@article {pmid42343158,
year = {2026},
author = {Aryal, S and Mell, B and Tummala, R and Manandhar, I and Kumariya, S and Kondapalli, N and Yeoh, BS and Ahlidja, W and Mautin Akinola, O and Pachhain, S and Bardhan, P and Saha, P and Zeydabadinejad, S and Osman, I and Thodeti, C and Yang, T and Vijay-Kumar, M and Reddivari, L and Joe, B},
title = {Gut microbiome drives glycodeoxycholic acid-mediated attenuation of hypertension.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2691346},
doi = {10.1080/19490976.2026.2691346},
pmid = {42343158},
issn = {1949-0984},
mesh = {Animals ; *Hypertension/microbiology/metabolism/physiopathology/drug therapy ; Receptors, G-Protein-Coupled/genetics/metabolism ; *Gastrointestinal Microbiome ; Rats, Inbred Dahl ; Blood Pressure/drug effects ; Rats ; Male ; *Glycodeoxycholic Acid/metabolism ; Bile Acids and Salts/metabolism ; Cecum/microbiology ; Fecal Microbiota Transplantation ; },
abstract = {Gut microbiota and bile acids are increasingly recognized to regulate blood pressure, but the mechanisms remain unclear. Takeda G-protein coupled receptor 5 (TGR5) is a major receptor for secondary bile acids. We hypothesized that loss of TGR5 function remodels gut microbiota and influences blood pressure. Using CRISPR/Cas9, TGR5 knockout (Tgr5KO) rats on the Dahl Salt-Sensitive (S) background were generated and characterized. Compared to the control S rats, Tgr5KO rats demonstrated significantly lower blood pressure, a distinct shift in gut microbiota composition, and an increase in the secondary bile acid, particularly, glycodeoxycholic acid. Supplementation of glycodeoxycholic acid to the control S rats produced a similar gut microbial shift and lowered blood pressure. Furthermore, cecal microbiota transplantation from Tgr5KO to control S rats lowered blood pressure in the recipient rats. This first loss-of-function study demonstrates that deletion of TGR5 remodels gut microbiota, increases glycodeoxycholic acid, and lowers blood pressure regardless of TGR5 signaling status, identifying a promising gut-liver axis target for lowering hypertension.},
}

Animals
*Hypertension/microbiology/metabolism/physiopathology/drug therapy
Receptors, G-Protein-Coupled/genetics/metabolism
*Gastrointestinal Microbiome
Rats, Inbred Dahl
Blood Pressure/drug effects
Rats
Male
*Glycodeoxycholic Acid/metabolism
Bile Acids and Salts/metabolism
Cecum/microbiology
Fecal Microbiota Transplantation

@article {pmid42343209,
year = {2026},
author = {Jiang, M and Liu, R and Li, Z and Xu, H and Zeng, J and Qu, W and Hu, Z and Chen, Y and Feng, D and Wu, W},
title = {Aspergillus niger ZJ-17 enhances the yield and quality of Angelica dahurica var. formosana by modulating beneficial rhizobacteria: a sustainable strategy for plant production.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09252-9},
pmid = {42343209},
issn = {1471-2229},
support = {Grant No. 2021YFYZ0012//the Key R & D projects of the Sichuan Provincial Department of Science and Technology/ ; Grant No. 2021-16-4//the Key Discipline Construction Project of Traditional Chinese Medicine in Sichuan Province/ ; Grant No. 2024-55//the Sichuan Qihuang Scholar Capability Enhancement Project/ ; },
abstract = {BACKGROUND: Angelica dahurica var. formosana is a medicinal and edible plant. Higher abundance of Proteobacteria is an excellent characteristic of its rhizosphere bacterial community. Aspergillus niger ZJ-17 (AN17) significantly improved plant yield and quality while reducing fertilizer input application in both pot and field experiments. However, the impact of inoculants on resident soil bacteria directly determines their field application. Therefore, to systematically analyze how AN17 remodels host rhizosphere bacterial communities, we inoculated AN17 into the roots of A. dahurica var. formosana. The rhizosphere bacterial communities and root exudates were investigated at the harvest stage. Rhizosphere bacteria were isolated for in vitro experiments to elucidate the reasons for the changes in the rhizosphere bacterial community.

RESULTS: AN17 promoted nutrient utilization and absorption in rhizosphere soil and increased the accumulation of IAA and JA in plant roots. In the microbiome, the relative abundance of rhizosphere Proteobacteria increased after inoculation. A total of 832 bacterial strains were isolated from the rhizosphere of the host for in vitro experiments. In in vitro experiments, AN17 induced the enrichment of Proteobacteria through microbial interactions and the modulation of host root exudates. These root exudates promoted the proliferation of bacterial genera with higher abundance and diversity. In the metabolome, host root activity increased following AN17 inoculation. According to the KEGG analysis of root exudates, AN17 upregulated microbial metabolism in diverse environments, the biosynthesis of alkaloids derived from the shikimate pathway and tryptophan metabolism. Correlation analysis and in vitro tests revealed that AN17 regulated the secretion of phenolic acids (4-chlorophenol, 2-oxoadipic acid, pyrogallol, and vanillic acid) from roots, which serve as crucial components driving the enrichment of Proteobacteria. In both plate and pot experiments, these bacteria promoted the growth of A. dahurica var. formosana and activated nutrient availability.

CONCLUSIONS: We supplemented multiple growth-promoting strategies by which AN17 improves rhizosphere bacterial communities. Phenolic acids in root exudates were recognized during the stimulation of rhizosphere bacterial proliferation by AN17. The interaction relationships among plants, beneficial fungi and rhizobacteria were explored and revealed. This result provides a sustainable approach for rhizosphere bacterial optimization and chemical fertilizer reduction in agricultural production.},
}

@article {pmid42343255,
year = {2026},
author = {Grzyb, T and Szulc, J},
title = {Integrated functional genomics and safety assessment of plant-growth-promoting Caryophanales from post-maize-cultivation soils.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13058-2},
pmid = {42343255},
issn = {1471-2164},
support = {00077.DDD.6509.000167.2022.05//The Agency for Restructuring and Modernisation of Agriculture, Poland/ ; },
abstract = {This study aimed to evaluate six environmental bacterial strains isolated from post-maize cultivation soils as candidates for agricultural biopreparation development, using an integrated functional genomic and safety assessment framework. Building on experimental validation of plant-growth-promoting activities, the analysis included: plant-growth-promoting traits (PGPT-Pred) using PLABase; carbohydrate-active enzymes (CAZymes) relevant for lignocellulosic crop residue degradation (dbCAN3); secondary metabolite profiles (antiSMASH); and screening for virulence factors and antibiotic resistance genes (ABRicate, BTyper3).All analyzed strains possess 1,449-1,617 predicted PGPT-encoding genes (24.1-35.9% of total genes), which are strongly shaped by taxonomic relatedness, as confirmed by congruence testing against ANI-based genomic divergence. Paenibacillus amylolyticus 5mez and Priestia megaterium 7psych showed distinct functional profiles compared to Bacillus spp., while Bacillus subtilis sensu lato strains were most similar to each other. Genomic predictions suggest involvement in nutrient acquisition (N, P, K, Fe) and stress mitigation. Secondary metabolite analysis revealed high biosynthetic potential, with non-Bacillus species harbouring a large proportion of unknown gene clusters, indicating underexplored metabolite diversity. CAZyme profiling identified P. amylolyticus 5mez as the most enzyme-rich strain, while B. cereus s.s. zielonkawy showed ligninolytic potential despite low overall CAZyme abundance. The safety assessment identified B. cereus s.s. zielonkawy as toxigenic and unsuitable for use. Of the remaining strains, P. amylolyticus 5mez and Pr. megaterium 7psych demonstrated the most favourable safety profiles, exhibiting no detectable virulence factors or antibiotic resistance genes, justifying their priority use in agricultural biopreparations, pending phenotypic validation. Given the high-dimensional, low-sample-size nature of multi-trait datasets in applied microbial genomics, tailored statistical approaches, including noise-reduction-validated PCA and distance-based congruence testing, were applied; their rationale and limitations are discussed.},
}

@article {pmid42343426,
year = {2026},
author = {Mehta, V and Galletti, C and Mathur, A and Suresh, N and Nandi, D and Flores-Fraile, J},
title = {Efficacy of probiotics in the management of oral candidiasis: an umbrella review of systematic reviews and meta-analyses.},
journal = {Systematic reviews},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13643-026-03249-z},
pmid = {42343426},
issn = {2046-4053},
abstract = {BACKGROUND: Oral candidiasis (OC) is among the most prevalent oral infections, frequently associated with immunosuppression, denture wearing, advanced age, and excessive antibiotic use. Given the growing concerns about antifungal resistance, probiotics are being explored as potential adjuncts in the management of oral Candida overgrowth. Existing literature provides fragmented evidence; thus, an umbrella review was planned to synthesize the available evidence on the effectiveness of probiotic interventions in reducing oral Candida spp.

METHODS: A comprehensive, independent search was conducted in four databases (PubMed, Embase, Scopus, and Web of Science) covering literature from inception to 31st January 2026. Systematic reviews (SRs) with or without meta-analyses (MAs) assessing the effectiveness of probiotics in reducing oral Candida spp. count in terms of colony-forming units/mL (CFU/mL) were included. The quality assessment of the evidence was evaluated using A Measurement Tool to Assess Systematic Reviews 2 (AMSTAR 2) tool and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.

RESULTS: Out of the 157 retrieved records, 7 studies were included in this umbrella review, out of which 5 were SRMAs, and 2 were SRs. The interventions involved multi-strain probiotics delivered through various formulations, routes, and treatment durations. Across the 5 SRMAs, probiotic interventions demonstrated beneficial effects by reducing Candida spp. with effect estimates ranging from odds ratio (OR) 0.06 to 0.71; however, wide interstudy heterogeneity (I[2] = 0-78%) restricts the reliability and comparability of these findings. These effect estimates were derived from individual meta-analyses with heterogeneous study populations. Methodological assessment of the 7 included studies using the AMSTAR 2 tool identified 3 studies (42.8%) as having low confidence, while 4 studies (57.1%) were rated critically low. Similarly, the overall quality of evidence, as assessed by GRADE, ranged from low for the adult population to very low for the pediatric population, across three key clinical outcomes: reduction in oral Candida spp., clinical cure rate of OC, and recurrence rate.

CONCLUSIONS: Probiotics may have a potential role in the prevention and treatment of OC; however, the current evidence base cannot be generalized due to significant heterogeneity and methodological constraints. Probiotics can supplement conventional antifungal treatment, but their standalone use is not recommended yet. High-quality, standardized randomized controlled trials and comprehensive SRMAs are necessary to better understand the effectiveness of probiotics in OC management.

PROSPERO CRD420251117392.},
}

@article {pmid42343457,
year = {2026},
author = {Wang, C and Li, S and Liu, Y and Zhao, X and Wang, F and You, Y and Zhao, X},
title = {Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02453-2},
pmid = {42343457},
issn = {2049-2618},
abstract = {BACKGROUND: Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition.

RESULTS: Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and​ a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in​ stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.

CONCLUSIONS: Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.},
}

@article {pmid42343653,
year = {2026},
author = {Bruggeman, A and Vandenbroucke, RE and Santens, P},
title = {Rationale and current status of fecal microbiota transplantations for Parkinson's disease.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X261455608},
doi = {10.1177/1877718X261455608},
pmid = {42343653},
issn = {1877-718X},
abstract = {Treating a neurological disorder through the gut may seem counterintuitive, yet multiple lines of evidence highlight the gut's important role in Parkinson's disease (PD). Prodromal gastrointestinal symptoms, the presence of aggregated α-synuclein in enteric neurons, increased intestinal inflammation, and impaired epithelial barrier integrity all point to gut-level involvement in PD pathophysiology. The gut microbiome, markedly altered in individuals with PD, may be a key driver of these changes. Fecal microbiota transplantation (FMT) is currently the most effective strategy for achieving broad and durable modifications of gut microbiota composition. However, FMT is a complex, multi-step procedure requiring stringent methodological control. Modulating gut bacteria has demonstrated therapeutic potential in preclinical models of PD, and recent clinical trials have begun evaluating FMT in patients, although outcomes have been variable. In this review, we examine potential explanations for these divergent results, with a particular focus on methodological differences across trials. We also outline future directions for optimizing FMT study design in PD and discuss how these insights may guide the development of next-generation microbiota-targeted therapies.},
}

@article {pmid42343855,
year = {2026},
author = {Baños-Quintana, AP and de Carvalho, ASP and Kaltenpoth, M},
title = {Symbiotic organs in insects: diversity, functional implications, and terminology.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1953},
pages = {},
doi = {10.1098/rstb.2024.0386},
pmid = {42343855},
issn = {1471-2970},
support = {//Deutsche Forschungsgemeinschaft/ ; //H2020 European Research Council/ ; //Max-Planck-Gesellschaft/ ; },
mesh = {Animals ; *Symbiosis ; *Insecta/microbiology/physiology/anatomy & histology ; Terminology as Topic ; *Fungi/physiology ; *Microbiota ; *Bacterial Physiological Phenomena ; },
abstract = {With over a million described species, insects represent the most successful group of animals on Earth. One of the drivers of insect diversity is their ability to engage in multifold beneficial symbioses with microorganisms, often involving specialized host organs to accommodate intra- or extracellular symbionts. The existence of such organs and their importance for sustaining and transmitting beneficial symbionts has been known for over a century, and specific terms have been established for categorizing organs harbouring intracellular bacteria (bacteriomes) or fungi (mycetomes), or cuticular crypts containing extracellular fungi (mycetangia). For others, however, general terms are lacking, e.g. organs containing extracellular bacteria associated with the cuticle or with the digestive tract. Furthermore, previously established terms have been misused in other contexts. Notably, 'bacteriome' has been increasingly employed in the microbiome field to refer to bacterial communities, instead of the term's original meaning of specialized organs housing intracellular bacterial symbionts. Here, we review and categorize the diversity of symbiotic organs in insects and propose a unified terminology. Our hope is that this common language will facilitate communication and thereby support the field of symbiosis research in unravelling commonalities and differences in the evolution, ecology, development, physiology and molecular basis across symbiotic interactions. This article is part of the theme issue 'Life in natural microcosms'.},
}

Animals
*Symbiosis
*Insecta/microbiology/physiology/anatomy & histology
Terminology as Topic
*Fungi/physiology
*Microbiota
*Bacterial Physiological Phenomena

@article {pmid42343916,
year = {2026},
author = {Liu, F and Xue, H and Jiang, Y and Chen, S and Zhang, Y and Yu, J and Qin, Y and Dong, X and Ou, Y and Qiu, R},
title = {Fluoride varnish application and the temporal evolution of supragingival microbiota in children with differential caries risk.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2682471},
pmid = {42343916},
issn = {2000-2297},
abstract = {BACKGROUND: Fluoride varnish is used to prevent early childhood caries, but its longitudinal ecological impact on the supragingival microbiome beyond enamel remineralization remains poorly understood, especially long-term.

OBJECTIVE: To characterize 24‑month supragingival plaque microbiome evolution in young children under biannual fluoride varnish, stratified by caries risk, and fluoride's ecological effect on microbial structure, interactions, and metabolism.

DESIGN: A total of 48 children were categorized into low‑, moderate‑, and high‑caries‑risk groups using the modified caries-risk assessment tool for preschool children (PSC-MCAT). All received fluoride varnish every six months. Supragingival plaque collected at five timepoints over 24 months. 16S rRNA sequencing assessed diversity, key taxa, co-occurrence networks, and PICRUSt2 metabolic pathways.

RESULTS: Baseline alpha‑ and beta‑diversity differed significantly across risk groups (p<0.05). After sustained fluoride, intergroup differences diminished. High‑risk group retained caries‑associated genera (e.g. Leptotrichia, Prevotella, Veillonella) with suppressed abundance. Fluoride increased network complexity and negative correlations in moderate‑/high‑risk groups. Glycolysis, TCA cycle, and starch/sucrose metabolism were inhibited in the high‑risk group post‑intervention.

CONCLUSIONS: Regular fluoride varnish reduces ecological disparities across risk groups, suppresses cariogenic taxa, and alters microbial interactions and carbohydrate metabolism, promoting homeostasis. High‑risk children may require more frequent interventions.},
}

@article {pmid42343917,
year = {2026},
author = {Krasaesin, A and Wongbanthit, Y and Chaiboonyarak, T and Wang, DH and Alinejad-Rokny, H and Samaranayake, L and Pongpanich, M and Porntaveetus, T},
title = {Shotgun metagenomic profiling reveals ecological and functional alterations of the oral microbiome in craniosynostosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2687219},
pmid = {42343917},
issn = {2000-2297},
abstract = {OBJECTIVE: To elucidate the microbial drivers underlying of craniosynostosis (CS) , which involves premature suture fusion and secondary dentofacial malformations likely to increase dental disease burden.

METHODS: Shotgun metagenomic sequencing of supragingival plaque from 44 participants (22 CS patients and 22 matched healthy controls, aged 6-17 years) were performed, following by bioinformatics evaluation.

RESULTS: Beta diversity demonstrated significant differences between groups (p < 0.01), whereas alpha diversity trended lower in the CS cohort. Taxonomic profiling revealed a dysbiotic signature in CS with high caries burden, defined by the enrichment of saccharolytic and anaerobic taxa (Scardovia, Actinomyces sp. oral taxon 448, Selenomonas sp. F0473, and Treponema lecithinolyticum)) alongside reduced health-associated genera like Haemophilus and Neisseria. Functional pathway analysis indicated metabolic remodeling, with upregulated fructan biosynthesis and starch degradation III pathways, consistent with caries-active biofilms.

CONCLUSION: These findings demonstrate that orofacial anomalies in CS favor the assembly of an acidogenic, virulent plaque biofilm. The first shotgun metagenomic profile of the oral microbiome in CS establishes a foundation for future investigations. Furthermore, clinical management of CS should extend beyond structural correction to incorporate microbiological monitoring and preventive strategies, reducing the elevated risk of dental disease in this vulnerable population.},
}

@article {pmid42343918,
year = {2026},
author = {J Rus, M and R Nieto, M and Oh, HJ and Yoo, H and Areal-Quecuty, V and Duarte Faria, F and Lendines-Cordero, D and Simon-Soro, A},
title = {Salivary estrone and estradiol are associated with oral microbiome profiles in aging women.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2690784},
pmid = {42343918},
issn = {2000-2297},
abstract = {OBJECTIVES: To explore whether salivary estrogens (estrone and estradiol) are associated with oral microbiome composition in aging women, and to assess the oral cavity as a potential sentinel of systemic hormonal changes during midlife.

MATERIALS AND METHODS: Cross-sectional study including 30 women aged 40-65 years. Saliva and microbial specimens were collected from four oral ecological niches (buccal mucosa, tongue dorsum, supragingival plaque, subgingival plaque). Microbiome composition and diversity were assessed by 16S rRNA gene sequencing, ecological indices, and co-occurrence network analysis. Salivary estrone and estradiol were quantified, and associations with oral health and microbial profiles were evaluated.

RESULTS: Estrone levels declined significantly with age and were associated with hyposalivation and lower oral health scores. Estrone was linked to increased microbial diversity on the tongue dorsum and enrichment of taxa such as Porphyromonas. In contrast, estradiol was positively associated with commensal genera (Streptococcus, Lactobacillus) and negatively with periodontal-associated taxa (Fusobacterium, Prevotella). Co-occurrence networks revealed niche-specific microbial shifts associated with estrogen levels.

CONCLUSIONS: Salivary estrogens, particularly estrone, shape oral microbial communities in aging women. The oral cavity may act as a window into systemic hormonal changes, supporting its role as a non-invasive sentinel of women's health during midlife.},
}

@article {pmid42343919,
year = {2026},
author = {Nicot, C},
title = {From Cold to Constrained: Why MSS Colorectal Cancer Resists Immunotherapy.},
journal = {Cancer biome and targeted therapy},
volume = {1},
number = {2},
pages = {320-327},
pmid = {42343919},
issn = {3070-9989},
}

@article {pmid42343926,
year = {2026},
author = {Kim, H and Zhou, M and Lin, L and Zhu, W and McAllister, TA and Guan, LL},
title = {PacBio full-length 16S rRNA gene sequencing processed with Emu and GTDB provides the highest taxonomic resolution for rumen bacteriome profiling.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag148},
pmid = {42343926},
issn = {2730-6151},
abstract = {Although full-length 16S rRNA gene sequencing has substantially improved taxonomic resolution compared to short-read approaches, a high proportion of unclassified taxa are reported in rumen microbiome studies. This limitation is largely driven by platform-specific analytical workflows and the insufficient representation of rumen-associated lineages in commonly used reference databases. Here, we identified the optimal combination of sequencing platform, analytical workflow, and reference database to improve rumen bacteriome classification. We analyzed short-read and full-length 16S rRNA gene sequences from rumen samples collected from two beef cattle populations. Short-read sequences were generated using Illumina NextSeq2000 and processed with QIIME2. Full-length sequences were generated using PacBio Revio (PacBio-16S) and Nanopore MinION (ONT-16S); PacBio-16S data were analyzed using QIIME2 and Emu, while Nanopore data were analyzed using EPI2ME and Emu. Five reference databases were evaluated across all analytical approaches: SILVA 138.2, SILVA 138.2 with Hungate1000 collection, NCBI, Greengenes2, and GTDB. The comparisons showed that PacBio-16S (Emu) achieved the highest proportion of classified reads among all platform-specific workflows, while GTDB consistently produced the highest number of non-redundant classified taxa. Prevotella, a dominant rumen genus, was abundant in Illumina and PacBio-16S datasets but was underrepresented in ONT-16S workflows. Species-level analyses further demonstrated that PacBio-16S (Emu) reliably provided more consistent and high-resolution identification of Prevotella species under GTDB across two beef populations. Overall, our results demonstrate that sequencing platform, workflow choice, and database selection strongly influence rumen bacteriome profiles. We recommend PacBio-16S (Emu) under GTDB as the most reliable workflow for achieving high-resolution taxonomic classification of rumen bacteriome.},
}

@article {pmid42343927,
year = {2026},
author = {González-Ramírez, IS and Song, MJ and Mehlferber, EC and Mishler, BD},
title = {Off-target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica.},
journal = {Applications in plant sciences},
volume = {14},
number = {3},
pages = {e70064},
pmid = {42343927},
issn = {2168-0450},
abstract = {PREMISE: The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable the use of short reads to study bacterial communities associated with organisms.

METHODS: We utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.

RESULTS: The bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well-known plant symbionts. While diversity metrics of bacteria composition were similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality.

DISCUSSION: Our results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. The novel off-target metagenomics approach can be applied to any population-level resequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using repurposed data from landscape genomics.},
}

@article {pmid42343970,
year = {2026},
author = {Das, R and Kumar, R and Tamang, B},
title = {Microbial community structure, functional potential, probiotic signatures, and MAG reconstruction of fermented bamboo shoots from Northeast India.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag032},
pmid = {42343970},
issn = {2633-6685},
abstract = {Fermented bamboo shoot (FBS) products are widely consumed traditional foods across the Northeast region (NER) of India, yet their microbiome structure, functional capacity, biosynthetic potential, and safety attributes remain insufficiently explored. Here, comparative shotgun metagenomics of ten traditional FBS products from six NER states was used to address these gaps integrating previously generated metagenomic data from Tripura with newly generated datasets from Manipur, Meghalaya, Arunachal Pradesh, Nagaland, and Sikkim thereby bringing the total number of samples to 24. Taxonomic profiling revealed a predominance of lactic acid bacteria, primarily members of Lactiplantibacillus, Levilactobacillus, Lactobacillus, Lactococcus, and Pediococcus, with pronounced product- and region-specific community signatures. Functional annotation demonstrated predominance of genes involved in carbohydrate metabolism, stress response, quorum sensing, ABC transporters, vitamin biosynthesis, and energy metabolism, supporting strong probiotic-associated functional potential across FBS types. AntiSMASH analysis enabled the identification of diverse biosynthetic gene clusters (BGCs) responsible for the production of various secondary metabolites, including bacteriocins, non-ribosomal peptides, terpenes, and siderophores, with higher biosynthetic diversity observed in Mesu (Sikkim), Tuaithar (Manipur), Lung-Seij (Meghalaya), and Bastenga (Nagaland). Antimicrobial resistance (AMR) profiling revealed a generally low resistome burden, dominated by intrinsic resistance determinants, with FBS Sikkim and Tripura exhibiting the lowest AMR prevalence among all products. High-quality metagenome-assembled genomes affiliated with Lactiplantibacillus plantarum, Lactobacillus acetotolerans, and Pediococcus pentosaceus exhibited conserved probiotic traits, carbohydrate-active enzymes, biosynthetic pathways, and a limited presence of mobile genetic elements. Overall, the microbiome-based comparative analysis provides a framework for understanding the microbial community structure and functional potential across the NER, demonstrating broad probiotic potential and biosynthetic richness, with mesu samples from Sikkim showed a comparatively consistent distribution of functional pathways, biosynthetic gene clusters, and AMR-related features relative to the other FBS samples analysed.},
}

@article {pmid42343982,
year = {2026},
author = {van Mourik, DJM and Balvers, M and Jansen, VLBI and de Jonge, PA and Coppens, M and Nieuwdorp, M and Middeldorp, S and Eikenboom, JCJ and Voorberg, J and van Mens, TE},
title = {Cross-Reactivity of Antiphospholipid Antibodies with Gut Commensal Proteins in Antiphospholipid Syndrome.},
journal = {TH open : companion journal to thrombosis and haemostasis},
volume = {10},
number = {},
pages = {a28685248},
pmid = {42343982},
issn = {2512-9465},
abstract = {BACKGROUND: Antiphospholipid syndrome (APS) is an autoimmune disease characterized by the persistent presence of antiphospholipid antibodies (aPL), mainly targeted against β2 glycoprotein 1 (β2GP1). The autoimmune response to β2GP1 is aimed at several B-cell and T-cell epitopes. Molecular mimicry of these epitopes by gut commensal proteins, so-called mimotopes, causing cross-immunization, might contribute to the formation of aPL.

