE-003-2022.//Lancaster University and Sunway University/ ; },
abstract = {Inflammatory bowel disease (IBD) comprises mainly Crohn's disease (CD) and Ulcerative Colitis (UC). The Western model suggests that environmental factors, immunological factors, the gut microbiome, and genetic disposition all contribute to the onset and sustained symptoms that define CD, although the pathogenesis of CD remains unresolved. Current studies propose that in individuals who are genetically susceptible, genetic factors linked to immune dysregulation, in combination with environmental exposure, can result in dysbiosis of the gut microbiome and intestinal barrier dysfunction, leading to immune dysregulation. In Malaysia, the incidence of IBD is rising with CD increasing disproportionally compared to UC, and the incidence of CD currently mirrors that of the United Kingdom in the 1930s, which now has one of the highest incidences worldwide. Given the suggested role of Mycobacterium avium subspecies paratuberculosis (MAP) in CD in Western countries, which is subject to some controversy, this review summarises for the first time the current evidence on genetic, environmental, and microbial factors that could contribute to the rise of Crohn's disease in Malaysia and proposes preventive approaches. We note the increasing reliance of Malaysia on imported cattle and milk products from areas of high Johne's Disease prevalence to meet increasing demand and changes in milk preferences in the Malaysian population, both key indicators for human-MAP exposure in the Western model. Therefore, should MAP be shown to be associated with CD in Malaysia, some preventative measures are suggested, such as screening imported and native beef and dairy cattle, dairy products and ultimately water, both recreational and potable.},
}

@article {pmid41753572,
year = {2026},
author = {Lohbrunner, L and Baessler, C and Becker, E and Döhla, C and Droll, N and Hagen, RM and Klein, N and Mutters, NT and Reyhe, A and Weppler, R and Döhla, M},
title = {Hospital Wing Opening Sparks Antimicrobial Resistance in Wastewater Microbial Community Within the First Twelve Months.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020285},
pmid = {41753572},
issn = {2076-2607},
support = {Open Access Publication Fund//University of Bonn/ ; },
abstract = {Antimicrobial resistance (AMR) in hospital wastewater is a recognized public health concern, yet the dynamics of its emergence remain poorly understood. This study aimed to characterize the quantitative and qualitative changes in the microbial community of a newly built internal medicine intensive care hospital wing following the start of patient treatment. Wastewater samples were collected regularly from eight relevant sites, including seven patient-associated locations within the intensive care ward and the central sanitary sewer where all effluent converged. Culture-based analyses targeted the "ESCAPE-SO" bacterial and fungal groups ("Enterococci", "Staphylococci", "Candida", "Acinetobacter", "Pseudomonas", "Enterobacteriaceae", "Stenotrophomonas", "Others"). Comparisons were made between a 12-month pre-operation period (only flushing every 72 h to prevent contamination of the drinking water system) and the first 12 months of patient treatment. The results showed a significant increase in mean bacterial concentrations from 53 [0-349] CFU/mL before patient treatment to 8423 [3054-79,490] CFU/mL during patient treatment (p = 0.0224) with a particular focus on Pseudomonas spp. as the dominant genus. Resistance against all four main antibiotic classes of the WHO AWaRe essential "watch" list (carbapenems, third-generation cephalosporins, broad-spectrum penicillin and ciprofloxacin) emerged within the first twelve months and depended on the amount of prescribed antibiotics and the number of patients treated. These findings indicate that hospital activity drives rapid development of antimicrobial resistance in wastewater microbial communities, highlighting the critical role of clinical antibiotic use in shaping environmental resistomes. This study provides quantitative evidence that resistance can emerge within months of hospital operation, emphasizing the need for early monitoring and targeted interventions to mitigate the spread of AMR from hospital effluents into broader environmental systems.},
}

@article {pmid41753563,
year = {2026},
author = {Ding, Y and Liu, A and Ma, B and Zhang, H and Zhang, C and Li, J and Han, J and Shi, C},
title = {Perinatal Antibiotic Timing Impairs Maternal IgG Transfer via FcRn and Shapes the Neonatal Gut Microbiome in Mice.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020276},
pmid = {41753563},
issn = {2076-2607},
abstract = {Perinatal antibiotic exposure poses a significant risk to maternal-offspring immune programming and infant gut microbiota development. This study investigated the time-specific effects of maternal cefoperazone sodium (CPZ) administration on IgG transfer and offspring gut microbiota in a murine model. Pregnant C57BL/6J mice were assigned to control (CON), gestational (G-CPZ), lactational (L-CPZ), and combined gestational/lactational (GL-CPZ) treatment groups. Results showed that all CPZ treatments significantly reduced IgG and its subtype levels in maternal serum, colostrum, and offspring serum (p < 0.05). Concurrently, mRNA expression of the neonatal Fc receptor (FcRn), critical for IgG transport, was downregulated in both maternal breast and offspring intestinal tissues (p < 0.05). Furthermore, 16S rRNA sequencing revealed that CPZ exposure altered offspring gut microbiota diversity and composition. Alpha diversity was reduced, particularly in the G-CPZ group, while beta diversity showed significant separation in L-CPZ and GL-CPZ groups (p < 0.05). Taxonomic shifts included decreased Bacteroidetes and Lactobacillus, and in the GL-CPZ group, a marked increase in Firmicutes and potential pathobionts like Enterococcus and Hungatella (p < 0.05). These findings demonstrate that perinatal antibiotic exposure, depending on its timing, impairs maternal-offspring IgG transfer via the FcRn pathway and induces distinct, persistent alterations in the offspring's gut microbiota, which may have implications for neonatal immunity and long-term health.},
}

