@article {pmid42878649,
year = {2026},
author = {Fansler, RT and Zhu, W},
title = {Small RNAs as emerging regulators of commensal adaptation in the mammalian gut.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0029226},
doi = {10.1128/iai.00292-26},
pmid = {42878649},
issn = {1098-5522},
abstract = {The commensal bacteria of the intestinal microbiota inhabit one of the most densely populated and dynamic microbial ecosystems known, where fluctuations in nutrient availability, host-derived stresses, and microbial competition require highly coordinated regulatory responses to maintain colonization and fitness. As a stable, homeostatic microbiota performs essential functions for the host, understanding how commensals adapt to the fluctuating intestinal environment is important for maintaining intestinal homeostasis and informing the development of new microbiota-targeted therapeutics. Throughout diverse bacterial species, rapid adaptation to environmental perturbations is mediated in part by small regulatory RNAs (sRNAs). While most sRNA research has focused on a limited number of model organisms, particularly bacterial pathogens, recent studies have uncovered important roles for these noncoding RNAs in promoting the fitness and resilience of gut commensals. Advances in differential RNA sequencing, comparative genomics, and functional genetics have revealed diverse repertoires of sRNAs in prominent gut symbionts, with regulatory roles in nutrient acquisition, stress responses, and host colonization. This minireview highlights recent advances and outlines future directions to further elucidate sRNA-mediated regulation as a pillar of commensal resilience in the mammalian gut.},
}

@article {pmid42878705,
year = {2026},
author = {Keuschnig, C and Feord, H and Broadwell, ELM and Zervas, A and Tranter, M and Anesio, AM and Benning, LG},
title = {Aerobic anoxygenic phototrophs are widespread and active members of Greenland Ice Sheet microbiomes.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag116},
pmid = {42878705},
issn = {1574-6941},
abstract = {The Greenland Ice Sheet (GrIS) hosts diverse microbial communities where glacier ice algae, snow algae, and cyanobacteria act as key primary producers across bare ice, snow, and cryoconite habitats, yet the ecological roles of associated heterotrophic prokaryotes remain poorly understood. Aerobic anoxygenic phototrophs (AAPs), known to couple light harvesting to heterotrophy and enter trophic relationships with algae in marine systems, suggesting they may represent an important but underexplored functional group in supraglacial ecosystems. Using genome-resolved analyses of supraglacial metagenomes and metatranscriptomes from Greenland, we recovered nine AAP metagenome-assembled genomes (MAGs) (4% of the 229 recovered MAGs) consistently enriched in bare ice and cryoconite communities, but nearly absent in snow. A meta-analysis of 2 451 public metagenomes supported this cryospheric habitat association. AAP_MAGs were disproportionally enriched in thiosulfate oxidation and bicarbonate-dependent carbon assimilation pathways relative to other MAGs. Iron and CO oxidation pathways were broadly distributed across the GrIS microbiome, including in AAPs, together suggesting adaptation strategies in supraglacial ecosystems. Genomic evidence for algal coupling via sulfoquinovose degradation was limited. Overall, we document that AAPs are active and widespread in weathering crust habitats, highlighting their potential contributions to biogeochemical cycling in supraglacial ecosystems.},
}

@article {pmid42879303,
year = {2026},
author = {Ahearn-Ford, S and Aboklaish, A and Young, GR and Lowe, J and Masi, AC and Gallacher, D and Marchesi, JR and Berrington, JE and Kotecha, S and Stewart, CJ},
title = {The impact of prophylactic azithromycin on the developing preterm gut microbiome and resistome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748147},
doi = {10.1080/19490976.2026.2748147},
pmid = {42879303},
issn = {1949-0984},
mesh = {Humans ; *Azithromycin/administration & dosage ; *Anti-Bacterial Agents/administration & dosage ; Infant, Newborn ; *Infant, Premature/growth & development ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Drug Resistance, Bacterial ; *Bacteria/genetics/drug effects/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Female ; *Antibiotic Prophylaxis ; Probiotics/administration & dosage ; Male ; },
abstract = {Early-life antibiotic exposure can profoundly impact the developing preterm gut microbiome and resistome, with short- and long-term consequences for health. In a large multi-center (n = 28) study of 693 preterm infants, we investigated the effects of 10 d of prophylactic intravenous azithromycin on the gut microbiome and antibiotic resistance genes (ARGs). The AZithromycin ThErapy for Chronic Lung Disease of Prematurity (AZTEC) study was a double blind, randomized, placebo-controlled trial of preterm infants (born < 30 weeks of gestation), treated from birth for 10 d with either intravenous azithromycin or placebo, and sampled longitudinally for 21 d or discharge. Using 16S rRNA gene sequencing, antibiotic susceptibility testing, and quantitative PCR, we show azithromycin reduced microbial diversity and the relative abundance of health-associated Bifidobacterium and increased relative abundances of pathobionts Staphylococcus and Enterobacter/Klebsiella. This early azithromycin treatment increased the number of macrolide-resistant genes, including the presence of erm (C), which persisted for the duration of the study. Probiotic use (at individual unit discretion) increased alpha diversity and Bifidobacterium relative abundance, but did not fully mitigate the effects of azithromycin receipt. Combined azithromycin and probiotics further increased the enrichment of Enterobacter/Klebsiella and total ARGs, including erm(C). These findings highlight the impacts of antibiotic and probiotic use, both important in balancing infection control issues and microbiome disruption and antimicrobial resistance.},
}

Humans
*Azithromycin/administration & dosage
*Anti-Bacterial Agents/administration & dosage
Infant, Newborn
*Infant, Premature/growth & development
*Gastrointestinal Microbiome/drug effects
Double-Blind Method
Drug Resistance, Bacterial
*Bacteria/genetics/drug effects/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Female
*Antibiotic Prophylaxis
Probiotics/administration & dosage
Male

@article {pmid42879678,
year = {2026},
author = {Lin, ZR and Shi, JC and Qiu, CC and Wu, ZX and Lin, XQ and He, GQ and Liu, SD and Du, QW and Lin, HB and Wu, LP and Sun, F and Jiang, XG},
title = {Metagenomic insights into the pulmonary microbiome of drug-sensitive and multidrug-resistant tuberculosis patients.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2720327},
doi = {10.1080/07853890.2026.2720327},
pmid = {42879678},
issn = {1365-2060},
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Female ; Male ; Metagenomics ; *Lung/microbiology ; Middle Aged ; Adult ; Prospective Studies ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {BACKGROUND: While the pulmonary microbiota may influence TB pathogenesis, direct comparisons between drug-sensitive (DS-TB) and multidrug-resistant (MDR-TB) patients remain scarce. This study explored microbiome differences between these groups.

METHODS: Bronchoalveolar lavage fluid (BALF) from 30 prospective patients (11 DS-TB, 19 MDR-TB) was analysed via metagenomic sequencing.

RESULTS: Patients with MDR-TB showed lower α-diversity and distinct β-diversity compared with patients with DS-TB. Streptococcus and Prevotella were relatively enriched in DS-TB, whereas Staphylococcus, Cutibacterium, and Mycobacterium were more abundant in MDR-TB. DS-TB showed enrichment of 45 carbohydrate-active enzyme families and core metabolic annotations, whereas MDR-TB showed enrichment of infection- and immunity-related functional annotations and a less connected taxonomic network. An exploratory random forest analysis identified six candidate genera and yielded an internally cross-validated AUC of 0.957.

CONCLUSIONS: MDR-TB was associated with lower pulmonary microbial diversity, altered community composition, and shifts in predicted microbial functions. These findings characterise lower-airway microbiome differences between DS-TB and MDR-TB and provide a basis for further validation.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Tuberculosis, Multidrug-Resistant/microbiology/drug therapy
Female
Male
Metagenomics
*Lung/microbiology
Middle Aged
Adult
Prospective Studies
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid42879794,
year = {2026},
author = {Beck, EA and Smith, CA and Currey, MC and Small, CM and Bohannan, BJM and Cresko, WA},
title = {Spontaneous hypopigmentation mutant in threespine stickleback fish exhibits changes in the gut microbiome consistent with inflammatory bowel diseases.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkag284},
pmid = {42879794},
issn = {2160-1836},
abstract = {Albinism is a large group of disorders characterized by a loss of pigment in ectoderm-derived tissues - most noticeably impacting the skin, hair, and eyes. Albinism is categorized as either syndromic or non-syndromic. Syndromic albinisms include a wide range of disorders with mutations impacting not just pigmentation but other cellular functions. These include, non-exclusively, melanogenesis disorders, endosome trafficking disorders like lysosomal storage disorders, and cell migration disorders. Mutations leading to syndromic albinisms can cause multi-organ system symptoms due to broad disruption lysosome related organelles (LROs) function. Various genetic mutations impact biogenesis, cell maturation, or trafficking at different stages which can lead to a range of severity. Syndromic albinisms also present with different combinations of symptoms depending on the impacted organelles; including oculocutaneous albinism (OCA) (melanosomes), blood diathesis (platelet dense granules), pulmonary fibrosis (lamellar bodies), or chronic inflammation (multiple cellular sources). Animal models for these multisymptomatic complex disorders are needed to understand the effects on systemic health. One such area of interest is in gut health of those with syndromic albinism. Shared inflammatory patterns of syndromic albinisms like Hermansky-Pudlak Syndromes (HPS) and Inflammatory Bowel Disease (IBD) are well studied, with animal models of HPS jointly used to study patterns of inflammation in IBD. However, the impact of this shared gastrointestinal inflammation on the gut microbiome remains unexplored. Using a spontaneously identified mutant family of threespine stickleback fish, we characterize phenotypes consistent with oculocutaneous albinism and vision impairment and demonstrate shared features of gut health to IBD extend from inflammation to the gut microbiome. We argue syndromic albinism models should be explored as models to study the gut microbiome in addition to inflammatory phenotypes in IBD, and importantly, be used to test microbial/dietary interventions for both IBD and syndromic albinisms.},
}

@article {pmid42879796,
year = {2026},
author = {Vicente-Díez, I and Mooney, KA and Vázquez-González, C},
title = {Contrasting effects of native soil microbiomes on direct and indirect herbivore resistance in a dominant shrub species.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcag334},
pmid = {42879796},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: The soil microbiome is known to modulate plant resistance to insect herbivores. Research on this topic has traditionally focused on bottom-up effects of plants on insects (direct resistance). However, how soil microbiomes affect plant resistance via top-down control of insects by natural enemies (indirect resistance) remains understudied. We conducted a greenhouse experiment using Baccharis salicifolia as a model to test the effects of native soil microbiomes on (i) direct resistance against the generalist aphid Aphis gossypii and (ii) indirect resistance by natural enemies.

METHODS: We grew B. salicifolia plants in a common sterilized substrate that was either inoculated with 10% native field soil or left uninoculated as a sterile control and performed a bioassay with A. gossypii to assess direct resistance by measuring aphid performance (age at first reproduction and reproductive rate). Then, we assessed indirect resistance by excluding natural enemies and estimating effects on aphid colony size in plants growing in inoculated vs. uninoculated soil.

KEY RESULTS: Plants in inoculated soil exhibited a 15% increase in growth, while aphid reproduction was reduced by 18% compared to uninoculated soil. Moreover, soil inoculation significantly altered the strength of top-down control by natural enemies. Access to natural enemies reduced aphid colony size by 23% in uninoculated soils but only by 11% in inoculated soils, indicating weaker indirect resistance under soil inoculation.

CONCLUSIONS: We show that native microbial communities regulate plant-insect-natural enemy interactions via contrasting effects on direct and indirect resistance, underscoring the need to consider both pathways to understand microbial impacts on plant resistance.},
}

@article {pmid42879892,
year = {2026},
author = {Muoghalu, C and Sun, Z and Guo, J and Kaboggoza, HC and Lubwama, I and Manga, M},
title = {Effects of substrate moisture content on physiological development, performance, and gut microbiome of black soldier fly larvae during swine waste treatment.},
journal = {Waste management (New York, N.Y.)},
volume = {227},
number = {},
pages = {115924},
doi = {10.1016/j.wasman.2026.115924},
pmid = {42879892},
issn = {1879-2456},
abstract = {Black soldier fly larvae (BSFL) composting is a sustainable approach for treating swine waste. BSFL's performance depends on its digestive enzyme activity, which is shaped and enhanced by the gut microbiome. Moisture content influences gut microbiome composition and function; however, it is often overlooked, and its role remains poorly understood. We evaluated the effects of three moisture levels (65%, 75%, and 85%) on the larval gut microbiome, digestive enzyme activity, larval growth, protein content, and contaminant removal. Microbial communities in larval guts and substrates were characterized using 16S rRNA sequencing and multivariate analyses. Larvae reared at 65% moisture had the highest protein content (40.8% DM) and achieved significantly greater reductions in total organic carbon (85.4%), total nitrogen (47.9%), and total phosphorus (47.7%) than those reared at higher moisture levels. However, protease activity was highest at 75% moisture and alpha-amylase activity was highest at 85% moisture. Linear discriminant analysis effect size identified a more functionally enriched gut microbiome at 65% moisture, characterized by taxa associated with organic matter degradation, including Bacillaceae, Paenibacillaceae, and Caryophanaceae, and genera such as Paenibacillus, Peribacillus, and Stenotrophomonas, whereas higher moisture levels favored anaerobic and fermentative taxa. Spearman correlation analysis further identified associations between specific bacterial genera and enzyme activities, including a strong positive association between Enterococcus (enriched at 85% moisture) and alpha-amylase activity (ρ = 0.90). This study contributes to optimizing BSFL-based waste management and highlights the need for microbial enhancement strategies and research on antimicrobial resistance.},
}

@article {pmid42879932,
year = {2026},
author = {Medriano, CA and Chow, KW and Oh, JY and Bae, S},
title = {Weathering chemistry shapes the gut microbiome-metabolome-transcriptome response of adult zebrafish to aged polyethylene microplastics.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143884},
doi = {10.1016/j.jhazmat.2026.143884},
pmid = {42879932},
issn = {1873-3336},
abstract = {Microplastics (MPs) in aquatic environments undergo continuous weathering, yet most toxicological studies still rely on pristine commercial particles, leaving biological consequences of distinct aging chemistries poorly resolved. Here, polyethylene (PE) MPs were aged through oxidative and hydrolytic pathways (UV+H2O, H2SO4, HNO3, and NaOH), characterized by FTIR (Fourier Transform Infrared Spectroscopy) and SEM (Scanning Electron Microscopy), and administered to zebrafish to link surface chemistry with the multilayered gut microbiome, metabolome, and host transcriptome responses. Weathering chemistry governed surface oxidation and morphological damage, with strong-acid treatment (H2SO4 ≫ HNO3) causing the most severe fragmentation. These surface differences propagated into chemistry-specific effects: an abundance-driven restructuring of the gut microbiota, including suppression of the core commensal Cetobacterium under alkaline aging and expansion of stress-tolerant environmental taxa; weathering-specific remodeling of the metabolome (NAD[+]/nicotinamide and glycosphingolipid); and low but treatment-specific transcriptional changes (6-13 DEGs per treatment, including a shared ∼800-fold induction of lhfpl5b under NaOH and UV+H2O). Multi-omics integration resolved into three chemistry-specific cross-omics axes, with the metabolome and transcriptome showing the strongest cross-layer concordance (Procrustes 1-M[2] = 0.38, p < 0.01). Weathered MPs from different degradation pathways cannot be aggregated into a single "aged-MP" category, as their hazards are chemistry-specific at every molecular layer.},
}

@article {pmid42880058,
year = {2026},
author = {Li, D and Yin, J and Zhou, H and Ge, N and Wang, B and Wang, T},
title = {Integrative multi-omics analysis reveals the PFAS-gut microbiome-FN1 axis in chronic kidney disease: From exposome to therapeutic target.},
journal = {Computational biology and chemistry},
volume = {126},
number = {Pt 2},
pages = {109478},
doi = {10.1016/j.compbiolchem.2026.109478},
pmid = {42880058},
issn = {1476-928X},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent environmental pollutants associated with chronic kidney disease (CKD), yet the molecular mechanisms linking PFAS exposure to renal fibrosis remain incompletely understood. We developed a Chemical-Microbiome-Metabolite-Target-Pathway-Disease (C-M-M-T-P-D) network framework integrating differential expression analysis of real GEO transcriptomic data (GSE104954, n = 195 kidney biopsies), gene set enrichment analysis across four pathway databases, two-sample Mendelian randomization with four complementary methods, molecular docking and molecular dynamics simulation of deoxycholic acid (DCA) to fibronectin 1 (FN1), and transcription factor and protein-protein interaction network analyses. FN1 was significantly upregulated in CKD (log2FC = 0.322, FDR = 6.67e-11), accompanied by elevated COL1A2, VIM, and POSTN, whereas TGFBR3 was downregulated (log2FC = -0.746, FDR = 1.67e-14). GSEA identified ECM-receptor interaction (NES = 2.23), interferon gamma response (NES = 2.70), and epithelial-mesenchymal transition (NES = 1.99) as top enriched pathways. MR analysis using real MiBioGen and CKDGen GWAS data (19 SNPs for Akkermansia, 12 SNPs for Desulfovibrio) revealed contrasting findings: Akkermansia to CKD showed no significant genetic association (0/4 methods, all p > 0.30), whereas Desulfovibrio to CKD demonstrated a robust positive genetic association across all four methods (IVW p = 0.008, WM p = 4.70e-04, MR-RAPS p = 1.46e-05, MR-cML p = 2.08e-06), though the significant Egger intercept (p = 0.005) for Desulfovibrio warrants cautious interpretation regarding pleiotropy. Molecular docking and 15-ns MD simulation confirmed stable DCA binding to FN1 (PDB: 2CG7, 1.20 A X-ray; MM/GBSA ΔGbind = -32.4 kcal/mol). The C-M-M-T-P-D network positioned FN1 as the third highest-degree node, bridging metabolite and pathway layers. This integrative multi-omics analysis provides multi-omics evidence supporting the PFAS-gut microbiome-FN1 axis as a hypothesis-generating framework for understanding CKD pathogenesis, supported by transcriptomic, structural, and network-level evidence, with genetic associations warranting further experimental validation.},
}

@article {pmid42880079,
year = {2026},
author = {Cha, HE and Jeon, AJ and Cho, HS and Lee, JW and Seo, J and Lee, S and Lim, SK},
title = {Age-associated variation in the Korean salivary microbiome: Exploratory assessment of spousal cohabitation as a potential confounder for forensic inference.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {87},
number = {},
pages = {103038},
doi = {10.1016/j.legalmed.2026.103038},
pmid = {42880079},
issn = {1873-4162},
abstract = {The salivary microbiome reflects host physiology and environmental exposures and may provide complementary information for forensic trace interpretation. This study primarily investigated age-associated variation in salivary microbiome profiles from 182 Korean adults and secondarily explored reported spousal cohabitation as a potential contextual variable and source of confounding through ecological analyses and exploratory machine-learning approaches. An XGBoost regression model yielded a test-set mean absolute error of 7.49 years (R[2] = 0.31) for chronological age. Alpha diversity differed across age groups, and Bray-Curtis community composition varied modestly by age group (R[2] = 0.037). Binary classification of participants in their 20s and 30s versus those in their 40s and 50s achieved an accuracy of 0.741 and an area under the receiver operating characteristic curve of 0.76. For reported spousal cohabitation, an unadjusted exploratory analysis showed a small difference in community composition (R[2] = 0.012). However, in a multivariable marginal PERMANOVA including chronological age, sex, and cohabitation status simultaneously, age remained significantly associated with community composition (R[2] = 0.014, p = 0.0119), whereas cohabitation was not (R[2] = 0.004, p = 0.6898). This association also remained non-significant in a sensitivity analysis restricted to participants in their 30s-50s. These findings support a modest, distributed age-related signal, whereas the weaker cohabitation-associated pattern may partly reflect demographic confounding. This study extends limited population-specific evidence on age-associated salivary microbiome variation in Korean adults and supports further evaluation of salivary microbiome profiles as complementary, rather than stand-alone, forensic information requiring external validation, rigorous confounder control, and casework-relevant testing.},
}

@article {pmid42880184,
year = {2026},
author = {Erreygers, I and Pinedo-Bardales, M and Dey, H and Segata, N and Wittouck, S and Lebeer, S and Heidrich, V},
title = {Transmission of lactic acid bacteria: a case study of the human vaginal microbiome.},
journal = {Current opinion in microbiology},
volume = {94},
number = {},
pages = {102845},
doi = {10.1016/j.mib.2026.102845},
pmid = {42880184},
issn = {1879-0364},
abstract = {Lactic acid bacteria (LAB) are among the microorganisms to which humans are most frequently exposed, largely via consumption of fermented foods and probiotics and through interpersonal contact. Such continued exposure to LAB does not necessarily result in stable engraftment, raising fundamental questions about which factors mediate successful LAB transmission and niche specialization across human-associated microbiomes. Here, we rethink transmission of LAB across the human life course, spanning food-associated, within-host, and interindividual routes, highlighting that LAB transfer can occur across multiple contexts, but long-term engraftment depends less on exposure and more on host-mediated selection. As a paradigmatic case study, we present the human adult vaginal microbiome, a low-diversity environment generally dominated by strains of specific Lactobacillus species. These strains display clear signatures of niche specialization in the vaginal environment, making them taxonomically and functionally distinct from other LAB, and illustrating how host-mediated selection rather than exposure alone determines which LAB persist. This proposed conceptual framework, combined with the experimental and computational tractability of LAB, enables a better understanding of LAB engraftment in the human host, contributing to improved design and strain-level efficacy assessment of microbiome-based interventions, including probiotics, live biotherapeutic products, and microbiota transplants.},
}

@article {pmid42880228,
year = {2026},
author = {Corral, D and Belkaid, Y},
title = {Milking the niche: Microbial control of neonatal hematopoiesis.},
journal = {Cell},
volume = {189},
number = {21},
pages = {6561-6563},
doi = {10.1016/j.cell.2026.09.010},
pmid = {42880228},
issn = {1097-4172},
mesh = {Animals ; *Hematopoiesis ; Humans ; *Microbiota ; *Osteopontin/metabolism ; *Milk/immunology/microbiology ; Dendritic Cells/immunology ; },
abstract = {In this issue of Cell, Howard et al. reveal how the milk glycoprotein osteopontin shapes the neonatal microbiome to regulate hematopoiesis, promoting dendritic cell development and protection from severe respiratory infection. These findings uncover a maternal milk-microbiota pathway linking early-life nutrition to immune development and long-term disease susceptibility.},
}

Animals
*Hematopoiesis
Humans
*Microbiota
*Osteopontin/metabolism
*Milk/immunology/microbiology
Dendritic Cells/immunology

@article {pmid42880254,
year = {2026},
author = {Meyers, M and Medina Evora, G and Molina Tijeras, JA and Brauer, M and Benzarti, M and Jans, M and Delgado, LF and Schorr, L and Rodriguez, F and Ternes, D and Ouyang, KS and Moskal, K and Schlicker, L and Tsenkova, M and Lucchetti, M and Gilson, C and Gabola, M and Carpentier, A and Nuciforo, PG and Koncina, E and Pozdeev, VI and Vereecke, L and Wilmes, P and Puschhof, J and Letellier, E},
title = {Gemella morbillorum promotes colorectal tumorigenesis through barrier disruption and invasion-dependent DNA damage.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.09.016},
pmid = {42880254},
issn = {1934-6069},
abstract = {Bacteria are increasingly recognized as contributors to cancer, yet the underlying mechanisms remain unclear for most species. Here, we find that Gemella morbillorum (Gm) is enriched in feces and tumor tissues from patients with colorectal cancer (CRC) and reveal a multi-step host-pathogen mechanism that promotes colorectal tumorigenesis. In mouse models of CRC, Gm suppresses IL-22 production by type 3 innate lymphoid cells (ILC3s), impairing intestinal barrier function and facilitating bacterial translocation to early neoplastic lesions. At the tumor site, Gm utilizes an ANXA2-dependent, clathrin-mediated pathway to invade CRC cells. Gm induces profound lipid remodeling, characterized by the accumulation of oxidation-prone fatty acids and enhanced lipid peroxidation, which contributes to invasion-dependent DNA damage. Inhibition of lipid peroxidation attenuates Gm-induced DNA damage, functionally linking lipid oxidative stress to genotoxicity. Together, these findings identify Gm as a candidate onco-pathogen in CRC that uses multiple mechanisms to disarm the intestinal barrier and trigger genotoxicity.},
}

@article {pmid42880376,
year = {2026},
author = {Yu, Q and Zhang, Z and Tian, Z and Kuang, J and Corbin, KD and Oberlin, LE and Collins, A and Goodpaster, BH and Erickson, KI and Owen, N and Dunstan, DW and Hillman, CH and Kramer, A and Liu-Ambrose, T and Lowe, C and Heath, M and Moon, HY and Banks, WA and Paas, F and Feter, N and Raichlen, DA and Kelley, KW and Allen, JM and Herold, F and Zou, L},
title = {Sedentary behavior as a Gut-Brain metabolic state.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {107068},
doi = {10.1016/j.bbi.2026.107068},
pmid = {42880376},
issn = {1090-2139},
abstract = {Sedentary behavior (SB) is prevalent in daily life, with a growing number of studies reporting that higher SB exposure is associated with poorer cardiometabolic and brain health. Thus, in line with a broader paradigm shift, SB should be considered as a postural and low-contractile metabolic state, shaped by both total exposure and bout patterning, that is related to, but distinct from, physical activity (PA), rather than simply the absence of the latter. Regarding the gut microbiome, current evidence on the role of SB remains limited and indirect, as human studies have not yet experimentally manipulated the SB exposure. To generate novel, yet testable hypotheses on the role of SB on the gut microbiome and brain health, this article synthesizes the current evidence base by emphasizing limitations related to cross-sectional designs, measurement heterogeneity, potential confounding by diet, sleep, medications, and PA, and the absence of established quantitative thresholds for SB exposure. Building on broader microbiome, metabolic, inflammatory, and gut-brain axis literature, we outline candidate pathways through which SB exposure, especially prolonged uninterrupted sitting, may alter microbe-derived metabolites and host responses, focusing on short-chain fatty acids, bile acid signaling, and tryptophan-derived metabolism alongside barrier-immune activation and autonomic-vagal circuitry relevant for brain health. Thus, this review extends prior SB-brain health frameworks by positioning SB as a specific gut-brain metabolic state with potential unique effects on a range of brain health-related outcomes. To probe the prediction that changes in SB patterns can affect gut-derived metabolites and specific brain health domains, suitable study designs are discussed. More specifically, future studies should combine accurate measures of SB and PA exposure with gut microbiome and blood-based metabolite assessments, vascular and inflammatory markers, autonomic measures, and standardized tests of cognition and mood, collected at different times, such as after meals and across the day, to better quantify and understand temporal dynamics. Approaching the gut-brain axis by isolating the effects of SB exposure is likely to generate practically relevant and impactful insights that not only help to inform stakeholders, such as policymakers, but also provide the basis for more fine-grained lifestyle recommendations to preserve and improve brain health.},
}