OBJECTIVE: To study the potential role of gut microbiome cross-immunization in APS by examining cross-reactivity of aPL with gut commensal mimotope-containing proteins.

METHODS: Fecal microbial metagenome of APS patients was determined using shotgun sequencing. An in-house developed in silico pipeline was used to identify gut commensal proteins that show sequence homology with known β2GP1 B and T cell epitopes in the metagenomic data. An enzyme-linked immunosorbent assay was used to test the identified microbial proteins for IgG cross-reactivity, with plasma of 21 APS patients and 17 control participants.

RESULTS: The in silico pipeline resulted in the identification of six gut commensals with a B cell and T cell β2GP1 epitope homologue. Of these, YjjG family noncanonical pyrimidine nucleotidase, one of the candidate-β2GP1 B cell mimicking proteins, showed significantly increased IgG reactivity in APS patients compared to control participants, as well as higher binding of a specific anti-β2GP1 monoclonal antibody than a negative control.

CONCLUSION: Our study shows reactivity of IgG antibodies to YjjG family noncanonical pyrimidine nucleotidase from Roseburia amylophila in APS patients. Insights into the origins of antibody formation may yield new therapeutic targets for improvement of APS treatment.},
}

@article {pmid42344006,
year = {2026},
author = {Tepson, JA and Agyirifo, DS},
title = {Microbial Ecology at the Nexus of Food Safety and Biotechnology With Ecological Mechanisms, Risks, and Emerging Innovations.},
journal = {International journal of food science},
volume = {2026},
number = {},
pages = {6618960},
pmid = {42344006},
issn = {2314-5765},
abstract = {Food systems are complex microbial ecosystems in which microorganisms play dual and often contrasting roles as agents of foodborne contamination and as essential drivers of food production and biotechnological innovation. Microbial ecology provides an integrative framework for understanding how microbial interactions, environmental conditions, and human interventions shape food safety outcomes and technological processes. This narrative integrative review is aimed at synthesizing current literature on microbial ecology at the nexus of food safety and food biotechnology and at identifying key research gaps and future directions. In this study, peer-reviewed journal articles addressing microbial interactions, contamination pathways, and ecological mechanisms relevant to food safety and biotechnology published between 2015 and 2025 were retrieved from major scientific databases and were synthesized using a narrative integrative approach. The review highlights ecological factors including microbial competition, stress adaptation, and biofilm formation across pre- and postharvest environments. At the same time, these same ecological principles are harnessed in food biotechnology to drive controlled fermentations, enhance shelf life through biopreservation, develop functional probiotics and enzymes, and engineer microbial systems via synthetic biology. Advances in high-throughput sequencing technologies, including whole genome sequencing, metagenomics, and multiomics integration, are identified as transformative tools for linking food-associated microbial community structure to functional outcomes. Despite significant progress, challenges remain in translating ecological insights into reliable industrial and regulatory practices due to microbial complexity, data integration limitations, and safety considerations. The review positions microbial ecology as a strategic framework for advancing food safety, biotechnological innovation, and sustainable food systems.},
}

@article {pmid42344316,
year = {2026},
author = {Rachmatika, R and Prijono, SN and Sarwono, KA and Pakpahan, S and Sari, AP and Maharani, S and Saputra, S and Fitri, A and Ridwan, R and Widodo, W and Nugraha, RTP and Handayani, W and Sjahfirdi, L},
title = {Comparative characterization of oral and cloacal microbiomes in captive adult and juvenile coconut lorikeets (Trichoglossus haematodus) using full-length 16S rRNA sequencing.},
journal = {Veterinary world},
volume = {19},
number = {5},
pages = {2117-2132},
pmid = {42344316},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The coconut lorikeet (Trichoglossus haematodus) is a nectarivorous parrot species of conservation concern in Indonesia, where captive breeding programs are increasingly implemented to reduce pressure on wild populations. Dietary modifications in captivity may influence host-associated microbiota, which play a critical role in health, nutrition, and adaptation. This study aimed to characterize and compare the oral and cloacal microbiomes of adult and juvenile T. haematodus using full-length 16S rRNA sequencing to elucidate age- and site-specific microbial patterns.

MATERIALS AND METHODS: Six clinically healthy captive T. haematodus (three adults and three juveniles) were maintained under standardized environmental and dietary conditions. Oral and cloacal swabs were collected, yielding twelve samples, which were subsequently pooled into four groups: adult oral (AO), adult cloaca (AC), juvenile oral (JO), and juvenile cloaca (JC). DNA was extracted and subjected to full-length 16S rRNA sequencing using Oxford Nanopore Technology. Bioinformatic analyses included taxonomic classification, alpha diversity (Observed operational taxonomic unit (OTU), abundance-based coverage estimator (ACE), Simpson, Fisher)), and beta diversity (Venn diagram and principal coordinates analysis).

RESULTS: A total of 1859 bacterial species were identified across all groups. Microbial composition differed markedly by age and anatomical site. Cloacal samples in both adults and juveniles were dominated by Rosenbergiella, with higher abundance in adults (~42%) than juveniles (~24%). Oral microbiota showed greater diversity, with Alcaligenes predominating in adults and Psittacicella in juveniles. Alpha diversity indices indicated higher richness in juvenile cloacal and AO samples, whereas adult cloacal samples exhibited lower diversity. Beta diversity analysis demonstrated clear separation among groups, indicating distinct microbial community structures influenced by both age and sampling site. Core microbiota shared across groups were limited, with substantial unique operational taxonomic units in each category.

CONCLUSION: This study provides the first comprehensive characterization of oral and cloacal microbiomes in captive T. haematodus. Microbial diversity and composition are strongly influenced by age and anatomical location, with cloacal microbiota showing greater stability and oral microbiota reflecting dietary and developmental differences. The dominance of nectar-associated bacteria such as Rosenbergiella highlights the ecological linkage between host diet and microbiome. These findings offer valuable insights for optimizing captive nutrition, improving health monitoring, and supporting conservation strategies for nectarivorous parrots.},
}

@article {pmid42344332,
year = {2026},
author = {Karalyan, Z and Sedrakyan, A and Arakelova, K and Zakharyan, M and Hakobyan, S and Hakobyan, S and Avetisyan, A and Bayramyan, N and Arzumanyan, H and Gevorgyan, V and Vardanyan, T and Baghdasaryan, B and Karalyan, A and Hakobyan, L and Poghosyan, A and Abroyan, L and Karalova, E and Voskanyan, H and Semerjyan, Z and Arakelova, E and Avagyan, H},
title = {African swine fever virus alters soil microbial biomass and biodiversity: Evidence from experimental soil systems.},
journal = {Veterinary world},
volume = {19},
number = {5},
pages = {1984-1998},
pmid = {42344332},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: African swine fever virus (ASFV) has expanded beyond its traditional ecological niches, raising concerns not only for animal health but also for environmental sustainability. While extensive research has focused on its persistence and transmission, little is known about its ecological effects in soil systems. This study aimed to investigate the influence of ASFV on soil microbial biomass, biodiversity, and associated ecological parameters.

MATERIALS AND METHODS: Eighteen anthrosol soil samples collected from agricultural regions of Armenia were subjected to controlled experimental conditions. Soil samples were treated with active ASFV (aASFV), inactivated ASFV (iASFV), and mock controls. Physicochemical properties, including pH and moisture content, were assessed. Microbial biomass was evaluated through soil protein quantification and viral nucleic acid (DNA and RNA) measurements. Microbial diversity was analyzed by enumerating culturable bacteria and fungi using selective media. Dissolved oxygen levels were measured to assess microbial activity. Quantitative real-time polymerase chain reaction was employed to evaluate viral genome dynamics and transcriptional activity. Statistical analyses were performed to determine correlations among measured variables.

RESULTS: ASFV exposure resulted in a general reduction in total microbial biomass, as evidenced by decreased soil protein content and viral nucleic acid concentrations in most samples. In contrast, microbial diversity, particularly among bacterial and fungal populations, showed an increasing trend, suggesting a restructuring of the microbial community. Active ASFV induced greater changes compared to the inactivated virus. A significant positive correlation was observed between protein content and microbial indicators, while a negative correlation was noted between oxygen levels and nucleic acid content. Viral transcriptional activity was detected in selected samples, with no evidence of complete viral replication. Limited detection of giant viruses suggested potential but inconclusive ecological interactions.

CONCLUSION: ASFV alters soil ecosystems through complex, multidirectional effects, characterized by reduced biomass and increased microbial diversity. These findings indicate that ASFV may indirectly influence soil ecological processes, even in the absence of active replication. The study highlights the importance of incorporating environmental perspectives into ASFV research and provides a foundation for future investigations on virus-soil-microbiome interactions.},
}

@article {pmid42344333,
year = {2026},
author = {Montayeva, N and Nurgaliyev, B and Kereyev, A and Nagimova, G and Kushmukhanov, Z},
title = {One Health perspective on mycotoxins in poultry production: Ecology, toxicological effects, occupational and environmental exposure, food safety risks, and mitigation strategies (2020-2025).},
journal = {Veterinary world},
volume = {19},
number = {5},
pages = {2172-2207},
pmid = {42344333},
issn = {0972-8988},
abstract = {Mycotoxins produced by toxigenic fungi remain a major challenge in poultry production and global food safety. Contamination of poultry feed with aflatoxins, ochratoxin A, fumonisins, deoxynivalenol, T-2 toxin, zearalenone, and other emerging mycotoxins is frequently reported worldwide, particularly under intensive production systems and changing climatic conditions. This review summarizes current evidence published between 2020 and 2025 on the occurrence, ecological drivers, toxicological effects, environmental and occupational exposure, food safety risks, analytical detection methods, and mitigation strategies of mycotoxins in poultry production within a One Health framework. Recent studies indicate that multi-mycotoxin contamination is common in poultry feeds, and emerging and masked mycotoxins may remain undetected by routine analytical approaches, thereby increasing the risk of underestimating exposure. Mycotoxins adversely affect poultry health through hepatotoxicity, nephrotoxicity, oxidative stress, immunosuppression, intestinal barrier disruption, microbiome dysbiosis, impaired reproductive performance, and reduced productivity. In addition, residues of several mycotoxins have been detected in meat and eggs, raising concerns regarding consumer safety. Airborne fungal spores and contaminated dust in poultry houses also represent important occupational hazards for poultry workers. Advances in analytical technologies, particularly Liquid Chromatography-Tandem Mass Spectrometry, biosensors, molecular diagnostics, and multiplex detection systems, have improved the sensitivity and reliability of mycotoxin monitoring. Various mitigation approaches, including feed hygiene management, adsorbents, probiotics, biological detoxification, and enzymatic degradation, have shown potential to reduce contamination and minimize toxic effects. However, the complete elimination of mycotoxins remains difficult due to the complexity of fungal ecology and the widespread occurrence of co-contamination. Overall, this review highlights the importance of integrated surveillance, improved feed management, advanced detection systems, and coordinated mitigation strategies within a One Health approach to reduce the impact of mycotoxins on poultry health, environmental safety, occupational exposure, and food security.},
}

@article {pmid42344551,
year = {2026},
author = {Martínez-Hernández, JI and Villegas-Mercado, CE and Santana-Delgado, SA and Orozco-Molina, GG and Arreguín-Cano, JA and Ordóñez-Torres, K and Luján-Aguilar, MA and Duarte-Chávez, LI and González-Acosta, A and Casavantes-Lazo, C and Bujanda-Ríos, CI and Bermúdez, M},
title = {Clear aligner therapy beyond esthetics: oral health, polymer materials, and the environmental cost of digital orthodontics.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1810940},
pmid = {42344551},
issn = {2673-4915},
abstract = {Clear aligner therapy (CAT) has become a popular orthodontic option, driven by advances in digital workflows, increasing aesthetic demands, and perceived benefits in comfort and oral hygiene. Although its clinical effectiveness has been well documented, a thorough review of its biological and environmental effects remains incomplete. This narrative review consolidates current evidence on CAT, exploring their history, material makeup, impact on oral health, and emerging environmental concerns. Recent clinical and microbiological research indicates that CAT may improve plaque control and periodontal health compared with fixed appliances; however, these benefits are heavily influenced by patient behavior, baseline caries risk, treatment duration, and adherence to hygiene and dietary guidelines. Evidence shows that aligner materials can support bacterial and fungal biofilm growth and, under certain conditions, may lead to enamel demineralization or erosion, emphasizing the need for personalized risk assessments and proper aligner maintenance. From a materials standpoint, modern aligners are primarily made from thermoplastic and polyurethane polymers, designed to exert controlled orthodontic forces and ensure durability. While beneficial clinically, these materials are poorly degradable and have limited recyclability. Life cycle analyses reveal that the environmental impact of CAT extends beyond disposal to include polymer production, energy-intensive manufacturing, packaging, and distribution. Additionally, emerging research suggests that aligners may release microplastics during use, adding to concerns about plastic pollution beyond solid waste. Given the rapid growth of the global clear aligner market, even small amounts of material per patient can result in a significant environmental impact. Overall, the evidence indicates that clear aligner therapy involves a complex interplay among biomechanics, patient care, materials science, and environmental sustainability. An integrated, life-cycle-based strategy is crucial to guiding clinicians, researchers, and manufacturers toward treatments that are both effective and environmentally responsible.},
}

@article {pmid42344668,
year = {2026},
author = {Huang, F and Zhang, Z and Zhao, Y and Ye, S and Gan, M and Li, X and Zhang, Y and Chen, L and Zhang, Y and Chen, L and Wang, T and Huang, J and Zhang, X},
title = {Altitude-Associated Divergence of the Gut Microbiome in Endangered Forest Musk Deer: Evidence From Integrated Metagenomics, Metabolomics, and Culturomics.},
journal = {Evolutionary applications},
volume = {19},
number = {6},
pages = {e70285},
pmid = {42344668},
issn = {1752-4571},
abstract = {High-altitude environments expose mammals and their gut symbionts to multifaceted stressors-hypoxia, cold, and intense UV radiation. Whether gut microbial communities undergo compositional restructuring in response to these stressors, and whether such restructuring carries translational value for captive conservation, remain unresolved questions. Here, we integrated deep shotgun metagenomics (≥ 15 Gb per sample), untargeted fecal metabolomics, and culturomics in 75 captive forest musk deer (Moschus berezovskii Flerov, 1929) housed at high altitude (~3900 m) and low altitude (~1450 m) facilities under uniform husbandry. Neutral community modeling showed a greater contribution of deterministic processes at high altitude (only 34.3% of species conformed to neutral expectations vs. 89.3% at low altitude), consistent with stronger environmental filtering. At high altitude, we observed enrichment of a functionally coherent guild of short-chain fatty acid (SCFA)-producing bacteria-centered on Flavonifractor plautii, Intestinimonas butyriciproducens, and Enterococcus faecium-that formed antagonistic co-occurrence networks with opportunistic pathogens including Clostridioides difficile and Campylobacter species, mirroring SCFA enrichment in phylogenetically diverse high-altitude mammals. Fecal metabolomics revealed coordinated shifts in urolithin biosynthesis, branch-specific regulation of the tryptophan-kynurenine pathway, and energy metabolism remodeling, all robustly predicted by microbiome composition via neural network modeling. Culturomics yielded seven safety-validated isolates with confirmed gastrointestinal stress tolerance and broad-spectrum pathogen-antagonistic activity in vitro. These findings provide an actionable framework for altitude-informed facility siting, fecal microbiota transplantation (FMT) donor selection, host-derived probiotic development, and non-invasive health surveillance in captive endangered species, and are broadly transferable to other taxa facing microbiome-associated disease pressure in captivity.},
}

@article {pmid42344726,
year = {2026},
author = {Khanna, V and Kumar, S and Kumar, S and Verma, S and Grigoriadis, A and Kumar, A},
title = {The gut microbiome in oral health and disease: evidence toward bidirectional oral-gut axis communication.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1817689},
pmid = {42344726},
issn = {1664-302X},
abstract = {The oral-gut microbiome axis has largely been seen as a unidirectional framework, in which dysbiotic oral flora is considered to contribute to gastrointestinal and systemic disease. However, recent evidence now challenges this view, indicating that gut microbial imbalance can act upstream to modulate oral immune homeostasis and disease susceptibility. Therefore, in the current perspective paper, we present a structured narrative review that synthesizes recent evidence from human microbiome, immunological, and genetic studies to propose a hypothetical mechanistic model in which gut dysbiosis may contribute to oral pathology. The literature discussed was identified through a targeted keyword-based search of major databases and complemented by manual screening of reference lists to capture relevant studies. Analyzing the evidence from human case-control and longitudinal cohort studies, as well as Mendelian randomization analysis, we identify convergent pathways linking gut dysbiosis to oral disease. These include systemic immune priming in autoimmune disorders with oral manifestations, depletion of gut-derived metabolites, such as short-chain fatty acids, that regulate epithelial barrier function and inflammation, and dysbiosis-associated barrier disruption that facilitates the systemic dissemination of microbial products and inflammatory mediators. Through these mechanisms, gut microbial imbalance contributes to chronic inflammatory conditions, altering host response and susceptibility to dental and mucosal diseases. In contrast, studies in healthy individuals show minimal oral-gut microbial overlap, supporting a model in which physiological compartmentalization is maintained in health and disrupted primarily under dysbiotic conditions. This synthesis reframes oral disease as host-microbiome dysregulation, highlighting gut microbiota as a driver of oral immune pathology.},
}

@article {pmid42344729,
year = {2026},
author = {Qian, X and Wu, Y and Wang, W and Shao, H and Xu, Z},
title = {The selection of matching donors for patients in fecal microbiota transplantation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1859411},
pmid = {42344729},
issn = {1664-302X},
abstract = {Fecal microbiota transplantation (FMT) is an emerging therapeutic strategy with potential applications in the treatment of various diseases, particularly those associated with gut microbiome dysbiosis. However, clinical trials have demonstrated considerable variability in FMT efficacy-even among patients with the same disease. The heterogeneity of gut microbiota from donors is considered a key factor influencing patient outcomes. Consequently, the development of donor-recipient matching models has emerged as an advanced approach to enhance the effectiveness of FMT. As a practical clinical intervention, the therapeutic impact of FMT on specific diseases requires further investigation. This article reviews the development of donors and the matching patterns between donors and recipients, and summarizes the key factors influencing the transfer of the microbiota. It provides new insights for exploring novel and effective donor-recipient matching patterns.},
}

@article {pmid42344732,
year = {2026},
author = {Zapata-Contreras, D and Aldridge, J and González-Puelma, J and Navarrete, M and Urrea, C and Orellana, F and Iriarte, MJ and Delgado, C and Puente, M and Leiva, L and Godoy, L and Altamirano, A and Karelovic, S and Espinosa-Parrilla, Y},
title = {Microbial dynamics in gastric cancer: insights from full-length 16S rRNA nanopore sequencing in the MAGIC cohort.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1841026},
pmid = {42344732},
issn = {1664-302X},
abstract = {Gastric dysbiosis, characterized by shifts in the microbial composition, has been increasingly associated with the development of gastric cancer, the fifth leading cause of cancer-related deaths worldwide and the second in Chile, yet its characterization through disease stages remains limited and its study in Latin American populations almost non-existent. While Helicobacter pylori is a well-established risk factor, recent evidence supports the involvement of non-Helicobacter pylori bacteria associated with disease progression, emphasizing the need to characterize the gastric microbiome in diverse populations and through cancer stages. In this study, 162 endoscopic biopsy tissues and gastrectomy tissues from 83 Chilean individuals enrolled in the Magellanic gastric cohort MAGIC and the BTUCH cohort were analyzed using high throughput full-length 16S rRNA sequencing based on Nanopore technology. Diversity analysis demonstrated significant differences among disease progression and histological subtypes. Spearman correlation identified 34 genera significantly associated with gastric cancer progression, including enrichment of Lactobacillus and Limosilactobacillus. Helicobacter stratification analysis revealed lower diversity and distinct community structure at early stages of disease. Declining Helicobacter abundance was associated with shifts toward degradation and biosynthetic/energy metabolism pathways suggesting potential metabolic adaptation in carcinogenesis. These findings reveal stage-specific restructuring of the gastric microbiota along disease progression and identify non-Helicobacter taxa as part of microbial signatures associated with different stages of gastric carcinogenesis.},
}

@article {pmid42344797,
year = {2026},
author = {Zhang, M and Lu, Y and Yuan, X},
title = {The tumor microenvironment: a dynamic ecosystem and therapeutic nexus in modern oncology.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1836055},
pmid = {42344797},
issn = {1663-9812},
abstract = {The tumor microenvironment (TME) has emerged as a central orchestrator of carcinogenesis, therapeutic resistance, and immune evasion, fundamentally reshaping the understanding of cancer as an ecosystem disease rather than a cell-autonomous genetic disorder. This review synthesizes contemporary advances in deconstructing the cellular and acellular architecture of the TME, encompassing cancer-associated fibroblasts, tumor-associated macrophages, aberrant vasculature, and a dynamically remodeled extracellular matrix. The molecular underpinnings of TME-mediated pathogenesis are critically evaluated, including metabolic reprogramming, epigenetic dysregulation, and systemic microbiome crosstalk, which collectively enforce immunosuppression and drive adaptive resistance. Building on this mechanistic framework, a new generation of therapeutic strategies designed to reprogram this malignant niche is highlighted: precision nanotechnologies for targeted and stimuli-responsive delivery; next-generation immunotherapies such as logic-gated CAR-T cells, bispecific engagers, and oncolytic viruses; metabolic and epigenetic modulators; stromal and vascular normalization approaches; and microbiome-based interventions, for instance fecal microbiota transplantation and defined bacterial consortia. Transformative tools, including patient-derived organoids, tumor-on-a-chip systems, 3D bioprinting, and artificial intelligence-powered multi-omics, are now enabling predictive modeling and personalized therapeutic forecasting. Despite persistent challenges posed by intratumoral heterogeneity, cellular plasticity, and the complexity of combination trial design, the convergence of these multidisciplinary approaches provides an unprecedented toolkit to durably reprogram the TME. Mastering this dynamic ecosystem is paramount to overcoming therapeutic roadblocks, and the strategic integration of these advances heralds a definitive paradigm shift toward TME-centric, adaptive, and personalized cancer therapy.},
}

@article {pmid42345017,
year = {2026},
author = {Bautista, J and Calderón-Cevallos, S and Salvador-Baquero, AM and Naranjo-Castillo, X and López-Cortés, A},
title = {Programming the tumor microenvironment through microbiome-driven mechanisms.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1857151},
pmid = {42345017},
issn = {2235-2988},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Microbiota/immunology ; *Neoplasms/immunology/microbiology/pathology ; Animals ; Signal Transduction ; Toll-Like Receptors/metabolism ; Multiomics ; Fatty Acids, Volatile/metabolism ; Lipopolysaccharides/metabolism ; },
abstract = {The tumor microenvironment (TME) comprises interacting immune, stromal, and metabolic compartments that determine tumor behavior and treatment response. Microbial communities modulate host signaling within the TME through metabolite-driven and receptor-mediated mechanisms. Lipopolysaccharides (LPS), short-chain fatty acids (SCFAs), bile acids, and amino acid-derived metabolites engage host receptors, including Toll-like receptors, G protein-coupled receptors, and aryl hydrocarbon receptor pathways, to regulate immune cell differentiation, antigen presentation, and metabolic adaptation. These microbiome-derived signals promote context-dependent immune suppression or immune activation according to metabolite concentration, receptor engagement, and immune cell composition, thereby influencing tumor progression and immune evasion. Host-driven inflammation and metabolic constraints reshape microbial composition and function within tumor-associated niches. Microbiome-associated mechanisms contribute to tumor initiation, progression, and therapeutic response through modulation of immune checkpoint activity and drug metabolism. Major limitations include reliance on associative human data, methodological variability across sequencing approaches, contamination in low-biomass samples, and incomplete integration of multi-omics datasets. Clinical translation requires mechanistic validation, longitudinal study designs, and standardized analytical frameworks to define reproducible microbiome-associated signatures.},
}

Humans
*Tumor Microenvironment/immunology
*Microbiota/immunology
*Neoplasms/immunology/microbiology/pathology
Animals
Signal Transduction
Toll-Like Receptors/metabolism
Multiomics
Fatty Acids, Volatile/metabolism
Lipopolysaccharides/metabolism