@article {pmid41753553,
year = {2026},
author = {Li, Y and Yu, Z and Cao, Q and Wang, H and Zhang, R and Liu, C and Wang, T and Wang, C},
title = {A Novel Approach to Biodegradation and Detoxification of Ricinine in Castor Meal: Relationship Between the Gut Microbiota and Microbial Metabolites of Hermetia illucens.},
journal = {Microorganisms},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/microorganisms14020265},
pmid = {41753553},
issn = {2076-2607},
support = {42407180, 42077357//National Natural Science Foundation of China/ ; NRGC202208//Hubei key Laboratory of Novel Reactor and Green Chemical Technology/ ; GCX2024006//Key Laboratory for Green Chemical Process of Ministry of Education/ ; 2024DJC045//Hubei Province Science and Technology Talent Service Enterprise Project/ ; },
abstract = {Hermetia illucens can digest toxic castor meal and tolerate ricinine stress. However, the underlying mechanisms of ricinine degradation and detoxification within the larval gut microbiome remain largely unknown. Here, the enhanced degradation kinetic process, and the roles of the gut bacterial community and metabolomics were investigated. When the ricinine content was 1000 mg kg[-1] in feeding substrate, larval development was not significantly affected. The ricinine degradation kinetics, facilitated by larval digestion, were significantly enhanced, reducing the degradation half-life to 5.13 days. The gut bacterial community structure adjusted in response to ricinine stress, suggesting that genera such as Dysgonomonas, Actinomyces, Phascolarctobacterium, Lachnoclostridium and Sedimentibacter might play key roles in ricinine resistance and degradation. Furthermore, the gut microbial metabolism responded to toxin stress, reflected by variations in metabolite expression and the enrichment of key metabolic pathways involved in amino acid and vitamin metabolism. This emphasizes the potential role of microbial metabolism in ricinine degradation and detoxification. The close association between gut bacteria and metabolites suggests a cooperative metabolic network within the gut microbiota, where bacteria may participate in ricinine degradation and detoxification either directly or through metabolic cooperation. These findings provide insights into host-microbe interactions and ricinine resistance, highlighting the need for further exploration into the microbiota's role in host metabolism and the development of new therapeutic strategies.},
}

@article {pmid41753276,
year = {2026},
author = {Beca, AM and Folescu, R and Crăciun, AT and Olariu, L and Enatescu, I and Belei, B and Belei, O},
title = {Gut Microbiota Alterations and Dysbiosis Patterns in Pediatric Inflammatory Bowel Disease: Clinical Correlations and Therapeutic Impact.},
journal = {Journal of clinical medicine},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/jcm15041589},
pmid = {41753276},
issn = {2077-0383},
support = {Not applicable//Victor Babeș University of Medicine and Pharmacy Timișoara/ ; },
abstract = {Background: Gut microbiota alterations are increasingly recognized as key contributors to the development and clinical course of inflammatory bowel disease (IBD), particularly in pediatric patients, in whom microbial maturation and immune regulation are still evolving. Objective: This study aimed to assess intestinal microbiota composition and dysbiosis severity in pediatric IBD, with comparative analyses according to disease phenotype (Crohn's disease versus ulcerative colitis) and therapeutic strategy (biologic versus non-biologic treatment). Methods: A prospective cohort of 60 pediatric patients diagnosed with IBD based on Porto criteria was evaluated. Fecal samples were obtained at baseline and after three months of combined standard IBD treatment and adjunct microbiota-targeted therapy, and were analyzed using an AI-assisted microbiota profiling platform. A semi-quantitative dysbiosis score was calculated based on the relative abundance of proinflammatory taxa and depletion of short-chain fatty acid (SCFA)-producing bacteria. Microbial parameters were correlated with clinical and therapeutic variables, including the Organism of Interest metric and the Gut Microbiota Index (GMI). Results: Dysbiosis severity was significantly higher in patients with Crohn's disease compared with ulcerative colitis (9.65 ± 1.44 vs. 8.42 ± 1.88, p = 0.037). Patients receiving biologic therapy showed a trend toward lower dysbiosis scores and improved microbial indices, although statistical significance was not reached. Severe dysbiosis was identified in 46.7% of the cohort. Strong positive correlations were observed between the dysbiosis score, Organism of Interest metric and GMI (r = 0.68-0.72, p < 0.01). Conclusions: Pediatric IBD is associated with a reproducible dysbiotic profile, more pronounced in Crohn's disease and partially modulated by biologic therapy. The observed correlations between microbiota-derived indices support their potential utility as complementary markers of intestinal microbial imbalance and disease activity.},
}