@article {pmid42880461,
year = {2026},
author = {Mitrea, L and Calinoiu, LF and Martau, GA and Teleky, BE and Cocean, AM and Odocheanu, R and Stefanescu, BE and Vodnar, DC},
title = {From Gut Microbiome to Aging Brain: Butyrate as a Neurogeroscience Effector.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {107037},
doi = {10.1016/j.neubiorev.2026.107037},
pmid = {42880461},
issn = {1873-7528},
abstract = {Aging-related cognitive decline is increasingly linked to disruption of the microbiome-gut-brain axis, in which age-associated dysbiosis progressively reduces butyrate production, a short-chain fatty acid and central neuroactive metabolite generated by bacterial fermentation of dietary fiber. Experimental studies indicate that butyrate can influence multiple processes relevant to brain aging, including histone deacetylase activity, neuroinflammatory signaling, microglial phenotypes, blood-brain barrier integrity, synaptic plasticity, and neurogenesis. Through these mechanisms, butyrate may modulate several molecular and cellular processes involved in brain aging, although evidence for direct causal effects in the human brain remains limited. Preclinical studies report neuroprotective effects across several models of aging and neurological disease; however, direct evidence in humans remains limited and largely associative or indirect. Therefore, this review critically synthesizes current evidence on microbiome-derived butyrate in brain aging, encompassing its microbial production and age-related alterations, molecular and cellular mechanisms, associations with neurodegenerative and neuropsychiatric conditions, and emerging strategies for therapeutic modulation and delivery. It examines emerging biotechnological strategies - including prodrug design, nanoparticle- and liposomal-based delivery systems, gut-targeted formulations, and microbiome engineering - all developed to overcome the blood-brain barrier and restore therapeutically relevant butyrate concentrations in the aging brain. By bridging fundamental microbiome biology and translational neuroscience, this review positions butyrate as a mechanistically grounded neurogeroscience effector and charts a roadmap for its application in promoting brain health across the aging continuum.},
}

@article {pmid42880574,
year = {2026},
author = {Wei, Q and Wu, J and Kang, W and Xu, S and Han, B},
title = {Laboratory larval exposure to mixed-size polystyrene micro/nanoplastics disrupts lipid metabolism and reshapes the hemolymph metabolome and gut microbiota of adult honeybee workers.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129347},
doi = {10.1016/j.envpol.2026.129347},
pmid = {42880574},
issn = {1873-6424},
abstract = {Micro/nanoplastics are pervasive contaminants in terrestrial ecosystems, yet their developmental toxicity to pollinators remains insufficiently understood. Here, worker larvae of the honeybee (Apis mellifera) were orally exposed under controlled laboratory conditions to a mixed-size polystyrene micro/nanoplastic (PS-MNP) system containing 50 nm, 100 nm, and 5 μm particles at a 1:1:1 mass ratio across 1-500 mg/L. Survival was assessed using 48 larvae per group, and adult hemolymph metabolomics and gut microbiome analyses were conducted for adults derived from the 10 mg/L larval exposure group using six biological replicates per treatment. Larval PS-MNP exposure reduced survival, transiently increased larval body mass, and disrupted nutrient allocation, as reflected by decreased total protein and free fatty acids but increased glycogen and triglyceride. In the larval fat body, PS-MNPs induced oxidative stress and lipid droplet accumulation, accompanied by transcriptional changes consistent with enhanced lipid storage and impaired lipophagy. These developmental disturbances were followed by post-metamorphic effects. Newly emerged workers exhibited midgut injury and oxidative imbalance. Moreover, adults derived from exposed larvae displayed pronounced hemolymph metabolomic reprogramming and altered gut microbiota after colony reintroduction. More than 1,200 differential hemolymph metabolites were detected, with downregulated features enriched mainly in lipid-remodeling, eicosanoid-related, and autophagy-associated pathways. The adult gut microbiota showed depletion of Gilliamella apicola and Bartonella apis and enrichment of Lactobacillus apis and Frischella perrara. Collectively, these findings show that larval-only exposure to a mixed-size PS-MNP system can disturb developmental lipid/redox homeostasis and be followed by intestinal, hemolymph metabolic, and gut microbial alterations after metamorphosis. This integrated cross-stage evidence advances understanding of micro/nanoplastic developmental ecotoxicology in beneficial terrestrial insects and provides evidence for considering developmental windows in future pollinator risk assessment.},
}

@article {pmid42880617,
year = {2026},
author = {Chen, S and Xiao, Q and Liu, X and Jiang, J and Lei, W and Zhang, S and Zeng, Y and Liu, J and Li, J and Xie, Y and Hu, H and Chen, S and Rong, F and Cai, S},
title = {Development of a novel diagnostic tool for community-acquired pneumonia based on microbial community characteristics.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {106011},
doi = {10.1016/j.meegid.2026.106011},
pmid = {42880617},
issn = {1567-7257},
abstract = {BACKGROUND: The lung microbiota plays a key role in pneumonia. A correct diagnosis in the early stage helps treatment and limits severity progression of community-acquired pneumonia (CAP).

METHODS: There were 42 patients with CAP and 20 controls. Amplicon bacterial 16S sequencing from bronchoalveolar lavage fluid samples revealed indicator genera by linear discriminant analysis effect size, random forest and ROC analyses. The abundance of bacteria was combined with laboratory inflammatory indexes to construct logistic regression models for CAP diagnosis. The final predictive model with a lower Akaike information criterion (AIC) was internally validated by bootstrap resampling.

RESULTS: After confirming lower respiratory tract (LRT) microbiome dysbiosis in CAP patients, we identified five indicator genera: Moraxella (M), Prevotella_1 (P), Lautropia (L), Neisseria (N), and Fusobacterium (F). Their combined effect was incorporated by calculation of the joint prediction probability (PRE) based on their relative abundances as PRE = 1 / (1 + EXP (-4.39 + 18.96 M + 9.30P - 5.38 L + 0.89 N + 0.70F)). A nomogram was constructed for CAP diagnosis that incorporated PRE with serum levels of CRP (cut-off ≥5.23 mg/L) and Neutrophil % (cut-off ≥66.05%). After internal validation, this nomogram showed satisfactory diagnostic performance with the bootstrap-corrected AUC of 0.927 and a well-fitting calibration curve.

CONCLUSIONS: The LRT microbiome was altered in CAP patients. Indicator genera were shown to have the potential to serve as diagnosis biomarkers in the constructed predictive model. These results may provide further clues for the microbial pathogenesis, optimized diagnostics and new therapeutic targets of CAP.},
}

@article {pmid42880740,
year = {2026},
author = {Giono-Cerezo, S and López-Vidal, Y and Alcántar-Curiel, MD},
title = {Bacterial infections and their association with female infertility: diagnostic and therapeutic perspectives.},
journal = {Gaceta medica de Mexico},
volume = {162},
number = {1},
pages = {28-36},
doi = {10.24875/GMM.M26001104},
pmid = {42880740},
issn = {0016-3813},
mesh = {Humans ; Female ; *Infertility, Female/microbiology/etiology/therapy/diagnosis ; *Bacterial Infections/complications/diagnosis/therapy/microbiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Chlamydia Infections/complications/diagnosis ; Pregnancy ; },
abstract = {Infertility is a public health issue affecting millions of women of reproductive age worldwide. Bacterial infections caused by Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma hominis, and Ureaplasma urealyticum are among the most prevalent. They are associated with pelvic inflammatory disease, chronic endometritis, fallopian tube obstruction, impaired endometrial receptivity and implantation, and increased risk of ectopic pregnancy and pregnancy loss. Timely diagnosis using nucleic acid amplification testing represents the current standard, while advanced techniques, such as sequencing, enable the precise identification of pathogens and dysbiosis. The treatment of infections caused by these microorganisms involved the use of antibiotics, guided by the specific antimicrobial susceptibility pattern of each bacterium. Alternatives such as antioxidants, probiotics, or vaginal microbiota transplantation have been proposed for persistent infections. The clinical approach is interdisciplinary, incorporating imaging studies and inflammatory biomarkers. Understanding the pathogens and their interactions within the microbiome, along with the integration of reproductive medicine and clinical microbiology, provides valuable insights for managing and preserving female fertility.},
}

Humans
Female
*Infertility, Female/microbiology/etiology/therapy/diagnosis
*Bacterial Infections/complications/diagnosis/therapy/microbiology/drug therapy
Anti-Bacterial Agents/therapeutic use
Chlamydia Infections/complications/diagnosis
Pregnancy

@article {pmid42880793,
year = {2026},
author = {Stevens, NE and Botten, R and Geake, JB and Eden, GL and Lo, WK and Inauen, J and Solujic, J and Sawka, A and Yelland, LN and Reid, EW and Shaw, M and Zhu, X and Tam, TK and Jeon, H and Amenyogbe, N and Lynn, MA and Ryan, FJ and Feng, CG and Britton, WJ and Kollmann, TR and Barry, SE and Lynn, DJ},
title = {A randomised, placebo-controlled study to assess whether antibiotic-mediated disruption of the gut microbiota impairs BCG-induced specific and non-specific immunity in young, healthy adults: protocol for the Antibiotics and Vaccine Immune Responses Study (AVIRS).},
journal = {BMJ open},
volume = {16},
number = {10},
pages = {e126924},
doi = {10.1136/bmjopen-2026-126924},
pmid = {42880793},
issn = {2044-6055},
}

@article {pmid42880811,
year = {2026},
author = {Juanola, A and Moreta, MJ and Solé, C and Sánchez, J and Albillos, A and Martínez González, J and Poca Sans, M and Alvarado, E and Campos-Varela, I and Cespedes, C and Alonso, S and Bañares, R and Fortea, JI and Puente, Á and Llop, E and Fernández-Carrillo, C and Moya, A and Ruiz-Ruiz, S and Fernandez-Real, JM and Mayneris-Perxachs, J and Bonfill, E and Rivera, C and Pich, J and Piano, S and Solà, E and Torres, F and Iavarone, S and Pérez-Guasch, M and Casanova, NC and González-Suárez, B and Fabrellas, N and Graupera, I and Pose, E and Ginès, P},
title = {Randomised, double-blind, placebo-controlled trial of faecal microbiota transplantation in patients with decompensated cirrhosis: the Livergut protocol.},
journal = {BMJ open},
volume = {16},
number = {10},
pages = {e118486},
doi = {10.1136/bmjopen-2026-118486},
pmid = {42880811},
issn = {2044-6055},
}

@article {pmid42880833,
year = {2026},
author = {Moloney, GM and Clarke, G and Cryan, JF},
title = {Gut microbiota and epigenetic mechanisms in brain physiology and disorders.},
journal = {Handbook of clinical neurology},
volume = {219},
number = {},
pages = {147-167},
doi = {10.1016/B978-0-443-19043-8.00019-0},
pmid = {42880833},
issn = {0072-9752},
mesh = {Humans ; *Epigenesis, Genetic/physiology ; *Brain/physiology/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology ; *Nervous System Diseases/genetics/microbiology ; *Brain Diseases/genetics ; },
abstract = {The interplay between gut microbiota and epigenetic mechanisms plays a crucial role in brain physiology and disorders, highlighting a novel area of research with significant implications for understanding and treating neurologic conditions. The gut microbiota, the diverse community of microorganisms in the digestive tract, influences brain function and health through the gut-brain axis, a complex communication network linking the gastrointestinal tract and the central nervous system. Epigenetic mechanisms, including DNA methylation, histone modification, and noncoding RNA activity, regulate gene expression without altering the DNA sequence, thus shaping neuronal development and plasticity. Recent studies have elucidated how gut microbiota can modulate these epigenetic processes, affecting neurotransmission, neuroinflammation, and the integrity of the blood-brain barrier. Disruptions in the gut microbiome are associated with various psychiatric disorders, such as autism spectrum disorder or depression, and with neurodegenerative diseases, potentially through epigenetic alterations that affect brain function. Understanding the molecular interactions between gut microbiota and epigenetic regulation offers promising avenues for therapeutic interventions, including dietary modifications, probiotics, and epigenetic drugs. This chapter underscores the significance of gut microbiota and epigenetic mechanisms in brain health and disease, suggesting that targeted manipulation of these factors could lead to novel treatments for neurologic disorders.},
}

Humans
*Epigenesis, Genetic/physiology
*Brain/physiology/metabolism
Animals
*Gastrointestinal Microbiome/physiology
*Nervous System Diseases/genetics/microbiology
*Brain Diseases/genetics

@article {pmid42881160,
year = {2026},
author = {Fernandes, N and Cai, M and Warren, FJ and Duncan, A and Harris, H and Serrano Contreras, JI and Sidorczuk, K and Bernal, A and Castillo, A and Petropoulou, K and Blunt, D and Perez-Moral, N and Garcia-Perez, I and Edwards, C and Hildebrand, F and Holmes, E and Wist, J and Frost, G},
title = {Effect of dietary chickpea structures on the small intestine metabolome and microbiome: a randomised crossover trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881160},
issn = {2041-1723},
support = {BB/X018857/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; Cross-Over Studies ; *Metabolome ; Glucagon-Like Peptide 1/metabolism ; Postprandial Period ; *Cicer/chemistry ; *Intestine, Small/metabolism/microbiology ; Peptide YY/metabolism ; Female ; Adult ; Gastric Inhibitory Polypeptide/metabolism ; *Gastrointestinal Microbiome/physiology ; Ileum/microbiology/metabolism ; *Diet ; Young Adult ; },
abstract = {The human gastrointestinal tract (GIT) is central to human physiology, yet our understanding of the metabolite, microbial, and hormonal spatiotemporal dynamics in humans is limited. How these environments respond to complex food structures and homeostatic mechanisms they generate is unknown in humans. In this randomised study, ten participants consumed chickpea-based meals with intact versus broken cellular structures, with sampling of oral, gastric, duodenal and ileal fluids. The primary outcome was the postprandial enteroendocrine hormone responses (GIP, GLP-1 and PYY); secondary outcomes were GIT metabolite profiles ([1]H NMR) and ileal microbiota (shotgun metagenomics). We observed that food structure markedly altered the spatiotemporal trajectories of metabolites and dominant microbe, driving distinct enteroendocrine hormone responses. Broken-cell meals produced early GIT glucose and maltose peaks associated with rapid GIP responses, whereas intact-cell meals elevated duodenal amino acids and ileal sugars, amino acids and formate, enhancing GLP-1 and PYY responses. Microbial profiles exhibited rapid spatial reorganisation, with evidence that oral bacterial strains transmitted to the ileum, where their abundance was associated with local metabolites and PYY responses. These findings identify food structure as a determinant of postprandial gastrointestinal metabolism and enteroendocrine responses and suggest an underappreciated route for oral bacteria to reach the ileum via the food bolus and impact metabolism. ISRCTN registration: ISRCTN18097249.},
}

Humans
Cross-Over Studies
*Metabolome
Glucagon-Like Peptide 1/metabolism
Postprandial Period
*Cicer/chemistry
*Intestine, Small/metabolism/microbiology
Peptide YY/metabolism
Female
Adult
Gastric Inhibitory Polypeptide/metabolism
*Gastrointestinal Microbiome/physiology
Ileum/microbiology/metabolism
*Diet
Young Adult

@article {pmid42881193,
year = {2026},
author = {Seymour, CO and Ecklu-Mensah, G and Lee, Y and Nicols, AR and Cheng, WA and Jumarang, JM and Marentes Ruiz, CJ and Navarro, J and Navarro, R and Rodriguez-Angeles, Y and Durand, D and Allard, SM and Taylor, ZW and De León, RG and Ochoa, TJ and Gilbert, JA and Pannaraj, PS},
title = {Klebsiella-dominant gut communities are associated with impeded oral rotavirus vaccine response in infants.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881193},
issn = {2041-1723},
mesh = {Humans ; *Rotavirus Vaccines/immunology/administration & dosage ; *Rotavirus Infections/prevention & control/immunology/virology/microbiology ; Infant ; Feces/microbiology/chemistry ; Rotavirus/immunology ; *Klebsiella/isolation & purification/immunology ; *Gastrointestinal Microbiome/immunology ; Gastroenteritis/prevention & control/virology/microbiology/immunology ; Administration, Oral ; Virus Shedding ; Female ; Male ; Peru ; Leukocyte L1 Antigen Complex ; Immunogenicity, Vaccine ; },
abstract = {Rotavirus gastroenteritis is the leading cause of infant diarrheal death worldwide. Oral rotavirus vaccine (RVV) prevents illness and death, but efficacy differs between high- and low-income countries and the etiologies are unclear. Here, we describe the relationship between colonization of the infant gut by commensal bacteria, inflammation, and vaccine response across a cohort of infants from Panama, Peru, and the U.S. Vaccine immunogenicity was related to community composition in the first month of life and inverse to increased relative abundance of Klebsiella. Clustering communities into gut types revealed that microbiome configurations with elevated Klebsiella or Escherichia in the first month of life were negatively associated with both seroconversion and rotavirus shedding after vaccination, suggesting potential inhibition of vaccine function or host response. Infants without RVV strain shedding displayed elevated fecal calprotectin in the first month. These results implicate microbiome-augmented infant gut inflammation as a potential impediment to RVV response.},
}

Humans
*Rotavirus Vaccines/immunology/administration & dosage
*Rotavirus Infections/prevention & control/immunology/virology/microbiology
Infant
Feces/microbiology/chemistry
Rotavirus/immunology
*Klebsiella/isolation & purification/immunology
*Gastrointestinal Microbiome/immunology
Gastroenteritis/prevention & control/virology/microbiology/immunology
Administration, Oral
Virus Shedding
Female
Male
Peru
Leukocyte L1 Antigen Complex
Immunogenicity, Vaccine

@article {pmid42881207,
year = {2026},
author = {Haskell, J},
title = {Engineering gut microbiome states overcomes hepatic accumulation of nanomedicines.},
journal = {Nature biomedical engineering},
volume = {10},
number = {10},
pages = {1988},
doi = {10.1038/s41551-026-01811-7},
pmid = {42881207},
issn = {2157-846X},
}

@article {pmid42881491,
year = {2026},
author = {Zehra, H and Kuchma, N and Lin, AW and Morris, G and Solano, O and Lopez, S and Kabage, AJ and Vaughn, BP and Weingarden, A and Fischer, M and Khoruts, A and Teigen, L},
title = {The Trajectory of Gastrointestinal Symptom Experience Following Fecal Microbiota Transplant for Recurrent Clostridioides Difficile Infection.},
journal = {Journal of clinical gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCG.0000000000002424},
pmid = {42881491},
issn = {1539-2031},
abstract = {INTRODUCTION: Recurrent Clostridioides difficile infection (rCDI) increases the risk of persistent gastrointestinal symptoms after treatment. Although fecal microbiota transplantation (FMT) effectively prevents CDI recurrence after antibiotics, the trajectory of gastrointestinal symptom severity remains poorly characterized.

METHODS: We tracked gastrointestinal symptom severity in a prospective, multicenter cohort study of adults with rCDI after treatment with standardized FMT products. Patients who experienced a CDI recurrence during the follow-up period were excluded. The IBS Symptom Severity Scale (IBS-SSS) was used as a measure of symptom severity, not as a diagnostic tool. Patients completed the IBS-SSS at the time of FMT, 1-week, 1-month, and 3-months post-FMT. The primary outcome was the change in IBS-SSS score after treatment. Subgroup analyses were conducted among patients with baseline IBS-SSS ≥175 (moderate/severe symptom severity) and <175 (none/mild symptom severity). Linear mixed-effects models were used to evaluate longitudinal changes and identify clinical predictors of IBS-SSS scores.

RESULTS: Among 107 patients included, median IBS-SSS scores decreased from 170 (range: 0 to 440) at baseline to 76 (range: 0 to 390) at week 1 and 54 (0 to 445) at month 3 (P<0.001). In those with baseline IBS-SSS ≥175 (n=51), 64% had none or mild symptom severity at month 3. In those with baseline IBS-SSS <175 (n=53), symptom severity was observed to remain as none or mild at month 3 in all but one patient.

CONCLUSION: FMT administered for prevention of rCDI was followed by a rapid (1 wk) and sustained (3 mo) reduction in gastrointestinal symptom scores in patients who did not develop CDI recurrence. These data help characterize the expected early post-FMT symptom trajectory, providing foundational evidence to better inform patient expectations and future interventions for persistent symptoms.},
}

@article {pmid42881525,
year = {2026},
author = {Chen, C and Zhang, H and Cheng, T and Zhou, F and Chen, X and Fang, M and Qi, P},
title = {Oral microbiome and inflammatory bowel disease: A scoping review.},
journal = {American journal of dentistry},
volume = {39},
number = {5},
pages = {253-258},
pmid = {42881525},
issn = {0894-8275},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Mouth/microbiology ; Dysbiosis/microbiology ; Periodontitis/microbiology ; Saliva/microbiology ; },
abstract = {PURPOSE: To examine the association between the oral microbiome and IBD in terms of microbiota diversity, composition, function, and diagnostic potential through a scoping review of the existing literature.

METHODS: This scoping review was structured following the PRISMA-ScR guidelines. Literature searches were conducted in PubMed, Embase, and the Cochrane Library, with the time frame restricted from database inception to November 17, 2025.

RESULTS: This review included 31 studies, among which seven topics for patients with periodontitis and IBD-related periodontitis, three studies assessed single bacterial species, and the remaining 21 articles explored the diversity and phylum-level taxonomic shifts of oral microbiota in IBD patients, functional and metabolic pathway alterations associated with oral dysbiosis, as well as the diagnostic potential and biomarkers derived from oral microbial profiles.

CLINICAL SIGNIFICANCE: The oral microbiota of IBD patients exhibits characteristic dysbiosis, manifested by the enrichment of pathogenic taxa, depletion of anti-inflammatory species, and metabolic dysfunction, which are closely associated with gut microbial alterations and systemic inflammatory status. The salivary microbiome demonstrates significant diagnostic potential for IBD.},
}

Humans
*Inflammatory Bowel Diseases/microbiology
*Microbiota
*Mouth/microbiology
Dysbiosis/microbiology
Periodontitis/microbiology
Saliva/microbiology

@article {pmid42881712,
year = {2026},
author = {Ionaș, TH and Ionaș, M and Chicea, R and Stănilă, A and Boța, G},
title = {Self-Reported Prebiotics and Probiotics Recognition and Recommendation Practices Among Dentists in Sibiu County, Romania: A Cross-Sectional Questionnaire Survey.},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/healthcare14193274},
pmid = {42881712},
issn = {2227-9032},
abstract = {Background/Objectives: Probiotics and prebiotics are being investigated as adjuncts for the management of oral dysbiosis, but little is known about how dentists understand and recommend them. We describe self-reported recognition of oral microbiome concepts, identification of the definitions of prebiotics and probiotics, and recommendation practices among dentists in Sibiu County, Romania. Methods: A cross-sectional online questionnaire survey (comprising eight closed items; delivered using Google Forms) was distributed through the county professional association WhatsApp messaging channel and to personal contacts between 20 February 2026 and 9 March 2026. Of a target of 630 dentists, 107 completed the questionnaire (response rate: 17.0%), forming a voluntary local sample. Three pre-specified hypotheses (definition accuracy × recommendation; general recommendation × adjunct recommended during antibiotic therapy; and years of experience × definition accuracy and recommendation) were tested with exact tests, odds ratios (ORs), and 95% confidence intervals (CIs) with Holm adjustment; other item associations were exploratory and adjusted within families. Results: A microbial role was recognized for periodontal disease by 98.1% of respondents, for dental caries by 92.5%, for focal infection by 73.8%, and for bone infection of dental origin by 64.5%. Diet, antibiotics, oral hygiene, and smoking were recognized as microbial influencing factors by 78-84%, probiotics by 58.9%, and prebiotics by 52.3%. Definitions of the adjuncts were correctly identified by 83.2% (prebiotics) and 80.4% (probiotics). Prebiotics were recommended by 50.5% and probiotics by 86.0% of respondents. Correct definitions were not associated with recommendation (prebiotics: OR 1.76, 95% CI 0.62-4.95; probiotics: OR 1.60, 95% CI 0.46-5.65). During antibiotic therapy, dentists who recommended prebiotics were more likely to select a prebiotic-probiotic combination than those who did not (57.4% versus 3.8%; exact p < 0.001). No outcome differed by years of experience. Conclusions: In this self-selected sample, biotics were recognized as microbiome-influencing factors less often than classical factors, and knowing the definitions was not associated with recommending the products. The reasons behind recommendation habits were not measured and require dedicated study.},
}

@article {pmid42882080,
year = {2026},
author = {Caruso, F and Vigilante, L and Borrelli, D and Gallo, A and Strina, I and Di Spiezio Sardo, A and Fantuz, MR and Savarese, G},
title = {Recurrent Implantation Failure and the Gut-Endometrium Axis: A Pilot Study on Microbiota Crosstalk.},
journal = {Journal of clinical medicine},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/jcm15197620},
pmid = {42882080},
issn = {2077-0383},
abstract = {Objective: We aim to assess gut and endometrial microbiota simultaneously in women with unexplained recurrent implantation failure (RIF) and explore the hypothesis of a gut-endometrium microbial axis. Study design: This monocentric observational pilot study included women aged 38 years or younger with a history of RIF. Paired fecal and endometrial samples were collected on the same day and analyzed by 16S rRNA gene sequencing. Relative abundances of major phyla and alpha-diversity indices were compared between compartments. Results: Twenty-one women were included. Chronic endometritis was documented through hysteroscopy in all cases. Gut dysbiosis was observed in 20/21 patients (95.2%), whereas endometrial dysbiosis was found in 16/21 (76.2%); crude agreement between compartments was 71.4% (Gwet's AC1 0.62, 95% CI 0.25-0.90). The intestinal microbiota was dominated by Bacteroidetes (52.8% ± 14.9%) and Firmicutes (33.3% ± 11.0%), whereas the endometrial microbiota was enriched in Firmicutes (64.5% ± 33.5%) and Proteobacteria (30.9% ± 32.3%). Bacteroidetes were significantly more abundant in fecal than endometrial samples (p < 0.001), while Firmicutes were significantly enriched in the endometrium (p = 0.001). All alpha-diversity indices were significantly higher in feces, indicating greater microbial richness and complexity in the gut. Conclusions: In this pilot cohort of women with unexplained RIF, gut and endometrial dysbiosis frequently co-occurred. These findings support a potential gut-endometrium microbial axis and highlight the possible interplay between gut and endometrial microbiota in recurrent implantation failure. Further studies are warranted to better elucidate the clinical and biological implications of this relationship.},
}