@article {pmid42345020,
year = {2026},
author = {Ismaiel, A and Almonajjed, MB and Wardeh, M and Abdelghafar, A and Popa, SL and Sabo, C and Dumitrascu, DL},
title = {From dysbiosis to malignancy: decoding gut-driven pathways to clinical management in hepatocellular carcinoma.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1852380},
pmid = {42345020},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/complications ; *Liver Neoplasms/therapy/etiology/pathology/microbiology ; *Carcinoma, Hepatocellular/therapy/etiology/pathology/microbiology ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {Hepatocellular carcinoma (HCC) is undergoing a profound global epidemiological shift, transitioning from viral-driven etiologies to metabolic dysfunction-associated steatotic liver disease (MASLD). This transition challenges traditional cirrhosis-centric surveillance, as a significant proportion of MASLD-HCC develops in non-cirrhotic livers. Parallel to these metabolic shifts, the gut-liver axis has emerged as a central orchestrator of hepatocarcinogenesis. This review decodes the complex gut-driven pathways fueling HCC, highlighting the oncogenic consequences of structural and functional dysbiosis. Dietary patterns and etiology-specific microbial shifts compromise the intestinal and gut-vascular barriers, precipitating a structural "leaky gut". This disruption facilitates the robust translocation of pathogen-associated molecular patterns (PAMPs), particularly lipopolysaccharide (LPS), and toxic microbial metabolites like secondary bile acids, specifically deoxycholic acid, into the portal circulation. Consequently, hepatic innate immunity is chronically activated via Toll-like receptor 4 (TLR4) signaling on Kupffer and hepatic stellate cells, fostering metainflammation, cellular senescence, genomic instability, and a highly immunosuppressive, pro-tumorigenic microenvironment. Furthermore, the depletion of keystone commensals diminishes the protective reservoir of short-chain fatty acids (SCFAs), exacerbating oncogene activation. Translating these mechanistic insights into the clinic, we explore the utility of distinct microbial signatures and metabolomic profiles as non-invasive diagnostic biomarkers. Such tools are urgently needed to bridge the early-detection gap in the expanding MASLD demographic. Finally, we discuss the pivotal role of the microbiome in modulating responses to immune checkpoint inhibitors (ICIs), notably through immune-stimulating taxa like Akkermansia muciniphila, and outline emerging gut-targeted therapies, including next-generation probiotics and fecal microbiota transplantation, aimed at restoring host-microbiome homeostasis to prevent and manage HCC. By decoding these gut-driven pathways, this review provides a comprehensive framework for integrating the microbiome-onco axis into precision oncology, offering novel avenues to combat the rising global burden of hepatocellular carcinoma.},
}

Humans
*Dysbiosis/complications
*Liver Neoplasms/therapy/etiology/pathology/microbiology
*Carcinoma, Hepatocellular/therapy/etiology/pathology/microbiology
*Gastrointestinal Microbiome
Animals

@article {pmid42345222,
year = {2026},
author = {Yuan, J and Liu, M and He, Z and Li, H and Ma, L and Zhang, Q and Yin, Z and Guo, P and Yin, H},
title = {Fictibacillus tiangongensis sp. nov., isolated from the China Space Station.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {6},
pages = {},
doi = {10.1099/ijsem.0.007216},
pmid = {42345222},
issn = {1466-5034},
mesh = {China ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/chemistry ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Base Composition ; *Bacillaceae/classification/isolation & purification/genetics ; Nucleic Acid Hybridization ; *Spacecraft ; Peptidoglycan/chemistry ; Vitamin K 2/analogs & derivatives/chemistry/analysis ; Extreme Environments ; },
abstract = {The identification of novel microbial species in extreme environments significantly enhances our comprehension of Earth's biodiversity and concurrently offers invaluable resources and critical insights for scientific research, biotechnological innovation and environmental conservation. As part of the China Space Station Habitation Area Microbiome Program (CHAMP), a Gram-positive, facultatively anaerobic, motile, spore-forming, rod-shaped strain, designated JL2B1089[T], was isolated from the surface of hardware within the genus Fictibacillus. The strain grows optimally at 30-37 °C and pH 7-8 with 0-2.0% (w/v) NaCl. Phylogenetic analyses based on the genomic data revealed that JL2B1089[T] is closely related to Fictibacillus phosphorivorans Ca7[T], with average nucleotide identity and digital DNA-DNA hybridization values of 90.0 and 40.6%, respectively; both values are below the recommended thresholds for species delineation. Chemotaxonomic characteristics, including the major cellular fatty acids iso-C15:0 and anteiso-C15:0, the predominant menaquinone-7 and a cell-wall peptidoglycan containing meso-diaminopimelic acid, are consistent with those of the closely related taxa F. phosphorivorans Ca7[T] and Fictibacillus halophilus AS8[T]. Additionally, strain JL2B1089[T] shows specificity in utilizing certain substrates, such as amino acids and carboxylic acids. Pan-genome analysis and divergence analysis of the bacillithiol biosynthesis deacetylase (BshB1) protein suggest that this strain may adapt to the space environment through mechanisms involved in coping with cell morphological alterations, osmotic fluctuations and oxidative damage under microgravity conditions. Based on phenotypic, chemotaxonomic and genomic characteristics, strain JL2B1089[T] represents a novel species within the genus Fictibacillus, for which the name Fictibacillus tiangongensis sp. nov. is proposed. The type strain is JL2B1089[T] (=GDMCC 1.4870[T]=KCTC 43746[T]).},
}

China
*Phylogeny
RNA, Ribosomal, 16S/genetics
Fatty Acids/chemistry
DNA, Bacterial/genetics
Bacterial Typing Techniques
Sequence Analysis, DNA
Base Composition
*Bacillaceae/classification/isolation & purification/genetics
Nucleic Acid Hybridization
*Spacecraft
Peptidoglycan/chemistry
Vitamin K 2/analogs & derivatives/chemistry/analysis
Extreme Environments

@article {pmid42345379,
year = {2026},
author = {Goyal, M and Sandhu, NK},
title = {Lactase Deficiency in 2026: Understanding Pathophysiology, Global Persistence Trends, and Targeted Therapies for Lactose Intolerance.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/27697061.2026.2688511},
pmid = {42345379},
issn = {2769-707X},
abstract = {Lactose intolerance is a common digestive disorder found in many people around the world. It occurs when the body does not produce enough of the enzyme lactase needed to break down lactose, a type of sugar. Lactose is present in almost all mammal milk products, and for infants, this sugar is important for providing energy during their growth. There are many variations of adults with lactase persistence around the world; for example, in Nordic countries, more than 90% of adults produce lactase into adulthood, but in Southeast Asia, only around 10% of adults do so. Overall, about one-third of all adults can digest dairy products; however, many people believe that there will be negative side effects if they eat or drink dairy products. This leads to a restriction of dairy products that can hurt the body's ability to grow and get enough nutrients because dairy products contain many essential nutrient sources (protein, vitamins, minerals). About 68% of the world population is affected by lactose intolerance, but that figure has not changed much in the past decade. However, there are vast regional variations (5-28% in Europe and 70-98% in Asia and Africa). The therapeutic market, including enzyme supplements, probiotics, and dietary aids applicable in all of the severity stages of the condition, is estimated to be valued at $ 36.96 billion in 2026, which represents a 7.4% compound annual growth rate; to reach $ 49.13 billion in 2030 due to the creation of personalized interventions and dairy substitutes.},
}

@article {pmid42345435,
year = {2026},
author = {Low, WK},
title = {The Gut Microbiome May Play a Role in the Pathogenesis of Meniere's Disease.},
journal = {The journal of international advanced otology},
volume = {22},
number = {2},
pages = {1-8},
doi = {10.65717/iao.2026.262424},
pmid = {42345435},
issn = {2148-3817},
mesh = {Humans ; *Meniere Disease/microbiology/etiology/immunology/physiopathology ; *Gastrointestinal Microbiome/physiology/immunology ; Ear, Inner ; Animals ; Dysbiosis/complications ; },
abstract = {Meniere's disease (MD) was first described 650 years ago. It is now considered to be a multifactorial disorder involving immunological mechanisms, blood-labyrinth barrier breakdown, endolymphatic hydrops, vascular compromise, and genetic susceptibility. Chronic inflammation from both innate and adaptive immunity is evident in the inner ear, with autoimmunity and allergy possibly playing a role. Despite its long history, significant knowledge gaps in its pathogenesis remain. For example, there may be root causes from elsewhere that are contributing to these pathological processes occurring in the inner ear. In recent years, rapid progress has been made in research on the contributions of gut microbiome to human health and disease. In particular, changes in gut microbiome have been found to be associated with many disorders of the brain. The brain and the inner ear share similar vascular networks that create a physical barrier to limit paracellular diffusion. Emerging evidence shows gut dysbiosis can potentially result in sensori-neural hearing loss. Early evidence suggests changes in gut microbiome may be associated with MD, possibly via dysregulation of the arginine vasopressin/vasopressin type 2 receptor/aquaporin-2 (AVP-V2R-AQP2) signaling pathway in the inner ear from increased brain secretion of AVP. It remains to be seen if the belief that gut dysbiosis contributes to the pathogenesis of MD can be substantiated by future research. If so, addressing gut issues may prove to be an important strategy in the overall management of MD.},
}

Humans
*Meniere Disease/microbiology/etiology/immunology/physiopathology
*Gastrointestinal Microbiome/physiology/immunology
Ear, Inner
Animals
Dysbiosis/complications

@article {pmid42345569,
year = {2026},
author = {Guigard, L and Bal, V and Bintarti, AF and Buron, M and Chavan, E and Gonzalo, M and Liu, X and Zheng, W and Shade, A},
title = {From dividing to dormant: embracing the full activity spectrum for environmental microorganisms.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0035425},
doi = {10.1128/mmbr.00354-25},
pmid = {42345569},
issn = {1098-5557},
abstract = {SUMMARYMicroorganisms can cope with stress by entering dormancy, a viable state of reduced metabolic activity that enables persistence, dispersal, and long-term survival. However, microbial life in environmental systems is best understood as a spectrum of metabolic activity, spanning from highly active, dividing cells to deeply dormant phenotypes. This spectrum reflects dynamic survival strategies under fluctuating conditions, with critical implications for ecosystem stability, gene dissemination, and resilience to disturbances in natural and human-influenced systems. Yet, microbial activity is often treated as binary (active vs. dormant), oversimplifying a biological continuity that remains technically difficult to quantify. Here, we synthesize advances in microbial dormancy to reconceptualize activity as a spectrum. We review current and emerging methods to quantify environmental activity, linking each to the Central Dogma of molecular biology (DNA to RNA to protein) to guide interpretation along a generalizable continuum. Through a literature synthesis of terrestrial, aquatic, and wastewater treatment ecosystems, we compare how methods estimate active cells and populations. We recommend standardized reporting of total community size, active cell abundance, and proportional activity to enrich the interpretation of microbiome 'omics data, with activity intensity and active-inactive switching providing deeper insights. To achieve this, we advocate for increased accessibility and throughput of precise activity-discriminating technologies, alongside renewed use of reliable methods like direct cell counts and activity stains. Adopting this spectrum-based perspective will improve our ability to tackle key societal challenges, such as understanding microbial contributions to ecosystem function under climate change and gene dispersal at human-environment interfaces.},
}

@article {pmid42345642,
year = {2026},
author = {Ciesielska-Markowska, I and Mycroft-Rzeszotarska, K and Korczyński, P and Pulik, K and Górska, K},
title = {Characteristics of Respiratory Microbiome in COPD-A Literature Review.},
journal = {Advances in respiratory medicine},
volume = {94},
number = {3},
pages = {},
pmid = {42345642},
issn = {2543-6031},
support = {2019/35/B/NZ5/00694//National Science Centre/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Microbiota ; *Respiratory System/microbiology ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is a respiratory disease that progressively impairs airway function. Its aetiology and clinical presentation are very complex, resulting in an unpredictable course of the disease. The most important causes include smoking and environmental pollutants. However, upper airway microbiome dysbiosis has been linked with COPD severity. Through this review, we aim to compare the microbiome of the respiratory tract between its sites, and to see if there are any significant differences in the composition of the microbial flora of patients with COPD when compared to healthy individuals. While preparing this review, the PubMed database was searched using keywords such as bacteriome, COPD, exacerbation, and microbiome. Analysis of the airway microbiome shows that the three most abundant phyla are Firmicutes, Proteobacteria, and Bacteroidetes. The severity of the disease and the selected therapeutic methods influence the ratio of Proteobacteria and Firmicutes. It has been observed that a decrease in microbial diversity resulted in lower values of FEV1 in patients and could be related with COPD's progress and exacerbation events. While exacerbation cases need quick treatment, COPD's complex background makes it difficult to find a singular, microbial cause.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology
*Microbiota
*Respiratory System/microbiology

@article {pmid42345647,
year = {2026},
author = {Czyżak, B and Lasota, A and Majewski, S},
title = {Acute Exacerbation of Interstitial Lung Disease: A Case Series and a Narrative Literature Review.},
journal = {Advances in respiratory medicine},
volume = {94},
number = {3},
pages = {},
pmid = {42345647},
issn = {2543-6031},
mesh = {Humans ; *Lung Diseases, Interstitial/physiopathology/therapy/drug therapy ; Disease Progression ; Female ; Male ; Aged ; Middle Aged ; Idiopathic Pulmonary Fibrosis ; Risk Factors ; },
abstract = {Acute exacerbation of interstitial lung disease (AE-ILD) represents sudden, severe deterioration in patients with pre-existing ILD and is associated with high morbidity and mortality. Our work presents a case series of AE-ILD in patients with idiopathic pulmonary fibrosis (IPF), idiopathic non-specific interstitial pneumonia (iNSIP), and connective tissue disease-associated ILD (CTD-ILD) managed at our institution and provides a narrative review of AE-ILD. Across cases, AE-ILD manifested as rapid progression of dyspnea and extensive ground-glass opacities (GGOs) on imaging, often triggered by infections or immune-mediated processes. Despite treatment, all cases were fatal, confirming that mortality remains high in AE-ILD. In our literature review, we focus on dysregulated innate immunity, an altered microbiome, potential microaspiration, surgical procedures, and autoantibody-mediated inflammation as triggers, as well as the risk factors for and prevalence of AE-ILD. We also examine pharmacological and non-pharmacological interventions, with particular emphasis on the role of antifibrotic agents as a key protective factor. Evidence for and against corticosteroid use in AE-IPF and non-IPF AE-ILD is discussed, highlighting the radically different treatment approach for AE in melanoma differentiation-associated gene 5 (MDA5)-positive dermatomyositis (DM)-associated ILD compared to AE-IPF. Our findings underscore the heterogeneous presentation and poor prognosis of AE-ILD, emphasizing the urgent need for standardized diagnostic criteria, risk stratification, and prospective studies with larger cohorts to establish evidence-based therapeutic strategies.},
}

Humans
*Lung Diseases, Interstitial/physiopathology/therapy/drug therapy
Disease Progression
Female
Male
Aged
Middle Aged
Idiopathic Pulmonary Fibrosis
Risk Factors

@article {pmid42345774,
year = {2026},
author = {Giannoulis, T and Dovolou, E and Mamuris, Z and Amiridis, GS},
title = {Consequences of Heat Stress on Physiology, Microbiome Dynamics, and Multi-Omics in Dairy Cows: More than Meets the Eye.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345774},
issn = {2079-7737},
abstract = {Heat stress (HS) is at the top of the challenges facing modern dairy production, with annual losses according to global projections, under high-emission scenarios, reaching US$14.7-40.0 billion by the end of the century. This review emphasizes three interconnected topics that account for most of the proportion of the productive and reproductive losses during HS. First, the physiological consequences of HS are reviewed, with emphasis on the pair-fed thermal neutral (PFTN) paradigm, which established that reduced dry matter intake (DMI) accounts for only 35-50% of the observed milk yield decline, with the remainder arising from tissue-level effects of hyperthermia on mammary function, metabolism, and reproductive performance. Second, HS-induced microbiome disruption is examined as an active pathophysiological amplifier, whereby rumen dysbiosis compromises intestinal barrier integrity and drives systemic endotoxaemia, chronically amplifying the immune suppression already imposed by the thermal insult. Third, we focus on the integration of multi-omics platforms as a management approach, since single-omics analyses capture only a fraction of the biological complexity underlying the HS response. As the available datasets expand in coverage and scale, their integration through AI-driven analytical frameworks has the potential to substantially advance beyond the current fragmented picture, progressively building toward a systems-level model of thermal stress. Evidence-based mitigation strategies spanning environmental cooling, targeted nutritional supplementation, and genomic selection are critically evaluated within this framework, with emphasis on equity of access to evidence-based solutions across global dairy production systems.},
}

@article {pmid42345816,
year = {2026},
author = {Do, HT and Bhunyakarnjanarat, T and Dityen, K and Kaewopas, Y and Thammachareonrach, N and Paiboonkasarp, S and Jaroonwitchawan, T and Boonyasuppayakorn, S and Chancharoenthana, W and Leelahavanichkul, A},
title = {Abdominal Symptoms During the Febrile Phase Indicate Profound Innate Immune Responses in Dengue.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345816},
issn = {2079-7737},
support = {B48G6600112//the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; RA-MF-02/67//Rachadapisek Sompote Matching Fund/ ; RA-MF-01/68//Rachadapisek Sompote Matching Fund/ ; },
abstract = {Gastrointestinal symptoms (GI) (abdominal pain, vomiting, and diarrhea) during the febrile phase of dengue (less than 5 days from fever onset) might indicate prominent innate immune responses. Serum and feces samples from cases with GI symptoms versus those without GI symptoms (n = 20 per group) were analyzed. From these, only the neutrophil extracellular traps (NETs), serum fibroblast growth factor (FGF) 21, and fecal microbiome analyses, but not the routine parameters, endotoxemia, or serum cytokines, were higher in the GI cases than in the non-GI cases. From the in vitro experiments, both lipopolysaccharide (LPS) and the dengue virus (DENV) upregulated the FGF receptor 1 (FGFR1) and cytokines in hepatocytes (HepG2) and THP-1-differentiated macrophages. Meanwhile, LPS and DENV induced NETs in isolated neutrophils from healthy volunteers. Only the starvation protocol, but not LPS or DENV, enhanced supernatant FGF-21 from hepatocytes. Incubation of recombinant FGF-21 in LPS + DENV-activated cells (hepatocytes, macrophages, and neutrophils) attenuated inflammation, as determined by supernatant cytokines and NETs. Hence, abdominal symptoms in dengue during the febrile phase indicate prominent innate immune responses, as detected by NETs and FGF-21 (an acute-phase protein), implying significant hepatic stress with a possible counteracting anti-inflammation.},
}

@article {pmid42345817,
year = {2026},
author = {Stefan, G and Gurau, MR and Ciocîrlie, N and Tudor, L and Bărăităreanu, S and Tache-Codreanu, DL and Sporea, C and Gligor, A and Iancu, I and Herman, V},
title = {Horizontal Gene Transfer in Listeria monocytogenes: Evolution of Antimicrobial Resistance and Virulence in a One Health Context.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345817},
issn = {2079-7737},
abstract = {Listeria monocytogenes is a ubiquitous Gram-positive bacterium responsible for listeriosis, a foodborne zoonotic disease affecting humans and animals. Although infection in immunocompetent individuals is often asymptomatic or limited to mild self-limiting gastroenteritis, Listeria monocytogenes may cause severe invasive disease in vulnerable groups, including pregnant women, neonates, elderly individuals, and immunocompromised patients. Although the incidence of listeriosis is relatively low compared with many other foodborne pathogens, the high hospitalization and mortality rates associated with clinical cases make this bacterium a major concern for food safety and public health. The evolutionary success of L. monocytogenes reflects the interaction between a conserved core genome and a dynamic accessory genome shaped by horizontal gene transfer (HGT), ecological selection, and expansion of specific clones. Transient intestinal carriage in humans and animals, potentially influenced by gut microbiome composition, creates ecological interfaces where plasmids, transposons, prophages, and integrative conjugative elements contribute to the exchange of antimicrobial resistance determinants, virulence factors, and stress tolerance systems. Virulence diversification is further influenced by the differential distribution of pathogenicity islands such as LIPI-1, LIPI-3, and LIPI-4 across specific clonal lineages. These evolutionary processes occur across interconnected farm, food-production, environmental, and clinical ecosystems consistent with the One Health framework. Advances in whole-genome sequencing have clarified lineage-specific gene flow, expansion of specific clones, and the dynamics of the resistome and mobilome in L. monocytogenes populations. This narrative review aims to synthesize current knowledge on the mobile genetic elements and ecological interfaces that shape horizontal gene transfer in L. monocytogenes. Its novelty lies in integrating antimicrobial resistance, virulence-associated genomic islands, stress adaptation, and gut microbiome-mediated selection within a One Health and metapopulation framework. The main message of this review is that HGT should be interpreted as a context-dependent contributor to L. monocytogenes adaptation, acting together with clonal background, ecological selection, and mobile genetic elements.},
}

@article {pmid42345819,
year = {2026},
author = {Thingujam, D and Malacrinò, A and Pajerowska-Mukhtar, KM and Mukhtar, MS},
title = {Molecular, Microbial, and Ecological Drivers of Duckweed Phytoremediation in Aquatic Environments.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345819},
issn = {2079-7737},
support = {IOS-2038872//U.S. National Science Foundation/ ; OIA-2418230//U.S. National Science Foundation/ ; },
abstract = {Aquatic ecosystems are under severe stress from a diverse combination of contaminants, including heavy metals, pesticides, pharmaceuticals, and microplastics, driven by rapid industrialization, intensive agriculture, and urbanization. Globally, 80% of wastewater remains untreated, and conventional systems often fail to address emerging contaminants. Consequently, toxic heavy metals like lead and mercury can persist in water sources for decades. In response, phytoremediation has emerged as a scalable, eco-friendly, nature-based alternative. Among phytoremediation agents, duckweeds are increasingly recognized for their rapid growth, simple morphology, and continuous water-column contact. This review outlines the landscape of duckweed-based remediation, detailing molecular detoxification pathways and the synergistic role of associated microbiomes in enhancing environmental cleanup. Evidence indicates that contaminant removal is often supported by plant-microbe interactions. Despite extensive laboratory validation, field-scale implementation remains constrained by environmental complexity, pollutant mixtures, and variable climatic conditions. Furthermore, while duckweed systems hold promise within circular bioeconomy frameworks, converting wastewater into nutrient-rich biomass, contaminant accumulation in plant tissues raises concerns about biomass utilization and contaminant carryover. Addressing these challenges requires an integrative approach that links molecular detoxification, ecological interactions, and engineered system design to realize the full potential of duckweeds for sustainable aquatic pollution management.},
}

@article {pmid42345832,
year = {2026},
author = {Konwar, B and Kim, KS},
title = {The Programmable Microbiome: Integrative AI and Multi-Omics Frameworks for Precision T2DM Management.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345832},
issn = {2079-7737},
abstract = {The gut microbiota is recognized as a programmable metabolic organ that governs systemic homeostasis. Recent advances (2023-2025) have pivoted Type 2 Diabetes Mellitus (T2DM) research from a host-centric perspective toward a failure of bidirectional host-microbe metabolic flux. This review evaluates the molecular mechanisms underpinning this shift, focusing on microbial metabolite signaling, virome-mediated modulation, and the emergence of drug-microbiome interactions as critical therapeutic variables. We highlight the transformative role of AI-guided mapping and digital twin simulations in modeling high-resolution metabolic flux and predicting the stability of engineered microbial consortia. By integrating meta-transcriptomics and epigenomics, we characterize the functional plasticity of the microbiome under therapeutic stress. We argue that framing the microbiota as a programmable infrastructure-integrated with AI analytics and metabolic engineering-enables adaptive, real-time interventions. This synthesis offers a blueprint for transitioning from correlative observations toward precision microbiome engineering to achieve sustained metabolic resilience.},
}

@article {pmid42345977,
year = {2026},
author = {Enax, J and Schulze Zur Wiesche, E and Epple, M},
title = {Tooth Enamel Demineralization: Caries and Erosion from the Viewpoint of Chemistry.},
journal = {Dentistry journal},
volume = {14},
number = {6},
pages = {},
pmid = {42345977},
issn = {2304-6767},
abstract = {The demineralization of tooth enamel is the primary consequence of dental caries, leading to cavities and finally tooth loss. Erosive tooth wear from acidic beverages and food is another factor that degrades enamel. In both cases, an acidic environment leads to etching and the final dissolution of tooth mineral, i.e., hydroxyapatite. Here, this process is discussed from a chemical perspective, taking into account the solubility of calcium phosphate and the presence of the pellicle (protein layer) and plaque (bacterial biofilms), which both affect the dissolution rate. While low pH is definitely decisive, calcium-binding ligands (e.g., acid anions, proteins) contribute to dissolution by removing calcium ions from the equilibrium. This is an important effect in the oral cavity where the concentration of biomolecules is high. The situation is complicated by the fact that the composition of saliva and the oral microbiome vary considerably between individuals. The state of current knowledge on the demineralization of enamel is summarized and discussed, also in the context of approaches to prevent dental caries and erosive tooth wear.},
}

@article {pmid42346015,
year = {2026},
author = {Habtemariam, S},
title = {The Gut Microbiome Dependency Continuum in Drug Discovery: A Unified Pharmacology Framework Linking Clinical Drugs, Natural Products, and Engineered Microbial Therapeutics.},
journal = {Biotech (Basel (Switzerland))},
volume = {15},
number = {2},
pages = {},
pmid = {42346015},
issn = {2673-6284},
abstract = {Highlighting its pivotal role in modern pharmacology, the gut microbiome is emerging as a key determinant of drug efficacy, toxicity, and bioavailability. This review proposes the Gut Microbiome Dependency Continuum, a four-layer framework describing progressively deeper levels of microbiome involvement in drug discovery and therapeutic function. The first layer, intact functional microbiome-dependent therapeutics and includes interventions such as faecal microbiota transplantation and defined microbial consortia. The second layer, microbiome-modulated approved drugs include widely used therapeutics whose pharmacokinetics or pharmacodynamics are strongly influenced by microbial metabolism. Examples include metformin, irinotecan, levodopa, and digoxin, where gut microbial interactions influence efficacy, toxicity, and inter-individual variability in treatment outcomes. The third layer, microbiota-transformable natural products, encompasses dietary and plant-derived compounds such as polyphenols, ginsenosides, alkaloids, fibres, isoflavones, lignans, and glucosinolates. Their biological activity depends on microbial biotransformation into bioactive metabolites. The fourth layer, engineered microbiome therapeutics, includes synthetic biology approaches such as programmable microbial systems, engineered probiotics, CRISPR-based microbiome editing, and microbiome-responsive drug delivery systems. It also includes synthetic microbial consortia, enabling targeted sensing, therapeutic delivery, and ecological reprogramming of gut microbial communities. Altogether, these layers define a continuum in which the gut microbiome evolves from a passive modulator to an essential metabolic organ and ultimately a programmable therapeutic platform. The article provides an integrated framework for microbiome-informed drug discovery. It also supports the development of precision, ecology-aware, and engineered microbial therapeutics.},
}