@article {pmid41753013,
year = {2026},
author = {Crespo, J and Argos Vélez, P and Alonso-Peña, M and Cayón, L and Jiménez-González, C and Iruzubieta, P},
title = {MASLD Under the Umbrella of the Microbiota: A Narrative Review on Ecological Risk and Functional Transmissibility.},
journal = {Journal of clinical medicine},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/jcm15041325},
pmid = {41753013},
issn = {2077-0383},
support = {101095679//HORIZON-HLTH-2022-STAYHLTH-02/ ; PI22/01853//Fondo de In-601 vestigaciones Sanitarias, Instituto de Salud Carlos III, Spain/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of chronic liver disease worldwide, distinguished by pronounced clinical heterogeneity and a frequent dissociation between metabolic risk factors and the degree of hepatic injury. These observations, together with the limited contribution of genetic heritability, have prompted a re-evaluation of the traditional conceptual framework of the disease. In this context, the question has emerged as to whether MASLD could be, at least in part, a transmissible condition. While there is no evidence to suggest that MASLD is contagious in humans, as no data support person-to-person transmission, gnotobiotic animal studies demonstrate that human gut microbiota can transfer susceptibility to steatosis, inflammation, and systemic metabolic disturbances through immunometabolic mechanisms, independent of host genetics. In parallel, human studies involving microbiota-targeted interventions support the concept that the gut ecosystem is a modifiable determinant of metabolic and hepatic phenotypes. Crucially, these findings do not imply natural transmission of disease, but rather underscore the functional plasticity of microbiota-host interactions. This narrative review integrates epidemiological, experimental, and clinical data to explore the hypothesis that MASLD may be functionally transmissible. MASLD is increasingly recognized as an eco-biological disease, where liver disease risk is not only shaped by host genetics and environment, but also by the ecological configuration and functional outputs of the gut microbiome. This perspective redefines disease susceptibility as, in part, context-dependent and microbiota-mediated, without implying infectiousness in the traditional sense.},
}

@article {pmid41752979,
year = {2026},
author = {Schettini, G and Pieri, E and Rizzo, C and Giorgi, M and Mancini, V and Habib, N and Rovira, R and Centini, G},
title = {A Dive into the Invisible: The Vaginal and Endometrial Microbiota in Gynecologic and Obstetric Disorders: A Narrative Review.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/life16020344},
pmid = {41752979},
issn = {2075-1729},
abstract = {The human microbiota is increasingly recognized as a key component of women's reproductive health. This narrative review examines the vaginal, endometrial, and gut microbiota and their roles in the pathogenesis of gynecologic and obstetric disorders, aiming to integrate current evidence into a clinically relevant framework. We review intrinsic (genetic, hormonal, and immunological) and extrinsic (environmental, lifestyle, and pharmacological) factors shaping microbial composition, with particular focus on dysbiosis and the role of the gut estrobolome within the microbiome in estrogen metabolism. The review synthesizes data on microbiota alterations associated with endometriosis, adenomyosis, uterine fibroids, endometrial polyps and hyperplasia, gynecologic malignancies, pelvic inflammatory disease, bacterial vaginosis, infertility, and adverse obstetric outcomes, including preterm birth and fetal growth restriction. Methodological approaches used to characterize the reproductive tract microbiota, such as vaginal swabs, endometrial sampling, and fecal analysis, are critically discussed, together with limitations related to low-biomass environments and contamination risk. Evidence regarding therapeutic modulation of the microbiota, including antibiotics, probiotics, hormonal therapies, and emerging microbiota-based interventions, is summarized, alongside the impact of gynecologic surgery on microbial translocation and long-term microbial balance. Overall, the available literature supports an association between microbiota alterations and multiple reproductive conditions, although causality remains incompletely established. Further standardized and longitudinal studies are needed to clarify mechanisms and guide microbiota-informed diagnostic and therapeutic strategies.},
}

@article {pmid41752930,
year = {2026},
author = {Glavina, A and Martić, D and Perko, MA and Mešin Delić, D and Tadin, A and Lešić, S and Šupe-Domić, D},
title = {The Oral Microbiome and Systemic Health: Current Insights into the Mouth-Body Connection.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/life16020294},
pmid = {41752930},
issn = {2075-1729},
abstract = {The oral cavity contains a complex and dynamic microbial ecosystem that plays a central role in maintaining both local and systemic homeostasis. Emerging evidence indicates that disturbances in oral microbial communities-including genetic and functional diversity within species-are associated not only with oral diseases but may also contribute to the development and progression of systemic diseases. This narrative review summarises the current state of knowledge on bidirectional interactions between oral microbial communities and major organ systems. A comprehensive search of PubMed/MEDLINE, Web of Science, Scopus, and Cochrane databases was conducted for studies published between 2019 and 2025, prioritising systematic reviews, meta-analyses, and high-quality mechanistic studies. Ultimately, 40 articles were included in the narrative synthesis. The results provide clear evidence of an association between oral dysbiosis and cardiovascular disease (CVD), type 2 diabetes mellitus (T2DM), chronic respiratory infections, and adverse pregnancy outcomes (APOs). Recent data also suggest links with neurodegenerative disorders, chronic kidney disease (CKD), autoimmune diseases, and cancer. Proposed mechanisms include transient or persistent bacteraemia, systemic inflammation caused by microbial metabolites and endotoxins, disruption of immune homeostasis, molecular mimicry, and modulation of host metabolic pathways. Despite growing evidence linking oral microbial communities to systemic health, most findings are based on observational studies, and causal relationships remain to be established through longitudinal and interventional research. Understanding the connection between the mouth and the body highlights the potential for targeting oral microbial activity, virulence factors, and host inflammatory responses in disease prevention and treatment.},
}