@article {pmid42882437,
year = {2026},
author = {Nitsotolis, TN and Assimakopoulos, SF and Mastoridou, E and Kolios, NG and Biros, D and Oikonomidi, ED and Lagadinou, M and Papalexandrou, A and Milionis, H and Christaki, E and Kalambokis, G},
title = {Cellular Crosstalk at the Gut-Liver Interface in Liver Cirrhosis: Epithelial Barrier Failure, Bacterial Translocation and Immune Activation as a Bidirectional Network.},
journal = {Cells},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/cells15191739},
pmid = {42882437},
issn = {2073-4409},
mesh = {Humans ; *Bacterial Translocation ; *Liver Cirrhosis/immunology/microbiology/pathology ; Animals ; *Liver/pathology/immunology/microbiology ; Intestinal Barrier Function ; *Intestinal Mucosa/pathology ; },
abstract = {The gut-liver axis is central to the systemic complications of liver cirrhosis, but it is usually described as a linear cascade in which barrier failure releases microbial products that activate a downstream immune response. This review proposes instead a four-compartment framework, in which the epithelial/barrier, innate immune, adaptive effector, and stromal-endothelial compartments-the last including the gut-vascular barrier-are treated as reciprocally interacting nodes, and pathological bacterial translocation is treated as both an input to and an output of the network rather than as its endpoint. Applying this framework across the stages of cirrhosis, we examine how tight-junction disassembly, mucus-layer thinning, Paneth-cell dysfunction and reduced secretory IgA, together with dysbiosis and small-intestinal bacterial overgrowth, permit translocation; how translocated bacteria and pathogen-associated molecular patterns activate all four compartments; and how the resulting cytokine circuits further degrade the barrier, generating feed-forward loops that underlie cirrhosis-associated immune dysfunction and chronic systemic inflammation. We relate these circuits to spontaneous bacterial peritonitis, hepatic encephalopathy, aggravated portal hypertension, and acute-on-chronic liver failure, distinguishing throughout between mechanisms demonstrated in humans and those inferred from animal or in vitro models. We identified evidence through structured searches of PubMed/MEDLINE, Embase, and Web of Science, and report it according to the SANRA checklist. Framed as a network, biomarkers become compartment-specific reporters, and barrier-, microbiome-, and immune-directed therapies become interventions at defined nodes and edges-a view that clarifies both their rationale and the current limits of the evidence.},
}

Humans
*Bacterial Translocation
*Liver Cirrhosis/immunology/microbiology/pathology
Animals
*Liver/pathology/immunology/microbiology
Intestinal Barrier Function
*Intestinal Mucosa/pathology

@article {pmid42882498,
year = {2026},
author = {Siemińska, I},
title = {The Gut Microbiota-Immunity Axis in Colorectal Cancer: Implications for Immunotherapy and Clinical Translation.},
journal = {Cells},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/cells15191800},
pmid = {42882498},
issn = {2073-4409},
mesh = {Humans ; *Colorectal Neoplasms/immunology/therapy/microbiology ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology ; *Translational Research, Biomedical ; Animals ; *Immunity ; },
abstract = {Colorectal cancer (CRC) arises within a complex microbial ecosystem that may influence carcinogenesis, tumor immunity, and therapeutic response. This is particularly relevant in metastatic disease, where most tumors are microsatellite-stable/mismatch repair-proficient (MSS/pMMR) and derive little meaningful benefit from immune checkpoint inhibitor (ICI) monotherapy. Specific pathobionts, including Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, have been implicated in genotoxic, inflammatory, and checkpoint-related mechanisms that may contribute to tumor progression and immune evasion, whereas selected commensals and microbiota-derived metabolites may support antitumor immunity in a context-dependent manner. This review integrates translational evidence linking microbial taxa and functions, metabolites, neutrophil biology, bacterial extracellular vesicles, and T-cell dysfunction with CRC progression and immunotherapy response. This review critically examines emerging microbiome-directed strategies, including fecal microbiota transplantation, next-generation probiotics, defined bacterial consortia, dietary and perioperative interventions, postbiotics, and bacteriophage-based approaches, as potential means of modifying immune resistance in MSS/pMMR CRC. Although early clinical signals from microbiota-modulating combinations are encouraging, the available evidence remains limited by small cohorts, heterogeneous interventions, and the absence of randomized CRC-specific studies. Microbiome-based biomarkers and therapeutics therefore remain investigational, and standardized sampling, prospective validation, and carefully designed trials will be required before microbiome modulation enters routine CRC care.},
}

Humans
*Colorectal Neoplasms/immunology/therapy/microbiology
*Immunotherapy/methods
*Gastrointestinal Microbiome/immunology
*Translational Research, Biomedical
Animals
*Immunity

@article {pmid42882521,
year = {2026},
author = {Pînzariu, AC and Șerban, IL and Soroceanu, RP and Vlăsceanu, VI and Maxim, M and Miler, AA and Leonte, SM and Atodiresei, C and Moscalu, M and Manole, LM and Trandafir, LM and Șerban, DN and Timofte, DV},
title = {GDF-15/GFRAL Axis Dynamics and Vulnerability Windows in Bariatric Surgery: Pathophysiological, Microbiomic, and Pharmacological Perspectives.},
journal = {Cells},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/cells15191823},
pmid = {42882521},
issn = {2073-4409},
mesh = {Humans ; *Bariatric Surgery ; Animals ; *Growth Differentiation Factor 15/metabolism ; *Glial Cell Line-Derived Neurotrophic Factor Receptors/metabolism ; Gastrointestinal Microbiome ; Signal Transduction ; Obesity/surgery/metabolism ; },
abstract = {Bariatric surgery (BS) and new pharmacological treatments cause significant neurometabolic changes. However, the pathways linking peripheral stress to central metabolic control remain poorly understood. This review highlights the GDF-15/GFRAL/RET complex as a key integrator of multiorgan-to-brain stress signals that shape systemic metabolic adaptation after surgical and pharmacological interventions. Based on a structured search across PubMed, Embase, Scopus, Google Scholar, and Web of Science covering 2020-2026 alongside foundational studies, we integrated translational evidence from peer-reviewed human trials and mechanistic animal models to map the GDF-15/GFRAL/RET axis across bariatric and incretin domains. We examined the neurobiology of the GDF-15/GFRAL axis to clarify variability in metabolic and behavioral outcomes after BS. This axis links metabolic stress signals from the gut, liver, and adipose tissue to the hindbrain and hypothalamic regulation of energy balance. Changes in the gut microbiome and SCFA-FFAR2/FFAR3 signaling after surgery interact with GDF-15 and incretin pathways. Future studies should critically compare BS with synergistic or alternative non-invasive neurometabolic approaches such as incretin mimetics, exogenous GDF-15 therapies, and high-protein diets.},
}

Humans
*Bariatric Surgery
Animals
*Growth Differentiation Factor 15/metabolism
*Glial Cell Line-Derived Neurotrophic Factor Receptors/metabolism
Gastrointestinal Microbiome
Signal Transduction
Obesity/surgery/metabolism

@article {pmid42882861,
year = {2026},
author = {Machado, MV},
title = {Prediction of Response to Immunotherapy in Hepatocellular Carcinoma: Where Do We Stand?.},
journal = {Cancers},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/cancers18193167},
pmid = {42882861},
issn = {2072-6694},
abstract = {Worldwide, liver cancer is the seventh most common cancer and the third leading cause of cancer-related mortality, reflecting its dismal prognosis, with only approximately 20% of patients alive 5 years after diagnosis. At least 50% of patients ultimately require systemic treatment. In 2020, the systemic treatment landscape changed dramatically with the introduction of immune checkpoint inhibitor (ICI)-based therapies, which have demonstrated improved overall survival and longer preservation of quality of life compared with tyrosine kinase inhibitor (TKI)-based approaches. However, fewer than one third of patients achieve objective response, 10-25% experience severe immune-related adverse events, and ICI-based treatments represent a substantial economic burden for health systems. Importantly, robust and clinically validated predictive biomarkers of response to ICI remain an unmet need. This review summarizes current efforts to identify predictive biomarkers of ICI response in hepatocellular carcinoma (HCC), integrating clinical, pathological, molecular, microbiome, and imaging approaches, and discusses how these developments may shape the future of treatment selection.},
}

@article {pmid42883021,
year = {2026},
author = {Bao, J and Li, H and Jiang, K and Xu, J and Wu, Y and Ji, W and Li, S and Qi, B and Niu, H},
title = {Comparative Study on Growth Performance and Rumen Digestive Metabolism Between Cull Beef Cows and Fattening Bulls.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193052},
pmid = {42883021},
issn = {2076-2615},
support = {(32460813)//National Natural Science Foundation of China/ ; (2025YFDZ0123, 2025ZY0111, YZ2023010, TL20205TW004)//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; (GXKY26Z082).//Inner Mongolia University for Nationalities/ ; },
abstract = {Culled beef cows may retain practical value for fattening after reproductive use, but the rumen and host physiological characteristics associated with this response remain incompletely characterized. This study compared culled beef cows (CBC; n = 9) with fattening bulls (CON; n = 9) using 18 healthy Simmental crossbred cattle fed the same experimental total mixed ration (TMR) under identical feedlot conditions. Growth performance, body condition score (BCS), apparent nutrient digestibility, economic outcomes, blood indices, rumen fermentation, ruminal enzyme activities, rumen metagenomes, and plasma untargeted metabolomes were assessed. Compared with CON, CBC had higher final body weight, average daily gain, feed intake, and apparent digestibility of dry matter, crude protein, and neutral detergent fiber, whereas the feed-to-gain ratio did not differ significantly between groups (p = 0.692). BCS increased significantly from day 0 to day 60 within both cattle categories. Because different, non-cross-calibrated BCS reference frameworks were used, no between-group comparison of BCS was made. Economic analysis indicated that the value attributable to actual live-weight gain was similar between groups when within-category prices were held constant, whereas the relative economic outcome varied with feed costs and changes in live-cattle market prices. CBC also showed more propionate-oriented fermentation, greater fibrolytic enzyme activities, distinct carbohydrate-active enzyme profiles, higher insulin and leptin, and lower non-esterified fatty acids and β-hydroxybutyrate. Because lean and fat mass were not directly measured, the tissue basis of the greater weight gain remains unresolved. Overall, CBC exhibited a stronger fattening response accompanied by coordinated differences in rumen function and host metabolic profiles.},
}

@article {pmid42883069,
year = {2026},
author = {Kostyunina, O and Traspov, A and Ermilov, A and Bakoev, F and Nemkovskiy, G and Kusnetzov, A and Belyakov, V},
title = {Untargeted Metabolomic Profiling of Spermatozoa and Seminal Plasma Identifies Candidate Metabolic Indicators of Semen Quality in Holstein Bulls.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193098},
pmid = {42883069},
issn = {2076-2615},
support = {24-16-00198//Russian Science Foundation/ ; },
abstract = {This exploratory study applied untargeted LC-MS/MS metabolomic profiling to investigate metabolic differences between Holstein bulls with high-quality (HQ) and low-quality (LQ) semen in both spermatozoa and seminal plasma. Bulls were classified based on long-term routine semen quality records and ejaculate rejection rates, providing a stable and biologically meaningful grouping. A total of 249 unique metabolites were annotated across both biological matrices. Differential analysis identified 46 LC-MS features corresponding to 44 unique metabolites in spermatozoa and 11 LC-MS features corresponding to 9 unique metabolites in seminal plasma that met the predefined multi-criteria selection thresholds (FDR < 0.05, |log2FC| > 1, VIP > 1, and AUC ≥ 0.80 or ≤0.20). The HQ group was characterized by higher levels of metabolites involved in amino acid and energy metabolism, including glutamine, glutamate, aspartate, succinate, ornithine, citrulline, and arginine. Conversely, the LQ group showed increased abundance of metabolites potentially related to altered redox homeostasis and compounds potentially originating from dietary or microbial sources. As this is an exploratory study, mechanistic interpretations regarding oxidative stress, microbiome-derived metabolites, and actual fertility should be considered strictly hypothesis-generating. The annotated metabolites represent candidate indicators associated with semen quality parameters rather than validated biomarkers. Their relationship with actual field fertility and their underlying biological mechanisms require confirmation in larger, independent populations with direct functional assays and field fertility records.},
}

@article {pmid42883122,
year = {2026},
author = {Baka, E and Kovács-Weber, M and Ábrahám, R and Pap, TI and Táncsics, A and Szabó, G and Heincinger, M and Szabó, S and Dolányi, Á and Berta, AI and Kovács, B and Szabó, RT},
title = {A Paired Ileum-Caecum Study of the Goose Gut Microbiome in Response to Fattening Protocol and Postbiotic Supplementation.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193153},
pmid = {42883122},
issn = {2076-2615},
support = {//Hungarian University of Agriculture and Life Sciences/ ; },
abstract = {The gut microbiota plays a central role in poultry health and production performance, yet its response to intensive fattening protocols and postbiotic supplementation in geese remains poorly characterized. This study used 16S rRNA gene amplicon sequencing to profile ileal and caecal microbial communities from geese raised under two fattening protocols, with or without postbiotic supplementation, and assessed the effect of 24 h post-mortem chilling on apparent community composition. Fattening protocol was associated with the largest differences in gut microbial structure, producing significant shifts in beta diversity in both the ileum and the caecum (although protocol, age at slaughter, and duration of postbiotic exposure co-varied between cohorts and cannot be fully disentangled), accompanied by extensive taxon-level differences identified by LEfSe. Postbiotic supplementation did not significantly alter overall community structure under force-feeding conditions but produced a taxon-specific, trend-level shift in the caecum under restricted feeding, suggesting that its effect depends on the continuity of supplementation relative to slaughter. Alpha diversity did not differ significantly in the ileum, but caecal richness differed significantly between the G2 and G5 postbiotic-supplemented groups (Conover-Iman test, adjusted p < 0.05). The warm- and chilled-dissection groups differed in ileal but not caecal community composition (individual-animal variation cannot be separated from the effect of chilling in this comparison, as the two groups consisted of different birds), indicating that dissection timing is an important methodological variable in goose microbiome research. These findings highlight cohort- and protocol-related differences as key correlates of gut microbial composition in geese and provide a framework for optimizing postbiotic supplementation strategies and sampling standardization in waterfowl production.},
}

@article {pmid42883403,
year = {2026},
author = {Khan, ZA and Chowdhury, Z and Modi, R and Sumsuzzman, DM and Ju, LS and Labala, RK and Gravenstein, N and Martynyuk, AE},
title = {Gut Microbiome Disruption in Traumatic Brain Injury and Therapeutic Potential of Probiotics: A Systematic Review and Meta-Analysis.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191730},
pmid = {42883403},
issn = {2079-7737},
support = {1R01HD107722-05/NH/NIH HHS/United States ; 5R56HD102898-02/NH/NIH HHS/United States ; //I. Heerman Anesthesia Foundation/ ; },
abstract = {BACKGROUND: Traumatic brain injury (TBI) is increasingly recognized as a systemic disorder that may involve alterations in the brain-gut-microbiome (BGM) axis, a bidirectional network linking the brain, immune system, and gut microbiota. While animal studies suggest that disruption and restoration of the BGM axis influence TBI-related changes and recovery, respectively, human evidence remains fragmented.

METHODS: MEDLINE, Embase, Scopus, and Web of Science were searched through 2025; Global Health was additionally searched for Aim 2. This study had two aims: (1) to assess gut microbiome changes following TBI and (2) to evaluate the effects of probiotic supplementation in TBI patients. Data were synthesized using random-effects meta-analyses, and risk of bias was assessed using the Newcastle-Ottawa and Cochrane tools.

RESULTS: Five studies (Aim 1) and fifteen studies (Aim 2) met the inclusion criteria. TBI was associated with shifts in microbial composition, including reduced abundance of Prevotella (p < 0.001), and Parabacteroides merdae (p = 0.038), whereas overall alpha diversity did not differ significantly. Probiotic supplementation improved neurological outcomes [Glasgow Coma Scale (GCS): MD = 2.25, 95% CI 1.34-3.16, p < 0.001] and functional outcomes [Glasgow Outcome Scale (GOS): MD = 1.40, 95% CI 1.12-1.69, p < 0.001], and reduced inflammatory markers, including TNF-α (p = 0.006), IL-6 (p < 0.001), procalcitonin (p < 0.001), and D-lactic acid levels (p < 0.001). High heterogeneity was observed across several outcomes, with the GOS showing moderate heterogeneity. Neurocognitive outcomes were evaluated qualitatively and were not pooled in a meta-analysis because of limited available data.

CONCLUSIONS: The findings of this analysis suggest that TBI is associated with alterations in the gut microbiome and that microbiota-targeted therapies involving probiotics may improve inflammatory, gut-barrier, neurological, and functional outcomes. Although substantial heterogeneity was observed across several outcomes, particularly the GCS, the available evidence supports further investigation of microbiome-directed interventions as adjunctive strategies for TBI management. Standardized multicenter trials are warranted.

PROSPERO: CRD420251135998.},
}

@article {pmid42883405,
year = {2026},
author = {Hammami, I and Abdelaal, M and Ababutain, IM and Alsanie, SI and Al Hawas, GH and Alghamdi, AI and Alqazlan, NM and Alghamdi, RA and Alsubaie, FM and Alnabbat, JY},
title = {Integrated Phytoremediation and Microbial Mitigation Strategies for Sustainable Restoration of Toxic Metal-Contaminated Soils.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191732},
pmid = {42883405},
issn = {2079-7737},
abstract = {Toxic metal contamination of soil remains a critical global challenge due to the persistence, bioaccumulation, and irreversible toxicity of these metals. Cadmium (Cd), lead (Pb), mercury (Hg), arsenic (As), chromium (Cr) and nickel (Ni) are the most common toxic metals that threaten food security, ecosystem stability, and human health. While conventional physicochemical remediation technologies provide rapid pollutant removal, they are constrained by high economic costs, secondary pollution risks, and long-term soil degradation. Biological approaches, particularly phytoremediation and microbial mitigation, offer environmentally compatible alternatives; however, their field-scale performance is often limited by low biomass production, restricted metal bioavailability, microbial instability, and heterogeneous soil conditions. This review critically synthesizes recent advances that move beyond standalone biological strategies toward integrated, multi-scale remediation frameworks. We evaluate the mechanistic basis and performance of nano-assisted phytoremediation, biochar-mediated stabilization, omics-guided plant-microbe optimization, and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein systems (CRISPR/Cas) for enhancing metal transport, chelator biosynthesis, antioxidant defense, and microbial detoxification pathways. Emerging evidence indicates that nano-enabled amendments and biochar composites can reduce bioavailable Cd fractions by up to 75%, while omics-driven microbial consortia and targeted genome editing improve tolerance and accumulation efficiency in key crops such as rice and sorghum. Importantly, we assess translational barriers including nanoparticle ecotoxicity, off-target genome effects, regulatory constraints, biomass disposal, and life-cycle sustainability that currently limit large-scale deployment. By integrating mechanistic insights with field validation data, risk assessment considerations, and technology readiness evaluation, this review proposes a conceptual roadmap for scalable, eco-efficient soil restoration. The convergence of nanotechnology, systems biology, microbiome engineering, and precision genome editing represents a transformative pathway for next-generation remediation strategies capable of restoring contaminated soil while safeguarding environmental and public health.},
}

@article {pmid42883411,
year = {2026},
author = {Florez, JZ and Varela-Prieto, L and Zárate, A and Caselles-Osorio, A and Llanos-Lizcano, A and Bruna, P},
title = {Root Microbiome Assembly Underpins the Ecological Role of Emergent Macrophytes in a Pilot-Scale Constructed Wetland.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191739},
pmid = {42883411},
issn = {2079-7737},
support = {11250731//National Agency for Research and Development/ ; 3220504//National Agency for Research and Development/ ; 2023-21230832//National Agency for Research and Development/ ; },
abstract = {Constructed wetlands (CWs) depend on plant-microbe associations for pollutant transformation, yet the processes linking macrophyte identity to rhizosphere microbiome assembly remain insufficiently resolved. We compared bacterial communities associated with C. articulatus (Ca) and T. geniculata (Tg) roots with an unplanted treatment (Up) in pilot-scale CWs on the Colombian Caribbean coast. Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Co-occurrence networks, taxon-environment correlations, and the phylogenetic bin-based null model iCAMP were used to assess community structure, potential associations and assembly mechanisms. CaS supported significantly greater bacterial diversity than TgS and Up, while each macrophyte recruited a distinct community. A shared core microbiome dominated by Rhodocyclaceae, Sphingomonadaceae, Chitinophagaceae, Pirellulaceae, and Xanthomonadaceae comprised taxa with putative roles in nutrient and organic matter transformations. Several bacterial families were significantly associated with PO4[3-], NH4[+], and dissolved oxygen. Assembly was predominantly stochastic, with dispersal limitation (45.2%) and ecological drift (33.2%) exceeding deterministic selection (16.5%). Nevertheless, planted treatments displayed higher network modularity and connectivity and inferred functional redundancy than Up, consistent with niche differentiation. These findings suggest that species-specific macrophyte configurations are associated with differences in root-associated microbial community composition, while assembly and network analyses provide exploratory insights into community organization. The limited replication precludes causal attribution to plant identity or conclusions regarding treatment performance. Future studies integrating controlled planting densities, increased replication, meta-omics, and root exudate characterization are needed to clarify plant-microbiome relationships and evaluate their potential relevance to constructed wetland functioning.},
}

@article {pmid42883451,
year = {2026},
author = {Liu, L and Spaink, HP},
title = {TLR Signaling Beyond Immunity: Emerging Roles in Cell Migration, Metabolism, Development, and Host-Microbiome Crosstalk.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191778},
pmid = {42883451},
issn = {2079-7737},
abstract = {Recent findings support a broader view of TLR signaling as an integrative signaling hub that links immunity with cell migration, metabolism, development, and host-microbiome crosstalk. In cell migration, TLRs exert context-dependent effects through chemokine receptor regulation, adhesion and cytoskeletal modulation, and indirect cytokine-mediated signaling. In metabolism, TLRs orchestrate insulin resistance, obesity, and glucose homeostasis in a receptor- and tissue-specific manner. In tissue injury and development, TLR signaling exerts dual roles; it is detrimental in ischemia-reperfusion injury, but beneficial in vascular remodeling and neurogenesis. We then examine the bidirectional interplay between TLRs and the gut microbiome, where TLRs shape microbial community structure and intestinal immune homeostasis. Finally, we survey the therapeutic landscape of TLR modulators, highlighting that while TLR agonists are predominantly explored in oncology, TLR antagonists show promise in autoimmune diseases such as inflammatory bowel disease. Special attention is given to insights from organoid, rodent and zebrafish models, which have provided powerful in vitro and in vivo evidence for multiple roles of TLR signaling under both physiological and pathological conditions. A deeper understanding of these non-canonical functions will be essential for developing next-generation therapeutic strategies that selectively modulate TLR signaling in infectious, inflammatory, metabolic, and microbiome-associated diseases.},
}

@article {pmid42883591,
year = {2026},
author = {Jiang, X and Xu, H and Zhou, H and Xie, M and Xiong, T and Liu, Z},
title = {Exploring Dynamic Changes in Microbial Succession and Flavor-Active Metabolites During Pickled and Dried Mustard Fermentation of Traditional Fermented Vegetables.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/foods15193486},
pmid = {42883591},
issn = {2304-8158},
support = {32260576//National Natural Science Foundation of China/ ; 20232BBF60024//Jiangxi Provincial KeyR&D Program/ ; 202401AS070025//Yunnan Provincial Basic Research Program in 2024/ ; },
abstract = {Pickled and dried mustard (PDM) is a traditional dish of the Hakka people that is well-known in many parts of the world. However, past scientific studies on PDM provide little information on the relationship between the microbiome composition of the PDM fermentation process and flavor formation, which restricts the industrialization and improved quality control of PDM. Therefore, this study investigated the microbiome composition, flavor metabolites, physicochemical properties, and the relationships among them in PDM from Shaoxing. During fermentation, the main aromas of PDM are similar to pine and orange oils, with a strong fat aroma, and are mainly contributed by dodecanal in the early and middle stages of fermentation. As the fermentation progressed, the phenolic and aldehyde contents increased markedly; the major aldehydes in PDM were dodecanal, nonanal, and phenylacetaldehyde. The microbial succession during PDM fermentation was a gradual transition from Weissella sp. and Basidiomycota to Latilactobacillus, Lactiplantibacillus, and Ascomycota. We identified candidate core microorganisms potentially related to characteristic flavor development in PDM: Debaryomyces sp., Weissella cibaria, Lactiplantibacillus pentosus, Weissella sp. NBRC 107272, Latilactobacillus sakei, Cryptococcus sp., Filobasidium magnum, Cystofilobasidium macerans, Weissella hellenica, Levilactobacillus brevis, and Weissella sp. NBRC 107245. The findings of this study will be an important guide to optimizing the production process and quality of PDM.},
}

@article {pmid42883631,
year = {2026},
author = {Eltanty, MM and Shim, JH and Türkez, H and Bae, SJ and Bae, J and Abd El-Aty, AM},
title = {From Food Additives and Contaminants to the Human Exposome: A Precision Toxicology Framework for Next-Generation Food Safety.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/foods15193525},
pmid = {42883631},
issn = {2304-8158},
support = {2026-ANCHOR-15-110//Ministry of Education/ ; RS-2026-25477916//National Research Foundation of Korea/ ; },
abstract = {Human exposure to foodborne xenobiotics, including environmental contaminants that enter the food chain, is no longer adequately represented by isolated chemicals. Individuals encounter complex and dynamic mixtures of food additives, pesticide residues, veterinary drugs, mycotoxins, processing contaminants, packaging migrants, environmental pollutants, and other dietary chemicals that interact with genetics, metabolism, the gut microbiome, nutritional status, and lifestyle throughout life. The dietary exposome therefore represents a critical interface linking food contaminants, internal chemical exposure, molecular perturbation, and long-term human health. Conventional toxicology provides an indispensable foundation for food safety regulation through hazard characterization and population-based health guidance values but is less equipped to explain interindividual variability in biological response and chronic disease susceptibility. Precision toxicology provides an integrative and mechanism-informed framework that combines high-resolution analytical chemistry, human biomonitoring, exposomics, multiomics, new approach methodologies, and artificial intelligence. This integration enables the characterization of biologically effective exposure, the elucidation of exposure-response relationships, and the identification of interindividual variability in toxicological susceptibility. This perspective proposes a translational framework connecting external exposure → internal dose → biological response → individual susceptibility → health outcome. We position this framework relative to existing exposome, exposure-pathway, and adverse-outcome-pathway frameworks; specify the evidence required at each transition; make its life-course dimension explicit; illustrate it with a worked per- and polyfluoroalkyl substance (PFAS) example; and outline a stepwise route into food risk assessment together with its principal limitations. Such integration could advance food safety science beyond residue detection toward biologically informed exposure assessment, ultimately supporting more evidence-based regulatory decision-making, preventive strategies, and public health protection.},
}