@article {pmid42346116,
year = {2026},
author = {Khan, SU and Chauhan, V and Chaudhary, AA and Khan, M},
title = {The Gut-Brain-Immune Axis: Multi-Omics Insights into Neurodegenerative and Metabolic Diseases.},
journal = {Cells},
volume = {15},
number = {12},
pages = {},
pmid = {42346116},
issn = {2073-4409},
support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; },
mesh = {Humans ; Multiomics ; *Neurodegenerative Diseases/immunology/metabolism ; Animals ; *Brain/immunology/metabolism ; *Metabolic Diseases/immunology/metabolism ; Gastrointestinal Microbiome ; Metabolomics ; },
abstract = {The axis linking the gut to the brain to the immune system connects all tissues involved-bacteria, immune cells, metabolism and the CNS-through a multidirectional communication network. Several studies have confirmed that when this axis is disrupted, it can be responsible for Alzheimer's disease, Parkinson's disease, obesity, type 2 diabetes, and NAFLD, and the main consequences come from increased systemic inflammation, altered regulation of immune cells, the production of microbial metabolites that alter signals to the immune cells and nervous system, increase in oxidative stress, breakdown of the gut barrier, and more. In recent years, advanced multi-omics technologies, such as metagenomics, transcriptomics, metabolomics, proteomics, and single-cell sequencing, have provided significant advancement in our understanding of all of the interacting nodes involved in the gut-brain-immune axis. These advanced sequencing technologies can characterize the microbial communities, host immune cells, metabolic profiles, and the degree of cell heterogeneity during a specific disease. Combining multi-omics information can reveal a few shared pathways between neurodegenerative and metabolic disorders, such as NF-κB, NLRP3 inflammasome activation, mitochondrial dysfunction, changes in SCFA metabolism, and the alteration of microbial populations in Alzheimer's and Parkinson's disease; metabolic dysbiosis and increased risk for Parkinson's disease; or changes in gut-to-brain-to-immune signaling contributing to diabetes complications and NAFLD. Artificial intelligence (AI) and machine learning are becoming promising tools for detecting biomarkers from these datasets, extracting knowledge, interpreting systems biology, and helping with developing precision medicine. In this review, we summarize current evidence that supports the role of the gut-brain-immune axis in neurodegenerative and metabolic diseases, highlighting results gained with the utilization of multi-omics approaches. We will describe the key microbial, immune, and metabolic pathways involved in pathogenesis and therapeutic approaches including psychobiotics, tailored nutrition, modulation of the microbiome, and metabolite interventions, discussing future perspectives of the translation of the gut-brain-immune axis knowledge into clinical practice.},
}

Humans
Multiomics
*Neurodegenerative Diseases/immunology/metabolism
Animals
*Brain/immunology/metabolism
*Metabolic Diseases/immunology/metabolism
Gastrointestinal Microbiome
Metabolomics

@article {pmid42346277,
year = {2026},
author = {Bodurska, T and Totev, T and Konova, E},
title = {Presence and Dominance of Lactobacillus in the Endometrial Microbiome and Age-Related Associations in Patients with Recurrent Reproductive Failure.},
journal = {Diseases (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {42346277},
issn = {2079-9721},
abstract = {OBJECTIVES: To evaluate the presence and dominance of Lactobacillus in the endometrial microbiome and their age-related associations in a large group of Bulgarian patients with recurrent implantation failure (RIF) and recurrent pregnancy loss (RPL) who attend our clinic.

METHODS: This retrospective study included 199 patients (mean age: 35.69 ± 5.16) with RIF (n = 103) and RPL (n = 96) who visited our fertility clinic between October 2019 and November 2022. Endometrial samples were analyzed using real-time PCR for target DNA sequences.

RESULTS: Overall, 62.8% (n = 125) exhibited an absence of Lactobacilli in their endometrial samples, with 63.1% (n = 65) of the RIF group and 62.5% (n = 60) of the RPL group showing a lack of Lactobacilli, with no statistically significant difference between the groups (p = 0.926). A Lactobacillus-dominant microbiome was found in 23.6% of the entire cohort (n = 47), 25.2% of the RIF group (n = 26) and 21.9% of the RPL group (n = 21). A reduced abundance of Lactobacilli was identified in 13.5% of the cohort (n = 27), though to differing degrees. There was no significant relationship between the abundance of Lactobacilli and belonging to the RIF or RPL group. A statistically significant difference was found in the mean age of two groups in cases with a Lactobacillus-dominant microbiome (mean age of 36.4 ± 4.8 years in the RIF group and 32.5 ± 3.5 years in the RPL group) (p = 0.004).

CONCLUSIONS: Our findings demonstrate a high prevalence of non-Lactobacillus-dominant microbiomes in a large group of Bulgarian patients with RIF and RPL and significant age-related Lactobacillus changes in the microbiome of patients with RPL. These results point to the potential role of the uterine microbiome and support the need for further prospective studies, especially in cases of advanced maternal age.},
}

@article {pmid42346347,
year = {2026},
author = {He, J and Qin, L and Sun, X},
title = {Bile Acids and the Gut-X Axis: TCM-Mediated Systemic Protection and Therapeutic Opportunities for Multi-Organ Diseases.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060366},
pmid = {42346347},
issn = {2218-1989},
support = {82405310//National Natural Science Foundation of China/ ; 1020241792//Natural Science Foundation of the Jiangsu Higher Education Institutions of China/ ; },
abstract = {The gut microbiota regulates host physiology and drives extraintestinal diseases through the gut-X axis. Bile acids (BAs) function as key mediators of this interorgan crosstalk by activating nuclear and membrane receptors (FXR, TGR5, PXR, VDR). Traditional Chinese Medicine (TCM) demonstrates efficacy across multiple organ systems through multi-component formulations. This narrative review synthesizes evidence from preclinical and clinical studies supporting that TCM exerts systemic protection via strategic modulation of the microbiota-BA-host receptor axis, which functions as a core regulatory circuit within a larger network of microbial metabolites. Mechanistically, representative TCM formulas remodel gut microbial ecology and reinforce intestinal barrier integrity, leading to optimized BA profiles. These favorable BA signatures engage tissue-specific receptor signaling to resolve inflammation, mitigate fibrosis, and restore metabolic homeostasis across the gut-heart, gut-kidney, gut-liver, gut-bone, and gut-endocrine axes. Support for this causal relationship is provided by microbiota depletion, fecal transplantation, and multi-omics studies, collectively suggesting that TCM's benefits are microbiota-dependent and at least partially BA-mediated. Moreover, context-dependent modulation of BA receptors, such as differential regulation of FXR, enables TCM to achieve pathology-specific outcomes. Current evidence is derived predominantly from preclinical models, and clinical data remain lacking. Nonetheless, the microbiota-BA-organ axis thus provides a potential framework for understanding TCM's systemic actions and establishes a molecular basis for developing microbiome-informed precision therapeutics. Future directions include patient stratification and precision intervention design inspired by TCM's ecological modulation strategies.},
}

@article {pmid42346351,
year = {2026},
author = {Ezzi, MY},
title = {Probiotics After Metabolic and Bariatric Surgery: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060371},
pmid = {42346351},
issn = {2218-1989},
abstract = {Background/Objectives: Patients undergoing metabolic and bariatric surgery (MBS) are at risk of micronutrient deficiencies and gut dysbiosis. Probiotics (such as Lactobacillus, Bifidobacterium) have been proposed as adjunct therapy to optimize postoperative outcomes. This review aimed to evaluate the effect of postoperative probiotic supplementation on anthropometric, metabolic, inflammatory, and micronutrient outcomes in MBS patients. Methods: Nine electronic databases were systematically searched, including PubMed, Web of Science, Cochrane Library, Google Scholar, Popline, Global Health Library, Virtual Health Library, New York Academy of Medicine, and OpenGrey, from inception through October 2024. Only randomized controlled trials (RCTs) were included. The Cochrane Collaboration risk-off-bias tool was used for quality assessment. Meta-analyses were performed using Comprehensive Meta-Analysis software version 2. Fixed-effects or random-effects models based on heterogeneity (I[2] threshold: 50%) were applied. Mean differences (MD) and 95% confidence intervals (CI) were calculated for all continuous variables. Results: Thirteen RCTs encompassing 666 patients (probiotics group: n = 344; control group: n = 322) were included. Incomplete outcome data represented the most prevalent high-risk domain (23%). Probiotic supplementation was associated with significantly improved serum vitamin D (MD: 25.32 nmol/L, 95% CI: 6.96-43.67, p = 0.007) and vitamin B12 levels (MD: 39.36 pg/mL, 95% CI: 1.88-76.84, p = 0.04). No statistically significant differences were observed in anthropometric outcomes (%EWL, BMI, weight, or waist circumference), lipid profile, glycemic indices, or inflammatory markers (TNF-α, IL-6, CRP). Conclusions: Postoperative probiotic supplementation may significantly improve vitamin D and B12 levels in patients undergoing MBS, suggesting a supportive role in mitigating micronutrient deficiencies. However, these findings should be interpreted with caution due to substantial heterogeneity across studies. Probiotics did not significantly affect weight loss, metabolic parameters, or inflammatory markers. Clinicians may consider probiotics as an adjunct strategy to support micronutrient status in at-risk postoperative patients. Large-scale, strain-specific trials incorporating standardized dietary control and microbiome profiling are warranted.},
}

@article {pmid42346365,
year = {2026},
author = {Xie, T and Ding, Q and Yang, L and Wang, J and Wei, J and Du, X and Jin, L},
title = {Screening of "Cry for Help" Signals from Angelica sinensis Induced by Fusarium solani and Their Potential for Biological Control.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060385},
pmid = {42346365},
issn = {2218-1989},
support = {Nos. 82160714 and 82560755//National Natural Science Foundation of China/ ; 2024QNTD36//Gansu Provincial Young Talent Project/ ; 23JRRA1711//Natural Science Foundation of Gansu Province/ ; 2025A-101//Gansu University Teacher Innovation Fund Project/ ; ZYZL-2024-04//Open Fund Project of the Gansu Provincial Key Laboratory of Traditional Chinese Medicine Quality and Standardization/ ; },
abstract = {BACKGROUND: Root rot caused by Fusarium solani is a devastating disease in Angelica sinensis (danggui), leading to severe yield and quality losses. Sustainable control strategies are urgently needed. According to the plant "cry for help" theory, plants under pathogen attack may recruit beneficial microbes via root exudates. However, whether A. sinensis employs this strategy against F. solani remains unknown. This study aimed to identify potential "cry for help" metabolites and evaluate their biocontrol potential.

METHODS: LC-MS analysis revealed that F. solani infection significantly altered the metabolic profiles of both A. sinensis roots and rhizosphere soil.

RESULTS: Comparative analysis identified seven metabolites specifically upregulated in infected plants but not detected in the pathogen, including taurine, oxoadipic acid, quinolinic acid, 6-phosphogluconic acid, methyl cinnamate, 2-phenylethanol, and (R)-3-hydroxybutyric acid. Exogenous application of these seven metabolites revealed that taurine and methyl cinnamate significantly alleviated disease symptoms, improved plant growth (root length, biomass), and enhanced the activities of key defense enzymes (peroxidase, POD, phenylalanine ammonia-lyase, PAL, lipoxygenase, LOX, polyphenol oxidase, PPO). Furthermore, taurine and methyl cinnamate reshaped the rhizosphere microbiome. The incidence of root rot was reduced by 51.3% and 50.8%, respectively. Taurine enriched actinobacteria (e.g., Paeniglutamicibacter) and reduced the relative abundance of pathogenic Ascomycota fungi, while methyl cinnamate markedly enriched the nitrogen-fixing bacterium Azotobacter and the saprophytic fungus Schizothecium. Crucially, both treatments significantly suppressed the proliferation of F. solani in the rhizosphere.

CONCLUSIONS: Our findings demonstrate for the first time that A. sinensis activates a "cry for help" response upon attack by F. solani, with taurine and methyl cinnamate preliminarily identified as key signaling metabolites that can directly or indirectly inhibit the development of A. sinensis root rot. These compounds enhance plant resistance and recruit beneficial microorganisms, offering a novel and promising ecological strategy for the green control of A. sinensis root rot.},
}

@article {pmid42346385,
year = {2026},
author = {Li, J and Xu, X and Wang, H and Gao, R and Li, B and You, X},
title = {Relationship Between Calcium and Gut Microbial Composition and Metabolic Pathways in Children with Autism.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060405},
pmid = {42346385},
issn = {2218-1989},
support = {531100006787540685//Chinese Academy of Medical Sciences & Peking Union Medical College/ ; },
abstract = {Background/Objectives: Trace elements may influence autism spectrum disorder (ASD) severity through interactions with the gut microbiota and microbial metabolic functions, but calcium-related evidence remains limited. This cross-sectional study examined associations among hair calcium, gut microbial taxa, metabolic pathways, and behavioral phenotypes in children with ASD. Methods: We analyzed 183 children with ASD who had behavioral assessments, hair calcium measurements, and fecal shotgun metagenomic sequencing data. Participants in the lowest and highest calcium quartiles were first compared to characterize group-level microbiome differences. Full-sample analyses then tested associations among continuous hair calcium, microbial taxa, metabolic pathways, and behavioral measures after covariate adjustment. Benjamini-Hochberg false discovery rate correction was applied for multiple testing. Results: Hair calcium was positively associated with CARS, ATEC-Total, ATEC-1, and ATEC-3 scores, with the strongest associations involving ATEC-1 and ATEC-3. Alpha and beta diversity did not differ significantly between calcium quartile groups, but group-based microbiome analyses identified 63 differential species and 22 differential MetaCyc pathways. Full-sample integrated analyses connected calcium-associated microbial taxa, metabolic pathways, and ASD behavioral measures. Conclusions: Hair calcium was associated with ASD behavioral severity, selected gut microbial species, and microbial metabolic pathways. These findings support an association framework connecting longer-term calcium-related mineral profiles, gut microbial functional potential, and behavioral phenotypes, providing a basis for future longitudinal and multi-omics studies.},
}

@article {pmid42346391,
year = {2026},
author = {Cheng, F and Lv, C and Yi, Y and Wang, D and Wang, W and Li, T and Zhou, R and Li, Q and Qin, S},
title = {Multi-Targeted Intervention of Eucommia ulmoides and Its Bioactive Constituents Against Metabolic Syndrome: From Molecular Mechanisms and Gut Microbiota Modulation to Clinical Translation.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060411},
pmid = {42346391},
issn = {2218-1989},
support = {82305009//National Natural Science Foundation of China/ ; 2024JJ5225//Department of Science and Technology of Hunan Province/ ; },
abstract = {Background/Objectives: Metabolic syndrome (MetS) is a pressing global health challenge comprising obesity, hyperglycemia, hypertension, and hyperlipidemia. Conventional polypharmacy often presents long-term compliance issues and side effects. Eucommia ulmoides Oliv., a traditional medicinal and edible plant rich in iridoids, lignans, flavonoids, and polysaccharides, has emerged as a promising natural intervention. This review aims to systematically summarize the bioavailability and multifaceted pharmacological mechanisms of E. ulmoides and its bioactive components in alleviating MetS. Methods: We comprehensively reviewed the recent in vitro and in vivo literature to map the functional evidence, specific signaling pathways, and gut microbiota-host interactions associated with E. ulmoides extracts and its key phytochemicals (e.g., asperuloside) against various metabolic dysfunctions. Results: Current evidence indicates that E. ulmoides operates through a "multi-component, multi-target, and multi-pathway" paradigm. For hyperlipidemia and obesity, it activates hepatic lipid metabolism (PPARα/CPT1A, FXR/CYP7A1) and mitigates oxidative stress (Nrf2/ARE). Furthermore, it dose-dependently reshapes the gut microbiota by enriching beneficial bacteria like Akkermansia and increasing butyrate production, exerting profound gut-liver axis regulation. It also ameliorates hypertension by activating the ACE2-Ang-(1-7)-Mas axis, improves insulin resistance via the AMPK/PI3K/Akt cascade, and manages hyperuricemia by modulating XOD and renal transporters. Notably, the low oral bioavailability of its glycosides highlights the crucial role of gut microbial hydrolysis in its efficacy. Conclusions: E. ulmoides holds substantial therapeutic potential as a multi-target natural supplement for MetS. However, future translational applications necessitate large-scale randomized clinical trials, multi-omics studies to further clarify host-microbiome interactions, and the development of standardized formulations to ensure clinical efficacy.},
}

@article {pmid42346411,
year = {2026},
author = {Vankayala, USA and Sohail, A and George, B and Singh, M and Khayat, O and Kreidieh, M and Hasham, A and Quiel, L},
title = {The Gut Microbiome in Heart Failure: Pathways to Inflammation and Therapeutic Targets.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060431},
pmid = {42346411},
issn = {2218-1989},
abstract = {Heart failure (HF) continues to be a major global health burden, with persistent morbidity and mortality despite guideline-directed and device-based therapies. Evidence suggests the gut-heart axis is a critical and underrecognized contributor to HF progression. Alterations in cardiac output and systemic venous congestion in HF lead to intestinal hypoperfusion, mucosal edema, and loss of barrier integrity, increasing intestinal permeability, gut dysbiosis, and translocation of microbial products. This systemic translocation is associated with chronic low-grade inflammation that activates innate immune pathways that correlate with endothelial dysfunction, oxidative stress, fibroblast activation, and adverse cardiac remodeling. Gut-derived metabolites derived by microbial metabolism modulate cardiovascular health by altering the metabolic profiles. Dysbiosis results in loss of protective short-chain fatty acid (SCFA)-producing bacteria and enriches pro-inflammatory taxa such as trimethylamine N-oxide (TMAO)-producing bacteria. Elevated TMAO is associated with increased mortality and hospitalization in HF, whereas SCFAs enhance barrier integrity and immune tolerance. Secondary bile acids and uremic toxins such as indoxyl sulfate and p-cresyl sulfate further link dysbiosis to fibrosis and vascular stiffness. Circulating markers such as TMAO, lipopolysaccharide-binding protein (LBP), and soluble CD14 carry prognostic value beyond traditional cardiac biomarkers. This review highlights current experimental, translational, and clinical evidence describing gut dysbiosis and its molecular links to HF progression. Targeting the gut-heart axis represents a novel therapeutic approach in HF. Dietary modulation, probiotics/prebiotics, fecal microbiota transplantation, and inhibitors of microbial metabolic pathways show promise. Future research should emphasize microbiota-based interventions in HF management.},
}

@article {pmid42346510,
year = {2026},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {The Gut Microbiome in Early Ontogeny: Implications for Brain and Immune System Development.},
journal = {Journal of developmental biology},
volume = {14},
number = {2},
pages = {},
pmid = {42346510},
issn = {2221-3759},
abstract = {The gut microbiome plays a pivotal role in modulating multiple physiological processes from the earliest stages of life. However, the complete scope of its effects during childhood is yet to be fully elucidated, which underscores the importance of enhancing the understanding of this emerging area of research. This narrative review provides an overview of the influence of the gut microbiome in early human ontogeny by examining its role in brain and immune development, as well as its involvement in neurodevelopmental disorders and early-life mental health. The gut microbiome contributes to shaping the development and function of both the brain and the immune system. Its influence appears to be primarily mediated through the synthesis of neurotransmitters and microbial metabolites, as well as through the activation of specific pathways within the hypothalamic-pituitary-adrenal axis. Nevertheless, the exact mechanisms through which the gut microbiome exerts these effects, and the full extent of its impact on neurodevelopmental and immune health, remain incompletely understood and continue to be active areas of research and scientific debate. Ultimately, advances revealing how the gut microbiome shapes early brain and immune system development will create new opportunities for innovative interventions and predictive strategies aimed at transforming pediatric health outcomes.},
}

@article {pmid42346523,
year = {2026},
author = {Morales-Mora, LA and Maldonado-Mendoza, IE and Nava-Galicia, SB and Romero-Arenas, O and Arroyo-Becerra, A and Villalobos-López, MA and Cortés-Espinosa, DV and Bibbins-Martínez, MD},
title = {Trichoderma spp. Associated with Teosinte (Zea mays spp. mexicana) Rhizosphere Exhibit Potential Plant Growth-Promoting and Antagonistic Functional Traits.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
pmid = {42346523},
issn = {2309-608X},
support = {Research project grant SIP20251091//Instituto Politécnico Nacional/ ; },
abstract = {Wild maize (teosinte) has been reported to be less susceptible to biotic and abiotic stresses than its modern relative, corn. The composition of the teosinte root microbiome may be linked to traits such as drought tolerance and pest resistance. Trichoderma spp. are ubiquitous saprotrophic fungi found in the plant rhizosphere, enhancing host plant growth and crop productivity while alleviating biotic and abiotic stresses. The present study identified ten Trichoderma fungal isolates associated with the rhizosphere microbiome of teosinte (Zea mays spp. mexicana) and performed in vitro screening to assess both their multi-trait plant growth-promoting activities and their biological control potential against the phytopathogens Aspergillus flavus and Fusarium verticillioides. Additionally, interaction tests were conducted to evaluate the phytostimulant effect of Trichoderma spp. on maize (Zea mays) seed germination. Taxonomic and phylogenetic analysis identified five different Trichoderma species: T. rifaii (TA and TH); T. azevedoi (TB and TI); T. afroharzianum (TE); T. hamatum (TF and TG); and Trichoderma sp. (aff. bannaense) (TC, TD, and TJ). Partial least squares discriminant analysis revealed the isolates TF, TG, and TJ to have the highest potential for use as biocontrol and biostimulant agents. The present study is the first to examine Trichoderma species associated with the teosinte microbiome, and the results suggest that Trichoderma isolates are a potential sustainable alternative for improving maize cultivation.},
}

@article {pmid42346610,
year = {2026},
author = {Zagorianakou, N and Makrydimas, S and Moustakli, E and Oikonomou, ED and Mitrogiannis, I and Sintou, E and Makrydimas, G},
title = {Epigenetics, Oxidative Stress, and the Microbiome in Endometriosis: Toward an Integrated Mechanistic Framework for Precision Medicine.},
journal = {Journal of personalized medicine},
volume = {16},
number = {6},
pages = {},
pmid = {42346610},
issn = {2075-4426},
abstract = {Endometriosis (EM) is a chronic, estrogen-dependent inflammatory disorder affecting approximately 6-10% of women of reproductive age in the general population and remains a major cause of chronic pelvic pain and infertility. High recurrence rates and enduring symptoms despite current treatments underscore the need for a more thorough understanding of its intricate biology. There is growing evidence that the interaction among oxidative stress (OS), microbiome dysbiosis, and epigenetic dysregulation contributes to immunological activation, hormonal imbalance, and the persistence of ectopic lesions. Important disease mechanisms, such as progesterone resistance, inflammatory signaling, and aberrant cellular proliferation, are influenced by epigenetic changes, which include aberrant DNA methylation, histone modifications, and dysregulated non-coding RNAs. Simultaneously, high levels of reactive oxygen species (ROS) reinforce lesion survival and chronic inflammation by promoting angiogenesis, fibrosis, and tissue damage. Changes in the microbiome also affect immunological responses, oxidative balance, estrogen metabolism, and epigenetic control, indicating the existence of interrelated pathogenic loops. This narrative review presents an integrated mechanistic framework for endometriosis, summarizing the available data that connect these pathways. Furthermore, the growing implications of non-invasive biomarkers and precision medicine techniques highlight the potential for improved diagnosis, disease classification, and targeted treatment approaches.},
}

@article {pmid42346643,
year = {2026},
author = {Lee, H and Sajid, K and Lee, D},
title = {Bridging Ancestry-Stratified Bias in Pharmacogenomics AI: Toward Metabolomics-Inclusive Multi-Omics Precision Medicine.},
journal = {Journal of personalized medicine},
volume = {16},
number = {6},
pages = {},
pmid = {42346643},
issn = {2075-4426},
abstract = {Pharmacogenomics AI offers significant potential for individualized drug therapy; however, its clinical benefits remain unevenly distributed. Models trained predominantly on European-ancestry data consistently underperform in non-European populations, with polygenic risk scores (PRS) showing an estimated 39-73% reduction in predictive accuracy in African-ancestry cohorts across complex traits. These disparities have driven increased interest in moving beyond single-layer genomic approaches. Multi-omics frameworks integrating genomic, transcriptomic, proteomic, and metabolomic data have emerged as a promising strategy to improve prediction across heterogeneous clinical populations, as each molecular layer provides distinct and complementary biological information. Among these layers, metabolomics may represent a particularly transferable component across populations. Metabolite profiles capture the downstream functional output of biological systems influenced by genetic, environmental, dietary, and microbiome-related factors, and may therefore be less reliant on ancestry-stratified allele frequency structures that underlie performance disparities in genomic models. This review synthesizes evidence regarding the mechanistic basis of genomic bias in pharmacogenomics AI, the emerging role of multi-omics integration, especially metabolomics, in improving predictive performance, and the current landscape of computational strategies for bias mitigation, including federated learning, transfer learning, domain adaptation, and synthetic data generation. Collectively, current evidence supports metabolomics-inclusive multi-omics frameworks as a biologically plausible, hypothesis-generating strategy to reduce reliance on ancestry-linked genomic features. However, direct evidence that such frameworks reduce ancestry-related bias in clinical AI outputs remains limited, underscoring the need for globally diverse datasets and prospective multi-population validation.},
}

@article {pmid42346798,
year = {2026},
author = {Mizuno, S and Espinoza, JL and Vu, LQ and Banno, H and Iida, Y and Shinohara, S and Dac, DT and Nakagami, Y and Uchino, K and Horio, T and Hanamura, I and Asai, N and Enomoto, M and Tani, H and Nakayama, T and Suzuki, S and Takami, A},
title = {Ascophyllan Supplementation Is Safe and Associated with Exploratory Modulation of Innate Immune Phenotypes, Biochemical Parameters, and the Gut Microbiome in a Randomized Pilot Trial.},
journal = {Marine drugs},
volume = {24},
number = {6},
pages = {},
pmid = {42346798},
issn = {1660-3397},
support = {#21K08427//Ministry of Education, Culture, Sports, Science and Technology/ ; #24K11527//Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Humans ; Pilot Projects ; Male ; Adult ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Female ; *Immunity, Innate/drug effects ; Double-Blind Method ; *Polysaccharides/administration & dosage/pharmacology/adverse effects ; Phenotype ; Killer Cells, Natural/drug effects/immunology ; Young Adult ; Antioxidants ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Ascophyllan, a sulfated polysaccharide extracted from brown seaweed, has shown immunomodulatory and antioxidant effects in preclinical studies, yet human clinical evidence remains scarce. This randomized, double-blind, placebo-controlled pilot trial evaluated the safety and exploratory biological effects of daily ascophyllan supplementation in healthy adults.