@article {pmid41752919,
year = {2026},
author = {Suarez, B and Álvarez, AM and Mascardi, MF and Ramos, ALM and Woo, DH and Gutiérrez, MM and Alzueta, G and Basbus, MDC and Bruzone, S and Cuart, P and Dieuzeide, G and García, T and Escobar, O and Carulla, RDJ and Oviedo, C and Segura, N and Vera, ODV and Giunta, JN and Gadano, A and Trinks, J},
title = {Interactions Between the Gut Microbiome and Genetic and Clinical Risk Factors for Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) in Patients with Type 2 Diabetes Mellitus from Different Geographical Regions of Argentina.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/life16020283},
pmid = {41752919},
issn = {2075-1729},
support = {22920200100009CO//PUE CONICET/ ; 2023//Sociedad Argentina de Diabetes Translational Research Grant/ ; },
abstract = {Background: Local specific biomarkers for MASLD risk stratification are urgently needed in Argentina. Aim: The aim of the study was to characterize the interaction of gut microbiome signatures and genetic and clinical risk factors for MASLD in patients with diabetes from different regions of Argentina. Materials and Methods: We recruited 214 patients with diabetes from different regions of Argentina. Anthropometric, clinical, and lifestyle data were obtained from all participants, who also underwent abdominal ultrasound for MASLD diagnosis and oral swabbing. The PNPLA3 gene was amplified by PCR from the swabs, and the rs738409 genotype was determined via bidirectional sequencing. To profile the MASLD-associated microbiome, stool was collected from 170 participants. V4 16S rRNA gene sequencing was performed, and reads were analyzed using QIIME2 2024.10.1. R Studio 2023.05.1 was used for statistical analyses. Results: MASLD prevalence was 77.9%, with similar rates of occurrence in all regions represented. FIB-4 scores < 1.3 and > 2.67 were detected in 55.3% and 7.4% of patients, respectively. Half of the diabetic patients had the PNPLA3 GG genotype, with the highest rates occurring in patients from Northwestern Argentina (64.9%; p = 0.02 vs. Buenos Aires). The PNPLA3 GG genotype was an independent risk factor for FIB-4 score (p = 0.0008) and a protective factor against glycated hemoglobin (p = 0.004), fasting plasma glucose (p = 0.008), and cholesterol levels (p = 0.02). Marked regional differences were observed in microbiota diversity and composition in Argentina. After adjusting for geographical region, Negativibacillus genus was exclusively detected in diabetic patients with MASLD and GG carriers. The Catenibacterium genus was related to FIB-4 > 2.67. Short-chain fatty acid-producing bacteria were linked to the absence of MASLD. Conclusions: Although some geographical regions of Argentina were not represented in this study and these results therefore cannot be generalized to the country as a whole, these specific signatures could be useful as biomarkers for MASLD risk stratification in Argentines with diabetes.},
}

@article {pmid41752848,
year = {2026},
author = {Liu, Y and Wang, K and Jiang, X and Wang, G},
title = {The Ratio of S[2-]/SO4[2-] Induces the Transference of Cadmium in Rhizosphere Soil, Soil Pore Water and Root Iron Plaque.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/life16020211},
pmid = {41752848},
issn = {2075-1729},
support = {2024HPYKFYB03//Key Laboratory for Lake Pollution Control of the Ministry of Ecology and Environment/ ; },
abstract = {Rice (Oryza sativa L.) readily accumulates cadmium (Cd), posing dietary exposure risks in populations dependent on rice-based diets. This study investigated how sulfur (S) redox processes regulate Cd mobility in S-deficient, Cd-contaminated paddy soil under waterlogged conditions. A pot experiment was conducted with two S treatments (-S and +S, 30 mg kg[-1]) throughout the rice growing season. S addition markedly increased pore water S[2-] concentrations during early growth (tillering) and mid-season (booting) and suppressed the diffusion of SO4[2-] from non-rhizosphere to rhizosphere at later stages (filling-maturity). Consequently, Cd in soil pore water was significantly lower in +S than -S treatments at all stages. Sulfur-amended soil showed a redistribution of Cd from labile fractions (exchangeable and carbonate-bound) to more stable fractions (Fe/Mn oxide-bound). Sulfur application also altered the rhizosphere microbiome: the relative abundance of sulfate-reducing bacteria (SRB) increased at the booting and filling stages, while sulfur-oxidizing bacteria (SOB) became more dominant at maturity. Additionally, +S enhanced Cd sequestration on rice root iron plaque by 32-67% during the grain-filling and maturity stages compared to -S. Throughout the rice growing period, redox-driven shifts in the S[2-]/SO4[2-] ratio emerged as a key control on Cd behavior, with low pe + pH (strongly reducing conditions) promoting Cd sulfide precipitation and high pe + pH (more oxidizing conditions) causing Cd remobilization.},
}