@article {pmid42883703,
year = {2026},
author = {Pérez-Castro, S and Carballo-Quinta, M and Rodríguez-Costas, N and Freire-Rodríguez, A and Davina-Nunez, C and Bellas-Pereira, A and Taboada-Rodríguez, P and Pérez-Schoch, M and Cabrera-Alvargonzález, JJ and Muller-Arteaga, CA and Sánchez-García, JF and Cespón-Outeda, E and López-Díez, ME},
title = {Gut Microbiota Signatures Associated with Metastatic Prostatic Cancer Treated with Androgen Receptor Pathway Inhibitor (ARPI) Therapy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198454},
pmid = {42883703},
issn = {1422-0067},
support = {Leonardo de la Peña 2022 Grant//Urological Research Foundation/ ; GAIN IN607B-2022-19//Axencia Galega de Innovacion/ ; },
mesh = {Humans ; Male ; *Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Androgen Receptor Antagonists/therapeutic use/pharmacology ; *Receptors, Androgen/metabolism ; Neoplasm Metastasis ; Aged ; Disease Progression ; Metagenomics/methods ; },
abstract = {Metastatic prostate cancer (MPCa) remains an aggressive disease despite the introduction of androgen receptor pathway inhibitors (ARPIs), and biomarkers predicting progression are still lacking. The aim of this study was to investigate gut microbiota (GM) composition and functional potential associated with advanced disease and progression under ARPI therapy. The GM of 15 patients with metastatic PCa receiving ARPIs, including 5 patients with disease progression, was compared with that of 39 patients with untreated (UT) PCa using shallow shotgun metagenomic sequencing. The metastatic PCa cohort receiving ADT plus ARPI therapy showed reduced microbial alpha diversity and significant taxonomic and functional differences compared with the untreated, clinically localized PCa reference cohort. In patients with advanced disease, microbial functions related to dietary carbohydrate utilization, fermentation, epithelial interaction, and microbial structural maintenance were predominantly underrepresented, whereas stress-responsive and redox-associated functions were overrepresented. These alterations may reflect reduced metabolic and ecological versatility alongside increased adaptation to host-associated stress conditions. Compared with the UT group, in patients with progression we found that Bifidobacterium longum, Anaerobutyricum hallii, Ruminococcus sp., and Blautia obeum (LinDA coefficients 5.7, 2.6, 2.6 and 2.4, respectively) were enriched, whereas Sutterella wadsworthensis, Butyricimonas, Bilophila wadsworthia, Alistipes indistinctus, and Intestinimonas were depleted (LinDA coefficients -8.4, -5.9, -5, -5 and -3, respectively). Together, these findings identify distinct taxonomic and functional features associated with metastatic PCa under systemic therapy and microbial features observed in patients experiencing progression during ARPI treatment, providing potential candidates for biomarker development and generating testable hypotheses regarding microbiome-host metabolic interactions in treatment resistance. The GM may therefore represent a potential source of biomarkers for advanced PCa and progression under ARPI therapy, although longitudinal and multi-omics studies are required to determine their predictive value and functional relevance.},
}

Humans
Male
*Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/drug effects
*Androgen Receptor Antagonists/therapeutic use/pharmacology
*Receptors, Androgen/metabolism
Neoplasm Metastasis
Aged
Disease Progression
Metagenomics/methods

@article {pmid42883711,
year = {2026},
author = {Jurkiewicz, K and Smolinska-Wilczynska, S},
title = {Maternal-Fetal Exposome and Early-Life Microbiota-Pattern Recognition Receptors Signaling in Inflammatory Bowel Disease Susceptibility: A Mechanistic Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198458},
pmid = {42883711},
issn = {1422-0067},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/etiology/metabolism/immunology ; Female ; Pregnancy ; Animals ; Signal Transduction ; *Receptors, Pattern Recognition/metabolism ; Disease Susceptibility ; *Prenatal Exposure Delayed Effects ; *Gastrointestinal Microbiome ; Developmental Origins of Health and Disease ; *Microbiota ; *Maternal Exposure/adverse effects ; },
abstract = {Inflammatory bowel disease (IBD) develops through interactions among genetic susceptibility, intestinal microbiota, environmental exposures, and dysregulated mucosal immunity. Increasing evidence suggests that these interactions may begin before diagnosis-and possibly before birth-when maternal signals, microbial assembly, epithelial maturation, and immune education intersect. This narrative review synthesizes findings from human observational and cohort studies, experimental animal and cellular models, and mechanistic literature to examine how prenatal and early-life exposures may influence later IBD susceptibility. Human cohort studies associate later IBD with several early-life exposures, particularly repeated antibiotic use, whereas evidence for dietary, delivery, and household factors remains heterogeneous and vulnerable to confounding. Studies of pregnancies affected by IBD identify altered maternal and infant microbial and immune features but do not establish causality. Experimental models provide stronger mechanistic evidence that maternal microbial signals influence offspring immune development, neonatal epithelial cells acquire context-dependent tolerance, and microbial metabolites regulate regulatory T cells, type 17 immunity, barrier function, and chromatin-modifying enzymes. Histamine-receptor signaling further illustrates receptor-specific modulation of bacterial TLR (Toll-like receptors) responses in established IBD, although its role in early-life programming remains unproven. We propose a testable "developmental inflammatory set-point" model in which cell type, tissue compartment, timing, signal intensity, and host genotype determine whether microbial sensing promotes tolerance or persistent inflammatory readiness. This model is biologically plausible but remains unvalidated as a predictor of human IBD.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/etiology/metabolism/immunology
Female
Pregnancy
Animals
Signal Transduction
*Receptors, Pattern Recognition/metabolism
Disease Susceptibility
*Prenatal Exposure Delayed Effects
*Gastrointestinal Microbiome
Developmental Origins of Health and Disease
*Microbiota
*Maternal Exposure/adverse effects

@article {pmid42883716,
year = {2026},
author = {Jo, S and Seo, H and Shuvo, MSH and Ahmed, I and Kim, S and Jeong, JH and Song, HY},
title = {Gut Microbiome Signatures Associated with Osteoporotic Vertebral Compression Fracture.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198468},
pmid = {42883716},
issn = {1422-0067},
support = {No. RS-2023-00219563//National Research Foundation of Korea/ ; //Soonchunhyang University/ ; No. 2021R1A6A1A03046418//National Research Foundation of Korea/ ; NRF-2020R1F1A1069896//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Fractures, Compression/microbiology ; *Gastrointestinal Microbiome ; Female ; RNA, Ribosomal, 16S/genetics ; *Osteoporotic Fractures/microbiology ; Male ; Aged ; Bone Density ; *Spinal Fractures/microbiology ; Feces/microbiology ; *Osteoporosis/microbiology ; Middle Aged ; Case-Control Studies ; Fatty Acids, Volatile/metabolism ; },
abstract = {Osteoporotic vertebral compression fracture (OVCF) is a clinically important condition associated with pain, disability, and impaired quality of life. Although osteoporosis is commonly diagnosed based on bone mineral density (BMD), fracture occurrence cannot be fully explained by BMD alone, suggesting that additional systemic factors may contribute to fracture susceptibility. The gut microbiome has recently emerged as a potential regulator of bone metabolism; however, its association with OVCF remains insufficiently characterized. In this study, fecal microbiome profiling using 16S rRNA gene sequencing was performed in 29 healthy controls, 11 patients with osteoporosis, and 25 patients with OVCF. Compared with the healthy control and osteoporosis groups, the OVCF group exhibited more distinct gut microbial compositional differences and reduced microbial diversity. Differential abundance analyses identified an increased relative abundance of Alistipes in the OVCF group and a higher relative abundance of Prevotella in healthy controls, with these taxa showing negative and positive correlations with BMD, respectively. Functional profiling further suggested differences in microbial metabolic pathways associated with OVCF, including increased mucin-derived carbohydrate degradation and reduced polyamine metabolism pathways. Consistently, fecal short-chain fatty acid concentrations were significantly lower in the OVCF group, accompanied by a reduced abundance of short-chain fatty acid-producing taxa and alterations in related microbial pathways. Overall, these findings suggest that gut microbial and metabolic alterations are associated with OVCF status rather than osteoporosis alone. The identified microbial signatures provide preliminary evidence of OVCF-associated microbial alterations; however, further validation in independent cohorts and longitudinal studies is required before their diagnostic or predictive value can be established.},
}

Humans
*Fractures, Compression/microbiology
*Gastrointestinal Microbiome
Female
RNA, Ribosomal, 16S/genetics
*Osteoporotic Fractures/microbiology
Male
Aged
Bone Density
*Spinal Fractures/microbiology
Feces/microbiology
*Osteoporosis/microbiology
Middle Aged
Case-Control Studies
Fatty Acids, Volatile/metabolism

@article {pmid42883721,
year = {2026},
author = {Papacocea, RI and Adina Gabriela, M and Radu-Ștefan, V and Russomano, T and Papacocea, IR},
title = {Antipsychotic-Induced Remodeling of the Gut Microbiota: Drug-Specific Patterns and Molecular Links to Metabolic Adverse Effects.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198471},
pmid = {42883721},
issn = {1422-0067},
mesh = {Humans ; *Antipsychotic Agents/adverse effects/pharmacology/therapeutic use ; Animals ; *Gastrointestinal Microbiome/drug effects ; Schizophrenia/drug therapy/microbiology ; },
abstract = {Antipsychotic drugs are essential for the treatment of schizophrenia-spectrum disorders and other severe psychiatric conditions, but several agents produce clinically important metabolic and gastrointestinal adverse effects. Increasing evidence suggests that these outcomes may involve bidirectional interactions between antipsychotics and the gut microbiota. This structured narrative review integrates human, animal, gnotobiotic, in vitro, pharmacokinetic, and multi-omic evidence to examine drug-specific microbiome effects and microbiota-dependent modulation of host responses. Olanzapine has the strongest mechanistic evidence, with germ-free, antibiotic-depletion, colonization, and vagotomy studies supporting a contributory role of the microbiota in weight gain, adiposity, inflammation, altered microbial metabolites, and lipid dysregulation. Risperidone also shows microbiota-dependent metabolic and neurobiological effects, whereas findings for clozapine, quetiapine, aripiprazole, lurasidone, and amisulpride remain more heterogeneous or limited. Across agents, no universal taxonomic pattern has emerged. Functional pathways involving short-chain fatty acids, bile acids, epithelial barrier integrity, immune and neuroendocrine signaling, vagal pathways, and microbial drug metabolism appear more informative than individual taxa or the Firmicutes/Bacteroidota ratio. Current evidence remains limited by methodological heterogeneity, small cohorts, confounding, and predominantly preclinical mechanistic data. Prospective, treatment-naive, drug-specific longitudinal multi-omic studies are required.},
}

Humans
*Antipsychotic Agents/adverse effects/pharmacology/therapeutic use
Animals
*Gastrointestinal Microbiome/drug effects
Schizophrenia/drug therapy/microbiology

@article {pmid42883741,
year = {2026},
author = {Zhukov, IS and Alnefeesi, Y and Gladyshev, NS and Zolkin, A and Zalicheva, AB and Chalabiani, Y and Miklya, I and Ermolenko, EI and Gainetdinov, RR},
title = {Gut Microbiome Alterations in TAAR5 Knockout Mice and In Silico Ligand Prediction.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198493},
pmid = {42883741},
issn = {1422-0067},
support = {148723091//St Petersburg University/ ; },
mesh = {Animals ; *Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry ; Mice, Knockout ; Trace Amine-Associated Receptors ; Mice ; *Gastrointestinal Microbiome/genetics ; Molecular Docking Simulation ; Ligands ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Trace amine-associated receptors (TAARs) are a class of G protein-coupled receptors with roles in olfaction, behaviour, and immunity. Known best as an olfactory receptor, TAAR5 has been linked to emotional behaviour and hippocampal neurogenesis, yet its peripheral mechanisms remain poorly understood. Given bidirectional influences between the gut microbiota and the host, we investigated whether TAAR5 deletion alters the gut microbiome in mice. Using 16S rRNA sequencing, we compared the gut microbiota of TAAR5-knockout (TAAR5-KO) and wild-type mice. While alpha-diversity remained unchanged, beta-diversity analysis revealed significant separation between genotypes, with TAAR5-KO mice exhibiting markedly increased inter-individual variability. Taxonomically, KO mice showed a significant reduction in Ruminococcus and ASF356, alongside an enrichment of specific Lachnospiraceae and Prevotellaceae lineages. Functional metagenomic prediction (PICRUSt2) implied a reduction in the metagenomic capacity for central metabolic pathways (glycolysis, TCA cycle, fatty acid β-oxidation) and an increase in the capacity for guanosine nucleotide degradation pathways; these hypotheses remain untested. Molecular docking identified candidate microbial metabolites, including small amines (2-aminophenol, aminoacetone, butan-1-amine), with ligand efficiencies comparable to the known TAAR5 agonist trimethylamine. These findings suggest that TAAR5 may influence gut microbiome composition and function, with particular impact on Ruminococcus-a genus linked to intestinal inflammation. The increased compositional variability in TAAR5-KO mice suggests that TAAR5 may act as a homeostatic gatekeeper in gut microbial ecology. Our in silico results offer testable hypotheses for future validation of microbial metabolites as novel TAAR5 ligands.},
}

Animals
*Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry
Mice, Knockout
Trace Amine-Associated Receptors
Mice
*Gastrointestinal Microbiome/genetics
Molecular Docking Simulation
Ligands
RNA, Ribosomal, 16S/genetics

@article {pmid42883752,
year = {2026},
author = {Mafe, AN and Büsselberg, D},
title = {Microbiome-Guided Maternal and Child Nutrition: A Structured Narrative Review of Indigenous African Foods, Fermented Foods, and Emerging Evidence.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198503},
pmid = {42883752},
issn = {1422-0067},
support = {NPRP 14S0311-210033//Qatar National Research Fund/ ; },
mesh = {Humans ; *Fermented Foods ; Probiotics ; Female ; *Child Nutritional Physiological Phenomena ; *Gastrointestinal Microbiome/physiology ; *Maternal Nutritional Physiological Phenomena ; Child ; Africa ; },
abstract = {The gut microbiota is recognized as important to maternal and child health through associations with immune maturation, metabolic programming, barrier integrity, and early-life disease susceptibility. Indigenous food systems, fermented foods, probiotics, and postbiotics may influence gut microbial communities and functions, suggesting potential avenues for investigation into nutritional resilience, particularly in low-resource settings. This review synthesizes evidence on microbiome-informed maternal and child nutrition, focusing on indigenous foods, fermented foods, probiotics, postbiotics, and microbiome-mediated mechanisms. Literature was searched in PubMed, Scopus, Web of Science, ScienceDirect, and Google Scholar for studies, systematic reviews, and meta-analyses published between 2015 and 2025. Evidence indicates that microbiome-directed nutritional interventions may influence microbial metabolites, particularly short-chain fatty acids, and pathways associated with barrier integrity, immune regulation, and cellular signaling, including adenosine monophosphate-activated protein kinase (AMPK), mechanistic target of rapamycin (mTOR), mitogen-activated protein kinase (MAPK), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), toll-like receptor (TLR), and peroxisome proliferator-activated receptor (PPAR). Artificial intelligence, multi-omics, and precision nutrition may support the investigation and future development of more targeted approaches. However, gaps remain regarding population-specific microbiome profiles, standardized probiotic and postbiotic formulations, longitudinal maternal-infant relationships, and evidence from African and other low-resource settings. The Microbiome-Informed Nutrition Framework (MINF) is proposed as a hypothesis-generating model integrating indigenous food systems, microbiome-directed interventions, precision nutrition, and community-based primary healthcare as potential areas for future research, rather than established clinical or public health interventions.},
}

Humans
*Fermented Foods
Probiotics
Female
*Child Nutritional Physiological Phenomena
*Gastrointestinal Microbiome/physiology
*Maternal Nutritional Physiological Phenomena
Child
Africa

@article {pmid42883796,
year = {2026},
author = {Izotova, AO and Komova, AV and Zhinzhakova, LZ and Khazieva, KR and Kachmazov, GS and Chaika, CV and Toshchakov, SV},
title = {Water-Sediment Partitioning of a Neutrophilic Iron-Cycling Microbiome in the High-Altitude Dzhily-Su Mineral Springs (Mt. Elbrus).},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198549},
pmid = {42883796},
issn = {1422-0067},
support = {//National Research Center "Kurchatov Institute"/ ; },
mesh = {*Microbiota ; RNA, Ribosomal, 16S/genetics ; *Iron/metabolism ; *Geologic Sediments/microbiology ; Archaea/genetics/classification/metabolism ; Phylogeny ; Altitude ; *Natural Springs/microbiology ; },
abstract = {Mineral springs of the Northern Caucasus remain largely uncharacterized by culture-independent approaches. At the high-altitude Dzhily-Su spring complex, where isotope data indicate deep-seated magmatic fluid inputs, planktonic and sediment-associated communities were analyzed using 16S rRNA gene profiling to determine whether these inputs shape the local microbiome. Rather than a distinct magmatically influenced community, the results revealed a pronounced water-sediment partitioning of taxa with known iron-cycling representatives, microaerophilic Gallionellaceae dominating the water fractions and facultatively anaerobic Aeromonas and Shewanella dominating the sediments. Furthermore, analysis of the fine-size (0.22 µm) water fraction highlighted a notable enrichment of candidate lineages and archaea, including a prominent Nanoarchaeota population (58.6% of archaeal reads) lacking identified mesophilic hosts. The predominance of a typical neutrophilic iron-cycling assemblage, together with the observed water-sediment partitioning, is consistent with an important role of local physicochemical gradients in structuring the microbial community despite the unusual geochemical setting of the parent aquifer.},
}

*Microbiota
RNA, Ribosomal, 16S/genetics
*Iron/metabolism
*Geologic Sediments/microbiology
Archaea/genetics/classification/metabolism
Phylogeny
Altitude
*Natural Springs/microbiology

@article {pmid42883861,
year = {2026},
author = {Deng, L and Liu, L and Luo, Y and Dai, M and Ye, Z and Xiong, X and Li, Y and Kong, D and Tan, X},
title = {From Prediction to Mechanism: Explainable AI for Plant-Microbiome Multi-Omics Integration and Biological Discovery.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198615},
pmid = {42883861},
issn = {1422-0067},
support = {42577322//National Natural Science Foundation of China/ ; },
mesh = {Multiomics ; *Plants/microbiology/genetics ; *Artificial Intelligence ; *Microbiota ; Computational Biology/methods ; },
abstract = {Predicting complex phenotypes from plant-microbiome multi-omics data has advanced significantly with machine learning and deep learning. However, traditional black-box models remain limited by their focus on predictive performance rather than mechanistic biological understanding. To bridge this gap, explainable artificial intelligence (XAI) has emerged as a key framework to transform biological data analysis from correlation mapping to hypothesis-driven discovery. This review synthesizes current advances in XAI methodologies, including post hoc feature attribution techniques and intrinsically interpretable neural architectures, and their applications in plant-microbiome interactions. We highlight how XAI enables multi-scale insights by mapping model predictions to functional genes, metabolic pathways, and microbial interaction networks. Furthermore, we address critical challenges in distinguishing statistical importance from true biological causality and advocate for a closed-loop framework that continuously integrates computational reasoning with wet-lab experimental validation. Finally, we explore future avenues, including biologically informed neural networks, causal AI, and multi-omics knowledge graphs. By facilitating the transition from predictive analytics to biologically interpretable and experimentally testable hypotheses, XAI may contribute to mechanistic discovery in plant-microbiome systems.},
}

Multiomics
*Plants/microbiology/genetics
*Artificial Intelligence
*Microbiota
Computational Biology/methods

@article {pmid42883874,
year = {2026},
author = {Chew, YY and Sharma, A and Goh, SSL and Mat Ali, NA and Augustin, Y and Krishna, S and Chung, I and Magesvaran, MKA and Masood, A and Teh, CSJ},
title = {Vaginal Microbial Risk Factors Associated with Human Papillomavirus-Induced Cervical Intraepithelial Neoplasia: A Systematic Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198625},
pmid = {42883874},
issn = {1422-0067},
support = {UM.000814/HPV.PV//Rafulin Holdings Sdn. Bhd./ ; },
mesh = {Female ; Humans ; *Uterine Cervical Dysplasia/microbiology/virology ; Risk Factors ; *Human Papillomavirus Viruses ; *Papillomavirus Infections/microbiology/virology/complications ; *Microbiota ; *Vagina/microbiology/virology ; *Uterine Cervical Neoplasms/microbiology/virology ; Dysbiosis/microbiology ; Lactobacillus ; Papillomaviridae ; },
abstract = {Human papillomavirus (HPV) drives cervical carcinogenesis, but viral infection alone is insufficient for malignant transformation. The vaginal microbiome may modulate HPV persistence and cervical intraepithelial neoplasia (CIN) progression, yet existing reviews remain inconclusive. This systematic review identifies specific vaginal microbiome risk factors associated with HPV and CIN and proposes plausible mechanisms linking dysbiosis to disease progression. Following (PRISMA) guidelines, databases were searched for studies published through October 2025. Thirty-three studies from 2013 to 2025 across 10 countries met the inclusion criteria, with 87.9% exhibiting low risk of bias. Most studies demonstrated marked Lactobacillus depletion alongside Prevotella and Gardnerella enrichment in HPV/CIN cases. Disease severity correlated with shifts toward high-diversity anaerobe communities, though alpha and beta diversity metrics varied across cohorts. Importantly, longitudinal data suggests a temporal sequence where baseline dysbiosis precedes clinical progression. Crucially, although the included cohorts directly observed and quantified these taxonomic shifts, the underlying mechanisms of disease progression, such as enzymatic degradation of mucosal barriers mediated by Gardnerella and immunosuppression driven by Fusobacterium, remain largely inferred from external in vitro literature. Lactobacillus iners emerged as a notable species-level risk factor in HPV persistence. Vaginal dysbiosis, characterised by Lactobacillus depletion and anaerobic expansion, is strongly correlated with HPV persistence and CIN progression, potentially facilitated through convergent barrier degradation and immune subversion. These findings highlight targets for microbiome-based risk stratification and therapeutic intervention.},
}

Female
Humans
*Uterine Cervical Dysplasia/microbiology/virology
Risk Factors
*Human Papillomavirus Viruses
*Papillomavirus Infections/microbiology/virology/complications
*Microbiota
*Vagina/microbiology/virology
*Uterine Cervical Neoplasms/microbiology/virology
Dysbiosis/microbiology
Lactobacillus
Papillomaviridae

@article {pmid42883875,
year = {2026},
author = {Tkaczenko, H and Rymuszka, A and Kołodziejska, R and Kurhaluk, N},
title = {Fresh and Fermented Beetroot: From Microbial Biotransformation to Nitrate-Nitrite-NO Signalling, Redox Homeostasis and Microbiome Interactions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198629},
pmid = {42883875},
issn = {1422-0067},
support = {NdS-II/SN/0476/2023/01//Ministry of Science and Higher Education/ ; },
mesh = {*Beta vulgaris/metabolism/chemistry/microbiology ; *Nitrates/metabolism ; Humans ; Fermentation ; *Nitric Oxide/metabolism ; Oxidation-Reduction ; Biotransformation ; *Nitrites/metabolism ; Homeostasis ; Signal Transduction ; *Microbiota ; Plant Roots/metabolism/microbiology ; Betalains/metabolism ; Animals ; Gastrointestinal Microbiome ; },
abstract = {Beetroot (Beta vulgaris L.) is a rich source of dietary nitrates, polyphenols, and other bioactive compounds that have potential cardiovascular, metabolic, and health-promoting effects. While previous reviews have largely focused on the nitrate-derived nitric oxide (NO) signalling pathway or the antioxidant properties of the pigments known as 'betalains', there is an increasing body of evidence that suggests microbial transformation and fermentation can substantially modify the biological properties of beetroot. This narrative review summarises the latest research on beetroot phytochemistry, nitrate-nitrite-NO metabolism, microbial biotransformation, fermentation and host physiological responses. Particular attention is given to the impact of fermentation on phenolic compounds, betalains, and the metabolism of nitrates and nitrites, as well as to its effects on antioxidant activity, bioaccessibility, and interactions with the gut microbiome. The available evidence suggests that fermentation can alter the beetroot matrix, increasing the accessibility or recovery of certain bioactive compounds while producing additional microbial metabolites with potential biological activity. These changes may complement the well-established effects of beetroot-derived nitrates and betalains on vascular function, redox homeostasis, inflammation and exercise-related physiology. However, evidence specifically linking fermented beetroot to clinical outcomes is limited, and the effects of fermentation depend heavily on microbial strains, processing conditions, the food matrix and host characteristics. Interindividual differences in microbiome composition may further contribute to variability in responses to beetroot-derived compounds. Thus, fermentation is a promising strategy for increasing the functional potential of beetroot by altering the bioaccessibility of its bioactive constituents through microbial biotransformation. Further well-designed human studies are needed to establish whether these compositional and mechanistic changes result in clinically significant benefits, and to clarify how individual microbiome profiles contribute to responses to fermented beetroot.},
}

*Beta vulgaris/metabolism/chemistry/microbiology
*Nitrates/metabolism
Humans
Fermentation
*Nitric Oxide/metabolism
Oxidation-Reduction
Biotransformation
*Nitrites/metabolism
Homeostasis
Signal Transduction
*Microbiota
Plant Roots/metabolism/microbiology
Betalains/metabolism
Animals
Gastrointestinal Microbiome