METHODS: Twelve participants were randomized to receive either ascophyllan (n = 6) or placebo (n = 6) for 28 days. Safety was monitored through adverse event reporting and repeated laboratory assessments, including hematology, biochemistry, and inflammatory markers. Immune cell populations were analyzed via serial flow cytometry, serum total antioxidant capacity was measured at multiple time points, and gut microbiome composition was profiled using 16S rRNA gene sequencing. All analyses were exploratory in nature.

RESULTS: Ascophyllan supplementation proved well tolerated, with no adverse events observed and stable hematologic, renal, and biochemical parameters throughout the study. Exploratory longitudinal analyses suggested directional modulation of NK-cell-associated phenotypes during ascophyllan supplementation, including directional changes in CD57[+], NKp46[+], and NKG2D[+] NK-cell phenotypes; however, group × time interaction analyses did not remain statistically significant after correction for multiple comparisons. Serum antioxidant capacity showed inter-individual variability with a directional but non-significant increase in the ascophyllan group at intermediate time points. Exploratory microbiome analyses suggested modest directional compositional differences involving members of the Bacteroidaceae and Bifidobacteriaceae families; however, no taxon remained statistically significant after correction for multiple comparisons.

CONCLUSIONS: These preliminary findings indicate that ascophyllan is safe and well tolerated in healthy adults and may be associated with modulation of innate immune phenotypes, subtle microbiome compositional differences, and directional changes in antioxidant capacity. Larger, adequately powered clinical trials are warranted to confirm these observations and further investigate potential biological and clinical effects.},
}

Humans
Pilot Projects
Male
Adult
*Gastrointestinal Microbiome/drug effects
*Dietary Supplements
Female
*Immunity, Innate/drug effects
Double-Blind Method
*Polysaccharides/administration & dosage/pharmacology/adverse effects
Phenotype
Killer Cells, Natural/drug effects/immunology
Young Adult
Antioxidants
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid42347203,
year = {2026},
author = {Widyarman, AS and Udawatte, NS and Ma, SSSS and Theodorea, CF and Richi, M and Poedjiastoeti, W and Seneviratne, CJ},
title = {Nutritional Stunting Is Linked to Reduced Oral Microbiome Stability and Reconfigured Microbial Networks in Children: A Pilot Intervention Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060591},
pmid = {42347203},
issn = {2076-0817},
mesh = {Humans ; Child ; Pilot Projects ; Female ; Probiotics/administration & dosage ; Male ; *Microbiota ; *Growth Disorders/microbiology/complications ; Mouthwashes/administration & dosage ; *Mouth/microbiology ; Saliva/microbiology/chemistry ; Oral Health ; Bacteria/classification/genetics ; Oils, Volatile/administration & dosage ; },
abstract = {This non-randomized, open-labelled, controlled pilot trial investigated the impact of stunting on oral health and the oral microbiome, and evaluated the effect of 14-day probiotic or essential oil mouthwash interventions in children aged 8-12 years. Thirty-six participants (18 stunted, 18 non-stunted) were randomized into three parallel arms: probiotic lozenges (Limosilactobacillus reuteri DSM 17938 + ATCC PTA 5289), essential oil mouthwash, or water control. D-25OH level was assessed with ELISA, OHI-S, and PBI were examined, and oral microbiome was analyzed using 16S metagenomic sequencing. Stunted children demonstrated significantly higher gingival inflammation (PBI, F = 10.57, p = 0.002), reduced microbial alpha diversity, reductions in commensal Streptococcus spp., and increases in pathobionts, including Parvimonas micra, Fusobacterium nucleatum, and Tannerella forsythia. Beta-diversity analysis revealed distinct microbial communities (p = 0.001), with network analysis identifying these anaerobes as keystone hubs in stunted individuals. Salivary vitamin D and oral hygiene indices (OHI-S) also differed by stunting status. Fourteen-day interventions produced only modest, non-significant improvements in clinical indices and failed to induce significant shifts in microbial diversity or composition. These findings indicate that nutritional stunting is independently associated with oral dysbiosis and gingival inflammation. Short-term antiseptic interventions appear insufficient to reverse established microbial shifts, highlighting the need for sustained, integrated nutritional-oral health strategies.},
}

Humans
Child
Pilot Projects
Female
Probiotics/administration & dosage
Male
*Microbiota
*Growth Disorders/microbiology/complications
Mouthwashes/administration & dosage
*Mouth/microbiology
Saliva/microbiology/chemistry
Oral Health
Bacteria/classification/genetics
Oils, Volatile/administration & dosage

@article {pmid42347211,
year = {2026},
author = {Karthikeyan, A and Javaid, A and Charway, GNA and Tabassum, N and Kim, TH and Kim, YM and Jung, WK and Khan, F},
title = {Prophages in Skin Pathogens: From Virulence to Therapy.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060599},
pmid = {42347211},
issn = {2076-0817},
support = {RS-2023-00241461//Ministry of Education/ ; RS-2021-NR060118//Ministry of Education/ ; },
mesh = {*Prophages/genetics/physiology ; Humans ; Virulence ; Virulence Factors/genetics ; Animals ; *Skin Diseases, Bacterial/therapy/microbiology ; },
abstract = {Prophages are bacteriophage genomes that are part of bacterial chromosomes. They are not just dormant passengers; they actively shape pathogen biology. For example, in skin-infecting pathogens such as Staphylococcus aureus, Streptococcus pyogenes, and Pseudomonas aeruginosa, prophages carry important virulence factors, cytotoxins, superantigens, immune evasion clusters, and epigenetic regulators that directly affect the course of skin and soft tissue infections. This same prophage biology provides a therapeutic strategy: prophage-derived molecules, including endolysins, holins, spanins, and polysaccharide depolymerases, demonstrate potent antimicrobial and antibiofilm activity against drug-resistant skin pathogens, with several candidates now in clinical development. Engineered chimeric lysins, CRISPR-encoded prophage delivery systems, and the systematic mining of the skin microbiome phageome collectively enhance the translational potential of this biology. This review integrates mechanistic insights into prophage-mediated virulence. It assesses the translational landscape of prophage-derived therapeutics, delineating the conceptual and clinical frontiers that characterize the forthcoming chapter in this domain.},
}

*Prophages/genetics/physiology
Humans
Virulence
Virulence Factors/genetics
Animals
*Skin Diseases, Bacterial/therapy/microbiology

@article {pmid42347259,
year = {2026},
author = {Xu, ZY and Chen, GQ and Xue, J and Chi, YX and Jian, R and Guo, WP},
title = {Molecular Detection of Coxiella-like Endosymbionts in Ticks in Hebei, China.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060647},
pmid = {42347259},
issn = {2076-0817},
support = {C2022406003//Hebei Natural Science Foundation/ ; BJ2020024//Young Talent Program of Higher School in Hebei Province/ ; 202001//Scientific Research Foundation for High-level Talents of Chengde Medical University/ ; 213777109D//Key Research and Development Program of Hebei Province/ ; },
mesh = {Animals ; China ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Coxiella/genetics/isolation & purification/classification ; *Symbiosis ; *Haemaphysalis longicornis/microbiology ; DNA, Bacterial/genetics ; Chaperonin 60/genetics ; *Ticks/microbiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Ticks are widely distributed in China and can carry and transmit a variety of pathogens that potential to cause serious impacts on public health and the economy. Little is known about the broader spectrum of Coxiella-like endosymbiont (CLE) in ticks under natural conditions in China. The aim of this study was to detect, analyze, and characterize phylogenetically CLE found in ticks in Hebei Province, China. A total of 947 ticks collected from Hebei Province were identified as Haemaphysalis longicornis based on morphological characteristics and cytochrome c oxidase gene PCR analysis of extracted DNA. Subsequently, DNA was analyzed via PCR for the IS1111 gene (frequently associated with Coxiella burnetii), and the amplified DNA was then sequenced and analyzed phylogenetically using a set of primers targeting the 16S rRNA, groEL, and rpoB genes. A total of 8.24% (78/947) of ticks from the Chengde, Baoding, and Cangzhou regions were positive in the IS1111 PCR. Phylogenetic analysis using the 16S rRNA, groEL, and rpoB genes revealed the presence of CLE in Ha. longicornis ticks from these regions and the formation of two distinct clades, suggesting horizontal gene transfer events. Our results strengthen the growing evidence that CLE, not Coxiella burnetii, is ubiquitously associated with ticks across diverse geographic locations-a distinction critical for accurately interpreting tick microbiome surveys and avoiding false assumptions of zoonotic risk.},
}

Animals
China
Phylogeny
RNA, Ribosomal, 16S/genetics
*Coxiella/genetics/isolation & purification/classification
*Symbiosis
*Haemaphysalis longicornis/microbiology
DNA, Bacterial/genetics
Chaperonin 60/genetics
*Ticks/microbiology
Polymerase Chain Reaction
Sequence Analysis, DNA

@article {pmid42347405,
year = {2026},
author = {Zheng, J and Chen, X and Jiang, J and Wu, F},
title = {Glyphosate Promotes the Spread of Antibiotic Resistance Genes in the Intestine: An Overlooked Environmental Risk.},
journal = {Toxics},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/toxics14060506},
pmid = {42347405},
issn = {2305-6304},
support = {42407569//National Natural Science Foundation of China/ ; 2024M750585//China Postdoctoral Science Foundation/ ; 2022GDASZH-2022010104-2//GDAS' Project of Science and Technology Development/ ; 2022GDASZH-2022020402-01//GDAS' Project of Science and Technology Development/ ; 2022GDASZH-2022020402-02//GDAS' Project of Science and Technology Development/ ; 2023B0303000006//Guangdong Major Project of Basic and Applied Basic Research/ ; 2023B1212060044//Guangdong Foundation for Program of Science and Technology Research/ ; },
abstract = {Glyphosate (Gly) is currently the most commonly used broad-spectrum herbicide in the world. The extensive residues of Gly and its major metabolite aminomethylphosphonic acid (AMPA) in food and the environment make it inevitable for humans to consume them. Although Gly has been shown to disturb the homeostasis of gut microbiome by inhibiting the shikimic acid pathway of microorganisms, the potential health effects [such as the occurrence of antibiotic resistance genes (ARGs)] remain unclear. Furthermore, as antibiotics that also act on the intestinal microbiota, their extensive residues inevitably lead to co-exposure with Gly. For these reasons, this study used zebrafish as experimental organisms to explore the effects of Gly/AMPA and oxytetracycline (OTC) exposure alone or in combination on ARGs in the intestine. Our results indicate that Gly exposure, rather than AMPA exposure, led to a 1.67-fold increase in the relative abundance of ARGs in the zebrafish intestine. Combined exposure to Gly and OTC led to a 2.30-fold increase in the relative abundance of ARGs in the zebrafish intestine, indicating a synergistic effect, whereas the additive effect of AMPA and OTC was negligible. In conclusion, the health risk of antibiotic resistance caused by Gly through the gut microbiota is a neglected hot topic. Further studies are needed to clarify Gly-induced functional drug resistance and to assess the human relevance of these findings using more appropriate model organisms.},
}

@article {pmid42347420,
year = {2026},
author = {Berber, AA and Akbulut, C and Demir, ŞN and Kurnaz, M},
title = {Microplastic Contamination in Amphibians and Reptiles: An Ecotoxicological Synthesis of Exposure, Mechanisms, and Risk Implications.},
journal = {Toxics},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/toxics14060522},
pmid = {42347420},
issn = {2305-6304},
abstract = {Microplastic (MP) contamination has become a defining feature of twenty-first century environmental change, yet the toxicological and ecological consequences for amphibians and reptiles-two vertebrate classes already facing severe extinction pressures-remain fragmented across taxa, regions, and methodological traditions. Here, we synthesize field and experimental evidence from five continents to provide a taxonomically balanced, mechanistically grounded, and geographically explicit assessment of MP exposure, bioaccumulation, and toxicity in herpetofauna, drawing on a structured literature search in Web of Science, Scopus, and PubMed (January 2015-March 2026). Field detection rates of MPs in amphibian larvae range from 26% in conservatively screened Central European populations to 73-80% in anuran tadpoles from high-anthropogenic-pressure Anatolian catchments, with fibrous polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) particles dominating the detected burden. Mechanistic evidence converges on oxidative stress cascades, hypothalamic-pituitary-thyroid axis disruption, gut and cutaneous microbiome dysbiosis, and compromised antiviral and antifungal immunity, with the latter potentially amplifying vulnerability to Batrachochytrium dendrobatidis and to ranavirus. Among reptiles, sea turtles display near-universal MP ingestion with documented maternal transfer to eggs; freshwater turtles, terrestrial squamates, and crocodilians remain critically understudied. Three structural asymmetries constrain current ecotoxicological risk characterization: taxonomic bias toward anurans and sea turtles, geographic bias toward the Global North, and experimental bias toward acute, supra-environmental laboratory exposures using pristine, single-polymer particles that fail to capture the chemical complexity of weathered field mixtures. We argue that MP burden may warrant consideration as a candidate stressor criterion within IUCN Red List assessments and within environmental risk assessment frameworks for freshwater and terrestrial biodiversity once a robust quantitative relationship between MP burden and demographic decline or population-level fitness has been established, and propose six hypothesis-driven research priorities: methodological standardization, reptile toxicokinetics, transgenerational epigenetics, MP-pathogen microbiome interactions and their translation into population viability models, temperature × MP interaction under climate warming, and population-genetic consequences of contemporary MP-driven selection, as the most tractable avenues for ecotoxicological progress and for the development of herpetofauna-specific risk characterization frameworks.},
}

@article {pmid42347889,
year = {2026},
author = {Wang, M and Wu, OY and Wallen, OG and Mozaffarian, D},
title = {Artificial and Other Non-Nutritive Sweeteners, the Microbiome, and Cardiometabolic Health.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {},
pmid = {42347889},
issn = {1534-6242},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Non-Nutritive Sweeteners/adverse effects ; *Cardiovascular Diseases ; Animals ; *Diabetes Mellitus, Type 2 ; },
abstract = {PURPOSE OF REVIEW: In this narrative review complemented by a novel meta-analysis, we critically analyzed current scientific evidence from RCTs and cohort studies regarding the impact of non-nutritive sweeteners (NNS) on cardiometabolic health, and assessed the interplay with the gut microbiome as a potential mechanistic pathway. We focused on the question of direct physiological effects of NNS, rather than the additional effects of energy displacement by NNS, to inform future research and the development of dietary and clinical guidelines.

RECENT FINDINGS: Cohort studies assessing NNS from all dietary sources suggest that total NNS and each commonly used NNS are associated with higher risk of type 2 diabetes, and that total intake and specific agents are associated with certain cardiovascular disease outcomes. These findings are consistent with prior evidence from cohorts focusing on NNS in beverages. Such observational evidence may be confounded by reverse causation: people at higher cardiometabolic risk choosing to use NNS. However, our new meta-analysis of RCTs with non-caloric comparators and a recent RCT on glycemia outcomes with human-to-mice microbiota transplant suggest that NNS have harmful effects on glucose-insulin homeostasis including fasting insulin, HbA1c, and glucose area under the curve during oral glucose tolerance test (OGTT), potentially mediated by effects on the composition and functional potential of the gut microbiome. The summed evidence supports potential long-term risk of cardiometabolic diseases associated with NNS intake and short-term harmful effects of NNS on glycemia. Future clinical trials of physiologic effects and molecular mechanisms will strengthen interpretations and causal inference. Given potential for harm, caution is warranted for the use of NNS.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Non-Nutritive Sweeteners/adverse effects
*Cardiovascular Diseases
Animals
*Diabetes Mellitus, Type 2

@article {pmid42348069,
year = {2026},
author = {Ernst, S and Dirschka, T},
title = {The Bacterial Landscape of Facial Skin: From Homeostasis to Skin Conditions.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42348069},
issn = {2193-8210},
abstract = {The human facial skin microbiome is a complex and dynamic ecosystem that plays a central role in maintaining skin health, immune regulation, and preventing dermatological skin conditions. Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis) are the most prominent bacterial species, with shifts in their relative abundance correlating with skin site, age, skin site, and health status. Exploring the facial microbiome offers exciting opportunities, though it requires careful methodological consideration. Sampling techniques vary in invasiveness and depth, which can influence the accuracy and reproducibility of microbiome profiles. While traditional cultivation methods provide valuable insights, they often miss nonculturable microbes, limiting the view of microbial diversity. Molecular approaches such as amplicon sequencing and metagenomics enable a more comprehensive understanding of microbial communities, even though they currently cannot distinguish between viable and nonviable microbes. Addressing these challenges will help unlock the full potential of facial microbiome research. A balanced facial skin microbiome is associated with healthy skin, whereas a dysbiosis of C. acnes and S. epidermidis is commonly observed in acne-prone skin and more pronounced clinically manifest acne. A comprehensive understanding of the diversity and distribution of C. acnes phylotypes, as well as distinct lineages of S. epidermidis associated with skin disorders, is crucial for developing targeted, microbiome-based cosmetic and medical treatments. Emerging strategies aim to restore microbial balance by leveraging the skin's native microbiota, including probiotic approaches. These strategies represent a promising yet still emerging approach, as current clinical evidence remains limited and further well-controlled studies are required, although they may offer benefits by enhancing microbial diversity and supporting skin barrier function.},
}

@article {pmid42348560,
year = {2026},
author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S},
title = {Insights into spatial dynamics of the microbiome and resistome across the conventional and organic dairy farms.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0352336},
doi = {10.1371/journal.pone.0352336},
pmid = {42348560},
issn = {1932-6203},
mesh = {Animals ; *Dairying/methods ; *Microbiota/genetics ; Cattle ; Milk/microbiology ; Farms ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Organic Agriculture ; },
abstract = {Antimicrobial resistance (AMR) poses a serious global threat to human and animal health. While AMR has been reported in various environments, its distribution across different ecological compartments within dairy farms remains poorly characterized. In this study, we used large-scale shotgun metagenomic sequencing to characterize the microbiome and resistome across multiple sampling sites within one organic and one conventional dairy farm, including teats, liners, water troughs, feed area, milking parlour mats, bedding sand, and milk. Our results indicate that microbial community composition and resistance gene profiles were largely comparable between the two study farms, with sample type (ecological niche) exerting a stronger influence on community structure than farm management type. Pseudomonadota, Bacillota, and Actinomycetota were the dominant phyla, while Aerococcus, Glutamicibacter, and Pseudomonas were the most prevalent genera. Glycopeptide resistance genes were the most abundant ARG class, followed by lincosamide and tetracycline resistance genes. Milk samples exhibited a distinct microbiome and resistome composition compared to environmental samples. Strong correlations between microbiome structure, resistome profiles, virulence factors, and metal resistance genes were observed across farm niches, highlighting the interconnected nature of microbial communities and resistance elements across dairy farm environments. These findings provide foundational data for targeted surveillance and management strategies to mitigate antimicrobial resistance in dairy production systems.},
}

Animals
*Dairying/methods
*Microbiota/genetics
Cattle
Milk/microbiology
Farms
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial/genetics
Metagenome
Metagenomics
Organic Agriculture

@article {pmid42348668,
year = {2026},
author = {Zhang, Y and Xie, Y and Zhang, Z and Gu, F and Xi, S},
title = {Elucidating the Pathophysiology and Diagnostic Biomarkers of Sepsis-Associated Encephalopathy: A Multiomics Approach.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002899},
pmid = {42348668},
issn = {1540-0514},
abstract = {Sepsis-associated encephalopathy (SAE) is a diffuse neurological injury that results from severe sepsis, and its underlying pathophysiological mechanisms remain largely unknown. This study aimed to elucidate the pathological basis of SAE and identify potential diagnostic biomarkers by integrating analyses of the intestinal microbiome, plasma metabolomics, and circulating microRNAs (miRNAs). We analyzed data from 50 patients who were divided into SAE or non-SAE groups. The results revealed significant differences in microbial composition between these groups, with a marked decrease in Bacteroides abundance and an increase in Enterococcus abundance in SAE patients. Compared with non-SAE patients, SAE patients presented notable alterations in LysoPC 18:3, linoleic acid, and miRNA PC-3p-535_63045 levels. Multiomics association analysis revealed positive correlations between Enterococcus and LysoPC 18:3, whereas Bacteroides and PC-3p-535_63045 were negatively correlated with linoleic acid. Gene prediction analysis indicated that PC-3p-535_63045 was enriched in PIK3R1, and a KEGG pathway analysis underscored the role of the PI3K‒Akt signaling pathway. PC-3p-535_63045 exhibited strong diagnostic performance, with an AUC of 0.850 (specificity of 0.867, sensitivity of 0.800). Comparative ROC analysis revealed no significant difference between PC-3p-535_63045 alone and the multiomics model. The integrated results from multiomics LASSO regression and random forest analyses suggest that PC-3p-535_63045 is a promising biomarker for the diagnosis of SAE. In conclusion, our multiomics analysis revealed a significant association among Bacteroides, PC-3p-535_63045, and linoleic acid, which suggests that the PI3K-Akt signaling pathway may play an important role in SAE progression. These findings deepen our understanding of the pathophysiological mechanisms underlying SAE and may ultimately enhance diagnostic and predictive capabilities for this condition.},
}

@article {pmid42348782,
year = {2026},
author = {Xia, H and Du, J and Kong, Y and Wang, Y and Xi, Y and Hu, C and Wang, W and Lei, L and Pan, X and Kang, L and Shi, J},
title = {Harnessing a Functional Rhizobial Partnership with Astragalus sinicus L. to Unlock Phytoremediation Potential for Soil Heavy Metals.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01468},
pmid = {42348782},
issn = {1520-5118},
abstract = {Phytoremediation of heavy metal-contaminated soils is often limited by phytotoxicity and metal availability. This study evaluated the phytoremediation potential of Astragalus sinicus L. and its symbiotic rhizobia. A nationwide soil survey revealed significantly lower arsenic (As) in planted versus unplanted soils, and key factors governing metal retention were attenuated in planted soils, indicating plant-mediated interference. Pot experiments confirmed that A. sinicus L. cultivation significantly reduced soil cadmium (Cd) (33.33%), lead (Pb, 39.73%), copper (Cu, 12.92%), and As (23.70%). Among rhizobial isolates, Mesorhizobium sp. XS6-2 exhibited the highest heavy metal tolerance. Inoculation with XS6-2 increased plant biomass and specifically enhanced chromium (Cr) and Pb remediation. Microbiome analysis showed that XS6-2 reshaped the rhizosphere community and strengthened microbial interactions. Our findings demonstrate a potent plant-microbe synergy that alleviates phytotoxicity and increases metal availability, offering an effective strategy to advance phytoremediation.},
}