@article {pmid41752713,
year = {2026},
author = {Filippini, M and Sozzi, J and de Góis Speck, NM and Fusco, I and Kesserling Tso, F and Dores, E and Farinelli, M},
title = {Efficacy and Safety of CO2 Laser Therapy Combined with Collagen Cream in Managing Vulvo-Vaginal Atrophy: A Randomized, Controlled Study on Symptom Relief and Microbiome Modulation.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {2},
pages = {},
doi = {10.3390/medicina62020314},
pmid = {41752713},
issn = {1648-9144},
abstract = {Background and Objectives: Vulvo-vaginal atrophy (VVA), a prevalent condition among postmenopausal women, significantly impairs quality of life through symptoms like vaginal dryness, dyspareunia, and burning. Non-hormonal treatments, such as CO2 laser therapy, have shown promise in managing VVA symptoms with minimal side effects. The addition of adjunctive treatments may enhance efficacy and mitigate possible adverse effects. To evaluate the combined efficacy and safety of CO2 laser therapy and a collagen-based cream in treating VVA and to explore their potential impact on the vaginal microbiome. Materials and Methods: This was a single-center, randomized, interventional. Sixty postmenopausal women diagnosed with VVA were randomized into two groups: a control group receiving laser-only treatment and a treatment group receiving laser therapy with daily collagen-based cream application. Primary outcome measures included symptom improvement on the Visual Analog Scale (VAS) for VVA-associated symptoms. Secondary outcomes involved microbiome composition analysis. Results: Both groups showed significant symptom improvement, with the combination therapy group demonstrating superior reductions in burning, dyspareunia, and vaginal dryness (p < 0.05). Microbiome analysis revealed increased levels of beneficial species (Lactobacillus iners and Lactobacillus crispatus) and decreased pathogenic bacteria (Gardnerella vaginalis and Atopobium vaginae) in the treatment group, though these changes were not statistically significant. Mild side effects, such as burning and swelling in the first days following the treatment, were less frequent in the combination therapy group, likely due to the anti-inflammatory effects of the collagen-based cream. Conclusions: This study provides evidence supporting the use of CO2 laser therapy with collagen-based cream as an effective and well-tolerated treatment for VVA in postmenopausal women, achieving significant symptom relief. The combined therapy approach holds potential for enhanced efficacy and reduced side effects compared to laser-only treatment, offering a promising alternative for women ineligible for hormone-based therapies.},
}

@article {pmid41752210,
year = {2026},
author = {Mahmood, SM and Al-Nasrallah, HK and Aldossry, A and Al-Ansari, MM and Al-Alwan, M},
title = {Breast-Cancer-Derived Secretomes from MCF-7 Cells Modulate Bacterial Pathogenic Traits.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27042073},
pmid = {41752210},
issn = {1422-0067},
support = {RAC# 2240005//King Faisal Specialist Hospital and Research Centre/ ; },
abstract = {Breast cancer is the most frequently diagnosed malignancy among women worldwide, with the luminal A subtype being the most prevalent. Several studies have reported a complex interplay between breast cancer cells and the local microbiome; however, the mechanisms by which tumor cell-secreted factors influence bacterial biological properties remain insufficiently explored. In this study, we established an in vitro model that partially recapitulates the luminal A breast cancer microenvironment by exposing three breast-associated bacterial species, Pseudomonas aeruginosa, Enterococcus faecalis, and Escherichia coli, to conditioned media (CM) derived from MCF-7 (tumor) or MCF-10A (non-tumor control) cell lines. A combination of complementary approaches, including ultrastructural morphological assessment, biofilm formation assays, antimicrobial susceptibility testing, and virulence gene abundance profiling by genomic qPCR, was employed to reveal distinct tumor-microbiota interactions. Exposure to MCF-7 CM induced dose-dependent structural alterations in P. aeruginosa and E. faecalis, with pronounced membrane blebbing and structural disruption in E. faecalis. Biofilm formation was differentially modulated in a species- and concentration-dependent manner, with a persistent increase observed in E. coli. Antibiotic susceptibility profiles were selectively altered in E. faecalis, which displayed increased sensitivity to vancomycin, penicillin, and imipenem, along with decreased sensitivity to chloramphenicol. P. aeruginosa exhibited increased sensitivity to imipenem along with reduced sensitivity to meropenem and gentamicin, whereas no significant changes were observed in E. coli. qPCR analyses demonstrated that MCF-7 CM was associated with enrichment of multiple virulence-associated genes (e.g., lasB, exoS, pilB, plcH, fsrC, esp, fimH, and papG), reflecting enhanced pathogenic and adhesive potential. Collectively, these findings suggest that luminal A breast cancer-derived factors can reprogram microbial phenotypes in a species-specific manner, providing mechanistic insight into breast tumor-microbiome crosstalk and a platform to explore microbiome-targeted interventions.},
}

@article {pmid41752202,
year = {2026},
author = {Jung, S},
title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27042068},
pmid = {41752202},
issn = {1422-0067},
support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; },
abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.},
}

@article {pmid41752141,
year = {2026},
author = {Wu, Y and Wong, OWH and Chen, S and Wang, Y and Zhang, G and Gao, Y and Chan, FKL and Ng, SC and Su, Q},
title = {Gut Microbiome Mediates the Causal Link Between Autism Spectrum Disorder and Dietary Preferences: A Mendelian Randomization Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27042006},
pmid = {41752141},
issn = {1422-0067},
abstract = {Autism spectrum disorder (ASD) frequently co-occurs with malnutrition and gut dysbiosis, yet the underlying mechanisms remain poorly understood. Herein, this cross-sectional study first profiles dietary intake differences using dietary records from 210,874 participants (ASD = 232; non-ASD = 210,642; median age = 56.18) from the UK Biobank (UKB). Second, a bi-directional Mendelian Randomization (MR) approach serves to dissect relationships between ASD genetic susceptibility and dietary preferences by leveraging genome-wide association metadata from the iPSYCH-PGC (ASD) and UKB (dietary intake/food-liking traits). The same strategy is implemented to identify ASD-associated gut microbial species. Mediation analyses further assess the role of gut microbiota in the association between ASD and dietary preferences. Subjects with ASD exhibit higher consumption of cheese, processed meat, and oily fish, alongside lower intake of fruits, and demonstrate a preference for high-fat/salt and energy-dense foods. Additionally, the depletion of Turicibacter, Streptococcus, and Lachnospiraceae NK4A136 was causally related with ASD (all false discovery rate < 0.05; β = -0.15, β = -0.10, β = -0.093, respectively), which significantly mediates the ASD-associated elevated preference for high-fat/salt foods. In conclusion, ASD is associated with specific dietary preferences, likely mediated via gut microbiota, highlighting the future potential of gut microbiome-based therapeutics to modify eating disorders for ASD.},
}