@article {pmid42883929,
year = {2026},
author = {Charoenchon, N and Korprasertthaworn, P and Thammavoharnkul, J and Kiatsurayanon, N and Prathomthong, P and Chimmanee, D and Sitthipunya, A},
title = {Toxicological Evaluation of Zingiber purpureum Extract and Its Effects on Gut Microbiota in Zebrafish.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198684},
pmid = {42883929},
issn = {1422-0067},
support = {MU-SRF-ST-09B/69//The Mahidol University Strategic Research Fund/ ; },
mesh = {Animals ; *Zebrafish/microbiology/embryology ; *Gastrointestinal Microbiome/drug effects ; *Plant Extracts/toxicity/pharmacology/chemistry ; Female ; RNA, Ribosomal, 16S/genetics ; *Zingiberaceae/chemistry ; Intestines/drug effects ; },
abstract = {Zingiber purpureum Roscoe (Phlai) is renowned in Southeast Asia for its anti-inflammatory, antioxidant, and antibacterial activities, yet its safety and effects on gut health in vivo are not well characterized. This study investigated the biological effects of ethanolic-soluble Phlai extract (ESPE) in zebrafish (Danio rerio), focusing on chemical marker standardization in phenylbutanoids and cucurminoids, developmental toxicity, gut microbiota investigation, and tissue histopathology. Zebrafish embryos were exposed to ESPE to assess toxicity while adult females received an ESPE-enriched diet containing 20 mg ESPE/g diet (2% w/w) for 14 days. Post-treatment analyses included intestinal and multi-organ histology, and 16S rRNA sequencing for microbiome profiling. HPLC analysis confirmed that ESPE contained 9.91% (w/w) of (E)-1-(3,4-dimethoxyphenyl)butadiene (DMPBD) and 0.49% (w/w) curcumin. The 96-h LC50 for embryos was 45.54 µg/mL. In adults, ESPE improved gut health, as shown by greater mucosal thickness, increased goblet cells, and enhanced enterocyte organization. Microbiome analysis showed that overall gut microbial alpha diversity and beta diversity did not differ significantly between groups. However, exploratory differential abundance analysis identified differences in the relative abundance of specific genera in the ESPE-treated group, including Crenobacter, Cellvibrio, Pseudaeromonas, and Starkeya. Muscle tissue demonstrated healthy myofibril regeneration without fibrosis. ESPE was well tolerated, enhanced intestinal function, and without systemic toxicity. These findings support the potential of ESPE as a bioactive extract for further investigation of intestinal health and safety in translational pharmacology applications.},
}

Animals
*Zebrafish/microbiology/embryology
*Gastrointestinal Microbiome/drug effects
*Plant Extracts/toxicity/pharmacology/chemistry
Female
RNA, Ribosomal, 16S/genetics
*Zingiberaceae/chemistry
Intestines/drug effects

@article {pmid42883935,
year = {2026},
author = {Gazzolari, L and Di Domenico, L and Leone, N and La Bella, S and Di Filippo, P and Hoxha, D and Di Pillo, S and Chiarelli, F and Breda, L and Russo, D and Attanasi, M},
title = {The Gut-Lung-Joint Axis: A Conceptual Framework for Microbiome-Mediated Crosstalk Between Respiratory and Rheumatic Diseases in Childhood.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198692},
pmid = {42883935},
issn = {1422-0067},
mesh = {Humans ; *Lung/microbiology/immunology ; *Gastrointestinal Microbiome ; Child ; *Arthritis, Juvenile/microbiology/immunology ; *Joints/microbiology ; Dysbiosis ; *Asthma/microbiology ; Animals ; },
abstract = {There is growing interest in the role of the gut microbiome in immune development and homeostasis during childhood. Increasing evidence suggests that early alterations in microbial composition might influence susceptibility to both respiratory and rheumatic diseases through interconnected pathways. While the gut-lung and gut-joint axes have been investigated separately, their integration into a biologically specific and testable model remains largely unexplored. In this narrative review, the literature was searched in PubMed/MEDLINE and Scopus for evidence syntheses published from 2020 to 2026; 37 eligible evidence syntheses were included, comprising 26 addressing the gut-lung/respiratory domain and 11 addressing the gut-joint/rheumatic domain. We examine current knowledge of microbiome-mediated interactions linking the gut, lungs, and joints in childhood. We discuss the development of the paediatric microbiome and the influence of early-life factors, including mode of delivery, breastfeeding, infections, antibiotic exposure, and environmental determinants, on immune programming. We then summarise evidence supporting the gut-lung axis in paediatric respiratory diseases and the gut-joint axis in juvenile idiopathic arthritis (JIA), highlighting recurrent but non-specific findings such as dysbiosis, impaired epithelial barrier integrity, altered microbial metabolite production, and immune dysregulation. Recent paediatric epidemiological evidence also showed that JIA was more prevalent among children with asthma than among those without asthma (0.81% vs. 0.23%), with asthma associated with approximately twofold higher odds of JIA after propensity-score weighting (OR 2.10, 95% CI 1.56-2.81), although this association does not establish microbiome-mediated causality. We finally critically examine whether more specific mechanisms, including gut-primed immune-cell trafficking, antigen-specific amplification, and metabolite-receptor convergence, could provide testable links between pulmonary and articular inflammation. On this basis, we propose the gut-lung-joint axis as a conceptual, hypothesis-generating model. Future research integrating microbiome profiling, immune-cell clonality, immunophenotyping, and metabolomics will be required to test its predictions and clarify its clinical relevance.},
}

Humans
*Lung/microbiology/immunology
*Gastrointestinal Microbiome
Child
*Arthritis, Juvenile/microbiology/immunology
*Joints/microbiology
Dysbiosis
*Asthma/microbiology
Animals

@article {pmid42883955,
year = {2026},
author = {Wu, Y and Hou, L and Li, Y and Li, J and Hua, X and He, Y and Ding, S and Fang, J},
title = {Viral-Gut Microbiota Interactions: Implications for the Gut Mucosa in Inflammatory Bowel Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198711},
pmid = {42883955},
issn = {1422-0067},
support = {2024RC2053//Yuelushan Laboratory joint talent introduction project/ ; Grant No. kq2502176//Natural Science Foundation of Changsha, China/ ; 24B0219//Scientific Research Project of Hunan Provincial Department of Education/ ; 2023YFD1301200//National Key Research and Development Program of China/ ; HARS-06//Hunan Poultry Industry Technology System/ ; No. 2025JK2027//the Key R&D Program of Hunan Provincial Science and Technology Innovation Plan/ ; 5026301|1025034//Hunan Province Grain and Oil Science and Technology Tackling Program "Open Bidding for Selecting the Best Candidates" Technical Project/ ; },
mesh = {Humans ; Animals ; *Inflammatory Bowel Diseases/microbiology/virology ; *Intestinal Mucosa/virology/microbiology ; *Gastrointestinal Microbiome ; Intestinal Barrier Function ; Virome ; Bacteriophages ; Bacteria ; Dysbiosis ; },
abstract = {Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), arises from complex interactions among genetic susceptibility, immune dysregulation, environmental factors, and the gut microbiome. Bacterial dysbiosis has been extensively studied, whereas the gut virome-comprising eukaryotic viruses and bacteriophages-remains less understood. Viruses can affect the intestinal barrier directly by infecting epithelial and immune cells, or indirectly by reshaping bacterial communities and host immunity. However, current evidence is dominated by cross-sectional associations and animal models, and whether virome alterations drive or result from intestinal inflammation remains unresolved. In this review, we provide a focused overview of intestinal barrier components relevant to IBD, synthesize human and animal evidence on IBD-associated viruses, and distinguish direct viral effects, microbiota-mediated effects, and bidirectional virus-microbiota interactions. We highlight bacteriophage-bacteria interactions as a central and potentially causal axis, discuss UC- and CD-specific differences, and outline causality gaps, search methodology, and emerging therapeutic strategies. Finally, we propose key unresolved questions and future research directions.},
}

Humans
Animals
*Inflammatory Bowel Diseases/microbiology/virology
*Intestinal Mucosa/virology/microbiology
*Gastrointestinal Microbiome
Intestinal Barrier Function
Virome
Bacteriophages
Bacteria
Dysbiosis

@article {pmid42883965,
year = {2026},
author = {Schuren, FHJ and Baak, M and Daniel, N and Leijden, BV and Vanhoecke, B and Meynier, A and Heerikhuisen, M and Méance, S and Wiese, M},
title = {Cranberry Extract and Polyphenol Metabolites Modulate Luminal and Mucosal Microbiome.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198722},
pmid = {42883965},
issn = {1422-0067},
support = {//Health Holland/ ; },
mesh = {*Vaccinium macrocarpon/chemistry ; Humans ; *Plant Extracts/pharmacology/chemistry ; *Polyphenols/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Adult ; Fatty Acids, Volatile/metabolism ; *Microbiota/drug effects ; Male ; },
abstract = {Cranberry polyphenols (PPs) are associated with various health benefits, which can be exerted by the known parent compounds and/or through related metabolites resulting from microbial metabolization. Metabolite levels and profile/composition are often subject to extensive inter-individual variability, and many aspects of the relevant bidirectional interactions of PPs with the individual gut microbiota are still elusive. Both undigested and predigested cranberry extract were tested, next to procyanidin A2 and hyperoside controls, on the luminal and mucosa-associated gut microbial communities of six healthy adult donors in vitro. The composition of the microbial communities, polyphenolic substrate metabolization patterns, and microbial metabolites, including short-chain fatty acids (SCFAs), bile acids and aromatic acids, were analyzed at different timepoints. Both predigested and undigested cranberry extracts modulated the microbiota composition in all donors, albeit with individual variations. The mucosal samples responded differently than the luminal samples, and the type of extract also affected the composition of microbiota differently. Further, inter-individual differences in the metabolization patterns and metabolite production, such as 3,4 DHPPA (3,4-dihydroxyphenylpropionic acid), 3,4 DHPP-2-ol, and 3,4-dihydroxyphenyl acetic acid, were observed. SCFA production was stimulated with predigested cranberry extract. A semipolar compound analysis further showed much broader metabolic variations, both in cranberry-related metabolites, such as 4-vinylphenol and 3,4,5-trimethoxyphenylacetic acid, and in microbial metabolites such as indole-3-lactic acid. This study increases the knowledge on how individual microbiota samples are modulated upon exposure to cranberry-related PPs and how this influences their metabolic activity.},
}

*Vaccinium macrocarpon/chemistry
Humans
*Plant Extracts/pharmacology/chemistry
*Polyphenols/pharmacology/metabolism
*Gastrointestinal Microbiome/drug effects
Adult
Fatty Acids, Volatile/metabolism
*Microbiota/drug effects
Male

@article {pmid42883973,
year = {2026},
author = {Pagán-Rivera, LH and Godoy-Vitorino, F and Ocasio-Rivera, SE and Santiago-Gascot, ME and González, V and Santiago, JM and Salgado, I and Torrado-Tapias, A and Colón-Mercado, JM and García-Guay, C and Miranda, JD},
title = {Tamoxifen Promotes Sustained Bifidobacterium Enrichment in the Gut Microbiota of Male and Female Rats After Spinal Cord Injury.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198729},
pmid = {42883973},
issn = {1422-0067},
support = {4SC1GM144032-04/NH/NIH HHS/United States ; },
mesh = {Animals ; *Spinal Cord Injuries/microbiology/drug therapy ; Female ; Male ; Rats ; *Bifidobacterium/drug effects/genetics ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tamoxifen/pharmacology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {Spinal cord injury (SCI) triggers complex secondary injury cascades that limit neurological recovery. Tamoxifen (TAM), a selective estrogen receptor modulator, exerts neuroprotective effects in experimental SCI, although its underlying mechanisms remain unknown. Given the emerging role of gut microbiota dysregulation in SCI, we investigated whether TAM-associated recovery is accompanied by alterations in gut microbial composition and predicted function. We conducted a longitudinal, sex-inclusive analysis of 61 Sprague-Dawley rats of both sexes assigned to naïve (NAÏVE), sham-placebo (SHAM PLB), sham-TAM (SHAM TAM), injured-placebo (INJ PLB), or injured-TAM (INJ TAM) groups. Injured animals received a moderate T10 contusion followed by a 21-day TAM (0.71 mg/day) or placebo pellet, and fecal samples were collected at 0, 7, 14, 21, and 28 days post-injury. Fecal samples were analyzed by 16S rRNA gene sequencing. Results showed that TAM induced sustained shifts in microbial community composition, with treatment-associated divergence emerging at 14 days post-injury (DPI) in females and 21 DPI in males. Bifidobacterium exhibited the most consistent TAM-associated enrichment across sexes. Bifidobacterium abundance was negatively associated with recovery in INJ PLB animals and positively associated with INJ TAM animals; because behavioral and microbiome measurements were not made in the same animals, these associations are hypothesis-generating only. PICRUSt2 analysis revealed TAM-associated changes in predicted microbial function, including increased glycogen degradation pathways from 14 DPI onward in both sexes. Together, these findings identify sustained TAM-associated taxonomic and predicted functional remodeling of the gut microbiota following SCI.},
}

Animals
*Spinal Cord Injuries/microbiology/drug therapy
Female
Male
Rats
*Bifidobacterium/drug effects/genetics
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Tamoxifen/pharmacology
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid42883987,
year = {2026},
author = {Barańska, D and Panek, J and Pertile, G and Gryta, A and Różalska, S and Frąc, M},
title = {Comparative Genomic, Metabolic and Transcriptomic Profiling of Bacterial Isolates Reveals Strain-Specific Adaptation and Safety Traits.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198734},
pmid = {42883987},
issn = {1422-0067},
support = {2022/45/B/NZ9/04254//National Science Centre/ ; },
mesh = {Gene Expression Profiling ; *Transcriptome ; *Adaptation, Physiological/genetics ; *Genomics/methods ; *Genome, Bacterial ; Multiomics ; *Bacillus megaterium/genetics/metabolism/isolation & purification ; Gene Expression Regulation, Bacterial ; Stress, Physiological ; Food Microbiology ; *Metabolome ; *Bacteria/genetics/metabolism/isolation & purification ; Phenotype ; },
abstract = {Food-associated microorganisms represent a diverse reservoir of bacterial strains with functional traits potentially relevant to host-microbiome interactions, stress resilience, metabolic processes, and microbial competition. In this study, we performed a multi-omics characterization of food-origin bacterial isolates to identify a potential candidate strain for further studies on microbiome-microgreens interactions. Over one hundred bacterial isolates were initially recovered from various food products and subjected to molecular screening, followed by whole-genome sequencing, metabolic profiling, transcriptomic characterization and morphological analysis of selected strains. Comparative characterization revealed significant differences among the strains. Among the tested isolates, strain B107/23, identified as Priestia megaterium (formerly Bacillus megaterium), showed consistently high numbers of genes associated with stress responses, nutrient uptake, plant growth-promoting traits, and colonization mechanisms. Phenotypic characterization later demonstrated high metabolic flexibility and a low substrate stress index, while transcriptomic profiling revealed the expression of genes associated with stress responses and metabolic activity. Overall, the integration of genomic, phenotypic, and transcriptomic results distinguished B107/23 as the most promising candidate among the tested isolates and revealed the molecular traits potentially relevant to interactions between the microbe and the host. These findings provide a basis for the validation of the selected strain in microgreens systems, including studies addressing plant stress resilience and post-harvest quality.},
}

Gene Expression Profiling
*Transcriptome
*Adaptation, Physiological/genetics
*Genomics/methods
*Genome, Bacterial
Multiomics
*Bacillus megaterium/genetics/metabolism/isolation & purification
Gene Expression Regulation, Bacterial
Stress, Physiological
Food Microbiology
*Metabolome
*Bacteria/genetics/metabolism/isolation & purification
Phenotype

@article {pmid42884152,
year = {2026},
author = {Jenkins Sánchez, L and Poppe, J and Baudot, A and Vu, LD and Villella, W and Van den Abbeele, P},
title = {Impact of Triacetin- and Tributyrin-Based Formulations on IBS Microbiome Composition and SCFA Profiles: A Preclinical Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198910},
pmid = {42884152},
issn = {1422-0067},
mesh = {Humans ; *Triglycerides/pharmacology ; *Fatty Acids, Volatile/metabolism ; *Triacetin/pharmacology ; *Irritable Bowel Syndrome/microbiology/drug therapy/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Adult ; Male ; Prebiotics/administration & dosage ; Female ; Butyrates/metabolism ; },
abstract = {Irritable bowel syndrome (IBS) is a prevalent yet poorly understood functional gut disorder frequently associated with microbial dysbiosis, making microbiome-targeting interventions a promising management strategy. In this study, we evaluated the microbiome-modulating potential of three doses of triacetin (TA; ReBiome™; 100, 200 and 300 mg/day) and two finished formulations containing TA and/or tributyrin (TB): Active Biome™ (AB) and Bio Complete 3™ (BC3). Inulin served as a benchmark prebiotic. The validated ex vivo Systemic Intestinal Fermentation Research (SIFR[®]) technology pipeline was applied using fecal microbiota from eight adults with IBS. TA dose-dependently increased short-chain fatty acid (SCFA) levels from 100 mg/day, significantly increasing acetate and butyrate while maintaining low gas formation. In addition to acetate and butyrate, AB and BC3 also promoted propionate while BC3 induced a particularly pronounced butyrate increase. Overall, both formulations induced stronger SCFA but milder gas increases than inulin. TA, AB and BC3 enriched IBS-depleted, butyrate-associated OTUs related to Faecalibacterium and Anaerobutyricum species. AB and BC3 increased microbial diversity (community modulation score (CMS)) by promoting Bifidobacteriaceae, Lachnospiraceae and Bacteroidaceae. Overall, TA and TA/TB-containing formulations promoted butyrate production, potentially helping mitigate IBS symptom severity by inducing a favorable fermentation profile with limited gas formation.},
}

Humans
*Triglycerides/pharmacology
*Fatty Acids, Volatile/metabolism
*Triacetin/pharmacology
*Irritable Bowel Syndrome/microbiology/drug therapy/metabolism
Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Fermentation
Adult
Male
Prebiotics/administration & dosage
Female
Butyrates/metabolism

@article {pmid42884177,
year = {2026},
author = {Rodríguez-Costas, N and Rodríguez-Blanco, A and Expósito, CR and Cubiella, J and Stompel, ES and Fernández-de-Ana Portela, C and Martín, AID and Taboada-Rodríguez, P and Silva, BF and Fernández, MDR and Zarraquiños, S and Remedios, D and Gómez, CAS and Lorenzo, SA and Poceiro, RF and Parga, MLC and Ramírez, VH and Pérez-Castro, S},
title = {Beyond Taxonomy: Fungal Nutraceutical Supplementation Modifies the Functional Potential of the Gut Microbiome in Colorectal Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198936},
pmid = {42884177},
issn = {1422-0067},
support = {N.º Solicitud SOL-00105490, N.º Expediente EXP0010549//Centre for Industrial Technological Development/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Fungi/chemistry ; Female ; Male ; Feces/microbiology ; Metagenomics/methods ; Middle Aged ; Aged ; },
abstract = {The gut microbiome is increasingly recognized as an important determinant of host immune regulation, intestinal homeostasis, and recovery after colorectal cancer (CRC) surgery. Although our previous randomized, double-blind, placebo-controlled clinical trial demonstrated that fungal nutraceutical supplementation with Micodigest[®] was associated with favorable taxonomic and systemic inflammatory changes in patients undergoing CRC surgery with curative intent, the functional consequences of this intervention remain poorly understood. Here, we performed a functional metagenomic analysis of fecal samples collected from patients enrolled in the original clinical trial to investigate whether Micodigest[®] supplementation was associated with changes in the functional potential of the gut microbiome. A total of 37 patients were analyzed, including 24 receiving Micodigest[®] and 13 receiving placebo, with paired samples collected before supplementation and after 4-6 weeks of intervention. Shallow shotgun metagenomic sequencing was performed, and microbial functional potential was characterized using KEGG Orthologues (KOs). Differential abundance analysis identified 14 significantly different KOs between groups at baseline and 23 after intervention, with no overlap between the two sets of orthologues. Following supplementation, Micodigest[®]-treated patients exhibited increased representation of functions related to CRISPR-associated systems, bacteriophage biology, and chitin-derived carbohydrate utilization, together with reduced representation of nutrient acquisition systems, conjugative transfer, sulfur metabolism, and components of the Wood-Ljungdahl pathway. These functional signatures suggest coordinated changes in microbial ecological adaptation, nutrient utilization, genetic exchange, and metabolic activity following fungal nutraceutical supplementation. Integration with previously reported taxonomic and inflammatory findings supports the hypothesis that Micodigest[®] may promote coordinated remodeling of the gut microbiome and host-microbiota interactions during the perioperative period. Although the present study cannot establish causality or directly infer microbial activity from metagenomic potential, these findings provide novel functional insights into the microbiome response to fungal nutraceutical supplementation in patients with CRC and highlight functional metagenomics as a valuable complement to taxonomic profiling.},
}

Humans
*Colorectal Neoplasms/microbiology
*Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Fungi/chemistry
Female
Male
Feces/microbiology
Metagenomics/methods
Middle Aged
Aged

@article {pmid42884560,
year = {2026},
author = {McLaughlin, C and Krishnareddy, S},
title = {Probiotics in Celiac Disease: Current Evidence and Future Directions.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193108},
pmid = {42884560},
issn = {2072-6643},
mesh = {Humans ; *Celiac Disease/microbiology/therapy/immunology ; *Probiotics/therapeutic use ; Diet, Gluten-Free ; *Gastrointestinal Microbiome ; Glutens/immunology ; },
abstract = {Celiac disease is often associated with gut microbiome alterations, which may play a role in autoimmunity to gluten peptides and upregulation of other autoinflammatory pathways. Probiotics of various formulations have been evaluated in attempts to normalize the gut microbiome and/or improve symptoms in Celiac disease, and even to potentially prevent Celiac disease in at-risk individuals. These studies have shown mixed results at best, and conclusions about the effectiveness of probiotics to these ends are limited by the variations across studies' probiotic formulation, dietary regimen, and clinical outcome markers. This leaves many encouraging future directions for further investigation into the potential beneficial role of probiotics on a pathophysiological and clinical level in Celiac disease.},
}

Humans
*Celiac Disease/microbiology/therapy/immunology
*Probiotics/therapeutic use
Diet, Gluten-Free
*Gastrointestinal Microbiome
Glutens/immunology

@article {pmid42884562,
year = {2026},
author = {Xu, Z and Lau, RI and Qi, H and Wong, MCS and Chan, KHN and Lau, ISF and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC},
title = {Synbiotic HQP08 Supplementation for Hair Loss and Depressive Symptoms: An Open-Label Pilot Study of Clinical Outcomes and Gut Microbiome Changes.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193111},
pmid = {42884562},
issn = {2072-6643},
support = {//InnoHK/ ; },
mesh = {Humans ; Pilot Projects ; *Alopecia/microbiology/therapy ; Female ; Male ; Adult ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Synbiotics/administration & dosage ; Treatment Outcome ; *Depression/therapy/microbiology ; *Bifidobacterium longum ; Dietary Supplements ; Young Adult ; },
abstract = {Background: Gut microbiota dysregulation has been implicated in hair loss via the gut-skin axis, but human interventional data are limited. We previously showed that Bifidobacterium longum HK003 reverses alopecia-like phenotypes in mice. Methods: We conducted an open-label, single-arm pilot study to evaluate an HK003-containing synbiotic (HQP08) in 32 adults with self-reported hair loss over 8 weeks. The primary endpoint was the proportion of participants reporting improvement on the Patient Global Impression of Change (PGI-C) scale at week 8. Secondary outcomes included changes in hair loss severity, 60 s hair count, depressive symptoms (PHQ-9), safety, and gut microbiome composition (Chinese Clinical Trial Registry ChiCTR2500112698). Results: At week 8, 62.5% (20/32) of participants reported PGI-C improvement. Significant reductions were observed in hair loss severity (p = 0.0008), 60 s hair count (p = 0.0048), and PHQ-9 scores (p = 0.002). Younger age was associated with PGI-C response (OR per year 0.86, 95% CI: 0.73-0.98, p = 0.037). Metagenomic analysis identified engraftment of B. longum HK003-like profiles in a subset of participants at week 12. Changes in microbial pathways related to thiamine metabolism, vitamin B12 salvage, and lipopolysaccharide biosynthesis were associated with ΔPHQ-9 (FDR-adjusted p < 0.05), but not with hair-related endpoints. No serious adverse events occurred. Conclusions: This first-in-human pilot study suggests that HQP08 was well tolerated and was associated with within-participant changes in hair-loss measurements and PHQ-9 scores. Randomized controlled trials are warranted to confirm efficacy and further elucidate mechanisms within the gut-brain-skin axis.},
}

Humans
Pilot Projects
*Alopecia/microbiology/therapy
Female
Male
Adult
*Gastrointestinal Microbiome/drug effects
Middle Aged
*Synbiotics/administration & dosage
Treatment Outcome
*Depression/therapy/microbiology
*Bifidobacterium longum
Dietary Supplements
Young Adult

@article {pmid42884570,
year = {2026},
author = {Odonkor, CA and Dodurgali, MR and Cox, FR and Klimov, IJ and Abd-Elsayed, A},
title = {GLP-1 Receptor Agonists, Gut Microbiota, and Chronic Pain: Nutritional Signaling at the Gut-Brain Axis.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193120},
pmid = {42884570},
issn = {2072-6643},
mesh = {Humans ; *Chronic Pain/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects/physiology ; *Glucagon-Like Peptide-1 Receptor Agonists ; Animals ; Signal Transduction ; *Brain-Gut Axis/physiology/drug effects ; *Brain/metabolism ; Glucagon-Like Peptide-1 Receptor/metabolism ; Dysbiosis ; Glucagon-Like Peptide 1/metabolism ; },
abstract = {BACKGROUND/OBJECTIVES: Chronic pain affects more than one in five adults worldwide and is increasingly conceptualized as a disorder of the gut-brain axis. Gut microbial dysbiosis, characterized by reduced alpha-diversity and depletion of short-chain fatty acid (SCFA)-producing taxa such as Faecalibacterium prausnitzii, Lachnospiraceae, and Roseburia, has been mechanistically linked to pain sensitization. Glucagon-like peptide-1 (GLP-1), a nutrient-sensing enteroendocrine hormone, and its pharmacological receptor agonists (GLP-1RAs) both reshape the gut microbiota and modulate pain across multiple phenotypes. This review synthesizes preclinical and clinical evidence positioning the gut microbiota as a proposed nutritional intermediary that links GLP-1RA pharmacology to chronic pain modulation.

METHODS: We conducted a narrative synthesis of studies retrieved from PubMed, Embase, and Web of Science from inception through 30 June 2026, spanning GLP-1 nutrient sensing, gut microbial alterations in pain, GLP-1RA effects on the microbiome, microbiota-dependent mechanisms, and clinical pain outcomes.