@article {pmid42348961,
year = {2026},
author = {Li, Y and Ye, Y and Lou, L and Yao, Z and Ma, Y and Feng, Y and Liu, W and Wu, H and Sun, Z and Cheng, Z and Zhao, Y and Lai, Q},
title = {Multi-omics analysis of the gill-gut axis in Scylla paramamosain under acute low-salinity stress: Implications for ion and osmotic regulation.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108219},
doi = {10.1016/j.marenvres.2026.108219},
pmid = {42348961},
issn = {1879-0291},
abstract = {The mud crab Scylla paramamosain is a euryhaline species with significant potential for aquaculture in low-salinity environments. However, abrupt exposure of this species to very low saline conditions may exceed its osmoregulatory capacity. Here, we evaluated the physiological, gill transcriptomic, and gut microbiome responses of S. paramamosain after 48 h of acute exposure to salinities of 1-5‰, with a control salinity of 15‰. The survival rate exhibited a sharp decline at salinities ≤5‰ (After 48 h of acute exposure, the survival rates were 33.3% at 1‰, 56.7% at 2‰, 70% at 3‰, 76.7% at 4‰, 86.7% at 5‰, and 100.0% at 15‰), accompanied by increased gill Na[+]/K[+]-ATPase activity, reduced hemolymph osmolality, and elevated hemolymph ammonia content. These results indicate that ion-regulatory responses were activated but were insufficient to sustain osmotic homeostasis under severe acute low-salinity stress. Gill transcriptome analysis between the 1‰ and 15‰ groups identified 1853 differentially expressed genes. Upregulated genes were enriched in ion transport, ABC transporters, calcium signaling, and mitochondrial energy-related pathways, whereas downregulated genes were mainly associated with chitin metabolism, steroid hormone biosynthesis, and molting-related transcriptional processes. Gut 16S rRNA sequencing showed that acute exposure to 1‰ salinity reduced microbial alpha diversity and altered community composition, including reduced abundance of several marine-associated genera such as Photobacterium and enrichment of Lactobacillus. BugBase and PICRUSt2 based analyses indicated differences in predicted microbial phenotypes and inferred functional potential between the 1‰ and 15‰ groups; these predictions should not be interpreted as direct evidence of microbial functional activity. Overall, S. paramamosain showed coordinated physiological, gill transcriptional, and gut microbial responses to acute low salinity. Nevertheless, severe hypoosmotic exposure impaired osmotic balance and reduced survival. These findings provide baseline information for evaluating low-salinity tolerance and suggest that gradual acclimation should be considered when introducing this species into low-salinity culture systems.},
}

@article {pmid42349034,
year = {2026},
author = {Abdel-Moneim, AS and Al-Balushi, MS and Al-Jabri, AA},
title = {Post-COVID-19 immune dysregulation and autoimmune sequelae.},
journal = {Virology},
volume = {623},
number = {},
pages = {111017},
doi = {10.1016/j.virol.2026.111017},
pmid = {42349034},
issn = {1096-0341},
abstract = {SARS-CoV-2 infection induces profound immune dysregulation, including hyperinflammation, lymphopenia, and innate/adaptive immune imbalance. In some individuals, these responses persist beyond viral clearance, creating conditions that may disrupt immunological self-tolerance and precipitate autoimmune phenomena. We critically review mechanistic and clinical evidence linking SARS-CoV-2 infection to autoimmunity. Viral entry via ACE2/TMPRSS2, endothelial injury, and renin-angiotensin system dysregulation generates a pro-inflammatory milieu. Immune pathways, including molecular mimicry, bystander activation, epitope spreading, and persistent antigenic stimulation, can trigger the activation of autoreactive lymphocytes. Emerging evidence further implicates SARS-CoV-2-associated oral-gut microbiome dysbiosis and alterations in tryptophan and arginine metabolic checkpoints as contributors to chronic inflammatory signaling and impaired tolerance maintenance. We propose a mechanistic cascade from viral infection to dysbiosis to metabolic perturbation to loss of tolerance to autoantibody generation. Clinical manifestations encompass neurological, hematological, endocrine, and systemic autoimmune syndromes, with evidence of autoantibody emergence and post-COVID-19 immune sequelae. SARS-CoV-2 acts as an amplifier of autoimmune reaction in genetically susceptible hosts. Understanding these mechanisms is critical for identifying at-risk individuals and informing preventive and therapeutic strategies for post-COVID-19 autoimmune sequelae.},
}

@article {pmid42349523,
year = {2026},
author = {Muqaddas, K and Mahnoor, and Hayat, O and Islam, A and Khan, R and Naz, S},
title = {Cutaneous Leishmaniasis Promotes Skin Microbial Dysbiosis and Exacerbation of Local Inflammatory Responses.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108655},
doi = {10.1016/j.micpath.2026.108655},
pmid = {42349523},
issn = {1096-1208},
abstract = {Cutaneous leishmaniasis (CL) is a neglected tropical disease caused by protozoan parasites belongs to the genus Leishmania transmitted to humans by the bite of the infected female sand fly. Increasing evidence suggested that alterations in the skin microbiome may influence local inflammatory responses and disease progression in CL. This study aimed to investigate the microbial community shifts associated with CL lesions using paired lesional and contralateral healthy skin samples from infected individuals (n = 8). Leishmania tropica was identified in all clinical samples by ITS-1 real-time PCR analysis. Microbiome profiling was performed using 16S rRNA gene amplicon sequencing followed by quality filtering, taxonomic classification using Kraken2/Bracken and statistical analysis. Phylum level analysis demonstrated altered microbial composition in lesional skin, with predominance of Proteobacteria. At the genus and species levels, lesional samples exhibited reduced microbial evenness and enrichment of opportunistic bacterial genera, including Stenotrophomonas, Pseudomonas, Acinetobacter, and Staphylococcus. In comparison, contralateral healthy skin indicated dominance of environmental and commensal bacteria such as Luteibacter, Methylobacterium, and Paracoccus, representing a relatively stable microbial community (FDR p ≥ 0.05). Alpha diversity analysis showed reduced microbial diversity in CL infected samples, whereas beta diversity analysis indicated clear difference between CL infected and contralateral skin microbiomes. The findings indicate that CL is associated with localized microbial dysbiosis characterized by altered community structure. These findings highlight the significance of skin microbiome as a contributing factor in CL pathogenesis and suggest that microbiome targeted approach may complement existing therapeutic strategies.},
}

@article {pmid42349666,
year = {2026},
author = {Tang, E and Xiang, Q and Wang, N and Zhou, H and Chen, Z and He, Q and Yang, X and Liao, W},
title = {Nobiletin Ameliorates Hepatic Insulin Resistance by Modulating the Gut-Liver Axis.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110452},
doi = {10.1016/j.jnutbio.2026.110452},
pmid = {42349666},
issn = {1873-4847},
abstract = {Insulin resistance (IR) is a core pathological feature of type 2 diabetes mellitus (T2DM), with hepatic IR serving as a hallmark of systemic IR. Nobiletin (NOB) shows great potential in exerting hypoglycemic effects and improving IR; however, its molecular mechanisms remain incompletely elucidated. This study aims to investigate the molecular mechanisms by which nobiletin (NOB) ameliorates hepatic IR. Our results demonstrated that NOB effectively ameliorated IR in both high-fat diet/streptozotocin (HFD/STZ)-induced mice and palmitic acid (PA)-treated HepG2 cells. NOB administration improved dyslipidemia and attenuated histopathological damage in mouse liver tissue. Additionally, NOB reduced lipid accumulation in both the mouse liver and HepG2 cells by inhibiting de novo lipogenesis (DNL) and free fatty acids (FFA) uptake while enhancing mitochondrial fatty acid β-oxidation (FAO). Moreover, NOB suppressed hepatic gluconeogenesis by activating the PI3K/AKT/FOXO1 signaling pathway. NOB also enhanced the intestinal barrier function, as evidenced by the upregulation of ZO-1, Claudin-1, and Occludin proteins. Furthermore, NOB increased gut microbiome diversity, reduced the F/B ratio, and enriched beneficial taxa, including Verrucomicrobia, Lachnospiraceae, and Akkermansia muciniphila, thereby ameliorating gut microbiota dysbiosis. This study pioneers the elucidation of the cooperative mechanisms by which NOB ameliorates IR through the gut-liver axis and multi-target regulation of hepatic lipid metabolism, establishing a foundation for the development of NOB-derived nutraceuticals and pharmaceuticals.},
}

@article {pmid42349674,
year = {2026},
author = {El-Sehrawy, AAMA and Aljumaili, OI and Baig, MR and Nematov, O and Sapaev, IB and Badr, IH and Smerat, A and Basunduwah, TS},
title = {Diagnostic and prognostic biomarkers in PCOS: Navigating insulin resistance, systemic inflammation, and endometrial receptivity.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121197},
doi = {10.1016/j.cca.2026.121197},
pmid = {42349674},
issn = {1873-3492},
abstract = {Polycystic ovary syndrome (PCOS) is a highly prevalent and phenotypically diverse endocrine disorder in which insulin resistance (IR) serves as a central molecular driver of major metabolic and reproductive complications, including infertility, obesity, and increased long-term cardiovascular risk. This review examines the complex pathophysiology of PCOS, emphasizing how chronic systemic low-grade inflammation, gut microbiome dysbiosis, and oxidative stress interact to worsen hyperinsulinemia and hyperandrogenemia. It also highlights the clinical value of emerging diagnostic and prognostic biomarkers to improve risk stratification and patient management. Systemic biomarkers, such as pro-inflammatory cytokines, circulating endotoxemia arising from increased intestinal permeability, and epigenetic regulators including miR-146a, may provide prognostic insight into the trajectory of metabolic deterioration. In parallel, endometrial biomarkers, including the glucose transporter GLUT4, implantation-associated genes such as HOXA10, and inflammatory mediators like TNF-α, can support evaluation of impaired uterine receptivity, prediction of assisted reproductive technology (ART) outcomes, and stratification of miscarriage risk. By mapping key interactions within the gut-immune-metabolic axis and detailing localized endometrial dysfunction, this review proposes a framework for integrating targeted biomarker profiling into clinical practice to enable personalized, biomarker-informed interventions aimed at restoring fertility and metabolic health in patients with PCOS.},
}

@article {pmid42349701,
year = {2026},
author = {Huang, J and Older, CE and Heckman, TI and Jordan, HR and Griffin, MJ and Allen, PJ and Grant Reifers, J and Goodman, PM and Yamamoto, FY},
title = {Autochthonous probiotic Lactococcus lactis MA5 improves recovery from acute hypoxia stress and resistance to Edwardsiella ictaluri in hybrid catfish (Ictalurus punctatus × I. furcatus).},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111544},
doi = {10.1016/j.fsi.2026.111544},
pmid = {42349701},
issn = {1095-9947},
abstract = {Dietary supplementation with probiotics is considered an effective strategy to enhance aquaculture production efficiency and disease resistance. Recent research has highlighted the value of using autochthonous probiotics in aquaculture. Herein, an autochthonous probiotic strain (Lactococcus lactis MA5) isolated from pond-raised hybrid catfish (Ictalurus punctatus × I. furcatus) in a previous study was investigated for its ability to improve host recovery from acute hypoxia and resistance to bacterial infection. Hybrid catfish were fed a control diet, or diets containing either 10[4] or 10[6] CFU/g MA5 for 56 days. After the feeding trial, subsets of fish were subjected to either acute hypoxia stress challenge or Edwardsiella ictaluri challenge. Fish fed MA5 exhibited enhanced growth performance without changes to body condition indices. Following acute hypoxia challenge, MA5-supplemented fish showed increased blood hemoglobin, red blood cell counts, and total protein concentration compared to the control. In addition, MA5 led to upregulated expression of gpx1, a gene encoding an antioxidant enzyme, in the intestine. Lastly, fish fed 10[6] CFU/g of MA5 displayed significantly higher survival when exposed to E. ictaluri. These data suggest dietary supplementation with the autogenous probiotic L. lactis MA5 can promote growth, support acute hypoxia recovery, and improve resistance to E. ictaluri in hybrid catfish.},
}

@article {pmid42349924,
year = {2026},
author = {Jeong, YS and Kim, KO and Park, YE and Lee, YJ and Seo, J and Kim, TW and Kim, BH and Yim, SV and Kim, HS and Lee, JY and Bae, JW and Choe, BH and Kang, B and Lee, CK},
title = {Age-Related Microbial Differences in Newly Diagnosed Crohn's Disease Reveal the Distinct Enrichment of Oral-Associated Taxa in Pediatric Patients.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl260027},
pmid = {42349924},
issn = {2005-1212},
abstract = {BACKGROUND/AIMS: Crohn's disease (CD) presents differently by age of onset, but the microbial distinctions between pediatric and adult CD are currently unclear.

METHODS: In this study, the gut microbiota of fecal samples collected from newly diagnosed patients with CD (n=88; pediatric 44, adult 44) and their age- and sex-matched healthy controls (HCs, n=112) was analyzed using 16S rRNA gene amplicon sequencing. Differential abundance analysis was performed using MaAsLin2 to identify age-specific microbial signatures, and enterotypes were classified using Dirichlet multinomial mixture modeling.

RESULTS: Both pediatric and adult patients with CD exhibited shared dysbiosis characterized by reduced alpha diversity (p<0.001), enrichment of CD-associated pathobionts, such as Enterobacteriaceae and Enterococcaceae, and depletion of short-chain fatty acid-producing taxa within Ruminococcaceae and Lachnospiraceae. Notably, enterotyping revealed that individuals with CD converged toward a shared, pathobiont-dominated enterotype regardless of age, overriding the age-dependent stratification observed in HCs. Despite this shared convergence, differences in age-stratified comparisons were observed. Adult CD patients exhibited enrichment of resident pathobionts such as Ruminococcus gnavus and Clostridium innocuum, whereas pediatric CD patients exhibited unique and pronounced enrichment of Pasteurellaceae, Neisseriaceae, and Gemellaceae (false discovery rate <0.1).

CONCLUSIONS: In newly diagnosed patients, CD is characterized by shared dysbiosis and convergence toward a disease-specific enterotype across age groups. However, this was accompanied by distinct microbial features, specifically, the enrichment of taxa previously reported as prevalent in the oral microbiome in children versus resident pathobionts in adults. These findings suggest that age at disease onset is associated with age-stratified differences in microbial profiles in CD.},
}

@article {pmid42349990,
year = {2026},
author = {Cheng, X and Huang, H and Fan, Z and Wang, H and Zheng, X and Dong, L and Li, M and Zhang, G and Mi, S},
title = {Clinical efficacy of portable, cost-effective manual thermal pulsation for obstructive meibomian gland dysfunction and factors associated with therapeutic efficacy.},
journal = {BMJ open ophthalmology},
volume = {11},
number = {2},
pages = {},
doi = {10.1136/bmjophth-2026-002769},
pmid = {42349990},
issn = {2397-3269},
mesh = {Humans ; *Meibomian Gland Dysfunction/therapy/metabolism ; Female ; Male ; *Meibomian Glands/metabolism ; Tears/metabolism/chemistry ; Treatment Outcome ; Middle Aged ; *Hyperthermia, Induced/methods/economics/instrumentation ; Cost-Benefit Analysis ; Adult ; Aged ; Microbiota ; Follow-Up Studies ; },
abstract = {OBJECTIVE: To evaluate the efficacy and safety of portable, cost-effective manual thermal pulsation as a single therapy for meibomian gland dysfunction (MGD) and to compare the microbiota and lipid composition in subjects with different therapeutic efficacy.

METHODS AND ANALYSIS: In this single-centre, randomised, positive-controlled clinical trial, 84 subjects were randomly assigned (1:1) to receive a single treatment of manual (self-developed device) or automatic (Lipiflow) thermal pulsation and followed up for 4 weeks, 76 of which were finally analysed. Efficacy was evaluated by Δ Meibomian Gland Score (MGS) (Δ variable=parameter at follow-up-parameter at baseline), Δ non-invasive break-up time (NIBUT), Δ standard patient evaluation of eye dryness (SPEED), Δ Meibomian Gland Expressibility Score (MES) and Δ corneal fluorescein staining (CFS), with safety investigated. Subjects who underwent manual thermal pulsation were further divided into two subgroups based on whether ΔMGS ≥-2, meibum microbiome and lipid metabolomics in the subgroups were analysed.

RESULTS: ΔMGS, ΔNIBUT, ΔSPEED, ΔMES and ΔCFS were not significantly different between manual and automatic thermal pulsation groups in 4 weeks (both p>0.05), indicating non-inferior efficacy of manual thermal pulsation. No serious ocular or device-related adverse events were reported. A more complex meibum microorganism diversity and 46 differentially expressed lipids (such as triglycerides, diglycerides, ceramides and oxidised species) were identified in those with a relatively weak therapeutic efficacy.

CONCLUSIONS: Portable, cost-effective manual thermal pulsation demonstrated non-inferiority to automatic thermal pulsation for MGD during the 4-week follow-up period, with therapeutic efficacy associated with meibum micro-organism and lipid components.},
}

Humans
*Meibomian Gland Dysfunction/therapy/metabolism
Female
Male
*Meibomian Glands/metabolism
Tears/metabolism/chemistry
Treatment Outcome
Middle Aged
*Hyperthermia, Induced/methods/economics/instrumentation
Cost-Benefit Analysis
Adult
Aged
Microbiota
Follow-Up Studies

@article {pmid42350218,
year = {2026},
author = {Lee, GA and Tseng, LW and Wang, CC and Lee, CJ and Chang, YW and Yang, YSH and Chang, KW and Chen, YC and Tseng, SH},
title = {Spleen-tonifying formula alleviates social deficits, gut dysbiosis, and hypomyelination in a perinatal injury model.},
journal = {Pediatrics and neonatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pedneo.2026.02.008},
pmid = {42350218},
issn = {2212-1692},
abstract = {BACKGROUND: Perinatal injury has been shown to induce autism spectrum disorder (ASD)-like phenotypes in offspring, including social behavioral deficits, hypomyelination, and gut microbial imbalances. Spleen-tonifying formulas (STFs), derived from traditional Chinese medicine, have demonstrated efficacy in modulating the brain-gut axis, particularly by alleviating hypomyelination and microbial dysbiosis in offspring with maternal immune activation-induced perinatal injury. However, whether STF can improve behavioral deficits in such offspring with perinatal injury remains unclear.

METHODS: To evaluate the therapeutic efficacy of STF, a battery of behavioral tests-including the three-chamber social interaction, grooming, rotarod, and open-field tests-was conducted in a two-hit perinatal injury rat model induced by prenatal lipopolysaccharide (LPS) exposure and postnatal hypoxic stress. Starting at 6 weeks of age, rats received daily oral administration of STF extract or distilled water for 14 days before behavioral assessments. Myelination and oligodendrocyte density in the prefrontal cortex were examined via immunohistochemistry. Fecal microbiota composition was profiled using 16S rRNA gene sequencing, and in vitro oxidative stress assays were performed in human oligodendroglioma (HOG) cells.

RESULTS: STF treatment significantly improved social behavior and restored myelination in offspring with perinatal injury, as evidenced by increased MBP expression and elevated numbers of Olig2[+] and NG2[+] cells in the prefrontal cortex. In vitro, STF protected differentiated HOG cells from H2O2-induced oxidative stress and cell death by sustaining AKT activation and inhibiting ERK signaling. Gut microbiota analysis revealed that STF effectively ameliorated dysbiosis, notably enriching bacterial families such as Oscillospiraceae and Colidextribacter, which were positively correlated with improved social behavior, suggesting potential as biomarkers of therapeutic response.

CONCLUSIONS: Our results indicate that oral STF treatment is associated with improvements in social behavior, myelination, and gut microbial composition in offspring with perinatal injury, underscoring the need for future studies to elucidate the potential causal relationships among these outcomes.},
}

@article {pmid42350404,
year = {2026},
author = {Cui, J and Chen, Z and Yan, S and Zhao, L and Degermendzhi, AG and Liu, H and Fu, Y},
title = {Simulated microgravity weakens wheat root microbial network against pathogens.},
journal = {NPJ microgravity},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41526-026-00623-y},
pmid = {42350404},
issn = {2373-8065},
support = {No. 23-44-00059//Russian Science Foundation/ ; 32471289//National Natural Science Foundation of China/ ; 32261133528//International Cooperation and Exchange of the National Natural Science Foundation of China/ ; KJZ-YY-NSM0603//Space Utilization System of the China Manned Space Program/ ; },
abstract = {Fungal pathogens are well-recognized biotic stressors for plants under terrestrial gravity and also pose risks to space crop production, but their effects on root-associated microbial networks under microgravity conditions remain poorly understood. Here, we profiled bacterial and fungal communities in wheat seedlings with or without Fusarium graminearum infection under normal gravity and simulated microgravity, and linked network properties to plant growth and hormone profiles. Although bacterial and fungal α-diversity showed no significant differences among treatments and Bray-Curtis β-diversity showed limited separation, co-occurrence networks revealed that infection disrupted bacterial-bacterial and bacterial-fungal networks more strongly under simulated microgravity than under normal gravity, whereas fungal-fungal networks were largely unchanged. Bacterial network characteristics explained more variation in plant performance than bacterial-fungal network characteristics. Structural equation modeling showed that simulated microgravity reduced endosphere bacterial network stability, which was positively associated with plant performance, especially jasmonic acid and cytokinin levels. Random forest analysis identified Paenibacillus and Microbacteriaceae-related taxa as key predictors of bacterial network stability. These findings support microbiome-based strategies to enhance plant resilience in space systems.},
}

@article {pmid42350492,
year = {2026},
author = {Dini, H and Chenghang, S and Tong, X and Yixin, L and Tianchun, P and Shunfu, H and Yanqiang, Y and Yibo, H},
title = {Integrated analyses of metagenomics, metabolomics and culture-based assays reveal functional roles of gut microbiota in Felidae.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01066-9},
pmid = {42350492},
issn = {2055-5008},
support = {32370552//National Natural Science Foundation of China/ ; 32325010//National Natural Science Foundation of China/ ; 2023YFF1304800//National Key Program of Research and Development of Ministry of Science and Technology/ ; },
abstract = {The functional roles of gut microbiota in carnivores remain poorly understood. Here, we integrated metagenomics, metabolomics, proteomics and culture-based functional assays to characterize metabolic potential of gut microbiota across 14 captive Felidae species. Comparative metagenomics analysis revealed that the Felidae gut microbiome is distinct from that of non-Felidae and reflects carnivorous dietary patterns. Genus-level core microbiota were dominated by Clostridium, Collinsella and Bacteroides, with functional enrichment in carbohydrate and amino acid metabolism. Of 219 reconstructed metagenome-assembled genomes (MAGs), 27 were identified as core MAGs containing proteases- and lipases- encoding genes, with ATP-dependent Clp proteases predominating and enriched KEGG orthologs mainly associated with amino acid metabolism. Fecal metabolomics identified 1316 metabolites shared among Felidae species, with KEGG analysis showing they were involved in amino acid and lipid metabolism and significantly enriched in protein digestion and absorption pathway. The amino acid- and lipid-related metabolites were correlated with the relative abundance of core MAGs. Culture-based assays revealed proteolytic and lipolytic activities across isolates, supported by proteomics evidence of predominant ATP-dependent proteases. In vitro fermentation with representative isolates generated fatty-acid-dominated metabolites consistent with fecal metabolomic profiles. Together, our findings demonstrate that Felidae gut microbiota play a critical role in amino acid metabolism for carnivory.},
}

@article {pmid42350508,
year = {2026},
author = {Phumthanakorn, N and Tanpradit, N and Arya, N and Wattananit, P and Kusonmano, K and Sutheeworapong, S and Cheevadhanarak, S and Langkaphin, W and Kittisirikul, N and Toniti, W and Sangsuriya, P and Income, N and Boonyarittichaikij, R},
title = {Gut microbiome diversity across seasons and locations in thai captive Asian elephants (elephas maximus).},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42350508},
issn = {2045-2322},
mesh = {Animals ; *Seasons ; *Elephants/microbiology ; Thailand ; *Gastrointestinal Microbiome ; Feces/microbiology ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; },
abstract = {The gut health of captive Asian elephants (Elephas maximus) is strongly influenced by human management. However, studies simultaneously examining the effects of both geographical location and season on the gut microbiome of these elephants remain limited. In this study, we focused on two geographically distant and ecologically distinct provinces in Thailand, which differ markedly in management practices, climate, vegetation, and landscape. Fecal samples from 20 to 10 captive Asian elephants in Lampang and Kanchanaburi, respectively, were collected during the wet and dry seasons. The gut microbiome was dominated by the phyla Firmicutes and Bacteroidota across all seasons and locations. Alpha diversity indices indicated that samples from the Lampang-wet group presented the highest diversity, whereas those from the Kanchanaburi-dry group showed the lowest. Beta-diversity analysis revealed significant differences in microbial community structure among the four groups. Functional prediction analysis indicated that microbial metabolic pathways varied between seasons, with carbohydrate metabolism pathways being more enriched in the wet season. Differences in microbiome composition and specific bacterial taxa were observed between samples from Lampang and Kanchanaburi, reflecting the unique management and environmental conditions of each region. Overall, microbial diversity was generally higher during the wet season compared to the dry season.},
}

Animals
*Seasons
*Elephants/microbiology
Thailand
*Gastrointestinal Microbiome
Feces/microbiology
Biodiversity
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics

@article {pmid42350644,
year = {2026},
author = {Suissa, D and Fidelle, M and Reich, E and Pham, TN and Thomas, S and Björk, JR and Liu, P and Zhao, L and Kitaoka, K and Piard, E and Lebhar, I and Tian, AL and Thelemaque, C and Alves Costa Silva, C and Deutsch, E and Loriot, Y and Segata, N and Piccinno, G and Hospers, GAP and Maleki Vareki, S and Silverman, MS and Lenehan, JG and Bataille, V and Boulate, D and Kuznetsova, T and Weersma, RK and Messaoudene, M and Durand, S and van der Aalst, CM and de Koning, HJ and Schuler-Thurner, B and de Vries, IJM and Rafie, E and Saliby, RM and Machaalani, M and Haferkamp, S and Schilling, B and Porcari, S and Ciccarese, C and Iacovelli, R and Cremolini, C and Choueiri, TK and Elkrief, A and Kroemer, G and Heinzerling, L and Chamoto, K and Ianiro, G and Routy, B and Derosa, L and Paragios, N and Zitvogel, L},
title = {Metabolic determinants of cancer immunotherapy outcomes identified by plasma profiling.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {42350644},
issn = {1546-170X},
abstract = {Immune-checkpoint inhibitors benefit a subset of patients with advanced cancer, and the metabolic determinants of response remain unclear. Here, using targeted metabolomics and metagenomics, we profiled 4,336 plasma samples from 1,714 patients across five tumor types and 16 cohorts spanning Europe and North America, longitudinally sampled during five immune-checkpoint inhibitor-based treatment modalities, including fecal microbiota transplantation. A multimodal machine-learning framework integrating 154 metabolites with clinical variables identified five metabolites, age, body mass index and renal function as predictors of 12-month progression-free survival. The model achieved areas under the curve of 0.88 in training and 0.73 in validation cohorts of 105 and 30 patients, respectively and generalized across seven external cohorts. Histidine was a favorable prognostic feature of survival, whereas long-chain fatty acids and succinate were negatively associated with outcome. Histidine supplementation enhanced antitumor immunity in mice. Histidine-rich diets improved progression-free survival in patients lacking dysbiotic microbiome signatures associated with histidine catabolism.},
}