@article {pmid41752122,
year = {2026},
author = {Wang, SJ and Nian, HY and Chen, ZH and Cui, L},
title = {Human Microbiota-Associated Pig Models for Translational Microbiome Research: A Scoping Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27041987},
pmid = {41752122},
issn = {1422-0067},
support = {23141900100//Science and Technology Commission of Shanghai Municipality/ ; },
abstract = {The human microbiota-associated (HMA) pig model provides a physiologically relevant platform that bridges preclinical and translational research. However, its use remains limited, with existing studies showing considerable variation in establishment methods. This scoping review systematically evaluates methodological frameworks, engraftment outcomes, and research applications of HMA pig models. Additionally, it highlights their strengths, limitations, and implications for future studies. We conducted a comprehensive literature search in PubMed, Web of Science, Scopus, and Directory of Open Access Journals, following PRISMA guidelines for Scoping Reviews. The review examines the methodological foundations of HMA pig model generation and proposes a minimal reporting framework to promote standardization. It synthesizes studies on human microbiota engraftment in pigs, identifying factors that influence colonization efficiency. Finally, it summarizes current applications, discusses persistent limitations and translational challenges, and outlines opportunities for future research. Overall, these integrated insights aim to foster standardized, reproducible protocols for HMA pig model preparation and guide advancements in the field.},
}

@article {pmid41752118,
year = {2026},
author = {Kurdi, MA and Alotaibi, H and Alkhuraymi, AT and Aldahery, LN and Alhawaj, AF and Aldali, HJ},
title = {Amyotrophic Lateral Sclerosis (ALS) Genetics and Microbiota: A Comprehensive Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27041978},
pmid = {41752118},
issn = {1422-0067},
abstract = {Amyotrophic Lateral Sclerosis (ALS) is a severe, progressive neurodegenerative disorder characterized by the loss of upper and lower motor neurons, affecting 0.5 to 2.6 per 100,000 people, with a median survival of 2 to 5 years. It is increasingly seen as a multisystem disorder, sharing essential clinicopathological features with Frontotemporal Dementia (FTD). This convergence arises from overlapping molecular processes, including severe oxidative stress, glutamate-mediated excitotoxicity, mitochondrial dysfunction, and widespread aggregated TDP-43 proteinopathy in both sporadic and familial cases. Several key genetic factors have been identified, particularly mutations in C9orf72, SOD1, TARDBP, and FUS, which serve as important targets for novel treatments, such as Tofersen, a recently approved SOD1-specific antisense oligonucleotide (ASO) gene therapy. Additionally, there is increasing evidence of the gut-brain connection. Dysbiosis, involving species such as Akkermansia muciniphila, and lower levels of neuroprotective metabolites, such as nicotinamide, may affect the course of the disease. As a result, treatment strategies are shifting toward a personalized approach. This includes using gene therapy, ranging from ASOs and RNA interference (RNAi) to new CRISPR-based genome editing. It also involves exploring microbiome-modulating treatments, such as specific probiotics and Fecal Microbiota Transplantation (FMT). While microbiome and gene therapies remain largely experimental, their potential is promising, as highlighted by the recent approval of Tofersen. These novel approaches could be further enhanced and guided by more robust diagnostic criteria and by investigating early multimodal treatment strategies to slow the progression of this complex disease.},
}

@article {pmid41751979,
year = {2026},
author = {Eskildsen, J and Dong, M and Hanak, T and Madsen, CK and Holme, I and Plaszkó, T and Vestergård, M and Nicolaisen, M and Thordal-Christensen, H and Brinch-Pedersen, H},
title = {Novel CRISPR/Cas9-Derived mlo Alleles in Barley: Resistance to Powdery Mildew and Microbiome Implications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27041846},
pmid = {41751979},
issn = {1422-0067},
support = {NNF19OC0056580//Novo Nordisk Foundation/ ; BarleyMicroBreed, 101060057//EU Horizon research and innovation/ ; },
abstract = {Barley grown in temperate regions is often challenged by powdery mildew disease. An effective solution is mildew resistance locus o (mlo)-based resistance, which is monogenic, durable, and broad-spectrum. While the pleiotropic effects of mlo mutations on above-ground tissues are well documented, their impact on the root-associated microbiome remains underexplored. We utilized CRISPR/Cas9 to generate novel mlo mutant lines and evaluated their resistance to causal fungus Blumeria hordei. We further examined if mlo knockout has any impact on the overall root microbiome diversity and composition under field-like conditions and applied DESeq2 to compare the abundance of microbial taxa between mutants and wild type. We created five novel resistant mlo lines, including the first mutants with amino acid alterations in the protein's extracellular region. Mutant lines showed significantly reduced B. hordei colony formation (0.5-5%). While microbial alpha and beta diversity were not significantly altered, a few microbial taxa displayed time-dependent shifts in abundance. Overall, our study demonstrates the effectiveness of CRISPR/Cas9 in generating mlo-based resistance. Moreover, the study revealed functionally important residues in the protein's extracellular region. Finally, we present the first evidence of limited mlo-associated effects on root microbiome diversity and relative abundance of microbial taxa.},
}