RESULTS: GLP-1 is secreted by L-cells in response to nutrients and microbial SCFAs, signaling to the brain through vagal and humoral routes. GLP-1RAs enrich the same anti-inflammatory, SCFA-producing taxa that are depleted in chronic pain, and their anti-inflammatory actions require an intact microbiota. Mechanistically, GLP-1RAs suppress pain through spinal microglial GLP-1 receptor (GLP-1R)/interleukin-10/beta-endorphin signaling, Nucleotide-binding oligomerization domain (NOD)-, Leucine-rich repeat (LRR)-, and pyrin domain-containing protein 3 (NLRP3) inflammasome inhibition, and receptor-independent transient receptor potential vanilloid 1 (TRPV1) blockade, largely independent of glycemic control or weight loss. Clinically, evidence is strongest for knee osteoarthritis and idiopathic intracranial hypertension headache, with emerging signals in fibromyalgia, visceral pain, and reduced opioid use.

CONCLUSIONS: The gut microbiota is proposed to act as both a therapeutic target and a mechanistic intermediary in GLP-1RA-mediated analgesia, a model that awaits direct confirmation in humans. Pain-specific trials incorporating dietary and microbiome endpoints are needed.},
}

Humans
*Chronic Pain/drug therapy/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects/physiology
*Glucagon-Like Peptide-1 Receptor Agonists
Animals
Signal Transduction
*Brain-Gut Axis/physiology/drug effects
*Brain/metabolism
Glucagon-Like Peptide-1 Receptor/metabolism
Dysbiosis
Glucagon-Like Peptide 1/metabolism

@article {pmid42884589,
year = {2026},
author = {Miulescu, RG and Costescu, M and Marin, RC and Mușetescu, A and Muntean, C and Roşca, I and Adam, II and Ilici, A and Coman, OA},
title = {The Gut-Skin Axis in Pediatric Atopic Dermatitis: Nutritional Modulation, Microbiome Interactions, and Emerging Precision Approaches.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193138},
pmid = {42884589},
issn = {2072-6643},
mesh = {Humans ; *Dermatitis, Atopic/microbiology/diet therapy ; Child ; *Gastrointestinal Microbiome/physiology ; Probiotics ; Infant ; *Skin/microbiology ; Child, Preschool ; *Precision Medicine/methods ; Diet ; Female ; Breast Feeding ; },
abstract = {BACKGROUND/OBJECTIVES: Pediatric atopic dermatitis (AD) is a barrier-driven inflammatory skin disease with systemic immune and microbial correlates. The gut-skin axis offers a biologically plausible framework through which early-life nutrition, gut microbial metabolism, intestinal barrier function, and immune maturation may influence disease risk and expression, but much of the supporting evidence remains associative. This narrative review asks which nutritional strategies are supported by clinical evidence in children with AD, which remain investigational, and how far the field is from precision nutrition.

METHODS: PubMed/MEDLINE, Scopus, and Web of Science were searched up to 31 July 2026; guidelines, systematic reviews, randomized trials, birth cohorts, and mechanistic studies with pediatric relevance were prioritized and appraised narratively.

RESULTS: Breastfeeding when possible, dietary diversity during complementary feeding, avoidance of unnecessary elimination diets, correction of documented nutritional deficiencies, and management of confirmed food allergy are supported by current guidance. Probiotics and synbiotics lower SCORAD in meta-analyses, but the pooled effect is small, heterogeneous, and below the minimal clinically important difference, so they are best described as an optional adjunct rather than a recommended treatment; Mediterranean-style or high-fiber dietary patterns are backed mainly by observational data. Microbiome profiling, metabolomics, multi-omics endotyping, and artificial intelligence remain research tools without validated predictive value for dietary responses.

CONCLUSIONS: Nutrition is an adjunct to, not a substitute for, established topical and systemic therapy in pediatric AD. Precision nutrition is a promising research direction rather than an established component of routine care, and its clinical value will depend on standardized biomarkers and well-designed longitudinal and interventional studies.},
}

Humans
*Dermatitis, Atopic/microbiology/diet therapy
Child
*Gastrointestinal Microbiome/physiology
Probiotics
Infant
*Skin/microbiology
Child, Preschool
*Precision Medicine/methods
Diet
Female
Breast Feeding

@article {pmid42884594,
year = {2026},
author = {Ben Mohamed, A and Vauzour, D},
title = {Do Grape- and Wine-Derived (Poly)Phenols Contribute to the Hallmarks of Healthy Brain Ageing?.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193144},
pmid = {42884594},
issn = {2072-6643},
mesh = {Humans ; *Wine/analysis ; *Vitis/chemistry ; *Brain/drug effects/physiology ; *Polyphenols/pharmacology/pharmacokinetics ; *Aging/drug effects ; Gastrointestinal Microbiome/drug effects ; Animals ; Biological Availability ; Antioxidants/pharmacology ; Cognitive Aging ; Neuroprotective Agents/pharmacology ; *Phenols/pharmacology ; },
abstract = {Population ageing is associated with a rising burden of cognitive decline, dementia and late-life affective disorders. Grape- and wine-derived (poly)phenols represent a chemically diverse group of bioactives whose biological relevance is shaped by structural complexity, the intervention matrix, host conjugation and gut microbial metabolism. Rather than acting as simple antioxidants, these compounds and their derived metabolites may influence interrelated pathways implicated in brain ageing, including neuroinflammation, endothelial function, synaptic plasticity, oxidative stress and gut-brain axis signalling. The gut microbiota is central to this framework as it converts poorly absorbed parent compounds into smaller phenolic metabolites and is modulated by (poly)phenol exposure. This review summarises the chemical and bioavailability features that determine intestinal and colonic availability, evaluates preclinical evidence concerning the neuroprotective potential of grape- and wine-derived (poly)phenols, and integrates clinical evidence from studies of cognitive ageing, mild cognitive impairment and Alzheimer's disease. Current evidence supports biological plausibility and justifies further investigation, but clinical findings remain heterogeneous. Future studies should prioritise chemically standardised preparations, metabolomic profiling, functional microbiome readouts, and integrated cognitive, vascular and inflammatory endpoints.},
}

Humans
*Wine/analysis
*Vitis/chemistry
*Brain/drug effects/physiology
*Polyphenols/pharmacology/pharmacokinetics
*Aging/drug effects
Gastrointestinal Microbiome/drug effects
Animals
Biological Availability
Antioxidants/pharmacology
Cognitive Aging
Neuroprotective Agents/pharmacology
*Phenols/pharmacology

@article {pmid42884597,
year = {2026},
author = {Kamalakar, K and Akerele, C and Lafont, E and Koralnik, LR and Gilman, C and Litran, JC and Lee, J and Robinson-Papp, J and Malaspina, D},
title = {Gut Microbiome-Mediated Neuroprotective Effect of the Mediterranean Diet: A Narrative Review of Cognitive Aging, Alzheimer's Disease, and Parkinson's Disease.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193146},
pmid = {42884597},
issn = {2072-6643},
mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/prevention & control ; *Alzheimer Disease/prevention & control/microbiology ; *Cognitive Aging/physiology ; *Neuroprotection ; Animals ; },
abstract = {Background: Alzheimer's disease (AD) and Parkinson's disease (PD) are major neurodegenerative disorders for which disease-modifying therapies are limited. Increasingly, evidence suggests that diet influences neurodegenerative risk through interactions among the gut microbiome, immune system, and brain. The Mediterranean diet (MD) is associated with improved cognitive health, but the mechanisms underlying its potential neuroprotective effects remain incompletely understood. Objective: In this narrative review, evidence on microbiome-mediated mechanisms linking MD adherence to neuroprotection was synthesized, and how Mediterranean dietary components influence microbial ecology, metabolites, immune regulation, and neuroinflammation relevant to cognitive aging, AD, and PD was evaluated. Methods: Evidence from experimental, observational, and clinical studies was reviewed, focusing on microbial metabolites, intestinal barrier integrity, immune regulation, and inflammatory pathways. Discussion: Mediterranean dietary components, including fiber, polyphenols, whole grains, legumes, nuts, extra-virgin olive oil, and omega-3 fatty acids, may promote beneficial microbial communities and metabolite production. Short-chain fatty acids, secondary bile acids, indole derivatives, and phenolic metabolites may strengthen the intestinal and blood-brain barriers, regulate immune responses, and suppress neuroinflammation. Conversely, dysbiosis may increase intestinal permeability, lipopolysaccharide translocation, systemic inflammation, and microglial activation. However, evidence remains heterogeneous and largely observational or experimental. Conclusions: The MD may promote neuroprotection through interconnected diet-microbiome-immune pathways. Longitudinal and intervention studies integrating microbiome, metabolomic, inflammatory, neuroimaging, and cognitive measures are needed to establish causality and advance precision nutrition strategies to prevent neurodegenerative disease.},
}

Humans
*Diet, Mediterranean
*Gastrointestinal Microbiome/physiology
*Parkinson Disease/microbiology/prevention & control
*Alzheimer Disease/prevention & control/microbiology
*Cognitive Aging/physiology
*Neuroprotection
Animals

@article {pmid42884619,
year = {2026},
author = {Ibrahim, I and Lawrence, K and Forte, OA and Huitt, L and Naidu, NC and Ajibola, N and Xu, J and Boakai, RK and Akabanda, F and Owusu-Kwarteng, J and Ajayi, OS and Ayariga, JA},
title = {Diffuse Idiopathic Skeletal Hyperostosis (DISH): Potential Links Between Gut Microbiota and Spinal Degenerative Diseases.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193168},
pmid = {42884619},
issn = {2072-6643},
support = {Title III- HBGI-RES//United States Department of Education/ ; },
mesh = {Humans ; *Hyperostosis, Diffuse Idiopathic Skeletal/microbiology ; *Gastrointestinal Microbiome/physiology ; *Intervertebral Disc Degeneration/microbiology ; Dysbiosis ; Animals ; },
abstract = {Diffuse Idiopathic Skeletal Hyperostosis (DISH) is a systemic, non-inflammatory skeletal disorder characterized by progressive calcification and ossification of spinal ligaments and entheses. Its strong associations with aging, obesity, type 2 diabetes, and metabolic syndrome raise the possibility that metabolic and inflammatory pathways may contribute to disease development. The gut microbiota participates in nutrient metabolism, short-chain fatty acid production, bile-acid transformation, intestinal-barrier maintenance, and immune regulation; these functions provide a plausible framework for examining whether intestinal dysbiosis may influence spinal and musculoskeletal tissues. This narrative review therefore evaluates the potential relationship between gut microbiota, DISH, and related spinal degenerative diseases. It considers the nutritional, metabolic, immunological, and host-interaction functions of the gut microbiota before examining proposed gut-spine, gut-bone, gut-joint, gut-disc, gut-ligament, and gut-muscle pathways. Particular attention is given to the apparent paradox that most microbiome-bone evidence concerns osteoporosis and bone loss, whereas DISH is characterized by excessive ectopic bone formation. Differences in short-chain fatty acid concentration, receptor expression, local versus systemic signaling, and osteoblast-osteoclast microenvironments may produce divergent skeletal effects, but these mechanisms have not been tested directly in DISH. Recent studies support associations between selected microbial taxa and intervertebral disc degeneration or spinal stenosis; however, direct clinical evidence linking gut microbiota to DISH remains limited. Consequently, dietary modification, probiotics, prebiotics, and fecal microbiota transplantation should be regarded as research considerations rather than established treatments for DISH. Well-characterized case-control and longitudinal studies integrating microbiome profiling, metabolomics, inflammatory markers, and serial imaging are required to determine whether reproducible microbial or metabolite signatures precede DISH onset or progression. The pathways discussed in this review are therefore presented as biologically plausible, testable hypotheses and not as established causal relationships.},
}

Humans
*Hyperostosis, Diffuse Idiopathic Skeletal/microbiology
*Gastrointestinal Microbiome/physiology
*Intervertebral Disc Degeneration/microbiology
Dysbiosis
Animals

@article {pmid42884675,
year = {2026},
author = {Yang, F and Xie, S and Yang, W and Zhu, C and Chen, Y and Yang, H and Yuan, H and Li, Q},
title = {Multi-Omics Analysis Reveals the Potential Role of Inonotus obliquus in Mit-Igating Hemolytic Jaundice.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193225},
pmid = {42884675},
issn = {2072-6643},
support = {No. CKD/SXMU-2025-07//Shanxi Medical University/ ; No. 202303021221129//Shanxi Science and Technology Department/ ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; Phenylhydrazines ; Male ; Liver/metabolism/drug effects ; Multiomics ; Bilirubin/blood ; Disease Models, Animal ; Limosilactobacillus reuteri ; *Jaundice/drug therapy/chemically induced ; *Plant Extracts/pharmacology ; },
abstract = {Background: Hemolytic jaundice, characterized by excessive bilirubin production and hepatic dysfunction, currently lacks effective therapeutic strategies targeting its underlying mechanisms. Methods: This study evaluated the therapeutic potential of the aqueous extract of Inonotus obliquus (IO) in ameliorating hemolytic jaundice through modulation of the gut-liver axis. A murine model of hemolytic jaundice was induced by phenylhydrazine (PHZ) administration, and IO was orally administered as the intervention. Antibiotic depletion and FMT verified gut microbiota dependence. Liver injury, serum bilirubin, gut microbiome, and metabolites were assessed. Results: IO treatment significantly alleviated PHZ-induced hemolytic jaundice in mice. Notably, antibiotic-mediated depletion of the gut microbiota abolished the hepatoprotective effects of IO, whereas fecal microbiota transplantation (FMT) from IO-treated donors conferred marked amelioration of hyperbilirubinemia in recipient mice. Integrative multi-omics analysis identified Limosilactobacillus reuteri and Lactobacillus johnsonii as the predominant microbial species altered by IO. Furthermore, IO upregulated the expression of farnesoid X receptor (FXR) and pregnane X receptor (PXR) in both hepatic and intestinal tissues and also increased the expression of bile salt export pump (BSEP) and multidrug resistance-associated protein 2 (MRP2). These alterations were correlated with an increased excretion of bile acids and bilirubin into the intestinal lumen, thereby mitigating hepatic injury. This process may be associated with the modulation of gut microbiota. Conclusions: These findings collectively provide evidence of a significant correlation between IO treatment and the mitigation of hemolytic jaundice, achieved by modulating the enterohepatic circulation of bile acids and bilirubin through the regulation of gut microbiota. Our results highlight the potential of IO as a microbiota-directed nutritional strategy for the management of jaundice.},
}

Animals
Mice
*Gastrointestinal Microbiome/drug effects
Phenylhydrazines
Male
Liver/metabolism/drug effects
Multiomics
Bilirubin/blood
Disease Models, Animal
Limosilactobacillus reuteri
*Jaundice/drug therapy/chemically induced
*Plant Extracts/pharmacology

@article {pmid42884688,
year = {2026},
author = {Pasam, T and Bowers, C and Ahmed, S and Kaffman, A},
title = {A Hypothesis Linking Early-Life Adversity to Altered Synaptic Connectivity Through Disrupted Gut Microbiome-Microglia Communication.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193237},
pmid = {42884688},
issn = {2072-6643},
support = {R01MH136490/MH/NIMH NIH HHS/United States ; R01MH130825/MH/NIMH NIH HHS/United States ; //National Center for Post Traumatic Stress Disorder/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Microglia/physiology ; *Adverse Childhood Experiences ; Animals ; Neuronal Plasticity ; Brain/physiopathology/growth & development ; *Synapses/physiology ; },
abstract = {Childhood adversity is a major risk factor for the development of numerous psychiatric and medical disorders later in life. Individuals exposed to early adversity also tend to experience more severe, treatment-resistant, and highly comorbid conditions, suggesting that childhood adversity represents a distinct pathophysiological entity requiring specialized diagnostic and therapeutic approaches. However, the biological mechanisms underlying these diverse long-term outcomes remain poorly understood. Recent studies have implicated disruptions of the gut-immune-brain axis and persistent low-grade inflammation in mediating the long-term consequences of childhood adversity. Here, we propose a complementary and novel, but still speculative, hypothesis that shifts the focus away from chronic low-grade neuroinflammation and instead emphasizes the direct crosstalk between the gut microbiome and glia-mediated synaptic pruning during critical periods of brain development. Specifically, we hypothesize that alterations in microbiome-derived signals disrupt the normal maturation and function of glial cells, leading to aberrant synaptic pruning, long-lasting changes in neural circuit connectivity, and persistent deficits in cognition and emotional regulation. Although several lines of evidence are consistent with individual components of this model, direct evidence linking these processes into a causal pathway is currently limited. We therefore discuss the experimental findings that provide a rationale for this hypothesis, identify important gaps in the current literature, and propose specific experimental strategies to rigorously test its central predictions. If validated, this framework could transform our understanding of how childhood adversity becomes biologically embedded and provide a foundation for the development of novel diagnostic biomarkers and targeted therapeutic interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Microglia/physiology
*Adverse Childhood Experiences
Animals
Neuronal Plasticity
Brain/physiopathology/growth & development
*Synapses/physiology

@article {pmid42884713,
year = {2026},
author = {Shin, J and Kim, HH and Kim, SY and Kang, HM and Youn, YA},
title = {Timing of Full Enteral Feeding and Longitudinal Gut Microbiome Development in Infants Admitted to the Neonatal Intensive Care Unit.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193262},
pmid = {42884713},
issn = {2072-6643},
support = {2022R1A2C100399611, RS-2023-00279932, RS-2026-25487768//Ministry of Science and ICT/ ; },
mesh = {Humans ; *Enteral Nutrition/methods ; Infant, Newborn ; Female ; *Gastrointestinal Microbiome ; Male ; *Intensive Care Units, Neonatal ; Infant ; Feces/microbiology ; Time Factors ; Gestational Age ; RNA, Ribosomal, 16S/genetics ; Infant, Premature ; Bacteria/classification ; Longitudinal Studies ; },
abstract = {BACKGROUND/OBJECTIVES: Delayed achievement of full enteral feeding (FEF) is common in neonatal intensive care unit (NICU) infants but is closely linked to gestational age (GA). We examined whether time to FEF is associated with gut microbiome development from birth to 6 months of corrected age (CA) beyond GA.

METHODS: We profiled 694 stool samples from 328 NICU infants, collected at first stool, discharge, and 4- and 6-month CA, by 16S rRNA gene sequencing. Infants were classified as Early FEF (<14 days, n = 293) or Delayed FEF (≥14 days, n = 35), and time to FEF was also analyzed continuously. Linear mixed models and PERMANOVA were adjusted for GA.

RESULTS: Composition at first stool did not differ between groups. At discharge, the Delayed group had higher Proteobacteria, lower Firmicutes, lower Streptococcus (q = 0.028), and a different community structure in unadjusted analyses, but none of these differences remained after GA adjustment. No phylum showed a GA-adjusted trajectory difference, and alpha diversity did not differ. In an exploratory continuous analysis, longer time to FEF was associated with higher Bacteroidetes at discharge and 4-month CA.

CONCLUSIONS: Most microbiome differences associated with delayed FEF were not independent of GA. Time to FEF may reflect maturity and illness severity rather than act as an independent determinant of the gut microbiome.},
}

Humans
*Enteral Nutrition/methods
Infant, Newborn
Female
*Gastrointestinal Microbiome
Male
*Intensive Care Units, Neonatal
Infant
Feces/microbiology
Time Factors
Gestational Age
RNA, Ribosomal, 16S/genetics
Infant, Premature
Bacteria/classification
Longitudinal Studies

@article {pmid42884719,
year = {2026},
author = {Temneanu, OR and Trofin, F and Mihai, A and Lupu, A and Olariu, R and Ștefan, M and Buzilă, ER and Novac, O and Șerban, R and Lupu, VV and Anton, E and Oros, M and Simionescu, B},
title = {Before the Gut: Human Milk Oligosaccharides and Oral Microbial Colonization in Infancy.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193269},
pmid = {42884719},
issn = {2072-6643},
mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Oligosaccharides/metabolism ; Infant ; *Mouth/microbiology ; Biofilms/growth & development ; *Microbiota ; Female ; Streptococcus mutans ; },
abstract = {BACKGROUND/OBJECTIVES: Human milk oligosaccharides (HMOs) reach the oral cavity before any other compartment and resist hydrolysis by salivary enzymes, yet their behavior there has received far less attention than their intestinal fate. This review asks what follows from treating the mouth as a compartment rather than as a corridor.

METHODS: MEDLINE, Scopus and Web of Science were searched from inception to August 2026, combining oligosaccharide and oral terms, with forward citation tracking of the human studies. Each candidate mechanism was classified by its type of supporting evidence: human oral association, direct oral in vitro evidence, indirect evidence from other compartments, or unresolved hypothesis.

RESULTS: Only two human analyses, both from the same Western Australian cohort (BLOSOM), have related HMO exposure to infant oral bacterial communities; the larger concluded that the effect, while statistically detectable, was biologically limited. Residence time, and probably effective glycan concentration, differ from the intestinal case, as do the aerotolerant, Gemella- and Rothia-dominated community and the salivary films coating teeth and mucosa. In vitro, 6'-sialyllactose and free N-acetylneuraminic acid inhibited Streptococcus mutans biofilm formation, but only at concentrations (~100 mM) well above plausible oral exposure; 2'-fucosyllactose had no antibiofilm effect, reduced adhesion in two of three strains and did not support growth. Maternal FUT2 genotype shapes the oligosaccharide profile of milk, whereas the infant's own FUT2 genotype governs fucosylation of the salivary glycoproteins those oligosaccharides encounter; neither has been measured in infant oral microbiome studies.

CONCLUSIONS: Anti-adhesive and substrate-driven mechanisms may operate in parallel, and a possible asymmetry between commensal and cariogenic streptococci is framed as a testable hypothesis, as is the contribution of swallowed oral communities to gut colonization. Current evidence supports no change in practice regarding supplemented formula, donor milk, oropharyngeal colostrum, or breastfeeding and caries.},
}

Humans
*Milk, Human/chemistry/metabolism
*Oligosaccharides/metabolism
Infant
*Mouth/microbiology
Biofilms/growth & development
*Microbiota
Female
Streptococcus mutans

@article {pmid42884726,
year = {2026},
author = {Cai, H and Chen, C and Cai, H and Zhang, D and Huang, Q},
title = {Planetary Health Diet and the Gut-Liver-Brain Axis: Implications for MASLD and Cognitive Aging.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193275},
pmid = {42884726},
issn = {2072-6643},
mesh = {Humans ; Gastrointestinal Microbiome/physiology ; *Brain/metabolism ; *Cognitive Aging/physiology ; *Liver/metabolism ; *Diet, Healthy ; Animals ; *Fatty Liver ; *Brain-Gut Axis/physiology ; },
abstract = {Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) and cognitive aging are prevalent, interrelated conditions that share gut-derived pathomechanisms. The Planetary Health Diet (PHD), a sustainable plant-forward framework proposed by the EAT-Lancet Commission, may offer dual-target benefits for hepatic and neurological health through the gut-liver-brain axis. Methods: A structured narrative literature search of PubMed, Web of Science, and Scopus (2015-2026) was conducted to identify observational, mechanistic, and interventional studies addressing PHD adherence in relation to MASLD, cognitive aging, and gut-liver-brain axis pathways. Results: Epidemiological evidence from large cohorts links higher PHD adherence to lower MASLD prevalence and severity, slower cognitive decline, reduced dementia incidence, and more favorable Alzheimer's disease neuropathology. Mechanistically, PHD components may modulate gut microbiota composition and diversity, enhance short-chain fatty acid production, regulate bile acid signaling through farnesoid X receptor (FXR) and Takeda G-protein-coupled receptor 5 (TGR5), reinforce intestinal barrier integrity, and attenuate metabolic endotoxemia and neuroinflammation. Conclusions: Although current evidence remains predominantly observational, the PHD is a promising dietary framework for simultaneously supporting liver and brain health. Future research should prioritize randomized controlled trials integrating liver imaging, cognitive assessment, microbiome profiling, and culturally adapted dietary interventions.},
}

Humans
Gastrointestinal Microbiome/physiology
*Brain/metabolism
*Cognitive Aging/physiology
*Liver/metabolism
*Diet, Healthy
Animals
*Fatty Liver
*Brain-Gut Axis/physiology

@article {pmid42884737,
year = {2026},
author = {Neal, WN and Kemp, KM and Little, RB and Carter, SJ and Schleicher, EA and Motl, RW and Lu, J and Lefkowitz, EJ and Oster, RA and Norian, LA and Hunter, GR and Krontiras, H and Turan, B and Rogers, LQ},
title = {Associations Between Physical Activity Measurement Modality and Gut Microbiome in Breast Cancer Survivors.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193286},
pmid = {42884737},
issn = {2072-6643},
support = {5R01CA235598-06/NH/NIH HHS/United States ; 5P30DK056336-25/NH/NIH HHS/United States ; 5T32CA047888-36/NH/NIH HHS/United States ; 5U01TR003096-05/NH/NIH HHS/United States ; 5R25CA076023-20/NH/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Breast Neoplasms/therapy/microbiology ; *Exercise/physiology ; *Gastrointestinal Microbiome/physiology ; *Cancer Survivors ; Middle Aged ; Accelerometry ; Physical Fitness ; Aged ; Sedentary Behavior ; Self Report ; Adult ; },
abstract = {BACKGROUND/OBJECTIVES: Physical activity (PA), physiological fitness, and the gut microbiome have each been linked to health outcomes among breast cancer survivors (BCS); however, these associations have been inconsistent. Few studies have directly compared the associations of self-reported PA, accelerometer-derived PA, and physiological fitness with the gut microbiome within the same population. This study evaluated whether associations with gut microbiome outcomes vary by PA and fitness measurement modality in post-primary treatment BCS.

METHODS: Baseline data from 69 BCS enrolled in a randomized controlled trial were analyzed. PA was assessed using self-reported moderate-to-vigorous PA (MVPA) and accelerometer-derived light PA (LPA), MVPA, and sedentary behaviors. Physiological fitness was evaluated using peak oxygen uptake (V˙O2peak) and related fitness metrics. Gut microbiome outcomes included α-diversity, β-diversity, and exploratory taxa-level analyses derived from 16S rRNA sequencing. Associations were evaluated using correlation and regression analyses, with adjustment for relevant clinical covariates.

RESULTS: Accelerometer-derived PA, particularly MVPA, demonstrated the strongest and most consistent associations with α-diversity and β-diversity, whereas physiological fitness measures showed only weak associations. Sedentary behavior was inversely associated with both diversity metrics, while self-reported MVPA was not associated with diversity indices. Medication burden and comorbidity status attenuated several PA-microbiome associations, and no taxa-level associations remained significant after correction for multiple testing.