@article {pmid42350849,
year = {2026},
author = {Ceballos-Castillo, J and Echeverry-Gallego, RA and Martínez-Pachón, D and Moncayo-Lasso, A and Vanegas, J},
title = {Microbial communities and pharmaceutical contaminants in the water-soil-plant continuum of sugarcane crops irrigated with contaminated waters from the Cauca River Valley, Colombia.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42350849},
issn = {1614-7499},
abstract = {"Agricultural irrigation with contaminated water poses a major risk to food security and public health. This study examined contaminant transfer across the water-soil-plant continuum in sugarcane crops irrigated with water from the Cauca River, Colombia. Microbial community composition was characterized using 16S rRNA gene sequencing, while pharmaceutical active compounds (PhACs) in irrigation water and sugarcane plants were quantified by UHPLC-MS/MS. Microbial analyses revealed a potential biological pathway of microorganisms from water and soil into plant endophytic tissues. Bacterial diversity decreased markedly, from more than 400 genera identified in water and soil to only 64 genera detected within endophytic tissues. Nine potentially pathogenic genera-including Escherichia-Shigella, Pseudomonas, and Bacillus- were found across all matrices, suggesting microbial internalization. Bioinformatic predictions indicated the presence of genes associated with virulence traits (e.g., antimicrobial resistance and biofilm formation) as well as beneficial functions such as nitrogen fixation and phosphate solubilization. In parallel, high concentrations of PhACs were detected in irrigation water, including valsartan (up to 1309 ng L[-][1]) and diclofenac (up to 969 ng L[-][1]), whereas none or only low concentration detected in sugarcane tissues. Overall, the primary risk to human health appears to stem not from chemical uptake but from microbial infiltration shaped by environmental pressures. Therefore, managing plant-associated microbiomes is essential to mitigate health risks while harnessing biotechnological potential for sustainable agriculture."},
}

@article {pmid42350936,
year = {2026},
author = {Yang, L and Mi, X and Dai, H and Li, X and Wang, Q and Wu, X and Gong, X},
title = {Skin microbiome signatures track uremic pruritus severity in hemodialysis patients.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05332-w},
pmid = {42350936},
issn = {1471-2180},
support = {YLZLXZ25G015//National Institute of Hospital Administration (NIHA), National Health Commission, China/ ; },
abstract = {Chronic kidney disease-associated pruritus (CKD-aP) is frequent in patients receiving maintenance hemodialysis and is often difficult to control. While systemic drivers are recognized, how the chronically altered skin microenvironment and its microbiome relate to itch severity remains insufficiently defined. In this single-center study, hemodialysis patients and healthy controls underwent pooled skin microbiome profiling by full-length 16 S rRNA sequencing, with differential taxa, functional features, and clinical associations analyzed using multivariate and correlation-based approaches. Compared with healthy controls, hemodialysis patients showed higher skin microbial richness and a distinct overall community structure. Within the dialysis cohort, increasing pruritus burden coincided with compositional turnover and depletion of canonical commensals. Machine learning and LEfSe highlighted pruritus-associated species-level signatures, with Propionibacterium sp. LG among the most informative features and Epilithonimonas hominis recurring across models. Network analysis indicated progressive fragmentation with greater pruritus severity, reflected by reduced connectivity and increased modularity. Predicted functional profiles suggested dialysis-associated alterations in microbial functional potential, with higher predicted representation of lipid biosynthesis pathways and lower predicted representation of core energy and nucleotide metabolism; pruritus severity was further linked to reductions in aerobic/energy-related functions. Phenotype prediction indicated higher inferred stress-tolerant and potentially pathogenic traits in pruritic patients. Taken together, hemodialysis was associated with broad skin microbiome remodeling, and worsening CKD-aP was accompanied by commensal loss, disrupted microbial interaction networks, and predicted functional shifts consistent with a more stress-adapted community. These features may reflect responses to the altered pruritic skin environment and provide microbiome-informed biomarkers and hypotheses for future mechanistic studies in CKD-aP.},
}

@article {pmid42350938,
year = {2026},
author = {Giuliano, F and Petta, G and Terzaghi, M and Tangredi, DN and Guarino, F and Castiglione, S and Cicatelli, A},
title = {Integrated plant and rhizosphere response to gadolinium exposure in hydroponically grown tomato plants.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09341-9},
pmid = {42350938},
issn = {1471-2229},
support = {CUP D43C23001170006//Horizon 2020 Framework Programme/ ; ORSA229034//Fondo d'Ateneo per la Ricerca di Base FARB 2022/ ; ORSA238273//Fondo d'Ateneo per la Ricerca di Base FARB 2023/ ; },
abstract = {Rare earth elements (REEs), comprising the lanthanides, scandium, and yttrium, are increasingly released into the environment due to anthropogenic activities but are not routinely monitored as conventional environmental contaminants. Gadolinium (Gd), used as a contrast agent in magnetic resonance imaging, is continuously discharged into aquatic ecosystems. While Gd effects on plants have been partially explored, its impact on plant physiology and plant-microbiome interactions remains poorly understood. This study investigated the effects of 150 µM Gd (23.6 mg L[- 1], 23.6 ppm) on tomato plants (Solanum lycopersicum L.) grown in hydroponics using a phosphate-free nutrient solution to prevent Gd precipitation and ensure its bioavailability. A multidisciplinary approach was employed, integrating morphological, physiological, biochemical, and molecular analysis. Plant growth, root system architecture, antioxidant defence responses, calcium content, Gd accumulation and translocation were assessed, together with changes in the composition and predicted functional potential of the rhizosphere microbiome. Prolonged Gd exposure significantly impaired tomato growth reducing leaf fresh weight from 7.90 g in control plants to 3.15 g in treated seedlings and markedly altering root morphology. Stress conditions triggered strong oxidative responses, while Gd accumulated predominantly in roots (5.32 mg g[- 1]), with no detectable translocation to aerial tissues. Rhizosphere microbial community composition was severely altered (e.g., Burkholderiales declined to 42% in Gd-treated plants). This work represents one of the first integrated assessments of plant morphological, physiological, biochemical and microbiome-level responses of a crop plant and its rhizosphere microbiome to Gd exposure, providing new insights into the ecological and agronomic implications of emerging REEs contamination.},
}

@article {pmid42351035,
year = {2026},
author = {He, T and Ai, Z and Han, Q and Chen, F and Wang, H and Wu, M and Chen, Q and Li, S and Wang, L and Yang, Z and Wang, P and Wang, Z and Xiang, Z},
title = {Microbiome-host interactions in different pathomic subtypes of early-stage lung adenocarcinoma.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04440-7},
pmid = {42351035},
issn = {1471-2466},
support = {82171931//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Microbiome-host interactions in different pathological subtypes of the early-stage lung adenocarcinoma (LUAD) remain poorly understood.

METHODS: We conducted histopathological and imaging analysis on a cohort of 106 Chinese patients with LUAD. Further deep analysis of the lung tissue microbiome, serum metabolome, and host transcriptome was performed. Using correlation analysis, microbial genetic information, and established metabolite-human gene pairs, we integrated multi-omics data to explore potential associations between the microbiome, microbial metabolites, and host gene expression.

FINDINGS: We identified distinct groups based on malignancy severity. Massilia, Sphingomonas, Staphylococcus, and Brevundimonas may influence host gene expression through their metabolites, affecting the progression of LUAD. We used Mendelian Randomization(MR) and found suggestive evidence that the levels of key metabolites (serotonin, uric acid) are negatively associated with LUAD risk.

INTERPRETATIONS: This study demonstrates that pathological images of early-stage LUAD cells can reflect potential clinical differences, and some microbial-metabolite-gene potential associations have been found in early-stage LUAD, which may affect the development of early-stage lung adenocarcinoma.

FUNDING: This research was supported by grants from the National Natural Science Foundation of China (No. 82171931), the Guangdong Basic and Applied Basic Research Foundation Enterprise Joint Fund (2025).},
}

@article {pmid42351093,
year = {2026},
author = {Zhu, C and Wang, T and Zhang, W and Guo, A and Ji, S and Liu, C and Ma, R and Song, L and Wang, Y and Yao, P and Lin, L and Li, L},
title = {Comparative analysis of MinION and MiSeq using 16S rRNA gene amplicon sequencing in human gut microbiome.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-026-01182-6},
pmid = {42351093},
issn = {1472-6750},
abstract = {The genetic classification of microbial populations at high taxonomic resolution is crucial for clinical diagnosis and treatment. The classification of complex bacterial communities in the human gut was examined in this study by utilizing amplicon sequencing of the 16S ribosomal RNA (rRNA) gene. The influence of different sequencing platforms and amplicon regions on this classification was investigated. Nineteen human fecal samples were analyzed using both Nanopore MinION and Illumina MiSeq platforms.The main objective of the analysis was to assess how effectively these platforms can characterize gut microbiota at the Amplicon Sequence Variant (ASV), genus, and species levels, taking into account various amplicon regions within the 16S rRNA gene. The findings reveal significant disparities between the two platforms. In particular, the MinION platform demonstrates higher values in terms of ASV and species richness, as well as diversity (both alpha and beta diversity) compared to the MiSeq platform. These variations are dependent on the specific targeted amplicon region of the 16S rRNA gene. However, despite these differences in richness and diversity, there is a notable level of consistency observed in detecting the presence of dominant microbial taxa across both platforms, although their relative abundances varied significantly. Notably, the study emphasizes that the choice of primers used for amplification exerts the most significant impact on the classification results at the genus level, surpassing the influence of the sequencing platform itself. This research provides valuable insights into the strengths and limitations of long-read and short-read sequencing in the context of classifying complex gut microbiota, particularly in clinical microbiology.},
}

@article {pmid42351162,
year = {2026},
author = {Cui, Y and Liu, Y and Dou, F and Mao, J},
title = {Letter to the Editor Regarding "The microbiome of host saliva, gastric fluid, and gastric mucosa as accurate diagnostic tools for gastric cancer detection".},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42351162},
issn = {1479-5876},
support = {First Affiliated Hospital of Dalian Medical University//First Affiliated Hospital of Dalian Medical University/ ; },
}

@article {pmid42351261,
year = {2026},
author = {Takahashi, H and Fujii, T and Yamada, C and Fujiki, K and Kuramitsu, K and Okuda, S and Tanaka, M and Asahina, T and Funasaka, K and Ohno, E and Hirooka, Y and Tochio, T},
title = {Preventive effect of heat-killed Lactiplantibacillus plantarum FM8 in an ovalbumin-induced food allergy murine model.},
journal = {Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13223-026-01048-8},
pmid = {42351261},
issn = {1710-1484},
abstract = {BACKGROUND: Paraprobiotics, the non-viable microbial cells with health benefits, have gained interest as candidates for preventing food allergies owing to their safety and stability. Heat-killed Lactiplantibacillus plantarum FM8 (FM8) has been reported to induce interleukin (IL)-10 production in dendritic cells in vitro; however, its in vivo efficacy as a standalone intervention remains unexplored. We investigated the preventive effect of heat-killed FM8 in a murine model of ovalbumin (OVA)-induced food allergy.

METHODS: BALB/c mice were assigned to control, OVA-induced allergy, or three FM8 treatment groups receiving FM8 at low (2 × 10⁹ CFU/day), medium (1 × 10¹⁰ CFU/day), or high (5 × 10¹⁰ CFU/day) doses. Food allergy was induced by repeated OVA sensitization and challenge. Allergy symptoms, OVA-specific immunoglobulin E (IgE), and IL-10 levels were measured. Tight junction gene expression, mucin production, gut microbiota composition, and short-chain fatty acids (SCFAs) were also analyzed.

RESULTS: FM8 supplementation attenuated allergic responses in a dose-dependent manner. Allergy symptom scores were reduced in the High group, and the rectal temperature decline following OVA challenge was ameliorated in both the Med and High groups. The sensitization-induced increase in OVA-specific IgE was also attenuated in these groups. IL-4 expression in Peyer's patches was reduced, whereas colonic IL-10 expression and serum IL-10 levels were increased in the High group. FM8 supplementation was further associated with increased ileal expression of tight junction-related genes (Occludin, Claudin-1 and Zo-1) and Muc2, along with a trend toward increased fecal mucin levels; however, no comparable changes in tight junction-related gene expression were observed in the colon. Although taxa with reported SCFA-producing potential were enriched in the High group, cecal acetate and propionate levels remained unchanged, while butyrate levels were decreased.

CONCLUSIONS: FM8 may prevent food allergy by promoting IL-10-associated immunoregulation and enhancing gut barrier-related responses, without a corresponding increase in cecal SCFA concentrations. The contribution of SCFA-related mechanisms remains to be clarified, and further studies are needed to determine clinically feasible dosing and efficacy in humans.},
}

@article {pmid42351266,
year = {2026},
author = {Chen, T and Xiao, J and Li, S and Peng, R and Xu, Y and Zhuang, Y and Zhao, X and Sha, M and Wang, J and Ma, J and Wang, W and Gao, J and Ma, M and Li, S and Cao, Z and Liu, S},
title = {Differential rumen and hindgut microbiome and metabolome in Holstein female calves with divergent feed efficiency.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02446-1},
pmid = {42351266},
issn = {2049-2618},
abstract = {BACKGROUND: Significant environmental problems have challenged animal agriculture, improving feed efficiency in animals has become a vital research direction for sustainable agriculture. Bacteria play a critical role in the feed efficiency of animals. However, our current understanding of bacteria communities in the gastrointestinal tract of high-feed efficiency animals and their metabolic mechanisms remains unclear.

RESULTS: Twenty Holstein female calves were used in this multi-omics study that integrated metagenomic and metabolomic analyses of 20 Holstein female calves to investigate feed efficiency, as measured by residual feed intake (RFI). From an initial cohort of 84 calves, the 10 with the highest RFI (HRFI, low efficiency) and the 10 with the lowest RFI (LRFI, high efficiency) were selected at 84 days of age. Rumen fluid, feces, and serum samples from these calves were collected for subsequent analyses. We found that LRFI calves harbored rumen and fecal microbiomes with significantly different community structures and co-occurrence networks compared to HRFI calves. Multi-omics integration identified robust microbial and metabolite biomarkers discriminating RFI groups. These microbiomes were functionally linked to differential nutrient utilization, LRFI calves were characterized by enhanced starch and protein digestibility coupled with propionate-oriented fermentation, associated with key species like Erysipelotrichaceae_bacterium and Hungatella_sp. Conversely, HRFI calves showed higher fat digestibility and acetate production. Notably, serum glutamate was enriched in LRFI calves despite lower intake, correlating with potential microbial metabolites (ribitol, taurine). Subsequent validation confirmed that glutamate supplementation in mice improved nitrogen metabolism and gut barrier function.

CONCLUSIONS: In summary, this multi-omics study reveals that high feed efficiency in calves is associated with distinct microbial ecosystems characterized by functions such as starch degradation and propionate production, where glutamate metabolism serves as a central node. Video Abstract.},
}

@article {pmid42351283,
year = {2026},
author = {Salazar-Hamm, PS and Romero-Jiménez, MJ and Caimi, NA and Amses, KR and Marshall Hathaway, JJ and Buecher, DC and Valdez, EW and Caesar, LK and Porras-Alfaro, A and Northup, DE},
title = {Bat skin microbiome and the association of ecoregion and bat species that impacted isolation of members with bioactivity against Pseudogymnoascus destructans.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00591-4},
pmid = {42351283},
issn = {2524-4671},
abstract = {BACKGROUND: Microbiome constituents can serve as a primary defense against vertebrate pathogens. This may be crucial to the protection of North American bats who have been devastated over the last two decades by the fungal pathogen, Pseudogymnoascus destructans (Pd), which causes white-nose syndrome (WNS). The objectives of this study were to isolate members of the external microbiome of bats post-hibernation in Arizona and New Mexico before the arrival of WNS, to identify those bacteria with bioactivity against Pd, and to determine the variables associated with antifungal strains.

RESULTS: In this study we isolated 2,936 bacteria from the fur and skin of 314 bats across 12 bat species at 6 sites across New Mexico and Arizona from 2013 to 2016. Selective media were used to promote the isolation of Actinomycetota (2,594 isolates, 88.4%), particularly species of Streptomyces (2,045 isolates, 69.7%) known for their bioactivity. Although Actinomycetota isolation was targeted, this collection includes representatives from Pseudomonadota (Alpha-, Beta-, and Gamma-Proteobacteria), Bacillota, and Bacteroidota phyla also common to the bat microbiome. A bi-layer challenge assay performed on 1,089 isolates identified 61 bat-associated bacteria with activity against Pd. These results were pooled with efforts by Hamm et al. [1] to determine what metrics impacted isolation of bacteria that inhibit Pd (n = 97). Ecoregion and bat species were determinant variables associated with Pd inhibition.

CONCLUSIONS: This study represents, to our best knowledge, the largest culture collection of bacteria from bats' skin and fur before the impact of WNS. We identified bacteria with antifungal activity against Pd and found significant associations of bioactive strains with bat species and ecoregions.},
}

@article {pmid42351291,
year = {2026},
author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y},
title = {Whole metagenome sequencing: not deep enough for complete microbial function recovery.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02448-z},
pmid = {42351291},
issn = {2049-2618},
abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.

RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed.

CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.},
}

@article {pmid42351301,
year = {2026},
author = {Ma, W and Pi, J and Wan, H and Wang, H and Han, W and Hu, M and Liu, J},
title = {Integrated microbiome-metabolome analysis implicates Acinetobacter guillouiae in arachidonic acid metabolic remodeling and endometrial cancer cell proliferation.},
journal = {Biology direct},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13062-026-00877-2},
pmid = {42351301},
issn = {1745-6150},
abstract = {BACKGROUND: Lesion-associated microbiota have emerged as potential regulators of tumor biology. However, the ecological organization and metabolic relevance of the local endometrial microbiome in endometrial cancer (EC) remain incompletely defined. This study aimed to characterize microbiome-associated metabolic alterations in EC tissues.

METHODS: We performed integrated 16S rRNA sequencing and untargeted metabolomic analyses using paired EC and adjacent non-tumor endometrial tissues. Microbial diversity, taxonomic composition, co-occurrence network architecture, and metabolomic pathway alterations were evaluated. Conditioned medium derived from Acinetobacter guillouiae was used to explore its association with arachidonic acid (AA) metabolism and proliferative phenotypes in EC cells, followed by pharmacological pathway interrogation and xenograft validation.

RESULTS: Overall microbial diversity was not significantly different between EC and adjacent tissues, whereas EC tissues exhibited a more connected and centralized microbial co-occurrence network. Taxonomic analyses identified enrichment of A. guillouiae in EC tissues based on 16S rRNA taxonomic assignment. Untargeted metabolomics revealed a group-level metabolic shift in EC tissues, with AA metabolism among the most prominently enriched pathways. In EC cells, A. guillouiae-derived conditioned medium increased intracellular AA levels, enhanced cPLA2 phosphorylation, induced AA-metabolizing enzymes, and activated the TLR4/NF-κB/ALOX5 signaling axis. Pharmacological inhibition of cPLA2, ALOX5, TLR4, or NF-κB partially attenuated the metabolic or proliferative effects associated with A. guillouiae conditioned medium. In a xenograft model, intratumoral exposure to A. guillouiae was associated with accelerated tumor growth.

CONCLUSIONS: These findings suggest that A. guillouiae-associated microbial alterations may contribute to AA metabolic remodeling and proliferative phenotypes in EC. This study provides a microbiome-metabolome framework for understanding lipid metabolic heterogeneity in EC and supports further validation of bacteria-associated AA metabolism as a potential therapeutic target.},
}

@article {pmid42351570,
year = {2026},
author = {Loth, S and Hauer, J and Scholz, C and Krüger, M and Bieber, A and Brickmann, C},
title = {Maternal and Neonatal Determinants of Respiratory Outcome Following Second-Trimester PPROM: A Multi-Domain Machine Learning Analysis.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/diagnostics16121911},
pmid = {42351570},
issn = {2075-4418},
abstract = {Background: Preterm premature rupture of membranes (PPROM) before 32 weeks of gestation with prolonged latency is associated with substantial neonatal morbidity, including Dry Lung Syndrome (DLS), pulmonary hypoplasia (PH), bronchopulmonary dysplasia (BPD), and death. Accurate individualized risk stratification remains elusive, as the interacting contributions of amniotic fluid dynamics, inflammatory status, and microbiological burden are inadequately captured by traditional statistical approaches. Methods: We performed a retrospective, exploratory-predictive analysis of 66 pregnancies complicated by second-trimester PPROM with latency exceeding 14 days. Elastic Net and Random Forest models were trained across six clinically defined predictor domains using a multi-stage block modelling strategy. To address the clinically relevant distinction between antenatal and postnatal information, results are reported separately for Model A-comprising exclusively antenatal predictors available during expectant management (gestational age at PPROM, latency, amniotic fluid trajectory, inflammatory status, vaginal microbiome at admission)-and Model B, which additionally incorporates postnatal variables and characterizes the full mechanistic perinatal risk trajectory. Binary and ordinal outcomes included DLS, PH, BPD, intraventricular hemorrhage (IVH), and neonatal death. Pairwise interaction models were additionally computed to identify cross-domain risk constellations. Results: Distinct predictor architectures emerged per outcome. Pulmonary hypoplasia was most strongly associated with temporal features of oligohydramnios-particularly the persistence and timing of SDP < 1 cm-rather than isolated measurements. For DLS, the antenatal model (Model A) achieved AUC 0.776, driven by gestational maturity and inflammatory status; surfactant administration-a postnatal variable reflecting therapeutic response rather than an antenatal risk factor-dominated only the mechanistic Model B. Neonatal death was driven by a combined profile of respiratory support burden, amniotic fluid persistence, and co-morbidity. IVH showed consistently high ordinal predictability (accuracy 0.863), with amniotic fluid dynamics and microbiological burden as leading contributors. BPD remained the least linearly separable endpoint across all configurations. Conclusions: Multi-domain machine learning reveals outcome-specific, cross-domain risk architectures following second-trimester PPROM that are invisible to conventional statistical models. Longitudinal amniotic fluid trajectory is the dominant antenatal determinant of structural pulmonary morbidity, while microbiological burden independently shapes neurological risk. These findings support prospective validation of integrated ML-based risk stratification tools for individualized antenatal counselling in this high-risk population.},
}

@article {pmid42351579,
year = {2026},
author = {Papadopoulou, A and Stavros, S and Potiris, A and Tsoplou, P and Dioikitopoulou, K and Plastourgou, V and Papanikopoulos, C and Tournas, G and Moustakli, E and Zikopoulos, A and Anysiadou, S and Daskalaki, AM and Antsaklis, P and Daskalakis, G and Domali, E},
title = {Endometrial Microbiome Profiles in Women Evaluated for Infertility or Recurrent Miscarriage: A Single-Center Descriptive Study.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {12},
pages = {},
doi = {10.3390/diagnostics16121920},
pmid = {42351579},
issn = {2075-4418},
abstract = {Background/Objectives: The role of the endometrial microbiome in reproductive failure remains incompletely understood. This study aimed to describe the composition of the endometrial microbiome in women evaluated for infertility or recurrent miscarriage. Methods: In this single-center descriptive study, endometrial samples were collected from women evaluated for infertility or recurrent miscarriage. Microbiome profiling was performed using 16S rRNA gene next-generation sequencing. Samples were classified as Lactobacillus-dominant when Lactobacillus spp. accounted for ≥90% of the total bacterial community. Alpha diversity was assessed using the Shannon and Simpson indices, while beta diversity was evaluated using Bray-Curtis dissimilarity, principal coordinates analysis (PCoA), PERMANOVA, and PERMDISP. Results: Of the 60 samples, 20 (33.3%) were Lactobacillus-dominant and 40 (66.7%) were non-Lactobacillus-dominant. Across all samples, Firmicutes was the predominant phylum (76.6%). Non-Lactobacillus-dominant samples showed significantly higher alpha diversity than Lactobacillus-dominant samples for both the Shannon and Simpson indices (p = 1.19 × 10[-6] and p = 1.51 × 10[-6], respectively), as well as higher observed taxa richness (p = 0.000017). PCoA based on Bray-Curtis dissimilarity demonstrated clear separation between microbiome profiles, supported by PERMANOVA (pseudo-F = 13.87, R[2] = 0.193, p = 0.001). PERMDISP showed significantly greater dispersion among non-Lactobacillus-dominant samples (F = 566.94, p < 0.001). Non-Lactobacillus-dominant samples showed greater representation of Enterococcus and Prevotella. Conclusions: In this cohort non-Lactobacillus-dominant communities were more frequent with greater diversity, richness, and compositional heterogeneity than Lactobacillus-dominant communities. These findings highlight the need for larger, standardized studies with appropriate control populations to clarify their clinical significance.},
}