@article {pmid41751912,
year = {2026},
author = {Huang, S and Chaudhari, DS and Shukla, R and Kanani, P and Zeidan, RS and Lin, Y and Burrow, W and Mankowski, RT and Jain, S and Yadav, H},
title = {Global Microbiome: Core and Unique Signatures Across Diverse Populations.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27041776},
pmid = {41751912},
issn = {1422-0067},
abstract = {Earlier analyses evaluating patterns of gut microbiota in individuals from different geographies and age groups are heterogeneous in methodology, precluding broader conclusions about the relationship between the gut microbiome and geographic region, age, and clinical health. Here, we systematically conducted a meta-analysis of 16s rRNA gut microbiome sequencing data representing 10,878 samples across North America, Europe, Africa, Asia and Oceania. Our analysis included 27 countries and three age groups (neonate to age 17, or AG01; ages 18 to 64, or AG02; 65 and above, or AG03). We identified that Firmicutes, Bacteriodetes, and Proteobacteria constitute core phyla across geographic regions. A differing predominance of top families alongside core family Lachnospiracaeae across regions comprised unique microbiome signatures. Countries also differed in their relative abundances of Bifidobacterium, Faecalibacterium, Lactobacillus and Bacteroides. We found in our age analyses that Proteobacteria and Actinobacteria were the most abundant phyla in AG01, and Actinobacteria abundance declined across all continents with increasing age. The relative abundance of Bacteriodetes increased between AG01 and AG02. Enrichment of asthma-associated Enterobacterieaceae in AG01 was highest for North America, followed by Europe and then in Asia. We discuss the correlation of these gut microbial patterns in the context of dietary patterns, populations health, clinical health trends, and healthy aging.},
}

@article {pmid41751904,
year = {2026},
author = {Katiraei, P and Frye, RE and Theoharides, TC},
title = {Gut-Brain Inflammation and Disrupted Homeostasis Due to Activation of Mast Cells and Microglia.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27041768},
pmid = {41751904},
issn = {1422-0067},
abstract = {Recent data from the Centers for Disease Control (CDC) indicate that the incidence of Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized by deficits in social communication and the presence of restricted interests and repetitive behaviors, has increased to 1 in 31 children. Individuals with ASD have a constellation of neurological, behavioral, sensory, feeding, gastrointestinal, and immunological issues. Even though there is some genetic component to the pathogenesis of ASD, accumulation of environmental and pathogenic toxins could contribute to disruption of the gut-blood-barrier (GBB) and blood-brain barrier (BBB) via activation of mast cells (MCs) and microglia, resulting in a chronic cycle of gut-brain inflammation. Here we discuss how various environmental, pathogenic, and stress factors can disrupt gut-brain homeostasis to create susceptibility and epigenetic effects that contribute to the development of ASD. We also suggest simple ways to address some of the key pathogenetic processes involved in ASD.},
}

@article {pmid41751903,
year = {2026},
author = {Marton, J and Ciocan, RA and Bâldea, I and Gherman, ML and Gheban, D and Filip, A and Pașcalău, IR and Mihăileanu, FV and Pop, RM and Gherman, CD},
title = {Molecular Mechanisms, Dynamic Lesions, and Therapeutic Targets in Intestinal Ischemia-Reperfusion Injury: A Systematic Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27041763},
pmid = {41751903},
issn = {1422-0067},
abstract = {Intestinal ischemia-reperfusion injury (IRI) represents a major cause of morbidity and mortality in abdominal surgery, trauma, and intestinal transplantation. The pathophysiological process involves a biphasic cascade that begins with ischemic hypoxia and progresses to amplified cellular and molecular injury upon reperfusion. This review synthesizes recent mechanistic insights regarding endothelial and microvascular dysfunction, epithelial barrier breakdown, microbiota-driven systemic propagation, and the involvement of oxidative/nitrosative stress and inflammatory signaling. The novelty of our review's approach is the focus on experimental and translational studies and correlation of the data with future directions for mechanistic research and clinical implementation. Despite promising preclinical results, heterogeneity in study protocols or/and model limitations make clinical translation challenging. Recent studies have demonstrated that mitochondria, tight junction proteins, adhesion molecules and innate immune receptors are critical determinants of lesion evolution. Based on these, the current therapeutic strategies include antioxidants, adenosine pathway modulators, dexmedetomidine, ischemic conditioning, hyperbaric oxygen therapy, and microbiota-targeted interventions. Since each mechanism is acting on distinct molecular pathways, a multimodal therapy that integrates redox modulation, endothelial protection, microbiome regulation, and the identification and employment of precision biomarkers is likely to improve outcomes. Beyond summarizing established molecular mechanisms, this review critically reassesses why decades of promising experimental strategies for intestinal ischemia-reperfusion injury has largely failed to translate into effective clinical therapies. By distinguishing context-dependent mechanisms from pathways with consistent translational relevance, we highlight key methodological and biological barriers limiting clinical applicability. Furthermore, we propose a temporally structured, multimodal therapeutic framework that integrates phase-specific pathophysiology with targeted interventions, aiming to inform future experimental design and improve translational success.},
}