CONCLUSIONS: Associations between PA, fitness, and gut microbiome outcomes varied according to measurement modality. Accelerometer-derived MVPA demonstrated more consistent associations with microbiome diversity and composition than self-reported MVPA or physiological fitness. Future studies should incorporate multiple complementary measures of PA and fitness when examining PA-microbiome relationships.},
}

Humans
Female
*Breast Neoplasms/therapy/microbiology
*Exercise/physiology
*Gastrointestinal Microbiome/physiology
*Cancer Survivors
Middle Aged
Accelerometry
Physical Fitness
Aged
Sedentary Behavior
Self Report
Adult

@article {pmid42884747,
year = {2026},
author = {Lee, AH and Lee, SM and Kang, IY and Park, GR and Yoo, HH and Yu, JS and Kim, HS and Shin, JH and Nam, YD and Yoon, EL and Jun, DW},
title = {VSL#3 Co-Administration Is Associated with Altered Early-Phase Obeticholic Acid Exposure in MASLD Mice.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193296},
pmid = {42884747},
issn = {2072-6643},
support = {HY-202300000003034//Hanyang University/ ; 2026-ANCHOR-01-027-01//Seoul ANCHOR Center/ ; },
mesh = {Animals ; Male ; Mice, Inbred C57BL ; *Chenodeoxycholic Acid/analogs & derivatives/pharmacokinetics/administration & dosage/pharmacology ; Mice ; Bile Acids and Salts/metabolism ; Gastrointestinal Microbiome/drug effects ; Liver/metabolism ; Disease Models, Animal ; *Non-alcoholic Fatty Liver Disease/metabolism ; },
abstract = {Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease, and its global incidence continues to increase. MASLD can progress from simple steatosis to steatohepatitis, cirrhosis, and hepatocellular carcinoma. However, effective preventive and therapeutic options remain limited. In this study, obeticholic acid (OCA) and the probiotic mixture VSL#3 were co-administered to a mouse model of MASLD to modulate gut microbiota and bile acid metabolism. Methods: Male C57BL/6 mice were fed a WD to induce MASLD and treated with OCA, VSL#3, or both. Gut microbiota was analyzed by 16S rRNA sequencing, bile acid (BA) composition was assessed by LC-MS/MS, hepatic and intestinal gene expression was determined by quantitative real-time PCR (qPCR) and immunohistochemistry, and unconjugated OCA pharmacokinetics (PK) were evaluated. Results: VSL#3-containing groups showed differences in selected taxa with reported bile salt hydrolase (BSH) potential and in BA composition, including a numerical shift toward higher levels of deconjugated BAs. Co-administration of OCA and VSL#3 was accompanied by lower hepatic steatosis, numerically favorable serum markers of liver injury, and lower cholesterol and total bilirubin levels. In addition, mice receiving VSL#3 showed numerically higher early plasma concentrations of unconjugated OCA. Lower intestinal ATP-binding cassette subfamily C member 2 (Abcc2) expression was also observed as a separate exploratory finding. Conclusions: The co-administration of VSL#3 with OCA was accompanied by exploratory differences in selected biological parameters and early-phase unconjugated OCA exposure. Lower intestinal Abcc2/Mrp2 expression was observed as a separate exploratory finding, and no functional relationship between intestinal transporter expression and OCA pharmacokinetics was established.},
}

Animals
Male
Mice, Inbred C57BL
*Chenodeoxycholic Acid/analogs & derivatives/pharmacokinetics/administration & dosage/pharmacology
Mice
Bile Acids and Salts/metabolism
Gastrointestinal Microbiome/drug effects
Liver/metabolism
Disease Models, Animal
*Non-alcoholic Fatty Liver Disease/metabolism

@article {pmid42884751,
year = {2026},
author = {Ondrak, KS and Seicshnaydre, EA and Duffy, SJ and Rodriguez, CL and Scott, C and Gladish, S and Byerley, LO},
title = {Is There a Relationship Between the Gut Microbiome and the Functional Capabilities of Skeletal Muscle? A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193300},
pmid = {42884751},
issn = {2072-6643},
mesh = {Humans ; *Muscle, Skeletal/physiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Probiotics/administration & dosage ; *Diet ; Animals ; Sarcopenia/microbiology ; Prebiotics ; Fatty Acids, Volatile/metabolism ; },
abstract = {Diet is one of the primary determinants of gut microbiota composition and its metabolic output. That output is emerging as a critical determinant of systemic health and has been linked to most physiological systems in the body, yet its relationship to skeletal muscle physiology has only recently received attention. Evidence from experimental, observational, and clinical studies supports the existence of a gut-muscle axis, in which microbial composition and metabolic activity in the gut, influenced by diet, affect muscle metabolism, strength, function, and physical performance. Fiber, protein intake, probiotics, prebiotics, synbiotics, and fermented foods are examples of dietary constituents that transiently alter the gut microbiota, producing key metabolic mediators including short-chain fatty acids (SCFA), microbially generated amino acid products, and metabolites implicated in systemic inflammation and gut barrier integrity, alongside endocrine crosstalk involving myokines and hormones (e.g., cortisol and testosterone). Human studies consistently associate higher microbial diversity and enrichment of SCFA-producing taxa with improved muscle-related outcomes, while age-related dysbiosis has been linked to sarcopenia and functional decline. This narrative review summarizes current evidence of the gut-muscle axis and highlights potential mechanisms linking gut microbial composition to skeletal muscle function. Future advances in personalized nutrition may offer novel opportunities to preserve muscle health and functional capacity throughout aging.},
}

Humans
*Muscle, Skeletal/physiology/metabolism
*Gastrointestinal Microbiome/physiology
Probiotics/administration & dosage
*Diet
Animals
Sarcopenia/microbiology
Prebiotics
Fatty Acids, Volatile/metabolism

@article {pmid42884886,
year = {2026},
author = {Rezaee Danesh, Y and Mulet, JM and Porcel, R},
title = {Microbial Biostimulants for Drought Resilience in Plants: Mechanisms, Plant-Microbiome Interactions, and Sustainable Agricultural Applications.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/plants15193022},
pmid = {42884886},
issn = {2223-7747},
abstract = {Drought stress is one of the most significant challenges for global agriculture, adversely affecting crop yields and food security. In recent years, microbial biostimulants have emerged as a promising solution to enhance plant resilience against such abiotic stresses. This review explores the mechanisms by which microbial biostimulants, including beneficial bacteria and fungi, confer drought tolerance in plants. Key interactions between plants and their associated microbiomes are highlighted, emphasizing the roles of root-associated microbes in promoting plant growth, nutrient uptake, and stress mitigation. We examine microbial-induced plant responses, including improved water relations, photosynthetic performance, and osmotic adjustment. Additionally, the review examines the sustainability of microbial biostimulant use in agricultural practices, addressing their potential to reduce reliance on chemical inputs and improve soil health. Evidence from field studies across diverse crops is also discussed, highlighting the potential of microbial biostimulants to improve plant performance and yield stability under water-limited conditions while emphasizing the context-dependent nature of their efficacy. Furthermore, we underscore the importance of microbial diversity and community composition in maximizing the benefits of biostimulants. By integrating microbial biostimulants into conventional agricultural practices, farmers can enhance drought resilience, thereby contributing to sustainable food production systems. This review aims to provide a comprehensive understanding of the interactions between microbial biostimulants and plants under drought stress, and to highlight future research directions for optimizing their use in sustainable agriculture.},
}

@article {pmid42884891,
year = {2026},
author = {Dimkić, I},
title = {Advances in Microbial Solutions for Sustainable Agriculture.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/plants15193027},
pmid = {42884891},
issn = {2223-7747},
abstract = {This Special Issue, "Advances in Microbial Solutions for Sustainable Agriculture," comprises ten high-quality contributions that collectively reflect the current state of the art in plant-associated microbiome research [...].},
}

@article {pmid42884898,
year = {2026},
author = {Li, J and Wang, Q and Li, X and Zhang, Z and Liu, Y and Meng, Q and Zou, J and Liu, X and Luo, Y and Guo, Z},
title = {Long-Term Fertilisation Regimes, Crop Yield and Rhizosphere Microecology in a Wheat-Soybean Rotation System.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/plants15193034},
pmid = {42884898},
issn = {2223-7747},
support = {2023YFD1500700//National Key Research and Development Program of China/ ; },
abstract = {Long-term fertilisation must sustain crop yield and rhizosphere microbial functions in wheat-soybean rotations, but interannual responses remain unclear. We examined 12 treatments in a long-term field experiment established in 1979 and continuing through 2025 in Heilongjiang, China; three within-plot soil composites per treatment represented the 2025 microbiome snapshot. Long-term wheat and soybean grain and straw yield, rhizosphere and non-rhizosphere metagenomes, bacterial diversity, functional gene profiles, taxonomic composition, yield-microbe correlations, and structural equation modelling were assessed. The displayed wheat grain yields differed among treatments, with the median approaching 2500 kg ha[-1] under manure plus medium-rate mineral fertiliser. Soybean grain yield exceeded 2000 kg ha[-1] under manure plus low- or medium-rate mineral fertiliser and was higher than under high-rate mineral fertiliser alone. Separate exploratory treatment-only PERMANOVAs returned R[2] values of 0.7578 and 0.8227 for rhizosphere and non-rhizosphere functional profiles, respectively; the profiles were within-plot subsamples. Mesorhizobium, Lysobacter, Gemmatirosa, and Pseudolabrys were positively correlated with crop yield. Structural equation modelling linked available phosphorus to wheat yield and rhizosphere diversity and linked available potassium to soybean yield. These descriptive findings suggest crop-specific fertilisation patterns and possible associations of yield with soil nutrients and rhizosphere microbiota, indicating that productivity and microbial responses should inform long-term nutrient management.},
}

@article {pmid42884929,
year = {2026},
author = {Sun, R and Farooq, A and Chen, S and Shahani, AAA and Liu, T and Jiajin, L and Farooq, TH and Yan, W and Wang, J},
title = {Nitrogen Regulation Under Heavy Metal Stress in Soil-Plant Systems: Implications for Plant Growth and Phytoremediation.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/plants15193065},
pmid = {42884929},
issn = {2223-7747},
support = {32471842//National Natural Science Foundation of China/ ; },
abstract = {Nitrogen (N) is a vital macronutrient that dictates soil fertility and plant productivity. Heavy metal contamination threatens plant health by disrupting nutrient uptake and photosynthesis. Specifically, heavy metals accumulate in soils and inhibit key N-assimilatory enzymes, such as nitrate reductase. This inhibition restricts N availability, which limits protein synthesis and reduces overall plant biomass. This review synthesizes the recent literature to evaluate the mechanisms of heavy metal-N interactions, highlighting a critical scientific insight: N exerts a dual role in heavy metal stress. Externally, the chemical form of N uptake alters rhizosphere pH, which can either mobilize or precipitate toxic metal cations. Internally, optimal N assimilation fuels the synthesis of metal-chelating proteins (e.g., phytochelatins) required for cellular detoxification. A key conclusion of this review is that isolated agronomic or physiological interventions are insufficient to manage this stress in the field. Effective mitigation requires a coupled "soil-to-gene" approach. By combining macroscopic soil management (e.g., pH buffering and biochar application) to restrict external metal bioavailability with targeted molecular interventions (e.g., regulating root ion transporters and leveraging microbiome-assisted multi-omics) to enhance internal detoxification, researchers can improve phytoremediation efficiency and restore soil health in multi-contaminated environments.},
}

@article {pmid42885155,
year = {2026},
author = {Shabana, H and Gudnadottir, U and Hugerth, LW and Rodriguez-Wallberg, KA and Brusselaers, N},
title = {Vaginal microbiome composition and medically assisted reproduction outcomes: a systematic review and network meta-analysis of 2289 women across three WHO regions.},
journal = {Human reproduction update},
volume = {},
number = {},
pages = {},
doi = {10.1093/humupd/dmag033},
pmid = {42885155},
issn = {1460-2369},
support = {//Swedish Society of Reproductive Medicine 2023/ ; //Nordic Federation of Societies of Obstetrics and Gynaecology 2024/ ; 20 0170F//Swedish Cancer Society/ ; },
abstract = {BACKGROUND: The vaginal microbiome may influence the success of medically assisted reproduction (MAR), including IVF with or without ICSI, and IUI. However, findings across studies remain inconsistent, and previous meta-analyses have largely relied on binary microbiome classifications or pairwise comparisons. The relative associations between individual vaginal community state types (CSTs) and pregnancy outcomes therefore remain uncertain.

OBJECTIVE AND RATIONALE: To compare the associations between individual CSTs and pregnancy following MAR by integrating direct and indirect evidence in a systematic review and network meta-analysis (NMA) and to determine whether specific CSTs were associated with lower odds of pregnancy.

SEARCH METHODS: PubMed, Embase, Web of Science, and the Cochrane Library were searched from database inception to 2 April 2026. Eligible longitudinal studies assessed vaginal microbiome composition using sequencing-based profiling before embryo transfer or IUI and reported pregnancy following MAR. Cross-sectional studies, studies without CST classification, or pregnancy outcome data, and studies based solely on post-treatment sampling were excluded. Two reviewers independently performed study selection and risk-of-bias assessment. Odds ratios (ORs) with 95% CIs were synthesized across CSTs using NMA. Twelve longitudinal studies including 2289 women met the inclusion criteria. The prospectively registered review was reported in accordance with PRISMA and the PRISMA extension for NMA.

OUTCOMES: The NMA allowed integration of direct and indirect evidence across six CST categories. Compared with Lactobacillus (L.) crispatus, Lactobacillus jensenii-dominated CSTs (OR 0.42, 95% CI 0.19-0.92), and low-lactobacillus community CSTs (OR 0.59, 95% CI 0.38-0.91) were associated with significantly lower odds of pregnancy. No statistically significant differences were observed for other lactobacilli, including Lactobacillus gasseri and Lactobacillus iners, compared with L. crispatus. Tests found no evidence of overall or loop inconsistency in the primary network. Subgroup analyses showed broadly similar patterns but were limited by sparse data, imprecision, and local inconsistency in some subgroup networks. Interpretation was further limited by clinical and methodological heterogeneity, observational study designs, residual confounding, and sparse evidence for several CST comparisons. Live-birth evidence was particularly limited: only five studies reported a total of 57 live births. Transitivity could not be formally assessed because potential effect modifiers were not consistently reported for individual CSTs.

WIDER IMPLICATIONS: The findings indicate that general assumption of Lactobacillus-dominated CSTs being beneficial to MAR-treatment effects should be regarded with caution, as these may differ in their associations with pregnancy, depending on the specific Lactobacillus dominance. However, the available evidence is insufficient to support clinical implementation of CST profiling. Larger, standardized prospective longitudinal studies with CST-specific reporting, adjusted estimates, repeated microbiome sampling, and live-birth outcomes are required to determine whether CST profiling has clinically useful prognostic value and whether microbiome-targeted interventions improve reproductive outcomes.

REGISTRATION NUMBER: PROSPERO CRD420251066092.},
}

@article {pmid42885240,
year = {2026},
author = {Ghosh, SK and Wassel, MA and Wong, MK and Hyodo, S and Hamasaki, K},
title = {Functional Metagenomics Reveals Gut Microbial Biosynthetic Potential for Essential Nutrients in Juvenile Chum Salmon.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70448},
doi = {10.1111/1462-2920.70448},
pmid = {42885240},
issn = {1462-2920},
support = {//University of Tokyo/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Animals ; *Oncorhynchus keta/microbiology/metabolism/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Amino Acids/biosynthesis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; },
abstract = {The fish gut microbiota contributes to host nutrition, immunity and homeostasis, yet how its metabolic capacity relates to gaps in the host genome remains poorly characterized. Here we used shotgun metagenomic sequencing and KEGG module completion analysis to compare the biosynthetic potential of the gut microbiome with that of the host genome in juvenile chum salmon (Oncorhynchus keta) at 35 days posthatching, when exogenous feeding begins. Because small juvenile guts yield low microbial biomass and a high proportion of host DNA, we first optimized a protocol combining enzymatic lysis with NEBNext-based host DNA depletion. This raised the bacterial sequence fraction from 11.3% to 41.2% and increased the number of KEGG Orthology identifiers mapped to modules from 1128 to 1532. Module Completion Ratio analysis revealed complementation in functional potential: the chum salmon genome was incomplete for de novo biosynthesis of essential amino acids (threonine, leucine, valine/isoleucine, lysine) and B-vitamins (thiamine, riboflavin, biotin), whereas the gut metagenome encoded complete or near-complete modules for these pathways. Sequences assigned to Bartonella-like, Acinetobacter and Enterococcus lineages contributed most. These observations indicate that the gut microbiome encodes biosynthetic potential the host genome lacks, although demonstrating a nutritional benefit to the host will require experimental manipulation.},
}

Animals
*Oncorhynchus keta/microbiology/metabolism/genetics
Metagenomics
*Gastrointestinal Microbiome
Amino Acids/biosynthesis
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenome

@article {pmid42885316,
year = {2026},
author = {Jin, C and Wang, Y},
title = {Gut microbiota in patients receiving dialysis: Mechanisms, complications and the road to personalized microbiome‑based care (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {6},
pages = {},
doi = {10.3892/mmr.2026.14044},
pmid = {42885316},
issn = {1791-3004},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Renal Dialysis/adverse effects ; *Dysbiosis/microbiology/etiology ; *Precision Medicine/methods ; },
abstract = {Gut dysbiosis is increasingly recognized as a potential contributor to poor outcomes in patients receiving dialysis, yet its mechanistic complexity and therapeutic implications remain incompletely understood in clinical practice. The uremic environment, dietary restrictions, polypharmacy and dialysis modality‑specific factors collectively reshape the gut microbial ecology, promoting the overproduction of deleterious metabolites such as indoxyl sulfate, p‑cresyl sulfate and trimethylamine N‑oxide while depleting protective short‑chain fatty acids. These alterations compromise intestinal barrier integrity, fuel systemic inflammation through endotoxemia and NOD‑like receptor family pyrin domain containing 3 inflammasome activation and have been associated with cardiovascular disease, immune dysfunction, peritonitis, protein‑energy wasting and cognitive impairment. Although probiotic, prebiotic, synbiotic and dietary interventions show promise, heterogeneous responses across trials underscore the inadequacy of one‑size‑fits‑all strategies. Multi‑omics profiling has revealed substantial interindividual variability in microbial composition and metabolic capacity, providing a rationale for personalized approaches. The present review synthesizes current evidence on the mechanisms underlying dysbiosis and complications in patients receiving dialysis and proposes a roadmap toward personalized microbiome‑based care to improve clinical outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Renal Dialysis/adverse effects
*Dysbiosis/microbiology/etiology
*Precision Medicine/methods

@article {pmid42885608,
year = {2026},
author = {Ali, S and Touzout, N and Rasool, A and Almalki, MA},
title = {Root-Microbiome Signaling Under Co-Contaminant Stress: Rhizosphere Reassembly, Microbial Detoxification, and Plant Resilience Through Multiomics.},
journal = {Journal of basic microbiology},
volume = {66},
number = {10},
pages = {e70207},
doi = {10.1002/jobm.70207},
pmid = {42885608},
issn = {1521-4028},
support = {KFU265833//Deanship of Scientific Research, Vice Presidency for Graduate Studies and Scientific Research, King Faisal University, Saudi Arabia/ ; },
mesh = {*Rhizosphere ; *Plant Roots/microbiology/physiology ; Multiomics ; Soil Microbiology ; *Microbiota/physiology ; *Plants/microbiology/metabolism ; Stress, Physiological ; *Soil Pollutants/metabolism/toxicity ; Signal Transduction ; Biodegradation, Environmental ; },
abstract = {Agricultural soils contain mixture of metals, pesticides, antibiotics, pharmaceuticals, and plastics. Their combined effects are shaped by contaminant chemistry, root activity, and microbial interactions at the rhizosphere interface. This review develops a mechanistic framework linking co-contaminant exposure with root sensing, exudate reprogramming, microbiome reassembly, multitrophic interactions, microbial detoxification, and plant stress adaptation. We distinguish taxonomic shifts from functional resilience and microbial resistance from plant protection. Particular attention is given to cross-kingdom interactions and microbial processes that control contaminant sequestration, transformation, nutrient availability, and host signaling. Multi-omics approaches are evaluated alongside stable-isotope probing, synthetic communities, metabolite supplementation, and genetic validation to identify candidate mechanisms for targeted causal validation. We then discuss microbiome engineering strategies for moving beyond descriptive community profiling toward predictive and function-oriented rhizosphere engineering. These strategies can be guided by contaminant fate and plant performance. By integrating contaminant chemistry, root-microbiome signaling, microbial functional responses, and plant adaptation, this review provides a mechanistic framework for understanding and engineering rhizosphere resilience under co-contaminant stress.},
}

*Rhizosphere
*Plant Roots/microbiology/physiology
Multiomics
Soil Microbiology
*Microbiota/physiology
*Plants/microbiology/metabolism
Stress, Physiological
*Soil Pollutants/metabolism/toxicity
Signal Transduction
Biodegradation, Environmental

@article {pmid42885689,
year = {2026},
author = {Shannon, OM and Beck, L and Castro, C and Jennings, A and Gillings, R and Lee, VY and Elsworthy, R and Gulston, M and Langerova, T and Boldurat, C and Nazeer, A and Hardeman, W and Hanson, S and Nelson, A and Siervo, M and Aldred, S and White, B and Gerasimidis, K and Griffin, J and Minihane, AM and Stewart, C and Mathers, J},
title = {Impact of a Mediterranean diet and physical activity intervention on the gut microbiome and faecal metabolites: findings from the MedEx-UK randomised controlled trial - ERRATUM.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1},
doi = {10.1017/S0007114526109416},
pmid = {42885689},
issn = {1475-2662},
}

@article {pmid42885915,
year = {2026},
author = {Gries, M and Schäfer, KH and Endres, K},
title = {Targeting the microbiota-gut-brain axis in Alzheimer's and Parkinson´s disease: recent therapeutic approaches.},
journal = {Expert opinion on therapeutic targets},
volume = {},
number = {},
pages = {},
doi = {10.1080/14728222.2026.2748747},
pmid = {42885915},
issn = {1744-7631},
abstract = {INTRODUCTION: Alzheimer's disease (AD) and Parkinson's disease (PD) are the most common neurodegenerative disorders with limited disease-modifying treatment options. Evidence suggests that the microbiota-gut-brain axis (MGBA) plays a role in these diseases by facilitating communication between the gut and the central nervous system. Associations have been found between altered gut microbiota composition and function, impaired barrier integrity, dysregulated metabolite production, and immune activation to neuroinflammation and progressive neurodegeneration.

AREAS COVERED: This review summarizes and critically assesses recent studies from the past year to provide an updated overview of therapeutic strategies targeting the MGBA in both diseases. We discuss dietary interventions, probiotics, postbiotics, microbial metabolites, and approaches targeting gut barrier function. We also highlight strategies such as fecal transplantation, photobiomodulation, and PD-targeted metabolism therapies using butyrate and resistant starch.