@article {pmid42351611,
year = {2026},
author = {Donchev, D and Nikolova, R and Vaseva, K and Taskov, H and Murdjeva, M and Maes, M and Ivanov, IN},
title = {Comparative Gut Microbiome Alterations in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome and Long COVID-19 Syndrome.},
journal = {Biomedicines},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biomedicines14061183},
pmid = {42351611},
issn = {2227-9059},
support = {project № BG-RRP-2.004-0007-С03//European Union-NextGenerationEU, through the National Recovery and Resilience Plan of the Republic of Bulgaria/ ; },
abstract = {Background: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long COVID-19 syndrome (LC) show substantial clinical overlap, but direct comparative microbiome studies remain limited. Methods: In this cross-sectional study, we compared the fecal gut microbiome of patients with ME/CFS, LC, and healthy controls (HC) within a unified analytical framework using 16S rRNA profiling, differential abundance testing, and multivariate modeling. We also examined associations between microbiome variation and questionnaire-derived symptom-domain scores. Results: Alpha-diversity did not differ significantly among groups, whereas beta-diversity analyses showed small but significant disease-associated community differences with broad overlap between cohorts. Differential abundance analysis identified stronger signals in disease-versus-control contrasts than in the direct ME/CFS vs. LC contrast. Both ME/CFS and LC shared enrichment of Sutterella and depletion of Terrisporobacter and Lachnospiraceae relative to HC. Predicted functional profiling showed shared disease-versus-control changes in pathways related to anaerobic acetate/H2 carbon flow, inositol/polyol degradation, phosphonate/C1-related metabolism, and lysine-derived fermentation. Regression analyses showed the strongest microbiome associations with fatigue-related and physiosomatic domains, while affective, cognitive, and gastrointestinal outcomes showed weaker signals. Conclusions: Overall, these findings support the presence of overlapping but non-identical gut microbiome alterations in ME/CFS and LC. The results provide a basis for future longitudinal and multi-omics studies aimed at clarifying the stability, functional relevance, and clinical utility of these microbial patterns.},
}

@article {pmid42351636,
year = {2026},
author = {Loguercio, M and Giamundo, DM and Giglio, A and Buda, E and Ambrosetti, M and Perone, F},
title = {Gut Microbiota: Cardiovascular Disease Prevention and Targeted Therapies.},
journal = {Biomedicines},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biomedicines14061210},
pmid = {42351636},
issn = {2227-9059},
abstract = {The gut microbiota has emerged as a key regulator of cardiovascular health, influencing metabolic, inflammatory, and vascular pathways. Growing evidence indicates that gut dysbiosis, characterized by reduced microbial diversity, depletion of beneficial short-chain fatty acid-producing bacteria, and enrichment of pro-inflammatory taxa, is associated with major cardiovascular risk factors and disease progression. Microbial-derived metabolites, including trimethylamine/trimethylamine N-oxide, short-chain fatty acids, amino acids and bile acids, may play a central role in modulating lipid metabolism, endothelial function, inflammation, and thrombosis, although the underlying mechanisms remain incompletely understood. Recent multi-omics approaches have expanded this understanding by identifying personalized microbiome-metabolome signatures linked to cardiovascular risk, supporting a shift toward precision medicine. In this review, we summarize current evidence on the composition and functional role of the gut microbiota in cardiovascular disease and critically discuss emerging microbiota-targeted strategies. These include dietary interventions, prebiotics, probiotics, synbiotics, antibiotics, enzyme inhibitors, and fecal microbiota transplantation, which may contribute to both the prevention and adjunctive treatment of cardiovascular conditions. In addition, we address the challenges of integrating gut microbiota management into clinical practice and highlight the importance of tailored strategies, including exercise-based interventions, microbial enzyme inhibitors, and postbiotics. Despite promising preclinical and early clinical data, the translation of microbiome-based therapies into routine practice remains limited by heterogeneity in study design, the lack of standardized protocols, and incomplete mechanistic understanding. Overall, targeting the gut microbiota represents a novel and potentially complementary approach for cardiovascular disease prevention and management, warranting further well-designed clinical studies.},
}

@article {pmid42351647,
year = {2026},
author = {Dewi, SR and Matsumoto, T and Sugihartono, T and Miftahussurur, M and Yamaoka, Y},
title = {A Cross-Sectional Dual-Site Analysis of the Gastric Antral and Duodenal Mucosa-Associated Microbiome Across Gastroesophageal Reflux Disease Phenotypes.},
journal = {Biomedicines},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biomedicines14061221},
pmid = {42351647},
issn = {2227-9059},
support = {23K24133//Grants-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan/ ; 23836904//Japan Agency for Medical Research and Development (AMED) [Adopting Sustainable Partnerships for Innovative Research Ecosystem (ASPIRE)/ ; 21357105//Science and Technology Research Partnership for Sustainable Development (SATREPS)/ ; No. 5425/B/UN3.LPPM/PT.01.03/2025//The Indonesian Endowment Fund for Education (LPDP) on behalf of the Indonesian Ministry of Higher Education, Science and Technology and managed under the EQUITY Program (Contract No. 4300/B3/DT/03.08/2025; No. 297/UN3/HK.07.00/2025) and International Rese/ ; },
abstract = {Background/Objectives: Despite increasing GERD prevalence worldwide, the role of gastroduodenal microbiota in GERD phenotypes and symptom severity remains poorly understood. This study profiled mucosa-associated microbiota from the gastric antrum and duodenum across phenotypes and examined site-specific associations with symptom severity. Methods: In this cross-sectional study, forty individuals, including 26 with erosive reflux disease (ERD), 10 with non-erosive reflux disease (NERD), and 4 participants in the endoscopically normal comparator group, underwent 16S rRNA gene sequencing. Community differences were assessed using Bray-Curtis dissimilarity, differential taxa were explored by linear discriminant analysis effect size (LEfSe), and correlations with validated symptom questionnaires were evaluated. Results: Microbial community structure differed significantly between the antrum and duodenum, with Proteobacteria and Firmicutes predominating at both sites. LEfSe suggested enrichment of Streptococcus, Haemophilus, and Enterobacter in the duodenum, whereas Sphingobium, Acinetobacter, and Aquabacterium were more abundant in the antrum. The genus Helicobacter was relatively enriched in the antrum of ERD samples, whereas Streptococcus-dominant signatures were more prominent in the duodenum. Symptom severity showed stronger associations with duodenal taxa, including Fusobacterium with odynophagia, early satiety, and globus; Aquabacterium with postnatal drip and dyspnea, whereas gastric associations were fewer. Conclusions: In this small exploratory cross-sectional cohort, gastroduodenal microbiota exhibited both site-specific and phenotype-associated differences, with phenotype-related microbial variation being more evident in the duodenum than in the antrum. These hypothesis-generating findings highlight the importance of considering both anatomical context and GERD phenotype in upper gastrointestinal host-microbe interactions, and require confirmation in larger, phenotypically well-characterized cohorts.},
}

@article {pmid42351662,
year = {2026},
author = {Dinkov, B},
title = {Akkermansia muciniphila and GLP-1-Based Therapies: Bidirectional Interactions and Implications for Type 2 Diabetes and MASLD/MASH.},
journal = {Biomedicines},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biomedicines14061235},
pmid = {42351662},
issn = {2227-9059},
support = {European Union-NextGenerationEU National Recovery and Resilience Plan of the Republic of Bulgaria, project № BG-RRP-2.004-0003//Medical University Pleven/ ; },
abstract = {The global burden of type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated steatotic liver disease (MASLD) continues to rise at an alarming pace, with substantial pathophysiological overlap driven by insulin resistance, visceral obesity, and chronic low-grade inflammation. MASLD may progress to metabolic dysfunction-associated steatohepatitis (MASH), with increased risk of cirrhosis and hepatocellular carcinoma. Glucagon-like peptide 1 (GLP-1)-based therapies have transformed the management of T2DM and obesity. They exert pleiotropic effects whose basis remains incompletely understood. Concurrently, Akkermansia muciniphila has emerged as a keystone gut microbiota species with demonstrated hepatoprotective potential in preclinical models of MASLD/MASH. This narrative review positions A. muciniphila simultaneously as a target of GLP-1-mediated microbiome remodeling and as an independent modulator of hepatoprotection in MASLD/MASH. A structured search of PubMed, Scopus, and Web of Science (last searched: 12 April 2026) was conducted using terms related to Akkermansia muciniphila, GLP-1 receptor agonists, MASLD/MASH and T2DM. A total of 174 records were identified. Of these, 148 were excluded due to duplication or non-relevant study design. 26 studies (23 preclinical, 3 clinical) were included in the synthesis, directly addressing A. muciniphila. Preclinical evidence demonstrates that liraglutide, semaglutide, exenatide, and tirzepatide increase A. muciniphila abundance, while A. muciniphila in turn enhances endogenous GLP-1 secretion via the P9/ICAM-2 axis, forming a hypothetical positive feedback loop. A working mechanistic model integrating these bidirectional interactions is proposed, alongside a discussion of current limitations and future research priorities, including microbiome-guided clinical trials in MASLD/MASH populations.},
}

@article {pmid42351694,
year = {2026},
author = {Hijová, E and Bertková, I and Benetinová, V},
title = {Gut Microbiota as an Innovative Therapeutic Target in Cardiovascular Diseases from a Metabolic and Inflammatory Perspective.},
journal = {Biomedicines},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biomedicines14061267},
pmid = {42351694},
issn = {2227-9059},
abstract = {The gut microbiome plays a key role in the pathogenesis of cardiovascular disease through systemic inflammation, impaired lipid metabolism, and proatherogenic gut metabolites like trimethylamine N-oxide. Gut dysbiosis contributes to decreased level of microbial metabolites such as short-chain fatty acids, bile acids, coprostanol, and phenylacetylglutamine, as well as increased intestinal permeability and platelet hyper-reactivity, and exacerbating cardiovascular risk. New microbiome-focused treatments such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation are showing potential to help reduce cardiovascular diseases. However, bringing these therapies into clinical settings is difficult because they vary by strain and individual response. The gut-heart connection offers an innovative approach to preventing and treating heart condition, but additional research is needed to ensure lasting effectiveness and safety.},
}

@article {pmid42351718,
year = {2026},
author = {Tîrziu, AT and Romanescu, M and Ciordas, PD and Mercea, N and Munteanu, M and Horhat, FG and Chis, AR and Preda, MA},
title = {Metagenomic Profiling of the Gut Microbiome in Age-Related Macular Degeneration-A Pilot Study.},
journal = {Biomedicines},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biomedicines14061290},
pmid = {42351718},
issn = {2227-9059},
support = {CNFIS-FDI-2024-F-0451//Consiliul National pentru Finantarea Invatamantului Superior/ ; },
abstract = {Background/Objectives: Age-related macular degeneration (AMD) is a multifactorial retinal disease involving inflammatory, metabolic, and genetic factors. Increasing evidence suggests that the gut microbiome may contribute to systemic pathways involved in retinal homeostasis. This exploratory pilot study investigated gut microbiome alterations in AMD patients and controls using long-read whole-genome sequencing. Methods: Bacterial DNA was extracted from fecal samples and analyzed using Oxford Nanopore sequencing, followed by taxonomic profiling, alpha and beta diversity analyses, and differential abundance testing. Results: AMD patients showed significantly reduced microbial diversity, reflected by lower richness, Shannon and Simpson indices. Species-level beta diversity analyses revealed significant differences in microbial community composition, particularly with Bray-Curtis metrics, alongside increased inter-individual microbial heterogeneity in AMD samples. Differential abundance analyses identified the depletion of several potentially beneficial commensal taxa, including Faecalibacterium prausnitzii and Parabacteriodes distasonis, whereas Staphylococcus aureus was enriched in AMD patients. Comparisons between wet and dry subtypes showed no significant differences in alpha or beta diversity. Conclusions: Overall, the findings support the presence of gut microbial dysbiosis in AMD characterized by reduced diversity, abundance-driven community shifts, and increased microbiome heterogeneity. Given the small cohort size, cross-sectional design and lack of functional analysis, these results should be considered preliminary and hypothesis-generating.},
}

@article {pmid42351737,
year = {2026},
author = {Gavrilescu, DM and Mateescu, DM and Marginean, A and Tudoran, C and Ilie, AC and Badalica-Petrescu, M and Surducan, DA and Florescu, E and Tirinescu, R and Cotet, I and Constantinescu, FE and Tischer, A and Muresan, CO},
title = {Orthodontic Treatment-Induced Periodontal, Microbiological, and Local Inflammatory Changes: A Systematic Review and Meta-Analysis.},
journal = {Biomedicines},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/biomedicines14061308},
pmid = {42351737},
issn = {2227-9059},
support = {Victor Babeș University of Medicine and Pharmacy Timișoara//Victor Babeș University of Medicine and Pharmacy Timișoara/ ; },
abstract = {Background/Objectives: Orthodontic treatment induces controlled mechanical forces that alter the periodontal environment, including changes in oral microbiota composition and activation of local inflammatory pathways. Despite the widespread and growing use of orthodontic appliances across all age groups, the magnitude, timing, and multi-domain biological impact of these changes have not been comprehensively quantified in a single systematic synthesis. This systematic review and meta-analysis aimed to synthesize the available evidence on periodontal clinical parameters, oral microbiota composition, and local inflammatory biomarkers associated with orthodontic treatment using fixed appliances and clear aligners, and to provide a structured, GRADE-rated evidence base for clinical practice. Methods: A systematic review and meta-analysis was conducted in accordance with PRISMA 2020 guidelines. PubMed/MEDLINE, Scopus, and Web of Science were searched from inception to March 2026. Prospective cohort studies, longitudinal clinical studies, and randomized controlled trials evaluating periodontal parameters, oral microbiota, and inflammatory biomarkers during orthodontic treatment were included. Quantitative synthesis was performed using mean differences or standardized mean differences with 95% confidence intervals, primarily assessing within-group (pre-post) changes. Results: Eighteen studies (n = 812 patients; follow-up 3-12 months) met inclusion criteria. Fixed orthodontic appliances were consistently associated with transient increases in plaque index (MD 0.45, 95% CI 0.32-0.58; I[2] = 62%), gingival index (MD 0.38, 95% CI 0.25-0.51; I[2] = 55%), and bleeding on probing (MD 15.2%, 95% CI 10.1-20.3%; I[2] = 48%), particularly during early treatment phases. Microbiological analyses demonstrated within-group shifts toward increased prevalence of periodontopathogenic species (Streptococcus mutans OR 2.45, 95% CI 1.89-3.18; Porphyromonas spp. OR 2.14, 95% CI 1.67-2.75) in patients treated with fixed appliances. Local inflammatory responses were characterized by elevated IL-1β (MD 1.2, 95% CI 0.8-1.6) and IL-6 (MD 0.9, 95% CI 0.6-1.2) in gingival crevicular fluid. Certainty of evidence was rated moderate for plaque and gingival indices and low for microbiological and inflammatory outcomes (GRADE). Conclusions: Orthodontic treatment-particularly with fixed appliances-is associated with transient, reversible deterioration of periodontal indices, shifts toward a more dysbiotic oral microbiome, and elevation of local inflammatory mediators in gingival crevicular fluid during active treatment phases. These changes are manageable through structured preventive protocols and regular periodontal monitoring. Future prospective studies with concurrent control groups and standardized multi-domain outcome measures are needed to better define the magnitude and reversibility of these biological responses. PROSPERO: CRD420261336117.},
}

@article {pmid42352033,
year = {2026},
author = {Barakat, H and Alfheeaid, HA},
title = {Probiotic Modulation of Gut Microbiota: Antioxidant Mechanisms and Clinical Benefits in Obesity and Type 2 Diabetes Management.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/antiox15060727},
pmid = {42352033},
issn = {2076-3921},
support = {QU-APC-2026//Qassim University/ ; },
abstract = {Obesity and type 2 diabetes mellitus (T2DM) represent intertwined global epidemics driven by gut dysbiosis, chronic inflammation, and impaired SCFA production, identifying the microbiome as a therapeutic target. This review synthesizes mechanistic insights and clinical evidence on the role of probiotics as microbiome modulators in the management of metabolic disease. A comprehensive literature search across PubMed, Scopus, Web of Science, and Google Scholar up to May 2026 identified ~230 records using keywords such as probiotics, SCFAs, obesity, and T2DM; a narrative synthesis integrated preclinical, RCT, and meta-analytic data without formal pooling due to heterogeneity. Probiotics restore eubiosis via strain-specific mechanisms, Lacticaseibacillus rhamnosus GG enhances tight junctions (ZO-1), Bifidobacterium breve BBr60 boosts butyrate cross-feeding, and pasteurized Akkermansia muciniphila remodels bile acids (FXR/FGF19), activating G-Protein Coupled Receptor 41 (GPR41)/43-GLP-1 signaling, Treg expansion, and NF-κB suppression. Beyond immunometabolic effects, probiotics mitigate obesity- and T2DM-related oxidative stress by upregulating endogenous antioxidant enzymes (e.g., SOD, catalase, GPx), modulating Nrf2/Keap1 signaling, and reducing lipid peroxidation and other oxidative stress markers in experimental and clinical settings. Meta-analyses of RCTs reveal modest benefits: BMI reductions (~0.3 kg m[-2]), waist circumference (WC) reductions (1-2 cm), HbA1c reductions (0.3-0.4%), and improvements in homeostatic model assessment of insulin resistance (HOMA-IR), especially with multi-strain (>10[9] CFU day[-1], ≥12 weeks) synbiotics. Innovative strategies-synbiotics, postbiotics, AI-tailored consortia, and fermented dairy-address engraftment and response variability. Current guidelines recommend 10[9]-10[11] CFU day[-1] using multi-strain formulations for 12-24 weeks alongside lifestyle measures, with regimen selection tailored to the dysbiosis phenotype (e.g., NAFLD). Future longitudinal RCTs integrating multi-omics endpoints with AI-driven strain selection should refine-and ultimately individualize-precision probiotic strategies for metabolic therapy.},
}

@article {pmid42352087,
year = {2026},
author = {Caradonna, E and Ferrara, F and Costantino, L and Iannuzzo, F and Testa, N and Giordano, L and Faversani, A and Setacci, C and Novellino, E and Vanoli, E},
title = {Clonal Hematopoiesis and Gut Microbiota-Derived TMAO as Candidate Amplifiers of Cardiovascular Inflammation: The CHIDT Hypothesis.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/antiox15060781},
pmid = {42352087},
issn = {2076-3921},
abstract = {Clonal hematopoiesis of indeterminate potential (CHIP) and the gut microbiota-derived metabolite trimethylamine N-oxide (TMAO) are both linked to NLRP3-mediated cardiovascular inflammation, but their interaction has not previously been explored. This work proposes the CHIDT axis (clonal hematopoiesis-dysbiosis-TMAO), a feed-forward mechanism in which TET2 loss-of-function CHIP- and TMAO-generating Gram-negative gut dysbiosis mutually enhance cardiovascular risk. The model proceeds in three nodes. CHIP-associated intestinal immune dysregulation promotes luminal expansion of Gammaproteobacteria, which produce both trimethylamine via CntA/CntB-mediated L-carnitine oxidation and ADP-heptose as an obligate LPS biosynthetic intermediate. TMAO amplifies NLRP3 inflammasome activation through the SIRT3 → SOD2 → mtROS pathway. The evidence base of the CHIDT model is strongest for TET2-CHIP; the proposed extension to DNMT3A-CHIP rests on indirect, associative data and requires dedicated experimental confirmation before it can be considered established. TXNIP cascade, with predicted disproportionate potency in macrophages epigenetically primed by TET2 haploinsufficiency. High concentrations of TMAO have also been shown to suppress TET2 expression in endothelial cells through CYTB promoter hypermethylation, inducing NLRP3-GSDMD-dependent pyroptosis, although it remains unclear whether physiological TMAO levels can trigger this effect. Concurrently, ADP-heptose activates the ALPK1-TIFA-NF-κB pathway in bone marrow progenitors, favoring the expansion of mutant hematopoietic stem and progenitor cells. The model identifies three potential therapeutic strategies: NLRP3 inhibition, microbial TMA lyase inhibition, and microbiome-targeted reduction in Gram-negative bacteria. None has been tested in CHIP carriers stratified by plasma TMAO. Further studies in preclinical models and human cohorts integrating CHIP genotyping and TMAO quantification are needed to validate the CHIDT axis as a target for precision cardiovascular prevention.},
}

@article {pmid42352268,
year = {2026},
author = {Tita, GV and Fogas, CR and Slavescu, KC and Tantau, VM and Medan, SA and Serban, DE},
title = {Persistent Gut Microbiota Dysbiosis in Pediatric Crohn's Disease: A Next-Generation Sequencing Pilot Study.},
journal = {Biomolecules},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/biom16060801},
pmid = {42352268},
issn = {2218-273X},
mesh = {Humans ; *Crohn Disease/microbiology ; *Dysbiosis/microbiology/genetics ; Pilot Projects ; Female ; Male ; Child ; *Gastrointestinal Microbiome/genetics ; *High-Throughput Nucleotide Sequencing ; Prospective Studies ; Adolescent ; Metagenomics ; Eubacteriales ; },
abstract = {Background: Crohn's disease (CD) is characterized by gut microbiota alterations including reduced microbial diversity, loss of commensal species, and increased abundance of opportunistic taxa. Methods: This prospective study was conducted between 2022 and 2024 at the Emergency Clinical Hospital for Children, Cluj-Napoca. Children with CD and healthy controls were evaluated. The gut microbiota was analyzed using shotgun metagenomics. Bioinformatic processing assessed alpha and beta diversity, core microbiome composition, and differential taxa. Results: Ten patients with CD and eight healthy children were included; five patients were re-evaluated after a median interval of 14 weeks. The Shannon index was significantly lower in CD patients compared with controls (p = 0.037). Beta diversity analysis suggested partial separation between CD at diagnosis and controls (p = 0.041). An inverse correlation was observed between the Shannon index and the clinical score (p = 0.028). Ruminococcus gnavus was among the taxa contributing to group separation. At follow-up, all patients were in clinical remission, while 80% had achieved biological remission and mucosal healing. They showed persistently reduced alpha diversity and distinct microbial communities compared with controls (p = 0.028 and p = 0.005, respectively). Conclusions: Pediatric CD was correlated with dysbiosis that persisted despite remission. Reduced alpha diversity was associated with greater disease severity at diagnosis.},
}

Humans
*Crohn Disease/microbiology
*Dysbiosis/microbiology/genetics
Pilot Projects
Female
Male
Child
*Gastrointestinal Microbiome/genetics
*High-Throughput Nucleotide Sequencing
Prospective Studies
Adolescent
Metagenomics
Eubacteriales

@article {pmid42352285,
year = {2026},
author = {Tang, Y and Lu, P and Chen, H and Wong, S and Salahuddin, M and Hasan, M and Alake, SE and Kim, Y and Montgomery, M and Chowanadisai, W and Smith, BJ and Clarke, SL and Lucas, EA and Shen, CL and Tang, M and Lin, D},
title = {Zeaxanthin Modulates Early Metabolic and Inflammatory Responses in db/db Mice: Associations with Intestinal Lipid Handling and Gut Microbiome Remodeling.},
journal = {Biomolecules},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/biom16060818},
pmid = {42352285},
issn = {2218-273X},
support = {2020-67017-30842//National Institute of Food and Agriculture/ ; 2021-67018-34023//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; Male ; *Zeaxanthins/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Inflammation/metabolism/drug therapy ; *Lipid Metabolism/drug effects ; *Diabetes Mellitus, Type 2/metabolism/drug therapy ; *Diabetes Mellitus, Experimental/metabolism ; Liver/metabolism/drug effects ; Blood Glucose ; },
abstract = {Dietary zeaxanthin exhibits low intestinal absorption efficiency, and circulating levels are reduced in individuals with type 2 diabetes, suggesting potential metabolic relevance. However, its role during early-stage diabetes remains incompletely understood. This study examined whether dietary zeaxanthin modulates early metabolic and inflammatory responses and influences host-microbiome interactions during early T2DM progression. Four-week-old male db/db mice and wild-type C57BL/6J mice were fed an AIN-93M diet with or without 0.02% (w/w) zeaxanthin for 4 weeks. Zeaxanthin attenuated body weight gain, adiposity, hyperinsulinemia, and circulating keratinocyte-derived chemokine levels in diabetic mice. These effects were accompanied by reduced ileal membrane localization of Niemann-Pick C1-like protein 1 and decreased hepatic expression of CD36, nuclear factor kappa B p65, and phosphoenolpyruvate carboxykinase 1, without significant improvement in fasting blood glucose or hepatic triglyceride accumulation. Cecal microbiota analysis showed reduced microbial richness in diabetic mice that was not restored by zeaxanthin; however, zeaxanthin induced selective compositional shifts, including enrichment of fermentation-associated taxa (e.g., Ruminococcaceae) and normalization of Clostridium XIVb. Predicted microbial pathways related to fermentation, amino acid biosynthesis, and cofactor metabolism were also altered. Collectively, dietary zeaxanthin modulated early metabolic and inflammatory adaptation and was associated with alterations in intestinal lipid handling, inflammatory signaling, and gut microbiome composition during early T2DM progression.},
}

Animals
Male
*Zeaxanthins/pharmacology
Mice
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Inflammation/metabolism/drug therapy
*Lipid Metabolism/drug effects
*Diabetes Mellitus, Type 2/metabolism/drug therapy
*Diabetes Mellitus, Experimental/metabolism
Liver/metabolism/drug effects
Blood Glucose