@article {pmid41751881,
year = {2026},
author = {Abd-Elgawad, MMM},
title = {Grasping Molecular Biology Mechanisms to Optimize Plant Resistance and Advance Microbiome Role Against Phytonematodes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27041744},
pmid = {41751881},
issn = {1422-0067},
support = {No. 47725//STDF/ ; },
abstract = {Plant-parasitic nematodes (PPNs) cause big crop losses globally. Safe/reliable methods for their durable management strategies can harness various beneficial relationships among the plant immune system and related microbiomes. Molecular mechanisms basic to these relations reveal wide arrays of significant roles for plant-healthy growth. This review focuses on such relations of microbiomes to prime and immunize plants against PPNs. It also highlights molecular issues facing PPN-resistant varieties with possible solutions such as genetic breeding/engineering, grafting, PPN-antagonistic root exudates, and novel resistant cultivars. These issues call for optimal uses of various widespread groups of microbiomes. Related plant signaling hormones and transcription factors that regulate gene expression and modulate nematode-responsive genes to ease positive/negative adaptation are presented. Exploring PPN-resistance genes, their activation mechanisms, and signaling networks offers a holistic grasp of plant defense related to biotic/abiotic factors. Such factors relevant to systemic acquired resistance (SAR) via plant-microbe interactions to manage PPNs are stressed. The microbiomes can be added as inoculants and/or steering the indigenous rhizosphere ones. Consequently, SAR is mediated by the accumulation of salicylic acid and the subsequent expression of pathogenesis-related genes. To activate SAR, adequate priming and induction of plant defense against PPNs would rely on closely linked factors. They mainly include the engaged microbiome species/strains, plant genotypes, existing fauna/flora, compatibility with other involved biologicals, and methods/rates of the inoculants. To operationalize improved plant resistance and the microbiome's usage, novel actionable insights for research and field applications are necessary. Synthesis of adequate screening techniques in plant breeding would better use multiple parameters (molecular and classical ones)-based ratings for PPN-host suitability designation. Sound statistical analyses and interpretation approaches can better identify genotypes with high-level, stable resistance to PPNs than the commonly used ones. Linking molecular mechanisms to consistent field relevance can be progressed via dissemination of many advanced techniques. The CRISPR/Cas9 system has been effective in knocking out both the OsHPP04 gene in rice to confer resistance against Meloidogyne graminicola and the GhiMLO3 gene in cotton to minimize the Rotylenchulus reniformis reproduction. Its genetic modifications in crops synthesized "transgene-free" PPN-resistant plants without decreased growth/yield. Characterizing microbiome species/strains needed to prime and immunize plants requires better molecular tools for fine-scale taxonomic resolution than the common ones used. The former can distinguish closely related ones that exhibit divergent phenotypes for key attributes like stability and production of enzymes and secondary metabolites. As PPN-control strategies via tritrophic interactions are more sensitive to the relevant settings than chemical nematicides, it is suggested herein to test these settings on a case-by-case basis to avoid erratic/contradictory results. Moreover, expanding the use of automated systems to expedite detection/count processes of PPN and related microbes with objectivity/accuracy is discussed. When PPNs and their related microbial distribution patterns were modeled, more aspects of their field distributions were discovered in order to optimize their integrated management. Hence, the feasibility of site-specific microbiome application in PPN-hotspot infections can be evaluated. The main technical challenges and controversies in the field are also addressed herein. Their conceptual revision based on harnessing novel techniques/tools is direly needed for future clear trends. This review also engages raising growers' awareness to leverage such strategies for enhancing plant resistance and advancing the microbiome role. Microbiomes enjoy wide spectrum efficacy, low fitness cost, and inheritance to next generations in durable agriculture.},
}

@article {pmid41751793,
year = {2026},
author = {Ptáček, O and Musil, Z and Guarnieri, G and Vrbacká, A and Moudrá, P and Zlámalová, A and Röszlerová, P and Tonhajzer, M and Musil, V and Morelli, A and Zach, P},
title = {Amyotrophic Lateral Sclerosis: The State of the Art on Treatments and the Therapeutic Role of the Intestinal Microbiome in Human Studies.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
doi = {10.3390/ijms27041655},
pmid = {41751793},
issn = {1422-0067},
support = {Cooperatio 39 - Oncology and Haematology//Charles University/ ; Cooperatio 33-Intensive Care Medicine//Charles University/ ; Cooperatio 36-Medical Diagnostics and Basic Medical Sciences//Charles University/ ; #NEXTGENERATIONEU//European Commission/ ; MNESYS (PE0000006) - A Multiscale integrated approach to the study of the nervous system in health and disease (DR. 1553 11.10.2022)//Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP)/ ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a common neurodegenerative disorder; to date, there is no long-term effective treatment. Recently, a relationship has been discovered between the human intestinal microbiome and the pathogenesis of ALS, on which basis faecal microbiota transplantation (FMT) has been proposed as a potential treatment for ALS. In this review, we compare three existing case studies examining the effect of FMT on the course of ALS, highlighting differences in methodology and results. In two of the studies, a halt in the progression of ALS symptoms was observed following FMT, accompanied by improvement in patient health. However, in the third and largest study, no significant effect of FMT was observed. The possible explanation for this discrepancy may be the intentional depletion of intestinal microorganisms using antibiotics prior to FMT in the third study. Future studies and/or completion of the ongoing clinical studies will help clarify the therapeutic effectiveness of FMT in ALS patients.},
}