EXPERT OPINION: While these interventions have shown promising results in preclinical and early clinical trials, their clinical application is limited by methodological heterogeneity, interindividual variability and a lack of standardized protocols. Successful implementation requires carefully designed clinical trials, particularly longitudinal studies of presymptomatic cohorts, standardized microbiome analyses, and integrated multi-omics approaches to elucidate causal relations and facilitate personalized treatment strategies.},
}

@article {pmid42766464,
year = {2026},
author = {Moreno-Mirón, JM and Moreno-Mirón, A and Ruiz-Argüelles, GJ and Gale, RP},
title = {Helicobacter pylori in Haematology: Contextualising Established and Emerging Associations.},
journal = {Acta haematologica},
volume = {},
number = {},
pages = {1},
doi = {10.1159/aha/abkag012},
pmid = {42766464},
issn = {1421-9662},
}

@article {pmid42873131,
year = {2026},
author = {Navarro-Diaz, M and Bertram, K and Göbel, L and Camus, L and Ham, S and Angenent, LT and Gomez, JAV and Heilbronner, S and Stincone, P and Rapp, J and Petras, D and Link, H},
title = {Community composition drives metabolic competition and Staphylococcus aureus colonization resistance in synthetic nasal communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag268},
pmid = {42873131},
issn = {1751-7370},
abstract = {The human nasal microbiome is a low-diversity ecosystem whose assembly principles and mechanisms of colonization resistance remain poorly understood. Staphylococcus aureus is a member of the nasal microbiome of some individuals with variable abundance. We hypothesized that nutritional competition, strain-level diversity, and nutrient availability shape community stability and the ability of commensal species to inhibit S. aureus. To test this, we constructed 50 defined synthetic communities inoculated with 5 to 10 representative human nasal bacterial species differing in strain and species composition and tracked their compositional changes across serial passages, S. aureus growth, metabolic profiles, and nutritional interactions. The resulting consortia, which assembled into communities of up to 6 co-existing species converged in one of three community types. Synthetic communities dominated by specific Corynebacterium propinquum strains showed exclusion of most other community members, including S. aureus. Conversely, communities lacking C. propinquum dominance showed that exclusion of S. aureus was driven primarily by a combination of Staphylococcus epidermidis and Staphylococcus lugdunensis. Growth and coculture assays showed that C. propinquum outcompetes S. aureus in conditions that resemble the nasal environment, whereas S. aureus dominates in nutrient-rich conditions. Metabolomics analyses indicated that nutritional competition, including siderophore utilization and amino acid limitation, likely underlies this colonization resistance. These results establish a reproducible and tractable synthetic community model for the human nasal microbiome and suggest that nutrient-dependent competition and microbial metabolite production are key drivers of community structure and pathogen exclusion.},
}

@article {pmid42873224,
year = {2026},
author = {Tereucán, G and Tosi, N and Dobani, S and Carrieri, C and Del Rio, D and Henriquez-Aedo, K and Bresciani, L and Aranda, M and Mena, P},
title = {In vitro colonic fermentation of ferulic acid and trans-resveratrol: kinetic profiling and metabolic convergence.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
pmid = {42873224},
issn = {2042-650X},
abstract = {In vitro batch fecal fermentation offers a controlled approach to study colonic catabolism of dietary (poly)phenols and their microbial metabolites. Here, the bioconversion of two (poly)phenols, ferulic acid (FA) and trans-resveratrol (t-R), was followed over 48 h to assess metabolic convergence in their catabolic pathways. Using a human fecal inoculum, samples collected at 2, 6, 24 and 48 h were analyzed by UPLC-ESI-QqQ-MS/MS. FA and t-R displayed distinct degradation kinetics, consistent with their different molecular structures and steric constraints. FA was rapidly depleted within 2 h, whereas t-R persisted throughout incubation, with less than half converted by 6 h and ≈37% remaining at 48 h. Accordingly, FA catabolites peaked at 85% molar mass recovery at 2 h, while t-R-derived catabolites accumulated gradually, reaching ≈44% at 48 h. Despite these differences, both substrates were mainly processed through reduction followed by dehydroxylation, converging toward a shared pool of low-molecular-weight phenolic acids. FA degradation was characterized by phenylpropanoic acid formation after hydrogenation of the unsaturated side chain, whereas t-R catabolism yielded dibenzyl derivatives, mainly dihydroresveratrol and lunularin. Notably, 3-(4'-hydroxyphenyl)propanoic acid emerged as a major FA catabolite, and several phenolic acids were quantified as t-R-derived products, suggesting minor routes involving the cleavage of the stilbene central linkage and subsequent methyl oxidation. Overall, we propose a sequence of microbial enzymatic reactions underlying FA and t-R colonic catabolism. Future studies should validate these findings across donors and integrate microbiome functional readouts to explain inter-individual variability in bioconversion.},
}

@article {pmid42873245,
year = {2026},
author = {Tutun, H and Sevin, S and Taş, P and Özgenç Çınar, Ö and Erdem, B and Ceylan, A and Keskin, E},
title = {Chronic oral toxicity of lithium citrate in honeybees (Apis mellifera L.): impacts on survival, midgut histopathology and gut microbiota.},
journal = {Die Naturwissenschaften},
volume = {113},
number = {6},
pages = {},
pmid = {42873245},
issn = {1432-1904},
mesh = {Animals ; Bees/drug effects/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Citrates/toxicity/administration & dosage ; RNA, Ribosomal, 16S/genetics ; Administration, Oral ; Gastrointestinal Tract/drug effects/microbiology/pathology ; },
abstract = {The search for effective alternatives to conventional acaricides has positioned lithium as a promising experimental candidate for controlling Varroa destructor; however, its physiological impact on the honeybee (Apis mellifera) remains insufficiently characterized. This study evaluated the chronic oral toxicity of lithium citrate over a 10-day exposure period, focusing on survival, midgut histopathological changes, and gut microbiota dynamics. Newly emerged bees were exposed to sugar syrup containing 12.5, 25, and 50 mM lithium citrate. Mortality increased monotonically with dose: 10-day survival was 0.94 in the control and 0.84, 0.22, and 0 at 12.5, 25, and 50 mM, respectively (all pairwise contrasts significant, Benjamini-Hochberg correction). Histological analysis of the midgut revealed pronounced epithelial damage, characterized by severe desquamation and cellular shedding into the lumen, even at the lower dose of 12.5 mM, with the highest severity at 12.5 mM rather than 25 mM; the peritrophic membrane remained intact in all groups. Furthermore, 16S rRNA gene sequencing revealed variation in the relative abundance of several core gut bacteria across treatment groups, although neither alpha- nor beta-diversity differed significantly among groups. At the highest lithium concentration (25 mM), Gilliamella showed a markedly lower median relative abundance, whereas Frischella was relatively more abundant; however, these patterns were not statistically supported by differential abundance analysis and did not indicate a consistent concentration-dependent response. Given the limited number of biological replicates (n = 3 per group), these compositional patterns should be regarded as preliminary. These findings suggest that lithium citrate, despite its varroacidal potential, acts as a significant physiological stressor, compromising the structural integrity of the digestive tract and disrupting microbial homeostasis. Consequently, the development of lithium-based treatments must carefully consider both lethal and sublethal effects at the individual level, and colony-level consequences remain to be evaluated.},
}

Animals
Bees/drug effects/microbiology
*Gastrointestinal Microbiome/drug effects
*Citrates/toxicity/administration & dosage
RNA, Ribosomal, 16S/genetics
Administration, Oral
Gastrointestinal Tract/drug effects/microbiology/pathology

@article {pmid42873256,
year = {2026},
author = {Hassan, NF and Ahmed, SG and Aboul-Ella, H and Salem, MA and Gohar, A and El-Maghraby, AM and Hamed, DM and Essa, MA and Gad, ES},
title = {Bacillus-based probiotics ameliorate bleomycin-induced pulmonary fibrosis in rats: coupling intestinal barrier reinforcement to the modulation of M2 macrophage polarization/TGF-β/p38MAPK and inflammasome-driven pyroptosis.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42873256},
issn = {1432-1912},
abstract = {Pulmonary fibrosis (PF) is a chronic, progressive lung disorder with an 87.5% mortality rate recorded in aged patients. Emerging evidence bridges gut dysbiosis to PF pathogenesis. The consumption of a Bacillus-based probiotic exhibited immunomodulatory and anti-inflammatory effects by alleviating gut dysbiosis and restoring gut microbiome composition, positioning it as a promising therapeutic strategy for gut-organ axis disorders. The present study investigated the therapeutic effects of Bacillus-based probiotics in a rat model of PF by targeting the gut-lung axis. Rats were randomly assigned to five groups: Group I (the normal control group) and Group II received a single intratracheal instillation of bleomycin (BLM) (5 mg/kg). All treated groups received BLM and commenced treatment fourteen days later. Group III: received B. clausii. Group IV: received B. coagulans. Group V: received a combination of both strains. In vitro and in vivo analyses showed that the probiotic strains exhibited gut survivability, colonization associated with restoration of intestinal barrier integrity, and an SCFA profile. The dual therapy exerted a notable immunomodulatory effect by suppressing pulmonary M2 macrophage polarization (CD206 and Arg1), inhibiting the TGF-β/p38MAPK-JNK/NF-κB signaling cascade, mitigating inflammatory and fibrotic responses, and diminishing NLRP3/Caspase-1/IL-1β/GSDMD-N-mediated pyroptosis, thereby disrupting the vicious cycle of inflammation and fibrogenesis. Interplay with the Nrf2 axis activates antioxidant defense. This study resolves this knowledge gap by investigating the therapeutic potential of Bacillus-based probiotics to alleviate PF by modulating the gut-lung axis, offering an innovative platform for the treatment of PF that extends beyond current Lactobacillus-focused research.},
}

@article {pmid42873567,
year = {2026},
author = {Kueneman, JG and Argueta-Guzmán, M and McFrederick, QS and Vannette, RL and Steffan, SA and Buchmann, SL and Roubik, DW and Wcislo, WT and Danforth, BN},
title = {Acidogenic Bacteria Dominate Brood Pollen Provisions Across Diverse Bee Taxa.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70578},
doi = {10.1111/mec.70578},
pmid = {42873567},
issn = {1365-294X},
support = {1929499//National Science Foundation/ ; 1929572//National Science Foundation/ ; 2019-67013-29299//National Institute of Food and Agriculture/ ; //Smithsonian Tropical Research Institute Scholarly Studies Program/ ; //Cornell Atkinson Center for Sustainability Academic Venture Fund/ ; NC1173//USDA multistate grant/ ; },
mesh = {Animals ; Bees/microbiology/classification ; *Pollen/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Phylogeny ; *Microbiota/genetics ; Fungi/genetics/classification ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; },
abstract = {Bacteria and fungi play vital roles in bee health and development, yet microbial communities associated with pollen provisions remain largely uncharacterized for most bee species, particularly ground-nesting taxa. Microbial communities may prevent pollen provision spoilage, liberate nutrients from pollen, supply direct nutrition and/or suppress pathogens, though these functions appear context-dependent and variable among hosts. To determine whether bee evolutionary history and ecological traits structure pollen provision microbiomes, we analyzed 345 'live' brood cell pollen provisions representing 39 species, 18 tribes and six bee families spanning diverse life histories, diet breadths, floral resource use and nesting substrates. Microbial composition was determined by amplicon sequencing of bacterial 16S rRNA (V5-V7) and fungal ITS (1 and 2) regions. Bacterial richness and community composition were strongly structured by bee taxonomy and were also associated with several ecological traits, while community composition was significantly associated with host phylogeny. Fungal richness also varied among bee taxa and ecological groups, whereas fungal community composition showed greater variability and weaker, though detectable, taxonomic structure, with comparatively small ecological-trait effects. Across phylogenetically distant bee tribes, pollen provisions were often dominated by lactic- or acetic acid-producing bacteria, indicating a strategy of microbial fermentation that reduces bacterial richness and may enhance food preservation. Together, these results reveal broad evolutionary and ecological patterns underlying the microbiome of solitary bee brood cells and suggest that acid-producing bacteria play a stabilizing role in the preservation and function of pollen provisions.},
}

Animals
Bees/microbiology/classification
*Pollen/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
Phylogeny
*Microbiota/genetics
Fungi/genetics/classification
Sequence Analysis, DNA
DNA, Bacterial/genetics

@article {pmid42873652,
year = {2026},
author = {Pulvino, AT and Sardaro, MLS and Quinn, WG and Christopher, ER and Koenig, S and Lucore, JM and Vidal-Cruchez, O and Mallott, EK and Kuthyar, S and Lee, W and Chitta, S and Gray, S and Williams, LE and Curley, JP and Liechty, ER and Ben-Sahra, I and Amato, KR},
title = {Bile, sulphur and carbohydrate metabolic variation co-occur with host adiposity in mice colonized with primate microbiota.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001848},
pmid = {42873652},
issn = {2057-5858},
mesh = {Animals ; Mice ; Humans ; *Adiposity ; *Bile/metabolism ; Macaca mulatta ; *Sulfur/metabolism ; *Carbohydrate Metabolism ; Multiomics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Cecum/microbiology ; Liver/metabolism ; Metagenomics ; Primates/microbiology ; Microbiota ; },
abstract = {Although mechanistic links between the microbiome and chronic disease are increasingly well defined, how microbiomes facilitate normal variation in host metabolism remains less clear. Building on our recent demonstration that pooled faecal inocula from different primate species can cause relative differences in mouse host adiposity, we define potential mechanisms by which this could occur. Using existing samples from germ-free mice inoculated with faecal samples from humans (Homo sapiens), rhesus macaques (Macaca mulatta) and squirrel monkeys (Saimiri boliviensis), we integrate shotgun metagenomics of caecal contents, liquid chromatography-MS-MS metabolomics of serum and caecal contents and hepatic RNA-sequencing. Our multi-omic analysis reveals that the relative increase in adiposity previously observed in macaque-donor mice is associated with differences in hepatic cysteine catabolism and bile metabolism pathway features. These data suggest that bile and sulphur co-metabolic variation may mediate increased bile pool hydrophobicity. We also observed variation in caecal microbiome composition as well as host hepatic retinol signalling and lipid metabolism between treatments. When considered together with the observation that macaque-donor mice consumed less food than the other treatment groups, our results support the hypothesis that increased bile pool hydrophobicity results in increased dietary energy extraction. Our findings provide a foundation for future mechanistic testing of new hypotheses for understanding how the intestinal microbiomes of different primate species regulate lipid homeostasis in a mouse host.},
}

Animals
Mice
Humans
*Adiposity
*Bile/metabolism
Macaca mulatta
*Sulfur/metabolism
*Carbohydrate Metabolism
Multiomics
Feces/microbiology
*Gastrointestinal Microbiome
Cecum/microbiology
Liver/metabolism
Metagenomics
Primates/microbiology
Microbiota

@article {pmid42874001,
year = {2026},
author = {Chang, L and Freimer, NB and Hsiao, EY},
title = {The Brain-Gut-Microbiome Axis: Exploring the Link Between Depression and Irritable Bowel Syndrome.},
journal = {Annual review of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-physiol-040225-111420},
pmid = {42874001},
issn = {1545-1585},
abstract = {The brain-gut-microbiome system is an integrated communication network linking the central nervous system, enteric nervous system, immune pathways, and intestinal microbiota. Increasing evidence indicates that dysregulation of this bidirectional signaling system contributes to both gastrointestinal and psychiatric disorders. Irritable bowel syndrome (IBS), a disorder of gut-brain interaction, and major depressive disorder (MDD) frequently coexist and share multiple biological and environmental risk factors. Advances in microbiome science, neuroimaging, and multi-omics technologies have revealed that microbial metabolites, neuroimmune signaling, and stress-responsive neuroendocrine pathways influence neural circuits regulating mood, visceral perception, and gastrointestinal function. These interconnected mechanisms may explain the high comorbidity between IBS and MDD and suggest that both conditions arise from disturbances across overlapping biological systems. In this review, we synthesize current knowledge of genetic, neurobiological, and potential microbial contributors to IBS and depression, discuss emerging therapeutic approaches targeting the brain-gut-microbiome system, and highlight future directions for developing mechanistically informed treatment strategies.},
}

@article {pmid42874194,
year = {2026},
author = {Luo, ZN and Zhang, TY and Zhu, B and Zhang, DX and Lv, H and Shi, J and Peng, Z and Zhou, B and Xu, M and Zhao, HX and He, H and Zeng, C and Xu, B},
title = {Nitrification control and early microbiome-resistome transitions during permanent conversion from chloramine to free chlorine in a full-scale drinking water distribution system.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127125},
doi = {10.1016/j.watres.2026.127125},
pmid = {42874194},
issn = {1879-2448},
abstract = {Chloramine is widely used in drinking water distribution systems (DWDSs), but ammonia recycling can promote nitrification and disinfectant residual loss. As source water ammonia is controlled, permanent conversion to free chlorine may replace repeated temporary chlorine burns, yet its nitrogen control performance and microbiome-resistome consequences remain unresolved. We analyzed early responses of 16 bulk water metagenomes from four sites at chloramine baseline and free chlorine days 1, 5 and 8, with nitrification-related water quality monitored for 8 months. Conversion achieved nitrogen control benefits, with nitrite lower after conversion at multiple time points (p < 0.05), dominant nitrifying genera suppressed to <0.1%, and ammonia oxidation and hydroxylamine oxidation potentials decreasing from 125.84 to 2.77 TPM and from 20.35 to 0.45 TPM. Community restructuring was site-specific (PERMANOVA stage R[2] = 0.297, p = 0.001; site R[2] = 0.311, p = 0.002). Despite improved nitrification control, 21-50% of each site's baseline ARGs remained detectable after conversion. SEM linked chlorine speciation to community shift (β = 0.695) and ARG/16S shift (β = -0.344), while community shift and MGE/16S shift showed positive paths to ARG/16S shift (β = 0.426 and 0.819). The pathways suggest that the shift toward free chlorine was a potential driver of early microbiome-resistome reorganization. These early responses are consistent with succession from chloramine-resistant communities toward free chlorine-resistant, MGE-associated hosts that may facilitate ARG redistribution. Permanent conversion is a viable nitrification control option, but evaluation should include microbiome and resistome monitoring beyond residual and nitrification indicators.},
}

@article {pmid42874205,
year = {2026},
author = {Fang, K and Chu, S and Lu, Z and Ma, X and Zhang, D and Ding, W and Wei, L and Yang, H and Zhou, R and Zhang, D and Zhou, P},
title = {Sustained hydrogen delivery enhances microbiome-associated cadmium and copper immobilization in co-contaminated soils.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143893},
doi = {10.1016/j.jhazmat.2026.143893},
pmid = {42874205},
issn = {1873-3336},
abstract = {Molecular hydrogen (H2) is an important energy source for soil microbes and has been implicated in biogeochemical regulation; however, whether-and how-exogenous H2 inputs promote Cd and Cu immobilization in co-contaminated soils remains unclear. We engineered MgH2-biochar granules capable of sustained H2 release for up to 448 h. The granules exhibited high adsorption capacities in aqueous Cd-Cu systems (Cu: 59.76 mg g[-1]; Cd: 35.76 mg g[-1]). In soil, MgH2-biochar treatment was associated with enhanced microbial hydrogenase activity, reduced oxidative stress, and enrichment of functional taxa, together with significant reductions in available Cd (10.9-22.5%) and Cu (14.2-30.1%) (P < 0.05). Notably, Mg-associated alkalization elevated soil pH and contributed to physicochemical immobilization. Microbial community analyses further revealed H2-associated shifts in community structure and significant associations between H2 metabolism and metal resistance (Cd: P < 0.001; Cu: P < 0.03). Genome-resolved metagenomics identified 10 metagenome-assembled genomes (MAGs) that co-harbour [NiFe]-hydrogenases (Groups 1 and 4) and Cd/Cu resistance genes (e.g., actS, czcA, and copC). Exploratory pathway modeling further indicated associations of Cd/Cu immobilization with H2-associated microbial processes and Mg-associated physicochemical effects. This work provides integrated material, geochemical, and microbial evidence supporting an H2-associated contribution to heavy-metal immobilization in soils.},
}

@article {pmid42874435,
year = {2026},
author = {Guo, X and Peng, C and Zhang, S and Yin, R and Chen, X and Xin, X and Xiao, X and Dou, K and Liu, S and Jiang, Z and Gao, Y},
title = {Multi-perspective integration reveals the molecular and microbiological basis for differences in the biosynthesis of phenylpropanoid-related bioactive compounds in different medicinal parts of Angelica sinensis (Oliv.) Diels.},
journal = {Plant physiology and biochemistry : PPB},
volume = {239},
number = {},
pages = {111780},
doi = {10.1016/j.plaphy.2026.111780},
pmid = {42874435},
issn = {1873-2690},
abstract = {Angelica sinensis (Oliv.) Diels (Ang) is a major medicinal herb, and its phenylpropanoids constitute the key bioactive compounds. However, the molecular and microbiological basis underlying their accumulation remains unclear, particularly at the sub-regional level of root head, body, and tail (ARH, ARB and ART, respectively). To address this, we integrated whole-genome gene family analysis, differential gene expression profiling, network pharmacology, molecular docking, microbial community characterization, and mediation regression path analysis to systematically investigate the compositional differences across different root regions. The results indicated that phenylpropanoid biosynthesis and plant-pathogen interaction pathways were significantly enriched in ART. Eight key phenylpropanoid biosynthetic gene families were identified, the majority of which showed predominant expression in ART. Metabolic profiling further demonstrated that prenyl arabinosyl-(1 → 6)-glucoside, coumarin, and lawsone were markedly enriched in ART compared to both ARH and ARB, along with several other metabolites. Network pharmacology and molecular docking revealed that ART-enriched phenylpropanoid-related metabolites constitute a multi-target network, many of which exhibited anti-thrombotic, anti-blood-stasis, and anti-inflammatory activities. Microbiome profiling showed that dominant endophytic fungi reached their highest relative abundance in ART, with community assembly governed deterministically. Mediation regression path analysis further statistically supported that highly expressed phenylpropanoid biosynthetic genes in ART positively modulate phenylpropanoid-related metabolites, and these genes exerted a significant mediating effect on the shaping of metabolites by endophytic fungi. Overall, this study established a multidimensional analytical framework to elucidate the molecular and microbial basis for the preferential accumulation of phenylpropanoid-related metabolites in ART, offering new insights for precision medicine and quality control of Ang.},
}

@article {pmid42874443,
year = {2026},
author = {Rizky, D and Pramono, A and Setiawan, B and Pangarsa, EA and Santosa, D and Suharti, C},
title = {Microbiota modulation in colorectal cancer: A scoping review of its potential role in toxicity mitigation and treatment response.},
journal = {Cancer treatment and research communications},
volume = {49},
number = {},
pages = {101486},
doi = {10.1016/j.ctarc.2026.101486},
pmid = {42874443},
issn = {2468-2942},
abstract = {INTRODUCTION: Colorectal cancer (CRC) treatment remains limited by gastrointestinal toxicity, heterogeneous therapeutic responses, and treatment resistance. The gut microbiota has emerged as a modifiable factor implicated in these outcomes, particularly chemotherapy-induced toxicity. Probiotics, prebiotics, and synbiotics have been investigated as adjunctive strategies to mitigate chemotherapy-related harm. However, whether the field is ready to extend its focus toward oncologic endpoints, including treatment response, recurrence, and survival, remains unclear.

METHODS: We conducted a scoping review following the Arksey and O'Malley framework and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) guidance. PubMed, EBSCOhost, Scopus, and CENTRAL were searched through 18 February 2026 for studies evaluating probiotic, prebiotic, or synbiotic interventions in adults with CRC receiving systemic therapy. Primary clinical studies and systematic reviews were eligible. Outcomes included treatment-related toxicity, microbial composition, inflammatory and immune markers, and oncologic endpoints.

RESULTS: Of 114 records screened, 16 studies were included, comprising 9 primary studies and 7 systematic reviews. Most studies evaluated probiotic-only regimens in patients receiving fluoropyrimidine- or oxaliplatin-based chemotherapy. The most consistent benefit was a reduction in chemotherapy-induced gastrointestinal toxicity, particularly diarrhea, mucositis, and nausea, along with improved treatment tolerance. Effects on microbial diversity, systemic inflammation, and immune parameters were inconsistent. Only 2 trials directly addressed oncologic outcomes: one reported significantly higher 6-, 12-, and 24-month survival in the probiotic arm, whereas another identified a microbiota-based classifier that predicted treatment response, with an area under the curve (AUC) of 0.95. However, neither trial comprehensively reported conventional oncologic endpoints such as objective response rate or progression-free survival. In addition, strain, dose, and timing varied widely across studies.

DISCUSSION: Microbiota modulation is a plausible and well-tolerated adjunctive strategy in CRC. However, current evidence remains largely anchored to toxicity mitigation, while oncologic endpoints remain underexamined. The field appears ready to move beyond a supportive-care framework and prospectively test whether microbiota-targeted adjuncts influence treatment response, recurrence, and survival. Probiotics, prebiotics, and synbiotics should not be treated as interchangeable interventions. Advancing this research agenda will require adequately powered, strain-specific trials with prespecified oncologic endpoints, embedded microbiome and biomarker readouts, and harmonized reporting.},
}

@article {pmid42874557,
year = {2026},
author = {Jiao, N and Zhu, L and Zhu, R},
title = {Mutant KRAS favors a microbe that signals back.},
journal = {Cell host & microbe},
volume = {34},
number = {10},
pages = {1859-1861},
doi = {10.1016/j.chom.2026.09.007},
pmid = {42874557},
issn = {1934-6069},
mesh = {Humans ; Mutation ; Signal Transduction ; *Proto-Oncogene Proteins p21(ras)/genetics/metabolism ; *Bacteroides/genetics ; *Colorectal Neoplasms/microbiology/genetics ; Rho Guanine Nucleotide Exchange Factors/metabolism ; },
abstract = {Tumor genetics and the microbiome both shape colorectal cancer, but their reciprocal interplay remains poorly defined. In this issue of Cell Host & Microbe, Jiao et al. show that mutant KRAS favors Bacteroides acidifaciens, which signals back through a SusF-ARHGEF2 axis to reinforce RAS-MAPK signaling.},
}

Humans
Mutation
Signal Transduction
*Proto-Oncogene Proteins p21(ras)/genetics/metabolism
*Bacteroides/genetics
*Colorectal Neoplasms/microbiology/genetics
Rho Guanine Nucleotide Exchange Factors/metabolism

@article {pmid42874558,
year = {2026},
author = {Rose, AE and Zhu, W},
title = {From blunt to precision: Engineering microbiome therapeutics against cancer.},
journal = {Cell host & microbe},
volume = {34},
number = {10},
pages = {1862-1864},
doi = {10.1016/j.chom.2026.08.008},
pmid = {42874558},
issn = {1934-6069},
mesh = {Humans ; *Neoplasms/therapy/immunology ; *Immunotherapy/methods ; *Microbiota ; Animals ; *Gastrointestinal Microbiome ; },
abstract = {Two recent papers in Cell Host & Microbe move microbiome therapeutics beyond selecting "beneficial" strains. By turning bacterial surfaces into oral vaccine couriers and resident microbial metabolism into a controllable reactor, they show how location, control, and measurable output can transform the gut into a precision platform for cancer immunotherapy.},
}

Humans
*Neoplasms/therapy/immunology
*Immunotherapy/methods
*Microbiota
Animals
*Gastrointestinal Microbiome

@article {pmid42874560,
year = {2026},
author = {Suryavanshi, MV and Miller, AW},
title = {When microbial biofilms build kidney stones.},
journal = {Cell host & microbe},
volume = {34},
number = {10},
pages = {1868-1870},
doi = {10.1016/j.chom.2026.09.006},
pmid = {42874560},
issn = {1934-6069},
mesh = {*Biofilms/growth & development ; *Kidney Calculi/microbiology/chemistry ; Humans ; Calcium Oxalate/metabolism/chemistry ; *Corynebacterium/physiology/metabolism ; Crystallization ; Microbiota ; Hippurates/metabolism ; },
abstract = {Qi et al.[1] identify Corynebacterium glucuronolyticum-like bacteria as urinary pathobionts that promote calcium oxalate crystallization through two complementary mechanisms: degradation of the crystallization inhibitor hippuric acid and biofilm-mediated crystal aggregation. The work reframes microbiome contributions to stones as discrete, targetable microbial functions rather than generalized dysbiosis.},
}

*Biofilms/growth & development
*Kidney Calculi/microbiology/chemistry
Humans
Calcium Oxalate/metabolism/chemistry
*Corynebacterium/physiology/metabolism
Crystallization
Microbiota
Hippurates/metabolism

@article {pmid42874656,
year = {2026},
author = {McKay, JA and Harding-Crooks, R and Sangal, V},
title = {What is in the Dust? Species-Level Profiling Reveals Pathogenic and Protective Potential of Microbial Communities in Daycare and Home Environments.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70433},
doi = {10.1111/1758-2229.70433},
pmid = {42874656},
issn = {1758-2229},
support = {//Northumbria University/ ; },
mesh = {*Dust/analysis ; Humans ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Child Day Care Centers ; RNA, Ribosomal, 16S/genetics ; *Home Environment ; Animals ; Biodiversity ; },
abstract = {Indoor environments are rich in microbial diversity, which is influenced by multiple factors, including human activities, occupancy levels and the presence of pets. Environment-associated taxa were found to be prevalent in daycare and human-associated taxa in home environments during the COVID-19 pandemic, a period marked by profoundly altered social mixing and hygiene practices. In this study, we investigated the structure of microbial communities and their ecological profiles in daycare and home dust in the post-COVID-19 era. Microbial communities in household dust remain more heterogeneous, with a higher prevalence of human-associated species, than daycare samples. Full-length 16S rRNA gene sequencing enabled species-level taxonomic resolution, yet approximately 40% of amplicon sequence variants remained unclassified, underscoring the vast, novel microbial diversity within our indoor environments encountered in everyday life. AI-assisted ecological profiling revealed a higher burden of pathogens and opportunistic pathogens in home environments than in daycares. Interestingly, the presence of pets had limited influence on microbial diversity in household dust. Finally, several species with known probiotic properties and immunostimulatory potential were present in both environments, reinforcing the notion that microbial exposure during the critical window of early childhood may confer protection against various non-communicable diseases including asthma, childhood leukaemia and other cancers.},
}

*Dust/analysis
Humans
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
*Child Day Care Centers
RNA, Ribosomal, 16S/genetics
*Home Environment
Animals
Biodiversity